Pierrick Roger
| Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024) |
| git_url: https://git.bioconductor.org/packages/biodbChebi |
| git_branch: RELEASE_3_19 |
| git_last_commit: fad38a4 |
| git_last_commit_date: 2024-04-30 11:37:31 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-05-04 11:40:18 -0400 (Sat, 04 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4753 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" | 4486 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" | 4519 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4479 |
| 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 200/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodbChebi 1.10.0 (landing page) Pierrick Roger
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | TIMEOUT | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
|
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: biodbChebi |
| Version: 1.10.0 |
| Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings biodbChebi_1.10.0.tar.gz |
| StartedAt: 2024-05-04 05:23:06 -0000 (Sat, 04 May 2024) |
| EndedAt: 2024-05-04 05:38:54 -0000 (Sat, 04 May 2024) |
| EllapsedTime: 948.5 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: biodbChebi.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings biodbChebi_1.10.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/biodbChebi.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodbChebi/DESCRIPTION’ ... OK
* this is package ‘biodbChebi’ version ‘1.10.0’
* 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
ChebiConn 1.121 0.056 5.498
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
── Failure ('test_100_generic.R:16:1'): The peak table is correct. ─────────────
any(vapply(entries, is.null, FUN.VALUE = TRUE)) is not FALSE
`actual`: TRUE
`expected`: FALSE
One of the entries is NULL.
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<ChebiCnn>`, opt = `<named list>`)
3. └─testthat::expect_false(...)
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 444 ]
Error: Test failures
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR
See
‘/home/biocbuild/bbs-3.19-bioc/meat/biodbChebi.Rcheck/00check.log’
for details.
biodbChebi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL biodbChebi ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/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.fail
R version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 [2024-05-04 05:24:31.677][biodb::testContext]
biodb.INFO [2024-05-04 05:24:31.680][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-04 05:24:31.681][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-05-04 05:24:31.682][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-04 05:24:31.684][biodb::testContext]
biodb.INFO [2024-05-04 05:24:31.692][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-05-04 05:24:31.695][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-05-04 05:24:31.704][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-04 05:24:31.705][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-04 05:24:31.707][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-04 05:24:31.708][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:24:31.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:24:31.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:24:31.712][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-04 05:24:31.740][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-04 05:24:31.741][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:24:31.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:24:31.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:24:31.745][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-04 05:24:31.747][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-04 05:24:31.748][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:24:31.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:24:31.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:24:31.752][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-04 05:24:31.753][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-04 05:24:31.754][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-04 05:24:31.756][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:24:31.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:24:31.758][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.DEBUG[2024-05-04 05:24:31.759][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-04 05:24:31.761][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-04 05:24:31.762][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-04 05:24:31.763][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:24:31.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:24:31.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:24:31.767][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-04 05:24:31.769][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-04 05:24:31.770][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:24:31.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:24:31.772][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:24:31.774][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-04 05:24:31.775][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-04 05:24:31.776][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-04 05:24:31.778][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:24:31.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:24:31.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:24:31.781][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-04 05:24:31.783][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-04 05:24:31.784][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:24:31.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:24:31.787][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:24:31.788][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-04 05:24:31.789][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-04 05:24:31.791][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-04 05:24:31.792][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:24:31.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:24:31.795][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:24:31.796][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-04 05:24:31.797][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-04 05:24:31.799][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-04 05:24:31.800][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-04 05:24:31.801][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-04 05:24:31.803][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-04 05:24:31.804][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:24:31.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:24:31.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:24:31.808][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-04 05:24:31.809][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-04 05:24:31.810][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:24:31.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:24:31.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:24:31.814][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-04 05:24:31.816][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-04 05:24:31.817][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:24:31.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:24:31.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:24:31.821][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-04 05:24:31.822][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-04 05:24:31.823][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:24:31.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:24:31.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:24:31.827][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-04 05:24:31.829][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-04 05:24:31.830][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:24:31.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:24:31.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:24:31.834][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-04 05:24:31.835][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-04 05:24:31.836][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:24:31.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:24:31.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:24:31.841][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-04 05:24:31.843][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-04 05:24:31.849][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-04 05:24:31.850][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:24:31.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:24:31.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:24:31.854][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-04 05:24:31.856][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-04 05:24:31.857][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-04 05:24:31.859][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:24:31.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:24:31.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:24:31.866][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-04 05:24:31.916][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-04 05:24:31.952][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-05-04 05:24:31.953][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 05:24:31.955][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 05:24:31.956][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 05:24:31.957][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 05:24:31.959][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-04 05:24:31.960][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 05:24:31.961][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-04 05:24:31.963][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 05:24:31.964][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-04 05:24:31.966][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-04 05:24:31.967][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 05:24:31.968][self$setPropertyValue]
biodb.DEBUG[2024-05-04 05:24:31.970][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-04 05:24:31.971][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-04 05:24:31.971][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-04 05:24:31.971][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-04 05:24:31.971][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-04 05:24:31.971][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-04 05:24:31.973][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-04 05:24:31.974][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 05:24:31.975][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 05:24:31.977][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 05:24:31.978][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 05:24:31.979][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 05:24:31.981][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 05:24:31.982][self$setPropertyValue]
biodb.DEBUG[2024-05-04 05:24:31.984][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 05:24:31.985][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 05:24:31.986][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-04 05:24:31.988][self$setPropertyValue]
biodb.DEBUG[2024-05-04 05:24:31.989][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-04 05:24:31.992][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-04 05:24:31.993][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-04 05:24:31.995][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 05:24:31.996][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 05:24:31.998][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 05:24:31.999][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 05:24:32.000][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-04 05:24:32.002][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 05:24:32.003][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-04 05:24:32.005][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 05:24:32.006][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-04 05:24:32.007][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-04 05:24:32.009][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 05:24:32.010][self$setPropertyValue]
biodb.DEBUG[2024-05-04 05:24:32.012][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-04 05:24:32.013][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-04 05:24:32.013][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-04 05:24:32.013][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-04 05:24:32.013][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-04 05:24:32.013][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-04 05:24:32.014][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-04 05:24:32.016][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 05:24:32.017][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 05:24:32.018][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 05:24:32.020][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 05:24:32.021][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 05:24:32.022][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 05:24:32.024][self$setPropertyValue]
biodb.DEBUG[2024-05-04 05:24:32.025][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 05:24:32.026][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 05:24:32.028][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-04 05:24:32.029][self$setPropertyValue]
biodb.DEBUG[2024-05-04 05:24:32.031][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-04 05:24:32.033][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-04 05:24:32.035][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-05-04 05:24:32.036][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 05:24:32.037][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 05:24:32.039][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 05:24:32.041][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 05:24:32.042][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-04 05:24:32.044][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 05:24:32.045][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-04 05:24:32.046][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 05:24:32.048][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-04 05:24:32.049][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-04 05:24:32.051][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 05:24:32.052][self$setPropertyValue]
biodb.DEBUG[2024-05-04 05:24:32.054][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-04 05:24:32.055][self$setPropertyValue]
biodb.DEBUG[2024-05-04 05:24:32.056][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-04 05:24:32.058][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 05:24:32.059][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 05:24:32.060][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 05:24:32.062][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 05:24:32.063][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 05:24:32.064][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 05:24:32.065][self$setPropertyValue]
biodb.DEBUG[2024-05-04 05:24:32.067][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 05:24:32.068][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 05:24:32.069][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-04 05:24:32.071][self$setPropertyValue]
biodb.DEBUG[2024-05-04 05:24:32.072][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-04 05:24:32.075][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-04 05:24:32.076][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-04 05:24:32.078][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 05:24:32.079][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 05:24:32.080][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 05:24:32.082][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 05:24:32.083][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-04 05:24:32.084][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 05:24:32.086][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-04 05:24:32.087][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 05:24:32.089][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-04 05:24:32.090][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-04 05:24:32.091][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 05:24:32.093][self$setPropertyValue]
biodb.DEBUG[2024-05-04 05:24:32.094][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-04 05:24:32.095][self$setPropertyValue]
biodb.DEBUG[2024-05-04 05:24:32.097][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-04 05:24:32.098][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 05:24:32.099][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 05:24:32.101][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 05:24:32.102][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 05:24:32.103][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 05:24:32.105][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 05:24:32.106][self$setPropertyValue]
biodb.DEBUG[2024-05-04 05:24:32.107][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 05:24:32.109][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 05:24:32.110][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-04 05:24:32.111][self$setPropertyValue]
biodb.DEBUG[2024-05-04 05:24:32.116][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-04 05:24:32.118][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:24:32.119][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[2024-05-04 05:24:32.120][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:24:32.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:24:32.123][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:24:32.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:24:32.125][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:24:32.126][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:24:32.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:24:32.129][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:24:32.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:24:32.131][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:24:32.133][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:24:32.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:24:32.135][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:24:32.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:24:32.138][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.DEBUG[2024-05-04 05:24:32.139][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:24:32.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:24:32.142][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:24:32.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:24:32.144][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[2024-05-04 05:24:32.145][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:24:32.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:24:32.148][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:24:32.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:24:32.150][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[2024-05-04 05:24:32.151][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:24:32.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:24:32.154][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:24:32.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:24:32.156][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:24:32.158][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:24:32.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:24:32.160][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:24:32.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:24:32.162][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:24:32.164][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:24:32.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:24:32.166][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:24:32.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:24:32.169][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:24:32.170][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:24:32.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:24:32.172][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:24:32.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:24:32.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:24:32.176][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:24:32.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:24:32.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:24:32.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:24:32.181][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:24:32.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:24:32.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:24:32.185][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:24:32.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:24:32.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:24:32.188][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:24:32.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:24:32.191][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:24:32.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:24:32.193][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[2024-05-04 05:24:32.194][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:24:32.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:24:32.197][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:24:32.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:24:32.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:24:32.201][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:24:32.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:24:32.203][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:24:32.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:24:32.205][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:24:32.207][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:24:32.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:24:32.209][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:24:32.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:24:32.212][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:24:32.213][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:24:32.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:24:32.215][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:24:32.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:24:32.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:24:32.219][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:24:32.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:24:32.222][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:24:32.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:24:32.224][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[2024-05-04 05:24:32.226][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-04 05:24:32.232][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-04 05:24:32.234][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-04 05:24:32.236][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-04 05:24:32.238][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-04 05:24:32.240][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-04 05:24:32.243][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-04 05:24:32.246][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-04 05:24:32.248][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-04 05:24:32.250][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-04 05:24:32.253][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-04 05:24:32.255][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-04 05:24:32.257][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-04 05:24:32.259][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-04 05:24:32.261][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-04 05:24:32.263][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-04 05:24:32.265][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-04 05:24:32.267][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-04 05:24:32.269][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-04 05:24:32.271][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-04 05:24:32.273][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-04 05:24:32.275][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-04 05:24:32.277][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-04 05:24:32.279][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-04 05:24:32.281][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-04 05:24:32.283][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-04 05:24:32.285][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-04 05:24:32.287][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-04 05:24:32.289][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-04 05:24:32.291][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-04 05:24:32.293][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-04 05:24:32.295][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-04 05:24:32.297][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-04 05:24:32.307][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-04 05:24:32.310][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-04 05:24:32.312][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-04 05:24:32.314][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-04 05:24:32.316][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-04 05:24:32.318][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-04 05:24:32.320][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-04 05:24:32.323][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-04 05:24:32.325][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-04 05:24:32.327][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-04 05:24:32.329][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-04 05:24:32.331][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-04 05:24:32.333][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-04 05:24:32.335][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-04 05:24:32.337][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-04 05:24:32.339][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-04 05:24:32.342][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-04 05:24:32.344][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-04 05:24:32.346][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-04 05:24:32.348][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-04 05:24:32.350][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-04 05:24:32.352][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-04 05:24:32.354][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-04 05:24:32.356][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-04 05:24:32.358][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-04 05:24:32.361][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-04 05:24:32.363][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-04 05:24:32.365][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-04 05:24:32.367][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-04 05:24:32.369][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-04 05:24:32.371][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-04 05:24:32.373][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-04 05:24:32.375][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-04 05:24:32.377][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-04 05:24:32.379][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-04 05:24:32.381][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-04 05:24:32.383][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-04 05:24:32.385][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-04 05:24:32.387][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-04 05:24:32.390][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-04 05:24:32.392][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-04 05:24:32.394][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-04 05:24:32.396][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-04 05:24:32.398][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-04 05:24:32.400][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-04 05:24:32.402][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-04 05:24:32.404][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-04 05:24:32.407][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-04 05:24:32.409][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-04 05:24:32.411][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-04 05:24:32.420][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-04 05:24:32.422][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-05-04 05:24:32.427][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-04 05:24:32.428][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:24:32.430][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:24:32.431][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:24:32.433][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:24:32.440][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:24:32.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:24:32.443][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:24:32.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:24:32.446][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:24:32.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:24:32.448][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[2024-05-04 05:24:32.450][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:24:32.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:24:32.452][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:24:32.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:24:32.455][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:24:32.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:24:32.457][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[2024-05-04 05:24:32.458][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:24:32.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:24:32.462][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:24:32.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:24:32.464][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:24:32.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:24:32.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:24:32.468][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:24:32.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:24:32.470][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:24:32.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:24:32.473][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:24:32.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:24:32.475][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[2024-05-04 05:24:32.476][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:24:32.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:24:32.479][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:24:32.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:24:32.481][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:24:32.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:24:32.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:24:32.485][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:24:32.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:24:32.487][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:24:32.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:24:32.490][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:24:32.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:24:32.492][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:24:32.494][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:24:32.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:24:32.496][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:24:32.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:24:32.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:24:32.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:24:32.501][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.DEBUG[2024-05-04 05:24:32.502][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:24:32.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:24:32.504][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:24:32.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:24:32.507][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:24:32.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:24:32.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:24:32.511][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:24:32.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:24:32.513][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:24:32.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:24:32.515][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:24:32.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:24:32.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:24:32.519][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:24:32.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:24:32.522][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:24:32.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:24:32.524][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:24:32.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:24:32.526][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:24:32.528][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:24:32.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:24:32.530][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:24:32.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:24:32.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:24:32.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:24:32.535][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[2024-05-04 05:24:32.536][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:24:32.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:24:32.538][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:24:32.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:24:32.541][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:24:32.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:24:32.543][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:24:32.544][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:24:32.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:24:32.547][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:24:32.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:24:32.549][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:24:32.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:24:32.552][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:24:32.553][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:24:32.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:24:32.555][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:24:32.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:24:32.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:24:32.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:24:32.560][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:24:32.561][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:24:32.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:24:32.563][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:24:32.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:24:32.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:24:32.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:24:32.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:24:32.569][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:24:32.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:24:32.572][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:24:32.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:24:32.574][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:24:32.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:24:32.577][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:24:32.578][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:24:32.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:24:32.580][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:24:32.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:24:32.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:24:32.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:24:32.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:24:32.587][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-05-04 05:24:32.600][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-05-04 05:24:32.603][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-04 05:24:32.604][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-05-04 05:24:32.606][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 05:24:32.607][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 05:24:32.608][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 05:24:32.610][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 05:24:32.611][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-04 05:24:32.612][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-05-04 05:24:32.614][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-05-04 05:24:32.615][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 05:24:32.616][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-04 05:24:32.618][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-05-04 05:24:32.619][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 05:24:32.620][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-05-04 05:24:32.620][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-05-04 05:24:32.620][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-05-04 05:24:32.620][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-05-04 05:24:32.620][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-05-04 05:24:32.620][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-05-04 05:24:32.620][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-05-04 05:24:32.620][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-05-04 05:24:32.620][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-05-04 05:24:32.620][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-05-04 05:24:32.620][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-05-04 05:24:32.622][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-04 05:24:32.623][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-04 05:24:32.623][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-04 05:24:32.623][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-04 05:24:32.625][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-05-04 05:24:32.626][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 05:24:32.627][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 05:24:32.628][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 05:24:32.630][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 05:24:32.631][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 05:24:32.632][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 05:24:32.633][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-04 05:24:32.633][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-05-04 05:24:32.635][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 05:24:32.636][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 05:24:32.637][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-04 05:24:32.639][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-05-04 05:24:32.639][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-05-04 05:24:32.647][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-04 05:24:32.649][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-04 05:24:32.651][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-05-04 05:24:32.653][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-04 05:24:32.662][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-04 05:24:32.666][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-04 05:24:32.695][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-05-04 05:24:32.696][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-05-04 05:24:32.702][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-05-04 05:24:32.707][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-05-04 05:24:32.712][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-04 05:24:32.713][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-04 05:24:32.715][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-05-04 05:24:32.717][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-05-04 05:24:32.728][biodb::testThat]
biodb.INFO [2024-05-04 05:24:32.729][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2024-05-04 05:24:32.731][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 05:24:32.732][biodb::testThat]
biodb.TRACE[2024-05-04 05:24:32.737][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2024-05-04 05:24:32.739][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-04 05:24:32.744][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-04 05:24:32.754][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:24:32.755][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:24:32.756][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:24:32.772][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:24:32.773][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:24:32.774][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:24:32.776][FUN] Functions in observer BiodbConfig: [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[2024-05-04 05:24:32.787][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:24:32.789][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:24:32.790][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:32.791][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:32.794][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:24:32.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:24:32.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:32.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:32.816][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-04 05:24:32.817][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-04 05:24:32.818][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:32.819][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:32.857][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-04 05:24:32.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-04 05:24:32.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:32.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:32.863][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 05:24:32.864][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 05:24:32.866][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:32.867][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:32.869][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 05:24:32.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 05:24:32.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:32.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:32.875][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 05:24:32.877][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 05:24:32.878][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:32.879][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:32.881][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 05:24:32.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 05:24:32.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:32.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:32.886][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 05:24:32.888][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 05:24:32.889][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:32.890][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:32.892][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 05:24:32.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 05:24:32.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:32.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:32.898][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:24:32.899][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:24:32.900][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:32.902][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:32.903][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:24:32.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:24:32.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:32.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:32.909][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-04 05:24:32.910][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:24:32.912][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:32.913][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:32.915][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-04 05:24:32.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:24:32.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:32.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:32.920][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:24:32.922][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:24:32.923][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:32.924][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:32.926][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:24:32.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:24:32.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:32.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:32.931][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 05:24:32.933][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 05:24:32.934][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:32.935][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:32.937][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 05:24:32.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 05:24:32.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:32.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:32.943][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-04 05:24:32.944][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-04 05:24:32.946][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:32.947][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:32.949][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-04 05:24:32.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-04 05:24:32.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:32.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:32.954][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-04 05:24:32.956][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-04 05:24:32.957][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:32.958][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:32.960][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-04 05:24:32.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-04 05:24:32.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:32.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:32.966][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:24:32.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:24:32.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:32.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:32.971][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:24:32.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:24:32.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:32.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:32.976][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:24:32.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:24:32.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:32.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:32.982][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:24:32.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:24:32.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:32.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:32.987][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:24:32.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:24:32.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:32.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:32.992][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:24:32.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:24:32.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:32.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:32.998][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:24:32.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:24:33.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.066][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:24:33.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:24:33.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.072][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:24:33.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:24:33.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.078][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:24:33.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:24:33.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:24:33.083][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2024-05-04 05:24:33.086][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 05:24:33.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 05:24:33.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.092][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 05:24:33.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 05:24:33.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.130][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 05:24:33.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 05:24:33.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.136][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 05:24:33.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 05:24:33.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.141][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:24:33.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:24:33.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.146][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:24:33.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:24:33.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.151][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-04 05:24:33.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-04 05:24:33.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.156][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-04 05:24:33.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-04 05:24:33.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.162][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-04 05:24:33.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-04 05:24:33.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.167][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-04 05:24:33.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-04 05:24:33.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.191][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:24:33.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:24:33.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.213][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:24:33.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:24:33.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.223][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:24:33.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:24:33.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.229][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:24:33.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:24:33.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.234][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:24:33.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:24:33.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.242][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:24:33.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:24:33.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.248][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:24:33.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:24:33.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.253][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:24:33.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:24:33.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.259][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:24:33.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:24:33.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.264][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:24:33.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:24:33.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.269][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:24:33.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:24:33.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.284][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:24:33.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:24:33.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.290][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:24:33.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:24:33.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.295][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:24:33.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:24:33.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.301][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:24:33.302][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:24:33.303][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.305][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.306][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:24:33.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:24:33.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.358][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:24:33.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:24:33.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.364][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:24:33.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:24:33.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.369][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:24:33.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:24:33.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.374][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:24:33.375][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:24:33.377][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.378][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.379][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:24:33.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:24:33.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.394][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 05:24:33.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 05:24:33.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.400][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 05:24:33.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 05:24:33.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.405][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 05:24:33.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 05:24:33.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.410][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 05:24:33.412][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 05:24:33.413][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.414][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.416][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 05:24:33.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 05:24:33.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.431][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 05:24:33.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 05:24:33.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.437][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 05:24:33.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 05:24:33.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.442][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 05:24:33.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 05:24:33.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.448][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 05:24:33.449][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 05:24:33.451][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.452][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.453][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 05:24:33.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 05:24:33.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.469][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:24:33.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:24:33.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.475][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:24:33.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:24:33.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.480][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:24:33.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:24:33.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.486][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:24:33.487][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:24:33.489][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.490][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.491][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:24:33.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:24:33.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.507][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:24:33.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:24:33.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.512][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:24:33.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:24:33.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.517][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:24:33.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:24:33.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.523][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:24:33.524][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:24:33.526][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.527][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.528][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:24:33.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:24:33.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.544][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-04 05:24:33.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-04 05:24:33.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.549][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-04 05:24:33.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-04 05:24:33.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.555][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-04 05:24:33.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-04 05:24:33.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.560][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-04 05:24:33.562][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-04 05:24:33.563][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.564][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.565][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-04 05:24:33.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-04 05:24:33.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.581][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-05-04 05:24:33.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-04 05:24:33.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.586][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-05-04 05:24:33.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-04 05:24:33.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.592][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-05-04 05:24:33.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-04 05:24:33.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.597][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-05-04 05:24:33.599][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-04 05:24:33.600][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.601][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.603][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-05-04 05:24:33.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-04 05:24:33.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.618][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:24:33.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:24:33.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.624][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:24:33.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:24:33.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.629][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:24:33.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:24:33.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.634][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:24:33.636][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:24:33.637][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.638][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.640][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:24:33.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:24:33.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.662][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-04 05:24:33.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-04 05:24:33.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.668][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-04 05:24:33.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-04 05:24:33.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.674][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-04 05:24:33.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-04 05:24:33.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.680][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-04 05:24:33.682][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-04 05:24:33.683][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.685][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.686][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-04 05:24:33.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-04 05:24:33.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.702][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 05:24:33.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 05:24:33.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.709][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 05:24:33.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 05:24:33.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.714][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 05:24:33.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 05:24:33.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.720][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 05:24:33.722][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 05:24:33.723][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.725][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.726][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 05:24:33.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 05:24:33.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.743][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 05:24:33.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 05:24:33.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.749][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 05:24:33.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 05:24:33.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.754][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 05:24:33.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 05:24:33.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.760][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 05:24:33.762][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 05:24:33.763][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.764][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.766][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 05:24:33.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 05:24:33.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.781][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:24:33.783][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:24:33.784][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.786][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.792][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-04 05:24:33.793][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-04 05:24:33.795][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.796][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.802][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 05:24:33.804][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 05:24:33.805][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.806][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.812][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 05:24:33.814][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 05:24:33.815][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.816][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.822][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 05:24:33.824][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 05:24:33.825][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.826][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.833][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:24:33.834][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:24:33.836][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.837][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.843][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:24:33.844][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:24:33.846][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.847][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.853][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:24:33.854][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:24:33.856][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.857][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.863][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-05-04 05:24:33.865][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-04 05:24:33.866][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.867][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.873][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 05:24:33.875][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 05:24:33.876][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.878][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:33.884][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-04 05:24:33.885][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-04 05:24:33.887][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:33.888][ef$get] fields variable is a list.
biodb.INFO [2024-05-04 05:24:33.898][biodb::testThat]
biodb.INFO [2024-05-04 05:24:33.899][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-05-04 05:24:33.900][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 05:24:33.902][biodb::testThat]
biodb.DEBUG[2024-05-04 05:24:33.921][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2024-05-04 05:24:33.929][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-04 05:24:33.934][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2024-05-04 05:24:33.935][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-04 05:24:33.937][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2024-05-04 05:24:33.939][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-04 05:24:33.981][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-04 05:24:33.983][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-04 05:24:33.985][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:24:33.987][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:24:33.988][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:24:33.994][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:24:33.995][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:24:33.997][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:24:33.998][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 05:24:34.002][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:24:34.003][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:24:34.005][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:34.006][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:34.008][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:24:34.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:24:34.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:34.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:34.038][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-04 05:24:34.039][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-04 05:24:34.041][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:34.042][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:34.044][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-04 05:24:34.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-04 05:24:34.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:34.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:34.049][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 05:24:34.051][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 05:24:34.052][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:34.053][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:34.055][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 05:24:34.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 05:24:34.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:34.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:34.061][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 05:24:34.062][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 05:24:34.064][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:34.065][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:34.067][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 05:24:34.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 05:24:34.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:34.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:34.073][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 05:24:34.074][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 05:24:34.076][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:34.077][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:34.079][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 05:24:34.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 05:24:34.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:34.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:34.085][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:24:34.086][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:24:34.088][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:34.089][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:34.091][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:24:34.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:24:34.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:34.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:34.096][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-04 05:24:34.098][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:24:34.099][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:34.101][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:34.102][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-04 05:24:34.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:24:34.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:34.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:34.108][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:24:34.110][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:24:34.111][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:34.112][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:34.114][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:24:34.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:24:34.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:34.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:34.120][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 05:24:34.121][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 05:24:34.123][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:34.124][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:34.126][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 05:24:34.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 05:24:34.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:34.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:34.132][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-04 05:24:34.133][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-04 05:24:34.134][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:34.136][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:34.138][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-04 05:24:34.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-04 05:24:34.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:34.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:34.143][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-04 05:24:34.145][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-04 05:24:34.146][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:34.147][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:34.149][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-04 05:24:34.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-04 05:24:34.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:34.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:34.155][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:24:34.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:24:34.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:34.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:34.161][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:24:34.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:24:34.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:34.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:34.166][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:24:34.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:24:34.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:34.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:34.172][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:24:34.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:24:34.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:34.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:34.177][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:24:34.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:24:34.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:34.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:34.183][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:24:34.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:24:34.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:34.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:34.188][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:24:34.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:24:34.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:34.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:34.194][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:24:34.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:24:34.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:34.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:34.200][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:24:34.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:24:34.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:34.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:34.205][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:24:34.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:24:34.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:34.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:24:34.211][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2024-05-04 05:24:34.212][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-05-04 05:24:34.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-05-04 05:24:34.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:34.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:34.218][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-05-04 05:24:34.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-05-04 05:24:34.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:34.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:34.224][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-05-04 05:24:34.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-05-04 05:24:34.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:34.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-04 05:24:34.238][biodb::testThat]
biodb.INFO [2024-05-04 05:24:34.240][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2024-05-04 05:24:34.241][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 05:24:34.242][biodb::testThat]
biodb.TRACE[2024-05-04 05:24:34.246][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 05:24:34.248][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 05:24:34.249][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:34.251][ef$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:24:34.252][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2024-05-04 05:24:34.296][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 05:24:34.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 05:24:34.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:34.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:34.302][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 05:24:34.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 05:24:34.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:34.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:34.308][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 05:24:34.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 05:24:34.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:34.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:24:34.317][function(conn, opt)] With value "squalene".
biodb.DEBUG[2024-05-04 05:24:34.323][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-05-04 05:24:34.352][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-04 05:24:34.376][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-05-04 05:24:34.378][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-04 05:24:34.380][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-05-04 05:24:34.413][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[2024-05-04 05:24:34.419][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-04 05:24:34.421][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-05-04 05:24:34.423][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-04 05:24:34.425][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-05-04 05:24:34.428][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2024-05-04 05:24:34.444][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:24:34.446][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:24:34.447][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:34.449][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:34.450][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:24:34.452][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:24:34.453][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:34.454][ef$get] fields variable is a list.
