Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-04 11:37:28 -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. |
Package: biodbChebi |
Version: 1.10.0 |
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:biodbChebi.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings biodbChebi_1.10.0.tar.gz |
StartedAt: 2024-05-04 01:03:01 -0400 (Sat, 04 May 2024) |
EndedAt: 2024-05-04 01:16:49 -0400 (Sat, 04 May 2024) |
EllapsedTime: 828.0 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: biodbChebi.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:biodbChebi.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings biodbChebi_1.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/biodbChebi.Rcheck' * using R version 4.4.0 beta (2024-04-15 r86425 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * 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 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 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 3.72 2.39 94.37 * 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 384 ] 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 'F:/biocbuild/bbs-3.19-bioc/meat/biodbChebi.Rcheck/00check.log' for details.
biodbChebi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL biodbChebi ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.19-bioc/R/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 ucrt) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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 01:06:36.015][biodb::testContext] biodb.INFO [2024-05-04 01:06:36.021][biodb::testContext] ******************************************************************************** biodb.INFO [2024-05-04 01:06:36.024][biodb::testContext] Test context - Generic tests biodb.INFO [2024-05-04 01:06:36.027][biodb::testContext] ******************************************************************************** biodb.INFO [2024-05-04 01:06:36.029][biodb::testContext] biodb.INFO [2024-05-04 01:06:36.041][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0. biodb.DEBUG[2024-05-04 01:06:36.045][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc/R/library/biodb/definitions.yml". biodb.DEBUG[2024-05-04 01:06:36.057][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-05-04 01:06:36.060][self$getConfig()$define] Define config key allow.huge.downloads. biodb.DEBUG[2024-05-04 01:06:36.062][self$set] Set key allow.huge.downloads to TRUE. biodb.DEBUG[2024-05-04 01:06:36.065][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:06:36.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:06:36.070][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:06:36.072][self$getConfig()$define] Define config key autoload.extra.pkgs. biodb.DEBUG[2024-05-04 01:06:36.118][self$set] Set key autoload.extra.pkgs to TRUE. biodb.DEBUG[2024-05-04 01:06:36.120][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:06:36.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:06:36.124][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:06:36.126][self$getConfig()$define] Define config key cache.all.requests. biodb.DEBUG[2024-05-04 01:06:36.128][self$set] Set key cache.all.requests to TRUE. biodb.DEBUG[2024-05-04 01:06:36.130][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:06:36.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:06:36.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:06:36.136][self$getConfig()$define] Define config key cache.directory. biodb.DEBUG[2024-05-04 01:06:36.138][self$getConfig()$define] Define config key cache.read.only. biodb.DEBUG[2024-05-04 01:06:36.140][self$set] Set key cache.read.only to FALSE. biodb.DEBUG[2024-05-04 01:06:36.142][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:06:36.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:06:36.145][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 01:06:36.147][self$getConfig()$define] Define config key cache.subfolders. biodb.DEBUG[2024-05-04 01:06:36.149][self$getConfig()$define] Define config key cache.system. biodb.DEBUG[2024-05-04 01:06:36.151][self$set] Set key cache.system to TRUE. biodb.DEBUG[2024-05-04 01:06:36.153][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:06:36.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:06:36.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:06:36.157][self$getConfig()$define] Define config key use.cache.for.local.db. biodb.DEBUG[2024-05-04 01:06:36.159][self$set] Set key use.cache.for.local.db to FALSE. biodb.DEBUG[2024-05-04 01:06:36.161][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:06:36.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:06:36.165][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 01:06:36.167][self$getConfig()$define] Define config key dwnld.chunk.size. biodb.DEBUG[2024-05-04 01:06:36.169][self$getConfig()$define] Define config key dwnld.timeout. biodb.DEBUG[2024-05-04 01:06:36.171][self$set] Set key dwnld.timeout to 3600. biodb.DEBUG[2024-05-04 01:06:36.173][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:06:36.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:06:36.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:06:36.179][self$getConfig()$define] Define config key compute.fields. biodb.DEBUG[2024-05-04 01:06:36.181][self$set] Set key compute.fields to TRUE. biodb.DEBUG[2024-05-04 01:06:36.183][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:06:36.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:06:36.186][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 01:06:36.188][self$getConfig()$define] Define config key factory.cache. biodb.DEBUG[2024-05-04 01:06:36.190][self$getConfig()$define] Define config key force.locale. biodb.DEBUG[2024-05-04 01:06:36.193][self$set] Set key force.locale to TRUE. biodb.DEBUG[2024-05-04 01:06:36.194][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:06:36.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:06:36.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:06:36.200][self$getConfig()$define] Define config key longterm.cache.subfolder. biodb.DEBUG[2024-05-04 01:06:36.202][self$getConfig()$define] Define config key msg.caution.lvl. biodb.DEBUG[2024-05-04 01:06:36.203][self$getConfig()$define] Define config key msg.debug.lvl. biodb.DEBUG[2024-05-04 01:06:36.206][self$getConfig()$define] Define config key msg.info.lvl. biodb.DEBUG[2024-05-04 01:06:36.208][self$getConfig()$define] Define config key multival.field.sep. biodb.DEBUG[2024-05-04 01:06:36.210][self$set] Set key multival.field.sep to ";". biodb.DEBUG[2024-05-04 01:06:36.212][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:06:36.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:06:36.216][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:06:36.218][self$getConfig()$define] Define config key intra.field.name.sep. biodb.DEBUG[2024-05-04 01:06:36.220][self$set] Set key intra.field.name.sep to ".". biodb.DEBUG[2024-05-04 01:06:36.222][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:06:36.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:06:36.226][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:06:36.228][self$getConfig()$define] Define config key entries.sep. biodb.DEBUG[2024-05-04 01:06:36.230][self$set] Set key entries.sep to "|". biodb.DEBUG[2024-05-04 01:06:36.232][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:06:36.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:06:36.235][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:06:36.238][self$getConfig()$define] Define config key offline. biodb.DEBUG[2024-05-04 01:06:36.240][self$set] Set key offline to FALSE. biodb.DEBUG[2024-05-04 01:06:36.242][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:06:36.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:06:36.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:06:36.247][self$getConfig()$define] Define config key persistent.cache.impl. biodb.DEBUG[2024-05-04 01:06:36.250][self$set] Set key persistent.cache.impl to "custom". biodb.DEBUG[2024-05-04 01:06:36.252][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:06:36.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:06:36.256][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:06:36.258][self$getConfig()$define] Define config key proton.mass. biodb.DEBUG[2024-05-04 01:06:36.260][self$set] Set key proton.mass to 1.0072765. biodb.DEBUG[2024-05-04 01:06:36.262][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:06:36.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:06:36.265][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:06:36.266][self$getConfig()$define] Define config key shortterm.cache.subfolder. biodb.DEBUG[2024-05-04 01:06:36.268][self$getConfig()$define] Define config key svn.binary.path. biodb.DEBUG[2024-05-04 01:06:36.272][self$set] Set key svn.binary.path to "". biodb.DEBUG[2024-05-04 01:06:36.273][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:06:36.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:06:36.275][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 01:06:36.276][self$getConfig()$define] Define config key test.functions. biodb.DEBUG[2024-05-04 01:06:36.277][self$getConfig()$define] Define config key useragent. biodb.DEBUG[2024-05-04 01:06:36.279][self$set] Set key useragent to "R Bioconductor biodb library.". biodb.DEBUG[2024-05-04 01:06:36.280][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:06:36.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:06:36.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:06:36.286][self$getDbsInfo()$define] Define connector comp.csv.file. biodb.DEBUG[2024-05-04 01:06:36.315][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-05-04 01:06:36.331][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.". biodb.DEBUG[2024-05-04 01:06:36.333][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 01:06:36.334][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 01:06:36.335][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 01:06:36.337][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 01:06:36.338][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-04 01:06:36.339][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 01:06:36.341][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2024-05-04 01:06:36.342][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 01:06:36.343][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-05-04 01:06:36.344][self$setPropertyValue] Setting property "name" to "Compound CSV File". biodb.DEBUG[2024-05-04 01:06:36.346][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 01:06:36.347][self$setPropertyValue] biodb.DEBUG[2024-05-04 01:06:36.349][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-04 01:06:36.350][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-05-04 01:06:36.350][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-05-04 01:06:36.350][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2024-05-04 01:06:36.350][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2024-05-04 01:06:36.350][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2024-05-04 01:06:36.351][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 01:06:36.353][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 01:06:36.354][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 01:06:36.355][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 01:06:36.356][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 01:06:36.357][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 01:06:36.358][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 01:06:36.360][self$setPropertyValue] biodb.DEBUG[2024-05-04 01:06:36.362][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 01:06:36.365][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 01:06:36.367][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-04 01:06:36.369][self$setPropertyValue] biodb.DEBUG[2024-05-04 01:06:36.371][self$getDbsInfo()$define] Define connector comp.sqlite. biodb.DEBUG[2024-05-04 01:06:36.374][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-05-04 01:06:36.376][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.". biodb.DEBUG[2024-05-04 01:06:36.377][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 01:06:36.378][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 01:06:36.380][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 01:06:36.382][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 01:06:36.383][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-04 01:06:36.385][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 01:06:36.386][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2024-05-04 01:06:36.387][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 01:06:36.388][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-05-04 01:06:36.390][self$setPropertyValue] Setting property "name" to "Compound SQLite". biodb.DEBUG[2024-05-04 01:06:36.391][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 01:06:36.393][self$setPropertyValue] biodb.DEBUG[2024-05-04 01:06:36.394][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-04 01:06:36.401][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-05-04 01:06:36.401][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-05-04 01:06:36.401][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2024-05-04 01:06:36.401][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2024-05-04 01:06:36.401][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2024-05-04 01:06:36.403][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 01:06:36.404][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 01:06:36.405][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 01:06:36.407][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 01:06:36.408][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 01:06:36.410][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 01:06:36.412][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 01:06:36.414][self$setPropertyValue] biodb.DEBUG[2024-05-04 01:06:36.416][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 01:06:36.418][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 01:06:36.420][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-04 01:06:36.422][self$setPropertyValue] biodb.DEBUG[2024-05-04 01:06:36.425][self$getDbsInfo()$define] Define connector mass.csv.file. biodb.DEBUG[2024-05-04 01:06:36.427][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2024-05-04 01:06:36.428][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..". biodb.DEBUG[2024-05-04 01:06:36.430][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 01:06:36.431][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 01:06:36.433][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 01:06:36.434][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 01:06:36.436][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-04 01:06:36.437][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 01:06:36.438][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2024-05-04 01:06:36.439][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 01:06:36.441][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2024-05-04 01:06:36.442][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File". biodb.DEBUG[2024-05-04 01:06:36.443][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 01:06:36.444][self$setPropertyValue] biodb.DEBUG[2024-05-04 01:06:36.446][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-04 01:06:36.448][self$setPropertyValue] biodb.DEBUG[2024-05-04 01:06:36.449][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 01:06:36.450][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 01:06:36.451][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 01:06:36.452][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 01:06:36.454][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 01:06:36.455][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 01:06:36.456][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 01:06:36.457][self$setPropertyValue] biodb.DEBUG[2024-05-04 01:06:36.459][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 01:06:36.460][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 01:06:36.461][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-04 01:06:36.462][self$setPropertyValue] biodb.DEBUG[2024-05-04 01:06:36.465][self$getDbsInfo()$define] Define connector mass.sqlite. biodb.DEBUG[2024-05-04 01:06:36.467][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2024-05-04 01:06:36.469][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.". biodb.DEBUG[2024-05-04 01:06:36.470][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 01:06:36.471][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 01:06:36.472][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 01:06:36.474][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 01:06:36.475][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-04 01:06:36.476][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 01:06:36.477][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2024-05-04 01:06:36.479][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 01:06:36.480][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2024-05-04 01:06:36.481][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite". biodb.DEBUG[2024-05-04 01:06:36.483][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 01:06:36.484][self$setPropertyValue] biodb.DEBUG[2024-05-04 01:06:36.486][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-04 01:06:36.488][self$setPropertyValue] biodb.DEBUG[2024-05-04 01:06:36.490][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 01:06:36.492][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 01:06:36.493][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 01:06:36.495][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 01:06:36.497][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 01:06:36.499][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 01:06:36.501][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 01:06:36.502][self$setPropertyValue] biodb.DEBUG[2024-05-04 01:06:36.504][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 01:06:36.506][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 01:06:36.508][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-04 01:06:36.510][self$setPropertyValue] biodb.DEBUG[2024-05-04 01:06:36.515][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-05-04 01:06:36.517][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:06:36.519][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 01:06:36.520][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:06:36.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:06:36.524][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 01:06:36.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:06:36.528][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:06:36.529][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:06:36.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:06:36.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:06:36.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:06:36.536][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:06:36.538][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:06:36.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:06:36.541][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 01:06:36.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:06:36.545][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:06:36.546][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:06:36.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:06:36.550][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:06:36.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:06:36.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:06:36.555][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:06:36.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:06:36.558][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 01:06:36.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:06:36.562][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.DEBUG[2024-05-04 01:06:36.564][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:06:36.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:06:36.567][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:06:36.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:06:36.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:06:36.574][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:06:36.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:06:36.577][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 01:06:36.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:06:36.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:06:36.582][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:06:36.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:06:36.586][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:06:36.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:06:36.590][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:06:36.591][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:06:36.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:06:36.595][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 01:06:36.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:06:36.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:06:36.601][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:06:36.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:06:36.604][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:06:36.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:06:36.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:06:36.610][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:06:36.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:06:36.613][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:06:36.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:06:36.617][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 01:06:36.619][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:06:36.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:06:36.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:06:36.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:06:36.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:06:36.628][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:06:36.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:06:36.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:06:36.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:06:36.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:06:36.637][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:06:36.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:06:36.640][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:06:36.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:06:36.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:06:36.646][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:06:36.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:06:36.649][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:06:36.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:06:36.653][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:06:36.655][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:06:36.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:06:36.658][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:06:36.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:06:36.662][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 01:06:36.664][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:06:36.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:06:36.668][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 01:06:36.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:06:36.