Pierrick Roger
| Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/biodbChebi |
| git_branch: devel |
| git_last_commit: 6eb1625 |
| git_last_commit_date: 2023-10-24 11:36:37 -0400 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-28 11:36:14 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 199/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodbChebi 1.9.0 (landing page) Pierrick Roger
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the biodbChebi package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodbChebi.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: biodbChebi |
| Version: 1.9.0 |
| Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings biodbChebi_1.9.0.tar.gz |
| StartedAt: 2024-03-27 20:39:02 -0400 (Wed, 27 Mar 2024) |
| EndedAt: 2024-03-27 20:41:19 -0400 (Wed, 27 Mar 2024) |
| EllapsedTime: 136.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: biodbChebi.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings biodbChebi_1.9.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/biodbChebi.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘biodbChebi/DESCRIPTION’ ... OK
* this is package ‘biodbChebi’ version ‘1.9.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbChebi’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
biodbChebi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL biodbChebi ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘biodbChebi’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (biodbChebi)
biodbChebi.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # vi: fdm=marker
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbChebi)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbChebi")
biodb.INFO [2024-03-27 20:39:49.225][biodb::testContext]
biodb.INFO [2024-03-27 20:39:49.228][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-27 20:39:49.229][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-03-27 20:39:49.230][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-27 20:39:49.231][biodb::testContext]
biodb.INFO [2024-03-27 20:39:49.238][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.11.0.
biodb.DEBUG[2024-03-27 20:39:49.240][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-03-27 20:39:49.249][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-27 20:39:49.250][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-03-27 20:39:49.251][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-03-27 20:39:49.252][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:39:49.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:39:49.254][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:39:49.255][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-03-27 20:39:49.276][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-03-27 20:39:49.277][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:39:49.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:39:49.279][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:39:49.280][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-03-27 20:39:49.281][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-03-27 20:39:49.282][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:39:49.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:39:49.284][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:39:49.285][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-03-27 20:39:49.286][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-03-27 20:39:49.287][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-03-27 20:39:49.288][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:39:49.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:39:49.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:39:49.291][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-03-27 20:39:49.292][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-03-27 20:39:49.294][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-03-27 20:39:49.294][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:39:49.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:39:49.296][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:39:49.297][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-03-27 20:39:49.299][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-03-27 20:39:49.299][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:39:49.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:39:49.301][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:39:49.302][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-03-27 20:39:49.304][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-03-27 20:39:49.305][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-03-27 20:39:49.306][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:39:49.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:39:49.307][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:39:49.309][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-03-27 20:39:49.310][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-03-27 20:39:49.311][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:39:49.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:39:49.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:39:49.313][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-03-27 20:39:49.315][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-03-27 20:39:49.316][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-03-27 20:39:49.317][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:39:49.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:39:49.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:39:49.320][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-03-27 20:39:49.321][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-03-27 20:39:49.322][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-03-27 20:39:49.323][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-03-27 20:39:49.328][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-03-27 20:39:49.330][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-03-27 20:39:49.331][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:39:49.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:39:49.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:39:49.334][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-03-27 20:39:49.335][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-03-27 20:39:49.336][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:39:49.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:39:49.338][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:39:49.339][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-03-27 20:39:49.340][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-03-27 20:39:49.341][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:39:49.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:39:49.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:39:49.344][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-03-27 20:39:49.346][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-03-27 20:39:49.347][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:39:49.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:39:49.348][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:39:49.349][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-03-27 20:39:49.351][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-03-27 20:39:49.352][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:39:49.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:39:49.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:39:49.355][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-03-27 20:39:49.356][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-03-27 20:39:49.357][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:39:49.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:39:49.359][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:39:49.360][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-03-27 20:39:49.361][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-03-27 20:39:49.365][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-03-27 20:39:49.366][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:39:49.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:39:49.368][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:39:49.369][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-03-27 20:39:49.370][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-03-27 20:39:49.371][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-03-27 20:39:49.372][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:39:49.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:39:49.374][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:39:49.379][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-03-27 20:39:49.420][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-27 20:39:49.457][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-03-27 20:39:49.458][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 20:39:49.459][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 20:39:49.460][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 20:39:49.461][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 20:39:49.463][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-27 20:39:49.464][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 20:39:49.465][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-27 20:39:49.466][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 20:39:49.467][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-27 20:39:49.468][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-03-27 20:39:49.469][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 20:39:49.470][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:39:49.471][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-27 20:39:49.472][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-27 20:39:49.472][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-27 20:39:49.472][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-27 20:39:49.472][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-27 20:39:49.472][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-27 20:39:49.473][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 20:39:49.474][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:39:49.475][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:39:49.476][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 20:39:49.477][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:39:49.478][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:39:49.479][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 20:39:49.480][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:39:49.481][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 20:39:49.482][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 20:39:49.483][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-27 20:39:49.484][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:39:49.486][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-03-27 20:39:49.488][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-27 20:39:49.489][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-03-27 20:39:49.490][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 20:39:49.491][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 20:39:49.492][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 20:39:49.493][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 20:39:49.494][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-27 20:39:49.495][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 20:39:49.497][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-27 20:39:49.498][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 20:39:49.499][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-27 20:39:49.500][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-03-27 20:39:49.501][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 20:39:49.502][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:39:49.503][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-27 20:39:49.504][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-27 20:39:49.504][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-27 20:39:49.504][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-27 20:39:49.504][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-27 20:39:49.504][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-27 20:39:49.505][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 20:39:49.506][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:39:49.507][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:39:49.508][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 20:39:49.509][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:39:49.510][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:39:49.511][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 20:39:49.512][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:39:49.513][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 20:39:49.514][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 20:39:49.515][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-27 20:39:49.517][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:39:49.518][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-03-27 20:39:49.520][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-27 20:39:49.521][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-03-27 20:39:49.522][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 20:39:49.523][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 20:39:49.524][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 20:39:49.525][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 20:39:49.526][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-27 20:39:49.528][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 20:39:49.529][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-27 20:39:49.530][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 20:39:49.531][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-27 20:39:49.532][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-03-27 20:39:49.533][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 20:39:49.534][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:39:49.535][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-27 20:39:49.536][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:39:49.537][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 20:39:49.538][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:39:49.539][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:39:49.540][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 20:39:49.541][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:39:49.542][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:39:49.543][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 20:39:49.544][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:39:49.546][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 20:39:49.546][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 20:39:49.548][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-27 20:39:49.549][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:39:49.550][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-03-27 20:39:49.552][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-27 20:39:49.553][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-03-27 20:39:49.554][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 20:39:49.555][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 20:39:49.556][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 20:39:49.557][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 20:39:49.559][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-27 20:39:49.560][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 20:39:49.561][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-27 20:39:49.562][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 20:39:49.563][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-27 20:39:49.564][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-03-27 20:39:49.565][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 20:39:49.566][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:39:49.567][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-27 20:39:49.568][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:39:49.569][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 20:39:49.570][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:39:49.571][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:39:49.572][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 20:39:49.573][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:39:49.574][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:39:49.575][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 20:39:49.576][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:39:49.577][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 20:39:49.578][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 20:39:49.579][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-27 20:39:49.580][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:39:49.585][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-27 20:39:49.586][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:39:49.587][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:39:49.588][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:39:49.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:39:49.590][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:39:49.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:39:49.592][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:39:49.593][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:39:49.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:39:49.595][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:39:49.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:39:49.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:39:49.598][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:39:49.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:39:49.600][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:39:49.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:39:49.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:39:49.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:39:49.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:39:49.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:39:49.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:39:49.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:39:49.608][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:39:49.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:39:49.610][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:39:49.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:39:49.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:39:49.612][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:39:49.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:39:49.614][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:39:49.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:39:49.616][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:39:49.617][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:39:49.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:39:49.619][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:39:49.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:39:49.621][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:39:49.622][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:39:49.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:39:49.624][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:39:49.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:39:49.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:39:49.627][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:39:49.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:39:49.628][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:39:49.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:39:49.630][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:39:49.631][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:39:49.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:39:49.633][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:39:49.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:39:49.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:39:49.636][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:39:49.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:39:49.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:39:49.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:39:49.639][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:39:49.640][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:39:49.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:39:49.642][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:39:49.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:39:49.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:39:49.645][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:39:49.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:39:49.647][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:39:49.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:39:49.649][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:39:49.650][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:39:49.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:39:49.651][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:39:49.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:39:49.653][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:39:49.654][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:39:49.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:39:49.656][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:39:49.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:39:49.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:39:49.658][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:39:49.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:39:49.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:39:49.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:39:49.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:39:49.663][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:39:49.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:39:49.665][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:39:49.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:39:49.667][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:39:49.668][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-03-27 20:39:49.674][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-03-27 20:39:49.675][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-03-27 20:39:49.677][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-03-27 20:39:49.678][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-03-27 20:39:49.679][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-03-27 20:39:49.681][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-03-27 20:39:49.682][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-03-27 20:39:49.684][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-03-27 20:39:49.685][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-03-27 20:39:49.686][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-03-27 20:39:49.688][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-03-27 20:39:49.689][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-03-27 20:39:49.691][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-03-27 20:39:49.692][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-03-27 20:39:49.693][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-03-27 20:39:49.695][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-03-27 20:39:49.696][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-03-27 20:39:49.698][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-03-27 20:39:49.699][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-03-27 20:39:49.700][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-03-27 20:39:49.702][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-03-27 20:39:49.703][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-03-27 20:39:49.705][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-03-27 20:39:49.706][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-03-27 20:39:49.707][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-03-27 20:39:49.709][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-03-27 20:39:49.710][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-03-27 20:39:49.712][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-03-27 20:39:49.713][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-03-27 20:39:49.714][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-03-27 20:39:49.716][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-03-27 20:39:49.717][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-03-27 20:39:49.719][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-03-27 20:39:49.720][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-03-27 20:39:49.722][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-03-27 20:39:49.730][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-03-27 20:39:49.732][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-03-27 20:39:49.733][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-03-27 20:39:49.734][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-03-27 20:39:49.736][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-03-27 20:39:49.737][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-03-27 20:39:49.738][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-03-27 20:39:49.740][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-03-27 20:39:49.741][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-03-27 20:39:49.742][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-03-27 20:39:49.744][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-03-27 20:39:49.745][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-03-27 20:39:49.746][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-03-27 20:39:49.748][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-03-27 20:39:49.749][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-03-27 20:39:49.750][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-03-27 20:39:49.752][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-03-27 20:39:49.753][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-03-27 20:39:49.754][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-03-27 20:39:49.756][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-03-27 20:39:49.757][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-03-27 20:39:49.758][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-03-27 20:39:49.760][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-03-27 20:39:49.761][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-03-27 20:39:49.762][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-03-27 20:39:49.764][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-03-27 20:39:49.765][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-03-27 20:39:49.766][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-03-27 20:39:49.767][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-03-27 20:39:49.769][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-03-27 20:39:49.770][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-03-27 20:39:49.771][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-03-27 20:39:49.773][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-03-27 20:39:49.774][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-03-27 20:39:49.775][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-03-27 20:39:49.777][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-03-27 20:39:49.778][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-03-27 20:39:49.779][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-03-27 20:39:49.781][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-03-27 20:39:49.782][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-03-27 20:39:49.783][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-03-27 20:39:49.784][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-03-27 20:39:49.786][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-03-27 20:39:49.787][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-03-27 20:39:49.788][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-03-27 20:39:49.790][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-03-27 20:39:49.791][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-03-27 20:39:49.797][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-03-27 20:39:49.798][initialize] This is biodb version 1.11.0.
biodb.DEBUG[2024-03-27 20:39:49.802][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-27 20:39:49.802][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:39:49.803][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:39:49.804][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:39:49.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:39:49.810][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:39:49.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:39:49.811][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:39:49.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:39:49.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:39:49.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:39:49.815][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:39:49.816][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:39:49.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:39:49.818][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:39:49.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:39:49.819][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:39:49.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:39:49.821][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:39:49.822][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:39:49.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:39:49.824][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:39:49.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:39:49.825][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:39:49.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:39:49.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:39:49.828][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:39:49.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:39:49.830][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:39:49.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:39:49.831][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:39:49.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:39:49.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:39:49.834][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:39:49.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:39:49.835][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:39:49.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:39:49.837][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:39:49.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:39:49.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:39:49.840][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:39:49.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:39:49.841][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:39:49.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:39:49.843][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:39:49.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:39:49.845][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:39:49.846][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:39:49.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:39:49.847][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:39:49.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:39:49.849][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:39:49.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:39:49.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:39:49.852][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:39:49.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:39:49.853][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:39:49.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:39:49.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:39:49.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:39:49.857][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:39:49.858][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:39:49.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:39:49.859][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:39:49.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:39:49.861][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:39:49.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:39:49.863][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:39:49.864][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:39:49.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:39:49.865][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:39:49.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:39:49.867][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:39:49.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:39:49.869][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:39:49.870][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:39:49.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:39:49.871][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:39:49.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:39:49.873][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:39:49.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:39:49.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:39:49.876][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:39:49.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:39:49.877][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:39:49.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:39:49.879][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:39:49.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:39:49.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:39:49.882][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:39:49.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:39:49.883][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:39:49.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:39:49.885][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:39:49.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:39:49.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:39:49.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:39:49.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:39:49.889][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:39:49.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:39:49.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:39:49.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:39:49.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:39:49.894][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:39:49.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:39:49.895][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:39:49.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:39:49.897][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:39:49.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:39:49.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:39:49.900][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:39:49.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:39:49.901][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:39:49.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:39:49.903][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:39:49.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:39:49.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:39:49.906][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:39:49.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:39:49.908][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:39:49.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:39:49.909][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:39:49.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:39:49.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:39:49.913][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-03-27 20:39:49.923][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-03-27 20:39:49.925][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-27 20:39:49.926][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-03-27 20:39:49.927][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 20:39:49.928][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 20:39:49.929][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 20:39:49.930][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 20:39:49.931][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-03-27 20:39:49.932][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-03-27 20:39:49.933][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-03-27 20:39:49.934][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 20:39:49.935][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-27 20:39:49.936][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-03-27 20:39:49.936][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 20:39:49.938][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-03-27 20:39:49.938][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-03-27 20:39:49.938][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-03-27 20:39:49.938][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-03-27 20:39:49.938][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-03-27 20:39:49.938][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-03-27 20:39:49.938][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-03-27 20:39:49.938][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-03-27 20:39:49.938][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-03-27 20:39:49.938][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-03-27 20:39:49.938][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-03-27 20:39:49.939][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-03-27 20:39:49.940][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-27 20:39:49.940][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-27 20:39:49.940][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-27 20:39:49.941][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-03-27 20:39:49.942][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:39:49.943][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:39:49.944][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 20:39:49.945][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:39:49.946][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:39:49.947][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 20:39:49.948][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-27 20:39:49.948][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-03-27 20:39:49.949][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 20:39:49.950][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 20:39:49.951][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-03-27 20:39:49.952][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-03-27 20:39:49.952][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-03-27 20:39:49.958][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-03-27 20:39:49.960][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-03-27 20:39:49.961][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-03-27 20:39:49.963][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-03-27 20:39:49.964][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-03-27 20:39:49.966][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-03-27 20:39:49.998][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-03-27 20:39:50.000][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-03-27 20:39:50.005][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-03-27 20:39:50.009][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-03-27 20:39:50.014][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-03-27 20:39:50.015][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-03-27 20:39:50.017][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-03-27 20:39:50.018][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-03-27 20:39:50.028][biodb::testThat]
biodb.INFO [2024-03-27 20:39:50.029][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2024-03-27 20:39:50.030][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 20:39:50.031][biodb::testThat]
biodb.TRACE[2024-03-27 20:39:50.035][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2024-03-27 20:39:50.037][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-27 20:39:50.041][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-27 20:39:50.050][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:39:50.051][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:39:50.052][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:39:50.065][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:39:50.066][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:39:50.067][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:39:50.068][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:39:50.078][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:39:50.079][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:39:50.080][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.081][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.083][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:39:50.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:39:50.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.098][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-27 20:39:50.099][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-27 20:39:50.100][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.101][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.126][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-27 20:39:50.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-27 20:39:50.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.130][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:39:50.131][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:39:50.132][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.133][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.134][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:39:50.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:39:50.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.138][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-27 20:39:50.139][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-27 20:39:50.140][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.141][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.142][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-27 20:39:50.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-27 20:39:50.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.146][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-27 20:39:50.147][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-27 20:39:50.148][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.149][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.150][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-27 20:39:50.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-27 20:39:50.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.154][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:39:50.155][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:39:50.156][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.157][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.158][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:39:50.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:39:50.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.162][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-27 20:39:50.163][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:39:50.164][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.165][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.166][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-27 20:39:50.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:39:50.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.170][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:39:50.171][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:39:50.172][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.173][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.174][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:39:50.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:39:50.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.178][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:39:50.179][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:39:50.180][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.181][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.183][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:39:50.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:39:50.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.187][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-27 20:39:50.188][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-27 20:39:50.188][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.189][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.191][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-27 20:39:50.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-27 20:39:50.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.195][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-27 20:39:50.196][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-27 20:39:50.196][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.197][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.199][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-27 20:39:50.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-27 20:39:50.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.203][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:39:50.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:39:50.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.206][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:39:50.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:39:50.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.210][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:39:50.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:39:50.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.214][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:39:50.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:39:50.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.218][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:39:50.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:39:50.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.222][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:39:50.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:39:50.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.226][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:39:50.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:39:50.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.270][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:39:50.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:39:50.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.274][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:39:50.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:39:50.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.278][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:39:50.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:39:50.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:39:50.282][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2024-03-27 20:39:50.284][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-27 20:39:50.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-27 20:39:50.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.288][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-27 20:39:50.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-27 20:39:50.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.314][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-27 20:39:50.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-27 20:39:50.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.318][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-27 20:39:50.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-27 20:39:50.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.322][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:39:50.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:39:50.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.326][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:39:50.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:39:50.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.330][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-27 20:39:50.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-27 20:39:50.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.334][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-27 20:39:50.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-27 20:39:50.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.338][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-03-27 20:39:50.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-03-27 20:39:50.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.342][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-03-27 20:39:50.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-03-27 20:39:50.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.362][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:39:50.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:39:50.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.379][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:39:50.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:39:50.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.387][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:39:50.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:39:50.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.391][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:39:50.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:39:50.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.394][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:39:50.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:39:50.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.400][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:39:50.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:39:50.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.404][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:39:50.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:39:50.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.408][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:39:50.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:39:50.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.412][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:39:50.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:39:50.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.415][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:39:50.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:39:50.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.419][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:39:50.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:39:50.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.430][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:39:50.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:39:50.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.434][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:39:50.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:39:50.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.437][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:39:50.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:39:50.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.441][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:39:50.442][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:39:50.443][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.444][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.445][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:39:50.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:39:50.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.456][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:39:50.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:39:50.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.485][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:39:50.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:39:50.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.489][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:39:50.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:39:50.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.493][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:39:50.494][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:39:50.495][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.496][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.497][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:39:50.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:39:50.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.509][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:39:50.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:39:50.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.513][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:39:50.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:39:50.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.517][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:39:50.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:39:50.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.521][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:39:50.522][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:39:50.523][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.523][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.524][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:39:50.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:39:50.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.536][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:39:50.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:39:50.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.540][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:39:50.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:39:50.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.543][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:39:50.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:39:50.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.547][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:39:50.548][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:39:50.549][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.550][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.551][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:39:50.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:39:50.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.562][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:39:50.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:39:50.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.566][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:39:50.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:39:50.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.569][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:39:50.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:39:50.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.573][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:39:50.574][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:39:50.575][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.576][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.577][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:39:50.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:39:50.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.588][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:39:50.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:39:50.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.592][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:39:50.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:39:50.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.596][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:39:50.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:39:50.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.600][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:39:50.601][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:39:50.602][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.603][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.604][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:39:50.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:39:50.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.614][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-27 20:39:50.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-27 20:39:50.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.618][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-27 20:39:50.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-27 20:39:50.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.622][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-27 20:39:50.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-27 20:39:50.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.626][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-27 20:39:50.627][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-27 20:39:50.628][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.629][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.630][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-27 20:39:50.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-27 20:39:50.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.640][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-03-27 20:39:50.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-27 20:39:50.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.644][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-03-27 20:39:50.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-27 20:39:50.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.648][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-03-27 20:39:50.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-27 20:39:50.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.652][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-03-27 20:39:50.653][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-27 20:39:50.654][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.655][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.656][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-03-27 20:39:50.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-27 20:39:50.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.666][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:39:50.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:39:50.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.670][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:39:50.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:39:50.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.674][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:39:50.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:39:50.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.678][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:39:50.679][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:39:50.680][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.681][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.682][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:39:50.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:39:50.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.692][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-27 20:39:50.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-27 20:39:50.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.701][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-27 20:39:50.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-27 20:39:50.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.705][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-27 20:39:50.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-27 20:39:50.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.709][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-27 20:39:50.710][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-27 20:39:50.710][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.711][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.712][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-27 20:39:50.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-27 20:39:50.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.723][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-27 20:39:50.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-27 20:39:50.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.727][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-27 20:39:50.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-27 20:39:50.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.731][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-27 20:39:50.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-27 20:39:50.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.735][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-27 20:39:50.736][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-27 20:39:50.737][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.738][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.739][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-27 20:39:50.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-27 20:39:50.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.749][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-27 20:39:50.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-27 20:39:50.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.753][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-27 20:39:50.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-27 20:39:50.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.757][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-27 20:39:50.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-27 20:39:50.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.761][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-27 20:39:50.762][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-27 20:39:50.763][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.764][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.765][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-27 20:39:50.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-27 20:39:50.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.775][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:39:50.776][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:39:50.777][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.778][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.782][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-27 20:39:50.783][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-27 20:39:50.784][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.785][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.789][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:39:50.790][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:39:50.791][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.791][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.795][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-27 20:39:50.796][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-27 20:39:50.797][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.798][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.802][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-27 20:39:50.803][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-27 20:39:50.804][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.805][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.809][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:39:50.810][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:39:50.811][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.812][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.816][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:39:50.817][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:39:50.818][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.819][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.823][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:39:50.824][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:39:50.825][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.825][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.830][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-03-27 20:39:50.831][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-27 20:39:50.832][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.833][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.837][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:39:50.838][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:39:50.839][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.839][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.844][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-27 20:39:50.845][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-27 20:39:50.846][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.846][ef$get] fields variable is a list.