biodb.INFO [2024-05-04 05:24:34.460][biodb::testThat]
biodb.INFO [2024-05-04 05:24:34.461][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2024-05-04 05:24:34.463][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 05:24:34.464][biodb::testThat]
biodb.TRACE[2024-05-04 05:24:34.499][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 05:24:34.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 05:24:34.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:34.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:34.505][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 05:24:34.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 05:24:34.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:34.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:34.511][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 05:24:34.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 05:24:34.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:34.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:24:34.607][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[2024-05-04 05:24:34.612][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-04 05:24:34.614][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-05-04 05:24:34.616][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-04 05:24:34.619][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2024-05-04 05:24:34.640][biodb::testThat]
biodb.INFO [2024-05-04 05:24:34.641][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2024-05-04 05:24:34.643][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 05:24:34.644][biodb::testThat]
biodb.TRACE[2024-05-04 05:24:34.671][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 05:24:34.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 05:24:34.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:34.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:34.676][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 05:24:34.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 05:24:34.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:34.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:34.682][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 05:24:34.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 05:24:34.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:34.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:34.687][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 05:24:34.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 05:24:34.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:34.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:34.693][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:24:34.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:24:34.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:34.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:34.698][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:24:34.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:24:34.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:34.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:34.703][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-04 05:24:34.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-04 05:24:34.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:34.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:34.709][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-04 05:24:34.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-04 05:24:34.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:34.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:34.714][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-04 05:24:34.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-04 05:24:34.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:34.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:34.719][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-04 05:24:34.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-04 05:24:34.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:34.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:34.749][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 05:24:34.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 05:24:34.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:34.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:34.755][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 05:24:34.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 05:24:34.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:34.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:34.760][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 05:24:34.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 05:24:34.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:34.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:34.765][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 05:24:34.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 05:24:34.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:34.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:34.770][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:24:34.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:24:34.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:34.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:34.776][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:24:34.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:24:34.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:34.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:34.781][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-04 05:24:34.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-04 05:24:34.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:34.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:34.786][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-04 05:24:34.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-04 05:24:34.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:34.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:34.791][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-04 05:24:34.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-04 05:24:34.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:34.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:24:34.797][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-04 05:24:34.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-04 05:24:34.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:24:34.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-04 05:24:34.809][biodb::testThat]
biodb.INFO [2024-05-04 05:24:34.810][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-05-04 05:24:34.811][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 05:24:34.813][biodb::testThat]
biodb.INFO [2024-05-04 05:24:34.823][biodb::testThat]
biodb.INFO [2024-05-04 05:24:34.824][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-05-04 05:24:34.826][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 05:24:34.827][biodb::testThat]
biodb.INFO [2024-05-04 05:24:34.838][biodb::testThat]
biodb.INFO [2024-05-04 05:24:34.839][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2024-05-04 05:24:34.841][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 05:24:34.842][biodb::testThat]
biodb.DEBUG[2024-05-04 05:24:34.855][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2024-05-04 05:24:46.067][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2024-05-04 05:25:05.497][biodb::testThat]
biodb.INFO [2024-05-04 05:25:05.498][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2024-05-04 05:25:05.500][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 05:25:05.501][biodb::testThat]
biodb.DEBUG[2024-05-04 05:25:06.622][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[2024-05-04 05:25:08.914][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 05:25:08.915][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 05:25:08.917][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:25:08.918][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:25:08.919][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:25:08.921][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:25:08.922][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:25:08.923][ef$get] fields variable is a list.
biodb.INFO [2024-05-04 05:25:08.926][biodb::testThat]
biodb.INFO [2024-05-04 05:25:08.927][biodb::testThat] Running test function test.searchCompound (" We can search for a compound ").
biodb.INFO [2024-05-04 05:25:08.928][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 05:25:08.929][biodb::testThat]
biodb.TRACE[2024-05-04 05:25:08.943][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 05:25:08.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 05:25:08.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:25:08.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:25:08.949][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 05:25:08.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 05:25:08.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:25:08.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:25:08.954][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 05:25:08.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 05:25:08.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:25:08.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:25:09.082][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[2024-05-04 05:25:09.087][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-04 05:25:09.088][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-05-04 05:25:09.090][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-04 05:25:09.092][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-05-04 05:25:09.193][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[2024-05-04 05:25:09.198][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-04 05:25:09.200][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-05-04 05:25:09.202][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-04 05:25:09.204][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2024-05-04 05:25:09.224][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-04 05:25:09.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-04 05:25:09.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:25:09.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:25:09.236][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:25:09.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:25:09.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:25:09.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:25:09.242][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:25:09.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:25:09.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:25:09.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:25:09.248][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:25:09.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:25:09.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:25:09.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:25:09.254][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:25:09.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:25:09.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:25:09.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:25:09.260][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:25:09.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:25:09.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:25:09.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:25:09.276][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[2024-05-04 05:25:09.280][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-04 05:25:09.282][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-05-04 05:25:09.284][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-04 05:25:09.287][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-05-04 05:25:09.291][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:25:09.292][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:25:09.293][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:25:09.314][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:25:09.316][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:25:09.317][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:25:09.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:25:09.320][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2024-05-04 05:25:09.391][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-04 05:25:09.394][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2024-05-04 05:25:09.397][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-04 05:25:09.399][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-04 05:25:09.401][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-04 05:25:09.402][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-04 05:25:09.404][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-04 05:25:09.405][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-04 05:25:09.409][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:25:09.410][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:25:09.411][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:25:09.418][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:25:09.420][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:25:09.421][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:25:09.422][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:25:09.424][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2024-05-04 05:25:09.428][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 05:25:09.429][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 05:25:09.431][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2024-05-04 05:25:21.371][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2024-05-04 05:25:35.429][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-04 05:25:35.432][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2024-05-04 05:25:35.453][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2024-05-04 05:25:35.457][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2024-05-04 05:25:35.459][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-04 05:25:35.461][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-04 05:25:35.462][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-04 05:25:35.465][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:25:35.466][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:25:35.467][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:25:35.474][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:25:35.475][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:25:35.477][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:25:35.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 05:25:35.481][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:25:35.483][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:25:35.484][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:25:35.486][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:25:35.488][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:25:35.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:25:35.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:25:35.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:25:35.493][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-04 05:25:35.495][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-04 05:25:35.496][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:25:35.498][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:25:35.500][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 05:25:35.501][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 05:25:35.503][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:25:35.504][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:25:35.506][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 05:25:35.508][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 05:25:35.509][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:25:35.510][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:25:35.512][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 05:25:35.514][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 05:25:35.515][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:25:35.516][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:25:35.518][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:25:35.520][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:25:35.521][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:25:35.522][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:25:35.524][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-04 05:25:35.526][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:25:35.527][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:25:35.528][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:25:35.530][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:25:35.532][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:25:35.533][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:25:35.535][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:25:35.536][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 05:25:35.538][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 05:25:35.540][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:25:35.541][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:25:35.557][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-04 05:25:35.559][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-04 05:25:35.561][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:25:35.562][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:25:35.564][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-04 05:25:35.566][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-04 05:25:35.567][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:25:35.569][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:25:35.571][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:25:35.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:25:35.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:25:35.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:25:35.577][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:25:35.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:25:35.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:25:35.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:25:35.584][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:25:35.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:25:35.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:25:35.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:25:35.590][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:25:35.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:25:35.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:25:35.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:25:35.596][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:25:35.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:25:35.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:25:35.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:25:35.602][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:25:35.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:25:35.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:25:35.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:25:35.609][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:25:35.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:25:35.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:25:35.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:25:35.615][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:25:35.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:25:35.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:25:35.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:25:35.622][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:25:35.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:25:35.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:25:35.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:25:35.628][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:25:35.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:25:35.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:25:35.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:25:35.634][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-05-04 05:25:35.636][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-05-04 05:25:35.652][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-04 05:25:35.658][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-04 05:25:35.660][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-05-04 05:25:35.662][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-04 05:25:35.665][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-05-04 05:25:35.689][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:25:35.691][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:25:35.692][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:25:35.700][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:25:35.701][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:25:35.703][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:25:35.704][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 05:25:35.706][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:25:35.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:25:35.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:25:35.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:25:35.713][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:25:35.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:25:35.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:25:35.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:25:35.719][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:25:35.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:25:35.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:25:35.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:25:35.725][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:25:35.726][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:25:35.727][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:25:35.734][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:25:35.735][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:25:35.736][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:25:35.738][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:25:35.739][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2024-05-04 05:25:35.741][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-04 05:25:35.743][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2024-05-04 05:25:35.745][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-04 05:25:35.746][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-04 05:25:35.748][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-04 05:25:35.749][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-04 05:25:35.750][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-04 05:25:35.752][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-04 05:25:35.772][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:25:35.774][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:25:35.775][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:25:35.781][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:25:35.783][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:25:35.784][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:25:35.785][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:25:35.787][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2024-05-04 05:25:35.820][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 05:25:35.822][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 05:25:35.845][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2024-05-04 05:25:47.932][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2024-05-04 05:25:59.491][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-04 05:25:59.494][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2024-05-04 05:25:59.498][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2024-05-04 05:25:59.502][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2024-05-04 05:25:59.503][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-04 05:25:59.505][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-04 05:25:59.507][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-04 05:25:59.509][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:25:59.510][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:25:59.511][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:25:59.517][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:25:59.518][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:25:59.520][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:25:59.521][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[2024-05-04 05:25:59.524][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:25:59.525][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:25:59.526][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:25:59.528][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:25:59.529][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:25:59.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:25:59.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:25:59.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:25:59.535][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-04 05:25:59.536][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-04 05:25:59.537][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:25:59.539][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:25:59.540][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 05:25:59.542][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 05:25:59.543][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:25:59.544][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:25:59.546][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 05:25:59.548][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 05:25:59.549][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:25:59.550][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:25:59.552][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 05:25:59.553][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 05:25:59.555][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:25:59.556][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:25:59.557][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:25:59.559][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:25:59.560][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:25:59.562][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:25:59.563][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-04 05:25:59.565][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:25:59.566][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:25:59.567][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:25:59.569][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:25:59.570][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:25:59.572][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:25:59.573][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:25:59.575][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 05:25:59.576][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 05:25:59.577][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:25:59.579][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:25:59.581][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-04 05:25:59.582][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-04 05:25:59.583][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:25:59.585][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:25:59.586][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-04 05:25:59.588][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-04 05:25:59.589][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:25:59.590][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:25:59.592][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:25:59.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:25:59.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:25:59.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:25:59.598][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:25:59.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:25:59.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:25:59.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:25:59.603][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:25:59.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:25:59.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:25:59.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:25:59.608][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:25:59.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:25:59.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:25:59.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:25:59.614][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:25:59.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:25:59.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:25:59.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:25:59.619][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:25:59.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:25:59.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:25:59.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:25:59.625][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:25:59.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:25:59.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:25:59.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:25:59.630][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:25:59.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:25:59.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:25:59.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:25:59.635][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:25:59.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:25:59.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:25:59.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:25:59.641][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:25:59.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:25:59.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:25:59.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:25:59.646][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-05-04 05:25:59.647][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-05-04 05:25:59.650][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:25:59.651][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:25:59.652][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:25:59.658][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:25:59.659][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:25:59.661][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:25:59.662][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[2024-05-04 05:25:59.663][private$loadEntries] Creating entries from ids [1]: "227078".
biodb.DEBUG[2024-05-04 05:25:59.665][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-04 05:25:59.667][cch$loadFileContent] Trying to load 1 files from cache: [1]: "227078".
biodb.TRACE[2024-05-04 05:25:59.668][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-04 05:25:59.670][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-04 05:25:59.671][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-04 05:25:59.673][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-04 05:25:59.674][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-04 05:25:59.675][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-04 05:25:59.679][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:25:59.680][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:25:59.681][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:25:59.700][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:25:59.701][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:25:59.702][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:25:59.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:25:59.705][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=227078".
biodb.DEBUG[2024-05-04 05:25:59.709][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 05:25:59.710][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 05:25:59.711][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=227078".
biodb.TRACE[2024-05-04 05:26:11.623][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=227078).
biodb.DEBUG[2024-05-04 05:26:26.472][scheduler$sendRequest] Saving content of request to cache.
biodb.INFO [2024-05-04 05:26:26.475][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2024-05-04 05:26:26.477][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ccc0d17769ea5be638da2084b1bd4710.content"
biodb.TRACE[2024-05-04 05:26:26.481][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ccc0d17769ea5be638da2084b1bd4710.request"
biodb.TRACE[2024-05-04 05:26:26.485][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/227078.xml"
biodb.DEBUG[2024-05-04 05:26:26.487][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-04 05:26:26.488][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-04 05:26:26.490][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-04 05:26:26.492][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:26:26.493][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:26:26.495][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:26:26.501][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:26:26.502][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:26:26.504][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:26:26.505][FUN] Functions in observer BiodbConfig: [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[2024-05-04 05:26:26.508][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:26:26.510][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:26:26.511][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:26:26.512][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:26:26.514][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:26:26.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:26:26.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:26:26.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:26:26.520][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-04 05:26:26.522][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-04 05:26:26.523][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:26:26.525][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:26:26.526][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 05:26:26.528][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 05:26:26.529][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:26:26.531][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:26:26.533][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 05:26:26.534][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 05:26:26.536][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:26:26.537][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:26:26.539][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 05:26:26.540][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 05:26:26.542][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:26:26.543][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:26:26.545][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:26:26.547][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:26:26.548][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:26:26.550][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:26:26.551][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-04 05:26:26.553][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:26:26.554][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:26:26.556][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:26:26.557][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:26:26.559][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:26:26.560][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:26:26.562][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:26:26.564][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 05:26:26.565][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 05:26:26.566][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:26:26.568][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:26:26.570][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-04 05:26:26.571][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-04 05:26:26.573][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:26:26.574][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:26:26.576][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-04 05:26:26.577][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-04 05:26:26.579][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:26:26.580][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:26:26.582][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:26:26.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:26:26.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:26:26.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:26:26.588][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:26:26.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:26:26.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:26:26.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:26:26.593][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:26:26.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:26:26.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:26:26.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:26:26.599][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:26:26.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:26:26.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:26:26.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:26:26.605][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:26:26.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:26:26.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:26:26.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:26:26.611][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:26:26.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:26:26.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:26:26.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:26:26.616][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:26:26.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:26:26.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:26:26.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:26:26.622][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:26:26.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:26:26.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:26:26.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:26:26.628][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:26:26.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:26:26.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:26:26.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:26:26.633][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:26:26.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:26:26.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:26:26.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:26:26.639][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-05-04 05:26:26.640][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-05-04 05:26:26.643][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-04 05:26:26.647][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 05:26:26.649][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 05:26:26.651][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-05-04 05:26:28.482][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-05-04 05:26:31.570][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-04 05:26:31.573][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.content"
biodb.TRACE[2024-05-04 05:26:31.578][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.request"
biodb.DEBUG[2024-05-04 05:26:31.604][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-04 05:26:31.608][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 05:26:31.610][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 05:26:31.612][private$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[2024-05-04 05:26:34.700][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[2024-05-04 05:26:35.928][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-04 05:26:35.931][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2024-05-04 05:26:35.936][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2024-05-04 05:26:35.941][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:26:35.944][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:26:35.945][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:26:35.956][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:26:35.957][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:26:35.959][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:26:35.960][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[2024-05-04 05:26:35.962][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:26:35.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:26:35.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:26:35.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:26:35.968][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:26:35.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:26:35.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:26:35.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:26:35.973][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:26:35.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:26:35.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:26:35.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:26:35.979][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:26:35.980][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:26:35.981][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:26:35.988][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:26:35.989][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:26:35.990][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:26:35.991][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[2024-05-04 05:26:35.993][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2024-05-04 05:26:35.994][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-04 05:26:35.996][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2024-05-04 05:26:35.998][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-04 05:26:36.000][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-04 05:26:36.001][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-04 05:26:36.003][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-04 05:26:36.004][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-04 05:26:36.005][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-04 05:26:36.010][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:26:36.011][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:26:36.012][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:26:36.019][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:26:36.020][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:26:36.021][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:26:36.023][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[2024-05-04 05:26:36.024][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2024-05-04 05:26:36.028][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 05:26:36.029][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 05:26:36.031][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2024-05-04 05:26:47.861][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2024-05-04 05:26:58.970][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-04 05:26:58.972][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2024-05-04 05:26:58.977][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2024-05-04 05:26:58.980][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2024-05-04 05:26:58.982][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-04 05:26:58.983][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-04 05:26:58.985][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-04 05:26:58.987][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:26:58.988][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:26:58.989][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:26:58.995][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:26:58.997][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:26:58.998][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:26:58.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 05:26:59.002][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:26:59.003][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:26:59.005][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:26:59.006][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:26:59.007][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:26:59.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:26:59.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:26:59.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:26:59.013][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-04 05:26:59.014][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-04 05:26:59.015][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:26:59.017][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:26:59.018][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 05:26:59.020][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 05:26:59.021][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:26:59.022][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:26:59.024][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 05:26:59.026][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 05:26:59.027][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:26:59.028][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:26:59.030][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 05:26:59.031][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 05:26:59.032][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:26:59.034][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:26:59.035][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:26:59.036][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:26:59.038][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:26:59.039][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:26:59.041][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-04 05:26:59.042][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:26:59.043][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:26:59.044][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:26:59.046][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:26:59.047][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:26:59.049][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:26:59.050][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:26:59.051][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 05:26:59.053][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 05:26:59.054][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:26:59.055][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:26:59.057][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-04 05:26:59.059][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-04 05:26:59.060][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:26:59.061][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:26:59.063][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-04 05:26:59.064][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-04 05:26:59.065][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:26:59.066][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:26:59.068][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:26:59.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:26:59.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:26:59.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:26:59.073][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:26:59.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:26:59.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:26:59.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:26:59.079][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:26:59.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:26:59.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:26:59.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:26:59.084][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:26:59.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:26:59.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:26:59.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:26:59.089][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:26:59.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:26:59.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:26:59.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:26:59.094][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:26:59.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:26:59.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:26:59.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:26:59.100][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:26:59.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:26:59.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:26:59.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:26:59.119][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:26:59.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:26:59.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:26:59.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:26:59.125][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:26:59.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:26:59.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:26:59.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:26:59.130][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:26:59.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:26:59.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:26:59.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:26:59.135][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-05-04 05:26:59.136][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-05-04 05:26:59.138][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:26:59.139][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:26:59.140][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:26:59.146][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:26:59.148][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:26:59.149][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:26:59.150][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:26:59.152][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2024-05-04 05:26:59.153][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-04 05:26:59.155][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2024-05-04 05:26:59.157][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-04 05:26:59.158][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-04 05:26:59.160][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-04 05:26:59.161][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-04 05:26:59.162][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-04 05:26:59.164][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-04 05:26:59.167][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:26:59.168][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:26:59.170][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:26:59.176][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:26:59.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:26:59.179][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:26:59.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:26:59.182][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2024-05-04 05:26:59.185][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 05:26:59.187][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 05:26:59.189][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2024-05-04 05:27:11.101][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2024-05-04 05:27:22.179][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-04 05:27:22.182][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2024-05-04 05:27:22.186][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2024-05-04 05:27:22.189][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2024-05-04 05:27:22.191][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-04 05:27:22.193][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-04 05:27:22.194][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-04 05:27:22.196][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:27:22.198][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:27:22.199][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:27:22.205][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:27:22.206][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:27:22.208][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:27:22.209][FUN] Functions in observer BiodbConfig: [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[2024-05-04 05:27:22.212][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:27:22.213][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:27:22.214][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:27:22.216][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:27:22.217][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:27:22.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:27:22.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:27:22.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:27:22.223][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-04 05:27:22.224][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-04 05:27:22.225][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:27:22.227][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:27:22.228][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 05:27:22.230][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 05:27:22.231][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:27:22.232][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:27:22.234][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 05:27:22.235][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 05:27:22.237][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:27:22.238][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:27:22.240][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 05:27:22.241][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 05:27:22.242][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:27:22.243][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:27:22.245][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:27:22.246][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:27:22.248][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:27:22.249][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:27:22.250][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-04 05:27:22.252][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:27:22.253][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:27:22.254][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:27:22.256][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:27:22.257][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:27:22.259][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:27:22.260][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:27:22.261][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 05:27:22.263][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 05:27:22.264][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:27:22.265][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:27:22.267][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-04 05:27:22.268][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-04 05:27:22.270][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:27:22.271][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:27:22.273][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-04 05:27:22.274][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-04 05:27:22.275][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:27:22.276][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:27:22.278][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:27:22.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:27:22.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:27:22.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:27:22.283][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:27:22.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:27:22.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:27:22.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:27:22.289][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:27:22.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:27:22.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:27:22.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:27:22.294][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:27:22.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:27:22.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:27:22.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:27:22.299][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:27:22.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:27:22.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:27:22.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:27:22.304][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:27:22.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:27:22.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:27:22.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:27:22.310][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:27:22.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:27:22.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:27:22.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:27:22.315][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:27:22.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:27:22.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:27:22.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:27:22.320][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:27:22.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:27:22.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:27:22.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:27:22.326][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:27:22.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:27:22.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:27:22.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:27:22.331][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-05-04 05:27:22.344][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-05-04 05:27:22.345][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:27:22.346][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:27:22.347][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:27:22.353][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:27:22.355][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:27:22.356][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:27:22.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:27:22.359][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2024-05-04 05:27:22.360][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-04 05:27:22.362][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2024-05-04 05:27:22.364][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-04 05:27:22.365][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-04 05:27:22.367][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-04 05:27:22.368][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-04 05:27:22.369][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-04 05:27:22.371][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-04 05:27:22.374][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:27:22.375][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:27:22.376][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:27:22.383][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:27:22.384][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:27:22.385][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:27:22.386][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:27:22.388][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2024-05-04 05:27:22.391][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 05:27:22.393][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 05:27:22.395][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2024-05-04 05:27:38.643][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2024-05-04 05:27:52.393][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-04 05:27:52.396][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2024-05-04 05:27:52.401][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2024-05-04 05:27:52.405][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2024-05-04 05:27:52.407][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-04 05:27:52.409][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-04 05:27:52.410][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-04 05:27:52.413][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:27:52.414][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:27:52.415][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:27:52.422][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:27:52.424][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:27:52.425][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:27:52.426][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 05:27:52.430][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:27:52.431][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:27:52.433][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:27:52.434][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:27:52.436][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:27:52.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:27:52.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:27:52.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:27:52.442][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-04 05:27:52.444][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-04 05:27:52.445][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:27:52.447][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:27:52.448][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 05:27:52.450][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 05:27:52.451][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:27:52.453][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:27:52.455][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 05:27:52.457][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 05:27:52.458][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:27:52.459][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:27:52.461][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 05:27:52.463][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 05:27:52.464][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:27:52.466][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:27:52.467][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:27:52.469][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:27:52.470][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:27:52.472][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:27:52.474][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-04 05:27:52.475][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:27:52.477][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:27:52.478][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:27:52.480][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:27:52.482][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:27:52.483][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:27:52.484][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:27:52.486][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 05:27:52.488][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 05:27:52.489][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:27:52.491][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:27:52.493][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-04 05:27:52.494][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-04 05:27:52.496][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:27:52.497][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:27:52.499][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-04 05:27:52.500][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-04 05:27:52.502][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:27:52.503][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:27:52.505][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:27:52.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:27:52.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:27:52.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:27:52.511][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:27:52.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:27:52.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:27:52.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:27:52.516][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:27:52.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:27:52.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:27:52.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:27:52.522][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:27:52.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:27:52.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:27:52.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:27:52.528][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:27:52.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:27:52.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:27:52.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:27:52.533][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:27:52.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:27:52.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:27:52.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:27:52.539][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:27:52.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:27:52.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:27:52.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:27:52.545][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:27:52.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:27:52.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:27:52.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:27:52.551][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:27:52.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:27:52.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:27:52.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:27:52.557][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:27:52.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:27:52.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:27:52.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:27:52.563][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-05-04 05:27:52.564][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-05-04 05:27:52.566][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:27:52.567][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:27:52.569][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:27:52.575][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:27:52.577][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:27:52.578][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:27:52.580][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:27:52.581][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2024-05-04 05:27:52.583][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-04 05:27:52.585][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2024-05-04 05:27:52.595][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-04 05:27:52.601][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-04 05:27:52.603][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-04 05:27:52.604][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-04 05:27:52.606][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-04 05:27:52.607][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-04 05:27:52.611][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:27:52.613][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:27:52.614][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:27:52.621][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:27:52.622][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:27:52.623][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:27:52.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:27:52.626][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2024-05-04 05:27:52.633][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 05:27:52.636][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 05:27:52.639][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2024-05-04 05:28:11.440][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2024-05-04 05:28:26.404][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-04 05:28:26.408][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2024-05-04 05:28:26.413][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2024-05-04 05:28:26.417][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2024-05-04 05:28:26.419][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-04 05:28:26.421][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-04 05:28:26.423][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-04 05:28:26.425][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:28:26.427][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:28:26.428][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:28:26.436][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:28:26.437][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:28:26.439][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:28:26.440][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.TRACE[2024-05-04 05:28:26.443][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:28:26.445][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:28:26.446][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:26.448][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:26.450][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:28:26.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:28:26.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:26.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:26.455][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-04 05:28:26.457][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-04 05:28:26.458][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:26.460][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:26.461][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 05:28:26.463][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 05:28:26.464][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:26.466][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:26.468][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 05:28:26.469][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 05:28:26.471][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:26.472][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:26.474][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 05:28:26.476][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 05:28:26.477][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:26.479][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:26.481][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:28:26.482][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:28:26.484][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:26.485][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:26.487][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-04 05:28:26.488][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:28:26.490][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:26.491][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:26.493][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:28:26.495][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:28:26.496][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:26.497][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:26.499][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 05:28:26.501][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 05:28:26.502][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:26.504][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:26.506][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-04 05:28:26.507][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-04 05:28:26.509][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:26.510][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:26.512][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-04 05:28:26.514][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-04 05:28:26.515][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:26.517][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:26.518][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:28:26.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:28:26.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:26.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:26.524][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:28:26.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:28:26.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:26.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:26.530][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:28:26.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:28:26.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:26.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:26.536][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:28:26.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:28:26.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:26.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:26.542][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:28:26.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:28:26.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:26.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:26.548][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:28:26.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:28:26.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:26.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:26.554][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:28:26.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:28:26.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:26.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:26.560][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:28:26.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:28:26.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:26.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:26.566][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:28:26.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:28:26.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:26.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:26.572][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:28:26.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:28:26.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:26.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:28:26.578][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-05-04 05:28:26.580][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-05-04 05:28:26.581][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:28:26.582][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:28:26.584][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:28:26.591][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:28:26.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:28:26.593][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:28:26.595][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[2024-05-04 05:28:26.596][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2024-05-04 05:28:26.598][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-04 05:28:26.601][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2024-05-04 05:28:26.602][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-04 05:28:26.604][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-04 05:28:26.606][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-04 05:28:26.607][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-04 05:28:26.609][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-04 05:28:26.610][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-04 05:28:26.614][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:28:26.616][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:28:26.617][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:28:26.624][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:28:26.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:28:26.645][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:28:26.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:28:26.648][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2024-05-04 05:28:26.652][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 05:28:26.654][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 05:28:26.656][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2024-05-04 05:28:45.840][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2024-05-04 05:28:46.980][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-04 05:28:46.983][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2024-05-04 05:28:46.988][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2024-05-04 05:28:46.991][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2024-05-04 05:28:46.993][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-04 05:28:46.994][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-04 05:28:46.996][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-04 05:28:46.998][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:28:46.999][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:28:47.000][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:28:47.007][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:28:47.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:28:47.009][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:28:47.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 05:28:47.013][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:28:47.015][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:28:47.016][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:47.017][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:47.019][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:28:47.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:28:47.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:47.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:47.024][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-04 05:28:47.026][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-04 05:28:47.027][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:47.028][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:47.030][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-04 05:28:47.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-04 05:28:47.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:47.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:47.035][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 05:28:47.037][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 05:28:47.039][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:47.040][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:47.043][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 05:28:47.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 05:28:47.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:47.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:47.048][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 05:28:47.050][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 05:28:47.051][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:47.052][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:47.054][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 05:28:47.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 05:28:47.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:47.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:47.059][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 05:28:47.060][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 05:28:47.062][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:47.063][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:47.064][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 05:28:47.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 05:28:47.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:47.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:47.070][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:28:47.071][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:28:47.072][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:47.074][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:47.075][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:28:47.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:28:47.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:47.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:47.080][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-04 05:28:47.082][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:28:47.083][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:47.084][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:47.086][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-04 05:28:47.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:28:47.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:47.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:47.091][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:28:47.093][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:28:47.094][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:47.095][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:47.097][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:28:47.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:28:47.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:47.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:47.102][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 05:28:47.103][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 05:28:47.105][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:47.106][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:47.108][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 05:28:47.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 05:28:47.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:47.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:47.113][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-04 05:28:47.114][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-04 05:28:47.116][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:47.117][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:47.118][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-04 05:28:47.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-04 05:28:47.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:47.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:47.124][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-04 05:28:47.125][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-04 05:28:47.127][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:47.128][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:47.129][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-04 05:28:47.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-04 05:28:47.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:47.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:47.135][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:28:47.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:28:47.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:47.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:47.140][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:28:47.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:28:47.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:47.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:47.145][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:28:47.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:28:47.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:47.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:47.150][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:28:47.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:28:47.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:47.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:47.155][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:28:47.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:28:47.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:47.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:47.160][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:28:47.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:28:47.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:47.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:47.165][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:28:47.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:28:47.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:47.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:47.171][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:28:47.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:28:47.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:47.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:47.176][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:28:47.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:28:47.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:47.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:47.181][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:28:47.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:28:47.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:47.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:28:47.186][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2024-05-04 05:28:47.188][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:28:47.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:28:47.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:47.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:47.205][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:28:47.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:28:47.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:47.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:47.210][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:28:47.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:28:47.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:47.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:28:47.216][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:28:47.217][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:28:47.218][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:28:47.224][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:28:47.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:28:47.227][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:28:47.228][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:28:47.229][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2024-05-04 05:28:47.230][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-04 05:28:47.233][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2024-05-04 05:28:47.234][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-04 05:28:47.236][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-04 05:28:47.237][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-04 05:28:47.238][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-04 05:28:47.241][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-04 05:28:47.242][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-04 05:28:47.245][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:28:47.247][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:28:47.248][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:28:47.254][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:28:47.255][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:28:47.257][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:28:47.258][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:28:47.259][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2024-05-04 05:28:47.263][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 05:28:47.264][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 05:28:47.266][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2024-05-04 05:28:48.347][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2024-05-04 05:28:49.443][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-04 05:28:49.446][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2024-05-04 05:28:49.450][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2024-05-04 05:28:49.453][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2024-05-04 05:28:49.455][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-04 05:28:49.457][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-04 05:28:49.458][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-04 05:28:49.461][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:28:49.462][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:28:49.463][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:28:49.469][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:28:49.471][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:28:49.472][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:28:49.474][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 05:28:49.477][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:28:49.478][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:28:49.479][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:49.481][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:49.482][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:28:49.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:28:49.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:49.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:49.488][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-04 05:28:49.489][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-04 05:28:49.491][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:49.492][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:49.494][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-04 05:28:49.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-04 05:28:49.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:49.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:49.500][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 05:28:49.501][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 05:28:49.503][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:49.504][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:49.506][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 05:28:49.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 05:28:49.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:49.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:49.511][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 05:28:49.513][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 05:28:49.514][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:49.515][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:49.517][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 05:28:49.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 05:28:49.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:49.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:49.522][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 05:28:49.524][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 05:28:49.525][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:49.526][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:49.528][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 05:28:49.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 05:28:49.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:49.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:49.534][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:28:49.535][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:28:49.536][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:49.538][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:49.539][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-04 05:28:49.541][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:28:49.542][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:49.543][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:49.545][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-04 05:28:49.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:28:49.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:49.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:49.550][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:28:49.552][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:28:49.553][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:49.554][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:49.556][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:28:49.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:28:49.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:49.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:49.562][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 05:28:49.563][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 05:28:49.564][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:49.566][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:49.567][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 05:28:49.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 05:28:49.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:49.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:49.573][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-04 05:28:49.574][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-04 05:28:49.576][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:49.577][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:49.579][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-04 05:28:49.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-04 05:28:49.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:49.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:49.584][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-04 05:28:49.586][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-04 05:28:49.587][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:49.588][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:49.590][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-04 05:28:49.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-04 05:28:49.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:49.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:49.595][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:28:49.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:28:49.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:49.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:49.601][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:28:49.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:28:49.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:49.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:49.606][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:28:49.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:28:49.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:49.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:49.620][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:28:49.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:28:49.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:49.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:49.630][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:28:49.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:28:49.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:49.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:49.636][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:28:49.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:28:49.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:49.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:49.642][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:28:49.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:28:49.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:49.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:49.648][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:28:49.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:28:49.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:49.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:49.654][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:28:49.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:28:49.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:49.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:49.660][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:28:49.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:28:49.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:49.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:28:49.665][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2024-05-04 05:28:49.667][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:28:49.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:28:49.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:49.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:49.673][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:28:49.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:28:49.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:49.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:28:49.678][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:28:49.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:28:49.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:28:49.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:28:49.684][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:28:49.685][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:28:49.687][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:28:49.693][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:28:49.695][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:28:49.696][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:28:49.697][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[2024-05-04 05:28:49.699][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2024-05-04 05:28:49.700][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-04 05:28:49.702][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2024-05-04 05:28:49.704][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-04 05:28:49.706][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-04 05:28:49.707][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-04 05:28:49.709][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-04 05:28:49.710][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-04 05:28:49.711][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-04 05:28:49.715][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:28:49.716][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:28:49.717][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:28:49.724][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:28:49.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:28:49.727][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:28:49.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:28:49.730][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2024-05-04 05:28:49.734][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 05:28:49.735][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 05:28:49.737][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2024-05-04 05:29:00.871][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2024-05-04 05:29:12.007][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-04 05:29:12.010][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2024-05-04 05:29:12.015][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2024-05-04 05:29:12.018][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2024-05-04 05:29:12.020][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-04 05:29:12.022][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-04 05:29:12.024][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-04 05:29:12.026][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:29:12.027][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:29:12.029][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:29:12.035][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:29:12.037][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:29:12.038][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:29:12.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 05:29:12.042][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:29:12.044][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:29:12.045][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:12.047][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:12.048][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:29:12.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:29:12.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:12.