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:06:36.673][self$getEntryFields()$define] Define field accession. biodb.DEBUG[2024-05-04 01:06:36.679][self$getEntryFields()$define] Define field description. biodb.DEBUG[2024-05-04 01:06:36.682][self$getEntryFields()$define] Define field name. biodb.DEBUG[2024-05-04 01:06:36.685][self$getEntryFields()$define] Define field cas.id. biodb.DEBUG[2024-05-04 01:06:36.688][self$getEntryFields()$define] Define field chebi.id. biodb.DEBUG[2024-05-04 01:06:36.690][self$getEntryFields()$define] Define field chemspider.id. biodb.DEBUG[2024-05-04 01:06:36.693][self$getEntryFields()$define] Define field comp.csv.file.id. biodb.DEBUG[2024-05-04 01:06:36.696][self$getEntryFields()$define] Define field comp.sqlite.id. biodb.DEBUG[2024-05-04 01:06:36.699][self$getEntryFields()$define] Define field expasy.enzyme.id. biodb.DEBUG[2024-05-04 01:06:36.701][self$getEntryFields()$define] Define field hmdb.metabolites.id. biodb.DEBUG[2024-05-04 01:06:36.704][self$getEntryFields()$define] Define field kegg.compound.id. biodb.DEBUG[2024-05-04 01:06:36.706][self$getEntryFields()$define] Define field kegg.genes.id. biodb.DEBUG[2024-05-04 01:06:36.709][self$getEntryFields()$define] Define field mass.csv.file.id. biodb.DEBUG[2024-05-04 01:06:36.711][self$getEntryFields()$define] Define field mass.sqlite.id. biodb.DEBUG[2024-05-04 01:06:36.714][self$getEntryFields()$define] Define field ncbi.gene.id. biodb.DEBUG[2024-05-04 01:06:36.717][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id. biodb.DEBUG[2024-05-04 01:06:36.720][self$getEntryFields()$define] Define field compound.id. biodb.DEBUG[2024-05-04 01:06:36.722][self$getEntryFields()$define] Define field average.mass. biodb.DEBUG[2024-05-04 01:06:36.725][self$getEntryFields()$define] Define field molecular.mass. biodb.DEBUG[2024-05-04 01:06:36.728][self$getEntryFields()$define] Define field monoisotopic.mass. biodb.DEBUG[2024-05-04 01:06:36.731][self$getEntryFields()$define] Define field nominal.mass. biodb.DEBUG[2024-05-04 01:06:36.734][self$getEntryFields()$define] Define field peak.attr. biodb.DEBUG[2024-05-04 01:06:36.746][self$getEntryFields()$define] Define field peak.comp. biodb.DEBUG[2024-05-04 01:06:36.749][self$getEntryFields()$define] Define field peak.error.ppm. biodb.DEBUG[2024-05-04 01:06:36.752][self$getEntryFields()$define] Define field peak.formula. biodb.DEBUG[2024-05-04 01:06:36.754][self$getEntryFields()$define] Define field peak.intensity. biodb.DEBUG[2024-05-04 01:06:36.757][self$getEntryFields()$define] Define field peak.mass. biodb.DEBUG[2024-05-04 01:06:36.760][self$getEntryFields()$define] Define field peak.mztheo. biodb.DEBUG[2024-05-04 01:06:36.764][self$getEntryFields()$define] Define field peak.mzexp. biodb.DEBUG[2024-05-04 01:06:36.767][self$getEntryFields()$define] Define field peak.mz. biodb.DEBUG[2024-05-04 01:06:36.769][self$getEntryFields()$define] Define field peak.relative.intensity. biodb.DEBUG[2024-05-04 01:06:36.772][self$getEntryFields()$define] Define field peaks. biodb.DEBUG[2024-05-04 01:06:36.775][self$getEntryFields()$define] Define field chrom.col.constructor. biodb.DEBUG[2024-05-04 01:06:36.777][self$getEntryFields()$define] Define field chrom.col.diameter. biodb.DEBUG[2024-05-04 01:06:36.780][self$getEntryFields()$define] Define field chrom.col.id. biodb.DEBUG[2024-05-04 01:06:36.782][self$getEntryFields()$define] Define field chrom.col.length. biodb.DEBUG[2024-05-04 01:06:36.784][self$getEntryFields()$define] Define field chrom.col.method.protocol. biodb.DEBUG[2024-05-04 01:06:36.786][self$getEntryFields()$define] Define field chrom.col.name. biodb.DEBUG[2024-05-04 01:06:36.787][self$getEntryFields()$define] Define field chrom.flow.gradient. biodb.DEBUG[2024-05-04 01:06:36.790][self$getEntryFields()$define] Define field chrom.flow.rate. biodb.DEBUG[2024-05-04 01:06:36.791][self$getEntryFields()$define] Define field chrom.rt. biodb.DEBUG[2024-05-04 01:06:36.793][self$getEntryFields()$define] Define field chrom.rt.max. biodb.DEBUG[2024-05-04 01:06:36.796][self$getEntryFields()$define] Define field chrom.rt.min. biodb.DEBUG[2024-05-04 01:06:36.799][self$getEntryFields()$define] Define field chrom.rt.unit. biodb.DEBUG[2024-05-04 01:06:36.801][self$getEntryFields()$define] Define field chrom.solvent. biodb.DEBUG[2024-05-04 01:06:36.804][self$getEntryFields()$define] Define field aa.seq. biodb.DEBUG[2024-05-04 01:06:36.806][self$getEntryFields()$define] Define field aa.seq.length. biodb.DEBUG[2024-05-04 01:06:36.808][self$getEntryFields()$define] Define field aa.seq.location. biodb.DEBUG[2024-05-04 01:06:36.810][self$getEntryFields()$define] Define field nt.seq. biodb.DEBUG[2024-05-04 01:06:36.811][self$getEntryFields()$define] Define field nt.seq.length. biodb.DEBUG[2024-05-04 01:06:36.813][self$getEntryFields()$define] Define field ec. biodb.DEBUG[2024-05-04 01:06:36.815][self$getEntryFields()$define] Define field organism. biodb.DEBUG[2024-05-04 01:06:36.816][self$getEntryFields()$define] Define field pathway.class. biodb.DEBUG[2024-05-04 01:06:36.818][self$getEntryFields()$define] Define field catalytic.activity. biodb.DEBUG[2024-05-04 01:06:36.820][self$getEntryFields()$define] Define field cofactor. biodb.DEBUG[2024-05-04 01:06:36.823][self$getEntryFields()$define] Define field gene.symbol. biodb.DEBUG[2024-05-04 01:06:36.826][self$getEntryFields()$define] Define field charge. biodb.DEBUG[2024-05-04 01:06:36.828][self$getEntryFields()$define] Define field comp.iupac.name.allowed. biodb.DEBUG[2024-05-04 01:06:36.831][self$getEntryFields()$define] Define field comp.iupac.name.cas. biodb.DEBUG[2024-05-04 01:06:36.833][self$getEntryFields()$define] Define field comp.iupac.name.pref. biodb.DEBUG[2024-05-04 01:06:36.836][self$getEntryFields()$define] Define field comp.iupac.name.syst. biodb.DEBUG[2024-05-04 01:06:36.838][self$getEntryFields()$define] Define field comp.iupac.name.trad. biodb.DEBUG[2024-05-04 01:06:36.841][self$getEntryFields()$define] Define field comp.super.class. biodb.DEBUG[2024-05-04 01:06:36.844][self$getEntryFields()$define] Define field equation. biodb.DEBUG[2024-05-04 01:06:36.846][self$getEntryFields()$define] Define field formula. biodb.DEBUG[2024-05-04 01:06:36.849][self$getEntryFields()$define] Define field composition. biodb.DEBUG[2024-05-04 01:06:36.852][self$getEntryFields()$define] Define field inchi. biodb.DEBUG[2024-05-04 01:06:36.854][self$getEntryFields()$define] Define field inchikey. biodb.DEBUG[2024-05-04 01:06:36.857][self$getEntryFields()$define] Define field logp. biodb.DEBUG[2024-05-04 01:06:36.860][self$getEntryFields()$define] Define field ms.level. biodb.DEBUG[2024-05-04 01:06:36.862][self$getEntryFields()$define] Define field ms.mode. biodb.DEBUG[2024-05-04 01:06:36.865][self$getEntryFields()$define] Define field msdev. biodb.DEBUG[2024-05-04 01:06:36.867][self$getEntryFields()$define] Define field msdevtype. biodb.DEBUG[2024-05-04 01:06:36.870][self$getEntryFields()$define] Define field msprecannot. biodb.DEBUG[2024-05-04 01:06:36.872][self$getEntryFields()$define] Define field msprecmz. biodb.DEBUG[2024-05-04 01:06:36.875][self$getEntryFields()$define] Define field mstype. biodb.DEBUG[2024-05-04 01:06:36.878][self$getEntryFields()$define] Define field nb.compounds. biodb.DEBUG[2024-05-04 01:06:36.880][self$getEntryFields()$define] Define field nb.peaks. biodb.DEBUG[2024-05-04 01:06:36.883][self$getEntryFields()$define] Define field products. biodb.DEBUG[2024-05-04 01:06:36.885][self$getEntryFields()$define] Define field smiles. biodb.DEBUG[2024-05-04 01:06:36.888][self$getEntryFields()$define] Define field smiles.canonical. biodb.DEBUG[2024-05-04 01:06:36.890][self$getEntryFields()$define] Define field smiles.isomeric. biodb.DEBUG[2024-05-04 01:06:36.893][self$getEntryFields()$define] Define field substrates. biodb.DEBUG[2024-05-04 01:06:36.942][initialize] Created successfully new BiodbMain instance. biodb.DEBUG[2024-05-04 01:06:36.945][initialize] This is biodb version 1.12.0. biodb.DEBUG[2024-05-04 01:06:36.948][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-05-04 01:06:36.949][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:06:36.951][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:06:36.952][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:06:36.953][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:06:36.959][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:06:36.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:06:36.961][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:06:36.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:06:36.964][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:06:36.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:06:36.966][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:06:36.967][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:06:36.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:06:36.970][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:06:36.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:06:36.972][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:06:36.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:06:36.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:06:36.976][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:06:36.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:06:36.978][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:06:36.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:06:36.980][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:06:36.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:06:36.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:06:36.984][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:06:36.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:06:36.988][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:06:36.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:06:36.992][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:06:36.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:06:36.995][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.DEBUG[2024-05-04 01:06:36.997][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:06:36.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:06:36.999][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:06:37.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:06:37.001][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 01:06:37.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:06:37.003][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:06:37.005][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:06:37.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:06:37.007][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:06:37.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:06:37.009][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:06:37.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:06:37.011][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:06:37.013][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:06:37.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:06:37.015][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:06:37.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:06:37.018][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 01:06:37.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:06:37.020][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 01:06:37.021][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:06:37.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:06:37.023][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:06:37.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:06:37.025][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:06:37.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:06:37.028][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 01:06:37.029][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:06:37.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:06:37.031][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:06:37.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:06:37.034][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 01:06:37.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:06:37.036][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 01:06:37.037][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:06:37.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:06:37.039][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:06:37.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:06:37.041][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:06:37.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:06:37.044][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 01:06:37.045][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:06:37.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:06:37.047][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:06:37.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:06:37.050][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 01:06:37.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:06:37.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:06:37.055][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:06:37.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:06:37.059][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:06:37.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:06:37.063][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:06:37.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:06:37.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:06:37.077][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:06:37.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:06:37.081][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:06:37.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:06:37.084][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 01:06:37.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:06:37.088][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:06:37.090][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:06:37.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:06:37.093][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:06:37.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:06:37.097][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:06:37.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:06:37.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:06:37.102][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:06:37.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:06:37.105][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:06:37.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:06:37.108][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:06:37.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:06:37.112][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 01:06:37.114][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:06:37.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:06:37.117][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:06:37.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:06:37.119][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:06:37.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:06:37.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:06:37.122][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:06:37.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:06:37.125][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:06:37.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:06:37.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:06:37.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:06:37.129][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 01:06:37.134][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc/R/library/biodbChebi/definitions.yml". biodb.DEBUG[2024-05-04 01:06:37.150][self$getDbsInfo()$define] Define connector chebi. biodb.DEBUG[2024-05-04 01:06:37.154][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-05-04 01:06:37.157][self$setPropertyValue] Setting property "description" to "NA". biodb.DEBUG[2024-05-04 01:06:37.159][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 01:06:37.162][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 01:06:37.164][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 01:06:37.166][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 01:06:37.169][self$setPropertyValue] Setting property "editable" to "FALSE". biodb.DEBUG[2024-05-04 01:06:37.171][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8". biodb.DEBUG[2024-05-04 01:06:37.173][self$setPropertyValue] Setting property "entry.content.type" to "xml". biodb.DEBUG[2024-05-04 01:06:37.176][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 01:06:37.178][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-05-04 01:06:37.180][self$setPropertyValue] Setting property "name" to "ChEBI". biodb.DEBUG[2024-05-04 01:06:37.182][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 01:06:37.185][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')". biodb.DEBUG[2024-05-04 01:06:37.185][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge". biodb.DEBUG[2024-05-04 01:06:37.185][self$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 01:06:37.185][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi". biodb.DEBUG[2024-05-04 01:06:37.185][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey". biodb.DEBUG[2024-05-04 01:06:37.185][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data". biodb.DEBUG[2024-05-04 01:06:37.185][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass". biodb.DEBUG[2024-05-04 01:06:37.185][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass". biodb.DEBUG[2024-05-04 01:06:37.185][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")". biodb.DEBUG[2024-05-04 01:06:37.185][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar". biodb.DEBUG[2024-05-04 01:06:37.185][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles". biodb.DEBUG[2024-05-04 01:06:37.187][self$setPropertyValue] Setting property "remote" to "TRUE". biodb.DEBUG[2024-05-04 01:06:37.190][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-05-04 01:06:37.190][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-05-04 01:06:37.190][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2024-05-04 01:06:37.192][self$setPropertyValue] Setting property "scheduler.n" to "3". biodb.DEBUG[2024-05-04 01:06:37.194][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 01:06:37.196][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 01:06:37.198][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 01:06:37.200][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 01:06:37.202][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 01:06:37.205][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 01:06:37.206][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-05-04 01:06:37.206][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/". biodb.DEBUG[2024-05-04 01:06:37.208][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 01:06:37.209][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 01:06:37.210][self$setPropertyValue] Setting property "writable" to "FALSE". biodb.DEBUG[2024-05-04 01:06:37.211][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi". biodb.DEBUG[2024-05-04 01:06:37.211][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema". biodb.DEBUG[2024-05-04 01:06:37.217][self$getEntryFields()$define] Define field chebi.id. biodb.DEBUG[2024-05-04 01:06:37.220][self$getEntryFields()$define] Define field kegg.compound.id. biodb.DEBUG[2024-05-04 01:06:37.222][self$getEntryFields()$define] Define field n_stars. biodb.DEBUG[2024-05-04 01:06:37.223][self$getEntryFields()$define] Define field molecular.mass. biodb.DEBUG[2024-05-04 01:06:37.225][self$getEntryFields()$define] Define field inchi. biodb.DEBUG[2024-05-04 01:06:37.227][self$getEntryFields()$define] Define field inchikey. biodb.DEBUG[2024-05-04 01:06:37.251][super$initialize] Initialize connector chebi. biodb.DEBUG[2024-05-04 01:06:37.253][super$initialize] Register connector chebi with the request scheduler biodb.DEBUG[2024-05-04 01:06:37.259][private$bdb$getRequestScheduler()$re ...] Register connector chebi. biodb.DEBUG[2024-05-04 01:06:37.266][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi". biodb.DEBUG[2024-05-04 01:06:37.271][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2024-05-04 01:06:37.273][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2024-05-04 01:06:37.274][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk". biodb.DEBUG[2024-05-04 01:06:37.276][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi . biodb.INFO [2024-05-04 01:06:37.286][biodb::testThat] biodb.INFO [2024-05-04 01:06:37.287][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value "). biodb.INFO [2024-05-04 01:06:37.289][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 01:06:37.290][biodb::testThat] biodb.TRACE[2024-05-04 01:06:37.295][loadFileContents] Loaded 1 files from cache: [1]: "F:/biocbuild/bbs-3.19-bioc/R/library/biodbChebi/testref/entry-chebi-15440-content.xml". biodb.DEBUG[2024-05-04 01:06:37.297][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-05-04 01:06:37.301][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries. biodb.DEBUG[2024-05-04 01:06:37.308][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:06:37.309][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:06:37.311][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:06:37.339][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:06:37.340][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 01:06:37.341][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:06:37.342][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 01:06:37.351][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:06:37.353][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:06:37.354][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:37.355][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:37.358][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:06:37.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:06:37.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:37.383][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:37.384][ef$get] Asked field names are: charge. biodb.TRACE[2024-05-04 01:06:37.386][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-05-04 01:06:37.387][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:37.388][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:37.412][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-05-04 01:06:37.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-05-04 01:06:37.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:37.417][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:37.418][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-04 01:06:37.420][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 01:06:37.421][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:37.422][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:37.424][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 01:06:37.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 01:06:37.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:37.427][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:37.429][ef$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 01:06:37.430][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 01:06:37.431][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:37.433][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:37.434][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 01:06:37.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 01:06:37.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:37.438][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:37.440][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 01:06:37.441][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 01:06:37.442][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:37.443][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:37.445][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 01:06:37.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 01:06:37.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:37.449][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:37.450][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-04 01:06:37.451][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-04 01:06:37.453][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:37.455][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:37.458][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-04 01:06:37.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-04 01:06:37.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:37.464][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:37.466][ef$get] Asked field names are: mass. biodb.TRACE[2024-05-04 01:06:37.468][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:06:37.470][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:37.472][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:37.474][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-05-04 01:06:37.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:06:37.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:37.480][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:37.482][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:06:37.484][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:06:37.486][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:37.487][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:37.488][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:06:37.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:06:37.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:37.492][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:37.494][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 01:06:37.495][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 01:06:37.496][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:37.497][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:37.499][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 01:06:37.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 01:06:37.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:37.503][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:37.504][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-05-04 01:06:37.506][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-05-04 01:06:37.507][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:37.508][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:37.510][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-05-04 01:06:37.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-05-04 01:06:37.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:37.513][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:37.515][ef$get] Asked field names are: smiles. biodb.TRACE[2024-05-04 01:06:37.516][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-04 01:06:37.517][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:37.519][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:37.520][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-05-04 01:06:37.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-04 01:06:37.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:37.524][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:37.526][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:06:37.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:06:37.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:37.529][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:37.531][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:06:37.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:06:37.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:37.537][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:37.539][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:06:37.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:06:37.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:37.546][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:37.548][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:06:37.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:06:37.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:37.554][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:37.557][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:06:37.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:06:37.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:37.563][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:37.565][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:06:37.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:06:37.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:37.569][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:37.570][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:06:37.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:06:37.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:37.574][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:37.642][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:06:37.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:06:37.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:37.646][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:37.647][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:06:37.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:06:37.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:37.651][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:37.652][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:06:37.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:06:37.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:37.656][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:06:37.657][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440. biodb.TRACE[2024-05-04 01:06:37.706][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 01:06:37.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 01:06:37.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:37.713][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:37.715][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 01:06:37.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 01:06:37.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:37.721][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:37.759][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 01:06:37.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 01:06:37.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:37.766][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:37.768][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 01:06:37.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 01:06:37.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:37.774][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:37.776][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:06:37.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:06:37.