biodb.INFO [2024-03-27 20:39:50.853][biodb::testThat]
biodb.INFO [2024-03-27 20:39:50.854][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-03-27 20:39:50.855][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 20:39:50.856][biodb::testThat]
biodb.DEBUG[2024-03-27 20:39:50.869][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2024-03-27 20:39:50.876][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-27 20:39:50.880][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2024-03-27 20:39:50.882][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-27 20:39:50.883][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2024-03-27 20:39:50.884][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-27 20:39:50.911][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-27 20:39:50.912][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-27 20:39:50.914][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:39:50.915][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:39:50.915][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:39:50.920][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:39:50.921][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:39:50.921][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:39:50.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:39:50.925][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:39:50.926][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:39:50.927][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.928][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.929][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:39:50.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:39:50.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.948][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-27 20:39:50.949][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-27 20:39:50.950][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.951][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.953][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-27 20:39:50.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-27 20:39:50.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.956][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:39:50.957][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:39:50.958][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.959][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.961][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:39:50.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:39:50.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.964][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-27 20:39:50.965][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-27 20:39:50.966][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.967][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.968][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-27 20:39:50.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-27 20:39:50.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.972][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-27 20:39:50.973][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-27 20:39:50.974][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.975][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.976][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-27 20:39:50.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-27 20:39:50.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.980][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:39:50.981][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:39:50.982][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.983][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.984][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:39:50.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:39:50.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.988][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-27 20:39:50.989][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:39:50.990][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.991][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.992][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-27 20:39:50.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:39:50.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:50.996][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:39:50.997][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:39:50.998][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:50.999][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:51.000][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:39:51.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:39:51.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:51.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:51.004][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:39:51.005][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:39:51.006][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:51.006][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:51.008][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:39:51.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:39:51.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:51.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:51.012][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-27 20:39:51.013][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-27 20:39:51.014][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:51.014][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:51.016][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-27 20:39:51.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-27 20:39:51.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:51.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:51.020][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-27 20:39:51.021][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-27 20:39:51.022][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:51.022][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:51.024][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-27 20:39:51.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-27 20:39:51.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:51.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:51.028][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:39:51.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:39:51.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:51.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:51.031][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:39:51.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:39:51.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:51.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:51.035][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:39:51.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:39:51.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:51.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:51.039][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:39:51.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:39:51.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:51.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:51.043][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:39:51.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:39:51.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:51.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:51.047][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:39:51.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:39:51.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:51.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:51.050][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:39:51.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:39:51.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:51.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:51.054][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:39:51.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:39:51.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:51.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:51.058][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:39:51.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:39:51.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:51.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:51.062][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:39:51.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:39:51.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:51.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:39:51.065][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2024-03-27 20:39:51.066][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-03-27 20:39:51.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-03-27 20:39:51.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:51.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:51.070][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-03-27 20:39:51.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-03-27 20:39:51.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:51.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:51.074][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-03-27 20:39:51.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-03-27 20:39:51.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:51.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-03-27 20:39:51.084][biodb::testThat]
biodb.INFO [2024-03-27 20:39:51.085][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2024-03-27 20:39:51.086][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 20:39:51.087][biodb::testThat]
biodb.TRACE[2024-03-27 20:39:51.090][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:39:51.091][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:39:51.092][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:51.093][ef$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:39:51.094][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2024-03-27 20:39:51.122][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:39:51.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:39:51.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:51.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:51.126][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:39:51.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:39:51.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:51.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:51.130][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:39:51.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:39:51.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:51.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:39:51.137][function(conn, opt)] With value "squalene".
biodb.DEBUG[2024-03-27 20:39:51.141][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-03-27 20:39:51.160][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-27 20:39:51.175][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-03-27 20:39:51.176][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-27 20:39:51.178][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-03-27 20:39:51.199][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-03-27 20:39:51.202][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-27 20:39:51.204][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-03-27 20:39:51.205][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-27 20:39:51.206][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-03-27 20:39:51.208][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2024-03-27 20:39:51.218][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:39:51.219][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:39:51.220][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:51.221][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:51.222][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:39:51.223][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:39:51.224][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:51.225][ef$get] fields variable is a list.
biodb.INFO [2024-03-27 20:39:51.229][biodb::testThat]
biodb.INFO [2024-03-27 20:39:51.230][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2024-03-27 20:39:51.231][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 20:39:51.231][biodb::testThat]
biodb.TRACE[2024-03-27 20:39:51.253][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:39:51.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:39:51.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:51.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:51.257][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:39:51.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:39:51.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:51.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:51.261][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:39:51.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:39:51.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:51.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:39:51.325][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-03-27 20:39:51.328][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-27 20:39:51.329][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-03-27 20:39:51.330][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-27 20:39:51.332][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2024-03-27 20:39:51.346][biodb::testThat]
biodb.INFO [2024-03-27 20:39:51.347][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2024-03-27 20:39:51.348][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 20:39:51.349][biodb::testThat]
biodb.TRACE[2024-03-27 20:39:51.367][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-27 20:39:51.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-27 20:39:51.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:51.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:51.371][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-27 20:39:51.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-27 20:39:51.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:51.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:51.375][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-27 20:39:51.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-27 20:39:51.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:51.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:51.379][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-27 20:39:51.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-27 20:39:51.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:51.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:51.383][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:39:51.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:39:51.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:51.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:51.387][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:39:51.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:39:51.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:51.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:51.390][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-27 20:39:51.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-27 20:39:51.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:51.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:51.394][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-27 20:39:51.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-27 20:39:51.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:51.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:51.398][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-03-27 20:39:51.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-03-27 20:39:51.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:51.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:51.402][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-03-27 20:39:51.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-03-27 20:39:51.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:51.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:51.421][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-27 20:39:51.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-27 20:39:51.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:51.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:51.426][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-27 20:39:51.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-27 20:39:51.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:51.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:51.429][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-27 20:39:51.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-27 20:39:51.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:51.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:51.433][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-27 20:39:51.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-27 20:39:51.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:51.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:51.437][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:39:51.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:39:51.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:51.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:51.441][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:39:51.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:39:51.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:51.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:51.444][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-27 20:39:51.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-27 20:39:51.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:51.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:51.448][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-27 20:39:51.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-27 20:39:51.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:51.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:51.452][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-03-27 20:39:51.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-03-27 20:39:51.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:51.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:51.456][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-03-27 20:39:51.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-03-27 20:39:51.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:51.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-03-27 20:39:51.465][biodb::testThat]
biodb.INFO [2024-03-27 20:39:51.466][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-03-27 20:39:51.467][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 20:39:51.468][biodb::testThat]
biodb.INFO [2024-03-27 20:39:51.475][biodb::testThat]
biodb.INFO [2024-03-27 20:39:51.476][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-03-27 20:39:51.477][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 20:39:51.478][biodb::testThat]
biodb.INFO [2024-03-27 20:39:51.486][biodb::testThat]
biodb.INFO [2024-03-27 20:39:51.487][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2024-03-27 20:39:51.488][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 20:39:51.489][biodb::testThat]
biodb.DEBUG[2024-03-27 20:39:51.492][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2024-03-27 20:39:52.184][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2024-03-27 20:39:53.468][biodb::testThat]
biodb.INFO [2024-03-27 20:39:53.469][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2024-03-27 20:39:53.471][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 20:39:53.472][biodb::testThat]
biodb.DEBUG[2024-03-27 20:39:53.970][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/displayImage.do?defaultImage=true&imageIndex=0&chebiId=15440&dimensions=400.
biodb.TRACE[2024-03-27 20:39:54.460][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:39:54.463][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:39:54.465][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:54.468][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:54.470][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:39:54.472][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:39:54.474][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:54.476][ef$get] fields variable is a list.
biodb.INFO [2024-03-27 20:39:54.481][biodb::testThat]
biodb.INFO [2024-03-27 20:39:54.483][biodb::testThat] Running test function test.searchCompound (" We can search for a compound ").
biodb.INFO [2024-03-27 20:39:54.485][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 20:39:54.487][biodb::testThat]
biodb.TRACE[2024-03-27 20:39:54.507][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:39:54.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:39:54.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:54.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:54.515][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:39:54.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:39:54.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:54.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:54.519][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:39:54.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:39:54.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:54.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:39:54.617][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.INFO [2024-03-27 20:39:54.620][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.DEBUG[2024-03-27 20:39:54.621][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:39:54.622][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:39:54.624][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-03-27 20:39:55.225][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-03-27 20:39:55.833][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:39:55.835][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2024-03-27 20:39:55.850][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2024-03-27 20:39:55.909][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-03-27 20:39:55.912][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-27 20:39:55.914][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-03-27 20:39:55.915][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-27 20:39:55.917][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2024-03-27 20:39:55.929][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-03-27 20:39:55.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-03-27 20:39:55.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:55.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:55.938][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:39:55.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:39:55.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:55.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:55.942][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:39:55.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:39:55.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:55.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:55.946][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:39:55.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:39:55.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:55.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:55.950][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:39:55.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:39:55.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:55.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:55.962][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:39:55.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:39:55.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:55.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:39:55.974][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-03-27 20:39:55.990][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:39:55.991][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:39:56.006][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-03-27 20:39:56.450][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-03-27 20:39:56.905][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:39:56.909][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2024-03-27 20:39:56.918][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2024-03-27 20:39:56.923][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:39:56.926][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:39:56.928][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:39:56.937][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:39:56.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:39:56.942][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:39:56.944][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:39:56.946][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2024-03-27 20:39:57.004][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-27 20:39:57.006][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2024-03-27 20:39:57.007][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-27 20:39:57.008][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-27 20:39:57.009][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-27 20:39:57.010][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-27 20:39:57.011][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-27 20:39:57.012][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-27 20:39:57.014][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:39:57.015][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:39:57.016][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:39:57.021][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:39:57.021][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:39:57.022][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:39:57.023][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:39:57.024][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2024-03-27 20:39:57.027][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:39:57.028][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:39:57.029][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2024-03-27 20:39:57.475][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2024-03-27 20:39:57.986][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:39:57.990][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2024-03-27 20:39:57.998][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2024-03-27 20:39:58.003][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2024-03-27 20:39:58.007][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-27 20:39:58.009][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-27 20:39:58.012][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-27 20:39:58.033][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:39:58.035][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:39:58.037][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:39:58.045][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:39:58.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:39:58.048][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:39:58.049][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:39:58.053][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:39:58.055][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:39:58.056][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:58.057][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:58.059][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:39:58.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:39:58.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:58.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:58.064][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-27 20:39:58.065][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-27 20:39:58.066][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:58.067][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:58.069][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-27 20:39:58.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-27 20:39:58.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:58.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:58.073][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:39:58.074][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:39:58.075][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:58.076][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:58.078][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:39:58.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:39:58.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:58.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:58.082][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-27 20:39:58.083][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-27 20:39:58.084][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:58.085][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:58.086][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-27 20:39:58.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-27 20:39:58.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:58.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:58.090][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-27 20:39:58.091][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-27 20:39:58.092][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:58.093][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:58.094][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-27 20:39:58.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-27 20:39:58.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:58.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:58.098][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:39:58.099][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:39:58.100][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:58.101][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:58.102][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-27 20:39:58.103][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:39:58.104][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:58.105][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:58.106][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-27 20:39:58.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:39:58.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:58.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:58.110][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:39:58.111][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:39:58.112][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:58.112][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:58.114][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:39:58.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:39:58.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:58.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:58.118][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:39:58.119][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:39:58.119][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:58.120][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:58.122][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:39:58.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:39:58.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:58.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:58.126][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-27 20:39:58.127][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-27 20:39:58.128][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:58.129][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:58.130][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-27 20:39:58.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-27 20:39:58.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:58.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:58.134][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-27 20:39:58.135][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-27 20:39:58.136][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:58.136][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:58.138][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-27 20:39:58.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-27 20:39:58.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:58.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:58.142][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:39:58.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:39:58.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:58.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:58.145][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:39:58.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:39:58.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:58.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:58.149][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:39:58.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:39:58.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:58.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:58.153][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:39:58.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:39:58.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:58.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:58.157][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:39:58.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:39:58.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:58.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:58.161][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:39:58.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:39:58.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:58.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:58.165][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:39:58.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:39:58.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:58.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:58.169][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:39:58.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:39:58.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:58.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:58.172][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:39:58.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:39:58.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:58.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:58.176][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:39:58.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:39:58.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:58.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:39:58.180][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2024-03-27 20:39:58.189][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:39:58.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:39:58.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:58.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:58.193][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:39:58.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:39:58.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:58.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:58.197][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:39:58.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:39:58.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:58.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:39:58.202][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-03-27 20:39:58.205][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:39:58.206][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:39:58.208][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-03-27 20:39:58.654][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-03-27 20:39:59.108][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:39:59.110][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2024-03-27 20:39:59.114][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2024-03-27 20:39:59.129][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:39:59.131][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:39:59.132][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:39:59.136][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:39:59.137][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:39:59.138][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:39:59.139][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:39:59.140][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:39:59.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:39:59.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:59.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:59.144][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:39:59.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:39:59.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:59.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:39:59.148][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:39:59.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:39:59.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:39:59.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:39:59.152][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:39:59.153][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:39:59.153][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:39:59.158][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:39:59.159][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:39:59.160][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:39:59.161][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:39:59.162][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2024-03-27 20:39:59.163][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-27 20:39:59.164][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2024-03-27 20:39:59.165][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-27 20:39:59.166][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-27 20:39:59.167][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-27 20:39:59.168][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-27 20:39:59.169][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-27 20:39:59.170][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-27 20:39:59.183][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:39:59.184][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:39:59.185][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:39:59.190][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:39:59.191][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:39:59.192][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:39:59.193][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:39:59.194][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2024-03-27 20:39:59.196][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:39:59.197][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:39:59.199][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2024-03-27 20:39:59.709][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2024-03-27 20:40:00.156][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:40:00.159][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2024-03-27 20:40:00.163][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2024-03-27 20:40:00.166][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2024-03-27 20:40:00.168][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-27 20:40:00.169][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-27 20:40:00.170][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-27 20:40:00.173][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:00.174][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:00.175][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:00.181][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:00.182][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:00.183][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:00.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:00.186][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:00.188][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:00.189][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:00.190][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:00.191][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:00.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:00.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:00.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:00.195][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-27 20:40:00.197][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-27 20:40:00.198][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:00.199][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:00.200][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-27 20:40:00.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-27 20:40:00.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:00.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:00.204][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:40:00.205][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:40:00.206][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:00.207][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:00.209][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:40:00.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:40:00.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:00.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:00.213][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-27 20:40:00.214][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-27 20:40:00.215][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:00.216][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:00.218][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-27 20:40:00.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-27 20:40:00.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:00.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:00.222][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-27 20:40:00.223][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-27 20:40:00.224][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:00.225][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:00.226][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-27 20:40:00.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-27 20:40:00.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:00.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:00.231][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:00.232][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:00.233][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:00.234][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:00.235][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-27 20:40:00.254][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:00.255][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:00.256][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:00.257][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-27 20:40:00.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:00.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:00.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:00.261][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:00.263][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:00.264][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:00.265][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:00.266][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:00.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:00.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:00.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:00.270][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:00.272][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:00.273][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:00.274][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:00.275][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:00.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:00.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:00.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:00.279][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-27 20:40:00.280][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-27 20:40:00.281][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:00.282][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:00.283][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-27 20:40:00.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-27 20:40:00.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:00.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:00.288][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-27 20:40:00.289][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-27 20:40:00.290][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:00.291][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:00.292][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-27 20:40:00.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-27 20:40:00.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:00.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:00.296][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:00.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:00.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:00.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:00.300][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:00.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:00.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:00.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:00.304][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:00.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:00.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:00.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:00.308][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:00.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:00.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:00.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:00.312][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:00.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:00.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:00.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:00.317][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:00.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:00.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:00.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:00.321][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:00.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:00.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:00.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:00.325][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:00.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:00.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:00.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:00.329][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:00.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:00.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:00.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:00.333][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:00.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:00.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:00.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:00.337][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2024-03-27 20:40:00.339][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:00.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:00.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:00.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:00.343][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:00.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:00.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:00.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:00.347][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:00.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:00.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:00.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:00.369][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-03-27 20:40:00.372][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-27 20:40:00.373][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-03-27 20:40:00.374][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-27 20:40:00.376][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-03-27 20:40:00.378][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:00.379][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:00.380][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:00.384][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:00.385][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:00.386][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:00.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:00.388][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:00.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:00.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:00.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:00.392][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:00.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:00.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:00.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:00.395][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:00.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:00.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:00.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:00.399][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:00.400][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:00.401][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:00.405][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:00.406][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:00.407][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:00.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:00.409][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2024-03-27 20:40:00.410][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-27 20:40:00.412][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2024-03-27 20:40:00.413][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-27 20:40:00.414][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-27 20:40:00.415][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-27 20:40:00.416][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-27 20:40:00.417][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-27 20:40:00.418][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-27 20:40:00.420][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:00.421][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:00.422][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:00.426][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:00.427][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:00.428][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:00.434][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:00.435][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2024-03-27 20:40:00.438][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:40:00.439][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:40:00.440][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2024-03-27 20:40:00.902][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2024-03-27 20:40:01.350][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:40:01.354][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2024-03-27 20:40:01.362][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2024-03-27 20:40:01.367][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2024-03-27 20:40:01.371][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-27 20:40:01.373][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-27 20:40:01.376][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-27 20:40:01.380][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:01.382][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:01.384][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:01.393][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:01.395][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:01.396][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:01.398][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:01.402][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:01.404][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:01.405][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:01.407][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:01.409][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:01.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:01.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:01.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:01.415][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-27 20:40:01.416][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-27 20:40:01.417][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:01.419][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:01.420][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:40:01.422][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:40:01.423][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:01.424][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:01.426][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-27 20:40:01.427][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-27 20:40:01.428][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:01.429][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:01.430][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-27 20:40:01.432][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-27 20:40:01.433][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:01.434][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:01.435][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:01.436][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:01.437][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:01.438][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:01.439][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-27 20:40:01.440][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:01.441][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:01.442][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:01.443][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:01.444][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:01.445][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:01.446][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:01.447][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:01.448][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:01.449][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:01.450][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:01.451][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:01.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:01.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:01.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:01.455][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-27 20:40:01.456][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-27 20:40:01.457][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:01.458][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:01.459][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-27 20:40:01.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-27 20:40:01.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:01.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:01.463][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-27 20:40:01.464][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-27 20:40:01.465][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:01.466][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:01.467][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:01.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:01.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:01.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:01.471][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:01.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:01.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:01.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:01.475][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:01.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:01.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:01.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:01.478][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:01.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:01.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:01.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:01.482][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:01.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:01.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:01.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:01.486][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:01.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:01.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:01.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:01.490][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:01.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:01.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:01.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:01.494][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:01.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:01.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:01.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:01.498][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:01.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:01.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:01.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:01.501][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:01.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:01.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:01.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:01.505][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2024-03-27 20:40:01.506][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:01.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:01.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:01.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:01.510][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:01.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:01.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:01.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:01.514][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:01.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:01.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:01.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:01.518][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:01.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:01.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:01.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:01.522][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:01.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:01.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:01.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:01.526][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:01.527][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:01.528][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:01.533][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:01.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:01.534][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:01.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:01.536][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2024-03-27 20:40:01.537][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-27 20:40:01.539][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2024-03-27 20:40:01.540][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-27 20:40:01.541][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-27 20:40:01.542][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-27 20:40:01.543][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-27 20:40:01.544][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-27 20:40:01.550][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-27 20:40:01.556][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:01.556][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:01.557][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:01.562][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:01.563][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:01.564][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:01.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:01.566][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2024-03-27 20:40:01.568][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:40:01.569][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:40:01.571][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2024-03-27 20:40:02.038][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2024-03-27 20:40:02.511][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:40:02.515][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2024-03-27 20:40:02.523][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2024-03-27 20:40:02.528][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2024-03-27 20:40:02.531][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-27 20:40:02.534][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-27 20:40:02.537][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-27 20:40:02.540][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:02.542][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:02.544][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:02.554][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:02.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:02.557][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:02.559][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:02.564][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:02.565][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:02.567][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:02.568][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:02.570][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:02.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:02.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:02.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:02.576][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-27 20:40:02.578][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-27 20:40:02.579][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:02.580][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:02.582][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:40:02.583][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:40:02.585][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:02.586][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:02.588][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-27 20:40:02.589][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-27 20:40:02.590][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:02.591][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:02.593][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-27 20:40:02.594][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-27 20:40:02.595][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:02.596][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:02.597][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:02.598][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:02.599][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:02.600][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:02.602][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-27 20:40:02.603][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:02.604][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:02.605][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:02.606][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:02.607][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:02.608][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:02.609][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:02.610][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:02.611][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:02.612][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:02.613][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:02.615][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:02.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:02.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:02.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:02.619][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-27 20:40:02.620][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-27 20:40:02.621][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:02.621][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:02.623][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-27 20:40:02.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-27 20:40:02.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:02.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:02.627][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-27 20:40:02.628][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-27 20:40:02.629][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:02.629][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:02.631][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:02.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:02.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:02.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:02.634][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:02.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:02.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:02.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:02.638][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:02.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:02.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:02.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:02.642][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:02.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:02.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:02.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:02.646][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:02.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:02.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:02.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:02.650][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:02.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:02.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:02.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:02.653][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:02.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:02.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:02.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:02.657][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:02.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:02.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:02.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:02.661][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:02.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:02.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:02.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:02.665][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:02.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:02.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:02.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:02.669][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2024-03-27 20:40:02.670][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:02.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:02.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:02.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:02.674][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:02.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:02.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:02.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:02.678][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:02.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:02.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:02.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:02.681][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:02.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:02.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:02.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:02.685][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:02.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:02.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:02.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:02.689][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:02.690][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:02.691][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:02.695][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:02.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:02.705][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:02.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:02.707][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2024-03-27 20:40:02.708][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-27 20:40:02.709][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2024-03-27 20:40:02.711][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-27 20:40:02.712][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-27 20:40:02.713][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-27 20:40:02.714][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-27 20:40:02.715][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-27 20:40:02.716][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-27 20:40:02.718][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:02.719][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:02.720][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:02.725][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:02.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:02.726][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:02.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:02.728][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2024-03-27 20:40:02.731][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:40:02.732][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:40:02.733][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2024-03-27 20:40:03.207][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2024-03-27 20:40:03.688][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:40:03.692][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2024-03-27 20:40:03.698][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2024-03-27 20:40:03.703][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2024-03-27 20:40:03.706][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-27 20:40:03.708][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-27 20:40:03.710][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-27 20:40:03.713][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:03.715][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:03.717][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:03.725][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:03.726][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:03.728][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:03.729][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:03.733][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:03.735][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:03.737][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:03.738][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:03.740][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:03.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:03.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:03.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:03.746][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-27 20:40:03.748][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-27 20:40:03.749][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:03.751][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:03.752][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:40:03.754][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:40:03.755][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:03.756][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:03.758][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-27 20:40:03.759][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-27 20:40:03.760][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:03.761][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:03.763][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-27 20:40:03.764][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-27 20:40:03.765][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:03.766][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:03.767][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:03.769][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:03.770][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:03.771][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:03.772][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-27 20:40:03.773][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:03.774][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:03.775][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:03.776][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:03.777][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:03.778][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:03.779][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:03.780][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:03.781][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:03.782][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:03.783][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:03.785][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:03.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:03.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:03.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:03.789][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-27 20:40:03.790][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-27 20:40:03.791][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:03.792][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:03.793][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-27 20:40:03.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-27 20:40:03.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:03.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:03.797][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-27 20:40:03.798][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-27 20:40:03.799][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:03.800][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:03.801][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:03.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:03.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:03.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:03.805][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:03.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:03.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:03.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:03.809][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:03.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:03.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:03.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:03.813][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:03.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:03.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:03.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:03.817][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:03.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:03.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:03.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:03.820][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:03.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:03.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:03.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:03.824][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:03.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:03.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:03.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:03.828][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:03.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:03.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:03.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:03.832][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:03.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:03.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:03.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:03.836][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:03.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:03.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:03.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:03.839][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2024-03-27 20:40:03.840][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:03.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:03.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:03.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:03.844][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:03.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:03.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:03.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:03.848][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:03.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:03.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:03.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:03.852][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:03.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:03.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:03.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:03.863][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:03.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:03.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:03.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:03.867][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:03.868][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:03.869][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:03.873][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:03.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:03.875][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:03.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:03.877][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2024-03-27 20:40:03.878][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-27 20:40:03.880][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2024-03-27 20:40:03.881][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-27 20:40:03.882][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-27 20:40:03.883][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-27 20:40:03.884][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-27 20:40:03.885][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-27 20:40:03.886][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-27 20:40:03.888][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:03.889][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:03.890][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:03.895][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:03.895][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:03.896][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:03.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:03.898][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2024-03-27 20:40:03.901][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:40:03.902][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:40:03.903][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2024-03-27 20:40:04.363][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2024-03-27 20:40:04.851][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:40:04.853][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2024-03-27 20:40:04.857][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2024-03-27 20:40:04.859][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2024-03-27 20:40:04.860][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-27 20:40:04.862][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-27 20:40:04.863][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-27 20:40:04.864][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:04.865][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:04.866][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:04.871][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:04.872][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:04.872][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:04.873][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:04.875][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:04.876][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:04.877][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:04.878][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:04.879][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:04.