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:12.054][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-04 05:29:12.056][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-04 05:29:12.057][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:12.059][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:12.060][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 05:29:12.062][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 05:29:12.063][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:12.065][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:12.067][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 05:29:12.068][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 05:29:12.070][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:12.071][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:12.073][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 05:29:12.074][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 05:29:12.076][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:12.077][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:12.079][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:29:12.080][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:29:12.082][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:12.083][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:12.085][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-04 05:29:12.086][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:29:12.088][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:12.089][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:12.091][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:29:12.092][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:29:12.094][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:12.095][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:12.097][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 05:29:12.098][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 05:29:12.099][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:12.101][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:12.103][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-04 05:29:12.104][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-04 05:29:12.106][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:12.107][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:12.109][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-04 05:29:12.110][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-04 05:29:12.112][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:12.113][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:12.115][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:29:12.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:29:12.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:12.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:12.120][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:29:12.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:29:12.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:12.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:12.126][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:29:12.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:29:12.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:12.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:12.132][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:29:12.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:29:12.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:12.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:12.150][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:29:12.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:29:12.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:12.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:12.156][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:29:12.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:29:12.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:12.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:12.161][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:29:12.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:29:12.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:12.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:12.167][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:29:12.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:29:12.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:12.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:12.173][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:29:12.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:29:12.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:12.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:12.180][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:29:12.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:29:12.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:12.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:29:12.186][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-05-04 05:29:12.187][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-05-04 05:29:12.188][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:29:12.190][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:29:12.191][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:29:12.197][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:29:12.198][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:29:12.200][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:29:12.201][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:29:12.203][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2024-05-04 05:29:12.204][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-04 05:29:12.206][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2024-05-04 05:29:12.208][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-04 05:29:12.209][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-04 05:29:12.211][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-04 05:29:12.212][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-04 05:29:12.214][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-04 05:29:12.215][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-04 05:29:12.219][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:29:12.220][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:29:12.222][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:29:12.228][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:29:12.229][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:29:12.231][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:29:12.232][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:29:12.234][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2024-05-04 05:29:12.237][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 05:29:12.239][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 05:29:12.241][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2024-05-04 05:29:26.195][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2024-05-04 05:29:33.356][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-04 05:29:33.359][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2024-05-04 05:29:33.364][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2024-05-04 05:29:33.367][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2024-05-04 05:29:33.369][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-04 05:29:33.371][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-04 05:29:33.373][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-04 05:29:33.375][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:29:33.376][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:29:33.377][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:29:33.384][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:29:33.385][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:29:33.386][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:29:33.388][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[2024-05-04 05:29:33.391][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:29:33.392][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:29:33.394][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:33.395][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:33.397][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:29:33.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:29:33.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:33.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:33.403][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-04 05:29:33.404][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-04 05:29:33.405][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:33.407][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:33.409][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-04 05:29:33.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-04 05:29:33.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:33.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:33.414][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 05:29:33.416][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 05:29:33.417][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:33.419][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:33.420][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 05:29:33.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 05:29:33.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:33.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:33.426][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 05:29:33.428][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 05:29:33.429][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:33.430][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:33.432][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 05:29:33.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 05:29:33.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:33.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:33.438][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 05:29:33.440][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 05:29:33.441][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:33.442][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:33.444][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 05:29:33.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 05:29:33.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:33.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:33.450][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:29:33.451][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:29:33.453][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:33.454][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:33.456][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-04 05:29:33.457][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:29:33.458][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:33.460][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:33.462][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-04 05:29:33.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:29:33.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:33.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:33.467][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:29:33.469][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:29:33.470][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:33.471][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:33.473][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:29:33.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:29:33.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:33.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:33.479][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 05:29:33.480][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 05:29:33.482][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:33.483][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:33.485][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 05:29:33.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 05:29:33.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:33.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:33.491][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-04 05:29:33.492][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-04 05:29:33.494][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:33.495][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:33.497][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-04 05:29:33.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-04 05:29:33.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:33.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:33.503][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-04 05:29:33.504][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-04 05:29:33.518][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:33.520][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:33.521][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-04 05:29:33.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-04 05:29:33.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:33.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:33.527][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:29:33.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:29:33.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:33.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:33.533][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:29:33.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:29:33.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:33.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:33.539][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:29:33.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:29:33.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:33.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:33.544][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:29:33.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:29:33.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:33.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:33.550][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:29:33.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:29:33.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:33.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:33.556][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:29:33.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:29:33.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:33.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:33.561][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:29:33.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:29:33.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:33.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:33.567][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:29:33.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:29:33.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:33.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:33.573][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:29:33.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:29:33.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:33.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:33.579][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:29:33.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:29:33.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:33.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:29:33.585][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2024-05-04 05:29:33.587][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:29:33.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:29:33.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:33.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:33.593][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:29:33.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:29:33.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:33.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:33.598][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:29:33.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:29:33.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:33.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:29:33.604][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:29:33.605][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:29:33.607][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:29:33.613][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:29:33.615][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:29:33.616][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:29:33.617][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:29:33.619][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2024-05-04 05:29:33.620][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-04 05:29:33.622][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2024-05-04 05:29:33.624][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-04 05:29:33.626][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-04 05:29:33.627][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-04 05:29:33.629][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-04 05:29:33.630][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-04 05:29:33.632][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-04 05:29:33.636][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:29:33.637][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:29:33.639][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:29:33.645][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:29:33.647][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:29:33.648][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:29:33.649][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:29:33.651][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2024-05-04 05:29:33.655][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 05:29:33.657][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 05:29:33.659][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2024-05-04 05:29:35.061][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2024-05-04 05:29:36.203][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-04 05:29:36.207][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2024-05-04 05:29:36.212][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2024-05-04 05:29:36.216][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2024-05-04 05:29:36.218][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-04 05:29:36.220][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-04 05:29:36.222][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-04 05:29:36.225][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:29:36.226][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:29:36.228][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:29:36.235][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:29:36.236][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:29:36.238][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:29:36.239][FUN] Functions in observer BiodbConfig: [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[2024-05-04 05:29:36.243][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:29:36.245][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:29:36.246][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:36.248][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:36.249][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:29:36.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:29:36.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:36.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:36.256][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-04 05:29:36.257][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-04 05:29:36.259][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:36.260][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:36.262][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-04 05:29:36.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-04 05:29:36.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:36.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:36.270][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 05:29:36.272][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 05:29:36.273][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:36.275][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:36.277][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 05:29:36.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 05:29:36.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:36.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:36.283][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 05:29:36.285][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 05:29:36.286][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:36.287][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:36.289][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 05:29:36.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 05:29:36.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:36.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:36.295][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 05:29:36.297][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 05:29:36.299][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:36.300][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:36.302][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 05:29:36.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 05:29:36.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:36.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:36.308][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:29:36.310][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:29:36.311][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:36.312][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:36.314][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-04 05:29:36.324][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:29:36.331][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:36.332][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:36.334][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-04 05:29:36.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:29:36.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:36.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:36.341][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:29:36.342][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:29:36.344][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:36.345][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:36.347][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:29:36.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:29:36.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:36.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:36.353][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 05:29:36.355][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 05:29:36.356][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:36.358][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:36.360][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 05:29:36.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 05:29:36.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:36.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:36.366][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-04 05:29:36.368][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-04 05:29:36.369][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:36.371][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:36.373][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-04 05:29:36.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-04 05:29:36.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:36.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:36.379][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-04 05:29:36.381][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-04 05:29:36.382][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:36.384][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:36.386][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-04 05:29:36.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-04 05:29:36.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:36.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:36.392][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:29:36.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:29:36.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:36.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:36.399][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:29:36.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:29:36.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:36.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:36.405][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:29:36.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:29:36.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:36.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:36.412][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:29:36.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:29:36.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:36.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:36.418][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:29:36.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:29:36.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:36.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:36.425][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:29:36.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:29:36.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:36.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:36.431][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:29:36.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:29:36.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:36.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:36.438][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:29:36.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:29:36.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:36.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:36.444][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:29:36.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:29:36.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:36.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:36.449][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:29:36.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:29:36.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:36.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:29:36.455][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2024-05-04 05:29:36.457][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:29:36.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:29:36.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:36.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:36.463][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:29:36.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:29:36.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:36.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:36.469][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:29:36.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:29:36.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:36.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:29:36.475][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:29:36.476][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:29:36.478][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:29:36.484][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:29:36.486][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:29:36.487][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:29:36.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:29:36.490][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2024-05-04 05:29:36.491][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-04 05:29:36.493][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2024-05-04 05:29:36.495][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-04 05:29:36.497][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-04 05:29:36.498][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-04 05:29:36.500][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-04 05:29:36.501][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-04 05:29:36.502][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-04 05:29:36.506][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:29:36.507][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:29:36.509][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:29:36.515][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:29:36.517][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:29:36.518][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:29:36.519][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:29:36.521][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2024-05-04 05:29:36.525][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 05:29:36.526][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 05:29:36.528][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2024-05-04 05:29:37.892][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2024-05-04 05:29:39.009][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-04 05:29:39.011][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2024-05-04 05:29:39.016][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2024-05-04 05:29:39.019][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2024-05-04 05:29:39.021][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-04 05:29:39.023][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-04 05:29:39.024][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-04 05:29:39.027][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:29:39.028][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:29:39.029][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:29:39.036][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:29:39.037][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:29:39.038][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:29:39.039][FUN] Functions in observer BiodbConfig: [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[2024-05-04 05:29:39.043][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:29:39.044][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:29:39.046][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:39.047][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:39.049][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:29:39.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:29:39.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:39.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:39.054][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-04 05:29:39.056][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-04 05:29:39.057][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:39.058][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:39.106][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-04 05:29:39.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-04 05:29:39.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:39.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:39.113][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 05:29:39.115][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 05:29:39.116][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:39.117][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:39.119][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 05:29:39.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 05:29:39.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:39.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:39.125][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 05:29:39.126][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 05:29:39.128][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:39.129][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:39.131][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 05:29:39.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 05:29:39.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:39.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:39.136][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 05:29:39.138][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 05:29:39.139][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:39.140][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:39.142][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 05:29:39.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 05:29:39.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:39.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:39.148][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:29:39.149][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:29:39.151][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:39.152][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:39.154][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-04 05:29:39.155][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:29:39.156][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:39.158][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:39.160][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-04 05:29:39.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:29:39.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:39.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:39.165][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:29:39.167][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:29:39.168][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:39.169][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:39.171][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:29:39.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:29:39.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:39.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:39.177][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 05:29:39.179][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 05:29:39.180][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:39.181][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:39.183][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 05:29:39.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 05:29:39.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:39.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:39.189][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-04 05:29:39.190][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-04 05:29:39.192][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:39.193][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:39.195][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-04 05:29:39.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-04 05:29:39.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:39.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:39.201][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-04 05:29:39.202][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-04 05:29:39.204][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:39.205][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:39.207][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-04 05:29:39.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-04 05:29:39.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:39.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:39.212][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:29:39.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:29:39.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:39.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:39.218][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:29:39.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:29:39.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:39.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:39.224][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:29:39.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:29:39.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:39.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:39.230][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:29:39.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:29:39.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:39.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:39.236][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:29:39.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:29:39.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:39.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:39.241][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:29:39.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:29:39.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:39.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:39.247][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:29:39.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:29:39.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:39.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:39.252][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:29:39.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:29:39.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:39.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:39.258][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:29:39.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:29:39.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:39.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:39.264][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:29:39.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:29:39.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:39.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:29:39.269][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2024-05-04 05:29:39.271][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:29:39.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:29:39.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:39.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:39.276][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:29:39.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:29:39.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:39.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:39.282][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:29:39.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:29:39.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:39.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:29:39.287][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:29:39.289][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:29:39.290][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:29:39.297][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:29:39.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:29:39.300][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:29:39.301][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:29:39.303][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2024-05-04 05:29:39.304][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-04 05:29:39.306][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2024-05-04 05:29:39.308][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-04 05:29:39.310][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-04 05:29:39.311][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-04 05:29:39.313][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-04 05:29:39.314][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-04 05:29:39.315][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-04 05:29:39.319][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:29:39.320][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:29:39.321][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:29:39.328][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:29:39.329][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:29:39.330][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:29:39.331][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:29:39.333][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2024-05-04 05:29:39.337][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 05:29:39.338][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 05:29:39.340][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2024-05-04 05:29:40.474][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2024-05-04 05:29:41.567][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-04 05:29:41.570][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2024-05-04 05:29:41.586][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2024-05-04 05:29:41.590][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2024-05-04 05:29:41.593][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-04 05:29:41.594][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-04 05:29:41.596][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-04 05:29:41.598][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:29:41.600][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:29:41.601][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:29:41.608][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:29:41.609][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:29:41.610][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:29:41.612][FUN] Functions in observer BiodbConfig: [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[2024-05-04 05:29:41.615][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:29:41.616][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:29:41.618][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:41.619][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:41.621][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:29:41.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:29:41.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:41.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:41.627][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-04 05:29:41.628][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-04 05:29:41.630][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:41.631][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:41.633][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-04 05:29:41.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-04 05:29:41.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:41.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:41.639][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 05:29:41.640][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 05:29:41.642][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:41.643][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:41.645][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 05:29:41.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 05:29:41.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:41.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:41.651][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 05:29:41.652][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 05:29:41.654][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:41.655][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:41.657][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 05:29:41.658][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 05:29:41.660][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:41.661][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:41.663][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:29:41.664][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:29:41.666][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:41.667][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:41.669][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-04 05:29:41.670][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:29:41.672][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:41.673][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:41.675][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-04 05:29:41.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:29:41.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:41.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:41.681][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:29:41.682][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:29:41.684][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:41.685][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:41.687][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:29:41.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:29:41.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:41.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:41.693][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 05:29:41.694][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 05:29:41.696][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:41.697][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:41.699][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 05:29:41.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 05:29:41.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:41.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:41.705][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-04 05:29:41.706][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-04 05:29:41.708][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:41.709][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:41.711][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-04 05:29:41.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-04 05:29:41.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:41.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:41.717][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-04 05:29:41.718][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-04 05:29:41.720][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:41.721][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:41.723][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:29:41.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:29:41.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:41.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:41.729][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:29:41.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:29:41.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:41.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:41.734][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:29:41.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:29:41.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:41.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:41.740][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:29:41.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:29:41.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:41.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:41.746][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:29:41.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:29:41.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:41.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:41.751][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:29:41.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:29:41.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:41.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:41.757][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:29:41.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:29:41.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:41.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:41.763][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:29:41.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:29:41.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:41.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:41.769][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:29:41.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:29:41.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:41.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:41.775][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:29:41.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:29:41.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:41.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:29:41.781][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2024-05-04 05:29:41.782][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:29:41.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:29:41.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:41.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:41.788][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:29:41.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:29:41.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:41.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:29:41.794][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:29:41.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:29:41.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:29:41.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:29:41.800][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:29:41.801][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:29:41.802][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:29:41.809][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:29:41.811][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:29:41.812][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:29:41.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:29:41.815][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2024-05-04 05:29:41.817][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-04 05:29:41.819][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2024-05-04 05:29:41.821][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-04 05:29:41.822][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-04 05:29:41.824][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-04 05:29:41.826][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-04 05:29:41.827][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-04 05:29:41.829][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-04 05:29:41.832][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:29:41.834][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:29:41.835][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:29:41.851][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:29:41.852][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:29:41.854][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:29:41.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:29:41.857][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2024-05-04 05:29:41.861][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 05:29:41.862][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 05:29:41.864][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2024-05-04 05:29:52.960][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2024-05-04 05:30:04.092][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-04 05:30:04.095][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2024-05-04 05:30:04.100][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2024-05-04 05:30:04.103][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2024-05-04 05:30:04.106][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-04 05:30:04.107][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-04 05:30:04.109][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-04 05:30:04.111][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:30:04.113][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:30:04.114][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:30:04.120][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:30:04.122][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:30:04.123][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:30:04.124][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[2024-05-04 05:30:04.128][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:30:04.129][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:30:04.130][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:30:04.132][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:30:04.134][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:30:04.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:30:04.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:30:04.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:30:04.139][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-04 05:30:04.141][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-04 05:30:04.142][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:30:04.144][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:30:04.145][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 05:30:04.147][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 05:30:04.148][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:30:04.149][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:30:04.151][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 05:30:04.153][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 05:30:04.154][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:30:04.156][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:30:04.158][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 05:30:04.159][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 05:30:04.160][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:30:04.162][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:30:04.164][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:30:04.165][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:30:04.167][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:30:04.168][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:30:04.170][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-04 05:30:04.171][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:30:04.173][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:30:04.174][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:30:04.176][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:30:04.177][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:30:04.179][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:30:04.180][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:30:04.182][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 05:30:04.183][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 05:30:04.185][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:30:04.186][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:30:04.188][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-04 05:30:04.190][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-04 05:30:04.191][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:30:04.193][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:30:04.194][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-04 05:30:04.196][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-04 05:30:04.197][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:30:04.199][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:30:04.201][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:30:04.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:30:04.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:30:04.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:30:04.206][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:30:04.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:30:04.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:30:04.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:30:04.212][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:30:04.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:30:04.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:30:04.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:30:04.218][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:30:04.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:30:04.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:30:04.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:30:04.224][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:30:04.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:30:04.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:30:04.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:30:04.230][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:30:04.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:30:04.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:30:04.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:30:04.235][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:30:04.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:30:04.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:30:04.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:30:04.241][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:30:04.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:30:04.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:30:04.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:30:04.247][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:30:04.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:30:04.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:30:04.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:30:04.253][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:30:04.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:30:04.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:30:04.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:30:04.258][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-05-04 05:30:04.264][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-05-04 05:30:04.266][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:30:04.268][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:30:04.269][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:30:04.278][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:30:04.280][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:30:04.281][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:30:04.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:30:04.285][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2024-05-04 05:30:04.286][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-04 05:30:04.289][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2024-05-04 05:30:04.291][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-04 05:30:04.293][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-04 05:30:04.294][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-04 05:30:04.296][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-04 05:30:04.298][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-04 05:30:04.299][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-04 05:30:04.304][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:30:04.305][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:30:04.307][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:30:04.314][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:30:04.315][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:30:04.317][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:30:04.318][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[2024-05-04 05:30:04.320][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2024-05-04 05:30:04.325][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 05:30:04.326][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 05:30:04.328][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2024-05-04 05:30:15.409][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2024-05-04 05:30:26.689][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-04 05:30:26.707][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2024-05-04 05:30:26.720][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2024-05-04 05:30:26.724][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2024-05-04 05:30:26.727][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-04 05:30:26.728][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-04 05:30:26.730][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-04 05:30:26.733][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:30:26.734][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:30:26.735][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:30:26.742][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:30:26.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:30:26.745][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:30:26.746][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 05:30:26.749][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:30:26.751][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:30:26.752][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:30:26.754][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:30:26.756][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:30:26.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:30:26.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:30:26.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:30:26.762][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-04 05:30:26.763][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-04 05:30:26.765][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:30:26.766][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:30:26.768][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 05:30:26.769][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 05:30:26.771][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:30:26.772][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:30:26.774][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 05:30:26.776][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 05:30:26.777][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:30:26.779][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:30:26.780][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 05:30:26.782][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 05:30:26.783][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:30:26.785][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:30:26.787][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:30:26.788][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:30:26.789][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:30:26.791][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:30:26.793][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-04 05:30:26.794][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:30:26.796][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:30:26.797][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:30:26.799][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:30:26.800][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:30:26.802][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:30:26.803][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:30:26.805][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 05:30:26.807][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 05:30:26.808][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:30:26.809][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:30:26.811][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-04 05:30:26.813][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-04 05:30:26.814][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:30:26.816][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:30:26.818][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-04 05:30:26.819][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-04 05:30:26.821][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:30:26.822][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:30:26.824][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:30:26.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:30:26.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:30:26.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:30:26.830][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:30:26.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:30:26.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:30:26.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:30:26.836][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:30:26.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:30:26.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:30:26.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:30:26.842][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:30:26.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:30:26.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:30:26.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:30:26.848][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:30:26.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:30:26.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:30:26.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:30:26.853][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:30:26.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:30:26.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:30:26.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:30:26.859][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:30:26.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:30:26.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:30:26.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:30:26.866][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:30:26.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:30:26.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:30:26.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:30:26.872][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:30:26.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:30:26.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:30:26.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:30:26.878][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:30:26.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:30:26.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:30:26.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:30:26.885][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-05-04 05:30:26.887][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-05-04 05:30:26.888][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:30:26.890][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:30:26.891][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:30:26.898][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:30:26.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:30:26.901][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:30:26.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:30:26.904][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2024-05-04 05:30:26.905][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-04 05:30:26.908][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2024-05-04 05:30:26.910][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-04 05:30:26.911][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-04 05:30:26.913][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-04 05:30:26.914][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-04 05:30:26.916][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-04 05:30:26.917][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-04 05:30:26.921][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:30:26.923][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:30:26.924][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:30:26.931][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:30:26.932][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:30:26.933][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:30:26.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:30:26.936][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2024-05-04 05:30:26.940][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 05:30:26.942][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 05:30:26.944][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2024-05-04 05:30:38.077][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2024-05-04 05:30:49.155][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-04 05:30:49.158][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2024-05-04 05:30:49.163][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2024-05-04 05:30:49.166][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2024-05-04 05:30:49.169][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-04 05:30:49.171][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-04 05:30:49.173][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-04 05:30:49.176][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:30:49.177][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:30:49.178][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:30:49.199][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:30:49.200][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:30:49.202][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:30:49.203][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.TRACE[2024-05-04 05:30:49.207][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:30:49.209][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:30:49.210][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:30:49.212][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:30:49.214][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:30:49.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:30:49.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:30:49.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:30:49.220][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-04 05:30:49.222][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-04 05:30:49.224][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:30:49.225][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:30:49.227][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 05:30:49.229][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 05:30:49.230][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:30:49.232][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:30:49.234][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 05:30:49.235][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 05:30:49.237][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:30:49.238][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:30:49.240][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 05:30:49.242][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 05:30:49.244][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:30:49.245][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:30:49.247][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:30:49.249][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:30:49.250][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:30:49.252][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:30:49.254][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-04 05:30:49.255][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:30:49.257][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:30:49.258][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:30:49.260][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:30:49.262][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:30:49.263][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:30:49.265][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:30:49.266][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 05:30:49.268][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 05:30:49.270][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:30:49.271][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:30:49.273][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-04 05:30:49.275][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-04 05:30:49.276][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:30:49.277][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:30:49.279][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-04 05:30:49.281][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-04 05:30:49.283][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:30:49.284][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:30:49.286][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:30:49.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:30:49.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:30:49.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:30:49.292][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:30:49.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:30:49.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:30:49.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:30:49.298][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:30:49.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:30:49.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:30:49.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:30:49.304][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:30:49.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:30:49.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:30:49.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:30:49.310][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:30:49.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:30:49.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:30:49.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:30:49.316][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:30:49.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:30:49.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:30:49.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:30:49.322][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:30:49.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:30:49.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:30:49.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:30:49.329][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:30:49.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:30:49.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:30:49.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:30:49.334][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:30:49.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:30:49.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:30:49.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:30:49.341][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:30:49.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:30:49.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:30:49.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:30:49.348][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-05-04 05:30:49.350][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-05-04 05:30:49.351][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:30:49.353][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:30:49.354][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:30:49.362][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:30:49.363][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:30:49.365][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:30:49.366][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.DEBUG[2024-05-04 05:30:49.368][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2024-05-04 05:30:49.370][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-04 05:30:49.373][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2024-05-04 05:30:49.375][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-04 05:30:49.377][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-04 05:30:49.379][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-04 05:30:49.381][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-04 05:30:49.383][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-04 05:30:49.384][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-04 05:30:49.388][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:30:49.389][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:30:49.390][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:30:49.397][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:30:49.398][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:30:49.399][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:30:49.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:30:49.402][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2024-05-04 05:30:49.406][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 05:30:49.408][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 05:30:49.410][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2024-05-04 05:31:00.515][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2024-05-04 05:31:11.919][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-04 05:31:11.922][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2024-05-04 05:31:11.927][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2024-05-04 05:31:11.930][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2024-05-04 05:31:11.933][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-04 05:31:11.934][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-04 05:31:11.936][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-04 05:31:11.938][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:31:11.940][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:31:11.941][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:31:11.947][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:31:11.948][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:31:11.950][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:31:11.951][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 05:31:11.954][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:31:11.956][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:31:11.957][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:31:11.958][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:31:11.960][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:31:11.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:31:11.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:31:11.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:31:11.966][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-04 05:31:11.967][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-04 05:31:11.969][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:31:11.982][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:31:11.984][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 05:31:11.986][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 05:31:11.987][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:31:11.988][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:31:11.990][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 05:31:11.992][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 05:31:11.993][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:31:11.994][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:31:11.996][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 05:31:11.998][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 05:31:11.999][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:31:12.000][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:31:12.002][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:31:12.004][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:31:12.005][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:31:12.006][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:31:12.008][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-04 05:31:12.009][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:31:12.011][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:31:12.012][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:31:12.014][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:31:12.015][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:31:12.017][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:31:12.018][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:31:12.020][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 05:31:12.021][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 05:31:12.023][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:31:12.024][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:31:12.026][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-04 05:31:12.028][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-04 05:31:12.029][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:31:12.030][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:31:12.032][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-04 05:31:12.034][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-04 05:31:12.036][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:31:12.037][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:31:12.039][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:31:12.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:31:12.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:31:12.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:31:12.045][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:31:12.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:31:12.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:31:12.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:31:12.050][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:31:12.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:31:12.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:31:12.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:31:12.056][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:31:12.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:31:12.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:31:12.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:31:12.062][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:31:12.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:31:12.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:31:12.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:31:12.068][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:31:12.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:31:12.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:31:12.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:31:12.074][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:31:12.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:31:12.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:31:12.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:31:12.080][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:31:12.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:31:12.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:31:12.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:31:12.086][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:31:12.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:31:12.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:31:12.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:31:12.092][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:31:12.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:31:12.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:31:12.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:31:12.097][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-05-04 05:31:12.099][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-05-04 05:31:12.100][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:31:12.101][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:31:12.103][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:31:12.109][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:31:12.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:31:12.111][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:31:12.113][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:31:12.114][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2024-05-04 05:31:12.116][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-04 05:31:12.118][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2024-05-04 05:31:12.120][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-04 05:31:12.121][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-04 05:31:12.123][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-04 05:31:12.124][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-04 05:31:12.125][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-04 05:31:12.127][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-04 05:31:12.130][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:31:12.132][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:31:12.133][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:31:12.139][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:31:12.141][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:31:12.142][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:31:12.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:31:12.145][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2024-05-04 05:31:12.149][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 05:31:12.150][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 05:31:12.153][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2024-05-04 05:31:23.607][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2024-05-04 05:31:34.732][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-04 05:31:34.735][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2024-05-04 05:31:34.740][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2024-05-04 05:31:34.743][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2024-05-04 05:31:34.745][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-04 05:31:34.746][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-04 05:31:34.748][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-04 05:31:34.750][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:31:34.752][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:31:34.753][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:31:34.759][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:31:34.760][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:31:34.762][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:31:34.763][FUN] Functions in observer BiodbConfig: [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[2024-05-04 05:31:34.766][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:31:34.767][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:31:34.769][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:31:34.770][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:31:34.772][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:31:34.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:31:34.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:31:34.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:31:34.777][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-04 05:31:34.779][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-04 05:31:34.780][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:31:34.781][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:31:34.783][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 05:31:34.784][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 05:31:34.786][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:31:34.787][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:31:34.789][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 05:31:34.790][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 05:31:34.792][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:31:34.793][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:31:34.795][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 05:31:34.796][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 05:31:34.797][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:31:34.799][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:31:34.800][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:31:34.802][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:31:34.816][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:31:34.818][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:31:34.820][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-04 05:31:34.821][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:31:34.822][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:31:34.824][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:31:34.825][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:31:34.827][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:31:34.828][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:31:34.830][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:31:34.831][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 05:31:34.833][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 05:31:34.834][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:31:34.835][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:31:34.837][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-04 05:31:34.839][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-04 05:31:34.840][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:31:34.841][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:31:34.843][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-04 05:31:34.845][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-04 05:31:34.846][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:31:34.847][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:31:34.849][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:31:34.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:31:34.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:31:34.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:31:34.855][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:31:34.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:31:34.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:31:34.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:31:34.860][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:31:34.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:31:34.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:31:34.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:31:34.865][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:31:34.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:31:34.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:31:34.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:31:34.871][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:31:34.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:31:34.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:31:34.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:31:34.876][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:31:34.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:31:34.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:31:34.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:31:34.882][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:31:34.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:31:34.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:31:34.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:31:34.888][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:31:34.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:31:34.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:31:34.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:31:34.893][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:31:34.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:31:34.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:31:34.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:31:34.899][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:31:34.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:31:34.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:31:34.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:31:34.904][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-05-04 05:31:34.905][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-05-04 05:31:34.907][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:31:34.908][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:31:34.909][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:31:34.916][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:31:34.917][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:31:34.918][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:31:34.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:31:34.921][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2024-05-04 05:31:34.923][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-04 05:31:34.925][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2024-05-04 05:31:34.927][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-04 05:31:34.928][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-04 05:31:34.930][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-04 05:31:34.931][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-04 05:31:34.933][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-04 05:31:34.934][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-04 05:31:34.938][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:31:34.939][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:31:34.940][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:31:34.947][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:31:34.948][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:31:34.949][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:31:34.951][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.DEBUG[2024-05-04 05:31:34.952][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2024-05-04 05:31:34.956][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 05:31:34.958][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 05:31:34.960][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2024-05-04 05:31:46.035][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2024-05-04 05:31:57.561][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-04 05:31:57.565][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2024-05-04 05:31:57.570][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2024-05-04 05:31:57.574][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2024-05-04 05:31:57.576][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-04 05:31:57.578][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-04 05:31:57.580][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-04 05:31:57.583][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:31:57.585][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:31:57.586][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:31:57.593][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:31:57.595][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:31:57.597][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:31:57.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 05:31:57.602][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:31:57.604][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:31:57.605][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:31:57.607][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:31:57.609][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:31:57.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:31:57.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:31:57.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:31:57.616][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-04 05:31:57.617][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-04 05:31:57.619][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:31:57.620][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:31:57.622][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 05:31:57.623][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 05:31:57.625][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:31:57.626][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:31:57.628][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 05:31:57.629][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 05:31:57.631][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:31:57.632][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:31:57.634][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 05:31:57.635][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 05:31:57.637][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:31:57.638][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:31:57.640][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:31:57.641][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:31:57.642][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:31:57.644][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:31:57.646][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-04 05:31:57.647][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:31:57.648][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:31:57.650][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:31:57.651][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:31:57.653][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:31:57.654][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:31:57.656][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:31:57.657][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 05:31:57.659][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 05:31:57.660][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:31:57.661][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:31:57.663][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-04 05:31:57.677][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-04 05:31:57.678][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:31:57.680][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:31:57.681][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-04 05:31:57.683][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-04 05:31:57.684][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:31:57.685][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:31:57.687][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:31:57.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:31:57.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:31:57.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:31:57.692][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:31:57.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:31:57.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:31:57.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:31:57.698][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:31:57.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:31:57.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:31:57.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:31:57.703][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:31:57.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:31:57.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:31:57.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:31:57.709][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:31:57.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:31:57.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:31:57.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:31:57.714][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:31:57.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:31:57.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:31:57.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:31:57.719][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:31:57.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:31:57.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:31:57.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:31:57.725][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:31:57.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:31:57.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:31:57.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:31:57.730][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:31:57.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:31:57.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:31:57.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:31:57.736][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:31:57.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:31:57.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:31:57.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:31:57.741][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-05-04 05:31:57.742][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-05-04 05:31:57.744][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:31:57.745][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:31:57.746][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:31:57.752][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:31:57.753][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:31:57.755][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:31:57.756][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:31:57.757][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2024-05-04 05:31:57.759][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-04 05:31:57.761][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2024-05-04 05:31:57.763][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-04 05:31:57.764][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-04 05:31:57.766][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-04 05:31:57.767][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-04 05:31:57.768][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-04 05:31:57.770][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-04 05:31:57.773][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:31:57.775][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:31:57.776][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:31:57.782][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:31:57.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:31:57.785][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:31:57.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:31:57.788][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.DEBUG[2024-05-04 05:31:57.791][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 05:31:57.793][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 05:31:57.795][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.TRACE[2024-05-04 05:32:08.871][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655).