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:37.782][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:37.784][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:06:37.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:06:37.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:37.791][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:37.793][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-04 01:06:37.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-04 01:06:37.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:37.799][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:37.801][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-04 01:06:37.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-04 01:06:37.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:37.807][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:37.809][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2024-05-04 01:06:37.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2024-05-04 01:06:37.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:37.815][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:37.816][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2024-05-04 01:06:37.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2024-05-04 01:06:37.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:37.821][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:37.853][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:06:37.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:06:37.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:37.860][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:37.905][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:06:37.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:06:37.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:37.911][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:37.928][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:06:37.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:06:37.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:37.935][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:37.937][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:06:37.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:06:37.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:37.943][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:37.945][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:06:37.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:06:37.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:37.951][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:37.956][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:06:37.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:06:37.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:37.962][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:37.964][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:06:37.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:06:37.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:37.970][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:37.972][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:06:37.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:06:37.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:37.976][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:37.978][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:06:37.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:06:37.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:37.981][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:37.983][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:06:37.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:06:37.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:37.986][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:37.988][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:06:37.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:06:37.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:37.991][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.012][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:06:38.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:06:38.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.017][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.019][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:06:38.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:06:38.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.023][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.025][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:06:38.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:06:38.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.031][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.033][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:06:38.035][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:06:38.037][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.039][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.042][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:06:38.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:06:38.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.048][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.079][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:06:38.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:06:38.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.086][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.089][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:06:38.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:06:38.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.095][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.096][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:06:38.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:06:38.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.105][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.107][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:06:38.108][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:06:38.110][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.111][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.113][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:06:38.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:06:38.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.116][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.135][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 01:06:38.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 01:06:38.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.142][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.144][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 01:06:38.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 01:06:38.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.151][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.153][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 01:06:38.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 01:06:38.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.160][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.162][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 01:06:38.165][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 01:06:38.167][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.169][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.171][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 01:06:38.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 01:06:38.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.175][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.194][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 01:06:38.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 01:06:38.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.199][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.200][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 01:06:38.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 01:06:38.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.205][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.206][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 01:06:38.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 01:06:38.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.210][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.211][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-04 01:06:38.213][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 01:06:38.215][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.216][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.223][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 01:06:38.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 01:06:38.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.227][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.245][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:06:38.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:06:38.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.249][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.251][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:06:38.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:06:38.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.255][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.256][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:06:38.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:06:38.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.260][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.261][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:06:38.262][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:06:38.263][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.265][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.266][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:06:38.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:06:38.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.270][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.285][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:06:38.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:06:38.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.292][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.295][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:06:38.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:06:38.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.301][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.303][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:06:38.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:06:38.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.309][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.311][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:06:38.312][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:06:38.313][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.314][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.316][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:06:38.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:06:38.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.320][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.331][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-05-04 01:06:38.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-05-04 01:06:38.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.336][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.337][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-05-04 01:06:38.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-05-04 01:06:38.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.341][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.342][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-05-04 01:06:38.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-05-04 01:06:38.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.346][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.347][ef$get] Asked field names are: charge. biodb.TRACE[2024-05-04 01:06:38.349][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-05-04 01:06:38.350][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.351][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.352][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-05-04 01:06:38.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-05-04 01:06:38.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.358][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.379][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-05-04 01:06:38.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-05-04 01:06:38.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.383][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.385][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-05-04 01:06:38.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-05-04 01:06:38.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.389][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.390][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-05-04 01:06:38.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-05-04 01:06:38.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.394][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.395][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-05-04 01:06:38.397][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-05-04 01:06:38.398][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.399][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.401][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-05-04 01:06:38.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-05-04 01:06:38.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.404][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.426][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-04 01:06:38.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-04 01:06:38.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.430][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.432][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-04 01:06:38.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-04 01:06:38.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.436][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.437][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-04 01:06:38.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-04 01:06:38.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.441][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.442][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-04 01:06:38.443][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-04 01:06:38.444][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.446][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.447][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-04 01:06:38.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-04 01:06:38.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.451][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.469][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-05-04 01:06:38.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-04 01:06:38.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.482][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.484][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-05-04 01:06:38.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-04 01:06:38.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.490][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.491][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-05-04 01:06:38.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-04 01:06:38.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.495][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.496][ef$get] Asked field names are: smiles. biodb.TRACE[2024-05-04 01:06:38.498][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-04 01:06:38.499][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.500][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.501][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-05-04 01:06:38.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-04 01:06:38.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.505][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.523][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 01:06:38.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 01:06:38.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.528][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.529][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 01:06:38.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 01:06:38.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.533][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.534][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 01:06:38.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 01:06:38.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.538][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.539][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 01:06:38.540][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 01:06:38.542][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.543][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.544][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 01:06:38.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 01:06:38.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.548][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.570][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 01:06:38.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 01:06:38.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.574][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.575][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 01:06:38.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 01:06:38.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.579][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.580][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 01:06:38.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 01:06:38.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.584][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.585][ef$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 01:06:38.587][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 01:06:38.588][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.589][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.590][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 01:06:38.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 01:06:38.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.594][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.615][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:06:38.617][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:06:38.618][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.619][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.638][ef$get] Asked field names are: charge. biodb.TRACE[2024-05-04 01:06:38.640][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-05-04 01:06:38.641][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.642][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.650][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-04 01:06:38.652][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 01:06:38.653][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.654][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.673][ef$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 01:06:38.676][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 01:06:38.678][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.680][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.698][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 01:06:38.700][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 01:06:38.701][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.702][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.718][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-04 01:06:38.721][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-04 01:06:38.722][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.724][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.736][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:06:38.738][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:06:38.740][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.742][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.756][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:06:38.759][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:06:38.761][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.763][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.780][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-05-04 01:06:38.782][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-05-04 01:06:38.783][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.784][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.798][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 01:06:38.800][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 01:06:38.801][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.809][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:38.824][ef$get] Asked field names are: smiles. biodb.TRACE[2024-05-04 01:06:38.827][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-04 01:06:38.829][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:38.831][ef$get] fields variable is a list. biodb.INFO [2024-05-04 01:06:38.872][biodb::testThat] biodb.INFO [2024-05-04 01:06:38.874][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. "). biodb.INFO [2024-05-04 01:06:38.876][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 01:06:38.877][biodb::testThat] biodb.DEBUG[2024-05-04 01:06:38.898][private$loadEntries] Creating entries from ids [1]: "15440". biodb.DEBUG[2024-05-04 01:06:38.908][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-05-04 01:06:38.917][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440". biodb.TRACE[2024-05-04 01:06:38.920][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-05-04 01:06:38.924][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml". biodb.DEBUG[2024-05-04 01:06:38.926][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-05-04 01:06:38.966][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-05-04 01:06:38.969][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-05-04 01:06:38.972][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:06:38.974][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:06:38.976][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:06:38.993][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:06:38.995][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:06:38.997][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:06:38.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-04 01:06:39.004][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:06:39.006][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:06:39.008][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:39.010][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:39.013][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:06:39.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:06:39.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:39.019][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:39.047][ef$get] Asked field names are: charge. biodb.TRACE[2024-05-04 01:06:39.050][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-05-04 01:06:39.052][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:39.054][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:39.056][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-05-04 01:06:39.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-05-04 01:06:39.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:39.062][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:39.064][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-04 01:06:39.065][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 01:06:39.067][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:39.068][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:39.069][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 01:06:39.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 01:06:39.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:39.073][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:39.075][ef$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 01:06:39.076][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 01:06:39.077][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:39.079][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:39.080][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 01:06:39.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 01:06:39.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:39.084][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:39.086][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 01:06:39.087][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 01:06:39.088][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:39.090][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:39.098][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 01:06:39.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 01:06:39.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:39.102][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:39.104][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-04 01:06:39.105][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-04 01:06:39.106][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:39.108][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:39.110][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-04 01:06:39.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-04 01:06:39.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:39.114][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:39.115][ef$get] Asked field names are: mass. biodb.TRACE[2024-05-04 01:06:39.117][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:06:39.118][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:39.119][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:39.121][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-05-04 01:06:39.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:06:39.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:39.124][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:39.126][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:06:39.127][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:06:39.128][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:39.130][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:39.131][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:06:39.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:06:39.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:39.136][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:39.137][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 01:06:39.139][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 01:06:39.140][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:39.141][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:39.143][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 01:06:39.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 01:06:39.