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:04.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:04.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:04.883][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-27 20:40:04.884][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-27 20:40:04.885][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:04.886][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:04.888][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-27 20:40:04.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-27 20:40:04.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:04.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:04.892][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:40:04.893][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:40:04.893][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:04.894][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:04.896][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:40:04.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:40:04.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:04.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:04.900][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-27 20:40:04.901][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-27 20:40:04.901][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:04.902][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:04.904][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-27 20:40:04.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-27 20:40:04.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:04.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:04.908][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-27 20:40:04.909][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-27 20:40:04.909][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:04.910][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:04.912][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-27 20:40:04.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-27 20:40:04.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:04.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:04.916][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:04.917][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:04.917][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:04.918][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:04.920][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:04.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:04.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:04.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:04.924][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-27 20:40:04.925][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:04.926][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:04.927][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:04.928][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-27 20:40:04.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:04.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:04.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:04.932][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:04.933][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:04.934][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:04.935][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:04.936][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:04.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:04.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:04.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:04.940][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:04.941][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:04.942][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:04.943][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:04.945][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:04.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:04.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:04.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:04.949][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-27 20:40:04.950][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-27 20:40:04.951][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:04.952][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:04.953][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-27 20:40:04.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-27 20:40:04.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:04.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:04.957][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-27 20:40:04.958][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-27 20:40:04.959][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:04.960][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:04.961][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-27 20:40:04.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-27 20:40:04.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:04.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:04.965][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:04.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:04.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:04.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:04.969][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:04.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:04.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:04.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:04.973][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:04.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:04.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:04.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:04.984][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:04.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:04.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:04.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:04.988][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:04.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:04.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:04.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:04.992][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:04.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:04.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:04.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:04.996][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:04.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:04.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:04.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:05.000][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:05.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:05.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:05.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:05.004][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:05.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:05.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:05.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:05.007][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:05.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:05.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:05.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:05.011][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2024-03-27 20:40:05.012][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:05.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:05.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:05.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:05.016][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:05.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:05.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:05.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:05.020][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:05.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:05.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:05.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:05.024][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:05.025][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:05.025][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:05.030][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:05.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:05.032][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:05.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:05.034][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2024-03-27 20:40:05.035][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-27 20:40:05.036][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2024-03-27 20:40:05.038][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-27 20:40:05.039][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-27 20:40:05.040][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-27 20:40:05.041][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-27 20:40:05.042][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-27 20:40:05.042][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-27 20:40:05.045][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:05.046][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:05.047][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:05.051][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:05.052][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:05.053][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:05.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:05.055][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2024-03-27 20:40:05.058][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:40:05.059][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:40:05.060][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2024-03-27 20:40:05.538][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2024-03-27 20:40:06.021][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:40:06.024][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2024-03-27 20:40:06.030][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2024-03-27 20:40:06.035][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2024-03-27 20:40:06.037][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-27 20:40:06.039][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-27 20:40:06.042][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-27 20:40:06.044][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:06.046][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:06.047][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:06.054][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:06.056][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:06.057][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:06.058][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:06.062][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:06.063][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:06.065][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:06.066][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:06.068][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:06.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:06.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:06.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:06.074][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-27 20:40:06.076][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-27 20:40:06.077][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:06.078][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:06.080][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-27 20:40:06.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-27 20:40:06.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:06.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:06.086][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:40:06.088][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:40:06.089][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:06.091][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:06.093][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:40:06.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:40:06.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:06.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:06.099][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-27 20:40:06.101][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-27 20:40:06.102][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:06.103][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:06.105][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-27 20:40:06.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-27 20:40:06.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:06.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:06.109][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-27 20:40:06.110][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-27 20:40:06.110][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:06.111][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:06.113][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-27 20:40:06.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-27 20:40:06.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:06.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:06.116][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:06.117][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:06.118][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:06.119][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:06.120][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:06.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:06.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:06.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:06.124][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-27 20:40:06.125][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:06.126][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:06.127][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:06.128][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-27 20:40:06.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:06.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:06.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:06.132][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:06.133][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:06.134][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:06.135][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:06.136][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:06.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:06.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:06.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:06.148][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:06.149][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:06.150][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:06.151][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:06.152][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:06.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:06.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:06.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:06.156][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-27 20:40:06.157][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-27 20:40:06.158][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:06.159][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:06.160][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-27 20:40:06.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-27 20:40:06.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:06.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:06.164][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-27 20:40:06.165][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-27 20:40:06.166][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:06.167][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:06.168][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-27 20:40:06.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-27 20:40:06.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:06.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:06.172][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:06.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:06.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:06.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:06.175][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:06.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:06.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:06.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:06.179][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:06.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:06.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:06.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:06.183][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:06.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:06.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:06.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:06.187][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:06.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:06.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:06.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:06.190][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:06.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:06.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:06.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:06.194][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:06.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:06.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:06.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:06.198][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:06.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:06.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:06.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:06.202][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:06.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:06.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:06.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:06.205][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:06.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:06.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:06.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:06.209][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2024-03-27 20:40:06.210][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:06.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:06.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:06.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:06.214][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:06.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:06.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:06.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:06.218][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:06.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:06.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:06.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:06.221][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:06.222][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:06.223][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:06.227][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:06.228][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:06.229][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:06.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:06.231][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2024-03-27 20:40:06.232][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-27 20:40:06.233][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2024-03-27 20:40:06.234][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-27 20:40:06.235][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-27 20:40:06.237][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-27 20:40:06.237][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-27 20:40:06.238][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-27 20:40:06.239][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-27 20:40:06.242][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:06.243][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:06.243][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:06.248][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:06.249][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:06.250][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:06.250][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:06.252][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2024-03-27 20:40:06.254][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:40:06.255][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:40:06.256][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2024-03-27 20:40:06.706][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2024-03-27 20:40:07.188][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:40:07.190][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2024-03-27 20:40:07.194][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2024-03-27 20:40:07.196][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2024-03-27 20:40:07.197][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-27 20:40:07.199][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-27 20:40:07.200][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-27 20:40:07.201][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:07.202][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:07.203][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:07.207][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:07.208][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:07.209][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:07.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:07.212][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:07.213][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:07.214][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:07.215][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:07.216][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:07.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:07.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:07.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:07.220][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-27 20:40:07.221][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-27 20:40:07.222][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:07.223][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:07.224][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-27 20:40:07.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-27 20:40:07.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:07.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:07.228][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:40:07.229][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:40:07.230][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:07.230][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:07.232][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:40:07.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:40:07.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:07.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:07.235][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-27 20:40:07.236][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-27 20:40:07.237][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:07.246][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:07.247][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-27 20:40:07.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-27 20:40:07.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:07.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:07.251][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-27 20:40:07.252][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-27 20:40:07.253][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:07.254][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:07.255][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-27 20:40:07.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-27 20:40:07.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:07.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:07.259][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:07.260][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:07.261][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:07.261][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:07.263][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-27 20:40:07.264][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:07.265][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:07.265][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:07.267][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-27 20:40:07.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:07.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:07.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:07.270][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:07.272][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:07.272][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:07.273][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:07.274][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:07.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:07.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:07.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:07.278][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:07.279][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:07.280][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:07.281][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:07.282][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:07.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:07.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:07.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:07.286][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-27 20:40:07.287][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-27 20:40:07.288][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:07.289][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:07.290][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-27 20:40:07.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-27 20:40:07.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:07.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:07.294][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-27 20:40:07.295][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-27 20:40:07.296][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:07.297][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:07.298][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-27 20:40:07.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-27 20:40:07.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:07.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:07.302][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:07.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:07.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:07.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:07.306][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:07.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:07.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:07.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:07.309][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:07.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:07.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:07.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:07.313][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:07.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:07.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:07.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:07.317][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:07.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:07.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:07.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:07.321][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:07.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:07.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:07.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:07.324][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:07.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:07.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:07.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:07.328][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:07.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:07.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:07.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:07.332][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:07.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:07.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:07.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:07.336][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:07.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:07.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:07.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:07.340][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2024-03-27 20:40:07.341][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:07.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:07.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:07.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:07.345][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:07.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:07.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:07.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:07.349][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:07.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:07.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:07.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:07.353][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:07.354][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:07.354][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:07.359][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:07.360][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:07.361][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:07.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:07.362][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2024-03-27 20:40:07.363][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-27 20:40:07.365][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2024-03-27 20:40:07.366][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-27 20:40:07.367][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-27 20:40:07.368][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-27 20:40:07.369][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-27 20:40:07.370][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-27 20:40:07.371][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-27 20:40:07.374][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:07.374][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:07.375][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:07.380][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:07.381][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:07.381][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:07.382][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:07.383][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2024-03-27 20:40:07.386][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:40:07.387][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:40:07.388][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2024-03-27 20:40:07.838][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2024-03-27 20:40:08.282][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:40:08.285][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2024-03-27 20:40:08.288][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2024-03-27 20:40:08.291][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2024-03-27 20:40:08.292][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-27 20:40:08.293][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-27 20:40:08.295][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-27 20:40:08.296][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:08.297][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:08.298][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:08.322][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:08.324][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:08.325][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:08.327][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:08.331][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:08.333][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:08.334][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:08.335][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:08.337][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:08.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:08.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:08.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:08.342][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-27 20:40:08.343][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-27 20:40:08.344][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:08.346][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:08.347][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-27 20:40:08.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-27 20:40:08.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:08.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:08.352][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:40:08.353][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:40:08.354][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:08.355][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:08.356][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:40:08.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:40:08.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:08.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:08.360][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-27 20:40:08.361][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-27 20:40:08.362][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:08.363][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:08.365][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-27 20:40:08.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-27 20:40:08.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:08.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:08.369][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-27 20:40:08.370][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-27 20:40:08.371][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:08.372][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:08.373][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-27 20:40:08.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-27 20:40:08.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:08.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:08.378][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:08.379][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:08.380][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:08.381][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:08.382][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-27 20:40:08.383][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:08.384][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:08.385][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:08.386][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-27 20:40:08.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:08.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:08.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:08.390][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:08.392][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:08.393][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:08.393][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:08.395][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:08.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:08.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:08.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:08.399][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:08.400][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:08.401][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:08.402][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:08.404][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:08.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:08.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:08.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:08.408][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-27 20:40:08.409][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-27 20:40:08.410][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:08.411][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:08.412][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-27 20:40:08.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-27 20:40:08.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:08.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:08.416][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-27 20:40:08.417][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-27 20:40:08.418][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:08.419][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:08.421][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-27 20:40:08.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-27 20:40:08.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:08.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:08.425][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:08.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:08.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:08.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:08.429][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:08.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:08.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:08.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:08.433][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:08.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:08.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:08.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:08.437][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:08.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:08.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:08.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:08.441][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:08.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:08.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:08.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:08.446][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:08.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:08.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:08.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:08.450][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:08.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:08.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:08.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:08.454][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:08.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:08.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:08.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:08.458][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:08.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:08.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:08.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:08.462][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:08.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:08.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:08.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:08.466][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2024-03-27 20:40:08.467][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:08.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:08.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:08.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:08.472][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:08.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:08.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:08.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:08.476][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:08.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:08.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:08.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:08.480][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:08.481][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:08.482][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:08.487][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:08.488][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:08.489][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:08.490][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:08.491][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2024-03-27 20:40:08.492][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-27 20:40:08.494][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2024-03-27 20:40:08.495][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-27 20:40:08.496][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-27 20:40:08.497][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-27 20:40:08.498][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-27 20:40:08.500][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-27 20:40:08.501][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-27 20:40:08.504][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:08.505][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:08.506][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:08.521][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:08.522][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:08.523][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:08.524][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:08.525][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2024-03-27 20:40:08.528][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:40:08.529][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:40:08.530][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2024-03-27 20:40:08.979][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2024-03-27 20:40:09.454][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:40:09.457][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2024-03-27 20:40:09.463][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2024-03-27 20:40:09.467][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2024-03-27 20:40:09.470][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-27 20:40:09.472][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-27 20:40:09.474][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-27 20:40:09.477][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:09.479][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:09.480][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:09.488][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:09.490][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:09.491][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:09.493][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:09.496][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:09.498][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:09.500][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:09.501][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:09.503][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:09.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:09.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:09.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:09.509][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-27 20:40:09.511][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-27 20:40:09.512][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:09.513][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:09.515][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-27 20:40:09.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-27 20:40:09.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:09.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:09.520][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:40:09.521][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:40:09.522][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:09.523][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:09.525][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:40:09.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:40:09.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:09.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:09.529][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-27 20:40:09.530][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-27 20:40:09.531][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:09.532][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:09.533][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-27 20:40:09.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-27 20:40:09.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:09.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:09.537][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-27 20:40:09.538][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-27 20:40:09.539][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:09.540][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:09.541][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-27 20:40:09.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-27 20:40:09.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:09.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:09.545][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:09.546][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:09.547][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:09.548][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:09.549][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-27 20:40:09.550][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:09.551][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:09.552][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:09.553][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-27 20:40:09.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:09.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:09.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:09.557][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:09.558][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:09.559][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:09.560][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:09.561][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:09.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:09.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:09.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:09.565][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:09.566][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:09.566][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:09.567][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:09.569][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:09.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:09.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:09.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:09.572][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-27 20:40:09.573][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-27 20:40:09.574][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:09.575][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:09.576][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-27 20:40:09.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-27 20:40:09.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:09.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:09.580][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-27 20:40:09.581][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-27 20:40:09.582][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:09.583][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:09.584][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-27 20:40:09.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-27 20:40:09.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:09.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:09.588][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:09.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:09.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:09.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:09.592][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:09.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:09.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:09.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:09.596][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:09.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:09.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:09.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:09.599][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:09.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:09.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:09.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:09.603][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:09.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:09.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:09.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:09.607][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:09.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:09.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:09.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:09.611][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:09.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:09.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:09.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:09.615][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:09.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:09.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:09.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:09.619][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:09.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:09.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:09.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:09.623][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:09.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:09.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:09.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:09.626][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2024-03-27 20:40:09.628][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:09.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:09.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:09.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:09.640][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:09.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:09.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:09.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:09.644][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:09.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:09.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:09.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:09.647][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:09.648][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:09.649][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:09.654][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:09.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:09.655][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:09.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:09.657][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2024-03-27 20:40:09.658][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-27 20:40:09.660][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2024-03-27 20:40:09.661][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-27 20:40:09.662][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-27 20:40:09.663][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-27 20:40:09.664][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-27 20:40:09.665][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-27 20:40:09.666][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-27 20:40:09.669][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:09.670][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:09.670][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:09.675][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:09.676][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:09.677][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:09.678][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:09.679][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2024-03-27 20:40:09.682][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:40:09.683][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:40:09.684][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2024-03-27 20:40:10.138][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2024-03-27 20:40:10.585][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:40:10.588][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2024-03-27 20:40:10.591][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2024-03-27 20:40:10.593][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2024-03-27 20:40:10.595][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-27 20:40:10.596][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-27 20:40:10.597][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-27 20:40:10.599][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:10.599][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:10.600][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:10.605][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:10.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:10.606][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:10.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:10.609][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:10.610][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:10.611][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:10.612][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:10.614][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:10.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:10.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:10.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:10.619][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-27 20:40:10.621][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-27 20:40:10.622][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:10.623][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:10.624][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-27 20:40:10.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-27 20:40:10.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:10.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:10.629][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:40:10.630][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:40:10.631][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:10.632][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:10.634][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:40:10.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:40:10.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:10.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:10.638][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-27 20:40:10.639][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-27 20:40:10.640][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:10.641][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:10.642][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-27 20:40:10.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-27 20:40:10.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:10.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:10.646][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-27 20:40:10.647][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-27 20:40:10.648][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:10.649][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:10.650][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-27 20:40:10.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-27 20:40:10.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:10.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:10.654][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:10.655][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:10.656][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:10.656][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:10.658][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-27 20:40:10.659][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:10.660][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:10.660][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:10.662][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-27 20:40:10.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:10.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:10.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:10.666][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:10.667][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:10.667][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:10.668][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:10.670][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:10.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:10.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:10.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:10.673][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:10.674][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:10.675][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:10.676][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:10.678][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:10.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:10.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:10.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:10.681][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-27 20:40:10.682][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-27 20:40:10.683][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:10.684][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:10.685][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-27 20:40:10.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-27 20:40:10.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:10.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:10.689][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-27 20:40:10.690][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-27 20:40:10.691][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:10.692][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:10.693][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-27 20:40:10.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-27 20:40:10.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:10.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:10.697][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:10.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:10.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:10.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:10.701][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:10.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:10.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:10.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:10.705][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:10.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:10.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:10.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:10.744][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:10.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:10.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:10.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:10.748][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:10.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:10.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:10.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:10.752][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:10.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:10.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:10.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:10.755][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:10.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:10.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:10.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:10.760][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:10.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:10.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:10.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:10.763][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:10.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:10.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:10.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:10.767][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:10.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:10.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:10.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:10.771][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2024-03-27 20:40:10.772][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:10.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:10.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:10.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:10.776][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:10.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:10.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:10.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:10.779][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:10.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:10.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:10.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:10.783][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:10.784][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:10.785][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:10.789][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:10.790][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:10.791][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:10.792][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:10.793][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2024-03-27 20:40:10.794][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-27 20:40:10.795][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2024-03-27 20:40:10.797][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-27 20:40:10.798][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-27 20:40:10.799][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-27 20:40:10.800][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-27 20:40:10.801][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-27 20:40:10.802][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-27 20:40:10.804][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:10.805][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:10.806][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:10.810][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:10.811][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:10.812][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:10.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:10.814][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2024-03-27 20:40:10.817][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:40:10.818][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:40:10.819][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2024-03-27 20:40:11.271][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2024-03-27 20:40:11.758][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:40:11.762][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2024-03-27 20:40:11.770][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2024-03-27 20:40:11.775][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2024-03-27 20:40:11.778][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-27 20:40:11.781][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-27 20:40:11.783][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-27 20:40:11.787][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:11.789][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:11.791][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:11.800][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:11.802][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:11.804][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:11.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:11.809][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:11.811][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:11.812][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:11.814][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:11.816][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:11.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:11.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:11.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:11.821][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-27 20:40:11.823][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-27 20:40:11.824][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:11.825][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:11.827][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-27 20:40:11.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-27 20:40:11.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:11.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:11.832][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:40:11.834][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:40:11.835][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:11.836][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:11.837][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:40:11.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:40:11.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:11.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:11.842][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-27 20:40:11.843][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-27 20:40:11.844][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:11.845][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:11.846][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-27 20:40:11.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-27 20:40:11.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:11.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:11.850][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-27 20:40:11.851][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-27 20:40:11.852][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:11.853][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:11.854][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-27 20:40:11.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-27 20:40:11.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:11.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:11.858][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:11.859][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:11.860][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:11.861][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:11.862][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-27 20:40:11.863][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:11.864][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:11.865][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:11.866][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-27 20:40:11.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:11.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:11.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:11.870][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:11.871][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:11.872][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:11.873][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:11.874][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:11.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:11.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:11.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:11.878][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:11.879][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:11.880][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:11.881][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:11.889][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:11.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:11.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:11.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:11.894][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-27 20:40:11.895][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-27 20:40:11.895][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:11.896][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:11.898][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-27 20:40:11.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-27 20:40:11.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:11.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:11.902][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-27 20:40:11.903][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-27 20:40:11.903][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:11.904][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:11.906][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-27 20:40:11.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-27 20:40:11.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:11.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:11.910][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:11.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:11.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:11.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:11.913][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:11.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:11.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:11.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:11.917][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:11.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:11.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:11.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:11.921][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:11.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:11.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:11.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:11.925][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:11.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:11.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:11.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:11.928][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:11.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:11.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:11.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:11.932][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:11.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:11.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:11.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:11.936][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:11.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:11.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:11.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:11.940][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:11.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:11.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:11.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:11.944][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:11.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:11.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:11.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:11.948][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2024-03-27 20:40:11.949][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:11.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:11.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:11.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:11.953][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:11.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:11.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:11.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:11.956][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:11.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:11.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:11.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:11.960][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:11.961][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:11.962][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:11.967][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:11.967][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:11.968][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:11.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:11.970][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2024-03-27 20:40:11.971][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-27 20:40:11.973][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2024-03-27 20:40:11.974][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-27 20:40:11.975][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-27 20:40:11.976][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-27 20:40:11.977][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-27 20:40:11.978][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-27 20:40:11.979][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-27 20:40:11.982][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:11.983][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:11.983][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:11.988][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:11.989][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:11.990][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:11.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:11.992][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2024-03-27 20:40:11.994][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:40:11.995][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:40:11.997][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2024-03-27 20:40:12.449][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2024-03-27 20:40:12.937][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:40:12.940][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2024-03-27 20:40:12.946][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2024-03-27 20:40:12.951][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2024-03-27 20:40:12.954][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-27 20:40:12.956][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-27 20:40:12.958][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-27 20:40:12.961][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:12.962][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:12.964][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:12.972][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:12.974][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:12.975][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:12.977][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:12.981][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:12.983][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:12.984][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:12.986][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:12.988][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:12.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:12.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:12.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:12.993][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-27 20:40:12.995][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-27 20:40:12.996][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:12.997][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:12.999][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-27 20:40:13.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-27 20:40:13.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:13.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:13.004][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:40:13.005][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:40:13.006][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:13.007][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:13.008][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:40:13.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:40:13.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:13.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:13.013][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-27 20:40:13.014][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-27 20:40:13.015][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:13.016][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:13.017][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-27 20:40:13.018][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-27 20:40:13.019][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:13.020][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:13.021][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:13.030][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:13.031][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:13.032][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:13.033][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-27 20:40:13.035][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:13.035][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:13.036][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:13.038][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-27 20:40:13.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:13.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:13.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:13.041][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:13.042][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:13.043][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:13.044][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:13.045][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:13.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:13.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:13.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:13.049][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:13.050][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:13.051][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:13.052][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:13.054][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:13.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:13.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:13.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:13.057][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-27 20:40:13.058][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-27 20:40:13.059][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:13.060][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:13.061][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-27 20:40:13.