biodb.DEBUG[2024-05-04 05:32:20.007][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-04 05:32:20.010][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content"
biodb.TRACE[2024-05-04 05:32:20.015][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request"
biodb.TRACE[2024-05-04 05:32:20.018][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml"
biodb.DEBUG[2024-05-04 05:32:20.020][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-04 05:32:20.022][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-04 05:32:20.024][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-04 05:32:20.026][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:32:20.028][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:32:20.029][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:32:20.036][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:32:20.037][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:32:20.039][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:32:20.040][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.TRACE[2024-05-04 05:32:20.044][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:32:20.046][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:32:20.047][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:20.049][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:32:20.050][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:32:20.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:32:20.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:20.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:32:20.056][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-04 05:32:20.058][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-04 05:32:20.059][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:20.061][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:32:20.062][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 05:32:20.064][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 05:32:20.065][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:20.067][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:32:20.069][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 05:32:20.070][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 05:32:20.072][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:20.073][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:32:20.075][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 05:32:20.076][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 05:32:20.078][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:20.079][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:32:20.081][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:32:20.083][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:32:20.084][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:20.085][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:32:20.087][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-04 05:32:20.089][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:32:20.090][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:20.092][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:32:20.094][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:32:20.095][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:32:20.097][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:20.098][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:32:20.100][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 05:32:20.101][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 05:32:20.103][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:20.105][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:32:20.107][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-04 05:32:20.109][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-04 05:32:20.110][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:20.111][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:32:20.113][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-04 05:32:20.115][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-04 05:32:20.116][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:20.118][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:32:20.120][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:32:20.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:32:20.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:20.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:32:20.126][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:32:20.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:32:20.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:20.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:32:20.147][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:32:20.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:32:20.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:20.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:32:20.153][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:32:20.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:32:20.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:20.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:32:20.159][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:32:20.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:32:20.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:20.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:32:20.165][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:32:20.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:32:20.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:20.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:32:20.171][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:32:20.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:32:20.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:20.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:32:20.178][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:32:20.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:32:20.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:20.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:32:20.184][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:32:20.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:32:20.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:20.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:32:20.189][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:32:20.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:32:20.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:20.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:32:20.195][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-05-04 05:32:20.197][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-05-04 05:32:20.198][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:32:20.200][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:32:20.201][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:32:20.208][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:32:20.209][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:32:20.210][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:32:20.212][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:32:20.213][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2024-05-04 05:32:20.215][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-04 05:32:20.217][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2024-05-04 05:32:20.219][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-04 05:32:20.220][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-04 05:32:20.222][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-04 05:32:20.224][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-04 05:32:20.225][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-04 05:32:20.226][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-04 05:32:20.230][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:32:20.232][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:32:20.233][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:32:20.240][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:32:20.241][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:32:20.243][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:32:20.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:32:20.246][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.DEBUG[2024-05-04 05:32:20.250][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 05:32:20.251][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 05:32:20.254][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.TRACE[2024-05-04 05:32:31.358][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045).
biodb.DEBUG[2024-05-04 05:32:42.735][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-04 05:32:42.738][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.content"
biodb.TRACE[2024-05-04 05:32:42.743][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.request"
biodb.TRACE[2024-05-04 05:32:42.746][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml"
biodb.DEBUG[2024-05-04 05:32:42.748][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-04 05:32:42.750][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-04 05:32:42.752][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-04 05:32:42.754][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:32:42.755][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:32:42.756][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:32:42.763][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:32:42.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:32:42.766][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:32:42.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 05:32:42.770][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:32:42.772][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:32:42.773][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:42.774][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:32:42.776][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:32:42.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:32:42.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:42.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:32:42.782][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-04 05:32:42.784][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-04 05:32:42.785][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:42.786][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:32:42.788][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 05:32:42.789][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 05:32:42.791][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:42.792][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:32:42.794][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 05:32:42.796][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 05:32:42.797][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:42.798][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:32:42.801][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 05:32:42.803][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 05:32:42.804][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:42.805][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:32:42.807][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:32:42.809][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:32:42.810][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:42.811][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:32:42.813][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-04 05:32:42.815][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:32:42.816][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:42.817][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:32:42.819][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:32:42.820][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:32:42.822][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:42.823][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:32:42.825][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 05:32:42.826][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 05:32:42.828][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:42.829][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:32:42.831][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-04 05:32:42.833][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-04 05:32:42.834][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:42.836][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:32:42.837][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-04 05:32:42.839][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-04 05:32:42.840][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:42.842][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:32:42.844][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:32:42.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:32:42.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:42.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:32:42.850][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:32:42.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:32:42.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:42.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:32:42.856][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:32:42.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:32:42.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:42.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:32:42.861][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:32:42.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:32:42.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:42.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:32:42.867][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:32:42.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:32:42.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:42.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:32:42.873][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:32:42.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:32:42.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:42.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:32:42.892][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:32:42.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:32:42.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:42.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:32:42.898][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:32:42.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:32:42.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:42.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:32:42.904][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:32:42.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:32:42.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:42.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:32:42.910][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:32:42.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:32:42.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:42.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:32:42.916][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-05-04 05:32:42.917][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-05-04 05:32:42.943][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-04 05:32:42.948][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-04 05:32:42.950][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-05-04 05:32:42.952][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-04 05:32:42.954][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-05-04 05:32:42.958][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:32:42.960][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:32:42.961][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:32:42.967][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:32:42.969][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:32:42.970][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:32:42.971][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 05:32:42.973][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:32:42.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:32:42.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:42.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:32:42.979][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:32:42.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:32:42.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:42.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:32:42.985][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:32:42.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:32:42.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:42.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:32:42.990][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:32:42.992][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:32:42.993][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:32:43.000][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:32:43.001][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:32:43.003][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:32:43.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:32:43.006][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:32:43.008][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:32:43.009][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:32:43.016][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:32:43.017][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:32:43.019][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:32:43.020][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:32:43.022][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:32:43.023][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:32:43.025][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:32:43.031][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:32:43.033][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:32:43.034][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:32:43.035][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[2024-05-04 05:32:43.037][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:32:43.038][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:32:43.039][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:32:43.046][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:32:43.047][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:32:43.049][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:32:43.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:32:43.051][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:32:43.053][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:32:43.054][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:32:43.061][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:32:43.062][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:32:43.063][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:32:43.064][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[2024-05-04 05:32:43.066][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:32:43.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:32:43.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:43.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:32:43.072][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:32:43.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:32:43.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:43.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:32:43.077][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:32:43.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:32:43.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:43.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:32:43.083][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:32:43.084][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:32:43.086][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:32:43.092][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:32:43.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:32:43.095][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:32:43.097][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 05:32:43.098][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:32:43.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:32:43.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:43.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:32:43.104][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:32:43.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:32:43.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:43.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:32:43.110][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:32:43.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:32:43.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:43.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:32:43.116][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:32:43.117][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:32:43.118][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:32:43.125][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:32:43.126][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:32:43.128][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:32:43.129][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[2024-05-04 05:32:43.131][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:32:43.132][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:32:43.133][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:32:43.140][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:32:43.142][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:32:43.143][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:32:43.154][FUN] Functions in observer BiodbConfig: [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[2024-05-04 05:32:43.156][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:32:43.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:32:43.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:43.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:32:43.162][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:32:43.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:32:43.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:43.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:32:43.168][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:32:43.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:32:43.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:43.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:32:43.174][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:32:43.176][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:32:43.177][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:32:43.184][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:32:43.185][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:32:43.187][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:32:43.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 05:32:43.189][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:32:43.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:32:43.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:43.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:32:43.195][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:32:43.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:32:43.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:43.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:32:43.200][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:32:43.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:32:43.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:43.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:32:43.207][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:32:43.208][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:32:43.209][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:32:43.219][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:32:43.221][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:32:43.223][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:32:43.224][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 05:32:43.226][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:32:43.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:32:43.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:43.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:32:43.232][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:32:43.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:32:43.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:43.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:32:43.238][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:32:43.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:32:43.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:43.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:32:43.244][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:32:43.246][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:32:43.247][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:32:43.255][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:32:43.256][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:32:43.258][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:32:43.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 05:32:43.261][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:32:43.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:32:43.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:43.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:32:43.267][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:32:43.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:32:43.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:43.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:32:43.272][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:32:43.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:32:43.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:43.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:32:43.278][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:32:43.280][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:32:43.281][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:32:43.288][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:32:43.289][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:32:43.291][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:32:43.292][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[2024-05-04 05:32:43.294][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:32:43.295][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:32:43.297][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:32:43.304][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:32:43.305][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:32:43.307][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:32:43.308][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:32:43.310][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:32:43.311][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:32:43.312][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:32:43.319][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:32:43.321][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:32:43.322][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:32:43.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:32:43.325][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:32:43.326][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:32:43.328][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:32:43.334][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:32:43.336][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:32:43.337][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:32:43.339][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:32:43.340][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:32:43.342][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:32:43.343][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:32:43.350][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:32:43.352][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:32:43.353][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:32:43.354][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:32:43.356][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:32:43.357][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:32:43.359][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:32:43.365][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:32:43.367][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:32:43.368][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:32:43.370][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[2024-05-04 05:32:43.371][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:32:43.373][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:32:43.374][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:32:43.383][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:32:43.385][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:32:43.386][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:32:43.387][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.DEBUG[2024-05-04 05:32:43.389][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:32:43.390][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:32:43.392][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:32:43.398][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:32:43.400][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:32:43.401][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:32:43.402][FUN] Functions in observer BiodbConfig: [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[2024-05-04 05:32:43.441][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:32:43.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:32:43.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:43.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:32:43.448][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:32:43.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:32:43.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:43.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:32:43.454][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:32:43.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:32:43.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:43.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:32:43.460][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:32:43.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:32:43.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:43.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:32:43.465][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:32:43.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:32:43.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:32:43.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:32:43.510][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-04 05:32:43.515][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 05:32:43.516][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 05:32:43.519][private$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[2024-05-04 05:32:44.591][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[2024-05-04 05:32:45.673][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-04 05:32:45.676][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2024-05-04 05:32:45.681][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2024-05-04 05:32:45.686][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[2024-05-04 05:32:45.691][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 05:32:45.692][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 05:32:45.695][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-05-04 05:32:46.824][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-05-04 05:32:47.921][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-04 05:32:47.924][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2024-05-04 05:32:47.929][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2024-05-04 05:32:47.933][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:32:47.934][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:32:47.936][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:32:47.942][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:32:47.943][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:32:47.945][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:32:47.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:32:47.947][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2024-05-04 05:32:47.949][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-04 05:32:47.951][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2024-05-04 05:32:47.953][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-04 05:32:47.954][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-04 05:32:47.956][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-04 05:32:47.957][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-04 05:32:47.959][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-04 05:32:47.960][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-04 05:32:47.964][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:32:47.965][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:32:47.966][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:32:47.973][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:32:47.974][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:32:47.976][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:32:47.977][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:32:47.979][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2024-05-04 05:32:47.982][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 05:32:47.984][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 05:32:47.986][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2024-05-04 05:32:59.074][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2024-05-04 05:33:10.150][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-04 05:33:10.153][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2024-05-04 05:33:10.157][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2024-05-04 05:33:10.161][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2024-05-04 05:33:10.162][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-04 05:33:10.164][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-04 05:33:10.166][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-04 05:33:10.168][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:33:10.169][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:33:10.170][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:33:10.177][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:33:10.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:33:10.179][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:33:10.181][FUN] Functions in observer BiodbConfig: [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[2024-05-04 05:33:10.184][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:33:10.185][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:33:10.186][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:33:10.188][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:33:10.189][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:33:10.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:33:10.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:33:10.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:33:10.195][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-04 05:33:10.196][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-04 05:33:10.198][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:33:10.199][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:33:10.201][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 05:33:10.202][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 05:33:10.204][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:33:10.205][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:33:10.226][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 05:33:10.228][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 05:33:10.229][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:33:10.230][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:33:10.232][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 05:33:10.233][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 05:33:10.235][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:33:10.236][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:33:10.238][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:33:10.239][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:33:10.240][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:33:10.242][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:33:10.243][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-04 05:33:10.245][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:33:10.246][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:33:10.247][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:33:10.249][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:33:10.251][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:33:10.252][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:33:10.253][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:33:10.255][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 05:33:10.256][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 05:33:10.258][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:33:10.259][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:33:10.261][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-04 05:33:10.262][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-04 05:33:10.264][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:33:10.265][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:33:10.267][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-04 05:33:10.268][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-04 05:33:10.269][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:33:10.271][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:33:10.272][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:33:10.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:33:10.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:33:10.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:33:10.278][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:33:10.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:33:10.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:33:10.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:33:10.283][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:33:10.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:33:10.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:33:10.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:33:10.289][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:33:10.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:33:10.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:33:10.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:33:10.294][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:33:10.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:33:10.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:33:10.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:33:10.300][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:33:10.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:33:10.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:33:10.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:33:10.305][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:33:10.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:33:10.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:33:10.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:33:10.311][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:33:10.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:33:10.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:33:10.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:33:10.316][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:33:10.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:33:10.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:33:10.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:33:10.322][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:33:10.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:33:10.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:33:10.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:33:10.327][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-05-04 05:33:10.328][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-05-04 05:33:10.330][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:33:10.331][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:33:10.332][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:33:10.338][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:33:10.340][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:33:10.341][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:33:10.342][FUN] Functions in observer BiodbConfig: [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[2024-05-04 05:33:10.344][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:33:10.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:33:10.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:33:10.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:33:10.349][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:33:10.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:33:10.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:33:10.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:33:10.355][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:33:10.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:33:10.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:33:10.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:33:10.360][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:33:10.362][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:33:10.363][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:33:10.369][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:33:10.370][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:33:10.372][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:33:10.373][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:33:10.375][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2024-05-04 05:33:10.376][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-04 05:33:10.378][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2024-05-04 05:33:10.380][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-04 05:33:10.382][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-04 05:33:10.383][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-04 05:33:10.385][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-04 05:33:10.386][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-04 05:33:10.387][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-04 05:33:10.391][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:33:10.392][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:33:10.393][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:33:10.400][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:33:10.401][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:33:10.402][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:33:10.404][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.DEBUG[2024-05-04 05:33:10.405][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2024-05-04 05:33:10.409][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 05:33:10.410][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 05:33:10.412][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2024-05-04 05:33:21.468][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2024-05-04 05:33:32.570][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-04 05:33:32.573][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2024-05-04 05:33:32.578][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2024-05-04 05:33:32.581][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2024-05-04 05:33:32.583][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-04 05:33:32.585][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-04 05:33:32.587][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-04 05:33:32.589][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:33:32.590][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:33:32.592][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:33:32.598][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:33:32.600][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:33:32.601][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:33:32.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 05:33:32.605][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:33:32.607][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:33:32.609][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:33:32.611][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:33:32.612][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:33:32.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:33:32.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:33:32.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:33:32.631][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-04 05:33:32.633][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-04 05:33:32.635][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:33:32.636][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:33:32.638][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 05:33:32.640][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 05:33:32.641][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:33:32.642][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:33:32.644][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 05:33:32.646][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 05:33:32.647][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:33:32.649][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:33:32.651][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 05:33:32.652][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 05:33:32.654][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:33:32.655][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:33:32.657][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:33:32.658][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:33:32.660][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:33:32.661][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:33:32.663][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-04 05:33:32.664][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:33:32.666][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:33:32.667][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:33:32.669][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:33:32.670][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:33:32.672][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:33:32.673][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:33:32.675][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 05:33:32.677][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 05:33:32.678][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:33:32.679][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:33:32.681][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-04 05:33:32.683][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-04 05:33:32.684][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:33:32.686][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:33:32.688][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-04 05:33:32.689][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-04 05:33:32.690][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:33:32.692][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:33:32.694][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:33:32.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:33:32.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:33:32.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:33:32.700][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:33:32.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:33:32.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:33:32.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:33:32.706][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:33:32.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:33:32.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:33:32.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:33:32.712][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:33:32.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:33:32.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:33:32.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:33:32.718][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:33:32.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:33:32.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:33:32.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:33:32.724][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:33:32.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:33:32.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:33:32.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:33:32.730][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:33:32.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:33:32.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:33:32.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:33:32.736][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:33:32.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:33:32.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:33:32.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:33:32.742][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:33:32.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:33:32.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:33:32.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:33:32.748][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:33:32.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:33:32.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:33:32.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:33:32.754][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-05-04 05:33:32.755][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-05-04 05:33:32.757][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:33:32.758][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:33:32.759][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:33:32.766][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:33:32.768][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:33:32.769][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:33:32.770][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:33:32.772][private$loadEntries] Creating entries from ids [1]: "70786".
biodb.DEBUG[2024-05-04 05:33:32.774][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-04 05:33:32.776][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70786".
biodb.TRACE[2024-05-04 05:33:32.778][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-04 05:33:32.780][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-04 05:33:32.782][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-04 05:33:32.783][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-04 05:33:32.785][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-04 05:33:32.786][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-04 05:33:32.790][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:33:32.792][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:33:32.793][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:33:32.801][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:33:32.802][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:33:32.804][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:33:32.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:33:32.807][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70786".
biodb.DEBUG[2024-05-04 05:33:32.813][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 05:33:32.814][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 05:33:32.817][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70786".
biodb.TRACE[2024-05-04 05:33:43.891][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70786).
biodb.DEBUG[2024-05-04 05:33:55.660][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-04 05:33:55.663][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ea24f2a708fc4a90f6eff28b49d993c4.content"
biodb.TRACE[2024-05-04 05:33:55.668][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ea24f2a708fc4a90f6eff28b49d993c4.request"
biodb.TRACE[2024-05-04 05:33:55.672][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70786.xml"
biodb.DEBUG[2024-05-04 05:33:55.674][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-04 05:33:55.676][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-04 05:33:55.678][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-04 05:33:55.680][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:33:55.682][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:33:55.683][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:33:55.690][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:33:55.691][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:33:55.692][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:33:55.694][FUN] Functions in observer BiodbConfig: [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[2024-05-04 05:33:55.697][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:33:55.699][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:33:55.700][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:33:55.701][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:33:55.703][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:33:55.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:33:55.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:33:55.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:33:55.709][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-04 05:33:55.711][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-04 05:33:55.713][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:33:55.714][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:33:55.716][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 05:33:55.717][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 05:33:55.719][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:33:55.720][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:33:55.722][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 05:33:55.723][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 05:33:55.725][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:33:55.726][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:33:55.728][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 05:33:55.743][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 05:33:55.744][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:33:55.746][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:33:55.748][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:33:55.749][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:33:55.751][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:33:55.752][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:33:55.754][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-04 05:33:55.755][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:33:55.757][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:33:55.758][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:33:55.760][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:33:55.762][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:33:55.763][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:33:55.764][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:33:55.766][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 05:33:55.768][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 05:33:55.769][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:33:55.770][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:33:55.773][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-04 05:33:55.774][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-04 05:33:55.776][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:33:55.777][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:33:55.779][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-04 05:33:55.780][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-04 05:33:55.782][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:33:55.783][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:33:55.785][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:33:55.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:33:55.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:33:55.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:33:55.791][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:33:55.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:33:55.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:33:55.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:33:55.797][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:33:55.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:33:55.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:33:55.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:33:55.803][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:33:55.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:33:55.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:33:55.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:33:55.809][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:33:55.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:33:55.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:33:55.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:33:55.815][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:33:55.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:33:55.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:33:55.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:33:55.821][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:33:55.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:33:55.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:33:55.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:33:55.827][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:33:55.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:33:55.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:33:55.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:33:55.833][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:33:55.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:33:55.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:33:55.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:33:55.839][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:33:55.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:33:55.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:33:55.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:33:55.844][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-05-04 05:33:55.846][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-05-04 05:33:55.847][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:33:55.849][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:33:55.850][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:33:55.857][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:33:55.858][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:33:55.860][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:33:55.861][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.DEBUG[2024-05-04 05:33:55.863][private$loadEntries] Creating entries from ids [1]: "132464".
biodb.DEBUG[2024-05-04 05:33:55.864][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-04 05:33:55.867][cch$loadFileContent] Trying to load 1 files from cache: [1]: "132464".
biodb.TRACE[2024-05-04 05:33:55.869][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-04 05:33:55.870][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-04 05:33:55.872][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-04 05:33:55.874][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-04 05:33:55.875][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-04 05:33:55.877][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-04 05:33:55.880][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:33:55.882][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:33:55.883][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:33:55.890][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:33:55.892][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:33:55.893][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:33:55.894][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[2024-05-04 05:33:55.896][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=132464".
biodb.DEBUG[2024-05-04 05:33:55.900][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 05:33:55.902][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 05:33:55.904][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=132464".
biodb.TRACE[2024-05-04 05:34:07.027][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=132464).
biodb.DEBUG[2024-05-04 05:34:18.159][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-04 05:34:18.162][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5aef2e6eb54508978f23ad702144ac1d.content"
biodb.TRACE[2024-05-04 05:34:18.167][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5aef2e6eb54508978f23ad702144ac1d.request"
biodb.TRACE[2024-05-04 05:34:18.172][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/132464.xml"
biodb.DEBUG[2024-05-04 05:34:18.174][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-04 05:34:18.176][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-04 05:34:18.178][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-04 05:34:18.181][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:34:18.182][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:34:18.184][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:34:18.191][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:34:18.193][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:34:18.194][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:34:18.196][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 05:34:18.199][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:34:18.201][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:34:18.202][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:34:18.204][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:34:18.206][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:34:18.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:34:18.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:34:18.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:34:18.212][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-04 05:34:18.214][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-04 05:34:18.215][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:34:18.217][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:34:18.219][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 05:34:18.220][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 05:34:18.222][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:34:18.223][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:34:18.226][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 05:34:18.227][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 05:34:18.229][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:34:18.230][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:34:18.232][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 05:34:18.234][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 05:34:18.235][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:34:18.237][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:34:18.239][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:34:18.241][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:34:18.242][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:34:18.243][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:34:18.245][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-04 05:34:18.247][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:34:18.248][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:34:18.250][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:34:18.252][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:34:18.253][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:34:18.269][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:34:18.270][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:34:18.273][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 05:34:18.274][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 05:34:18.276][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:34:18.277][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:34:18.279][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-04 05:34:18.281][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-04 05:34:18.282][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:34:18.284][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:34:18.286][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-04 05:34:18.288][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-04 05:34:18.289][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:34:18.290][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:34:18.292][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:34:18.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:34:18.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:34:18.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:34:18.299][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:34:18.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:34:18.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:34:18.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:34:18.305][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:34:18.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:34:18.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:34:18.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:34:18.311][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:34:18.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:34:18.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:34:18.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:34:18.317][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:34:18.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:34:18.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:34:18.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:34:18.323][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:34:18.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:34:18.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:34:18.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:34:18.329][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:34:18.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:34:18.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:34:18.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:34:18.335][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:34:18.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:34:18.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:34:18.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:34:18.341][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:34:18.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:34:18.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:34:18.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:34:18.347][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:34:18.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:34:18.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:34:18.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:34:18.353][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-05-04 05:34:18.354][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-05-04 05:34:18.356][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:34:18.357][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:34:18.358][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:34:18.365][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:34:18.367][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:34:18.368][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:34:18.369][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:34:18.371][private$loadEntries] Creating entries from ids [1]: "132466".
biodb.DEBUG[2024-05-04 05:34:18.373][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-04 05:34:18.376][cch$loadFileContent] Trying to load 1 files from cache: [1]: "132466".
biodb.TRACE[2024-05-04 05:34:18.377][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-04 05:34:18.379][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-04 05:34:18.381][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-04 05:34:18.383][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-04 05:34:18.384][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-04 05:34:18.386][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-04 05:34:18.390][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:34:18.391][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:34:18.393][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:34:18.400][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:34:18.401][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:34:18.403][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:34:18.404][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:34:18.405][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=132466".
biodb.DEBUG[2024-05-04 05:34:18.409][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 05:34:18.411][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 05:34:18.413][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=132466".
biodb.TRACE[2024-05-04 05:34:29.493][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=132466).