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:39.147][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:39.148][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-05-04 01:06:39.150][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-05-04 01:06:39.152][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:39.154][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:39.156][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-05-04 01:06:39.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-05-04 01:06:39.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:39.162][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:39.164][ef$get] Asked field names are: smiles. biodb.TRACE[2024-05-04 01:06:39.166][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-04 01:06:39.167][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:39.169][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:39.170][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-05-04 01:06:39.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-04 01:06:39.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:39.174][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:39.176][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:06:39.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:06:39.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:39.179][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:39.181][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:06:39.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:06:39.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:39.187][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:39.188][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:06:39.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:06:39.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:39.194][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:39.196][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:06:39.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:06:39.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:39.201][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:39.203][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:06:39.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:06:39.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:39.208][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:39.210][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:06:39.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:06:39.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:39.215][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:39.217][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:06:39.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:06:39.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:39.222][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:39.224][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:06:39.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:06:39.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:39.230][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:39.231][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:06:39.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:06:39.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:39.237][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:39.238][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:06:39.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:06:39.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:39.244][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:06:39.245][self$createEntryFromContent] Accession numbers: 15440. biodb.TRACE[2024-05-04 01:06:39.247][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt. biodb.TRACE[2024-05-04 01:06:39.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt. biodb.TRACE[2024-05-04 01:06:39.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:39.253][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:39.254][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min. biodb.TRACE[2024-05-04 01:06:39.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min. biodb.TRACE[2024-05-04 01:06:39.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:39.260][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:39.262][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max. biodb.TRACE[2024-05-04 01:06:39.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max. biodb.TRACE[2024-05-04 01:06:39.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:39.268][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.INFO [2024-05-04 01:06:39.295][biodb::testThat] biodb.INFO [2024-05-04 01:06:39.298][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field "). biodb.INFO [2024-05-04 01:06:39.300][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 01:06:39.301][biodb::testThat] biodb.TRACE[2024-05-04 01:06:39.306][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 01:06:39.308][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 01:06:39.310][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:39.311][ef$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:06:39.313][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name". biodb.TRACE[2024-05-04 01:06:39.375][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 01:06:39.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 01:06:39.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:39.380][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:39.382][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 01:06:39.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 01:06:39.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:39.386][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:39.387][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 01:06:39.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 01:06:39.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:39.391][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:06:39.395][function(conn, opt)] With value "squalene". biodb.DEBUG[2024-05-04 01:06:39.400][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 01:06:39.421][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-05-04 01:06:39.439][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05". biodb.TRACE[2024-05-04 01:06:39.442][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-05-04 01:06:39.446][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content". biodb.DEBUG[2024-05-04 01:06:39.469][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 01:06:39.475][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-05-04 01:06:39.477][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2". biodb.TRACE[2024-05-04 01:06:39.479][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-05-04 01:06:39.494][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content". biodb.DEBUG[2024-05-04 01:06:39.498][function(conn, opt)] With found IDs [1]: "15440". biodb.TRACE[2024-05-04 01:06:39.542][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:06:39.544][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:06:39.546][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:39.548][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:39.549][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:06:39.551][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:06:39.552][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:39.554][ef$get] fields variable is a list. biodb.INFO [2024-05-04 01:06:39.571][biodb::testThat] biodb.INFO [2024-05-04 01:06:39.572][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. "). biodb.INFO [2024-05-04 01:06:39.573][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 01:06:39.574][biodb::testThat] biodb.TRACE[2024-05-04 01:06:39.613][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 01:06:39.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 01:06:39.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:39.618][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:39.619][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 01:06:39.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 01:06:39.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:39.624][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:39.625][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 01:06:39.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 01:06:39.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:39.629][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:06:39.692][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 01:06:39.697][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-05-04 01:06:39.699][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2". biodb.TRACE[2024-05-04 01:06:39.702][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-05-04 01:06:39.704][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content". biodb.INFO [2024-05-04 01:06:39.746][biodb::testThat] biodb.INFO [2024-05-04 01:06:39.749][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. "). biodb.INFO [2024-05-04 01:06:39.751][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 01:06:39.753][biodb::testThat] biodb.TRACE[2024-05-04 01:06:39.811][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 01:06:39.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 01:06:39.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:39.816][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:39.817][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 01:06:39.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 01:06:39.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:39.822][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:39.824][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 01:06:39.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 01:06:39.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:39.828][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:39.829][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 01:06:39.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 01:06:39.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:39.834][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:39.837][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:06:39.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:06:39.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:39.842][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:39.844][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:06:39.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:06:39.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:39.848][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:39.850][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-04 01:06:39.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-04 01:06:39.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:39.854][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:39.855][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-04 01:06:39.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-04 01:06:39.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:39.860][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:39.862][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2024-05-04 01:06:39.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2024-05-04 01:06:39.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:39.867][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:39.869][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2024-05-04 01:06:39.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2024-05-04 01:06:39.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:39.873][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:39.891][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 01:06:39.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 01:06:39.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:39.896][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:39.897][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 01:06:39.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 01:06:39.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:39.901][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:39.902][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 01:06:39.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 01:06:39.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:39.908][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:39.910][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 01:06:39.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 01:06:39.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:39.916][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:39.917][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:06:39.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:06:39.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:39.923][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:39.926][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:06:39.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:06:39.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:39.932][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:39.934][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-04 01:06:39.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-04 01:06:39.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:39.939][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:39.941][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-04 01:06:39.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-04 01:06:39.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:39.947][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:39.950][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2024-05-04 01:06:39.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2024-05-04 01:06:39.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:39.956][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:06:39.957][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2024-05-04 01:06:39.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2024-05-04 01:06:39.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:06:39.962][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.INFO [2024-05-04 01:06:39.986][biodb::testThat] biodb.INFO [2024-05-04 01:06:39.988][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. "). biodb.INFO [2024-05-04 01:06:39.989][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 01:06:39.990][biodb::testThat] biodb.INFO [2024-05-04 01:06:40.004][biodb::testThat] biodb.INFO [2024-05-04 01:06:40.006][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. "). biodb.INFO [2024-05-04 01:06:40.007][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 01:06:40.009][biodb::testThat] biodb.INFO [2024-05-04 01:06:40.028][biodb::testThat] biodb.INFO [2024-05-04 01:06:40.030][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. "). biodb.INFO [2024-05-04 01:06:40.031][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 01:06:40.033][biodb::testThat] biodb.DEBUG[2024-05-04 01:06:40.038][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440". biodb.DEBUG[2024-05-04 01:06:50.571][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440. biodb.INFO [2024-05-04 01:07:03.678][biodb::testThat] biodb.INFO [2024-05-04 01:07:03.679][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. "). biodb.INFO [2024-05-04 01:07:03.680][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 01:07:03.682][biodb::testThat] biodb.DEBUG[2024-05-04 01:07:08.774][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 01:07:15.569][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 01:07:15.571][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 01:07:15.572][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:07:15.573][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:07:15.575][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:07:15.576][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:07:15.577][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:07:15.579][ef$get] fields variable is a list. biodb.INFO [2024-05-04 01:07:15.594][biodb::testThat] biodb.INFO [2024-05-04 01:07:15.599][biodb::testThat] Running test function test.searchCompound (" We can search for a compound "). biodb.INFO [2024-05-04 01:07:15.600][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 01:07:15.602][biodb::testThat] biodb.TRACE[2024-05-04 01:07:15.625][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 01:07:15.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 01:07:15.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:07:15.629][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:07:15.630][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 01:07:15.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 01:07:15.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:07:15.634][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:07:15.636][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 01:07:15.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 01:07:15.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:07:15.640][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:07:15.729][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL". biodb.INFO [2024-05-04 01:07:15.734][self$getFolderPath] Create cache folder "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649". biodb.DEBUG[2024-05-04 01:07:15.736][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-04 01:07:15.738][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-04 01:07:15.740][private$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 01:07:23.830][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 01:07:24.382][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.INFO [2024-05-04 01:07:24.386][self$getFolderPath] Create cache folder "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649". biodb.TRACE[2024-05-04 01:07:24.389][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content" biodb.TRACE[2024-05-04 01:07:24.421][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request" biodb.DEBUG[2024-05-04 01:07:24.497][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-05-04 01:07:24.502][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-05-04 01:07:24.504][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2". biodb.TRACE[2024-05-04 01:07:24.506][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-05-04 01:07:24.510][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content". biodb.TRACE[2024-05-04 01:07:24.566][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-05-04 01:07:24.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-05-04 01:07:24.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:07:24.572][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:07:24.590][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:07:24.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:07:24.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:07:24.595][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:07:24.596][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:07:24.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:07:24.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:07:24.600][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:07:24.602][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:07:24.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:07:24.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:07:24.607][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:07:24.608][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:07:24.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:07:24.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:07:24.614][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:07:24.616][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:07:24.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:07:24.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:07:24.623][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:07:24.632][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-05-04 01:07:24.652][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-04 01:07:24.654][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-04 01:07:24.675][private$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 01:07:25.040][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 01:07:25.400][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-05-04 01:07:25.405][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content" biodb.TRACE[2024-05-04 01:07:25.413][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request" biodb.DEBUG[2024-05-04 01:07:25.419][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:07:25.422][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:07:25.424][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:07:25.440][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:07:25.442][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 01:07:25.451][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:07:25.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:07:25.455][private$loadEntries] Creating entries from ids [1]: "192288". biodb.DEBUG[2024-05-04 01:07:25.504][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-05-04 01:07:25.508][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288". biodb.TRACE[2024-05-04 01:07:25.510][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-05-04 01:07:25.513][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-05-04 01:07:25.515][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-05-04 01:07:25.516][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-05-04 01:07:25.518][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-05-04 01:07:25.519][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-05-04 01:07:25.522][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:07:25.524][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:07:25.526][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:07:25.543][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:07:25.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:07:25.547][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:07:25.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:07:25.551][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288". biodb.DEBUG[2024-05-04 01:07:25.556][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-04 01:07:25.558][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-04 01:07:25.561][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288". biodb.TRACE[2024-05-04 01:07:36.422][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 01:07:46.795][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-05-04 01:07:46.798][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content" biodb.TRACE[2024-05-04 01:07:46.803][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request" biodb.TRACE[2024-05-04 01:07:46.808][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml" biodb.DEBUG[2024-05-04 01:07:46.810][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-05-04 01:07:46.820][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-05-04 01:07:46.822][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-05-04 01:07:46.824][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:07:46.825][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:07:46.826][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:07:46.846][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:07:46.847][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:07:46.848][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:07:46.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-04 01:07:46.853][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:07:46.854][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:07:46.856][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:07:46.857][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:07:46.859][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:07:46.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:07:46.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:07:46.862][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:07:46.864][ef$get] Asked field names are: charge. biodb.TRACE[2024-05-04 01:07:46.865][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-05-04 01:07:46.867][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:07:46.868][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:07:46.870][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-04 01:07:46.871][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 01:07:46.872][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:07:46.874][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:07:46.875][ef$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 01:07:46.877][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 01:07:46.878][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:07:46.879][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:07:46.881][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 01:07:46.882][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 01:07:46.883][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:07:46.885][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:07:46.886][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-04 01:07:46.888][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-04 01:07:46.889][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:07:46.890][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:07:46.892][ef$get] Asked field names are: mass. biodb.TRACE[2024-05-04 01:07:46.893][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:07:46.895][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:07:46.896][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:07:46.898][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:07:46.899][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:07:46.901][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:07:46.902][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:07:46.903][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 01:07:46.905][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 01:07:46.906][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:07:46.907][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:07:46.909][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-05-04 01:07:46.910][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-05-04 01:07:46.911][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:07:46.912][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:07:46.914][ef$get] Asked field names are: smiles. biodb.TRACE[2024-05-04 01:07:46.916][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-04 01:07:46.917][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:07:46.918][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:07:46.920][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:07:46.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:07:46.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:07:46.923][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:07:46.924][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:07:46.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:07:46.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:07:46.928][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:07:46.930][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:07:46.