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-27 20:40:13.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:13.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:13.065][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-27 20:40:13.066][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-27 20:40:13.067][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:13.068][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:13.069][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:13.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:13.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:13.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:13.073][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:13.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:13.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:13.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:13.077][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:13.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:13.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:13.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:13.080][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:13.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:13.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:13.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:13.084][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:13.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:13.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:13.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:13.088][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:13.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:13.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:13.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:13.092][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:13.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:13.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:13.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:13.096][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:13.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:13.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:13.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:13.099][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:13.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:13.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:13.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:13.103][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:13.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:13.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:13.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:13.107][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2024-03-27 20:40:13.108][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:13.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:13.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:13.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:13.112][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:13.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:13.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:13.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:13.116][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:13.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:13.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:13.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:13.119][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:13.120][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:13.121][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:13.125][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:13.126][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:13.127][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:13.128][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:13.129][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2024-03-27 20:40:13.130][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-27 20:40:13.131][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2024-03-27 20:40:13.133][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-27 20:40:13.134][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-27 20:40:13.135][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-27 20:40:13.136][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-27 20:40:13.137][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-27 20:40:13.138][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-27 20:40:13.140][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:13.141][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:13.142][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:13.146][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:13.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:13.148][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:13.149][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:13.150][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2024-03-27 20:40:13.153][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:40:13.154][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:40:13.155][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2024-03-27 20:40:13.605][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2024-03-27 20:40:14.087][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:40:14.091][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2024-03-27 20:40:14.099][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2024-03-27 20:40:14.105][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2024-03-27 20:40:14.108][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-27 20:40:14.111][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-27 20:40:14.114][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-27 20:40:14.117][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:14.120][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:14.122][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:14.131][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:14.133][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:14.135][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:14.137][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:14.141][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:14.143][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:14.144][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:14.146][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:14.148][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:14.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:14.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:14.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:14.154][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-27 20:40:14.155][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-27 20:40:14.156][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:14.157][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:14.159][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-27 20:40:14.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-27 20:40:14.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:14.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:14.173][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:40:14.174][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:40:14.175][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:14.176][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:14.177][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:40:14.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:40:14.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:14.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:14.181][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-27 20:40:14.182][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-27 20:40:14.183][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:14.184][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:14.186][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-27 20:40:14.187][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-27 20:40:14.187][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:14.188][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:14.190][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:14.191][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:14.191][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:14.192][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:14.194][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-27 20:40:14.195][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:14.195][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:14.196][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:14.198][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-27 20:40:14.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:14.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:14.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:14.201][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:14.202][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:14.203][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:14.204][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:14.205][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:14.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:14.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:14.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:14.209][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:14.210][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:14.211][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:14.212][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:14.214][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:14.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:14.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:14.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:14.217][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-27 20:40:14.218][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-27 20:40:14.219][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:14.220][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:14.221][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-27 20:40:14.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-27 20:40:14.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:14.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:14.225][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-27 20:40:14.226][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-27 20:40:14.227][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:14.228][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:14.229][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:14.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:14.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:14.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:14.233][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:14.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:14.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:14.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:14.237][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:14.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:14.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:14.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:14.241][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:14.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:14.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:14.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:14.245][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:14.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:14.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:14.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:14.248][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:14.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:14.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:14.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:14.252][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:14.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:14.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:14.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:14.256][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:14.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:14.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:14.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:14.260][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:14.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:14.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:14.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:14.264][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:14.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:14.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:14.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:14.268][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2024-03-27 20:40:14.269][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:14.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:14.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:14.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:14.272][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:14.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:14.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:14.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:14.276][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:14.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:14.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:14.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:14.280][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:14.281][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:14.282][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:14.286][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:14.287][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:14.288][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:14.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:14.290][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2024-03-27 20:40:14.291][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-27 20:40:14.292][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2024-03-27 20:40:14.294][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-27 20:40:14.295][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-27 20:40:14.296][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-27 20:40:14.297][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-27 20:40:14.298][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-27 20:40:14.299][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-27 20:40:14.301][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:14.302][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:14.303][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:14.307][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:14.308][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:14.309][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:14.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:14.311][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2024-03-27 20:40:14.314][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:40:14.315][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:40:14.316][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2024-03-27 20:40:14.769][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2024-03-27 20:40:15.254][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:40:15.256][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2024-03-27 20:40:15.259][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2024-03-27 20:40:15.261][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2024-03-27 20:40:15.263][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-27 20:40:15.264][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-27 20:40:15.265][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-27 20:40:15.267][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:15.268][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:15.269][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:15.282][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:15.283][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:15.284][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:15.285][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:15.287][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:15.288][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:15.289][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:15.290][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:15.291][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:15.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:15.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:15.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:15.295][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-27 20:40:15.296][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-27 20:40:15.297][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:15.298][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:15.299][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-27 20:40:15.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-27 20:40:15.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:15.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:15.303][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:40:15.304][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:40:15.305][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:15.306][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:15.307][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:40:15.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:40:15.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:15.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:15.311][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-27 20:40:15.312][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-27 20:40:15.313][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:15.314][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:15.315][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-27 20:40:15.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-27 20:40:15.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:15.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:15.319][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-27 20:40:15.320][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-27 20:40:15.321][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:15.322][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:15.323][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-27 20:40:15.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-27 20:40:15.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:15.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:15.327][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:15.328][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:15.329][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:15.330][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:15.331][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-27 20:40:15.332][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:15.333][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:15.334][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:15.335][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-27 20:40:15.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:15.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:15.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:15.339][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:15.340][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:15.341][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:15.342][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:15.343][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:15.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:15.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:15.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:15.347][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:15.348][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:15.349][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:15.349][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:15.351][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:15.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:15.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:15.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:15.355][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-27 20:40:15.356][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-27 20:40:15.357][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:15.357][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:15.359][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-27 20:40:15.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-27 20:40:15.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:15.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:15.362][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-27 20:40:15.363][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-27 20:40:15.364][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:15.365][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:15.366][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-27 20:40:15.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-27 20:40:15.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:15.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:15.370][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:15.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:15.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:15.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:15.374][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:15.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:15.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:15.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:15.378][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:15.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:15.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:15.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:15.382][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:15.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:15.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:15.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:15.385][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:15.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:15.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:15.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:15.389][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:15.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:15.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:15.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:15.393][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:15.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:15.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:15.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:15.397][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:15.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:15.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:15.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:15.401][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:15.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:15.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:15.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:15.405][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:15.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:15.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:15.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:15.408][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2024-03-27 20:40:15.410][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:15.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:15.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:15.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:15.413][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:15.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:15.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:15.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:15.417][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:15.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:15.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:15.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:15.421][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:15.422][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:15.423][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:15.427][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:15.428][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:15.429][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:15.430][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:15.431][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2024-03-27 20:40:15.432][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-27 20:40:15.433][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2024-03-27 20:40:15.435][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-27 20:40:15.436][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-27 20:40:15.437][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-27 20:40:15.438][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-27 20:40:15.439][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-27 20:40:15.440][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-27 20:40:15.442][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:15.443][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:15.444][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:15.454][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:15.455][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:15.456][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:15.456][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:15.458][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2024-03-27 20:40:15.460][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:40:15.461][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:40:15.463][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2024-03-27 20:40:15.912][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2024-03-27 20:40:16.355][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:40:16.357][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2024-03-27 20:40:16.360][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2024-03-27 20:40:16.363][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2024-03-27 20:40:16.364][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-27 20:40:16.366][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-27 20:40:16.367][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-27 20:40:16.368][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:16.369][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:16.370][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:16.375][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:16.376][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:16.377][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:16.378][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:16.380][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:16.381][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:16.382][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:16.383][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:16.384][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:16.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:16.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:16.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:16.388][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-27 20:40:16.389][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-27 20:40:16.390][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:16.391][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:16.392][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-27 20:40:16.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-27 20:40:16.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:16.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:16.397][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:40:16.398][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:40:16.399][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:16.400][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:16.401][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:40:16.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:40:16.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:16.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:16.405][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-27 20:40:16.406][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-27 20:40:16.407][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:16.408][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:16.409][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-27 20:40:16.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-27 20:40:16.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:16.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:16.413][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-27 20:40:16.414][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-27 20:40:16.415][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:16.416][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:16.417][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-27 20:40:16.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-27 20:40:16.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:16.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:16.421][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:16.422][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:16.423][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:16.424][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:16.425][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-27 20:40:16.426][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:16.427][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:16.428][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:16.429][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-27 20:40:16.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:16.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:16.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:16.433][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:16.434][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:16.435][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:16.436][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:16.437][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:16.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:16.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:16.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:16.441][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:16.442][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:16.443][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:16.444][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:16.445][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:16.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:16.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:16.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:16.449][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-27 20:40:16.450][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-27 20:40:16.451][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:16.452][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:16.453][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-27 20:40:16.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-27 20:40:16.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:16.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:16.457][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-27 20:40:16.458][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-27 20:40:16.459][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:16.460][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:16.461][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-27 20:40:16.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-27 20:40:16.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:16.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:16.465][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:16.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:16.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:16.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:16.469][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:16.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:16.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:16.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:16.473][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:16.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:16.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:16.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:16.477][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:16.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:16.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:16.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:16.481][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:16.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:16.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:16.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:16.485][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:16.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:16.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:16.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:16.489][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:16.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:16.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:16.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:16.493][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:16.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:16.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:16.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:16.497][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:16.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:16.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:16.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:16.501][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:16.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:16.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:16.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:16.504][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2024-03-27 20:40:16.506][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:16.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:16.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:16.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:16.509][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:16.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:16.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:16.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:16.522][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:16.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:16.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:16.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:16.526][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:16.527][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:16.528][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:16.532][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:16.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:16.534][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:16.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:16.536][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2024-03-27 20:40:16.537][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-27 20:40:16.538][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2024-03-27 20:40:16.539][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-27 20:40:16.541][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-27 20:40:16.542][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-27 20:40:16.543][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-27 20:40:16.544][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-27 20:40:16.545][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-27 20:40:16.547][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:16.548][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:16.549][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:16.553][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:16.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:16.555][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:16.556][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:16.557][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2024-03-27 20:40:16.560][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:40:16.561][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:40:16.562][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2024-03-27 20:40:17.009][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2024-03-27 20:40:17.470][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:40:17.475][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2024-03-27 20:40:17.482][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2024-03-27 20:40:17.488][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2024-03-27 20:40:17.492][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-27 20:40:17.495][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-27 20:40:17.498][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-27 20:40:17.501][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:17.503][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:17.505][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:17.515][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:17.516][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:17.518][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:17.520][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:17.524][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:17.526][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:17.527][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:17.529][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:17.531][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:17.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:17.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:17.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:17.537][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-27 20:40:17.538][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-27 20:40:17.539][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:17.540][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:17.542][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-27 20:40:17.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-27 20:40:17.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:17.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:17.547][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:40:17.548][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:40:17.550][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:17.551][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:17.552][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:40:17.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:40:17.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:17.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:17.557][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-27 20:40:17.558][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-27 20:40:17.559][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:17.560][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:17.561][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-27 20:40:17.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-27 20:40:17.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:17.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:17.565][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-27 20:40:17.566][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-27 20:40:17.567][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:17.568][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:17.569][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-27 20:40:17.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-27 20:40:17.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:17.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:17.573][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:17.574][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:17.575][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:17.576][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:17.577][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-27 20:40:17.578][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:17.579][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:17.580][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:17.581][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-27 20:40:17.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:17.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:17.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:17.586][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:17.587][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:17.588][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:17.589][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:17.590][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:17.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:17.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:17.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:17.594][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:17.595][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:17.596][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:17.597][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:17.598][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:17.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:17.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:17.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:17.602][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-27 20:40:17.603][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-27 20:40:17.604][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:17.605][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:17.606][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-27 20:40:17.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-27 20:40:17.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:17.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:17.610][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-27 20:40:17.611][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-27 20:40:17.612][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:17.613][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:17.614][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-27 20:40:17.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-27 20:40:17.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:17.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:17.618][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:17.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:17.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:17.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:17.622][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:17.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:17.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:17.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:17.626][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:17.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:17.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:17.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:17.630][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:17.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:17.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:17.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:17.644][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:17.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:17.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:17.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:17.648][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:17.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:17.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:17.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:17.653][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:17.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:17.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:17.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:17.657][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:17.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:17.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:17.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:17.661][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:17.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:17.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:17.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:17.665][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:17.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:17.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:17.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:17.669][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2024-03-27 20:40:17.670][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:17.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:17.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:17.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:17.674][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:17.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:17.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:17.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:17.678][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:17.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:17.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:17.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:17.682][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:17.683][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:17.684][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:17.689][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:17.689][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:17.690][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:17.691][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:17.692][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2024-03-27 20:40:17.693][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-27 20:40:17.695][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2024-03-27 20:40:17.696][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-27 20:40:17.697][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-27 20:40:17.698][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-27 20:40:17.699][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-27 20:40:17.700][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-27 20:40:17.701][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-27 20:40:17.704][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:17.705][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:17.706][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:17.710][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:17.711][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:17.712][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:17.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:17.714][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2024-03-27 20:40:17.717][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:40:17.718][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:40:17.719][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2024-03-27 20:40:18.170][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2024-03-27 20:40:18.655][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:40:18.660][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2024-03-27 20:40:18.674][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2024-03-27 20:40:18.687][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2024-03-27 20:40:18.691][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-27 20:40:18.695][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-27 20:40:18.698][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-27 20:40:18.703][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:18.705][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:18.707][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:18.718][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:18.720][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:18.721][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:18.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:18.727][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:18.729][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:18.730][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:18.732][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:18.733][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:18.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:18.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:18.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:18.739][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-27 20:40:18.740][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-27 20:40:18.742][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:18.743][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:18.745][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-27 20:40:18.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-27 20:40:18.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:18.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:18.750][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:40:18.751][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:40:18.752][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:18.753][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:18.755][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:40:18.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:40:18.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:18.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:18.760][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-27 20:40:18.761][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-27 20:40:18.762][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:18.763][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:18.764][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-27 20:40:18.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-27 20:40:18.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:18.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:18.769][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-27 20:40:18.770][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-27 20:40:18.771][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:18.772][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:18.774][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-27 20:40:18.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-27 20:40:18.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:18.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:18.778][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:18.780][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:18.781][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:18.782][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:18.783][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-27 20:40:18.785][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:18.786][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:18.787][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:18.788][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-27 20:40:18.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:18.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:18.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:18.793][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:18.794][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:18.795][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:18.796][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:18.797][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:18.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:18.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:18.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:18.802][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:18.803][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:18.804][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:18.805][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:18.807][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:18.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:18.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:18.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:18.834][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-27 20:40:18.836][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-27 20:40:18.837][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:18.838][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:18.839][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-27 20:40:18.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-27 20:40:18.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:18.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:18.844][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-27 20:40:18.846][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-27 20:40:18.847][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:18.848][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:18.849][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-27 20:40:18.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-27 20:40:18.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:18.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:18.854][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:18.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:18.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:18.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:18.859][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:18.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:18.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:18.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:18.863][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:18.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:18.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:18.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:18.867][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:18.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:18.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:18.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:18.872][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:18.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:18.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:18.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:18.876][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:18.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:18.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:18.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:18.880][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:18.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:18.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:18.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:18.885][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:18.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:18.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:18.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:18.889][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:18.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:18.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:18.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:18.893][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:18.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:18.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:18.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:18.897][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2024-03-27 20:40:18.898][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:18.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:18.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:18.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:18.903][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:18.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:18.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:18.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:18.907][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:18.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:18.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:18.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:18.911][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:18.912][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:18.913][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:18.918][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:18.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:18.920][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:18.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:18.922][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2024-03-27 20:40:18.923][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-27 20:40:18.925][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2024-03-27 20:40:18.926][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-27 20:40:18.927][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-27 20:40:18.928][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-27 20:40:18.930][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-27 20:40:18.931][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-27 20:40:18.931][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-27 20:40:18.934][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:18.935][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:18.936][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:18.941][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:18.942][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:18.942][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:18.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:18.945][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2024-03-27 20:40:18.947][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:40:18.948][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:40:18.950][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2024-03-27 20:40:19.402][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2024-03-27 20:40:19.865][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:40:19.867][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2024-03-27 20:40:19.871][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2024-03-27 20:40:19.874][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2024-03-27 20:40:19.875][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-27 20:40:19.876][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-27 20:40:19.877][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-27 20:40:19.879][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:19.880][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:19.881][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:19.886][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:19.887][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:19.888][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:19.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:19.892][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:19.893][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:19.894][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:19.895][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:19.896][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:19.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:19.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:19.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:19.901][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-27 20:40:19.902][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-27 20:40:19.903][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:19.904][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:19.905][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-27 20:40:19.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-27 20:40:19.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:19.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:19.909][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:40:19.910][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:40:19.911][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:19.912][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:19.913][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:40:19.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:40:19.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:19.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:19.917][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-27 20:40:19.918][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-27 20:40:19.919][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:19.920][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:19.922][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-27 20:40:19.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-27 20:40:19.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:19.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:19.926][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-27 20:40:19.927][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-27 20:40:19.928][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:19.940][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:19.942][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-27 20:40:19.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-27 20:40:19.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:19.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:19.947][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:19.948][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:19.949][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:19.950][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:19.951][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-27 20:40:19.952][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:19.953][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:19.954][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:19.956][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-27 20:40:19.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:19.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:19.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:19.960][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:19.961][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:19.962][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:19.963][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:19.964][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:19.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:19.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:19.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:19.968][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:19.969][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:19.970][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:19.971][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:19.972][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:19.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:19.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:19.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:19.976][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-27 20:40:19.977][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-27 20:40:19.978][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:19.979][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:19.980][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-27 20:40:19.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-27 20:40:19.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:19.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:19.984][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-27 20:40:19.985][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-27 20:40:19.986][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:19.987][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:19.988][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-27 20:40:19.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-27 20:40:19.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:19.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:19.992][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:19.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:19.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:19.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:19.996][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:19.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:19.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:19.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:20.000][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:20.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:20.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:20.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:20.004][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:20.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:20.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:20.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:20.008][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:20.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:20.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:20.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:20.012][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:20.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:20.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:20.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:20.015][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:20.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:20.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:20.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:20.019][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:20.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:20.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:20.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:20.023][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:20.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:20.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:20.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:20.027][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:20.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:20.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:20.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:20.031][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2024-03-27 20:40:20.032][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:20.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:20.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:20.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:20.036][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:20.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:20.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:20.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:20.040][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:20.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:20.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:20.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:20.043][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:20.044][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:20.045][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:20.050][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:20.051][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:20.052][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:20.052][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:20.054][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2024-03-27 20:40:20.055][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-27 20:40:20.056][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2024-03-27 20:40:20.057][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-27 20:40:20.058][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-27 20:40:20.060][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-27 20:40:20.061][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-27 20:40:20.062][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-27 20:40:20.063][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-27 20:40:20.065][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:20.066][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:20.067][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:20.071][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:20.072][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:20.073][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:20.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:20.075][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.DEBUG[2024-03-27 20:40:20.078][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:40:20.079][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:40:20.080][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.TRACE[2024-03-27 20:40:20.532][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655).
biodb.DEBUG[2024-03-27 20:40:21.004][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:40:21.008][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content"
biodb.TRACE[2024-03-27 20:40:21.015][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request"
biodb.TRACE[2024-03-27 20:40:21.021][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml"
biodb.DEBUG[2024-03-27 20:40:21.024][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-27 20:40:21.027][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-27 20:40:21.029][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-27 20:40:21.033][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:21.035][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:21.037][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:21.046][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:21.048][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:21.050][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:21.052][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:21.056][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:21.057][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:21.065][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:21.071][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:21.073][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:21.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:21.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:21.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:21.078][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-27 20:40:21.079][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-27 20:40:21.080][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:21.082][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:21.083][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-27 20:40:21.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-27 20:40:21.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:21.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:21.088][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:40:21.089][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:40:21.090][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:21.091][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:21.092][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:40:21.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:40:21.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:21.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:21.097][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-27 20:40:21.098][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-27 20:40:21.099][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:21.099][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:21.101][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-27 20:40:21.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-27 20:40:21.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:21.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:21.105][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-27 20:40:21.106][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-27 20:40:21.106][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:21.107][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:21.109][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-27 20:40:21.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-27 20:40:21.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:21.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:21.112][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:21.113][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:21.114][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:21.115][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:21.117][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-27 20:40:21.118][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:21.118][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:21.119][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:21.121][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-27 20:40:21.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:21.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:21.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:21.124][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:21.125][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:21.126][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:21.127][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:21.128][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:21.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:21.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:21.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:21.132][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:21.133][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:21.134][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:21.135][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:21.137][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:21.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:21.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:21.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:21.141][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-27 20:40:21.142][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-27 20:40:21.142][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:21.143][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:21.145][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-27 20:40:21.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-27 20:40:21.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:21.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:21.148][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-27 20:40:21.149][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-27 20:40:21.150][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:21.151][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:21.152][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-27 20:40:21.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-27 20:40:21.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:21.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:21.156][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:21.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:21.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:21.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:21.160][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:21.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:21.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:21.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:21.164][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:21.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:21.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:21.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:21.168][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:21.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:21.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:21.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:21.172][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:21.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:21.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:21.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:21.175][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:21.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:21.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:21.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:21.179][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:21.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:21.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:21.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:21.183][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:21.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:21.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:21.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:21.187][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:21.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:21.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:21.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:21.191][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:21.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:21.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:21.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:21.195][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2024-03-27 20:40:21.196][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:21.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:21.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:21.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:21.200][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:21.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:21.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:21.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:21.203][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:21.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:21.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:21.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:21.207][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:21.208][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:21.209][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:21.214][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:21.215][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:21.215][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:21.216][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:21.217][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2024-03-27 20:40:21.218][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-27 20:40:21.220][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2024-03-27 20:40:21.221][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-27 20:40:21.222][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-27 20:40:21.223][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-27 20:40:21.224][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-27 20:40:21.225][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-27 20:40:21.226][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-27 20:40:21.229][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:21.230][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:21.231][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:21.235][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:21.236][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:21.237][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:21.238][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:21.243][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.DEBUG[2024-03-27 20:40:21.247][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:40:21.248][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:40:21.249][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.TRACE[2024-03-27 20:40:21.703][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045).