biodb.DEBUG[2024-05-04 05:34:40.865][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-04 05:34:40.868][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ec6b951c43591c7f32ac066d8d7eba7b.content"
biodb.TRACE[2024-05-04 05:34:40.872][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ec6b951c43591c7f32ac066d8d7eba7b.request"
biodb.TRACE[2024-05-04 05:34:40.876][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/132466.xml"
biodb.DEBUG[2024-05-04 05:34:40.878][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-04 05:34:40.879][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-04 05:34:40.881][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-04 05:34:40.884][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:34:40.885][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:34:40.886][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:34:40.893][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:34:40.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:34:40.895][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:34:40.897][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.TRACE[2024-05-04 05:34:40.900][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:34:40.901][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:34:40.902][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:34:40.904][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:34:40.905][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:34:40.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:34:40.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:34:40.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:34:40.911][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-04 05:34:40.912][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-04 05:34:40.914][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:34:40.915][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:34:40.917][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 05:34:40.918][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 05:34:40.920][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:34:40.921][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:34:40.923][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 05:34:40.924][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 05:34:40.926][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:34:40.927][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:34:40.929][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 05:34:40.930][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 05:34:40.931][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:34:40.933][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:34:40.934][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:34:40.936][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:34:40.937][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:34:40.938][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:34:40.940][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-04 05:34:40.941][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:34:40.943][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:34:40.944][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:34:40.946][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:34:40.947][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:34:40.949][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:34:40.950][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:34:40.951][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 05:34:40.953][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 05:34:40.954][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:34:40.955][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:34:40.957][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-04 05:34:40.959][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-04 05:34:40.960][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:34:40.961][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:34:40.963][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-04 05:34:40.964][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-04 05:34:40.978][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:34:40.980][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:34:40.982][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:34:40.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:34:40.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:34:40.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:34:40.988][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:34:40.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:34:40.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:34:40.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:34:40.993][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:34:40.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:34:40.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:34:40.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:34:40.999][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:34:41.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:34:41.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:34:41.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:34:41.004][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:34:41.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:34:41.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:34:41.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:34:41.010][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:34:41.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:34:41.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:34:41.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:34:41.015][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:34:41.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:34:41.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:34:41.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:34:41.021][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:34:41.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:34:41.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:34:41.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:34:41.026][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:34:41.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:34:41.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:34:41.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:34:41.031][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:34:41.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:34:41.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:34:41.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:34:41.037][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-05-04 05:34:41.038][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-05-04 05:34:41.040][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:34:41.041][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:34:41.042][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:34:41.048][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:34:41.050][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:34:41.051][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:34:41.052][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[2024-05-04 05:34:41.054][private$loadEntries] Creating entries from ids [1]: "5016".
biodb.DEBUG[2024-05-04 05:34:41.055][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-04 05:34:41.058][cch$loadFileContent] Trying to load 1 files from cache: [1]: "5016".
biodb.TRACE[2024-05-04 05:34:41.060][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-04 05:34:41.061][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-04 05:34:41.063][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-04 05:34:41.064][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-04 05:34:41.066][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-04 05:34:41.067][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-04 05:34:41.071][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:34:41.072][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:34:41.074][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:34:41.080][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:34:41.082][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:34:41.083][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:34:41.085][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:34:41.087][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=5016".
biodb.DEBUG[2024-05-04 05:34:41.091][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 05:34:41.092][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 05:34:41.094][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=5016".
biodb.TRACE[2024-05-04 05:34:52.504][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=5016).
biodb.DEBUG[2024-05-04 05:35:03.578][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-04 05:35:03.581][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/83362e749102f90322a226fbf099edda.content"
biodb.TRACE[2024-05-04 05:35:03.586][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/83362e749102f90322a226fbf099edda.request"
biodb.TRACE[2024-05-04 05:35:03.589][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5016.xml"
biodb.DEBUG[2024-05-04 05:35:03.592][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-04 05:35:03.593][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-04 05:35:03.595][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-04 05:35:03.597][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:35:03.599][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:35:03.600][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:35:03.607][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:35:03.608][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:35:03.610][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:35:03.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 05:35:03.614][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:35:03.616][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:35:03.617][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:03.618][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:03.620][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:35:03.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:35:03.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:03.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:03.626][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-04 05:35:03.627][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-04 05:35:03.628][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:03.630][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:03.632][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 05:35:03.633][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 05:35:03.635][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:03.637][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:03.638][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 05:35:03.640][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 05:35:03.641][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:03.643][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:03.644][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 05:35:03.646][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 05:35:03.647][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:03.649][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:03.651][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:35:03.652][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:35:03.654][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:03.655][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:03.657][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-04 05:35:03.658][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:35:03.660][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:03.661][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:03.663][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:03.664][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:03.666][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:03.667][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:03.669][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 05:35:03.670][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 05:35:03.672][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:03.673][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:03.675][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-04 05:35:03.676][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-04 05:35:03.678][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:03.679][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:03.681][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-04 05:35:03.682][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-04 05:35:03.684][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:03.685][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:03.687][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:35:03.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:35:03.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:03.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:03.693][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:35:03.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:35:03.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:03.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:03.698][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:35:03.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:35:03.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:03.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:03.717][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:35:03.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:35:03.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:03.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:03.722][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:35:03.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:35:03.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:03.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:03.728][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:35:03.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:35:03.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:03.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:03.733][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:35:03.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:35:03.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:03.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:03.739][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:35:03.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:35:03.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:03.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:03.745][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:35:03.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:35:03.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:03.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:03.750][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:35:03.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:35:03.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:03.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:35:03.756][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-05-04 05:35:03.757][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-05-04 05:35:03.758][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:35:03.760][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:35:03.761][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:35:03.767][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:35:03.768][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:35:03.769][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:35:03.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:35:03.772][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:35:03.773][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:35:03.774][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:35:03.781][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:35:03.782][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:35:03.783][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:35:03.785][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:35:03.787][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39126*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-04 05:35:03.792][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 05:35:03.793][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 05:35:03.796][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39126%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-05-04 05:35:04.893][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39126%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-05-04 05:35:06.010][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-04 05:35:06.013][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e98fcf727dab60128a5496d811825b6a.content"
biodb.TRACE[2024-05-04 05:35:06.018][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e98fcf727dab60128a5496d811825b6a.request"
biodb.DEBUG[2024-05-04 05:35:06.043][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[2024-05-04 05:35:06.047][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-04 05:35:06.049][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-05-04 05:35:06.050][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-04 05:35:06.052][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-05-04 05:35:06.056][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:35:06.057][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:35:06.058][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:35:06.064][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:35:06.066][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:35:06.067][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:35:06.068][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[2024-05-04 05:35:06.070][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:06.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:06.075][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:06.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:06.080][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:06.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:35:06.086][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:35:06.087][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:35:06.088][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:35:06.094][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:35:06.096][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:35:06.097][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:35:06.098][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[2024-05-04 05:35:06.100][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:35:06.101][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:35:06.102][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:35:06.108][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:35:06.109][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:35:06.110][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:35:06.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:35:06.113][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:35:06.114][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:35:06.116][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:35:06.122][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:35:06.123][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:35:06.124][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:35:06.125][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:35:06.127][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:35:06.128][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:35:06.129][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:35:06.135][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:35:06.136][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:35:06.138][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:35:06.139][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[2024-05-04 05:35:06.140][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:35:06.142][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:35:06.143][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:35:06.149][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:35:06.150][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:35:06.151][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:35:06.152][FUN] Functions in observer BiodbConfig: [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[2024-05-04 05:35:06.154][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:06.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:06.172][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:06.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:06.177][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:06.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:35:06.182][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:35:06.184][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:35:06.185][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:35:06.191][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:35:06.192][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:35:06.194][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:35:06.195][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.TRACE[2024-05-04 05:35:06.197][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:06.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:06.202][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:06.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:06.208][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:06.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:35:06.214][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:35:06.215][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:35:06.216][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:35:06.223][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:35:06.224][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:35:06.225][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:35:06.226][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.DEBUG[2024-05-04 05:35:06.228][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:35:06.229][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:35:06.230][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:35:06.236][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:35:06.238][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:35:06.239][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:35:06.240][FUN] Functions in observer BiodbConfig: [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[2024-05-04 05:35:06.242][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:06.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:06.247][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:06.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:06.252][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:06.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:35:06.258][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:35:06.259][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:35:06.260][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:35:06.266][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:35:06.268][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:35:06.269][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:35:06.270][FUN] Functions in observer BiodbConfig: [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[2024-05-04 05:35:06.272][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:06.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:06.277][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:06.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:06.282][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:06.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:35:06.288][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:35:06.289][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:35:06.290][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:35:06.297][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:35:06.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:35:06.300][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:35:06.301][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.TRACE[2024-05-04 05:35:06.302][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:06.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:06.308][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:06.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:06.313][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:06.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:35:06.319][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:35:06.320][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:35:06.321][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:35:06.327][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:35:06.328][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:35:06.330][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:35:06.331][FUN] Functions in observer BiodbConfig: [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[2024-05-04 05:35:06.333][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:06.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:06.339][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:06.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:06.344][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:06.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:35:06.350][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:35:06.351][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:35:06.352][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:35:06.358][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:35:06.360][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:35:06.361][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:35:06.362][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:35:06.364][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:35:06.365][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:35:06.366][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:35:06.372][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:35:06.373][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:35:06.374][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:35:06.376][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:35:06.377][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:35:06.378][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:35:06.380][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:35:06.386][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:35:06.387][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:35:06.388][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:35:06.389][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:35:06.391][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:35:06.392][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:35:06.393][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:35:06.399][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:35:06.408][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:35:06.410][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:35:06.411][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[2024-05-04 05:35:06.412][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:35:06.414][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:35:06.415][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:35:06.421][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:35:06.422][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:35:06.423][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:35:06.425][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[2024-05-04 05:35:06.426][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:35:06.427][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:35:06.428][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:35:06.434][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:35:06.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:35:06.437][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:35:06.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:35:06.440][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:35:06.441][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:35:06.442][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:35:06.448][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:35:06.449][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:35:06.451][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:35:06.452][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[2024-05-04 05:35:06.453][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:35:06.455][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:35:06.456][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:35:06.462][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:35:06.463][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:35:06.464][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:35:06.466][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[2024-05-04 05:35:06.490][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[2024-05-04 05:35:06.495][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-04 05:35:06.497][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-05-04 05:35:06.499][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-04 05:35:06.501][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-05-04 05:35:06.505][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:35:06.506][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:35:06.507][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:35:06.513][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:35:06.514][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:35:06.516][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:35:06.517][FUN] Functions in observer BiodbConfig: [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[2024-05-04 05:35:06.518][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:06.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:06.524][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:06.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:06.529][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:06.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:35:06.534][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:35:06.536][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:35:06.537][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:35:06.543][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:35:06.544][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:35:06.545][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:35:06.547][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.DEBUG[2024-05-04 05:35:06.548][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:35:06.549][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:35:06.551][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:35:06.557][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:35:06.558][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:35:06.559][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:35:06.560][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:35:06.562][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:35:06.563][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:35:06.564][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:35:06.570][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:35:06.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:35:06.573][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:35:06.574][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:35:06.575][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:35:06.576][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:35:06.578][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:35:06.584][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:35:06.585][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:35:06.586][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:35:06.587][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[2024-05-04 05:35:06.589][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:35:06.590][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:35:06.591][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:35:06.597][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:35:06.598][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:35:06.600][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:35:06.601][FUN] Functions in observer BiodbConfig: [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[2024-05-04 05:35:06.602][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:06.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:06.608][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:06.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:06.613][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:06.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:35:06.618][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:35:06.620][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:35:06.621][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:35:06.627][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:35:06.628][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:35:06.629][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:35:06.630][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.TRACE[2024-05-04 05:35:06.632][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:06.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:06.637][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:06.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:06.652][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:06.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:35:06.657][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:35:06.658][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:35:06.659][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:35:06.669][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:35:06.670][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:35:06.672][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:35:06.673][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[2024-05-04 05:35:06.675][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:35:06.676][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:35:06.677][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:35:06.684][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:35:06.686][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:35:06.687][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:35:06.688][FUN] Functions in observer BiodbConfig: [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[2024-05-04 05:35:06.690][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:06.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:06.696][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:06.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:06.702][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:06.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:35:06.708][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:35:06.710][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:35:06.711][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:35:06.718][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:35:06.720][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:35:06.721][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:35:06.722][FUN] Functions in observer BiodbConfig: [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[2024-05-04 05:35:06.724][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:06.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:06.729][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:06.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:06.735][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:06.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:35:06.741][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:35:06.742][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:35:06.743][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:35:06.750][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:35:06.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:35:06.753][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:35:06.754][FUN] Functions in observer BiodbConfig: [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[2024-05-04 05:35:06.756][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:06.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:06.761][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:06.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:06.767][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:06.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:35:06.772][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:35:06.773][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:35:06.775][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:35:06.781][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:35:06.783][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:35:06.784][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:35:06.785][FUN] Functions in observer BiodbConfig: [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[2024-05-04 05:35:06.787][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:06.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:06.793][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:06.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:06.798][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:06.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:06.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:35:06.804][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:35:06.805][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:35:06.806][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:35:06.813][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:35:06.814][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:35:06.815][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:35:06.816][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:35:06.818][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:35:06.819][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:35:06.820][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:35:06.827][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:35:06.828][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:35:06.830][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:35:06.831][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.DEBUG[2024-05-04 05:35:06.832][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:35:06.834][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:35:06.835][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:35:06.842][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:35:06.843][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:35:06.844][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:35:06.846][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.DEBUG[2024-05-04 05:35:06.847][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:35:06.848][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:35:06.850][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:35:06.856][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:35:06.858][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:35:06.859][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:35:06.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:35:06.862][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:35:06.863][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:35:06.865][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:35:06.871][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:35:06.873][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:35:06.874][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:35:06.875][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[2024-05-04 05:35:06.877][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:35:06.878][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:35:06.879][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:35:06.885][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:35:06.887][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:35:06.888][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:35:06.889][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.DEBUG[2024-05-04 05:35:06.891][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:35:06.892][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:35:06.893][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:35:06.916][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:35:06.918][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:35:06.919][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:35:06.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:35:06.922][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:35:06.923][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:35:06.924][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:35:06.931][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:35:06.932][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:35:06.933][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:35:06.934][FUN] Functions in observer BiodbConfig: [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[2024-05-04 05:35:06.954][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-05-04 05:35:06.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-05-04 05:35:06.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:06.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-04 05:35:06.969][biodb::testThat]
biodb.INFO [2024-05-04 05:35:06.970][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-05-04 05:35:06.972][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 05:35:06.973][biodb::testThat]
biodb.TRACE[2024-05-04 05:35:06.977][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-04 05:35:06.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-04 05:35:06.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:06.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:06.982][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:35:06.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:35:06.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:06.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:06.987][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:35:06.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:35:06.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:06.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:06.993][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:35:06.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:35:06.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:06.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:06.998][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:35:07.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:35:07.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:07.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:35:07.007][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:35:07.009][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:35:07.010][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:35:07.016][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:35:07.017][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:35:07.018][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:35:07.020][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:35:07.024][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[2024-05-04 05:35:07.028][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 05:35:07.030][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 05:35:07.032][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-05-04 05:35:08.403][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-05-04 05:35:09.474][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-04 05:35:09.477][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2024-05-04 05:35:09.482][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2024-05-04 05:35:09.485][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:35:09.486][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:35:09.487][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:35:09.493][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:35:09.495][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:35:09.496][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:35:09.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:35:09.499][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-04 05:35:09.504][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 05:35:09.505][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 05:35:09.507][private$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[2024-05-04 05:35:10.621][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[2024-05-04 05:35:11.688][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-04 05:35:11.690][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2024-05-04 05:35:11.696][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2024-05-04 05:35:11.699][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:35:11.701][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:35:11.702][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:35:11.708][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:35:11.710][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:35:11.711][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:35:11.712][FUN] Functions in observer BiodbConfig: [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[2024-05-04 05:35:11.714][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:35:11.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:35:11.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:11.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:11.719][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:35:11.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:35:11.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:11.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:11.724][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:35:11.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:35:11.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:11.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:35:11.729][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:35:11.730][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:35:11.732][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:35:11.738][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:35:11.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:35:11.740][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:35:11.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:35:11.743][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:35:11.744][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:35:11.745][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:35:11.752][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:35:11.753][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:35:11.754][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:35:11.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:35:11.758][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-04 05:35:11.778][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-04 05:35:11.780][cch$loadFileContent] Trying to load 1 files from cache: [1]: "94c7655c8f372fb2982c15119402bcba".
biodb.TRACE[2024-05-04 05:35:11.782][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-04 05:35:11.784][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.content".
biodb.DEBUG[2024-05-04 05:35:11.788][private$bdb$entriesToDataframe] 1 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-04 05:35:11.790][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:35:11.791][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:35:11.792][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:35:11.798][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:35:11.800][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:35:11.801][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:35:11.802][FUN] Functions in observer BiodbConfig: [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[2024-05-04 05:35:11.804][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:35:11.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:35:11.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:11.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:11.809][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:35:11.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:35:11.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:11.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:11.814][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-04 05:35:11.815][private$selectFields]
biodb.TRACE[2024-05-04 05:35:11.817][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-04 05:35:11.818][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-04 05:35:11.819][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-04 05:35:11.820][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:35:11.822][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:35:11.823][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:11.824][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:11.825][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:35:11.827][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:35:11.828][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:11.829][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:11.831][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-04 05:35:11.832][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-04 05:35:11.833][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:35:11.835][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:35:11.836][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:11.837][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:11.838][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-04 05:35:11.840][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:35:11.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:35:11.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:11.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:11.845][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:35:11.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:35:11.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:11.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:11.850][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:35:11.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:35:11.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:11.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:11.868][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-05-04 05:35:11.870][private$entriesToListOfDataframes] Converted 1 entry/ies to data frame(s).
biodb.DEBUG[2024-05-04 05:35:11.871][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-05-04 05:35:11.882][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:11.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:11.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:11.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:11.888][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:11.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:11.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:11.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:11.893][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:11.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:11.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:11.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:11.898][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:11.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:11.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:11.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:35:11.979][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:35:11.980][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:35:11.981][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:35:11.996][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:35:11.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:35:11.999][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:35:12.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:35:12.004][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[2024-05-04 05:35:12.009][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 05:35:12.010][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 05:35:12.013][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-05-04 05:35:13.148][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-05-04 05:35:14.215][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-04 05:35:14.217][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2024-05-04 05:35:14.222][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2024-05-04 05:35:14.227][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-04 05:35:14.232][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 05:35:14.233][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 05:35:14.235][private$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[2024-05-04 05:35:15.286][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[2024-05-04 05:35:16.366][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-04 05:35:16.369][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2024-05-04 05:35:16.375][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2024-05-04 05:35:16.379][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:35:16.380][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:35:16.381][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:35:16.388][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:35:16.389][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:35:16.391][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:35:16.392][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[2024-05-04 05:35:16.394][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:35:16.395][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:35:16.396][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:35:16.403][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:35:16.404][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:35:16.406][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:35:16.407][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.TRACE[2024-05-04 05:35:16.409][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:16.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:16.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:16.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:16.415][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:16.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:16.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:16.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:16.421][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:16.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:16.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:16.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:35:16.426][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:35:16.428][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:35:16.429][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:35:16.436][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:35:16.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:35:16.439][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:35:16.440][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[2024-05-04 05:35:16.442][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:35:16.443][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:35:16.445][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:35:16.451][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:35:16.452][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:35:16.454][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:35:16.455][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:35:16.457][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:35:16.458][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:35:16.459][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:35:16.466][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:35:16.467][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:35:16.468][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:35:16.470][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[2024-05-04 05:35:16.471][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:35:16.473][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:35:16.474][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:35:16.480][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:35:16.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:35:16.483][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:35:16.485][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:35:16.486][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:35:16.488][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:35:16.489][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:35:16.495][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:35:16.497][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:35:16.498][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:35:16.500][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[2024-05-04 05:35:16.502][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:35:16.503][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:35:16.504][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:35:16.511][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:35:16.512][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:35:16.514][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:35:16.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:35:16.517][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:35:16.518][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:35:16.520][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:35:16.527][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:35:16.528][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:35:16.530][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:35:16.531][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.DEBUG[2024-05-04 05:35:16.534][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.4*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-04 05:35:16.539][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 05:35:16.541][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 05:35:16.543][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.4%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-05-04 05:35:17.618][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.4%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-05-04 05:35:18.727][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-04 05:35:18.730][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aaf802ce66e9d9898733b018b57315f1.content"
biodb.TRACE[2024-05-04 05:35:18.735][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aaf802ce66e9d9898733b018b57315f1.request"
biodb.DEBUG[2024-05-04 05:35:18.739][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:35:18.741][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:35:18.742][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:35:18.770][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:35:18.771][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:35:18.773][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:35:18.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:35:18.776][private$loadEntries] Creating entries from ids [1]: "28243".
biodb.DEBUG[2024-05-04 05:35:18.778][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-04 05:35:18.780][cch$loadFileContent] Trying to load 1 files from cache: [1]: "28243".
biodb.TRACE[2024-05-04 05:35:18.782][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-04 05:35:18.784][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-04 05:35:18.785][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-04 05:35:18.787][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-04 05:35:18.789][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-04 05:35:18.790][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-04 05:35:18.794][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:35:18.795][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:35:18.797][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:35:18.803][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:35:18.805][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:35:18.806][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:35:18.808][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:35:18.810][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=28243".
biodb.DEBUG[2024-05-04 05:35:18.814][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 05:35:18.815][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 05:35:18.817][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=28243".
biodb.TRACE[2024-05-04 05:35:29.953][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=28243).
biodb.DEBUG[2024-05-04 05:35:41.360][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-04 05:35:41.362][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/177c3a227615d232b537605885883911.content"
biodb.TRACE[2024-05-04 05:35:41.367][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/177c3a227615d232b537605885883911.request"
biodb.TRACE[2024-05-04 05:35:41.370][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/28243.xml"
biodb.DEBUG[2024-05-04 05:35:41.372][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-04 05:35:41.374][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-04 05:35:41.375][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-04 05:35:41.378][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:35:41.379][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:35:41.380][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:35:41.386][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:35:41.388][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:35:41.389][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:35:41.390][FUN] Functions in observer BiodbConfig: [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[2024-05-04 05:35:41.393][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:35:41.395][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:35:41.396][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:41.397][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:41.399][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:35:41.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:35:41.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:41.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:41.404][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-04 05:35:41.406][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-04 05:35:41.407][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:41.408][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:41.410][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 05:35:41.411][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 05:35:41.413][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:41.414][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:41.416][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 05:35:41.417][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 05:35:41.419][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:41.420][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:41.422][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 05:35:41.423][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 05:35:41.424][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:41.426][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:41.428][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:35:41.429][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:35:41.430][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:41.432][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:41.433][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-04 05:35:41.435][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:35:41.436][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:41.437][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:41.439][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:41.441][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:35:41.442][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:41.443][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:41.445][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 05:35:41.446][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 05:35:41.448][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:41.449][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:41.451][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-04 05:35:41.452][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-04 05:35:41.454][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:41.455][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:41.457][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-04 05:35:41.458][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-04 05:35:41.459][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:41.461][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:41.462][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:35:41.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:35:41.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:41.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:41.468][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:35:41.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:35:41.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:41.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:41.473][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:35:41.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:35:41.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:41.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:41.478][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:35:41.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:35:41.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:41.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:41.484][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:35:41.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:35:41.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:41.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:41.489][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:35:41.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:35:41.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:41.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:41.495][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:35:41.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:35:41.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:41.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:41.500][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:35:41.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:35:41.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:41.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:41.506][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:35:41.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:35:41.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:41.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:35:41.511][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:35:41.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:35:41.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:35:41.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:35:41.517][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-05-04 05:35:41.518][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-05-04 05:35:41.519][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:35:41.520][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:35:41.522][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:35:41.528][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:35:41.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:35:41.530][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:35:41.531][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.DEBUG[2024-05-04 05:35:41.533][private$loadEntries] Creating entries from ids [1]: "78144".
biodb.DEBUG[2024-05-04 05:35:41.534][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-04 05:35:41.537][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78144".
biodb.TRACE[2024-05-04 05:35:41.538][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-04 05:35:41.540][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-04 05:35:41.541][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-04 05:35:41.543][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-04 05:35:41.544][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-04 05:35:41.558][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-04 05:35:41.563][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:35:41.564][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:35:41.566][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:35:41.572][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:35:41.574][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:35:41.575][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:35:41.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:35:41.578][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78144".
biodb.DEBUG[2024-05-04 05:35:41.582][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 05:35:41.584][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 05:35:41.586][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78144".
biodb.TRACE[2024-05-04 05:35:52.674][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78144).
biodb.DEBUG[2024-05-04 05:36:03.773][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-04 05:36:03.776][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ede5a640bd42c7611e16282ef185b74.content"
biodb.TRACE[2024-05-04 05:36:03.780][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ede5a640bd42c7611e16282ef185b74.request"
biodb.TRACE[2024-05-04 05:36:03.784][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78144.xml"
biodb.DEBUG[2024-05-04 05:36:03.785][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-04 05:36:03.787][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-04 05:36:03.789][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-04 05:36:03.791][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:36:03.792][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:36:03.793][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:36:03.800][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:36:03.801][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:36:03.802][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:36:03.803][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 05:36:03.806][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:36:03.808][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:36:03.809][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:36:03.810][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:36:03.812][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:36:03.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:36:03.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:36:03.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:36:03.817][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-04 05:36:03.818][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-04 05:36:03.820][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:36:03.821][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:36:03.822][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 05:36:03.824][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 05:36:03.825][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:36:03.826][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:36:03.828][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 05:36:03.830][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 05:36:03.831][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:36:03.832][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:36:03.834][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 05:36:03.835][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 05:36:03.836][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:36:03.838][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:36:03.839][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:36:03.841][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:36:03.842][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:36:03.843][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:36:03.845][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-04 05:36:03.846][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:36:03.847][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:36:03.849][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:36:03.850][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:36:03.852][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:36:03.853][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:36:03.854][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:36:03.856][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 05:36:03.857][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 05:36:03.858][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:36:03.860][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:36:03.861][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-04 05:36:03.863][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-04 05:36:03.864][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:36:03.865][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:36:03.867][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-04 05:36:03.868][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-04 05:36:03.870][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:36:03.871][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:36:03.873][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:36:03.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:36:03.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:36:03.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:36:03.878][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:36:03.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:36:03.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:36:03.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:36:03.884][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:36:03.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:36:03.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:36:03.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:36:03.889][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:36:03.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:36:03.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:36:03.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:36:03.894][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:36:03.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:36:03.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:36:03.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:36:03.900][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:36:03.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:36:03.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:36:03.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:36:03.905][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:36:03.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:36:03.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:36:03.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:36:03.911][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:36:03.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:36:03.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:36:03.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:36:03.916][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:36:03.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:36:03.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:36:03.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:36:03.921][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:36:03.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:36:03.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:36:03.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:36:03.927][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-05-04 05:36:03.928][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-05-04 05:36:03.930][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:36:03.931][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:36:03.932][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:36:03.938][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:36:03.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:36:03.941][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:36:03.942][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:36:03.943][private$loadEntries] Creating entries from ids [1]: "78710".
biodb.DEBUG[2024-05-04 05:36:03.945][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-04 05:36:03.947][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78710".
biodb.TRACE[2024-05-04 05:36:03.948][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-04 05:36:03.950][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-04 05:36:03.952][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-04 05:36:03.953][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-04 05:36:03.955][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-04 05:36:03.956][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-04 05:36:03.959][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:36:03.961][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:36:03.962][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:36:03.968][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:36:03.969][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:36:03.970][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:36:03.971][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:36:03.985][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78710".
biodb.DEBUG[2024-05-04 05:36:03.989][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 05:36:03.990][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 05:36:03.993][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78710".
biodb.TRACE[2024-05-04 05:36:15.074][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78710).
biodb.DEBUG[2024-05-04 05:36:26.205][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-04 05:36:26.208][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/9ef05dfa4d90ed64df5daace690a9bea.content"
biodb.TRACE[2024-05-04 05:36:26.213][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/9ef05dfa4d90ed64df5daace690a9bea.request"
biodb.TRACE[2024-05-04 05:36:26.216][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78710.xml"
biodb.DEBUG[2024-05-04 05:36:26.218][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-04 05:36:26.220][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-04 05:36:26.222][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-04 05:36:26.224][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:36:26.225][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:36:26.227][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:36:26.233][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:36:26.235][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:36:26.236][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:36:26.237][FUN] Functions in observer BiodbConfig: [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[2024-05-04 05:36:26.241][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:36:26.242][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:36:26.244][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:36:26.245][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:36:26.247][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:36:26.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:36:26.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:36:26.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:36:26.253][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-04 05:36:26.254][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-04 05:36:26.255][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:36:26.257][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:36:26.258][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 05:36:26.260][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 05:36:26.261][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:36:26.262][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:36:26.264][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 05:36:26.265][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 05:36:26.267][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:36:26.268][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:36:26.270][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 05:36:26.271][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 05:36:26.272][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:36:26.274][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:36:26.275][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:36:26.277][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:36:26.278][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:36:26.279][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:36:26.281][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-04 05:36:26.283][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:36:26.284][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:36:26.285][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:36:26.287][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:36:26.288][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:36:26.289][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:36:26.291][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:36:26.292][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 05:36:26.294][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 05:36:26.295][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:36:26.296][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:36:26.298][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-04 05:36:26.300][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-04 05:36:26.301][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:36:26.302][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:36:26.304][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-04 05:36:26.306][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-04 05:36:26.307][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:36:26.308][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:36:26.310][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:36:26.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:36:26.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:36:26.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:36:26.315][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:36:26.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:36:26.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:36:26.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:36:26.320][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:36:26.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:36:26.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:36:26.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:36:26.326][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:36:26.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:36:26.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:36:26.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:36:26.332][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:36:26.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:36:26.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:36:26.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:36:26.337][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:36:26.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:36:26.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:36:26.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:36:26.343][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:36:26.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:36:26.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:36:26.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:36:26.348][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:36:26.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:36:26.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:36:26.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:36:26.353][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:36:26.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:36:26.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:36:26.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:36:26.359][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:36:26.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:36:26.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:36:26.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:36:26.364][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-05-04 05:36:26.365][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-05-04 05:36:26.366][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:36:26.368][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:36:26.369][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:36:26.375][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:36:26.376][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:36:26.377][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:36:26.378][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[2024-05-04 05:36:26.380][private$loadEntries] Creating entries from ids [1]: "84884".