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:07:46.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:07:46.934][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:07:46.935][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:07:46.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:07:46.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:07:46.939][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:07:46.940][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:07:46.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:07:46.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:07:46.945][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:07:46.947][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:07:46.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:07:46.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:07:46.951][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:07:46.953][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:07:46.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:07:46.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:07:46.957][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:07:46.959][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:07:46.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:07:46.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:07:46.965][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:07:46.967][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:07:46.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:07:46.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:07:46.973][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:07:46.982][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:07:46.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:07:46.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:07:46.986][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:07:46.988][self$createEntryFromContent] Accession numbers: . biodb.DEBUG[2024-05-04 01:07:46.989][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL. biodb.DEBUG[2024-05-04 01:07:47.001][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-05-04 01:07:47.005][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-04 01:07:47.007][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-04 01:07:47.009][private$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 01:07:47.363][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 01:07:47.713][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-05-04 01:07:47.716][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content" biodb.TRACE[2024-05-04 01:07:47.722][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request" biodb.DEBUG[2024-05-04 01:07:47.737][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:07:47.738][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:07:47.740][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:07:47.778][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:07:47.779][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:07:47.781][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:07:47.783][FUN] Functions in observer BiodbConfig: [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 01:07:47.785][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:07:47.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:07:47.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:07:47.791][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:07:47.793][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:07:47.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:07:47.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:07:47.799][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:07:47.801][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:07:47.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:07:47.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:07:47.808][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:07:47.810][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:07:47.812][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:07:47.814][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:07:47.856][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:07:47.858][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 01:07:47.859][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:07:47.860][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 01:07:47.862][private$loadEntries] Creating entries from ids [1]: "209892". biodb.DEBUG[2024-05-04 01:07:47.863][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-05-04 01:07:47.866][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892". biodb.TRACE[2024-05-04 01:07:47.868][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-05-04 01:07:47.870][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-05-04 01:07:47.872][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-05-04 01:07:47.874][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-05-04 01:07:47.876][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-05-04 01:07:47.878][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-05-04 01:07:47.906][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:07:47.907][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:07:47.909][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:07:47.916][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:07:47.918][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 01:07:47.919][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:07:47.920][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 01:07:47.922][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892". biodb.DEBUG[2024-05-04 01:07:47.925][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-04 01:07:47.927][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-04 01:07:47.929][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892". biodb.TRACE[2024-05-04 01:07:58.731][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 01:08:09.097][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-05-04 01:08:09.102][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content" biodb.TRACE[2024-05-04 01:08:09.109][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request" biodb.TRACE[2024-05-04 01:08:09.115][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml" biodb.DEBUG[2024-05-04 01:08:09.119][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-05-04 01:08:09.121][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-05-04 01:08:09.124][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-05-04 01:08:09.127][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:08:09.129][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:08:09.131][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:08:09.145][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:08:09.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:08:09.148][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:08:09.149][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-04 01:08:09.152][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:08:09.153][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:08:09.155][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:08:09.156][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:08:09.157][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:08:09.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:08:09.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:08:09.161][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:08:09.163][ef$get] Asked field names are: charge. biodb.TRACE[2024-05-04 01:08:09.164][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-05-04 01:08:09.165][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:08:09.167][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:08:09.168][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-04 01:08:09.170][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 01:08:09.171][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:08:09.172][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:08:09.174][ef$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 01:08:09.175][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 01:08:09.176][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:08:09.178][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:08:09.179][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 01:08:09.181][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 01:08:09.182][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:08:09.183][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:08:09.184][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-04 01:08:09.186][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-04 01:08:09.187][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:08:09.188][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:08:09.190][ef$get] Asked field names are: mass. biodb.TRACE[2024-05-04 01:08:09.191][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:08:09.192][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:08:09.194][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:08:09.195][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:08:09.197][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:08:09.198][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:08:09.200][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:08:09.201][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 01:08:09.203][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 01:08:09.204][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:08:09.205][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:08:09.207][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-05-04 01:08:09.208][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-05-04 01:08:09.210][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:08:09.211][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:08:09.213][ef$get] Asked field names are: smiles. biodb.TRACE[2024-05-04 01:08:09.215][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-04 01:08:09.226][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:08:09.227][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:08:09.230][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:08:09.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:08:09.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:08:09.235][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:08:09.236][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:08:09.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:08:09.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:08:09.240][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:08:09.241][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:08:09.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:08:09.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:08:09.245][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:08:09.246][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:08:09.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:08:09.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:08:09.250][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:08:09.251][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:08:09.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:08:09.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:08:09.255][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:08:09.257][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:08:09.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:08:09.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:08:09.260][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:08:09.262][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:08:09.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:08:09.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:08:09.265][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:08:09.267][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:08:09.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:08:09.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:08:09.271][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:08:09.272][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:08:09.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:08:09.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:08:09.276][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:08:09.277][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:08:09.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:08:09.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:08:09.281][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:08:09.282][self$createEntryFromContent] Accession numbers: . biodb.DEBUG[2024-05-04 01:08:09.283][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL. biodb.DEBUG[2024-05-04 01:08:09.285][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:08:09.286][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:08:09.287][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:08:09.300][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:08:09.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:08:09.303][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:08:09.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:08:09.306][private$loadEntries] Creating entries from ids [1]: "227078". biodb.DEBUG[2024-05-04 01:08:09.307][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-05-04 01:08:09.309][cch$loadFileContent] Trying to load 1 files from cache: [1]: "227078". biodb.TRACE[2024-05-04 01:08:09.311][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-05-04 01:08:09.312][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-05-04 01:08:09.314][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-05-04 01:08:09.315][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-05-04 01:08:09.316][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-05-04 01:08:09.317][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-05-04 01:08:09.320][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:08:09.321][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:08:09.323][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:08:09.339][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:08:09.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:08:09.342][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:08:09.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:08:09.345][scheduler$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 01:08:09.348][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-04 01:08:09.349][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-04 01:08:09.351][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=227078". biodb.TRACE[2024-05-04 01:08:19.704][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=227078). biodb.DEBUG[2024-05-04 01:08:30.059][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-05-04 01:08:30.064][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ccc0d17769ea5be638da2084b1bd4710.content" biodb.TRACE[2024-05-04 01:08:30.071][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ccc0d17769ea5be638da2084b1bd4710.request" biodb.TRACE[2024-05-04 01:08:30.078][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/227078.xml" biodb.DEBUG[2024-05-04 01:08:30.082][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-05-04 01:08:30.085][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-05-04 01:08:30.088][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-05-04 01:08:30.091][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:08:30.093][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:08:30.095][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:08:30.118][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:08:30.120][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:08:30.122][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:08:30.124][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 01:08:30.128][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:08:30.131][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:08:30.133][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:08:30.134][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:08:30.137][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:08:30.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:08:30.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:08:30.143][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:08:30.145][ef$get] Asked field names are: charge. biodb.TRACE[2024-05-04 01:08:30.147][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-05-04 01:08:30.149][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:08:30.151][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:08:30.154][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-04 01:08:30.156][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 01:08:30.158][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:08:30.160][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:08:30.163][ef$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 01:08:30.165][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 01:08:30.167][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:08:30.169][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:08:30.171][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 01:08:30.173][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 01:08:30.175][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:08:30.177][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:08:30.179][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-04 01:08:30.181][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-04 01:08:30.183][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:08:30.185][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:08:30.188][ef$get] Asked field names are: mass. biodb.TRACE[2024-05-04 01:08:30.190][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:08:30.192][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:08:30.194][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:08:30.196][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:08:30.199][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:08:30.201][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:08:30.202][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:08:30.205][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 01:08:30.207][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 01:08:30.209][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:08:30.211][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:08:30.214][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-05-04 01:08:30.216][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-05-04 01:08:30.218][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:08:30.220][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:08:30.222][ef$get] Asked field names are: smiles. biodb.TRACE[2024-05-04 01:08:30.224][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-04 01:08:30.226][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:08:30.228][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:08:30.231][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:08:30.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:08:30.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:08:30.237][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:08:30.239][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:08:30.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:08:30.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:08:30.245][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:08:30.247][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:08:30.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:08:30.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:08:30.253][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:08:30.255][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:08:30.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:08:30.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:08:30.261][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:08:30.263][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:08:30.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:08:30.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:08:30.269][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:08:30.271][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:08:30.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:08:30.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:08:30.277][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:08:30.279][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:08:30.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:08:30.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:08:30.285][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:08:30.288][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:08:30.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:08:30.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:08:30.294][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:08:30.296][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:08:30.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:08:30.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:08:30.302][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:08:30.304][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:08:30.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:08:30.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:08:30.311][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:08:30.313][self$createEntryFromContent] Accession numbers: . biodb.DEBUG[2024-05-04 01:08:30.315][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL. biodb.DEBUG[2024-05-04 01:08:30.327][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 01:08:30.332][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-04 01:08:30.333][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-04 01:08:30.336][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.TRACE[2024-05-04 01:08:30.682][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL). biodb.DEBUG[2024-05-04 01:08:31.040][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-05-04 01:08:31.044][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.content" biodb.TRACE[2024-05-04 01:08:31.052][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.request" biodb.DEBUG[2024-05-04 01:08:31.118][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-05-04 01:08:31.122][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-05-04 01:08:31.124][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2". biodb.TRACE[2024-05-04 01:08:31.126][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-05-04 01:08:31.128][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content". biodb.DEBUG[2024-05-04 01:08:31.132][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:08:31.133][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:08:31.134][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:08:31.141][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:08:31.143][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:08:31.144][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:08:31.145][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-04 01:08:31.147][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:08:31.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:08:31.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:08:31.151][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:08:31.152][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:08:31.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:08:31.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:08:31.156][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:08:31.157][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:08:31.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:08:31.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:08:31.161][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:08:31.163][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:08:31.164][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:08:31.166][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:08:31.180][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:08:31.182][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:08:31.183][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:08:31.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:08:31.186][private$loadEntries] Creating entries from ids [1]: "26747". biodb.DEBUG[2024-05-04 01:08:31.187][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-05-04 01:08:31.190][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747". biodb.TRACE[2024-05-04 01:08:31.192][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-05-04 01:08:31.193][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-05-04 01:08:31.194][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-05-04 01:08:31.196][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-05-04 01:08:31.197][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-05-04 01:08:31.198][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-05-04 01:08:31.201][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:08:31.202][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:08:31.204][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:08:31.211][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:08:31.213][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:08:31.214][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:08:31.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:08:31.217][scheduler$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 01:08:31.227][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-04 01:08:31.228][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-04 01:08:31.230][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747". biodb.TRACE[2024-05-04 01:08:41.585][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747). biodb.DEBUG[2024-05-04 01:08:51.940][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-05-04 01:08:51.945][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content" biodb.TRACE[2024-05-04 01:08:51.950][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request" biodb.TRACE[2024-05-04 01:08:51.955][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml" biodb.DEBUG[2024-05-04 01:08:51.959][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-05-04 01:08:51.962][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-05-04 01:08:51.965][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-05-04 01:08:51.968][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:08:51.970][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:08:51.972][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:08:51.994][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:08:51.995][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 01:08:51.997][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:08:51.998][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 01:08:52.001][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:08:52.002][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:08:52.003][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:08:52.004][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:08:52.006][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:08:52.