biodb.DEBUG[2024-03-27 20:40:22.203][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:40:22.207][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.content"
biodb.TRACE[2024-03-27 20:40:22.215][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.request"
biodb.TRACE[2024-03-27 20:40:22.220][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml"
biodb.DEBUG[2024-03-27 20:40:22.224][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-27 20:40:22.226][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-27 20:40:22.229][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-27 20:40:22.233][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:22.235][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:22.237][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:22.246][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:22.248][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:22.250][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:22.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:22.256][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:22.258][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:22.260][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.261][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.263][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:22.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:22.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.269][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-27 20:40:22.270][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-27 20:40:22.272][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.273][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.275][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-27 20:40:22.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-27 20:40:22.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.280][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:40:22.281][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:40:22.282][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.283][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.285][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:40:22.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:40:22.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.289][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-27 20:40:22.291][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-27 20:40:22.292][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.293][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.294][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-27 20:40:22.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-27 20:40:22.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.298][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-27 20:40:22.299][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-27 20:40:22.300][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.301][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.302][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-27 20:40:22.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-27 20:40:22.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.306][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:22.307][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:22.308][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.309][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.310][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-27 20:40:22.311][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.312][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.313][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.314][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-27 20:40:22.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.318][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:22.319][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:22.320][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.321][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.322][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:22.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:22.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.326][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:22.327][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:22.328][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.329][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.330][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:22.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:22.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.334][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-27 20:40:22.335][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-27 20:40:22.336][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.337][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.338][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-27 20:40:22.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-27 20:40:22.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.342][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-27 20:40:22.343][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-27 20:40:22.344][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.345][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.346][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-27 20:40:22.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-27 20:40:22.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.350][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:22.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:22.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.354][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:22.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:22.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.358][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:22.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:22.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.362][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:22.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:22.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.366][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:22.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:22.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.370][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:22.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:22.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.374][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:22.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:22.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.378][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:22.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:22.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.382][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:22.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:22.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.386][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:22.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:22.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:22.390][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2024-03-27 20:40:22.391][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.394][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.398][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:22.429][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-03-27 20:40:22.433][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-27 20:40:22.434][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-03-27 20:40:22.435][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-27 20:40:22.437][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-03-27 20:40:22.440][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:22.441][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:22.441][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:22.446][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:22.447][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:22.448][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:22.449][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:22.450][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.454][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.458][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:22.462][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:22.462][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:22.463][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:22.468][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:22.469][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:22.470][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:22.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:22.472][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.476][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.480][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.484][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.488][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:22.492][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:22.493][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:22.494][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:22.499][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:22.499][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:22.500][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:22.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:22.502][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.506][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.510][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.514][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.518][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:22.522][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:22.523][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:22.524][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:22.529][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:22.530][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:22.531][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:22.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:22.534][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.538][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.542][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.547][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.551][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:22.555][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:22.556][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:22.557][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:22.562][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:22.563][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:22.564][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:22.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:22.566][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.570][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.574][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:22.578][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:22.579][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:22.580][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:22.584][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:22.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:22.593][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:22.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:22.595][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.599][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.604][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:22.608][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:22.609][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:22.610][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:22.614][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:22.615][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:22.616][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:22.617][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:22.618][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.622][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.626][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:22.630][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:22.631][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:22.632][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:22.637][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:22.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:22.638][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:22.639][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:22.640][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.644][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.648][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:22.652][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:22.653][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:22.654][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:22.658][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:22.659][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:22.660][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:22.661][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:22.662][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.666][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.670][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:22.674][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:22.675][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:22.676][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:22.681][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:22.682][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:22.683][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:22.683][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:22.684][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.688][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.692][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:22.696][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:22.697][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:22.698][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:22.702][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:22.703][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:22.704][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:22.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:22.706][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.710][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.714][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:22.718][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:22.719][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:22.720][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:22.724][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:22.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:22.726][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:22.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:22.728][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.732][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.735][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:22.739][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:22.740][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:22.741][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:22.745][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:22.746][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:22.747][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:22.748][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:22.749][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.753][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.756][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:22.766][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:22.767][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:22.768][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:22.773][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:22.774][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:22.774][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:22.775][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:22.776][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.780][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.784][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:22.788][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:22.789][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:22.790][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:22.794][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:22.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:22.796][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:22.796][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:22.798][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.801][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.805][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:22.809][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:22.810][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:22.811][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:22.815][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:22.816][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:22.817][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:22.818][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:22.819][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.823][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.827][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:22.831][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:22.831][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:22.832][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:22.837][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:22.838][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:22.838][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:22.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:22.840][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.844][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.848][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:22.852][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:22.853][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:22.854][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:22.858][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:22.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:22.860][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:22.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:22.862][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.866][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.869][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:22.873][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:22.874][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:22.875][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:22.879][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:22.880][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:22.881][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:22.882][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:22.883][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.887][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.891][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:22.895][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:22.896][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:22.897][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:22.901][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:22.902][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:22.903][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:22.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:22.905][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.909][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.913][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:22.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.929][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:22.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:22.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.939][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:22.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:22.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.943][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:22.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:22.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.946][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:22.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:22.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:22.950][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:22.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:22.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:22.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:22.978][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-03-27 20:40:22.981][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:40:22.982][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:40:22.984][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-03-27 20:40:23.427][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-03-27 20:40:23.898][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:40:23.900][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2024-03-27 20:40:23.904][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2024-03-27 20:40:23.908][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-03-27 20:40:23.911][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:40:23.915][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:40:23.919][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-03-27 20:40:24.377][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-03-27 20:40:24.856][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:40:24.859][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2024-03-27 20:40:24.863][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2024-03-27 20:40:24.868][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:24.869][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:24.870][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:24.877][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:24.878][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:24.879][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:24.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:24.881][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2024-03-27 20:40:24.883][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-27 20:40:24.884][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2024-03-27 20:40:24.886][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-27 20:40:24.887][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-27 20:40:24.888][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-27 20:40:24.890][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-27 20:40:24.891][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-27 20:40:24.892][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-27 20:40:24.895][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:24.896][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:24.897][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:24.902][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:24.903][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:24.904][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:24.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:24.907][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2024-03-27 20:40:24.910][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:40:24.911][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:40:24.913][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2024-03-27 20:40:25.357][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2024-03-27 20:40:25.806][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:40:25.809][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2024-03-27 20:40:25.812][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2024-03-27 20:40:25.815][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2024-03-27 20:40:25.817][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-27 20:40:25.818][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-27 20:40:25.819][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-27 20:40:25.821][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:25.822][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:25.823][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:25.828][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:25.829][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:25.830][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:25.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:25.833][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:25.834][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:25.835][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:25.836][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:25.837][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:25.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:25.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:25.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:25.842][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-27 20:40:25.843][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-27 20:40:25.844][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:25.845][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:25.846][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-27 20:40:25.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-27 20:40:25.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:25.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:25.850][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:40:25.851][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:40:25.852][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:25.876][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:25.878][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:40:25.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:40:25.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:25.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:25.882][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-27 20:40:25.884][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-27 20:40:25.885][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:25.885][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:25.887][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-27 20:40:25.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-27 20:40:25.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:25.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:25.891][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-27 20:40:25.892][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-27 20:40:25.893][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:25.894][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:25.896][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-27 20:40:25.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-27 20:40:25.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:25.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:25.900][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:25.901][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:25.902][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:25.903][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:25.904][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:25.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:25.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:25.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:25.908][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-27 20:40:25.909][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:25.910][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:25.911][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:25.913][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-27 20:40:25.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:25.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:25.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:25.917][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:25.918][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:25.919][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:25.920][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:25.921][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:25.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:25.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:25.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:25.925][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:25.926][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:25.927][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:25.928][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:25.930][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:25.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:25.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:25.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:25.934][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-27 20:40:25.935][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-27 20:40:25.936][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:25.937][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:25.938][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-27 20:40:25.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-27 20:40:25.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:25.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:25.942][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-27 20:40:25.943][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-27 20:40:25.944][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:25.945][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:25.947][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-27 20:40:25.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-27 20:40:25.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:25.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:25.951][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:25.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:25.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:25.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:25.954][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:25.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:25.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:25.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:25.958][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:25.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:25.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:25.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:25.962][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:25.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:25.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:25.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:25.966][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:25.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:25.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:25.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:25.970][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:25.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:25.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:25.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:25.974][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:25.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:25.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:25.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:25.978][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:25.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:25.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:25.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:25.982][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:25.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:25.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:25.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:25.986][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:25.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:25.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:25.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:25.990][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2024-03-27 20:40:25.991][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:25.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:25.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:25.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:25.995][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:25.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:25.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:25.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:25.999][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:26.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:26.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:26.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:26.003][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:26.004][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:26.005][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:26.009][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:26.010][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:26.011][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:26.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:26.014][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:26.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:26.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:26.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:26.018][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:26.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:26.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:26.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:26.022][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:26.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:26.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:26.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:26.026][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:26.027][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:26.028][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:26.033][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:26.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:26.035][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:26.036][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:26.037][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2024-03-27 20:40:26.038][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-27 20:40:26.040][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2024-03-27 20:40:26.041][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-27 20:40:26.042][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-27 20:40:26.043][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-27 20:40:26.044][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-27 20:40:26.045][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-27 20:40:26.046][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-27 20:40:26.056][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:26.057][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:26.058][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:26.064][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:26.065][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:26.065][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:26.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:26.068][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2024-03-27 20:40:26.071][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:40:26.072][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:40:26.073][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2024-03-27 20:40:26.632][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2024-03-27 20:40:27.082][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:40:27.087][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2024-03-27 20:40:27.095][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2024-03-27 20:40:27.101][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2024-03-27 20:40:27.105][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-27 20:40:27.108][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-27 20:40:27.110][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-27 20:40:27.114][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:27.116][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:27.118][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:27.128][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:27.130][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:27.131][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:27.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:27.137][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:27.139][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:27.140][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.142][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.143][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:27.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:27.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.149][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-27 20:40:27.151][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-27 20:40:27.152][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.153][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.155][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-27 20:40:27.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-27 20:40:27.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.160][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:40:27.161][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:40:27.163][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.164][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.165][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:40:27.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:40:27.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.170][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-27 20:40:27.171][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-27 20:40:27.172][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.173][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.174][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-27 20:40:27.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-27 20:40:27.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.179][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-27 20:40:27.180][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-27 20:40:27.181][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.182][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.183][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-27 20:40:27.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-27 20:40:27.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.187][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:27.188][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:27.189][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.190][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.192][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-27 20:40:27.193][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:27.194][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.195][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.196][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-27 20:40:27.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:27.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.200][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.201][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.202][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.203][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.204][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.209][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:27.210][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:27.211][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.212][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.213][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:27.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:27.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.219][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-27 20:40:27.221][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-27 20:40:27.222][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.224][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.226][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-27 20:40:27.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-27 20:40:27.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.232][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-27 20:40:27.233][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-27 20:40:27.234][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.236][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.238][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-27 20:40:27.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-27 20:40:27.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.244][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:27.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:27.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.249][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:27.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:27.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.255][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:27.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:27.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.261][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:27.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:27.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.267][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:27.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:27.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.273][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:27.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:27.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.278][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:27.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:27.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.284][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:27.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:27.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.290][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:27.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:27.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.296][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:27.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:27.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:27.315][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2024-03-27 20:40:27.317][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.330][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.338][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:27.373][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-03-27 20:40:27.380][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-27 20:40:27.382][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-03-27 20:40:27.384][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-27 20:40:27.387][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-03-27 20:40:27.392][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:27.394][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:27.395][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:27.401][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:27.402][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:27.403][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:27.404][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:27.406][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.410][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.415][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:27.420][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:27.421][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:27.422][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:27.427][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:27.428][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:27.429][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:27.430][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:27.431][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.436][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.441][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.445][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.449][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:27.454][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:27.455][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:27.456][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:27.461][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:27.462][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:27.463][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:27.464][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:27.465][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.469][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.474][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.478][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.482][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:27.487][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:27.488][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:27.489][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:27.495][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:27.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:27.497][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:27.498][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:27.499][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.504][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.508][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.513][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.517][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:27.521][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:27.522][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:27.523][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:27.528][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:27.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:27.530][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:27.531][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:27.533][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.537][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.555][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:27.559][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:27.560][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:27.561][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:27.566][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:27.567][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:27.568][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:27.569][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:27.570][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.574][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.578][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:27.582][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:27.583][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:27.584][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:27.589][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:27.590][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:27.591][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:27.592][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:27.593][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.597][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.601][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:27.606][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:27.607][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:27.608][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:27.612][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:27.613][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:27.614][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:27.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:27.617][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.621][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.625][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:27.629][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:27.630][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:27.631][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:27.636][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:27.637][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:27.638][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:27.639][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:27.640][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.644][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.648][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:27.652][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:27.653][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:27.654][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:27.659][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:27.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:27.661][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:27.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:27.663][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.667][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.671][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:27.675][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:27.676][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:27.677][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:27.681][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:27.682][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:27.683][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:27.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:27.685][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.689][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.693][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:27.697][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:27.698][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:27.699][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:27.704][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:27.705][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:27.706][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:27.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:27.708][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.712][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.717][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:27.721][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:27.721][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:27.722][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:27.727][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:27.728][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:27.734][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:27.735][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:27.736][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.740][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.745][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:27.749][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:27.749][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:27.750][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:27.755][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:27.756][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:27.757][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:27.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:27.759][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.763][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.767][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:27.772][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:27.772][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:27.773][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:27.778][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:27.779][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:27.780][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:27.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:27.783][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.787][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.791][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:27.795][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:27.796][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:27.797][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:27.801][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:27.802][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:27.803][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:27.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:27.805][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.809][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.813][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:27.817][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:27.818][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:27.819][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:27.823][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:27.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:27.825][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:27.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:27.827][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.831][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.835][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:27.839][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:27.840][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:27.841][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:27.845][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:27.846][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:27.847][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:27.848][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:27.849][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.853][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.857][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:27.861][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:27.862][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:27.863][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:27.868][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:27.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:27.869][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:27.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:27.872][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.876][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.880][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:27.883][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:27.884][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:27.885][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:27.890][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:27.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:27.892][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:27.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:27.894][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.898][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.902][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:27.931][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-03-27 20:40:27.934][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-27 20:40:27.936][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-03-27 20:40:27.937][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-27 20:40:27.939][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-03-27 20:40:27.942][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:27.943][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:27.944][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:27.948][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:27.949][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:27.950][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:27.951][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:27.952][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.956][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.960][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:27.964][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:27.965][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:27.966][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:27.970][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:27.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:27.972][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:27.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:27.974][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.978][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.983][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.987][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:27.990][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:27.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:27.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:27.995][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:27.995][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:27.996][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:28.001][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:28.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:28.003][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:28.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:28.005][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.009][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.013][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.017][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.021][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:28.025][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:28.026][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:28.026][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:28.031][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:28.032][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:28.033][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:28.034][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:28.035][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.039][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.043][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.047][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.051][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:28.055][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:28.056][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:28.057][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:28.061][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:28.062][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:28.063][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:28.064][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:28.065][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.069][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.073][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:28.077][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:28.078][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:28.079][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:28.083][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:28.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:28.085][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:28.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:28.093][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.097][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.101][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:28.106][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:28.106][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:28.107][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:28.112][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:28.113][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:28.114][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:28.115][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:28.116][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.120][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.124][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:28.128][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:28.129][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:28.130][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:28.135][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:28.136][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:28.137][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:28.138][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:28.139][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.143][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.147][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:28.151][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:28.152][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:28.152][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:28.157][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:28.158][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:28.159][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:28.160][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:28.161][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.165][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.169][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:28.173][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:28.173][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:28.174][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:28.179][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:28.180][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:28.181][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:28.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:28.183][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.187][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.191][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:28.195][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:28.196][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:28.196][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:28.201][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:28.202][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:28.203][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:28.204][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:28.205][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.209][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.213][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:28.217][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:28.218][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:28.219][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:28.223][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:28.224][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:28.225][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:28.226][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:28.227][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.231][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.235][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:28.239][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:28.240][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:28.241][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:28.246][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:28.247][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:28.247][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:28.248][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:28.249][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.253][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.257][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:28.261][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:28.262][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:28.263][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:28.273][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:28.274][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:28.275][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:28.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:28.277][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.281][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.286][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:28.290][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:28.291][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:28.292][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:28.296][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:28.297][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:28.298][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:28.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:28.300][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.304][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.308][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:28.312][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:28.313][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:28.314][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:28.319][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:28.320][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:28.320][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:28.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:28.323][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.327][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.331][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:28.335][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:28.335][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:28.336][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:28.341][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:28.342][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:28.343][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:28.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:28.345][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.349][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.353][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:28.357][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:28.358][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:28.359][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:28.363][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:28.364][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:28.365][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:28.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:28.367][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.371][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.375][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:28.379][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:28.380][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:28.381][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:28.386][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:28.386][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:28.387][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:28.388][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:28.389][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.394][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.398][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:28.402][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:28.403][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:28.404][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:28.409][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:28.410][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:28.410][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:28.411][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:28.413][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.417][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.421][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.439][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-03-27 20:40:28.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-03-27 20:40:28.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-03-27 20:40:28.459][biodb::testThat]
biodb.INFO [2024-03-27 20:40:28.460][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-03-27 20:40:28.461][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 20:40:28.462][biodb::testThat]
biodb.TRACE[2024-03-27 20:40:28.465][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-03-27 20:40:28.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-03-27 20:40:28.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.470][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:28.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:28.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.474][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:28.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:28.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.479][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:28.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:28.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.483][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:28.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:28.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:28.490][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:28.491][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:28.492][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:28.496][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:28.497][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:28.498][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:28.499][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:28.502][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-03-27 20:40:28.505][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-27 20:40:28.506][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-03-27 20:40:28.508][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-27 20:40:28.509][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-03-27 20:40:28.512][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:28.512][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:28.513][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:28.518][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:28.519][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:28.520][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:28.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:28.522][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:28.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:28.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.526][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:28.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:28.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.530][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:28.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:28.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:28.535][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-03-27 20:40:28.538][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-27 20:40:28.539][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-03-27 20:40:28.540][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-27 20:40:28.542][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-03-27 20:40:28.544][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:28.545][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:28.546][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:28.550][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:28.551][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:28.552][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:28.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:28.554][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:28.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:28.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.558][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:28.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:28.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.562][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:28.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:28.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:28.566][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:28.567][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:28.568][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:28.573][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:28.574][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:28.575][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:28.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:28.577][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:28.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:28.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.581][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:28.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:28.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.585][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:28.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:28.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:28.589][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-03-27 20:40:28.591][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:28.592][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:28.593][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:28.597][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:28.598][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:28.599][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:28.600][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:28.601][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:28.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:28.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.605][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:28.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:28.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.609][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:28.610][private$selectFields]
biodb.TRACE[2024-03-27 20:40:28.611][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-27 20:40:28.612][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-27 20:40:28.613][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:28.614][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:28.615][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:28.616][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.617][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.618][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:28.619][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:28.620][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.621][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.622][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:28.623][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:28.624][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:28.625][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:28.626][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.627][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.628][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-03-27 20:40:28.629][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:28.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:28.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.639][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:28.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:28.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.643][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:28.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:28.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.657][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-03-27 20:40:28.658][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:28.659][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:28.660][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:28.665][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:28.666][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:28.667][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:28.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:28.669][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:28.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:28.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.673][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:28.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:28.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.677][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:28.678][private$selectFields]
biodb.TRACE[2024-03-27 20:40:28.679][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-27 20:40:28.680][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-27 20:40:28.681][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:28.682][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:28.683][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:28.684][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.685][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.686][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:28.687][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:28.688][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.689][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.690][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:28.691][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:28.692][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:28.693][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:28.694][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.694][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.695][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-03-27 20:40:28.697][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:28.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:28.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.700][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:28.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:28.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.704][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:28.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:28.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.709][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-03-27 20:40:28.710][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:28.711][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:28.711][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:28.716][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:28.717][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:28.718][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:28.718][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:28.720][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:28.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:28.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.724][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:28.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:28.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.727][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:28.728][private$selectFields]
biodb.TRACE[2024-03-27 20:40:28.729][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-27 20:40:28.730][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-27 20:40:28.731][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:28.732][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:28.733][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:28.734][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.735][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.736][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:28.737][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:28.738][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.739][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.740][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:28.741][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:28.742][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:28.743][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:28.744][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.745][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.746][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-03-27 20:40:28.747][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:28.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:28.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.751][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:28.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:28.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.755][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:28.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:28.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.764][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-03-27 20:40:28.766][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-03-27 20:40:28.767][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-03-27 20:40:28.781][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.786][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.791][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:28.795][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:28.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:28.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:28.878][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:28.879][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:28.880][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:28.885][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:28.886][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:28.887][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:28.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:28.891][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-03-27 20:40:28.894][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:40:28.895][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:40:28.897][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-03-27 20:40:29.351][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-03-27 20:40:29.798][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:40:29.801][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2024-03-27 20:40:29.808][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2024-03-27 20:40:29.814][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-03-27 20:40:29.819][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:40:29.821][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:40:29.824][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-03-27 20:40:30.287][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-03-27 20:40:30.732][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:40:30.734][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2024-03-27 20:40:30.738][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2024-03-27 20:40:30.741][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:30.742][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:30.743][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:30.748][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:30.749][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:30.750][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:30.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:30.752][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:30.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:30.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:30.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:30.757][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:30.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:30.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:30.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:30.761][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:30.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:30.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:30.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:30.765][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:30.766][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:30.767][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:30.771][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:30.772][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:30.773][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:30.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:30.775][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:30.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:30.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:30.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:30.779][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:30.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:30.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:30.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:30.783][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:30.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:30.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:30.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:30.787][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:30.787][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:30.788][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:30.793][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:30.794][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:30.794][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:30.795][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:30.796][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:30.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:30.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:30.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:30.800][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:30.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:30.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:30.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:30.804][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:30.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:30.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:30.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:30.843][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-03-27 20:40:30.866][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:30.867][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:30.868][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:30.873][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:30.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:30.875][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:30.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:30.877][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:30.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:30.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:30.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:30.882][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:30.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:30.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:30.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:30.886][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:30.887][private$selectFields]