biodb.DEBUG[2024-05-04 05:36:26.381][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-04 05:36:26.383][cch$loadFileContent] Trying to load 1 files from cache: [1]: "84884".
biodb.TRACE[2024-05-04 05:36:26.385][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-04 05:36:26.387][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-04 05:36:26.388][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-04 05:36:26.389][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-04 05:36:26.391][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-04 05:36:26.392][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-04 05:36:26.395][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:36:26.397][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:36:26.398][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:36:26.404][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:36:26.406][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:36:26.407][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:36:26.408][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[2024-05-04 05:36:26.409][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=84884".
biodb.DEBUG[2024-05-04 05:36:26.413][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 05:36:26.414][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 05:36:26.416][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=84884".
biodb.TRACE[2024-05-04 05:36:37.521][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=84884).
biodb.DEBUG[2024-05-04 05:36:48.648][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-04 05:36:48.651][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/155a67d7448ef21628a46ed39d5e791d.content"
biodb.TRACE[2024-05-04 05:36:48.670][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/155a67d7448ef21628a46ed39d5e791d.request"
biodb.TRACE[2024-05-04 05:36:48.674][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/84884.xml"
biodb.DEBUG[2024-05-04 05:36:48.676][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-04 05:36:48.678][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-04 05:36:48.679][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-04 05:36:48.681][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:36:48.682][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:36:48.684][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:36:48.690][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:36:48.691][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:36:48.692][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:36:48.694][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 05:36:48.696][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:36:48.698][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:36:48.699][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:36:48.700][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:36:48.702][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:36:48.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:36:48.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:36:48.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:36:48.707][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-04 05:36:48.709][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-04 05:36:48.710][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:36:48.711][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:36:48.713][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 05:36:48.714][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 05:36:48.715][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:36:48.716][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:36:48.718][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 05:36:48.720][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 05:36:48.721][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:36:48.722][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:36:48.724][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 05:36:48.725][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 05:36:48.726][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:36:48.727][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:36:48.729][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:36:48.730][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:36:48.731][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:36:48.733][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:36:48.734][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-04 05:36:48.736][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:36:48.738][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:36:48.739][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:36:48.740][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:36:48.742][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:36:48.743][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:36:48.744][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:36:48.746][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 05:36:48.747][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 05:36:48.748][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:36:48.749][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:36:48.751][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-04 05:36:48.753][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-04 05:36:48.754][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:36:48.755][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:36:48.757][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-04 05:36:48.758][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-04 05:36:48.759][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:36:48.760][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:36:48.762][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:36:48.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:36:48.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:36:48.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:36:48.767][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:36:48.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:36:48.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:36:48.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:36:48.773][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:36:48.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:36:48.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:36:48.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:36:48.778][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:36:48.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:36:48.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:36:48.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:36:48.784][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:36:48.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:36:48.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:36:48.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:36:48.789][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:36:48.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:36:48.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:36:48.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:36:48.794][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:36:48.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:36:48.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:36:48.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:36:48.800][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:36:48.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:36:48.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:36:48.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:36:48.806][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:36:48.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:36:48.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:36:48.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:36:48.812][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:36:48.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:36:48.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:36:48.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:36:48.817][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-05-04 05:36:48.818][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-05-04 05:36:48.820][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:36:48.821][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:36:48.822][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:36:48.829][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:36:48.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:36:48.831][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:36:48.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:36:48.834][private$loadEntries] Creating entries from ids [1]: "84918".
biodb.DEBUG[2024-05-04 05:36:48.835][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-04 05:36:48.837][cch$loadFileContent] Trying to load 1 files from cache: [1]: "84918".
biodb.TRACE[2024-05-04 05:36:48.839][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-04 05:36:48.841][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-04 05:36:48.842][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-04 05:36:48.844][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-04 05:36:48.845][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-04 05:36:48.846][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-04 05:36:48.850][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:36:48.851][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:36:48.852][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:36:48.859][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:36:48.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:36:48.861][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:36:48.863][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:36:48.864][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=84918".
biodb.DEBUG[2024-05-04 05:36:48.868][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 05:36:48.869][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 05:36:48.871][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=84918".
biodb.TRACE[2024-05-04 05:37:00.128][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=84918).
biodb.DEBUG[2024-05-04 05:37:11.253][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-04 05:37:11.256][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/6813f369a455f895cb7b91ba45338bf2.content"
biodb.TRACE[2024-05-04 05:37:11.260][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/6813f369a455f895cb7b91ba45338bf2.request"
biodb.TRACE[2024-05-04 05:37:11.263][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/84918.xml"
biodb.DEBUG[2024-05-04 05:37:11.265][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-04 05:37:11.267][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-04 05:37:11.268][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-04 05:37:11.270][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:37:11.272][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:37:11.273][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:37:11.290][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:37:11.292][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:37:11.293][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:37:11.294][FUN] Functions in observer BiodbConfig: [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[2024-05-04 05:37:11.297][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:37:11.299][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:37:11.300][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:11.301][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:11.303][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:37:11.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:37:11.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:11.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:11.308][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-04 05:37:11.309][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-04 05:37:11.310][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:11.312][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:11.313][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 05:37:11.315][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 05:37:11.316][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:11.317][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:11.319][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 05:37:11.320][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 05:37:11.321][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:11.323][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:11.324][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 05:37:11.326][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 05:37:11.327][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:11.328][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:11.330][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:37:11.331][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:37:11.332][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:11.333][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:11.335][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-04 05:37:11.336][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:37:11.338][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:11.339][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:11.341][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:37:11.342][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:37:11.343][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:11.345][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:11.346][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 05:37:11.348][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 05:37:11.349][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:11.350][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:11.352][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-04 05:37:11.354][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-04 05:37:11.355][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:11.356][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:11.358][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-04 05:37:11.359][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-04 05:37:11.360][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:11.361][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:11.363][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:37:11.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:37:11.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:11.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:11.368][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:37:11.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:37:11.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:11.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:11.373][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:37:11.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:37:11.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:11.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:11.378][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:37:11.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:37:11.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:11.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:11.384][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:37:11.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:37:11.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:11.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:11.389][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:37:11.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:37:11.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:11.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:11.394][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:37:11.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:37:11.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:11.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:11.399][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:37:11.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:37:11.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:11.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:11.404][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:37:11.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:37:11.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:11.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:11.409][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:37:11.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:37:11.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:11.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:37:11.414][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-05-04 05:37:11.415][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-05-04 05:37:11.417][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:37:11.418][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:37:11.419][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:37:11.425][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:37:11.426][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:37:11.427][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:37:11.428][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[2024-05-04 05:37:11.431][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.41*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-04 05:37:11.436][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 05:37:11.437][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 05:37:11.439][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.41%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-05-04 05:37:12.526][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.41%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-05-04 05:37:13.621][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-04 05:37:13.624][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/6fb67f2addef198a43a9c7e2c87e0df9.content"
biodb.TRACE[2024-05-04 05:37:13.629][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/6fb67f2addef198a43a9c7e2c87e0df9.request"
biodb.DEBUG[2024-05-04 05:37:13.632][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:37:13.633][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:37:13.634][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:37:13.640][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:37:13.641][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:37:13.642][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:37:13.643][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:37:13.645][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:37:13.646][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:37:13.647][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:37:13.653][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:37:13.654][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:37:13.655][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:37:13.656][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[2024-05-04 05:37:13.658][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:37:13.659][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:37:13.660][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:37:13.666][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:37:13.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:37:13.669][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:37:13.670][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:37:13.715][private$bdb$entriesToDataframe] 1 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-04 05:37:13.747][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:37:13.748][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:37:13.749][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:37:13.755][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:37:13.756][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:37:13.757][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:37:13.759][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 05:37:13.776][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:37:13.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:37:13.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:13.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:13.781][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:37:13.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:37:13.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:13.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:13.814][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-04 05:37:13.815][private$selectFields]
biodb.TRACE[2024-05-04 05:37:13.816][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-04 05:37:13.817][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-04 05:37:13.819][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-04 05:37:13.820][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:37:13.821][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:37:13.822][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:13.823][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:13.825][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:37:13.826][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:37:13.827][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:13.828][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:13.829][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-04 05:37:13.843][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-04 05:37:13.845][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:37:13.846][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:37:13.847][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:13.848][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:13.850][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-04 05:37:13.851][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:37:13.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:37:13.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:13.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:13.856][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:37:13.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:37:13.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:13.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:13.860][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:37:13.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:37:13.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:13.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:13.866][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-05-04 05:37:13.867][private$entriesToListOfDataframes] Converted 1 entry/ies to data frame(s).
biodb.DEBUG[2024-05-04 05:37:13.869][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-05-04 05:37:13.886][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-05-04 05:37:13.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-05-04 05:37:13.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:13.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-04 05:37:13.895][biodb::testThat]
biodb.INFO [2024-05-04 05:37:13.896][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-05-04 05:37:13.898][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 05:37:13.899][biodb::testThat]
biodb.TRACE[2024-05-04 05:37:13.902][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-04 05:37:13.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-04 05:37:13.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:13.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:13.908][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:37:13.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:37:13.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:13.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:13.913][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:37:13.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:37:13.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:13.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:13.918][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:37:13.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:37:13.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:13.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:13.923][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:37:13.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:37:13.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:13.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:37:13.930][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:37:13.932][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:37:13.933][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:37:13.938][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:37:13.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:37:13.941][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:37:13.942][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:37:13.945][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-04 05:37:13.949][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-04 05:37:13.951][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-05-04 05:37:13.953][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-04 05:37:13.954][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-05-04 05:37:13.957][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:37:13.958][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:37:13.959][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:37:13.965][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:37:13.966][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:37:13.967][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:37:13.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:37:13.971][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-04 05:37:13.975][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-04 05:37:13.976][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-05-04 05:37:13.978][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-04 05:37:13.980][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-05-04 05:37:13.983][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:37:13.984][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:37:13.985][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:37:13.991][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:37:13.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:37:13.994][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:37:13.995][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 05:37:13.996][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:37:13.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:37:13.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:14.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:14.002][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:37:14.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:37:14.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:14.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:14.007][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:37:14.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:37:14.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:14.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:37:14.012][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:37:14.013][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:37:14.014][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:37:14.020][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:37:14.021][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:37:14.023][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:37:14.024][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[2024-05-04 05:37:14.025][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:37:14.026][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:37:14.027][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:37:14.033][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:37:14.035][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:37:14.036][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:37:14.037][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:37:14.039][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-04 05:37:14.043][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-04 05:37:14.045][cch$loadFileContent] Trying to load 1 files from cache: [1]: "94c7655c8f372fb2982c15119402bcba".
biodb.TRACE[2024-05-04 05:37:14.046][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-04 05:37:14.048][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.content".
biodb.DEBUG[2024-05-04 05:37:14.051][private$bdb$entriesToDataframe] 1 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-04 05:37:14.053][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:37:14.054][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:37:14.055][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:37:14.061][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:37:14.062][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:37:14.063][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:37:14.064][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 05:37:14.066][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:37:14.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:37:14.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:14.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:14.071][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:37:14.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:37:14.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:14.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:14.076][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-04 05:37:14.077][private$selectFields]
biodb.TRACE[2024-05-04 05:37:14.079][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-04 05:37:14.080][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-04 05:37:14.081][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-04 05:37:14.082][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:37:14.084][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:37:14.085][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:14.086][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:14.087][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:37:14.088][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:37:14.089][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:14.091][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:14.092][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-04 05:37:14.093][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-04 05:37:14.094][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:37:14.096][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:37:14.097][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:14.098][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:14.099][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-04 05:37:14.101][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:37:14.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:37:14.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:14.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:14.113][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:37:14.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:37:14.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:14.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:14.119][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:37:14.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:37:14.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:14.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:14.124][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-05-04 05:37:14.125][private$entriesToListOfDataframes] Converted 1 entry/ies to data frame(s).
biodb.DEBUG[2024-05-04 05:37:14.126][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-05-04 05:37:14.136][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:37:14.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:37:14.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:14.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:14.141][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:37:14.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:37:14.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:14.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:14.146][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:37:14.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:37:14.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:14.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:14.151][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:37:14.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:37:14.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:14.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:37:14.159][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:37:14.160][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:37:14.161][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:37:14.167][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:37:14.168][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:37:14.169][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:37:14.170][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:37:14.173][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-04 05:37:14.177][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-04 05:37:14.179][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-05-04 05:37:14.181][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-04 05:37:14.182][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-05-04 05:37:14.186][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-04 05:37:14.190][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-04 05:37:14.192][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-05-04 05:37:14.193][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-04 05:37:14.195][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-05-04 05:37:14.198][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:37:14.199][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:37:14.200][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:37:14.206][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:37:14.207][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:37:14.208][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:37:14.209][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:37:14.211][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:37:14.212][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:37:14.213][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:37:14.219][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:37:14.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:37:14.221][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:37:14.222][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[2024-05-04 05:37:14.224][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:37:14.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:37:14.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:14.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:14.228][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:37:14.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:37:14.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:14.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:14.233][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:37:14.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:37:14.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:14.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:37:14.238][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:37:14.239][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:37:14.240][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:37:14.246][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:37:14.247][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:37:14.248][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:37:14.249][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:37:14.251][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:37:14.252][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:37:14.253][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:37:14.259][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:37:14.260][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:37:14.261][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:37:14.262][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:37:14.263][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:37:14.265][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:37:14.266][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:37:14.272][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:37:14.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:37:14.274][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:37:14.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:37:14.277][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:37:14.278][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:37:14.279][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:37:14.285][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:37:14.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:37:14.287][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:37:14.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:37:14.290][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:37:14.291][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:37:14.292][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:37:14.297][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:37:14.299][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:37:14.300][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:37:14.301][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[2024-05-04 05:37:14.302][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:37:14.303][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:37:14.304][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:37:14.310][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:37:14.312][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:37:14.313][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:37:14.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:37:14.315][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:37:14.317][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:37:14.318][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:37:14.324][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:37:14.325][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:37:14.334][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:37:14.336][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:37:14.338][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.4*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-04 05:37:14.342][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-04 05:37:14.344][cch$loadFileContent] Trying to load 1 files from cache: [1]: "aaf802ce66e9d9898733b018b57315f1".
biodb.TRACE[2024-05-04 05:37:14.346][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-04 05:37:14.347][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aaf802ce66e9d9898733b018b57315f1.content".
biodb.DEBUG[2024-05-04 05:37:14.350][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:37:14.351][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:37:14.352][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:37:14.358][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:37:14.359][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:37:14.360][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:37:14.361][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[2024-05-04 05:37:14.363][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:37:14.364][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:37:14.365][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:37:14.371][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:37:14.372][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:37:14.373][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:37:14.374][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[2024-05-04 05:37:14.376][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:37:14.377][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:37:14.378][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:37:14.384][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:37:14.385][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:37:14.386][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:37:14.387][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.DEBUG[2024-05-04 05:37:14.389][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:37:14.390][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:37:14.391][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:37:14.397][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:37:14.398][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:37:14.399][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:37:14.400][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[2024-05-04 05:37:14.402][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:37:14.403][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:37:14.404][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:37:14.410][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:37:14.411][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:37:14.412][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:37:14.413][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[2024-05-04 05:37:14.414][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:37:14.416][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:37:14.417][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:37:14.423][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:37:14.424][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:37:14.425][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:37:14.426][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:37:14.428][private$bdb$entriesToDataframe] 1 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-04 05:37:14.430][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:37:14.431][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:37:14.432][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:37:14.437][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:37:14.439][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:37:14.440][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:37:14.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 05:37:14.442][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:37:14.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:37:14.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:14.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:14.447][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:37:14.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:37:14.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:14.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:14.452][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-04 05:37:14.453][private$selectFields]
biodb.TRACE[2024-05-04 05:37:14.454][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-04 05:37:14.455][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-04 05:37:14.457][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-04 05:37:14.458][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:37:14.459][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:37:14.460][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:14.461][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:14.463][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:37:14.464][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:37:14.465][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:14.466][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:14.468][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-04 05:37:14.469][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-04 05:37:14.470][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:37:14.472][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:37:14.473][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:14.474][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:14.475][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-04 05:37:14.477][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:37:14.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:37:14.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:14.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:14.481][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:37:14.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:37:14.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:14.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:14.486][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:37:14.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:37:14.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:14.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:14.491][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-05-04 05:37:14.493][private$entriesToListOfDataframes] Converted 1 entry/ies to data frame(s).
biodb.DEBUG[2024-05-04 05:37:14.494][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-05-04 05:37:14.504][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-05-04 05:37:14.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-05-04 05:37:14.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:14.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-04 05:37:14.513][biodb::testThat]
biodb.INFO [2024-05-04 05:37:14.514][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-05-04 05:37:14.515][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 05:37:14.517][biodb::testThat]
biodb.TRACE[2024-05-04 05:37:14.520][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-04 05:37:14.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-04 05:37:14.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:14.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:14.525][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:37:14.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:37:14.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:14.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:14.530][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:37:14.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:37:14.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:14.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:14.535][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:37:14.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:37:14.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:14.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:14.540][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:37:14.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:37:14.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:14.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:37:14.558][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:37:14.559][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:37:14.561][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:37:14.567][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:37:14.568][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:37:14.569][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:37:14.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:37:14.574][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-04 05:37:14.578][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-04 05:37:14.579][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-05-04 05:37:14.581][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-04 05:37:14.583][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-05-04 05:37:14.586][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:37:14.587][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:37:14.588][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:37:14.594][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:37:14.596][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:37:14.597][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:37:14.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:37:14.601][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-04 05:37:14.605][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-04 05:37:14.606][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-05-04 05:37:14.608][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-04 05:37:14.609][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-05-04 05:37:14.612][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:37:14.613][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:37:14.615][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:37:14.620][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:37:14.622][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:37:14.623][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:37:14.624][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 05:37:14.625][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:37:14.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:37:14.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:14.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:14.630][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:37:14.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:37:14.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:14.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:14.635][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 05:37:14.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:37:14.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:14.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:37:14.641][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:37:14.642][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:37:14.643][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:37:14.649][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:37:14.650][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:37:14.651][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:37:14.652][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:37:14.654][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:37:14.655][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:37:14.656][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:37:14.662][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:37:14.663][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:37:14.664][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:37:14.665][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:37:14.668][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-04 05:37:14.672][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-04 05:37:14.674][cch$loadFileContent] Trying to load 1 files from cache: [1]: "94c7655c8f372fb2982c15119402bcba".
biodb.TRACE[2024-05-04 05:37:14.675][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-04 05:37:14.677][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.content".
biodb.DEBUG[2024-05-04 05:37:14.680][private$bdb$entriesToDataframe] 1 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-04 05:37:14.682][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:37:14.683][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:37:14.684][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:37:14.690][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:37:14.691][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:37:14.693][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:37:14.694][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 05:37:14.695][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:37:14.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:37:14.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:14.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:14.700][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:37:14.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:37:14.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:14.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:14.705][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-04 05:37:14.706][private$selectFields]
biodb.TRACE[2024-05-04 05:37:14.708][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-04 05:37:14.709][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-04 05:37:14.710][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-04 05:37:14.711][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:37:14.713][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:37:14.714][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:14.715][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:14.716][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:37:14.718][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:37:14.719][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:14.720][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:14.721][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-04 05:37:14.723][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-04 05:37:14.724][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:37:14.725][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:37:14.726][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:14.728][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:14.729][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-04 05:37:14.730][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:37:14.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:37:14.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:14.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:14.735][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:37:14.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:37:14.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:14.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:14.741][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:37:14.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:37:14.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:14.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:14.746][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-05-04 05:37:14.748][private$entriesToListOfDataframes] Converted 1 entry/ies to data frame(s).
biodb.DEBUG[2024-05-04 05:37:14.749][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-05-04 05:37:14.773][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:37:14.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:37:14.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:14.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:14.787][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:37:14.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:37:14.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:14.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:14.792][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:37:14.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:37:14.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:14.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:14.797][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:37:14.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:37:14.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:14.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:37:14.807][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:37:14.808][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:37:14.809][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:37:14.816][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:37:14.817][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:37:14.818][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:37:14.820][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:37:14.823][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-04 05:37:14.827][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-04 05:37:14.829][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-05-04 05:37:14.831][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-04 05:37:14.832][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-05-04 05:37:14.836][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-04 05:37:14.840][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-04 05:37:14.842][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-05-04 05:37:14.844][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-04 05:37:14.845][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-05-04 05:37:14.849][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:37:14.850][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:37:14.851][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:37:14.857][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:37:14.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:37:14.860][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:37:14.861][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.DEBUG[2024-05-04 05:37:14.863][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:37:14.864][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:37:14.865][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:37:14.871][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:37:14.873][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:37:14.874][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:37:14.875][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.TRACE[2024-05-04 05:37:14.877][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:37:14.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:37:14.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:14.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:14.882][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:37:14.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:37:14.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:14.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:14.887][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:37:14.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:37:14.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:14.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:37:14.892][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:37:14.893][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:37:14.895][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:37:14.901][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:37:14.902][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:37:14.904][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:37:14.905][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[2024-05-04 05:37:14.906][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:37:14.908][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:37:14.909][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:37:14.915][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:37:14.917][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:37:14.918][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:37:14.919][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:37:14.921][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:37:14.922][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:37:14.923][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:37:14.929][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:37:14.930][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:37:14.931][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:37:14.933][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:37:14.934][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:37:14.935][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:37:14.936][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:37:14.942][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:37:14.944][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:37:14.945][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:37:14.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:37:14.947][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:37:14.949][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:37:14.950][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:37:14.956][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:37:14.957][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:37:14.958][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:37:14.959][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:37:14.961][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:37:14.962][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:37:14.963][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:37:14.969][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:37:14.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:37:14.972][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:37:14.973][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.DEBUG[2024-05-04 05:37:14.975][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:37:14.976][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:37:14.977][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:37:14.983][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:37:14.985][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:37:14.986][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:37:14.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:37:14.990][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.4*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-04 05:37:14.994][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-04 05:37:14.996][cch$loadFileContent] Trying to load 1 files from cache: [1]: "aaf802ce66e9d9898733b018b57315f1".
biodb.TRACE[2024-05-04 05:37:14.998][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-04 05:37:15.000][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aaf802ce66e9d9898733b018b57315f1.content".
biodb.DEBUG[2024-05-04 05:37:15.003][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:37:15.004][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:37:15.005][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:37:15.012][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:37:15.020][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:37:15.022][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:37:15.023][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[2024-05-04 05:37:15.025][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:37:15.026][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:37:15.027][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:37:15.033][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:37:15.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:37:15.035][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:37:15.037][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:37:15.038][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:37:15.039][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:37:15.040][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:37:15.046][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:37:15.047][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:37:15.049][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:37:15.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:37:15.051][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:37:15.052][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:37:15.053][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:37:15.059][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:37:15.061][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:37:15.062][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:37:15.063][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:37:15.064][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:37:15.065][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:37:15.066][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:37:15.072][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:37:15.074][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:37:15.075][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:37:15.076][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:37:15.078][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:37:15.079][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:37:15.080][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:37:15.086][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:37:15.088][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:37:15.089][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:37:15.090][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:37:15.093][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.41*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-04 05:37:15.097][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-04 05:37:15.099][cch$loadFileContent] Trying to load 1 files from cache: [1]: "6fb67f2addef198a43a9c7e2c87e0df9".
biodb.TRACE[2024-05-04 05:37:15.101][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-04 05:37:15.103][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/6fb67f2addef198a43a9c7e2c87e0df9.content".
biodb.DEBUG[2024-05-04 05:37:15.106][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:37:15.107][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:37:15.108][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:37:15.114][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:37:15.116][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:37:15.117][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:37:15.118][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:37:15.120][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:37:15.121][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:37:15.122][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:37:15.128][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:37:15.129][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:37:15.130][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:37:15.132][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".
biodb.DEBUG[2024-05-04 05:37:15.133][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:37:15.134][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:37:15.135][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:37:15.141][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:37:15.143][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:37:15.144][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:37:15.145][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:37:15.147][private$bdb$entriesToDataframe] 1 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-04 05:37:15.149][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:37:15.150][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:37:15.151][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:37:15.157][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:37:15.159][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:37:15.160][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:37:15.161][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 05:37:15.163][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:37:15.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:37:15.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:15.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:15.168][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:37:15.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:37:15.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:15.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:15.173][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-04 05:37:15.174][private$selectFields]
biodb.TRACE[2024-05-04 05:37:15.175][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-04 05:37:15.176][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-04 05:37:15.178][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-04 05:37:15.179][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:37:15.180][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:37:15.182][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:15.183][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:15.184][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:37:15.185][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:37:15.187][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:15.188][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:15.189][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-04 05:37:15.190][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-04 05:37:15.192][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:37:15.193][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:37:15.194][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:15.196][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:15.197][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-04 05:37:15.198][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:37:15.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:37:15.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:15.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:15.204][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:37:15.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:37:15.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:15.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:15.209][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:37:15.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:37:15.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:15.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:15.214][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-05-04 05:37:15.215][private$entriesToListOfDataframes] Converted 1 entry/ies to data frame(s).