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:08:52.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:08:52.012][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:08:52.014][ef$get] Asked field names are: charge. biodb.TRACE[2024-05-04 01:08:52.017][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-05-04 01:08:52.019][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:08:52.021][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:08:52.024][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-04 01:08:52.027][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 01:08:52.028][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:08:52.030][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:08:52.033][ef$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 01:08:52.035][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 01:08:52.037][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:08:52.039][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:08:52.040][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 01:08:52.042][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 01:08:52.043][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:08:52.044][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:08:52.046][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-04 01:08:52.047][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-04 01:08:52.048][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:08:52.049][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:08:52.051][ef$get] Asked field names are: mass. biodb.TRACE[2024-05-04 01:08:52.052][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:08:52.054][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:08:52.055][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:08:52.056][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:08:52.058][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:08:52.059][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:08:52.061][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:08:52.063][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 01:08:52.065][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 01:08:52.066][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:08:52.067][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:08:52.069][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-05-04 01:08:52.071][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-05-04 01:08:52.072][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:08:52.073][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:08:52.075][ef$get] Asked field names are: smiles. biodb.TRACE[2024-05-04 01:08:52.076][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-04 01:08:52.077][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:08:52.079][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:08:52.080][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:08:52.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:08:52.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:08:52.084][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:08:52.086][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:08:52.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:08:52.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:08:52.090][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:08:52.091][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:08:52.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:08:52.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:08:52.095][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:08:52.096][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:08:52.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:08:52.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:08:52.100][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:08:52.102][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:08:52.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:08:52.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:08:52.106][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:08:52.142][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:08:52.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:08:52.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:08:52.149][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:08:52.152][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:08:52.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:08:52.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:08:52.156][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:08:52.157][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:08:52.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:08:52.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:08:52.161][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:08:52.163][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:08:52.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:08:52.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:08:52.167][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:08:52.168][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:08:52.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:08:52.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:08:52.172][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:08:52.174][self$createEntryFromContent] Accession numbers: . biodb.DEBUG[2024-05-04 01:08:52.175][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL. biodb.DEBUG[2024-05-04 01:08:52.177][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:08:52.178][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:08:52.179][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:08:52.195][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:08:52.197][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 01:08:52.198][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:08:52.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:08:52.201][private$loadEntries] Creating entries from ids [1]: "59285". biodb.DEBUG[2024-05-04 01:08:52.202][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-05-04 01:08:52.205][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285". biodb.TRACE[2024-05-04 01:08:52.207][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-05-04 01:08:52.208][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-05-04 01:08:52.209][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-05-04 01:08:52.211][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-05-04 01:08:52.213][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-05-04 01:08:52.214][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-05-04 01:08:52.217][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:08:52.219][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:08:52.220][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:08:52.234][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:08:52.236][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 01:08:52.238][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:08:52.239][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.DEBUG[2024-05-04 01:08:52.241][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285". biodb.DEBUG[2024-05-04 01:08:52.244][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-04 01:08:52.245][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-04 01:08:52.247][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285". biodb.TRACE[2024-05-04 01:09:02.623][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 01:09:12.989][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-05-04 01:09:12.993][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content" biodb.TRACE[2024-05-04 01:09:13.001][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request" biodb.TRACE[2024-05-04 01:09:13.007][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml" biodb.DEBUG[2024-05-04 01:09:13.010][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-05-04 01:09:13.013][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-05-04 01:09:13.016][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-05-04 01:09:13.019][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:09:13.021][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:09:13.023][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:09:13.036][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:09:13.039][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:09:13.040][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:09:13.042][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-04 01:09:13.046][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:09:13.048][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:09:13.049][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:09:13.050][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:09:13.052][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:09:13.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:09:13.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:09:13.056][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:09:13.058][ef$get] Asked field names are: charge. biodb.TRACE[2024-05-04 01:09:13.061][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-05-04 01:09:13.064][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:09:13.066][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:09:13.068][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-04 01:09:13.070][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 01:09:13.072][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:09:13.083][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:09:13.089][ef$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 01:09:13.092][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 01:09:13.094][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:09:13.096][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:09:13.097][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 01:09:13.099][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 01:09:13.100][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:09:13.102][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:09:13.104][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-04 01:09:13.105][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-04 01:09:13.106][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:09:13.108][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:09:13.109][ef$get] Asked field names are: mass. biodb.TRACE[2024-05-04 01:09:13.111][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:09:13.112][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:09:13.114][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:09:13.116][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:09:13.119][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:09:13.121][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:09:13.123][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:09:13.125][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 01:09:13.128][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 01:09:13.130][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:09:13.132][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:09:13.134][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-05-04 01:09:13.135][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-05-04 01:09:13.136][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:09:13.138][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:09:13.139][ef$get] Asked field names are: smiles. biodb.TRACE[2024-05-04 01:09:13.140][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-04 01:09:13.142][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:09:13.143][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:09:13.145][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:09:13.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:09:13.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:09:13.148][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:09:13.150][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:09:13.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:09:13.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:09:13.153][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:09:13.155][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:09:13.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:09:13.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:09:13.159][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:09:13.160][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:09:13.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:09:13.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:09:13.164][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:09:13.165][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:09:13.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:09:13.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:09:13.169][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:09:13.170][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:09:13.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:09:13.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:09:13.174][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:09:13.175][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:09:13.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:09:13.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:09:13.179][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:09:13.181][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:09:13.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:09:13.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:09:13.185][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:09:13.186][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:09:13.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:09:13.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:09:13.190][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:09:13.191][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:09:13.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:09:13.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:09:13.195][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:09:13.196][self$createEntryFromContent] Accession numbers: . biodb.DEBUG[2024-05-04 01:09:13.198][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL. biodb.DEBUG[2024-05-04 01:09:13.199][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:09:13.200][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:09:13.201][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:09:13.234][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:09:13.236][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:09:13.237][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:09:13.238][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:09:13.240][private$loadEntries] Creating entries from ids [1]: "75174". biodb.DEBUG[2024-05-04 01:09:13.241][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-05-04 01:09:13.243][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174". biodb.TRACE[2024-05-04 01:09:13.245][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-05-04 01:09:13.247][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-05-04 01:09:13.248][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-05-04 01:09:13.249][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-05-04 01:09:13.251][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-05-04 01:09:13.252][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-05-04 01:09:13.255][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:09:13.256][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:09:13.257][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:09:13.300][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:09:13.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:09:13.303][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:09:13.305][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:09:13.307][scheduler$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 01:09:13.310][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-04 01:09:13.311][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-04 01:09:13.313][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174". biodb.TRACE[2024-05-04 01:09:23.669][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174). biodb.DEBUG[2024-05-04 01:09:34.773][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-05-04 01:09:34.778][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content" biodb.TRACE[2024-05-04 01:09:34.785][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request" biodb.TRACE[2024-05-04 01:09:34.791][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml" biodb.DEBUG[2024-05-04 01:09:34.798][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-05-04 01:09:34.800][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-05-04 01:09:34.803][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-05-04 01:09:34.806][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:09:34.808][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:09:34.810][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:09:34.829][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:09:34.832][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:09:34.834][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:09:34.836][FUN] Functions in observer BiodbConfig: [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 01:09:34.840][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:09:34.842][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:09:34.844][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:09:34.846][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:09:34.848][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:09:34.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:09:34.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:09:34.855][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:09:34.857][ef$get] Asked field names are: charge. biodb.TRACE[2024-05-04 01:09:34.858][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-05-04 01:09:34.860][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:09:34.861][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:09:34.863][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-04 01:09:34.864][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 01:09:34.865][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:09:34.867][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:09:34.869][ef$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 01:09:34.870][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 01:09:34.871][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:09:34.873][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:09:34.874][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 01:09:34.876][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 01:09:34.877][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:09:34.878][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:09:34.880][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-04 01:09:34.881][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-04 01:09:34.883][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:09:34.885][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:09:34.887][ef$get] Asked field names are: mass. biodb.TRACE[2024-05-04 01:09:34.888][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:09:34.890][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:09:34.891][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:09:34.893][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:09:34.895][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:09:34.897][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:09:34.899][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:09:34.902][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 01:09:34.904][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 01:09:34.906][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:09:34.908][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:09:34.911][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-05-04 01:09:34.913][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-05-04 01:09:34.915][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:09:34.917][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:09:34.920][ef$get] Asked field names are: smiles. biodb.TRACE[2024-05-04 01:09:34.922][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-04 01:09:34.924][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:09:34.926][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:09:34.928][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:09:34.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:09:34.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:09:34.935][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:09:34.937][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:09:34.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:09:34.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:09:34.944][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:09:34.946][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:09:34.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:09:34.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:09:34.952][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:09:34.954][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:09:34.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:09:34.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:09:34.972][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:09:34.974][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:09:34.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:09:34.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:09:34.980][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:09:34.983][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:09:34.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:09:34.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:09:34.989][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:09:34.991][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:09:34.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:09:34.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:09:34.998][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:09:35.000][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:09:35.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:09:35.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:09:35.007][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:09:35.009][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:09:35.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:09:35.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:09:35.015][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:09:35.017][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:09:35.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:09:35.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:09:35.023][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:09:35.025][self$createEntryFromContent] Accession numbers: . biodb.DEBUG[2024-05-04 01:09:35.028][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL. biodb.DEBUG[2024-05-04 01:09:35.030][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:09:35.032][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:09:35.034][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:09:35.230][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:09:35.232][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:09:35.234][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:09:35.235][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:09:35.237][private$loadEntries] Creating entries from ids [1]: "15441". biodb.DEBUG[2024-05-04 01:09:35.239][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-05-04 01:09:35.241][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441". biodb.TRACE[2024-05-04 01:09:35.243][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-05-04 01:09:35.244][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-05-04 01:09:35.245][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-05-04 01:09:35.247][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-05-04 01:09:35.248][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-05-04 01:09:35.250][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-05-04 01:09:35.253][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:09:35.255][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:09:35.256][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:09:35.273][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:09:35.275][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:09:35.277][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:09:35.279][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:09:35.282][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441". biodb.DEBUG[2024-05-04 01:09:35.287][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-04 01:09:35.288][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-04 01:09:35.290][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441". biodb.TRACE[2024-05-04 01:09:45.648][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 01:09:56.008][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-05-04 01:09:56.012][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content" biodb.TRACE[2024-05-04 01:09:56.020][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request" biodb.TRACE[2024-05-04 01:09:56.026][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml" biodb.DEBUG[2024-05-04 01:09:56.030][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-05-04 01:09:56.033][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-05-04 01:09:56.036][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-05-04 01:09:56.039][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:09:56.041][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:09:56.043][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:09:56.061][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:09:56.063][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:09:56.065][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:09:56.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-04 01:09:56.071][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:09:56.074][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:09:56.076][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:09:56.079][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:09:56.081][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:09:56.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:09:56.