biodb.TRACE[2024-03-27 20:40:30.888][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-27 20:40:30.889][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-27 20:40:30.890][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:30.891][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:30.892][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:30.893][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:30.894][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:30.895][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:30.896][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:30.897][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:30.898][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:30.899][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:30.900][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:30.901][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:30.902][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:30.903][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:30.904][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:30.905][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-03-27 20:40:30.906][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:30.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:30.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:30.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:30.910][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:30.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:30.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:30.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:30.914][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:30.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:30.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:30.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:30.919][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-03-27 20:40:30.920][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:30.921][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:30.921][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:30.926][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:30.927][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:30.928][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:30.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:30.941][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:30.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:30.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:30.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:30.945][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:30.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:30.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:30.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:30.974][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:30.975][private$selectFields]
biodb.TRACE[2024-03-27 20:40:30.976][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-27 20:40:30.977][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-27 20:40:30.978][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:30.979][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:30.980][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:30.981][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:30.982][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:30.983][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:30.984][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:30.985][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:30.986][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:30.986][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:30.996][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:30.997][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:30.999][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.000][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.000][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.001][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-03-27 20:40:31.002][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.006][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.010][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.014][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-03-27 20:40:31.015][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:31.016][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:31.017][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:31.021][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:31.022][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:31.023][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:31.024][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:31.025][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.029][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.033][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:31.034][private$selectFields]
biodb.TRACE[2024-03-27 20:40:31.035][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-27 20:40:31.036][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-27 20:40:31.036][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:31.037][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.038][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.039][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.040][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.041][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.042][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.043][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.044][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.045][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:31.046][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:31.047][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.048][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.049][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.050][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.051][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-03-27 20:40:31.052][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.055][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.059][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.063][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-03-27 20:40:31.064][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-03-27 20:40:31.065][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-03-27 20:40:31.073][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-03-27 20:40:31.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-03-27 20:40:31.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-03-27 20:40:31.080][biodb::testThat]
biodb.INFO [2024-03-27 20:40:31.081][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-03-27 20:40:31.082][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 20:40:31.083][biodb::testThat]
biodb.TRACE[2024-03-27 20:40:31.086][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-03-27 20:40:31.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-03-27 20:40:31.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.090][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:31.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:31.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.094][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:31.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:31.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.098][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:31.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:31.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.102][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:31.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:31.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:31.108][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:31.109][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:31.110][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:31.114][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:31.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:31.116][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:31.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:31.120][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-03-27 20:40:31.123][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-27 20:40:31.124][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-03-27 20:40:31.125][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-27 20:40:31.126][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-03-27 20:40:31.128][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:31.135][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:31.136][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:31.141][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:31.141][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:31.142][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:31.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:31.144][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:31.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:31.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.148][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:31.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:31.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.152][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:31.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:31.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:31.157][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-03-27 20:40:31.160][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-27 20:40:31.161][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-03-27 20:40:31.162][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-27 20:40:31.164][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-03-27 20:40:31.167][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:31.168][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:31.169][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:31.173][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:31.174][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:31.175][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:31.176][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:31.177][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:31.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:31.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.181][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:31.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:31.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.185][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:31.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:31.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:31.189][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:31.190][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:31.191][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:31.195][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:31.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:31.197][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:31.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:31.199][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:31.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:31.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.203][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:31.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:31.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.207][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:31.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:31.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:31.211][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-03-27 20:40:31.213][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:31.214][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:31.215][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:31.220][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:31.221][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:31.221][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:31.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:31.224][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.228][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.232][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:31.233][private$selectFields]
biodb.TRACE[2024-03-27 20:40:31.234][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-27 20:40:31.235][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-27 20:40:31.236][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:31.237][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.238][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.239][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.240][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.241][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.242][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.243][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.244][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.245][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:31.246][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:31.247][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.248][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.249][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.250][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.251][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-03-27 20:40:31.252][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.256][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.260][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.264][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-03-27 20:40:31.265][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:31.266][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:31.267][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:31.271][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:31.272][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:31.273][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:31.274][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:31.275][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.279][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.283][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:31.284][private$selectFields]
biodb.TRACE[2024-03-27 20:40:31.285][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-27 20:40:31.286][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-27 20:40:31.287][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:31.288][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.289][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.290][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.291][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.292][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.293][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.293][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.294][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.295][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:31.296][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:31.297][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.298][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.299][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.300][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.301][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-03-27 20:40:31.302][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.315][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.321][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.327][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-03-27 20:40:31.329][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:31.330][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:31.331][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:31.338][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:31.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:31.340][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:31.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:31.342][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.347][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.351][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:31.352][private$selectFields]
biodb.TRACE[2024-03-27 20:40:31.353][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-27 20:40:31.354][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-27 20:40:31.355][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:31.356][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.358][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.359][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.360][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.361][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.362][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.363][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.364][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.365][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:31.366][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:31.367][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.368][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.369][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.370][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.371][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-03-27 20:40:31.372][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.377][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.381][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.386][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-03-27 20:40:31.387][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-03-27 20:40:31.388][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-03-27 20:40:31.397][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:31.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:31.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.402][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:31.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:31.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.406][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:31.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:31.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.410][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:31.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:31.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:31.417][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:31.418][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:31.419][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:31.424][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:31.425][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:31.426][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:31.427][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:31.430][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-03-27 20:40:31.434][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-27 20:40:31.436][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-03-27 20:40:31.437][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-27 20:40:31.438][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-03-27 20:40:31.442][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-03-27 20:40:31.445][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-27 20:40:31.447][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-03-27 20:40:31.448][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-27 20:40:31.449][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-03-27 20:40:31.452][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:31.453][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:31.454][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:31.459][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:31.460][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:31.461][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:31.462][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:31.463][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:31.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:31.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.468][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:31.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:31.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.472][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:31.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:31.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:31.476][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:31.477][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:31.478][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:31.483][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:31.484][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:31.485][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:31.486][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:31.487][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:31.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:31.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.491][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:31.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:31.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.495][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:31.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:31.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:31.500][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:31.501][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:31.502][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:31.520][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:31.521][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:31.522][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:31.523][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:31.524][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:31.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:31.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.528][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:31.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:31.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.532][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:31.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:31.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:31.536][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-03-27 20:40:31.538][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:31.538][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:31.539][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:31.544][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:31.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:31.546][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:31.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:31.548][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.552][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.556][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:31.557][private$selectFields]
biodb.TRACE[2024-03-27 20:40:31.558][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-27 20:40:31.559][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-27 20:40:31.560][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:31.561][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.562][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.563][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.563][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.564][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.565][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.566][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.567][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.568][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:31.569][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:31.570][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.571][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.572][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.573][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.574][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-03-27 20:40:31.575][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.579][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.582][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.587][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-03-27 20:40:31.588][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:31.588][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:31.589][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:31.594][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:31.595][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:31.595][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:31.596][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:31.597][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.601][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.605][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:31.606][private$selectFields]
biodb.TRACE[2024-03-27 20:40:31.607][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-27 20:40:31.608][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-27 20:40:31.609][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:31.610][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.611][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.611][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.612][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.613][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.614][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.615][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.616][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.617][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:31.618][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:31.619][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.620][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.621][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.622][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.623][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-03-27 20:40:31.624][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.628][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.632][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.636][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-03-27 20:40:31.637][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:31.638][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:31.639][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:31.643][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:31.644][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:31.645][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:31.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:31.647][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.651][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.655][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:31.656][private$selectFields]
biodb.TRACE[2024-03-27 20:40:31.657][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-27 20:40:31.657][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-27 20:40:31.658][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:31.659][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.660][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.661][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.662][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.663][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.664][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.665][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.666][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.667][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:31.668][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:31.669][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.670][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.671][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.672][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.673][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-03-27 20:40:31.674][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.683][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.688][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.692][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-03-27 20:40:31.693][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-03-27 20:40:31.694][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-03-27 20:40:31.702][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-03-27 20:40:31.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-03-27 20:40:31.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-03-27 20:40:31.710][biodb::testThat]
biodb.INFO [2024-03-27 20:40:31.711][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-03-27 20:40:31.712][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 20:40:31.713][biodb::testThat]
biodb.TRACE[2024-03-27 20:40:31.716][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-03-27 20:40:31.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-03-27 20:40:31.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.720][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:31.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:31.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.723][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:31.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:31.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.727][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:31.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:31.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.731][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:31.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:31.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:31.739][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:31.740][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:31.741][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:31.746][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:31.746][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:31.747][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:31.748][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:31.751][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-03-27 20:40:31.754][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-27 20:40:31.755][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-03-27 20:40:31.757][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-27 20:40:31.758][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-03-27 20:40:31.760][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:31.761][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:31.762][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:31.767][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:31.768][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:31.768][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:31.769][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:31.770][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:31.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:31.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.774][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:31.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:31.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.778][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:31.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:31.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:31.783][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-03-27 20:40:31.786][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-27 20:40:31.787][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-03-27 20:40:31.788][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-27 20:40:31.789][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-03-27 20:40:31.792][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:31.792][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:31.793][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:31.798][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:31.799][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:31.800][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:31.800][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:31.802][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:31.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:31.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.805][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:31.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:31.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.809][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:31.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:31.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:31.813][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:31.814][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:31.815][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:31.820][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:31.820][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:31.821][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:31.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:31.823][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:31.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:31.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.827][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:31.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:31.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.831][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:31.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:31.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:31.835][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-03-27 20:40:31.837][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:31.838][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:31.839][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:31.843][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:31.844][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:31.845][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:31.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:31.847][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.851][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.861][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:31.862][private$selectFields]
biodb.TRACE[2024-03-27 20:40:31.863][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-27 20:40:31.864][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-27 20:40:31.865][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:31.866][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.867][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.868][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.869][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.870][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.871][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.872][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.873][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.874][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:31.875][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:31.876][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.877][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.878][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.879][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.880][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-03-27 20:40:31.881][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.884][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.888][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.892][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-03-27 20:40:31.893][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:31.894][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:31.895][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:31.899][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:31.900][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:31.901][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:31.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:31.903][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.907][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.910][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:31.911][private$selectFields]
biodb.TRACE[2024-03-27 20:40:31.912][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-27 20:40:31.913][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-27 20:40:31.914][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:31.915][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.916][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.917][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.918][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.919][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.920][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.921][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.921][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.922][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:31.923][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:31.924][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.925][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.926][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.927][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.928][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-03-27 20:40:31.929][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.933][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.937][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.941][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-03-27 20:40:31.942][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:31.943][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:31.943][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:31.948][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:31.949][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:31.950][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:31.950][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:31.952][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.955][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.959][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:31.960][private$selectFields]
biodb.TRACE[2024-03-27 20:40:31.961][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-27 20:40:31.962][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-27 20:40:31.963][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:31.964][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.965][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.966][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.967][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.968][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.969][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.970][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.970][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.971][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:31.972][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:31.973][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.974][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.975][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.976][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.977][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-03-27 20:40:31.978][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.982][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.986][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:31.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:31.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:31.990][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-03-27 20:40:31.991][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-03-27 20:40:31.992][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-03-27 20:40:32.010][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:32.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:32.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:32.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:32.015][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:32.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:32.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:32.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:32.024][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:32.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:32.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:32.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:32.029][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:32.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:32.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:32.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:32.036][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:32.037][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:32.038][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:32.043][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:32.044][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:32.045][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:32.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:32.049][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-03-27 20:40:32.053][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-27 20:40:32.054][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-03-27 20:40:32.056][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-27 20:40:32.057][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-03-27 20:40:32.060][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-03-27 20:40:32.064][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-27 20:40:32.067][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-03-27 20:40:32.070][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-27 20:40:32.073][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-03-27 20:40:32.080][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:32.082][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:32.084][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:32.091][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:32.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:32.095][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:32.097][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:32.099][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:32.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:32.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:32.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:32.105][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:32.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:32.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:32.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:32.110][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:32.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:32.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:32.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:32.115][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:32.116][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:32.117][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:32.122][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:32.123][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:32.124][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:32.124][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:32.126][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:32.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:32.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:32.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:32.129][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:32.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:32.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:32.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:32.133][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:32.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:32.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:32.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:32.137][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:32.138][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:32.139][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:32.143][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:32.144][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:32.145][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:32.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:32.148][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:32.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:32.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:32.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:32.155][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:32.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:32.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:32.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:32.161][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:32.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:32.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:32.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:32.168][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-03-27 20:40:32.171][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:32.172][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:32.174][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:32.181][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:32.183][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:32.185][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:32.186][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:32.188][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:32.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:32.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:32.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:32.194][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:32.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:32.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:32.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:32.200][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:32.201][private$selectFields]
biodb.TRACE[2024-03-27 20:40:32.203][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-27 20:40:32.204][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-27 20:40:32.206][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:32.207][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:32.209][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:32.210][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:32.212][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:32.213][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:32.215][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:32.216][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:32.218][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:32.219][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:32.221][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:32.222][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:32.224][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:32.225][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:32.226][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:32.228][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-03-27 20:40:32.229][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:32.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:32.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:32.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:32.235][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:32.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:32.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:32.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:32.241][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:32.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:32.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:32.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:32.248][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-03-27 20:40:32.249][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:32.251][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:32.252][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:32.271][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:32.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:32.275][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:32.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:32.279][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:32.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:32.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:32.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:32.285][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:32.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:32.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:32.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:32.292][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:32.293][private$selectFields]
biodb.TRACE[2024-03-27 20:40:32.295][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-27 20:40:32.296][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-27 20:40:32.298][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:32.299][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:32.301][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:32.302][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:32.304][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:32.305][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:32.307][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:32.308][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:32.310][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:32.312][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:32.313][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:32.315][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:32.317][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:32.319][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:32.320][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:32.322][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-03-27 20:40:32.324][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:32.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:32.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:32.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:32.330][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:32.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:32.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:32.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:32.336][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:32.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:32.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:32.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:32.343][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-03-27 20:40:32.345][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:32.347][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:32.348][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:32.356][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:32.357][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:32.359][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:32.360][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:32.362][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:32.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:32.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:32.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:32.369][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:32.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:32.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:32.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:32.375][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:32.376][private$selectFields]
biodb.TRACE[2024-03-27 20:40:32.378][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-27 20:40:32.379][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-27 20:40:32.381][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:32.382][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:32.384][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:32.385][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:32.387][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:32.388][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:32.390][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:32.391][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:32.392][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:32.394][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:32.395][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-27 20:40:32.397][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:32.398][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:32.399][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:32.401][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:32.402][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-03-27 20:40:32.404][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:32.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:32.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:32.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:32.409][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:32.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:32.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:32.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:32.415][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:32.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:32.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:32.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:32.422][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-03-27 20:40:32.423][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-03-27 20:40:32.424][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-03-27 20:40:32.453][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-03-27 20:40:32.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-03-27 20:40:32.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:32.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-03-27 20:40:32.462][biodb::testThat]
biodb.INFO [2024-03-27 20:40:32.463][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2024-03-27 20:40:32.464][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 20:40:32.465][biodb::testThat]
biodb.DEBUG[2024-03-27 20:40:32.467][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-03-27 20:40:32.469][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-27 20:40:32.471][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-03-27 20:40:32.473][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-27 20:40:32.474][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-27 20:40:32.476][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-27 20:40:32.477][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-27 20:40:32.478][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-27 20:40:32.479][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-27 20:40:32.484][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:32.485][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:32.487][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:32.494][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:32.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:32.497][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:32.498][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:32.499][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2024-03-27 20:40:32.504][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:40:32.505][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:40:32.507][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2024-03-27 20:40:33.017][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2024-03-27 20:40:33.536][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:40:33.541][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2024-03-27 20:40:33.549][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2024-03-27 20:40:33.556][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2024-03-27 20:40:33.595][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-27 20:40:33.599][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-27 20:40:33.603][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-27 20:40:33.608][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:33.610][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:33.612][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:33.619][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:33.621][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:33.622][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:33.623][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:33.627][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:33.629][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:33.631][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:33.634][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:33.637][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:33.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:33.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:33.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:33.643][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-27 20:40:33.644][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-27 20:40:33.645][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:33.646][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:33.648][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:40:33.650][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:40:33.651][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:33.653][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:33.655][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-27 20:40:33.657][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-27 20:40:33.658][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:33.660][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:33.662][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-27 20:40:33.663][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-27 20:40:33.665][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:33.666][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:33.668][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:33.671][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:33.673][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:33.675][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:33.678][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-27 20:40:33.680][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:33.682][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:33.684][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:33.687][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:33.689][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:33.691][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:33.693][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:33.696][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:33.699][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:33.701][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:33.703][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:33.705][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-27 20:40:33.707][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-27 20:40:33.709][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:33.711][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:33.714][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-27 20:40:33.716][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-27 20:40:33.718][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:33.721][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:33.723][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:33.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:33.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:33.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:33.731][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:33.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:33.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:33.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:33.739][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:33.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:33.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:33.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:33.746][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:33.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:33.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:33.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:33.754][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:33.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:33.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:33.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:33.762][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:33.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:33.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:33.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:33.769][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:33.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:33.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:33.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:33.776][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:33.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:33.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:33.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:33.781][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:33.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:33.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:33.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:33.785][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:33.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:33.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:33.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:33.790][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-03-27 20:40:33.791][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-03-27 20:40:33.807][biodb::testThat]
biodb.INFO [2024-03-27 20:40:33.810][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-03-27 20:40:33.812][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 20:40:33.814][biodb::testThat]
biodb.DEBUG[2024-03-27 20:40:33.832][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2024-03-27 20:40:33.835][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2024-03-27 20:40:33.838][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2024-03-27 20:40:33.842][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2024-03-27 20:40:33.845][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2024-03-27 20:40:33.848][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-27 20:40:33.851][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-27 20:40:33.853][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-27 20:40:33.855][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-27 20:40:33.857][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-27 20:40:33.862][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:33.864][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:33.866][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:33.874][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:33.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:33.877][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:33.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:33.880][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2024-03-27 20:40:33.883][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:40:33.884][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:40:33.886][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2024-03-27 20:40:34.356][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2024-03-27 20:40:34.844][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:40:34.850][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2024-03-27 20:40:34.857][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2024-03-27 20:40:34.861][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:34.890][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:34.893][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:34.904][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:34.906][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:34.908][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:34.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:34.913][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.DEBUG[2024-03-27 20:40:34.920][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:40:34.923][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:40:34.926][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.TRACE[2024-03-27 20:40:35.406][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
biodb.DEBUG[2024-03-27 20:40:35.888][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:40:35.895][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.content"
biodb.TRACE[2024-03-27 20:40:35.902][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.request"
biodb.DEBUG[2024-03-27 20:40:35.906][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:35.908][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:35.910][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:35.920][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:35.922][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:35.924][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:35.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:35.928][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2024-03-27 20:40:35.934][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:40:35.936][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:40:35.939][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2024-03-27 20:40:36.423][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2024-03-27 20:40:36.913][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:40:36.918][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2024-03-27 20:40:36.926][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2024-03-27 20:40:36.930][private$doSaveContentToFile] Saving to cache [3]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml, /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml"
biodb.DEBUG[2024-03-27 20:40:36.934][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-27 20:40:36.936][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2024-03-27 20:40:36.937][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2024-03-27 20:40:36.941][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:36.942][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:36.944][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:36.955][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:36.957][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:36.959][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:36.960][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:36.965][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:36.967][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:36.969][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:36.971][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:36.974][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:36.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:36.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:36.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:36.982][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-27 20:40:36.984][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-27 20:40:36.986][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:36.987][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:36.990][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:40:36.992][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:40:36.993][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:36.994][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:36.997][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-27 20:40:36.998][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-27 20:40:36.999][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.000][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.002][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-27 20:40:37.003][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-27 20:40:37.004][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.006][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.009][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:37.011][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:37.013][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.015][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.017][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-27 20:40:37.020][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:37.021][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.023][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.024][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:37.027][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:37.029][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.030][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.032][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:37.034][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:37.036][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.038][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.040][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-27 20:40:37.042][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-27 20:40:37.044][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.046][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.047][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-27 20:40:37.049][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-27 20:40:37.050][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.051][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.053][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:37.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:37.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.058][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:37.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:37.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.066][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:37.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:37.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.074][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:37.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:37.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.081][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:37.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:37.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.089][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:37.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:37.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.096][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:37.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:37.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:37.104][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:37.106][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:37.107][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:37.117][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:37.119][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:37.120][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:37.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:37.127][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:37.129][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:37.132][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.134][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.135][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:37.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:37.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.141][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-27 20:40:37.142][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-27 20:40:37.187][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.190][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.194][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-27 20:40:37.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-27 20:40:37.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.203][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:40:37.204][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:40:37.206][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.207][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.209][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:40:37.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:40:37.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.216][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-27 20:40:37.218][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-27 20:40:37.220][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.222][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.224][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-27 20:40:37.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-27 20:40:37.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.230][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-27 20:40:37.232][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-27 20:40:37.234][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.235][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.237][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-27 20:40:37.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-27 20:40:37.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.243][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:37.245][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:37.246][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.248][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.250][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:37.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:37.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.257][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-27 20:40:37.258][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:37.260][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.261][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.263][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-27 20:40:37.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:37.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.269][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:37.271][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:37.272][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.274][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.276][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:37.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:37.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.282][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:37.284][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:37.285][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.286][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.289][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:37.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:37.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.295][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-27 20:40:37.296][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-27 20:40:37.298][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.299][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.301][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-27 20:40:37.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-27 20:40:37.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.307][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-27 20:40:37.308][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-27 20:40:37.310][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.311][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.313][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-27 20:40:37.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-27 20:40:37.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.319][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:37.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:37.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.326][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:37.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:37.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.331][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:37.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:37.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.337][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:37.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:37.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.343][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:37.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:37.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.349][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:37.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:37.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.354][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:37.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:37.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:37.360][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:37.362][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:37.363][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:37.370][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:37.371][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:37.373][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:37.374][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:37.378][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:37.380][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:37.381][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.382][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.384][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:37.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:37.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.391][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-27 20:40:37.393][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-27 20:40:37.394][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.396][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.398][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-27 20:40:37.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-27 20:40:37.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.404][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:40:37.406][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:40:37.407][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.409][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.411][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:40:37.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:40:37.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.417][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-27 20:40:37.419][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-27 20:40:37.420][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.421][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.423][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-27 20:40:37.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-27 20:40:37.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.429][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-27 20:40:37.430][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-27 20:40:37.432][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.433][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.435][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-27 20:40:37.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-27 20:40:37.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.441][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:37.443][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:37.444][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.455][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.458][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:37.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:37.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.463][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-27 20:40:37.464][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:37.465][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.466][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.468][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-27 20:40:37.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:37.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.472][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:37.474][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:37.475][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.476][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.477][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:37.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:37.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.481][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:37.482][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:37.483][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.485][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.486][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:37.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:37.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.491][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-27 20:40:37.492][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-27 20:40:37.493][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.494][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.496][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-27 20:40:37.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-27 20:40:37.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.500][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-27 20:40:37.501][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-27 20:40:37.503][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.504][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.506][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-27 20:40:37.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-27 20:40:37.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.513][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:37.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:37.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.521][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:37.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:37.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.528][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:37.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:37.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.534][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:37.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:37.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.541][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:37.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:37.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.548][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:37.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:37.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.554][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:37.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:37.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.561][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:37.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:37.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.566][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:37.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:37.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.573][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:37.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:37.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.579][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:37.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:37.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.585][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:37.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:37.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.590][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:37.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:37.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.595][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:37.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:37.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.599][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:37.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:37.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:37.604][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:37.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:37.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:37.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:37.608][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2024-03-27 20:40:37.609][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-03-27 20:40:37.610][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2024-03-27 20:40:37.625][biodb::testThat]
biodb.INFO [2024-03-27 20:40:37.627][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2024-03-27 20:40:37.628][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 20:40:37.629][biodb::testThat]
biodb.INFO [2024-03-27 20:40:37.656][biodb::testThat]
biodb.INFO [2024-03-27 20:40:37.658][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2024-03-27 20:40:37.659][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 20:40:37.660][biodb::testThat]
biodb.INFO [2024-03-27 20:40:37.670][biodb::testThat]
biodb.INFO [2024-03-27 20:40:37.680][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2024-03-27 20:40:37.681][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 20:40:37.683][biodb::testThat]
biodb.DEBUG[2024-03-27 20:40:37.686][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1*&searchCategory=CHEBI ID&maximumResults=100&starsCategory=ALL".
biodb.DEBUG[2024-03-27 20:40:37.689][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:40:37.691][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:40:37.693][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL".
biodb.TRACE[2024-03-27 20:40:38.238][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL).
biodb.DEBUG[2024-03-27 20:40:38.875][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:40:38.880][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2024-03-27 20:40:38.887][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2024-03-27 20:40:38.905][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:38.907][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:38.908][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:38.909][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:38.910][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:38.911][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:38.912][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:38.913][ef$get] fields variable is a list.
biodb.INFO [2024-03-27 20:40:38.915][biodb::testThat]
biodb.INFO [2024-03-27 20:40:38.916][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. ").
biodb.INFO [2024-03-27 20:40:38.917][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 20:40:38.918][biodb::testThat]
biodb.ERROR[2024-03-27 20:40:38.935][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-03-27 20:40:38.954][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-03-27 20:40:38.969][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-03-27 20:40:38.971][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-03-27 20:40:38.972][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-03-27 20:40:38.973][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-03-27 20:40:38.974][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:38.975][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:38.976][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:38.977][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:38.978][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:38.979][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-03-27 20:40:38.990][biodb::testContext]
biodb.INFO [2024-03-27 20:40:38.991][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-27 20:40:38.992][biodb::testContext] Test context - Test conversions
biodb.INFO [2024-03-27 20:40:38.993][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-27 20:40:38.994][biodb::testContext]
biodb.INFO [2024-03-27 20:40:38.996][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.11.0.