biodb.DEBUG[2024-05-04 05:37:15.217][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-05-04 05:37:15.241][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-05-04 05:37:15.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-05-04 05:37:15.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:15.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-04 05:37:15.260][biodb::testThat]
biodb.INFO [2024-05-04 05:37:15.261][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2024-05-04 05:37:15.263][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 05:37:15.264][biodb::testThat]
biodb.DEBUG[2024-05-04 05:37:15.267][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-05-04 05:37:15.268][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-04 05:37:15.270][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-05-04 05:37:15.272][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-04 05:37:15.273][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-04 05:37:15.275][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-04 05:37:15.277][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-04 05:37:15.278][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-04 05:37:15.280][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-04 05:37:15.283][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:37:15.284][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:37:15.286][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:37:15.292][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:37:15.293][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:37:15.295][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:37:15.296][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:37:15.298][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2024-05-04 05:37:15.301][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 05:37:15.303][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 05:37:15.305][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2024-05-04 05:37:16.409][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2024-05-04 05:37:17.533][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-04 05:37:17.536][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2024-05-04 05:37:17.540][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2024-05-04 05:37:17.543][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2024-05-04 05:37:17.545][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-04 05:37:17.546][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-04 05:37:17.548][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-04 05:37:17.550][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:37:17.551][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:37:17.552][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:37:17.558][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:37:17.559][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:37:17.560][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:37:17.562][FUN] Functions in observer BiodbConfig: [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[2024-05-04 05:37:17.564][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:37:17.566][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:37:17.567][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:17.568][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:17.570][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:37:17.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:37:17.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:17.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:17.575][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-04 05:37:17.576][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-04 05:37:17.578][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:17.579][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:17.580][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 05:37:17.582][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 05:37:17.583][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:17.584][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:17.586][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 05:37:17.587][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 05:37:17.588][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:17.590][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:17.591][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 05:37:17.592][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 05:37:17.594][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:17.595][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:17.596][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:37:17.598][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:37:17.599][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:17.600][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:17.602][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-04 05:37:17.603][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:37:17.604][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:17.606][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:17.607][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:37:17.608][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:37:17.610][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:17.611][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:17.612][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 05:37:17.614][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 05:37:17.615][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:17.616][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:17.618][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-04 05:37:17.619][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-04 05:37:17.620][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:17.622][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:17.623][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-04 05:37:17.625][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-04 05:37:17.626][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:17.627][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:17.628][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:37:17.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:37:17.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:17.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:17.634][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:37:17.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:37:17.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:17.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:17.639][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:37:17.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:37:17.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:17.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:17.644][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:37:17.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:37:17.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:17.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:17.649][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:37:17.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:37:17.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:17.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:17.654][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:37:17.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:37:17.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:17.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:17.659][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:37:17.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:37:17.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:17.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:17.664][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:37:17.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:37:17.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:17.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:17.669][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:37:17.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:37:17.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:17.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:37:17.675][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:37:17.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:37:17.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:37:17.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:37:17.680][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-05-04 05:37:17.681][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-05-04 05:37:17.691][biodb::testThat]
biodb.INFO [2024-05-04 05:37:17.692][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-05-04 05:37:17.694][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 05:37:17.695][biodb::testThat]
biodb.DEBUG[2024-05-04 05:37:17.721][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2024-05-04 05:37:17.722][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2024-05-04 05:37:17.724][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2024-05-04 05:37:17.726][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2024-05-04 05:37:17.727][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2024-05-04 05:37:17.729][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-04 05:37:17.730][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-04 05:37:17.731][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-04 05:37:17.733][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-04 05:37:17.734][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-04 05:37:17.739][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:37:17.740][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:37:17.741][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:37:17.747][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:37:17.749][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:37:17.750][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:37:17.751][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.DEBUG[2024-05-04 05:37:17.752][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2024-05-04 05:37:17.756][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 05:37:17.757][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 05:37:17.759][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2024-05-04 05:37:18.847][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2024-05-04 05:37:20.921][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-04 05:37:20.924][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2024-05-04 05:37:20.928][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2024-05-04 05:37:20.930][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:37:20.931][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:37:20.933][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:37:20.939][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:37:20.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:37:20.942][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:37:20.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:37:20.944][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.DEBUG[2024-05-04 05:37:20.948][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 05:37:20.950][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 05:37:20.952][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.TRACE[2024-05-04 05:37:32.073][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
biodb.DEBUG[2024-05-04 05:37:43.150][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-04 05:37:43.153][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.content"
biodb.TRACE[2024-05-04 05:37:43.157][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.request"
biodb.DEBUG[2024-05-04 05:37:43.159][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:37:43.160][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:37:43.162][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:37:43.167][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:37:43.169][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:37:43.170][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:37:43.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:37:43.172][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2024-05-04 05:37:43.176][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 05:37:43.177][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 05:37:43.179][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2024-05-04 05:37:54.292][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2024-05-04 05:38:05.366][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-04 05:38:05.369][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2024-05-04 05:38:05.373][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2024-05-04 05:38:05.376][private$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[2024-05-04 05:38:05.378][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-04 05:38:05.379][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2024-05-04 05:38:05.381][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2024-05-04 05:38:05.383][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:38:05.384][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:05.385][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:05.391][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:05.392][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:05.393][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:05.394][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 05:38:05.397][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:38:05.398][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:38:05.400][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:05.401][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:05.402][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:38:05.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:38:05.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:05.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:05.407][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-04 05:38:05.409][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-04 05:38:05.410][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:05.411][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:05.413][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 05:38:05.414][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 05:38:05.415][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:05.416][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:05.418][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 05:38:05.419][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 05:38:05.420][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:05.422][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:05.423][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 05:38:05.425][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 05:38:05.426][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:05.427][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:05.428][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:38:05.430][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:38:05.431][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:05.432][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:05.434][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-04 05:38:05.435][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:38:05.436][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:05.437][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:05.439][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:38:05.440][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:38:05.441][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:05.443][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:05.444][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 05:38:05.445][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 05:38:05.447][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:05.448][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:05.450][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-04 05:38:05.451][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-04 05:38:05.452][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:05.453][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:05.455][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-04 05:38:05.456][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-04 05:38:05.457][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:05.459][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:05.460][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:38:05.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:38:05.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:05.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:05.482][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:38:05.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:38:05.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:05.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:05.487][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:38:05.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:38:05.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:05.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:05.493][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:38:05.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:38:05.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:05.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:05.497][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:38:05.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:38:05.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:05.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:05.502][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:38:05.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:38:05.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:05.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:05.507][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:38:05.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:38:05.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:05.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:38:05.512][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:38:05.514][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:05.515][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:05.520][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:05.522][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:05.523][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:05.524][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 05:38:05.527][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:38:05.528][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:38:05.529][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:05.531][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:05.532][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:38:05.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:38:05.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:05.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:05.537][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-04 05:38:05.538][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-04 05:38:05.540][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:05.541][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:05.542][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 05:38:05.544][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 05:38:05.545][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:05.546][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:05.548][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 05:38:05.549][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 05:38:05.550][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:05.551][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:05.553][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 05:38:05.554][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 05:38:05.555][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:05.556][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:05.558][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:38:05.559][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:38:05.560][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:05.561][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:05.563][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-04 05:38:05.564][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:38:05.565][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:05.567][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:05.568][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:38:05.569][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:38:05.570][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:05.572][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:05.573][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 05:38:05.574][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 05:38:05.576][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:05.577][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:05.578][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-04 05:38:05.580][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-04 05:38:05.581][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:05.582][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:05.584][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-04 05:38:05.585][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-04 05:38:05.586][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:05.587][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:05.589][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:38:05.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:38:05.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:05.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:05.594][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:38:05.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:38:05.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:05.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:05.599][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:38:05.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:38:05.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:05.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:05.604][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:38:05.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:38:05.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:05.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:05.609][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:38:05.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:38:05.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:05.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:05.614][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:38:05.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:38:05.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:05.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:05.619][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:38:05.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:38:05.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:05.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:38:05.624][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:38:05.625][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:05.626][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:05.632][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:05.633][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:05.634][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:05.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 05:38:05.638][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:38:05.640][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:38:05.641][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:05.642][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:05.644][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:38:05.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:38:05.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:05.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:05.649][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-04 05:38:05.650][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-04 05:38:05.651][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:05.653][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:05.654][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 05:38:05.656][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 05:38:05.657][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:05.658][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:05.660][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 05:38:05.661][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 05:38:05.662][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:05.663][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:05.665][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 05:38:05.666][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 05:38:05.667][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:05.668][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:05.670][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:38:05.671][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:38:05.672][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:05.674][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:05.675][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-04 05:38:05.676][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:38:05.678][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:05.679][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:05.680][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:38:05.681][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:38:05.683][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:05.684][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:05.685][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 05:38:05.694][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 05:38:05.696][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:05.697][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:05.699][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-04 05:38:05.701][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-04 05:38:05.702][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:05.703][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:05.704][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-04 05:38:05.706][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-04 05:38:05.707][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:05.708][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:05.709][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:38:05.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:38:05.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:05.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:05.714][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:38:05.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:38:05.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:05.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:05.719][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:38:05.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:38:05.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:05.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:05.724][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:38:05.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:38:05.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:05.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:05.729][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:38:05.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:38:05.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:05.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:05.734][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:38:05.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:38:05.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:05.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:05.738][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:38:05.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:38:05.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:05.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:05.743][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:38:05.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:38:05.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:05.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:05.748][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:38:05.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:38:05.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:05.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:05.753][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:38:05.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:38:05.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:05.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:05.758][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:38:05.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:38:05.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:05.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:05.763][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:38:05.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:38:05.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:05.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:05.769][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:38:05.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:38:05.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:05.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:05.774][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:38:05.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:38:05.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:05.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:05.779][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:38:05.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:38:05.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:05.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:05.784][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:38:05.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:38:05.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:05.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:38:05.788][self$createEntryFromContent] Accession numbers: , , .
biodb.DEBUG[2024-05-04 05:38:05.790][self$createEntryFromContent] Found 3 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-05-04 05:38:05.791][function(conn, opt)] Entries: [4]: "NULL, <environment>, NULL, NULL"
biodb.INFO [2024-05-04 05:38:05.990][biodb::testThat]
biodb.INFO [2024-05-04 05:38:05.991][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2024-05-04 05:38:05.993][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 05:38:05.994][biodb::testThat]
biodb.INFO [2024-05-04 05:38:06.050][biodb::testThat]
biodb.INFO [2024-05-04 05:38:06.052][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2024-05-04 05:38:06.053][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 05:38:06.054][biodb::testThat]
biodb.INFO [2024-05-04 05:38:06.065][biodb::testThat]
biodb.INFO [2024-05-04 05:38:06.066][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2024-05-04 05:38:06.067][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 05:38:06.068][biodb::testThat]
biodb.DEBUG[2024-05-04 05:38:06.071][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1*&searchCategory=CHEBI ID&maximumResults=100&starsCategory=ALL".
biodb.DEBUG[2024-05-04 05:38:06.076][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 05:38:06.077][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 05:38:06.079][private$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[2024-05-04 05:38:07.262][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[2024-05-04 05:38:08.991][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-04 05:38:08.994][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2024-05-04 05:38:08.999][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2024-05-04 05:38:09.028][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 05:38:09.030][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 05:38:09.032][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:09.033][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:09.035][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:38:09.037][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:38:09.038][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:09.040][ef$get] fields variable is a list.
biodb.INFO [2024-05-04 05:38:09.042][biodb::testThat]
biodb.INFO [2024-05-04 05:38:09.043][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. ").
biodb.INFO [2024-05-04 05:38:09.045][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 05:38:09.046][biodb::testThat]
biodb.ERROR[2024-05-04 05:38:09.065][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-05-04 05:38:09.089][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-05-04 05:38:09.108][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-04 05:38:09.110][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-05-04 05:38:09.112][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-05-04 05:38:09.113][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-04 05:38:09.114][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:09.116][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:09.117][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:09.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:09.119][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:09.120][FUN] Functions in observer BiodbConfig: [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 [2024-05-04 05:38:09.133][biodb::testContext]
biodb.INFO [2024-05-04 05:38:09.134][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-04 05:38:09.136][biodb::testContext] Test context - Test conversions
biodb.INFO [2024-05-04 05:38:09.137][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-04 05:38:09.138][biodb::testContext]
biodb.INFO [2024-05-04 05:38:09.140][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-05-04 05:38:09.143][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-05-04 05:38:09.147][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-04 05:38:09.149][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-04 05:38:09.150][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-04 05:38:09.151][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:09.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:09.153][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:09.154][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-04 05:38:09.156][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-04 05:38:09.157][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:09.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:09.159][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[2024-05-04 05:38:09.160][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-04 05:38:09.162][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-04 05:38:09.163][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:09.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:09.165][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:09.166][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-04 05:38:09.168][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-04 05:38:09.169][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-04 05:38:09.170][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:09.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:09.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:09.173][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-04 05:38:09.175][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-04 05:38:09.176][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-04 05:38:09.177][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:09.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:09.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:09.181][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-04 05:38:09.182][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-04 05:38:09.183][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:09.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:09.186][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.DEBUG[2024-05-04 05:38:09.187][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-04 05:38:09.189][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-04 05:38:09.190][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-04 05:38:09.191][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:09.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:09.193][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:09.416][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-04 05:38:09.418][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-04 05:38:09.419][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:09.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:09.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:09.422][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-04 05:38:09.424][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-04 05:38:09.425][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-04 05:38:09.426][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:09.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:09.428][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:09.429][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-04 05:38:09.430][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-04 05:38:09.432][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-04 05:38:09.433][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-04 05:38:09.434][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-04 05:38:09.435][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-04 05:38:09.436][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:09.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:09.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:09.440][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-04 05:38:09.441][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-04 05:38:09.442][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:09.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:09.444][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:09.445][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-04 05:38:09.447][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-04 05:38:09.448][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:09.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:09.450][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:09.451][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-04 05:38:09.452][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-04 05:38:09.453][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:09.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:09.455][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:09.457][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-04 05:38:09.458][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-04 05:38:09.459][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:09.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:09.461][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[2024-05-04 05:38:09.462][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-04 05:38:09.464][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-04 05:38:09.465][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:09.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:09.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:09.468][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-04 05:38:09.469][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-04 05:38:09.474][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-04 05:38:09.475][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:09.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:09.477][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:09.479][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-04 05:38:09.480][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-04 05:38:09.481][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-04 05:38:09.482][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:09.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:09.485][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:09.486][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-04 05:38:09.488][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-04 05:38:09.490][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-05-04 05:38:09.491][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 05:38:09.493][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 05:38:09.494][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 05:38:09.495][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 05:38:09.496][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-04 05:38:09.498][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 05:38:09.499][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-04 05:38:09.500][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 05:38:09.501][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-04 05:38:09.503][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-04 05:38:09.504][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 05:38:09.505][self$setPropertyValue]
biodb.DEBUG[2024-05-04 05:38:09.506][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-04 05:38:09.508][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-04 05:38:09.508][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-04 05:38:09.508][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-04 05:38:09.508][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-04 05:38:09.508][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-04 05:38:09.509][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-04 05:38:09.510][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 05:38:09.511][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 05:38:09.512][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 05:38:09.514][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 05:38:09.515][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 05:38:09.516][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 05:38:09.517][self$setPropertyValue]
biodb.DEBUG[2024-05-04 05:38:09.518][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 05:38:09.520][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 05:38:09.521][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-04 05:38:09.522][self$setPropertyValue]
biodb.DEBUG[2024-05-04 05:38:09.523][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-04 05:38:09.526][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-04 05:38:09.527][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-04 05:38:09.528][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 05:38:09.530][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 05:38:09.531][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 05:38:09.532][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 05:38:09.534][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-04 05:38:09.535][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 05:38:09.536][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-04 05:38:09.537][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 05:38:09.538][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-04 05:38:09.540][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-04 05:38:09.541][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 05:38:09.542][self$setPropertyValue]
biodb.DEBUG[2024-05-04 05:38:09.543][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-04 05:38:09.545][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-04 05:38:09.545][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-04 05:38:09.545][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-04 05:38:09.545][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-04 05:38:09.545][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-04 05:38:09.546][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-04 05:38:09.548][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 05:38:09.549][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 05:38:09.550][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 05:38:09.551][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 05:38:09.552][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 05:38:09.553][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 05:38:09.555][self$setPropertyValue]
biodb.DEBUG[2024-05-04 05:38:09.556][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 05:38:09.557][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 05:38:09.558][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-04 05:38:09.559][self$setPropertyValue]
biodb.DEBUG[2024-05-04 05:38:09.561][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-04 05:38:09.563][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-04 05:38:09.564][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-05-04 05:38:09.566][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 05:38:09.567][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 05:38:09.568][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 05:38:09.569][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 05:38:09.571][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-04 05:38:09.572][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 05:38:09.573][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-04 05:38:09.574][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 05:38:09.576][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-04 05:38:09.577][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-04 05:38:09.578][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 05:38:09.579][self$setPropertyValue]
biodb.DEBUG[2024-05-04 05:38:09.580][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-04 05:38:09.582][self$setPropertyValue]
biodb.DEBUG[2024-05-04 05:38:09.583][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-04 05:38:09.584][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 05:38:09.585][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 05:38:09.587][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 05:38:09.588][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 05:38:09.589][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 05:38:09.590][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 05:38:09.592][self$setPropertyValue]
biodb.DEBUG[2024-05-04 05:38:09.593][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 05:38:09.594][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 05:38:09.596][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-04 05:38:09.597][self$setPropertyValue]
biodb.DEBUG[2024-05-04 05:38:09.598][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-04 05:38:09.601][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-04 05:38:09.602][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-04 05:38:09.603][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 05:38:09.605][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 05:38:09.606][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 05:38:09.607][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 05:38:09.608][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-04 05:38:09.609][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 05:38:09.610][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-04 05:38:09.612][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 05:38:09.613][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-04 05:38:09.614][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-04 05:38:09.615][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 05:38:09.616][self$setPropertyValue]
biodb.DEBUG[2024-05-04 05:38:09.617][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-04 05:38:09.618][self$setPropertyValue]
biodb.DEBUG[2024-05-04 05:38:09.620][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-04 05:38:09.621][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 05:38:09.622][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 05:38:09.623][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 05:38:09.624][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 05:38:09.625][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 05:38:09.626][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 05:38:09.628][self$setPropertyValue]
biodb.DEBUG[2024-05-04 05:38:09.629][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 05:38:09.630][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 05:38:09.632][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-04 05:38:09.633][self$setPropertyValue]
biodb.DEBUG[2024-05-04 05:38:09.635][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-04 05:38:09.636][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:09.637][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:09.638][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:09.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:09.641][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:09.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:09.643][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:09.644][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:09.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:09.647][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:09.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:09.649][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[2024-05-04 05:38:09.650][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:09.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:09.653][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:09.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:09.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:09.657][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:09.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:09.659][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:09.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:09.661][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[2024-05-04 05:38:09.662][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:09.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:09.665][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:09.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:09.667][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[2024-05-04 05:38:09.668][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:09.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:09.671][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:09.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:09.673][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[2024-05-04 05:38:09.674][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:09.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:09.677][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:09.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:09.679][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[2024-05-04 05:38:09.680][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:09.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:09.683][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:09.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:09.685][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[2024-05-04 05:38:09.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:09.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:09.689][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:09.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:09.691][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[2024-05-04 05:38:09.692][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:09.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:09.694][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:09.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:09.697][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[2024-05-04 05:38:09.698][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:09.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:09.700][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:09.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:09.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:09.704][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:09.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:09.706][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:09.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:09.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:09.710][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:09.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:09.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:09.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:09.715][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:09.716][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:09.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:09.719][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:09.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:09.721][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:09.722][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:09.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:09.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:09.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:09.727][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[2024-05-04 05:38:09.728][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:09.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:09.731][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:09.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:09.734][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:09.735][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:09.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:09.737][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:09.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:09.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:09.741][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-04 05:38:09.743][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-04 05:38:09.745][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-04 05:38:09.747][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-04 05:38:09.749][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-04 05:38:09.751][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-04 05:38:09.753][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-04 05:38:09.754][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-04 05:38:09.756][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-04 05:38:09.758][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-04 05:38:09.760][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-04 05:38:09.762][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-04 05:38:09.764][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-04 05:38:09.766][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-04 05:38:09.768][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-04 05:38:09.770][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-04 05:38:09.772][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-04 05:38:09.774][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-04 05:38:09.776][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-04 05:38:09.777][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-04 05:38:09.779][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-04 05:38:09.781][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-04 05:38:09.783][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-04 05:38:09.785][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-04 05:38:09.787][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-04 05:38:09.789][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-04 05:38:09.791][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-04 05:38:09.793][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-04 05:38:09.795][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-04 05:38:09.797][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-04 05:38:09.799][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-04 05:38:09.801][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-04 05:38:09.803][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-04 05:38:09.805][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-04 05:38:09.807][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-04 05:38:09.809][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-04 05:38:09.811][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-04 05:38:09.813][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-04 05:38:09.814][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-04 05:38:09.816][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-04 05:38:09.818][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-04 05:38:09.820][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-04 05:38:09.822][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-04 05:38:09.824][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-04 05:38:09.826][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-04 05:38:09.828][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-04 05:38:09.830][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-04 05:38:09.832][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-04 05:38:09.834][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-04 05:38:09.836][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-04 05:38:09.838][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-04 05:38:09.840][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-04 05:38:09.842][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-04 05:38:09.844][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-04 05:38:09.846][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-04 05:38:09.848][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-04 05:38:09.850][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-04 05:38:09.852][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-04 05:38:09.854][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-04 05:38:09.855][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-04 05:38:09.857][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-04 05:38:09.859][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-04 05:38:09.861][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-04 05:38:09.863][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-04 05:38:09.865][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-04 05:38:09.867][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-04 05:38:09.869][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-04 05:38:09.871][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-04 05:38:09.873][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-04 05:38:09.875][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-04 05:38:09.877][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-04 05:38:09.879][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-04 05:38:09.881][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-04 05:38:09.882][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-04 05:38:09.884][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-04 05:38:09.886][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-04 05:38:09.888][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-04 05:38:09.890][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-04 05:38:09.892][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-04 05:38:09.894][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-04 05:38:09.896][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-04 05:38:09.898][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-04 05:38:09.900][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-04 05:38:09.902][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-04 05:38:09.904][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-05-04 05:38:09.905][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-04 05:38:09.907][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:09.908][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:09.909][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:09.917][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:09.919][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:09.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:09.921][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:09.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:09.923][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:09.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:09.925][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:09.926][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:09.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:09.929][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:09.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:09.931][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:09.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:09.934][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:09.935][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:09.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:09.937][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:09.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:09.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:09.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:09.941][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:09.942][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:09.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:09.945][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:09.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:09.947][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:09.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:09.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:09.950][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:09.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:09.952][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:09.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:09.955][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:09.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:09.957][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:09.958][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:09.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:09.960][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:09.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:09.962][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:09.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:09.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:09.966][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:09.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:09.968][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:09.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:09.970][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:09.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:09.972][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:09.974][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:09.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:09.976][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:09.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:09.978][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:09.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:09.980][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:09.981][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:09.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:09.984][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:09.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:09.986][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:09.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:09.988][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:09.989][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:09.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:09.991][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:09.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:09.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:09.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:09.996][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:09.997][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:09.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:09.999][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:10.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:10.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:10.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:10.004][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.DEBUG[2024-05-04 05:38:10.005][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:10.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:10.008][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:10.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:10.010][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:10.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:10.012][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.DEBUG[2024-05-04 05:38:10.014][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:10.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:10.016][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:10.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:10.018][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:10.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:10.020][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:10.022][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:10.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:10.024][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:10.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:10.026][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:10.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:10.028][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:10.029][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:10.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:10.032][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:10.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:10.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:10.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:10.036][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[2024-05-04 05:38:10.037][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:10.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:10.040][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:10.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:10.042][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:10.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:10.044][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:10.045][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:10.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:10.047][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:10.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:10.050][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:10.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:10.052][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[2024-05-04 05:38:10.054][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-05-04 05:38:10.056][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-05-04 05:38:10.058][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-04 05:38:10.059][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-05-04 05:38:10.061][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 05:38:10.062][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 05:38:10.063][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 05:38:10.064][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 05:38:10.065][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-04 05:38:10.067][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-05-04 05:38:10.068][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-05-04 05:38:10.069][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 05:38:10.070][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-04 05:38:10.072][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-05-04 05:38:10.073][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 05:38:10.074][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-05-04 05:38:10.074][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-05-04 05:38:10.074][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-05-04 05:38:10.074][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-05-04 05:38:10.074][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-05-04 05:38:10.074][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-05-04 05:38:10.074][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-05-04 05:38:10.074][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-05-04 05:38:10.074][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-05-04 05:38:10.074][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-05-04 05:38:10.074][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-05-04 05:38:10.076][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-04 05:38:10.077][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-04 05:38:10.077][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-04 05:38:10.077][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-04 05:38:10.078][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-05-04 05:38:10.080][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 05:38:10.081][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 05:38:10.082][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 05:38:10.083][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 05:38:10.084][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 05:38:10.086][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 05:38:10.087][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-04 05:38:10.087][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-05-04 05:38:10.088][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 05:38:10.089][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 05:38:10.091][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-04 05:38:10.092][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-05-04 05:38:10.092][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-05-04 05:38:10.094][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-04 05:38:10.096][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-04 05:38:10.098][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-05-04 05:38:10.100][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-04 05:38:10.102][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-04 05:38:10.104][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-04 05:38:10.108][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-05-04 05:38:10.110][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-05-04 05:38:10.111][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-05-04 05:38:10.113][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-05-04 05:38:10.115][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-04 05:38:10.116][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-04 05:38:10.118][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-05-04 05:38:10.119][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-05-04 05:38:10.121][biodb::testThat]
biodb.INFO [2024-05-04 05:38:10.122][biodb::testThat] Running test function test_chebi_convCasToChebi (" convCasToChebi() works. ").
biodb.INFO [2024-05-04 05:38:10.123][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 05:38:10.124][biodb::testThat]
biodb.DEBUG[2024-05-04 05:38:10.129][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-05-04 05:38:10.133][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 05:38:10.135][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 05:38:10.137][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2024-05-04 05:38:11.222][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2024-05-04 05:38:12.563][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-04 05:38:12.566][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2024-05-04 05:38:12.570][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2024-05-04 05:38:12.575][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-05-04 05:38:12.580][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 05:38:12.581][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 05:38:12.583][private$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[2024-05-04 05:38:13.682][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[2024-05-04 05:38:14.770][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-04 05:38:14.773][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2024-05-04 05:38:14.778][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2024-05-04 05:38:14.780][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:38:14.782][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:14.783][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:14.789][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:14.790][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:14.792][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:14.793][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:14.795][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[2024-05-04 05:38:14.800][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 05:38:14.801][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 05:38:14.803][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-05-04 05:38:15.878][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-05-04 05:38:16.963][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-04 05:38:16.966][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2024-05-04 05:38:16.971][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request"
biodb.DEBUG[2024-05-04 05:38:16.973][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:38:16.975][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:16.976][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:16.981][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:16.983][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:16.984][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:16.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:17.008][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:38:17.009][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:17.010][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:17.016][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:17.017][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:17.018][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:17.019][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:17.025][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-05-04 05:38:17.029][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-04 05:38:17.031][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-05-04 05:38:17.032][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-04 05:38:17.034][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-05-04 05:38:17.036][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:38:17.037][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:17.038][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:17.044][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:17.045][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:17.046][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:17.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:17.049][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-05-04 05:38:17.054][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-04 05:38:17.055][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-05-04 05:38:17.057][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-04 05:38:17.059][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-05-04 05:38:17.061][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:38:17.062][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:17.063][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:17.069][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:17.071][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:17.072][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:17.073][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:17.074][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:38:17.075][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:17.077][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:17.082][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:17.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:17.085][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:17.086][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.DEBUG[2024-05-04 05:38:17.091][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-05-04 05:38:17.096][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-04 05:38:17.097][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-05-04 05:38:17.099][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-04 05:38:17.101][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-05-04 05:38:17.103][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:38:17.104][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:17.105][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:17.111][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:17.112][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:17.113][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:17.115][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:17.117][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-05-04 05:38:17.121][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-04 05:38:17.123][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-05-04 05:38:17.124][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-04 05:38:17.126][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-05-04 05:38:17.128][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:38:17.129][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:17.131][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:17.137][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:17.138][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:17.139][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:17.140][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:17.143][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-05-04 05:38:17.147][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 05:38:17.149][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 05:38:17.151][private$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[2024-05-04 05:38:18.278][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[2024-05-04 05:38:19.327][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-04 05:38:19.329][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2024-05-04 05:38:19.334][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2024-05-04 05:38:19.337][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:38:19.338][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:19.339][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:19.345][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:19.346][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:19.354][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:19.368][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.INFO [2024-05-04 05:38:19.376][biodb::testThat]
biodb.INFO [2024-05-04 05:38:19.377][biodb::testThat] Running test function test_chebi_convInchiToChebi (" convInchiToChebi() works. ").