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:09:56.087][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:09:56.098][ef$get] Asked field names are: charge. biodb.TRACE[2024-05-04 01:09:56.103][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-05-04 01:09:56.105][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:09:56.107][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:09:56.110][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-04 01:09:56.112][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 01:09:56.114][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:09:56.116][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:09:56.119][ef$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 01:09:56.121][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 01:09:56.123][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:09:56.125][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:09:56.128][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 01:09:56.130][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 01:09:56.132][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:09:56.134][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:09:56.136][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-04 01:09:56.138][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-04 01:09:56.140][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:09:56.142][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:09:56.145][ef$get] Asked field names are: mass. biodb.TRACE[2024-05-04 01:09:56.147][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:09:56.149][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:09:56.151][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:09:56.154][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:09:56.156][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:09:56.158][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:09:56.160][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:09:56.162][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 01:09:56.165][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 01:09:56.167][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:09:56.169][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:09:56.172][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-05-04 01:09:56.174][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-05-04 01:09:56.175][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:09:56.176][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:09:56.178][ef$get] Asked field names are: smiles. biodb.TRACE[2024-05-04 01:09:56.179][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-04 01:09:56.180][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:09:56.182][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:09:56.184][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:09:56.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:09:56.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:09:56.190][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:09:56.192][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:09:56.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:09:56.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:09:56.199][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:09:56.201][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:09:56.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:09:56.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:09:56.206][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:09:56.207][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:09:56.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:09:56.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:09:56.211][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:09:56.212][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:09:56.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:09:56.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:09:56.216][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:09:56.218][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:09:56.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:09:56.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:09:56.222][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:09:56.223][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:09:56.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:09:56.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:09:56.227][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:09:56.228][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:09:56.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:09:56.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:09:56.232][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:09:56.233][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:09:56.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:09:56.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:09:56.237][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:09:56.238][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:09:56.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:09:56.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:09:56.242][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:09:56.243][self$createEntryFromContent] Accession numbers: . biodb.DEBUG[2024-05-04 01:09:56.244][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL. biodb.DEBUG[2024-05-04 01:09:56.246][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:09:56.247][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:09:56.248][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:09:56.256][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:09:56.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:09:56.258][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:09:56.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:09:56.261][private$loadEntries] Creating entries from ids [1]: "15442". biodb.DEBUG[2024-05-04 01:09:56.262][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-05-04 01:09:56.265][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442". biodb.TRACE[2024-05-04 01:09:56.267][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-05-04 01:09:56.268][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-05-04 01:09:56.269][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-05-04 01:09:56.276][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-05-04 01:09:56.278][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-05-04 01:09:56.279][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-05-04 01:09:56.283][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:09:56.284][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:09:56.285][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:09:56.293][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:09:56.294][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:09:56.295][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:09:56.296][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:09:56.298][scheduler$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 01:09:56.302][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-04 01:09:56.303][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-04 01:09:56.305][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442". biodb.TRACE[2024-05-04 01:10:06.667][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442). biodb.DEBUG[2024-05-04 01:10:17.036][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-05-04 01:10:17.041][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content" biodb.TRACE[2024-05-04 01:10:17.048][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request" biodb.TRACE[2024-05-04 01:10:17.055][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml" biodb.DEBUG[2024-05-04 01:10:17.060][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-05-04 01:10:17.062][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-05-04 01:10:17.065][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-05-04 01:10:17.068][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:10:17.070][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:10:17.072][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:10:17.092][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:10:17.094][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 01:10:17.096][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:10:17.099][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.TRACE[2024-05-04 01:10:17.104][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:10:17.106][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:10:17.108][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:10:17.110][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:10:17.113][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:10:17.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:10:17.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:10:17.120][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:10:17.122][ef$get] Asked field names are: charge. biodb.TRACE[2024-05-04 01:10:17.124][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-05-04 01:10:17.126][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:10:17.129][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:10:17.131][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-04 01:10:17.134][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 01:10:17.136][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:10:17.138][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:10:17.141][ef$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 01:10:17.143][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 01:10:17.145][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:10:17.147][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:10:17.150][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 01:10:17.152][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 01:10:17.154][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:10:17.156][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:10:17.159][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-04 01:10:17.161][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-04 01:10:17.164][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:10:17.166][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:10:17.168][ef$get] Asked field names are: mass. biodb.TRACE[2024-05-04 01:10:17.171][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:10:17.173][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:10:17.175][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:10:17.177][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:10:17.180][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:10:17.182][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:10:17.184][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:10:17.186][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 01:10:17.189][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 01:10:17.191][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:10:17.193][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:10:17.196][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-05-04 01:10:17.198][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-05-04 01:10:17.200][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:10:17.202][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:10:17.205][ef$get] Asked field names are: smiles. biodb.TRACE[2024-05-04 01:10:17.207][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-04 01:10:17.209][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:10:17.211][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:10:17.214][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:10:17.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:10:17.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:10:17.220][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:10:17.223][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:10:17.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:10:17.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:10:17.241][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:10:17.244][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:10:17.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:10:17.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:10:17.250][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:10:17.253][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:10:17.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:10:17.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:10:17.259][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:10:17.261][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:10:17.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:10:17.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:10:17.268][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:10:17.270][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:10:17.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:10:17.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:10:17.276][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:10:17.278][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:10:17.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:10:17.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:10:17.285][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:10:17.287][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:10:17.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:10:17.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:10:17.294][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:10:17.296][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:10:17.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:10:17.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:10:17.302][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:10:17.304][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:10:17.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:10:17.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:10:17.311][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:10:17.313][self$createEntryFromContent] Accession numbers: . biodb.DEBUG[2024-05-04 01:10:17.315][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL. biodb.DEBUG[2024-05-04 01:10:17.317][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:10:17.319][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:10:17.320][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:10:17.335][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:10:17.338][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:10:17.340][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:10:17.342][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.DEBUG[2024-05-04 01:10:17.345][private$loadEntries] Creating entries from ids [1]: "57310". biodb.DEBUG[2024-05-04 01:10:17.347][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-05-04 01:10:17.351][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310". biodb.TRACE[2024-05-04 01:10:17.354][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-05-04 01:10:17.357][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-05-04 01:10:17.359][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-05-04 01:10:17.362][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-05-04 01:10:17.363][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-05-04 01:10:17.364][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-05-04 01:10:17.368][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:10:17.369][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:10:17.370][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:10:17.383][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:10:17.385][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 01:10:17.387][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:10:17.388][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 01:10:17.390][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310". biodb.DEBUG[2024-05-04 01:10:17.393][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-04 01:10:17.394][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-04 01:10:17.396][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310". biodb.TRACE[2024-05-04 01:10:27.763][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 01:10:38.216][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-05-04 01:10:38.219][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content" biodb.TRACE[2024-05-04 01:10:38.224][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request" biodb.TRACE[2024-05-04 01:10:38.228][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml" biodb.DEBUG[2024-05-04 01:10:38.231][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-05-04 01:10:38.233][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-05-04 01:10:38.234][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-05-04 01:10:38.236][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:10:38.237][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:10:38.239][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:10:46.249][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:10:46.250][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:10:46.252][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:10:46.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-04 01:10:46.263][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:10:46.265][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:10:46.267][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:10:46.268][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:10:46.270][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:10:46.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:10:46.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:10:46.274][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:10:46.277][ef$get] Asked field names are: charge. biodb.TRACE[2024-05-04 01:10:46.279][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-05-04 01:10:46.280][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:10:46.281][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:10:46.283][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-04 01:10:46.284][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 01:10:46.286][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:10:46.287][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:10:46.289][ef$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 01:10:46.291][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 01:10:46.292][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:10:46.293][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:10:46.295][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 01:10:46.296][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 01:10:46.297][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:10:46.299][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:10:46.300][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-04 01:10:46.301][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-04 01:10:46.303][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:10:46.304][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:10:46.305][ef$get] Asked field names are: mass. biodb.TRACE[2024-05-04 01:10:46.307][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:10:46.308][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:10:46.309][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:10:46.310][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:10:46.312][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:10:46.314][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:10:46.315][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:10:46.317][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 01:10:46.318][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 01:10:46.319][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:10:46.320][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:10:46.322][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-05-04 01:10:46.323][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-05-04 01:10:46.325][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:10:46.326][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:10:46.327][ef$get] Asked field names are: smiles. biodb.TRACE[2024-05-04 01:10:46.329][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-04 01:10:46.331][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:10:46.333][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:10:46.336][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:10:46.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:10:46.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:10:46.342][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:10:46.343][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:10:46.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:10:46.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:10:46.347][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:10:46.348][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:10:46.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:10:46.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:10:46.352][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:10:46.354][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:10:46.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:10:46.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:10:46.358][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:10:46.359][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:10:46.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:10:46.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:10:46.363][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:10:46.364][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:10:46.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:10:46.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:10:46.368][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:10:46.369][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:10:46.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:10:46.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:10:46.373][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:10:46.374][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:10:46.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:10:46.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:10:46.378][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:10:46.380][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:10:46.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:10:46.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:10:46.383][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:10:46.385][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:10:46.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:10:46.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:10:46.388][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:10:46.390][self$createEntryFromContent] Accession numbers: . biodb.DEBUG[2024-05-04 01:10:46.392][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL. biodb.DEBUG[2024-05-04 01:10:46.393][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:10:46.394][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:10:46.396][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:10:46.410][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:10:46.412][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:10:46.424][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:10:46.426][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:10:46.429][private$loadEntries] Creating entries from ids [1]: "66216". biodb.DEBUG[2024-05-04 01:10:46.431][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-05-04 01:10:46.434][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216". biodb.TRACE[2024-05-04 01:10:46.437][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-05-04 01:10:46.439][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-05-04 01:10:46.441][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-05-04 01:10:46.443][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-05-04 01:10:46.445][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-05-04 01:10:46.447][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-05-04 01:10:46.452][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:10:46.454][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:10:46.456][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:10:46.469][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:10:46.471][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:10:46.473][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:10:46.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:10:46.479][scheduler$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 01:10:46.485][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-04 01:10:46.487][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-04 01:10:46.490][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216". biodb.TRACE[2024-05-04 01:10:58.130][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216). biodb.DEBUG[2024-05-04 01:11:18.000][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-05-04 01:11:18.005][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content" biodb.TRACE[2024-05-04 01:11:18.013][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request" biodb.TRACE[2024-05-04 01:11:18.019][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml" biodb.DEBUG[2024-05-04 01:11:18.023][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-05-04 01:11:18.026][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-05-04 01:11:18.029][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-05-04 01:11:18.032][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:11:18.034][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:11:18.036][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:11:18.055][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:11:18.059][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:11:18.061][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:11:18.063][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.TRACE[2024-05-04 01:11:18.067][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:11:18.070][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:11:18.072][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:18.074][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:18.076][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:11:18.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:11:18.