biodb.DEBUG[2024-03-27 20:40:38.998][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-03-27 20:40:39.002][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-27 20:40:39.004][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-03-27 20:40:39.005][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-03-27 20:40:39.006][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:39.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:39.008][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:39.009][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-03-27 20:40:39.010][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-03-27 20:40:39.011][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:39.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:39.013][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:39.014][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-03-27 20:40:39.015][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-03-27 20:40:39.016][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:39.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:39.018][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:39.019][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-03-27 20:40:39.020][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-03-27 20:40:39.021][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-03-27 20:40:39.022][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:39.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:39.024][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:39.025][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-03-27 20:40:39.026][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-03-27 20:40:39.027][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-03-27 20:40:39.028][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:39.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:39.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:39.031][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-03-27 20:40:39.032][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-03-27 20:40:39.033][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:39.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:39.035][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:39.036][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-03-27 20:40:39.037][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-03-27 20:40:39.038][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-03-27 20:40:39.039][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:39.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:39.041][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:39.042][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-03-27 20:40:39.043][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-03-27 20:40:39.044][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:39.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:39.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:39.047][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-03-27 20:40:39.048][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-03-27 20:40:39.049][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-03-27 20:40:39.050][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:39.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:39.052][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:39.053][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-03-27 20:40:39.071][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-03-27 20:40:39.073][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-03-27 20:40:39.074][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-03-27 20:40:39.075][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-03-27 20:40:39.076][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-03-27 20:40:39.077][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:39.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:39.079][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:39.080][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-03-27 20:40:39.081][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-03-27 20:40:39.082][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:39.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:39.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:39.085][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-03-27 20:40:39.086][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-03-27 20:40:39.087][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:39.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:39.089][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:39.090][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-03-27 20:40:39.091][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-03-27 20:40:39.092][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:39.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:39.093][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:39.094][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-03-27 20:40:39.095][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-03-27 20:40:39.096][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:39.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:39.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:39.099][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-03-27 20:40:39.100][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-03-27 20:40:39.101][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:39.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:39.102][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:39.103][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-03-27 20:40:39.104][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-03-27 20:40:39.108][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-03-27 20:40:39.108][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:39.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:39.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:39.111][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-03-27 20:40:39.112][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-03-27 20:40:39.113][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-03-27 20:40:39.114][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:39.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:39.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:39.117][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-03-27 20:40:39.119][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-27 20:40:39.119][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-03-27 20:40:39.120][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:39.121][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 20:40:39.122][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:39.123][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 20:40:39.124][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-27 20:40:39.125][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 20:40:39.126][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-27 20:40:39.127][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 20:40:39.128][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:39.129][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-03-27 20:40:39.130][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 20:40:39.131][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:40:39.132][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:39.133][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-27 20:40:39.133][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-27 20:40:39.133][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-27 20:40:39.133][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-27 20:40:39.133][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-27 20:40:39.134][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 20:40:39.135][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:40:39.135][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:40:39.136][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 20:40:39.137][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:40:39.138][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:40:39.139][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 20:40:39.140][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:40:39.141][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 20:40:39.142][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 20:40:39.143][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-27 20:40:39.144][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:40:39.145][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-03-27 20:40:39.146][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-27 20:40:39.147][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-03-27 20:40:39.148][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:39.149][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 20:40:39.150][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:39.151][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 20:40:39.152][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-27 20:40:39.153][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 20:40:39.154][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-27 20:40:39.155][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 20:40:39.156][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:39.157][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-03-27 20:40:39.158][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 20:40:39.159][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:40:39.160][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:39.161][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-27 20:40:39.161][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-27 20:40:39.161][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-27 20:40:39.161][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-27 20:40:39.161][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-27 20:40:39.162][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 20:40:39.163][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:40:39.163][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:40:39.164][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 20:40:39.165][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:40:39.166][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:40:39.167][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 20:40:39.168][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:40:39.169][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 20:40:39.170][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 20:40:39.171][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-27 20:40:39.172][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:40:39.173][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-03-27 20:40:39.174][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:39.175][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-03-27 20:40:39.176][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:39.177][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 20:40:39.178][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:39.179][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 20:40:39.180][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-27 20:40:39.181][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 20:40:39.182][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-27 20:40:39.183][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 20:40:39.184][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-27 20:40:39.185][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-03-27 20:40:39.186][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 20:40:39.187][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:40:39.188][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:39.189][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:40:39.190][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 20:40:39.191][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:40:39.191][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:40:39.192][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 20:40:39.193][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:40:39.194][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:40:39.195][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 20:40:39.196][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:40:39.197][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 20:40:39.198][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 20:40:39.199][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-27 20:40:39.200][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:40:39.201][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-03-27 20:40:39.203][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:39.204][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-03-27 20:40:39.204][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:39.205][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 20:40:39.206][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:39.207][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 20:40:39.208][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-27 20:40:39.209][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 20:40:39.210][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-27 20:40:39.211][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 20:40:39.212][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-27 20:40:39.213][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-03-27 20:40:39.214][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 20:40:39.215][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:40:39.216][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:39.217][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:40:39.218][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 20:40:39.219][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:40:39.220][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:40:39.220][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 20:40:39.221][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:40:39.222][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:40:39.223][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 20:40:39.224][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:40:39.225][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 20:40:39.226][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 20:40:39.399][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-27 20:40:39.400][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:40:39.401][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-27 20:40:39.402][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:39.403][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:39.404][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:39.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:39.405][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:39.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:39.407][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:39.408][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:39.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:39.410][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:39.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:39.411][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:39.412][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:39.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:39.414][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:39.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:39.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:39.416][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:39.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:39.418][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:39.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:39.419][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:39.420][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:39.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:39.422][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:39.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:39.424][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:39.424][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:39.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:39.426][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:39.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:39.428][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:39.428][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:39.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:39.430][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:39.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:39.432][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:39.432][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:39.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:39.434][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:39.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:39.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:39.436][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:39.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:39.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:39.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:39.440][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:39.441][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:39.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:39.442][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:39.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:39.444][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:39.445][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:39.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:39.447][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:39.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:39.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:39.449][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:39.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:39.451][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:39.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:39.452][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:39.453][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:39.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:39.455][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:39.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:39.456][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:39.457][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:39.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:39.459][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:39.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:39.461][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:39.461][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:39.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:39.463][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:39.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:39.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:39.465][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:39.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:39.467][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:39.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:39.469][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:39.469][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:39.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:39.471][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:39.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:39.473][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:39.474][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-03-27 20:40:39.475][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-03-27 20:40:39.476][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-03-27 20:40:39.478][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-03-27 20:40:39.479][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-03-27 20:40:39.480][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-03-27 20:40:39.481][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-03-27 20:40:39.483][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-03-27 20:40:39.484][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-03-27 20:40:39.485][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-03-27 20:40:39.486][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-03-27 20:40:39.488][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-03-27 20:40:39.489][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-03-27 20:40:39.490][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-03-27 20:40:39.491][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-03-27 20:40:39.493][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-03-27 20:40:39.494][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-03-27 20:40:39.495][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-03-27 20:40:39.496][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-03-27 20:40:39.498][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-03-27 20:40:39.499][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-03-27 20:40:39.500][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-03-27 20:40:39.501][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-03-27 20:40:39.503][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-03-27 20:40:39.504][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-03-27 20:40:39.505][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-03-27 20:40:39.506][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-03-27 20:40:39.508][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-03-27 20:40:39.509][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-03-27 20:40:39.510][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-03-27 20:40:39.511][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-03-27 20:40:39.513][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-03-27 20:40:39.514][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-03-27 20:40:39.515][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-03-27 20:40:39.517][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-03-27 20:40:39.518][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-03-27 20:40:39.519][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-03-27 20:40:39.520][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-03-27 20:40:39.522][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-03-27 20:40:39.523][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-03-27 20:40:39.524][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-03-27 20:40:39.526][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-03-27 20:40:39.527][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-03-27 20:40:39.528][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-03-27 20:40:39.529][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-03-27 20:40:39.531][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-03-27 20:40:39.532][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-03-27 20:40:39.533][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-03-27 20:40:39.535][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-03-27 20:40:39.536][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-03-27 20:40:39.537][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-03-27 20:40:39.539][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-03-27 20:40:39.540][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-03-27 20:40:39.541][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-03-27 20:40:39.542][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-03-27 20:40:39.544][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-03-27 20:40:39.545][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-03-27 20:40:39.546][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-03-27 20:40:39.548][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-03-27 20:40:39.549][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-03-27 20:40:39.550][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-03-27 20:40:39.552][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-03-27 20:40:39.553][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-03-27 20:40:39.554][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-03-27 20:40:39.556][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-03-27 20:40:39.557][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-03-27 20:40:39.559][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-03-27 20:40:39.560][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-03-27 20:40:39.561][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-03-27 20:40:39.563][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-03-27 20:40:39.564][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-03-27 20:40:39.566][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-03-27 20:40:39.567][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-03-27 20:40:39.568][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-03-27 20:40:39.570][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-03-27 20:40:39.571][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-03-27 20:40:39.573][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-03-27 20:40:39.574][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-03-27 20:40:39.575][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-03-27 20:40:39.577][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-03-27 20:40:39.578][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-03-27 20:40:39.579][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-03-27 20:40:39.581][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-03-27 20:40:39.582][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-03-27 20:40:39.584][initialize] This is biodb version 1.11.0.
biodb.DEBUG[2024-03-27 20:40:39.585][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-27 20:40:39.586][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:39.587][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:39.588][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:39.589][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:39.590][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:39.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:39.591][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:39.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:39.593][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:39.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:39.595][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:39.596][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:39.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:39.598][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:39.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:39.600][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:39.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:39.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:39.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:39.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:39.605][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:39.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:39.606][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:39.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:39.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:39.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:39.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:39.611][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:39.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:39.613][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:39.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:39.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:39.616][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:39.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:39.618][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:39.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:39.619][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:39.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:39.621][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:39.622][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:39.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:39.624][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:39.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:39.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:39.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:39.628][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:39.629][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:39.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:39.631][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:39.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:39.633][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:39.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:39.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:39.635][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:39.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:39.637][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:39.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:39.639][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:39.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:39.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:39.642][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:39.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:39.644][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:39.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:39.646][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:39.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:39.648][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:39.649][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:39.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:39.650][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:39.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:39.652][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:39.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:39.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:39.655][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:39.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:39.657][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:39.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:39.659][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:39.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:39.661][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:39.662][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:39.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:39.664][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:39.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:39.665][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:39.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:39.667][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:39.668][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:39.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:39.670][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:39.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:39.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:39.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:39.674][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:39.675][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:39.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:39.677][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:39.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:39.679][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:39.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:39.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:39.681][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:39.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:39.683][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:39.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:39.685][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:39.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:39.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:39.688][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:39.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:39.695][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:39.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:39.697][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:39.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:39.699][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:39.700][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:39.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:39.701][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:39.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:39.703][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:39.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:39.704][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:39.706][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-03-27 20:40:39.715][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-03-27 20:40:39.717][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-27 20:40:39.718][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-03-27 20:40:39.719][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:39.720][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 20:40:39.721][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:39.722][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 20:40:39.723][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:39.724][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-03-27 20:40:39.725][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-03-27 20:40:39.726][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 20:40:39.727][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:39.728][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-03-27 20:40:39.729][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 20:40:39.730][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-03-27 20:40:39.730][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-03-27 20:40:39.730][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-03-27 20:40:39.730][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-03-27 20:40:39.730][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-03-27 20:40:39.730][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-03-27 20:40:39.730][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-03-27 20:40:39.730][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-03-27 20:40:39.730][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-03-27 20:40:39.730][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-03-27 20:40:39.730][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-03-27 20:40:39.731][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-03-27 20:40:39.732][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-27 20:40:39.732][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-27 20:40:39.732][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-27 20:40:39.733][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-03-27 20:40:39.734][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:40:39.735][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:40:39.736][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 20:40:39.737][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:40:39.738][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:40:39.739][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 20:40:39.740][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-27 20:40:39.740][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-03-27 20:40:39.741][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 20:40:39.742][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 20:40:39.743][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:39.744][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-03-27 20:40:39.744][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-03-27 20:40:39.746][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-03-27 20:40:39.747][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-03-27 20:40:39.749][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-03-27 20:40:39.751][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-03-27 20:40:39.752][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-03-27 20:40:39.754][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-03-27 20:40:39.757][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-03-27 20:40:39.759][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-03-27 20:40:39.760][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-03-27 20:40:39.761][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-03-27 20:40:39.762][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-03-27 20:40:39.763][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-03-27 20:40:39.765][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-03-27 20:40:39.766][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-03-27 20:40:39.767][biodb::testThat]
biodb.INFO [2024-03-27 20:40:39.768][biodb::testThat] Running test function test_chebi_convCasToChebi (" convCasToChebi() works. ").
biodb.INFO [2024-03-27 20:40:39.769][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 20:40:39.770][biodb::testThat]
biodb.DEBUG[2024-03-27 20:40:39.773][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-03-27 20:40:39.777][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:40:39.778][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:40:39.779][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2024-03-27 20:40:40.229][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2024-03-27 20:40:40.897][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:40:40.901][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2024-03-27 20:40:40.905][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2024-03-27 20:40:40.913][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-03-27 20:40:40.918][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:40:40.919][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:40:40.921][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-03-27 20:40:41.408][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-03-27 20:40:41.865][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:40:41.869][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2024-03-27 20:40:41.877][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2024-03-27 20:40:41.882][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:41.883][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:41.885][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:41.896][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:41.898][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:41.900][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:41.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:41.907][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-03-27 20:40:41.914][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:40:41.916][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:40:41.920][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-03-27 20:40:42.404][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-03-27 20:40:42.861][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:40:42.865][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2024-03-27 20:40:42.873][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request"
biodb.DEBUG[2024-03-27 20:40:42.876][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:42.878][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:42.880][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:42.887][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:42.889][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:42.891][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:42.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:42.923][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:42.925][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:42.926][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:42.935][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:42.937][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:42.939][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:42.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:42.950][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-03-27 20:40:42.956][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-27 20:40:42.959][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-03-27 20:40:42.962][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-27 20:40:42.964][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-03-27 20:40:42.970][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:42.971][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:42.973][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:42.982][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:42.983][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:42.990][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:42.992][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:42.997][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-03-27 20:40:43.004][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-27 20:40:43.007][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-03-27 20:40:43.010][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-27 20:40:43.013][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-03-27 20:40:43.017][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:43.019][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:43.022][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:43.034][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:43.036][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:43.038][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:43.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:43.043][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:43.046][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:43.048][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:43.059][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:43.062][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:43.063][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:43.065][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:43.073][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-03-27 20:40:43.079][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-27 20:40:43.082][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-03-27 20:40:43.084][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-27 20:40:43.086][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-03-27 20:40:43.089][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:43.091][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:43.093][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:43.101][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:43.103][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:43.105][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:43.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:43.109][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-03-27 20:40:43.115][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-27 20:40:43.117][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-03-27 20:40:43.120][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-27 20:40:43.122][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-03-27 20:40:43.125][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:43.126][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:43.128][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:43.136][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:43.138][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:43.140][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:43.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:43.146][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-03-27 20:40:43.151][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:40:43.154][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:40:43.158][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-03-27 20:40:43.636][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-03-27 20:40:44.130][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:40:44.134][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2024-03-27 20:40:44.141][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2024-03-27 20:40:44.145][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:44.146][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:44.148][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:44.156][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:44.157][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:44.158][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:44.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-03-27 20:40:44.167][biodb::testThat]
biodb.INFO [2024-03-27 20:40:44.168][biodb::testThat] Running test function test_chebi_convInchiToChebi (" convInchiToChebi() works. ").
biodb.INFO [2024-03-27 20:40:44.170][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 20:40:44.171][biodb::testThat]
biodb.DEBUG[2024-03-27 20:40:44.174][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11?,12?,13?,14?,15-/m0/s1&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-03-27 20:40:44.212][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:40:44.214][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:40:44.216][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-03-27 20:40:44.701][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-03-27 20:40:45.182][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:40:45.186][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2024-03-27 20:40:45.194][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2024-03-27 20:40:45.207][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:45.210][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:45.211][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:45.218][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:45.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:45.221][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:45.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:45.227][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-03-27 20:40:45.231][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:40:45.232][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:40:45.234][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-03-27 20:40:45.682][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-03-27 20:40:46.167][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:40:46.169][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2024-03-27 20:40:46.173][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2024-03-27 20:40:46.175][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:46.176][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:46.177][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:46.181][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:46.182][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:46.183][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:46.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-03-27 20:40:46.189][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-03-27 20:40:46.191][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-03-27 20:40:46.192][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-03-27 20:40:46.193][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-03-27 20:40:46.194][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:46.194][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:46.195][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:46.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:46.197][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:46.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-03-27 20:40:46.202][biodb::testContext]
biodb.INFO [2024-03-27 20:40:46.203][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-27 20:40:46.204][biodb::testContext] Test context - Test web services
biodb.INFO [2024-03-27 20:40:46.205][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-27 20:40:46.206][biodb::testContext]
biodb.INFO [2024-03-27 20:40:46.209][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.11.0.
biodb.DEBUG[2024-03-27 20:40:46.210][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-03-27 20:40:46.215][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-27 20:40:46.216][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-03-27 20:40:46.217][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-03-27 20:40:46.218][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:46.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:46.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:46.221][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-03-27 20:40:46.222][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-03-27 20:40:46.223][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:46.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:46.224][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:46.225][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-03-27 20:40:46.227][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-03-27 20:40:46.228][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:46.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:46.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:46.231][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-03-27 20:40:46.232][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-03-27 20:40:46.233][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-03-27 20:40:46.234][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:46.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:46.236][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:46.237][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-03-27 20:40:46.238][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-03-27 20:40:46.239][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-03-27 20:40:46.240][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:46.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:46.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:46.242][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-03-27 20:40:46.244][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-03-27 20:40:46.244][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:46.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:46.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:46.247][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-03-27 20:40:46.248][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-03-27 20:40:46.249][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-03-27 20:40:46.250][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:46.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:46.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:46.253][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-03-27 20:40:46.254][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-03-27 20:40:46.255][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:46.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:46.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:46.258][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-03-27 20:40:46.259][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-03-27 20:40:46.260][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-03-27 20:40:46.261][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:46.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:46.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:46.264][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-03-27 20:40:46.265][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-03-27 20:40:46.266][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-03-27 20:40:46.267][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-03-27 20:40:46.268][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-03-27 20:40:46.269][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-03-27 20:40:46.270][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:46.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:46.272][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:46.273][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-03-27 20:40:46.274][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-03-27 20:40:46.275][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:46.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:46.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:46.278][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-03-27 20:40:46.279][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-03-27 20:40:46.280][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:46.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:46.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:46.283][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-03-27 20:40:46.284][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-03-27 20:40:46.285][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:46.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:46.287][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:46.288][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-03-27 20:40:46.289][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-03-27 20:40:46.290][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:46.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:46.292][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:46.293][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-03-27 20:40:46.294][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-03-27 20:40:46.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:46.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:46.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:46.298][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-03-27 20:40:46.299][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-03-27 20:40:46.302][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-03-27 20:40:46.303][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:46.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:46.305][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:46.306][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-03-27 20:40:46.307][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-03-27 20:40:46.308][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-03-27 20:40:46.309][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:46.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:46.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:46.312][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-03-27 20:40:46.314][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-27 20:40:46.315][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-03-27 20:40:46.316][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:46.317][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 20:40:46.318][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:46.319][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 20:40:46.320][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-27 20:40:46.321][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 20:40:46.322][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-27 20:40:46.323][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 20:40:46.324][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:46.325][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-03-27 20:40:46.326][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 20:40:46.327][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:40:46.328][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:46.329][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-27 20:40:46.329][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-27 20:40:46.329][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-27 20:40:46.329][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-27 20:40:46.329][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-27 20:40:46.331][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 20:40:46.332][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:40:46.333][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:40:46.334][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 20:40:46.335][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:40:46.335][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:40:46.336][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 20:40:46.338][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:40:46.339][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 20:40:46.340][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 20:40:46.341][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-27 20:40:46.342][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:40:46.343][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-03-27 20:40:46.345][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-27 20:40:46.346][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-03-27 20:40:46.347][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:46.348][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 20:40:46.349][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:46.350][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 20:40:46.351][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-27 20:40:46.352][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 20:40:46.353][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-27 20:40:46.354][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 20:40:46.355][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:46.356][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-03-27 20:40:46.357][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 20:40:46.358][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:40:46.359][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:46.360][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-27 20:40:46.360][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-27 20:40:46.360][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-27 20:40:46.360][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-27 20:40:46.360][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-27 20:40:46.361][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 20:40:46.362][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:40:46.363][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:40:46.364][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 20:40:46.365][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:40:46.366][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:40:46.367][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 20:40:46.368][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:40:46.369][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 20:40:46.370][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 20:40:46.371][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-27 20:40:46.372][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:40:46.373][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-03-27 20:40:46.375][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:46.376][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-03-27 20:40:46.377][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:46.378][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 20:40:46.379][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:46.380][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 20:40:46.381][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-27 20:40:46.382][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 20:40:46.383][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-27 20:40:46.384][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 20:40:46.385][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-27 20:40:46.386][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-03-27 20:40:46.387][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 20:40:46.389][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:40:46.390][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:46.391][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:40:46.392][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 20:40:46.393][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:40:46.393][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:40:46.394][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 20:40:46.395][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:40:46.396][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:40:46.397][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 20:40:46.398][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:40:46.399][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 20:40:46.400][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 20:40:46.401][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-27 20:40:46.402][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:40:46.403][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-03-27 20:40:46.405][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:46.406][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-03-27 20:40:46.407][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:46.408][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 20:40:46.409][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:46.410][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 20:40:46.411][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-27 20:40:46.412][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 20:40:46.413][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-27 20:40:46.414][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 20:40:46.416][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-27 20:40:46.417][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-03-27 20:40:46.418][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 20:40:46.419][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:40:46.420][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:46.421][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:40:46.422][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 20:40:46.423][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:40:46.423][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:40:46.424][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 20:40:46.425][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:40:46.426][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:40:46.427][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 20:40:46.428][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:40:46.429][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 20:40:46.430][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 20:40:46.431][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-27 20:40:46.432][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:40:46.434][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-27 20:40:46.434][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:46.435][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:46.436][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:46.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:46.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:46.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:46.440][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:46.441][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:46.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:46.443][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:46.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:46.444][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:46.445][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:46.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:46.447][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:46.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:46.466][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:46.467][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:46.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:46.468][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:46.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:46.470][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:46.471][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:46.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:46.473][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:46.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:46.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:46.475][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:46.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:46.477][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:46.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:46.479][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:46.480][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:46.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:46.481][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:46.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:46.483][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:46.484][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:46.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:46.486][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:46.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:46.487][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:46.488][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:46.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:46.490][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:46.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:46.491][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:46.492][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:46.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:46.494][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:46.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:46.496][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:46.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:46.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:46.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:46.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:46.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:46.501][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:46.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:46.502][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:46.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:46.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:46.505][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:46.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:46.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:46.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:46.508][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:46.509][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:46.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:46.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:46.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:46.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:46.513][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:46.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:46.514][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:46.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:46.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:46.517][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:46.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:46.519][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:46.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:46.520][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:46.521][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:46.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:46.523][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:46.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:46.524][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:46.525][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-03-27 20:40:46.527][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-03-27 20:40:46.528][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-03-27 20:40:46.529][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-03-27 20:40:46.530][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-03-27 20:40:46.532][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-03-27 20:40:46.533][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-03-27 20:40:46.534][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-03-27 20:40:46.536][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-03-27 20:40:46.537][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-03-27 20:40:46.538][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-03-27 20:40:46.539][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-03-27 20:40:46.541][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-03-27 20:40:46.542][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-03-27 20:40:46.543][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-03-27 20:40:46.544][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-03-27 20:40:46.546][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-03-27 20:40:46.547][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-03-27 20:40:46.548][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-03-27 20:40:46.549][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-03-27 20:40:46.551][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-03-27 20:40:46.552][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-03-27 20:40:46.553][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-03-27 20:40:46.555][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-03-27 20:40:46.556][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-03-27 20:40:46.557][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-03-27 20:40:46.558][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-03-27 20:40:46.560][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-03-27 20:40:46.561][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-03-27 20:40:46.562][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-03-27 20:40:46.564][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-03-27 20:40:46.565][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-03-27 20:40:46.566][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-03-27 20:40:46.567][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-03-27 20:40:46.569][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-03-27 20:40:46.570][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-03-27 20:40:46.571][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-03-27 20:40:46.573][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-03-27 20:40:46.574][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-03-27 20:40:46.575][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-03-27 20:40:46.576][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-03-27 20:40:46.578][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-03-27 20:40:46.579][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-03-27 20:40:46.580][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-03-27 20:40:46.582][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-03-27 20:40:46.583][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-03-27 20:40:46.584][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-03-27 20:40:46.586][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-03-27 20:40:46.587][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-03-27 20:40:46.588][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-03-27 20:40:46.590][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-03-27 20:40:46.591][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-03-27 20:40:46.592][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-03-27 20:40:46.593][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-03-27 20:40:46.595][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-03-27 20:40:46.596][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-03-27 20:40:46.597][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-03-27 20:40:46.599][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-03-27 20:40:46.600][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-03-27 20:40:46.601][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-03-27 20:40:46.603][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-03-27 20:40:46.604][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-03-27 20:40:46.605][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-03-27 20:40:46.607][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-03-27 20:40:46.608][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-03-27 20:40:46.609][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-03-27 20:40:46.610][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-03-27 20:40:46.612][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-03-27 20:40:46.613][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-03-27 20:40:46.614][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-03-27 20:40:46.616][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-03-27 20:40:46.617][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-03-27 20:40:46.618][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-03-27 20:40:46.619][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-03-27 20:40:46.621][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-03-27 20:40:46.622][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-03-27 20:40:46.623][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-03-27 20:40:46.625][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-03-27 20:40:46.626][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-03-27 20:40:46.627][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-03-27 20:40:46.628][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-03-27 20:40:46.630][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-03-27 20:40:46.631][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-03-27 20:40:46.632][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-03-27 20:40:46.634][initialize] This is biodb version 1.11.0.