biodb.INFO [2024-05-04 05:38:19.379][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 05:38:19.380][biodb::testThat]
biodb.DEBUG[2024-05-04 05:38:19.384][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[2024-05-04 05:38:19.388][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 05:38:19.389][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 05:38:19.392][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-05-04 05:38:20.471][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-05-04 05:38:21.753][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-04 05:38:21.756][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2024-05-04 05:38:21.762][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2024-05-04 05:38:21.765][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:38:21.766][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:21.768][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:21.774][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:21.776][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:21.777][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:21.779][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:21.785][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-05-04 05:38:21.790][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 05:38:21.791][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 05:38:21.794][private$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[2024-05-04 05:38:22.870][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[2024-05-04 05:38:24.023][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-04 05:38:24.026][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2024-05-04 05:38:24.031][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2024-05-04 05:38:24.033][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:38:24.035][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:24.036][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:24.041][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:24.043][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:24.044][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:24.045][FUN] Functions in observer BiodbConfig: [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 [2024-05-04 05:38:24.051][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-04 05:38:24.053][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-05-04 05:38:24.054][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-05-04 05:38:24.055][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-04 05:38:24.056][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:24.057][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:24.058][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:24.060][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:24.061][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:24.062][FUN] Functions in observer BiodbConfig: [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 [2024-05-04 05:38:24.066][biodb::testContext]
biodb.INFO [2024-05-04 05:38:24.068][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-04 05:38:24.069][biodb::testContext] Test context - Test web services
biodb.INFO [2024-05-04 05:38:24.070][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-04 05:38:24.071][biodb::testContext]
biodb.INFO [2024-05-04 05:38:24.074][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-05-04 05:38:24.076][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-05-04 05:38:24.080][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-04 05:38:24.082][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-04 05:38:24.083][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-04 05:38:24.084][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:24.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:24.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:24.088][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-04 05:38:24.089][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-04 05:38:24.090][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:24.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:24.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:24.094][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-04 05:38:24.096][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-04 05:38:24.097][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:24.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:24.099][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:24.101][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-04 05:38:24.102][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-04 05:38:24.104][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-04 05:38:24.105][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:24.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:24.108][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:24.110][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-04 05:38:24.111][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-04 05:38:24.112][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-04 05:38:24.113][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:24.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:24.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:24.117][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-04 05:38:24.118][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-04 05:38:24.119][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:24.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:24.122][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.DEBUG[2024-05-04 05:38:24.123][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-04 05:38:24.124][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-04 05:38:24.125][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-04 05:38:24.127][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:24.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:24.129][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:24.130][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-04 05:38:24.131][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-04 05:38:24.133][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:24.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:24.135][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:24.136][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-04 05:38:24.137][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-04 05:38:24.139][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-04 05:38:24.140][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:24.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:24.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:24.144][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-04 05:38:24.145][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-04 05:38:24.146][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-04 05:38:24.148][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-04 05:38:24.149][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-04 05:38:24.150][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-04 05:38:24.151][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:24.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:24.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:24.155][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-04 05:38:24.157][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-04 05:38:24.158][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:24.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:24.160][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:24.161][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-04 05:38:24.163][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-04 05:38:24.164][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:24.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:24.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:24.168][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-04 05:38:24.169][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-04 05:38:24.170][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:24.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:24.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:24.173][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-04 05:38:24.175][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-04 05:38:24.176][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:24.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:24.178][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:24.180][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-04 05:38:24.181][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-04 05:38:24.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:24.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:24.185][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:24.186][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-04 05:38:24.187][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-04 05:38:24.193][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-04 05:38:24.194][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:24.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:24.196][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:24.197][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-04 05:38:24.199][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-04 05:38:24.200][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-04 05:38:24.201][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:24.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:24.204][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:24.205][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-04 05:38:24.207][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-04 05:38:24.209][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-05-04 05:38:24.210][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 05:38:24.211][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 05:38:24.213][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 05:38:24.214][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 05:38:24.216][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-04 05:38:24.217][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 05:38:24.218][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-04 05:38:24.220][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 05:38:24.221][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-04 05:38:24.222][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-04 05:38:24.224][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 05:38:24.225][self$setPropertyValue]
biodb.DEBUG[2024-05-04 05:38:24.226][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-04 05:38:24.228][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-04 05:38:24.228][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-04 05:38:24.228][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-04 05:38:24.228][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-04 05:38:24.228][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-04 05:38:24.229][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-04 05:38:24.230][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 05:38:24.232][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 05:38:24.233][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 05:38:24.234][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 05:38:24.235][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 05:38:24.237][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 05:38:24.238][self$setPropertyValue]
biodb.DEBUG[2024-05-04 05:38:24.239][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 05:38:24.240][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 05:38:24.242][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-04 05:38:24.243][self$setPropertyValue]
biodb.DEBUG[2024-05-04 05:38:24.244][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-04 05:38:24.247][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-04 05:38:24.248][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-04 05:38:24.249][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 05:38:24.251][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 05:38:24.252][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 05:38:24.253][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 05:38:24.255][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-04 05:38:24.256][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 05:38:24.257][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-04 05:38:24.259][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 05:38:24.260][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-04 05:38:24.261][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-04 05:38:24.262][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 05:38:24.264][self$setPropertyValue]
biodb.DEBUG[2024-05-04 05:38:24.265][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-04 05:38:24.266][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-04 05:38:24.266][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-04 05:38:24.266][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-04 05:38:24.266][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-04 05:38:24.266][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-04 05:38:24.268][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-04 05:38:24.269][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 05:38:24.270][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 05:38:24.271][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 05:38:24.273][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 05:38:24.274][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 05:38:24.275][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 05:38:24.276][self$setPropertyValue]
biodb.DEBUG[2024-05-04 05:38:24.278][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 05:38:24.279][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 05:38:24.280][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-04 05:38:24.282][self$setPropertyValue]
biodb.DEBUG[2024-05-04 05:38:24.283][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-04 05:38:24.285][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-04 05:38:24.287][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-05-04 05:38:24.288][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 05:38:24.289][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 05:38:24.290][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 05:38:24.292][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 05:38:24.293][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-04 05:38:24.294][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 05:38:24.296][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-04 05:38:24.297][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 05:38:24.298][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-04 05:38:24.300][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-04 05:38:24.301][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 05:38:24.302][self$setPropertyValue]
biodb.DEBUG[2024-05-04 05:38:24.303][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-04 05:38:24.305][self$setPropertyValue]
biodb.DEBUG[2024-05-04 05:38:24.306][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-04 05:38:24.308][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 05:38:24.309][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 05:38:24.310][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 05:38:24.312][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 05:38:24.313][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 05:38:24.314][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 05:38:24.315][self$setPropertyValue]
biodb.DEBUG[2024-05-04 05:38:24.317][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 05:38:24.318][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 05:38:24.320][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-04 05:38:24.321][self$setPropertyValue]
biodb.DEBUG[2024-05-04 05:38:24.323][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-04 05:38:24.326][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-04 05:38:24.327][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-04 05:38:24.328][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 05:38:24.330][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 05:38:24.331][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 05:38:24.333][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 05:38:24.334][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-04 05:38:24.335][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 05:38:24.337][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-04 05:38:24.338][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 05:38:24.340][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-04 05:38:24.341][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-04 05:38:24.343][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 05:38:24.344][self$setPropertyValue]
biodb.DEBUG[2024-05-04 05:38:24.346][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-04 05:38:24.347][self$setPropertyValue]
biodb.DEBUG[2024-05-04 05:38:24.348][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-04 05:38:24.349][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 05:38:24.351][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 05:38:24.352][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 05:38:24.353][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 05:38:24.354][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 05:38:24.355][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 05:38:24.357][self$setPropertyValue]
biodb.DEBUG[2024-05-04 05:38:24.358][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 05:38:24.359][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 05:38:24.360][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-04 05:38:24.362][self$setPropertyValue]
biodb.DEBUG[2024-05-04 05:38:24.363][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-04 05:38:24.364][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:24.366][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.DEBUG[2024-05-04 05:38:24.367][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:24.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:24.369][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:24.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:24.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:24.372][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:24.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:24.375][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:24.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:24.377][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:24.378][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:24.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:24.380][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:24.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:24.382][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[2024-05-04 05:38:24.384][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:24.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:24.386][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:24.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:24.388][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.DEBUG[2024-05-04 05:38:24.389][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:24.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:24.392][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:24.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:24.394][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:24.395][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:24.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:24.397][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:24.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:24.400][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[2024-05-04 05:38:24.401][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:24.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:24.403][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:24.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:24.406][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[2024-05-04 05:38:24.407][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:24.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:24.409][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:24.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:24.411][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[2024-05-04 05:38:24.412][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:24.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:24.415][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:24.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:24.417][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:24.418][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:24.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:24.420][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:24.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:24.422][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:24.424][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:24.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:24.426][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:24.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:24.428][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[2024-05-04 05:38:24.429][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:24.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:24.432][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:24.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:24.434][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[2024-05-04 05:38:24.435][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:24.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:24.437][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:24.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:24.439][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[2024-05-04 05:38:24.440][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:24.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:24.443][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:24.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:24.445][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:24.446][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:24.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:24.448][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:24.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:24.451][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[2024-05-04 05:38:24.452][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:24.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:24.468][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:24.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:24.470][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[2024-05-04 05:38:24.471][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:24.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:24.473][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:24.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:24.475][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[2024-05-04 05:38:24.477][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-04 05:38:24.478][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-04 05:38:24.480][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-04 05:38:24.482][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-04 05:38:24.483][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-04 05:38:24.485][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-04 05:38:24.487][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-04 05:38:24.489][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-04 05:38:24.490][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-04 05:38:24.492][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-04 05:38:24.494][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-04 05:38:24.496][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-04 05:38:24.497][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-04 05:38:24.499][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-04 05:38:24.501][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-04 05:38:24.502][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-04 05:38:24.504][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-04 05:38:24.506][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-04 05:38:24.508][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-04 05:38:24.510][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-04 05:38:24.512][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-04 05:38:24.513][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-04 05:38:24.515][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-04 05:38:24.517][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-04 05:38:24.519][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-04 05:38:24.520][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-04 05:38:24.522][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-04 05:38:24.524][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-04 05:38:24.526][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-04 05:38:24.527][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-04 05:38:24.530][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-04 05:38:24.532][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-04 05:38:24.533][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-04 05:38:24.535][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-04 05:38:24.537][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-04 05:38:24.539][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-04 05:38:24.541][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-04 05:38:24.542][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-04 05:38:24.544][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-04 05:38:24.546][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-04 05:38:24.548][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-04 05:38:24.550][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-04 05:38:24.552][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-04 05:38:24.554][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-04 05:38:24.555][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-04 05:38:24.557][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-04 05:38:24.559][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-04 05:38:24.561][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-04 05:38:24.562][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-04 05:38:24.564][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-04 05:38:24.566][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-04 05:38:24.567][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-04 05:38:24.569][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-04 05:38:24.571][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-04 05:38:24.573][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-04 05:38:24.574][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-04 05:38:24.576][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-04 05:38:24.578][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-04 05:38:24.580][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-04 05:38:24.581][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-04 05:38:24.583][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-04 05:38:24.585][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-04 05:38:24.586][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-04 05:38:24.588][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-04 05:38:24.590][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-04 05:38:24.592][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-04 05:38:24.593][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-04 05:38:24.595][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-04 05:38:24.597][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-04 05:38:24.599][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-04 05:38:24.600][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-04 05:38:24.602][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-04 05:38:24.604][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-04 05:38:24.606][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-04 05:38:24.607][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-04 05:38:24.609][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-04 05:38:24.611][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-04 05:38:24.613][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-04 05:38:24.615][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-04 05:38:24.617][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-04 05:38:24.618][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-04 05:38:24.620][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-04 05:38:24.622][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-04 05:38:24.624][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-04 05:38:24.626][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-05-04 05:38:24.627][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-04 05:38:24.628][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:24.629][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:24.630][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:24.631][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:24.632][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:24.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:24.634][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:24.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:24.637][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:24.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:24.639][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[2024-05-04 05:38:24.640][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:24.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:24.642][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:24.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:24.645][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:24.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:24.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:24.648][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:24.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:24.650][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:24.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:24.652][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:24.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:24.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:24.656][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:24.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:24.658][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:24.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:24.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:24.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:24.662][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[2024-05-04 05:38:24.664][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:24.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:24.666][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:24.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:24.668][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:24.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:24.670][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:24.671][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:24.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:24.673][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:24.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:24.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:24.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:24.678][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[2024-05-04 05:38:24.679][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:24.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:24.681][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:24.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:24.683][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:24.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:24.685][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[2024-05-04 05:38:24.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:24.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:24.689][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:24.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:24.691][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:24.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:24.693][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:24.695][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:24.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:24.697][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:24.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:24.699][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:24.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:24.701][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:24.702][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:24.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:24.705][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:24.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:24.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:24.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:24.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:24.710][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:24.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:24.712][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:24.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:24.715][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:24.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:24.718][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.DEBUG[2024-05-04 05:38:24.719][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:24.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:24.722][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:24.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:24.724][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:24.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:24.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:24.727][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:24.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:24.730][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:24.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:24.732][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:24.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:24.734][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:24.735][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:24.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:24.737][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:24.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:24.740][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:24.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:24.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:24.743][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:24.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:24.745][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:24.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:24.748][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:24.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:24.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:24.751][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:24.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:24.753][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:24.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:24.755][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:24.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:24.758][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.DEBUG[2024-05-04 05:38:24.759][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:24.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:24.761][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:24.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:24.763][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:24.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:24.765][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:24.768][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-05-04 05:38:24.769][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-05-04 05:38:24.772][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-04 05:38:24.773][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-05-04 05:38:24.774][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 05:38:24.776][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 05:38:24.777][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 05:38:24.778][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 05:38:24.780][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-04 05:38:24.781][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-05-04 05:38:24.782][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-05-04 05:38:24.783][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 05:38:24.785][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-04 05:38:24.786][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-05-04 05:38:24.788][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 05:38:24.789][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-05-04 05:38:24.789][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-05-04 05:38:24.789][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-05-04 05:38:24.789][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-05-04 05:38:24.789][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-05-04 05:38:24.789][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-05-04 05:38:24.789][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-05-04 05:38:24.789][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-05-04 05:38:24.789][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-05-04 05:38:24.789][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-05-04 05:38:24.789][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-05-04 05:38:24.790][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-04 05:38:24.792][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-04 05:38:24.792][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-04 05:38:24.792][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-04 05:38:24.793][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-05-04 05:38:24.794][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 05:38:24.796][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 05:38:24.797][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 05:38:24.798][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 05:38:24.799][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 05:38:24.801][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 05:38:24.802][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-04 05:38:24.802][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-05-04 05:38:24.803][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 05:38:24.804][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 05:38:24.805][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-04 05:38:24.807][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-05-04 05:38:24.807][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-05-04 05:38:24.808][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-04 05:38:24.810][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-04 05:38:24.812][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-05-04 05:38:24.814][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-04 05:38:24.816][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-04 05:38:24.818][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-04 05:38:24.823][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-05-04 05:38:24.824][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-05-04 05:38:24.825][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-05-04 05:38:24.827][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-05-04 05:38:24.829][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-04 05:38:24.830][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-04 05:38:24.831][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-05-04 05:38:24.833][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-05-04 05:38:24.834][biodb::testThat]
biodb.INFO [2024-05-04 05:38:24.836][biodb::testThat] Running test function test.chebi.wsGetLiteEntity (" Web service getLiteEntity works fine. ").
biodb.INFO [2024-05-04 05:38:24.837][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 05:38:24.838][biodb::testThat]
biodb.DEBUG[2024-05-04 05:38:24.842][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-05-04 05:38:24.847][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-04 05:38:24.849][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-05-04 05:38:24.850][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-04 05:38:24.853][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-05-04 05:38:24.857][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[2024-05-04 05:38:24.861][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 05:38:24.862][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 05:38:24.864][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-05-04 05:38:25.942][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-05-04 05:38:27.051][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-04 05:38:27.054][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2024-05-04 05:38:27.059][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2024-05-04 05:38:27.069][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-04 05:38:27.071][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-05-04 05:38:27.073][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-05-04 05:38:27.074][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-04 05:38:27.075][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:27.076][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:27.078][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:27.079][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:27.080][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:27.081][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-05-04 05:38:27.086][biodb::testContext]
biodb.INFO [2024-05-04 05:38:27.088][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-04 05:38:27.089][biodb::testContext] Test context - Non regression tests
biodb.INFO [2024-05-04 05:38:27.090][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-04 05:38:27.092][biodb::testContext]
biodb.INFO [2024-05-04 05:38:27.094][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-05-04 05:38:27.097][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-05-04 05:38:27.102][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-04 05:38:27.103][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-04 05:38:27.105][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-04 05:38:27.106][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:27.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:27.109][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:27.110][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-04 05:38:27.112][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-04 05:38:27.113][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:27.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:27.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:27.117][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-04 05:38:27.119][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-04 05:38:27.120][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:27.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:27.123][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:27.125][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-04 05:38:27.126][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-04 05:38:27.128][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-04 05:38:27.129][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:27.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:27.131][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:27.133][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-04 05:38:27.134][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-04 05:38:27.136][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-04 05:38:27.149][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:27.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:27.153][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:27.154][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-04 05:38:27.155][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-04 05:38:27.157][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:27.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:27.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:27.161][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-04 05:38:27.162][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-04 05:38:27.164][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-04 05:38:27.165][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:27.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:27.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:27.169][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-04 05:38:27.170][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-04 05:38:27.172][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:27.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:27.174][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:27.176][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-04 05:38:27.177][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-04 05:38:27.179][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-04 05:38:27.180][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:27.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:27.182][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.DEBUG[2024-05-04 05:38:27.184][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-04 05:38:27.185][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-04 05:38:27.187][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-04 05:38:27.188][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-04 05:38:27.189][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-04 05:38:27.191][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-04 05:38:27.192][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:27.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:27.195][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:27.196][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-04 05:38:27.198][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-04 05:38:27.199][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:27.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:27.201][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:27.203][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-04 05:38:27.204][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-04 05:38:27.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:27.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:27.208][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:27.209][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-04 05:38:27.211][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-04 05:38:27.212][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:27.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:27.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:27.216][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-04 05:38:27.217][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-04 05:38:27.219][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:27.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:27.221][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:27.223][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-04 05:38:27.224][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-04 05:38:27.225][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:27.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:27.228][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:27.229][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-04 05:38:27.231][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-04 05:38:27.236][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-04 05:38:27.237][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:27.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:27.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:27.242][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-04 05:38:27.243][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-04 05:38:27.245][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-04 05:38:27.246][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:27.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:27.249][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:27.250][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-04 05:38:27.253][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-04 05:38:27.254][self$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[2024-05-04 05:38:27.255][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 05:38:27.256][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 05:38:27.258][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 05:38:27.259][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 05:38:27.260][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-04 05:38:27.262][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 05:38:27.263][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-04 05:38:27.264][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 05:38:27.266][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-04 05:38:27.267][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-04 05:38:27.268][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 05:38:27.270][self$setPropertyValue]
biodb.DEBUG[2024-05-04 05:38:27.271][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-04 05:38:27.272][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-04 05:38:27.272][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-04 05:38:27.272][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-04 05:38:27.272][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-04 05:38:27.272][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-04 05:38:27.274][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-04 05:38:27.275][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 05:38:27.276][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 05:38:27.277][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 05:38:27.278][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 05:38:27.280][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 05:38:27.281][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 05:38:27.282][self$setPropertyValue]
biodb.DEBUG[2024-05-04 05:38:27.283][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 05:38:27.285][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 05:38:27.286][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-04 05:38:27.287][self$setPropertyValue]
biodb.DEBUG[2024-05-04 05:38:27.289][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-04 05:38:27.291][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-04 05:38:27.292][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-04 05:38:27.293][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 05:38:27.295][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 05:38:27.296][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 05:38:27.297][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 05:38:27.299][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-04 05:38:27.300][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 05:38:27.301][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-04 05:38:27.303][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 05:38:27.304][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-04 05:38:27.306][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-04 05:38:27.307][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 05:38:27.309][self$setPropertyValue]
biodb.DEBUG[2024-05-04 05:38:27.310][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-04 05:38:27.311][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-04 05:38:27.311][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-04 05:38:27.311][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-04 05:38:27.311][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-04 05:38:27.311][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-04 05:38:27.313][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-04 05:38:27.314][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 05:38:27.316][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 05:38:27.317][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 05:38:27.318][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 05:38:27.319][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 05:38:27.321][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 05:38:27.322][self$setPropertyValue]
biodb.DEBUG[2024-05-04 05:38:27.323][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 05:38:27.324][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 05:38:27.326][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-04 05:38:27.327][self$setPropertyValue]
biodb.DEBUG[2024-05-04 05:38:27.328][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-04 05:38:27.331][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-04 05:38:27.332][self$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[2024-05-04 05:38:27.333][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 05:38:27.335][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 05:38:27.336][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 05:38:27.338][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 05:38:27.339][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-04 05:38:27.341][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 05:38:27.342][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-04 05:38:27.343][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 05:38:27.344][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-04 05:38:27.346][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-04 05:38:27.347][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 05:38:27.348][self$setPropertyValue]
biodb.DEBUG[2024-05-04 05:38:27.350][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-04 05:38:27.351][self$setPropertyValue]
biodb.DEBUG[2024-05-04 05:38:27.353][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-04 05:38:27.354][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 05:38:27.355][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 05:38:27.356][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 05:38:27.358][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 05:38:27.359][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 05:38:27.360][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 05:38:27.361][self$setPropertyValue]
biodb.DEBUG[2024-05-04 05:38:27.363][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 05:38:27.364][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 05:38:27.365][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-04 05:38:27.366][self$setPropertyValue]
biodb.DEBUG[2024-05-04 05:38:27.368][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-04 05:38:27.370][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-04 05:38:27.372][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-04 05:38:27.373][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 05:38:27.374][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 05:38:27.376][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 05:38:27.377][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 05:38:27.378][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-04 05:38:27.380][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 05:38:27.381][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-04 05:38:27.382][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 05:38:27.384][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-04 05:38:27.385][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-04 05:38:27.386][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 05:38:27.388][self$setPropertyValue]
biodb.DEBUG[2024-05-04 05:38:27.389][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-04 05:38:27.390][self$setPropertyValue]
biodb.DEBUG[2024-05-04 05:38:27.392][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-04 05:38:27.393][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 05:38:27.394][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 05:38:27.395][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 05:38:27.397][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 05:38:27.398][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 05:38:27.399][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 05:38:27.400][self$setPropertyValue]
biodb.DEBUG[2024-05-04 05:38:27.402][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 05:38:27.403][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 05:38:27.404][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-04 05:38:27.405][self$setPropertyValue]
biodb.DEBUG[2024-05-04 05:38:27.407][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-04 05:38:27.408][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:27.409][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:27.410][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:27.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:27.413][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:27.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:27.415][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[2024-05-04 05:38:27.416][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:27.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:27.419][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:27.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:27.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:27.422][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:27.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:27.424][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:27.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:27.427][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[2024-05-04 05:38:27.428][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:27.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:27.430][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:27.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:27.433][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:27.434][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:27.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:27.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:27.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:27.439][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[2024-05-04 05:38:27.440][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:27.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:27.442][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:27.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:27.444][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[2024-05-04 05:38:27.446][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:27.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:27.448][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:27.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:27.450][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:27.452][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:27.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:27.454][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:27.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:27.456][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[2024-05-04 05:38:27.457][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:27.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:27.460][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:27.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:27.462][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.DEBUG[2024-05-04 05:38:27.463][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:27.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:27.465][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:27.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:27.468][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:27.469][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:27.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:27.471][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:27.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:27.474][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:27.475][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:27.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:27.477][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:27.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:27.479][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[2024-05-04 05:38:27.481][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:27.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:27.483][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:27.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:27.485][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:27.486][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:27.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:27.489][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:27.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:27.491][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[2024-05-04 05:38:27.492][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:27.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:27.495][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:27.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:27.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:27.498][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:27.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:27.500][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:27.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:27.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:27.504][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:27.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:27.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:27.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:27.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:27.510][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-04 05:38:27.512][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-04 05:38:27.514][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-04 05:38:27.515][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-04 05:38:27.517][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-04 05:38:27.519][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-04 05:38:27.521][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-04 05:38:27.523][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-04 05:38:27.525][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-04 05:38:27.527][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-04 05:38:27.529][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-04 05:38:27.531][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-04 05:38:27.533][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-04 05:38:27.535][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-04 05:38:27.537][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-04 05:38:27.539][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-04 05:38:27.541][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-04 05:38:27.543][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-04 05:38:27.545][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-04 05:38:27.547][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-04 05:38:27.549][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-04 05:38:27.551][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-04 05:38:27.553][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-04 05:38:27.555][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-04 05:38:27.558][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-04 05:38:27.560][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-04 05:38:27.562][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-04 05:38:27.564][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-04 05:38:27.566][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-04 05:38:27.568][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-04 05:38:27.570][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-04 05:38:27.573][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-04 05:38:27.575][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-04 05:38:27.577][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-04 05:38:27.579][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-04 05:38:27.581][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-04 05:38:27.583][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-04 05:38:27.585][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-04 05:38:27.587][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-04 05:38:27.589][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-04 05:38:27.591][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-04 05:38:27.593][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-04 05:38:27.595][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-04 05:38:27.597][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-04 05:38:27.599][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-04 05:38:27.601][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-04 05:38:27.603][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-04 05:38:27.605][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-04 05:38:27.607][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-04 05:38:27.609][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-04 05:38:27.611][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-04 05:38:27.613][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-04 05:38:27.615][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-04 05:38:27.617][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-04 05:38:27.620][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-04 05:38:27.622][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-04 05:38:27.624][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-04 05:38:27.626][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-04 05:38:27.628][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-04 05:38:27.630][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-04 05:38:27.632][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-04 05:38:27.634][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-04 05:38:27.636][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-04 05:38:27.638][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-04 05:38:27.641][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-04 05:38:27.643][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-04 05:38:27.645][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-04 05:38:27.647][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-04 05:38:27.649][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-04 05:38:27.651][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-04 05:38:27.653][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-04 05:38:27.655][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-04 05:38:27.657][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-04 05:38:27.666][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-04 05:38:27.668][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-04 05:38:27.670][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-04 05:38:27.672][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-04 05:38:27.674][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-04 05:38:27.676][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-04 05:38:27.677][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-04 05:38:27.679][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-04 05:38:27.681][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-04 05:38:27.682][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-04 05:38:27.684][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-04 05:38:27.686][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-05-04 05:38:27.688][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-04 05:38:27.689][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:27.690][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:27.691][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:27.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:27.693][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:27.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:27.695][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:27.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:27.698][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:27.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:27.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:27.701][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:27.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:27.703][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:27.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:27.705][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:27.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:27.708][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[2024-05-04 05:38:27.709][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:27.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:27.711][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:27.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:27.713][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:27.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:27.716][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:27.717][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:27.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:27.719][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:27.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:27.721][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:27.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:27.724][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:27.725][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:27.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:27.727][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:27.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:27.729][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:27.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:27.731][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[2024-05-04 05:38:27.732][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:27.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:27.735][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:27.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:27.737][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:27.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:27.739][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:27.740][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:27.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:27.742][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:27.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:27.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:27.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:27.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:27.749][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:27.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:27.751][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:27.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:27.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:27.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:27.756][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:27.757][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:27.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:27.760][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:27.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:27.762][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:27.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:27.765][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:27.766][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:27.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:27.768][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:27.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:27.770][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:27.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:27.773][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:27.774][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:27.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:27.776][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:27.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:27.778][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:27.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:27.781][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.DEBUG[2024-05-04 05:38:27.782][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:27.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:27.784][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:27.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:27.786][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:27.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:27.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:27.789][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:27.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:27.792][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:27.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:27.794][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:27.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:27.796][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.DEBUG[2024-05-04 05:38:27.797][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:27.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:27.799][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:27.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:27.801][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:27.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:27.804][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.DEBUG[2024-05-04 05:38:27.805][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:27.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:27.807][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:27.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:27.809][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:27.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:27.811][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:27.813][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:27.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:27.815][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:27.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:27.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:27.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:27.820][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:27.822][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 05:38:27.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:27.824][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:27.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:27.826][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:27.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:27.828][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:27.830][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-05-04 05:38:27.832][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-05-04 05:38:27.834][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-04 05:38:27.836][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-05-04 05:38:27.837][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 05:38:27.838][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 05:38:27.840][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 05:38:27.841][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 05:38:27.842][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-04 05:38:27.843][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-05-04 05:38:27.845][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-05-04 05:38:27.846][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 05:38:27.847][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-04 05:38:27.849][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-05-04 05:38:27.850][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 05:38:27.851][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-05-04 05:38:27.851][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-05-04 05:38:27.851][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-05-04 05:38:27.851][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-05-04 05:38:27.851][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-05-04 05:38:27.851][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-05-04 05:38:27.851][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-05-04 05:38:27.851][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-05-04 05:38:27.851][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-05-04 05:38:27.851][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-05-04 05:38:27.851][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-05-04 05:38:27.853][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-04 05:38:27.854][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-04 05:38:27.854][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-04 05:38:27.854][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-04 05:38:27.855][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-05-04 05:38:27.856][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 05:38:27.857][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 05:38:27.859][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 05:38:27.860][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 05:38:27.861][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 05:38:27.862][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 05:38:27.864][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-04 05:38:27.864][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-05-04 05:38:27.865][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 05:38:27.866][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 05:38:27.867][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-04 05:38:27.869][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-05-04 05:38:27.869][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-05-04 05:38:27.871][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-04 05:38:27.873][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-04 05:38:27.876][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-05-04 05:38:27.878][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-04 05:38:27.880][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-04 05:38:27.882][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-04 05:38:27.886][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-05-04 05:38:27.888][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-05-04 05:38:27.890][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-05-04 05:38:27.892][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-05-04 05:38:27.894][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-04 05:38:27.896][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-04 05:38:27.898][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-05-04 05:38:27.899][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-05-04 05:38:27.901][biodb::testThat]
biodb.INFO [2024-05-04 05:38:27.902][biodb::testThat] Running test function test.chebi.encoding.issue.in.xml (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2024-05-04 05:38:27.903][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 05:38:27.905][biodb::testThat]
biodb.DEBUG[2024-05-04 05:38:27.909][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-05-04 05:38:27.913][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-04 05:38:27.915][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-05-04 05:38:27.917][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-04 05:38:27.919][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-05-04 05:38:27.924][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-05-04 05:38:27.928][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-04 05:38:27.930][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2024-05-04 05:38:27.932][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-04 05:38:27.933][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2024-05-04 05:38:27.939][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2024-05-04 05:38:27.940][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-04 05:38:27.943][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2024-05-04 05:38:27.944][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-04 05:38:27.946][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-04 05:38:27.947][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-04 05:38:27.949][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-04 05:38:27.950][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-04 05:38:27.952][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-04 05:38:27.955][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:38:27.956][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:27.958][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:27.964][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:27.965][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:27.966][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:27.967][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 05:38:27.969][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2024-05-04 05:38:27.972][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 05:38:27.974][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 05:38:27.975][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2024-05-04 05:38:39.083][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2024-05-04 05:38:51.613][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-04 05:38:51.615][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2024-05-04 05:38:51.620][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2024-05-04 05:38:51.624][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2024-05-04 05:38:51.626][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-04 05:38:51.628][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-04 05:38:51.629][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-04 05:38:51.632][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 05:38:51.633][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:51.634][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:51.641][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:51.642][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:51.643][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:51.645][FUN] Functions in observer BiodbConfig: [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[2024-05-04 05:38:51.648][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:38:51.649][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:38:51.651][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:51.652][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:51.654][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:38:51.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:38:51.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:51.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:51.660][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-04 05:38:51.661][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-04 05:38:51.663][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:51.664][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:51.666][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 05:38:51.667][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 05:38:51.669][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:51.670][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:51.672][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 05:38:51.674][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 05:38:51.675][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:51.676][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:51.678][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 05:38:51.680][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 05:38:51.681][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:51.682][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:51.684][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:38:51.686][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-04 05:38:51.687][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:51.689][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:51.690][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-04 05:38:51.692][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 05:38:51.693][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:51.695][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:51.696][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:38:51.698][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-04 05:38:51.699][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:51.701][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:51.702][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 05:38:51.704][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 05:38:51.705][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:51.706][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:51.708][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-04 05:38:51.710][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-04 05:38:51.711][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:51.712][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:51.714][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-04 05:38:51.715][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-04 05:38:51.717][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:51.718][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:51.720][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:38:51.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:38:51.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:51.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:51.725][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:38:51.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:38:51.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:51.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:51.731][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:38:51.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:38:51.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:51.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:51.737][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-04 05:38:51.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-04 05:38:51.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:51.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:51.742][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:38:51.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:38:51.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:51.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:51.748][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:38:51.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:38:51.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:51.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:51.753][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:38:51.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:38:51.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:51.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:51.759][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:38:51.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:38:51.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:51.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:51.764][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:38:51.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:38:51.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:51.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 05:38:51.769][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 05:38:51.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 05:38:51.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 05:38:51.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 05:38:51.775][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-05-04 05:38:51.776][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-05-04 05:38:51.781][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-04 05:38:51.782][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-05-04 05:38:51.784][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-05-04 05:38:51.785][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-04 05:38:51.786][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 05:38:51.787][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 05:38:51.788][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 05:38:51.789][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 05:38:51.791][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 05:38:51.792][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".
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 444 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_100_generic.R:16:1'): One wrong entry does not block the retrieval of good ones ──
any(vapply(entries[2:length(entries)], is.null, FUN.VALUE = TRUE)) is not FALSE
`actual`: TRUE
`expected`: FALSE
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<ChebiCnn>`, opt = `<named list>`)
3. └─testthat::expect_false(...)
── Failure ('test_100_generic.R:16:1'): The peak table is correct. ─────────────
any(vapply(entries, is.null, FUN.VALUE = TRUE)) is not FALSE
`actual`: TRUE
`expected`: FALSE
One of the entries is NULL.
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<ChebiCnn>`, opt = `<named list>`)
3. └─testthat::expect_false(...)
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 444 ]
Error: Test failures
Execution halted
biodbChebi.Rcheck/biodbChebi-Ex.timings
| name | user | system | elapsed | |
| ChebiConn | 1.121 | 0.056 | 5.498 | |
| ChebiEntry | 0.215 | 0.000 | 0.216 | |