biodb.DEBUG[2024-03-27 20:40:46.635][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-27 20:40:46.636][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:46.636][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:46.637][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:46.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:46.639][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:46.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:46.641][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:46.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:46.642][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:46.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:46.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:46.645][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:46.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:46.646][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:46.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:46.648][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:46.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:46.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:46.651][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:46.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:46.652][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:46.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:46.654][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:46.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:46.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:46.657][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:46.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:46.658][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:46.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:46.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:46.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:46.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:46.663][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:46.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:46.664][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:46.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:46.666][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:46.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:46.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:46.668][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:46.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:46.670][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:46.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:46.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:46.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:46.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:46.674][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:46.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:46.676][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:46.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:46.678][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:46.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:46.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:46.680][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:46.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:46.682][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:46.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:46.683][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:46.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:46.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:46.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:46.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:46.687][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:46.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:46.689][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:46.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:46.691][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:46.692][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:46.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:46.693][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:46.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:46.695][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:46.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:46.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:46.697][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:46.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:46.699][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:46.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:46.701][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:46.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:46.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:46.703][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:46.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:46.705][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:46.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:46.706][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:46.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:46.708][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:46.709][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:46.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:46.711][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:46.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:46.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:46.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:46.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:46.715][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:46.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:46.716][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:46.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:46.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:46.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:46.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:46.720][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:46.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:46.722][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:46.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:46.724][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:46.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:46.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:46.726][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:46.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:46.728][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:46.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:46.729][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:46.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:46.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:46.732][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:46.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:46.734][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:46.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:46.735][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:46.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:46.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:46.739][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-03-27 20:40:46.745][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-03-27 20:40:46.747][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-27 20:40:46.748][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-03-27 20:40:46.748][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:46.749][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 20:40:46.750][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:46.751][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 20:40:46.752][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:46.753][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-03-27 20:40:46.754][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-03-27 20:40:46.755][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 20:40:46.756][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:46.757][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-03-27 20:40:46.758][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 20:40:46.759][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-03-27 20:40:46.759][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-03-27 20:40:46.759][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-03-27 20:40:46.759][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-03-27 20:40:46.759][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-03-27 20:40:46.759][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-03-27 20:40:46.759][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-03-27 20:40:46.759][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-03-27 20:40:46.759][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-03-27 20:40:46.759][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-03-27 20:40:46.759][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-03-27 20:40:46.760][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-03-27 20:40:46.761][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-27 20:40:46.761][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-27 20:40:46.761][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-27 20:40:46.761][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-03-27 20:40:46.762][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:40:46.763][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:40:46.764][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 20:40:46.765][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:40:46.766][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:40:46.767][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 20:40:46.768][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-27 20:40:46.768][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-03-27 20:40:46.769][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 20:40:46.769][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 20:40:46.770][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:46.771][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-03-27 20:40:46.771][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-03-27 20:40:46.772][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-03-27 20:40:46.774][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-03-27 20:40:46.775][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-03-27 20:40:46.777][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-03-27 20:40:46.778][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-03-27 20:40:46.779][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-03-27 20:40:46.783][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-03-27 20:40:46.783][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-03-27 20:40:46.785][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-03-27 20:40:46.786][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-03-27 20:40:46.787][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-03-27 20:40:46.788][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-03-27 20:40:46.789][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-03-27 20:40:46.790][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-03-27 20:40:46.791][biodb::testThat]
biodb.INFO [2024-03-27 20:40:46.792][biodb::testThat] Running test function test.chebi.wsGetLiteEntity (" Web service getLiteEntity works fine. ").
biodb.INFO [2024-03-27 20:40:46.793][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 20:40:46.794][biodb::testThat]
biodb.DEBUG[2024-03-27 20:40:46.797][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-03-27 20:40:46.800][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-27 20:40:46.801][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-03-27 20:40:46.802][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-27 20:40:46.803][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-03-27 20:40:46.807][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-03-27 20:40:46.809][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:40:46.810][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:40:46.812][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-03-27 20:40:47.255][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-03-27 20:40:47.728][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:40:47.733][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2024-03-27 20:40:47.739][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2024-03-27 20:40:47.754][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-03-27 20:40:47.756][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-03-27 20:40:47.758][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-03-27 20:40:47.760][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-03-27 20:40:47.762][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:47.763][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:47.764][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:47.765][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:47.767][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:47.768][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-03-27 20:40:47.773][biodb::testContext]
biodb.INFO [2024-03-27 20:40:47.774][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-27 20:40:47.776][biodb::testContext] Test context - Non regression tests
biodb.INFO [2024-03-27 20:40:47.777][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-27 20:40:47.778][biodb::testContext]
biodb.INFO [2024-03-27 20:40:47.781][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.11.0.
biodb.DEBUG[2024-03-27 20:40:47.783][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-03-27 20:40:47.788][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-27 20:40:47.790][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-03-27 20:40:47.791][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-03-27 20:40:47.792][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:47.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:47.795][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:47.796][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-03-27 20:40:47.797][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-03-27 20:40:47.798][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:47.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:47.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:47.802][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-03-27 20:40:47.803][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-03-27 20:40:47.805][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:47.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:47.807][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:47.808][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-03-27 20:40:47.809][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-03-27 20:40:47.810][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-03-27 20:40:47.811][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:47.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:47.814][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:47.815][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-03-27 20:40:47.817][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-03-27 20:40:47.818][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-03-27 20:40:47.819][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:47.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:47.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:47.823][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-03-27 20:40:47.825][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-03-27 20:40:47.826][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:47.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:47.829][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:47.830][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-03-27 20:40:47.832][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-03-27 20:40:47.833][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-03-27 20:40:47.834][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:47.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:47.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:47.838][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-03-27 20:40:47.840][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-03-27 20:40:47.841][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:47.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:47.844][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:47.845][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-03-27 20:40:47.846][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-03-27 20:40:47.848][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-03-27 20:40:47.849][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:47.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:47.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:47.853][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-03-27 20:40:47.854][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-03-27 20:40:47.855][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-03-27 20:40:47.857][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-03-27 20:40:47.858][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-03-27 20:40:47.859][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-03-27 20:40:47.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:47.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:47.863][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:47.864][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-03-27 20:40:47.866][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-03-27 20:40:47.867][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:47.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:47.869][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:47.871][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-03-27 20:40:47.872][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-03-27 20:40:47.873][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:47.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:47.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:47.877][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-03-27 20:40:47.879][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-03-27 20:40:47.880][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:47.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:47.882][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:47.884][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-03-27 20:40:47.885][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-03-27 20:40:47.886][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:47.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:47.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:47.889][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-03-27 20:40:47.890][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-03-27 20:40:47.891][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:47.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:47.894][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:47.895][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-03-27 20:40:47.896][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-03-27 20:40:47.900][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-03-27 20:40:47.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:47.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:47.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:47.907][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-03-27 20:40:47.909][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-03-27 20:40:47.911][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-03-27 20:40:47.912][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:47.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:47.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:47.916][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-03-27 20:40:47.918][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-27 20:40:47.919][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-03-27 20:40:47.920][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:47.923][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 20:40:47.925][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:47.926][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 20:40:47.927][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-27 20:40:47.929][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 20:40:47.931][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-27 20:40:47.933][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 20:40:47.934][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:47.936][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-03-27 20:40:47.938][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 20:40:47.940][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:40:47.942][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:47.944][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-27 20:40:47.944][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-27 20:40:47.944][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-27 20:40:47.944][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-27 20:40:47.944][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-27 20:40:47.946][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 20:40:47.948][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:40:47.950][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:40:47.952][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 20:40:47.954][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:40:47.955][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:40:47.956][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 20:40:47.958][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:40:47.959][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 20:40:47.961][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 20:40:47.962][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-27 20:40:47.964][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:40:47.965][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-03-27 20:40:47.968][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-27 20:40:47.970][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-03-27 20:40:47.972][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:47.973][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 20:40:47.975][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:47.976][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 20:40:47.978][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-27 20:40:47.979][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 20:40:47.981][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-27 20:40:47.982][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 20:40:47.984][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:47.986][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-03-27 20:40:47.988][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 20:40:47.989][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:40:47.990][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:47.992][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-27 20:40:47.992][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-27 20:40:47.992][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-27 20:40:47.992][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-27 20:40:47.992][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-27 20:40:47.994][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 20:40:47.995][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:40:47.997][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:40:47.999][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 20:40:48.001][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:40:48.003][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:40:48.005][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 20:40:48.007][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:40:48.008][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 20:40:48.009][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 20:40:48.011][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-27 20:40:48.013][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:40:48.015][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-03-27 20:40:48.018][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:48.020][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-03-27 20:40:48.022][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:48.023][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 20:40:48.025][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:48.027][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 20:40:48.029][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-27 20:40:48.031][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 20:40:48.033][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-27 20:40:48.035][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 20:40:48.037][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-27 20:40:48.038][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-03-27 20:40:48.040][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 20:40:48.041][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:40:48.043][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:48.044][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:40:48.045][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 20:40:48.046][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:40:48.047][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:40:48.048][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 20:40:48.049][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:40:48.050][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:40:48.051][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 20:40:48.052][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:40:48.053][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 20:40:48.054][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 20:40:48.055][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-27 20:40:48.056][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:40:48.057][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-03-27 20:40:48.060][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:48.061][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-03-27 20:40:48.062][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:48.063][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 20:40:48.064][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:48.066][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 20:40:48.067][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-27 20:40:48.068][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 20:40:48.069][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-27 20:40:48.071][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 20:40:48.072][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-27 20:40:48.091][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-03-27 20:40:48.093][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 20:40:48.094][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:40:48.095][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:48.096][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:40:48.098][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 20:40:48.099][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:40:48.100][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:40:48.101][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 20:40:48.102][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:40:48.103][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:40:48.104][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 20:40:48.106][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:40:48.107][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 20:40:48.108][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 20:40:48.109][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-27 20:40:48.110][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:40:48.112][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-27 20:40:48.113][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:48.114][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:48.115][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:48.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:48.117][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:48.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:48.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:48.120][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:48.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:48.122][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:48.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:48.124][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:48.125][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:48.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:48.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:48.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:48.129][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:48.130][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:48.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:48.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:48.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:48.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:48.135][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:48.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:48.137][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:48.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:48.139][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:48.140][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:48.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:48.142][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:48.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:48.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:48.146][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:48.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:48.148][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:48.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:48.150][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:48.152][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:48.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:48.156][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:48.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:48.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:48.161][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:48.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:48.164][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:48.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:48.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:48.168][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:48.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:48.170][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:48.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:48.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:48.175][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:48.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:48.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:48.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:48.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:48.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:48.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:48.185][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:48.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:48.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:48.189][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:48.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:48.192][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:48.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:48.195][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:48.197][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:48.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:48.200][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:48.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:48.203][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:48.205][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:48.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:48.207][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:48.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:48.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:48.211][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:48.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:48.214][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:48.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:48.216][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:48.217][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:48.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:48.219][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:48.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:48.221][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:48.222][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-03-27 20:40:48.223][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-03-27 20:40:48.225][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-03-27 20:40:48.227][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-03-27 20:40:48.228][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-03-27 20:40:48.230][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-03-27 20:40:48.231][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-03-27 20:40:48.233][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-03-27 20:40:48.235][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-03-27 20:40:48.236][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-03-27 20:40:48.237][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-03-27 20:40:48.239][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-03-27 20:40:48.241][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-03-27 20:40:48.242][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-03-27 20:40:48.244][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-03-27 20:40:48.245][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-03-27 20:40:48.247][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-03-27 20:40:48.248][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-03-27 20:40:48.250][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-03-27 20:40:48.252][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-03-27 20:40:48.253][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-03-27 20:40:48.255][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-03-27 20:40:48.256][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-03-27 20:40:48.258][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-03-27 20:40:48.260][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-03-27 20:40:48.261][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-03-27 20:40:48.263][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-03-27 20:40:48.264][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-03-27 20:40:48.266][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-03-27 20:40:48.268][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-03-27 20:40:48.269][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-03-27 20:40:48.271][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-03-27 20:40:48.273][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-03-27 20:40:48.275][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-03-27 20:40:48.276][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-03-27 20:40:48.278][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-03-27 20:40:48.279][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-03-27 20:40:48.281][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-03-27 20:40:48.283][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-03-27 20:40:48.284][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-03-27 20:40:48.286][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-03-27 20:40:48.288][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-03-27 20:40:48.289][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-03-27 20:40:48.291][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-03-27 20:40:48.292][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-03-27 20:40:48.294][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-03-27 20:40:48.296][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-03-27 20:40:48.297][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-03-27 20:40:48.299][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-03-27 20:40:48.301][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-03-27 20:40:48.302][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-03-27 20:40:48.304][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-03-27 20:40:48.306][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-03-27 20:40:48.307][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-03-27 20:40:48.309][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-03-27 20:40:48.310][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-03-27 20:40:48.312][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-03-27 20:40:48.314][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-03-27 20:40:48.315][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-03-27 20:40:48.317][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-03-27 20:40:48.319][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-03-27 20:40:48.320][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-03-27 20:40:48.322][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-03-27 20:40:48.324][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-03-27 20:40:48.325][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-03-27 20:40:48.326][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-03-27 20:40:48.328][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-03-27 20:40:48.329][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-03-27 20:40:48.331][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-03-27 20:40:48.333][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-03-27 20:40:48.334][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-03-27 20:40:48.336][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-03-27 20:40:48.338][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-03-27 20:40:48.339][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-03-27 20:40:48.341][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-03-27 20:40:48.342][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-03-27 20:40:48.344][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-03-27 20:40:48.346][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-03-27 20:40:48.348][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-03-27 20:40:48.349][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-03-27 20:40:48.351][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-03-27 20:40:48.353][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-03-27 20:40:48.354][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-03-27 20:40:48.356][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-03-27 20:40:48.358][initialize] This is biodb version 1.11.0.
biodb.DEBUG[2024-03-27 20:40:48.359][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-27 20:40:48.360][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:48.361][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:48.362][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:48.363][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:48.364][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:48.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:48.366][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:48.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:48.369][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:48.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:48.370][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:48.371][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:48.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:48.373][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:48.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:48.375][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:48.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:48.378][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:48.379][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:48.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:48.381][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:48.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:48.383][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:48.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:48.385][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:48.386][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:48.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:48.388][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:48.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:48.390][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:48.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:48.392][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:48.393][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:48.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:48.396][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:48.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:48.398][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:48.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:48.400][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:48.401][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:48.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:48.403][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:48.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:48.404][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:48.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:48.406][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:48.407][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:48.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:48.409][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:48.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:48.411][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:48.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:48.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:48.414][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:48.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:48.415][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:48.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:48.417][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:48.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:48.419][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:48.420][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:48.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:48.422][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:48.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:48.424][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:48.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:48.425][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:48.426][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:48.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:48.428][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:48.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:48.430][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:48.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:48.432][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:48.433][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:48.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:48.435][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:48.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:48.437][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:48.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:48.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:48.440][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:48.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:48.442][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:48.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:48.443][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:48.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:48.451][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:48.452][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:48.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:48.454][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:48.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:48.456][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:48.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:48.457][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:48.458][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:48.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:48.460][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:48.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:48.463][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:48.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:48.464][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:48.466][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:48.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:48.467][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:48.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:48.469][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:48.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:48.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:48.473][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:48.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:48.475][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:48.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:48.478][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:48.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:48.481][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:48.482][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:40:48.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:48.485][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:48.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:48.487][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:48.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:48.490][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:48.493][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-03-27 20:40:48.495][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-03-27 20:40:48.498][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-27 20:40:48.500][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-03-27 20:40:48.501][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:48.503][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 20:40:48.504][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:48.506][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 20:40:48.507][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:48.509][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-03-27 20:40:48.510][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-03-27 20:40:48.511][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 20:40:48.513][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:48.514][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-03-27 20:40:48.516][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 20:40:48.518][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-03-27 20:40:48.518][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-03-27 20:40:48.518][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-03-27 20:40:48.518][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-03-27 20:40:48.518][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-03-27 20:40:48.518][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-03-27 20:40:48.518][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-03-27 20:40:48.518][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-03-27 20:40:48.518][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-03-27 20:40:48.518][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-03-27 20:40:48.518][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-03-27 20:40:48.520][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-03-27 20:40:48.522][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-27 20:40:48.522][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-27 20:40:48.522][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-27 20:40:48.523][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-03-27 20:40:48.525][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:40:48.526][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:40:48.527][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 20:40:48.528][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:40:48.529][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:40:48.530][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 20:40:48.532][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-27 20:40:48.532][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-03-27 20:40:48.533][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 20:40:48.535][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 20:40:48.536][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-03-27 20:40:48.537][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-03-27 20:40:48.537][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-03-27 20:40:48.539][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-03-27 20:40:48.541][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-03-27 20:40:48.544][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-03-27 20:40:48.546][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-03-27 20:40:48.549][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-03-27 20:40:48.551][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-03-27 20:40:48.557][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-03-27 20:40:48.558][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-03-27 20:40:48.560][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-03-27 20:40:48.561][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-03-27 20:40:48.563][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-03-27 20:40:48.564][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-03-27 20:40:48.565][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-03-27 20:40:48.566][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-03-27 20:40:48.568][biodb::testThat]
biodb.INFO [2024-03-27 20:40:48.569][biodb::testThat] Running test function test.chebi.encoding.issue.in.xml (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2024-03-27 20:40:48.570][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 20:40:48.571][biodb::testThat]
biodb.DEBUG[2024-03-27 20:40:48.574][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-03-27 20:40:48.579][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-27 20:40:48.580][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-03-27 20:40:48.582][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-27 20:40:48.584][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-03-27 20:40:48.589][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-03-27 20:40:48.592][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-27 20:40:48.594][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2024-03-27 20:40:48.595][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-27 20:40:48.597][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2024-03-27 20:40:48.602][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2024-03-27 20:40:48.603][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-27 20:40:48.605][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2024-03-27 20:40:48.607][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-27 20:40:48.608][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-27 20:40:48.609][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-27 20:40:48.610][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-27 20:40:48.612][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-27 20:40:48.613][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-27 20:40:48.616][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:48.617][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:48.618][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:48.622][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:48.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:48.625][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:48.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:40:48.627][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2024-03-27 20:40:48.631][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:40:48.632][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:40:48.633][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2024-03-27 20:40:49.524][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2024-03-27 20:40:50.857][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:40:50.860][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2024-03-27 20:40:50.867][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2024-03-27 20:40:50.872][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2024-03-27 20:40:50.875][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-27 20:40:50.877][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-27 20:40:50.879][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-27 20:40:50.882][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:40:50.883][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:50.885][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:50.891][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:50.893][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:50.894][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:50.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:40:50.902][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:50.904][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:50.906][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:50.907][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:50.909][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:50.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:50.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:50.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:50.915][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-27 20:40:50.917][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-27 20:40:50.918][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:50.920][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:50.922][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-27 20:40:50.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-27 20:40:50.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:50.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:50.928][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:40:50.929][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:40:50.931][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:50.932][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:50.934][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:40:50.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:40:50.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:50.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:50.940][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-27 20:40:50.942][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-27 20:40:50.943][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:50.945][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:50.947][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-27 20:40:50.948][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-27 20:40:50.950][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:50.951][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:50.953][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:50.955][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:50.956][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:50.957][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:50.959][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:50.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:40:50.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:50.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:50.965][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-27 20:40:50.967][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:50.968][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:50.970][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:50.972][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-27 20:40:50.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:40:50.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:50.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:50.979][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:50.980][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:50.982][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:50.983][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:50.985][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:50.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:40:50.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:50.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:50.991][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:51.001][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:51.004][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:51.006][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:51.010][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:40:51.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:40:51.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:51.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:51.018][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-27 20:40:51.020][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-27 20:40:51.022][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:51.023][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:51.025][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-27 20:40:51.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-27 20:40:51.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:51.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:51.032][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-27 20:40:51.033][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-27 20:40:51.035][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:51.036][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:51.038][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-27 20:40:51.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-27 20:40:51.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:51.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:51.045][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:51.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:51.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:51.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:51.051][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:51.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:51.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:51.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:51.057][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:51.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:51.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:51.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:51.063][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:40:51.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:40:51.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:51.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:51.070][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:51.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:51.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:51.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:51.076][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:51.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:51.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:51.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:51.083][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:51.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:51.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:51.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:51.090][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:51.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:51.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:51.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:51.097][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:51.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:51.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:51.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:40:51.103][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:40:51.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:40:51.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:40:51.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:40:51.110][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2024-03-27 20:40:51.117][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-03-27 20:40:51.120][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-03-27 20:40:51.122][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-03-27 20:40:51.124][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-03-27 20:40:51.125][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:40:51.127][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:40:51.128][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:40:51.129][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:40:51.131][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:40:51.132][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 386 ]
>
> proc.time()
user system elapsed
24.706 1.276 63.959
biodbChebi.Rcheck/biodbChebi-Ex.timings
| name | user | system | elapsed | |
| ChebiConn | 1.033 | 0.041 | 1.901 | |
| ChebiEntry | 0.144 | 0.002 | 0.145 | |