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:18.082][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:18.085][ef$get] Asked field names are: charge. biodb.TRACE[2024-05-04 01:11:18.087][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-05-04 01:11:18.089][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:18.090][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:18.093][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-04 01:11:18.095][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 01:11:18.097][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:18.098][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:18.101][ef$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 01:11:18.103][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 01:11:18.105][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:18.107][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:18.109][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 01:11:18.111][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 01:11:18.113][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:18.115][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:18.117][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-04 01:11:18.121][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-04 01:11:18.123][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:18.124][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:18.127][ef$get] Asked field names are: mass. biodb.TRACE[2024-05-04 01:11:18.129][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:11:18.131][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:18.133][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:18.135][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:11:18.137][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:11:18.139][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:18.141][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:18.143][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 01:11:18.145][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 01:11:18.147][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:18.149][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:18.152][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-05-04 01:11:18.154][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-05-04 01:11:18.156][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:18.170][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:18.173][ef$get] Asked field names are: smiles. biodb.TRACE[2024-05-04 01:11:18.176][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-04 01:11:18.178][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:18.180][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:18.183][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:11:18.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:11:18.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:18.189][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:18.192][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:11:18.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:11:18.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:18.198][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:18.200][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:11:18.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:11:18.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:18.206][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:18.208][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:11:18.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:11:18.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:18.215][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:18.217][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:11:18.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:11:18.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:18.223][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:18.225][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:11:18.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:11:18.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:18.232][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:18.234][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:11:18.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:11:18.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:18.240][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:18.242][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:11:18.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:11:18.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:18.248][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:18.250][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:11:18.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:11:18.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:18.256][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:18.258][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:11:18.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:11:18.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:18.264][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:11:18.266][self$createEntryFromContent] Accession numbers: . biodb.DEBUG[2024-05-04 01:11:18.268][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL. biodb.DEBUG[2024-05-04 01:11:18.270][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:11:18.272][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:11:18.273][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:11:18.289][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:11:18.291][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:11:18.293][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:11:18.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:11:18.298][private$loadEntries] Creating entries from ids [1]: "70860". biodb.DEBUG[2024-05-04 01:11:18.300][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-05-04 01:11:18.302][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860". biodb.TRACE[2024-05-04 01:11:18.304][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-05-04 01:11:18.305][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-05-04 01:11:18.307][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-05-04 01:11:18.308][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-05-04 01:11:18.309][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-05-04 01:11:18.310][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-05-04 01:11:18.313][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:11:18.315][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:11:18.316][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:11:18.325][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:11:18.326][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:11:18.328][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:11:18.329][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:11:18.331][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860". biodb.DEBUG[2024-05-04 01:11:18.334][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-04 01:11:18.336][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-04 01:11:18.339][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860". biodb.TRACE[2024-05-04 01:11:18.840][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 01:11:19.205][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-05-04 01:11:19.210][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content" biodb.TRACE[2024-05-04 01:11:19.217][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request" biodb.TRACE[2024-05-04 01:11:19.224][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml" biodb.DEBUG[2024-05-04 01:11:19.228][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-05-04 01:11:19.231][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-05-04 01:11:19.233][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-05-04 01:11:19.241][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:11:19.244][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:11:19.246][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:11:19.262][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:11:19.264][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:11:19.267][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:11:19.268][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-04 01:11:19.272][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:11:19.273][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:11:19.274][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:19.276][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:19.278][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:11:19.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:11:19.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:19.282][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:19.283][ef$get] Asked field names are: charge. biodb.TRACE[2024-05-04 01:11:19.284][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-05-04 01:11:19.286][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:19.287][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:19.289][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-05-04 01:11:19.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-05-04 01:11:19.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:19.293][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:19.294][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-04 01:11:19.296][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 01:11:19.297][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:19.298][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:19.301][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 01:11:19.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 01:11:19.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:19.305][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:19.306][ef$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 01:11:19.307][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 01:11:19.309][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:19.310][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:19.311][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 01:11:19.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 01:11:19.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:19.315][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:19.317][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 01:11:19.318][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 01:11:19.319][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:19.321][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:19.322][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 01:11:19.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 01:11:19.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:19.326][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:19.327][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-04 01:11:19.329][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-04 01:11:19.330][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:19.331][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:19.333][ef$get] Asked field names are: mass. biodb.TRACE[2024-05-04 01:11:19.334][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:11:19.336][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:19.338][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:19.339][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-05-04 01:11:19.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:11:19.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:19.343][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:19.344][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:11:19.346][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:11:19.348][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:19.349][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:19.351][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:11:19.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:11:19.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:19.354][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:19.356][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 01:11:19.357][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 01:11:19.358][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:19.359][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:19.361][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 01:11:19.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 01:11:19.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:19.365][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:19.366][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-05-04 01:11:19.368][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-05-04 01:11:19.369][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:19.371][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:19.373][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-05-04 01:11:19.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-05-04 01:11:19.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:19.376][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:19.378][ef$get] Asked field names are: smiles. biodb.TRACE[2024-05-04 01:11:19.379][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-04 01:11:19.380][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:19.382][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:19.383][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-05-04 01:11:19.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-04 01:11:19.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:19.387][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:19.388][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:11:19.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:11:19.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:19.398][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:19.400][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:11:19.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:11:19.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:19.404][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:19.405][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:11:19.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:11:19.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:19.409][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:19.410][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:11:19.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:11:19.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:19.414][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:19.416][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:11:19.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:11:19.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:19.419][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:19.421][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:11:19.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:11:19.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:19.425][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:19.426][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:11:19.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:11:19.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:19.430][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:19.432][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:11:19.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:11:19.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:19.436][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:19.437][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:11:19.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:11:19.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:19.441][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:19.442][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:11:19.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:11:19.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:19.446][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:11:19.448][self$createEntryFromContent] Accession numbers: 70860. biodb.TRACE[2024-05-04 01:11:19.449][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:11:19.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:11:19.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:19.453][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:19.454][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:11:19.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:11:19.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:19.458][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:19.460][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:11:19.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:11:19.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:19.464][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:11:19.465][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:11:19.466][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:11:19.467][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:11:19.482][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:11:19.483][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 01:11:19.485][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:11:19.486][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:11:19.487][private$loadEntries] Creating entries from ids [1]: "70861". biodb.DEBUG[2024-05-04 01:11:19.489][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-05-04 01:11:19.491][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861". biodb.TRACE[2024-05-04 01:11:19.493][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-05-04 01:11:19.494][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-05-04 01:11:19.495][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-05-04 01:11:19.497][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-05-04 01:11:19.498][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-05-04 01:11:19.499][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-05-04 01:11:19.502][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:11:19.503][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:11:19.504][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:11:19.512][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:11:19.513][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:11:19.515][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:11:19.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:11:19.517][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861". biodb.DEBUG[2024-05-04 01:11:19.521][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-04 01:11:19.522][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-04 01:11:19.524][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861". biodb.TRACE[2024-05-04 01:11:30.740][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 01:11:41.100][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-05-04 01:11:41.105][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content" biodb.TRACE[2024-05-04 01:11:41.112][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request" biodb.TRACE[2024-05-04 01:11:41.118][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml" biodb.DEBUG[2024-05-04 01:11:41.122][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-05-04 01:11:41.136][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-05-04 01:11:41.139][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-05-04 01:11:41.142][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:11:41.144][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:11:41.146][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:11:41.158][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:11:41.160][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:11:41.162][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:11:41.164][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-04 01:11:41.168][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:11:41.170][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:11:41.172][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:41.174][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:41.177][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:11:41.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:11:41.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:41.183][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:41.185][ef$get] Asked field names are: charge. biodb.TRACE[2024-05-04 01:11:41.187][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-05-04 01:11:41.189][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:41.191][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:41.193][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-04 01:11:41.195][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 01:11:41.197][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:41.199][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:41.202][ef$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 01:11:41.204][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 01:11:41.206][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:41.208][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:41.210][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 01:11:41.212][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 01:11:41.214][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:41.216][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:41.218][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-04 01:11:41.220][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-04 01:11:41.222][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:41.224][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:41.226][ef$get] Asked field names are: mass. biodb.TRACE[2024-05-04 01:11:41.228][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:11:41.230][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:41.232][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:41.234][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:11:41.236][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:11:41.238][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:41.240][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:41.242][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 01:11:41.244][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 01:11:41.246][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:41.248][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:41.251][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-05-04 01:11:41.253][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-05-04 01:11:41.255][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:41.256][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:41.259][ef$get] Asked field names are: smiles. biodb.TRACE[2024-05-04 01:11:41.261][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-04 01:11:41.262][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:41.264][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:41.267][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:11:41.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:11:41.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:41.272][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:41.274][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:11:41.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:11:41.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:41.280][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:41.282][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:11:41.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:11:41.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:41.288][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:41.290][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:11:41.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:11:41.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:41.296][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:41.298][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:11:41.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:11:41.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:41.304][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:41.306][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:11:41.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:11:41.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:41.312][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:41.314][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:11:41.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:11:41.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:41.319][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:41.322][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:11:41.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:11:41.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:41.328][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:41.330][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:11:41.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:11:41.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:41.344][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:11:41.347][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:11:41.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:11:41.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:11:41.353][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:11:41.355][self$createEntryFromContent] Accession numbers: . biodb.DEBUG[2024-05-04 01:11:41.357][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL. biodb.DEBUG[2024-05-04 01:11:41.359][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:11:41.361][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:11:41.363][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:11:41.375][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:11:41.377][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:11:41.379][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:11:41.380][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:11:41.383][private$loadEntries] Creating entries from ids [1]: "78662". biodb.DEBUG[2024-05-04 01:11:41.385][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-05-04 01:11:41.388][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662". biodb.TRACE[2024-05-04 01:11:41.390][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-05-04 01:11:41.393][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-05-04 01:11:41.395][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-05-04 01:11:41.397][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-05-04 01:11:41.399][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-05-04 01:11:41.401][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-05-04 01:11:41.406][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:11:41.407][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:11:41.409][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:11:41.421][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:11:41.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:11:41.425][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:11:41.427][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:11:41.429][scheduler$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 01:11:41.435][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-04 01:11:41.436][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-04 01:11:41.439][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662". biodb.TRACE[2024-05-04 01:11:51.809][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662). biodb.DEBUG[2024-05-04 01:12:02.315][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-05-04 01:12:02.319][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content" biodb.TRACE[2024-05-04 01:12:02.326][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request" biodb.TRACE[2024-05-04 01:12:02.332][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml" biodb.DEBUG[2024-05-04 01:12:02.336][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-05-04 01:12:02.339][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-05-04 01:12:02.341][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-05-04 01:12:02.345][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:12:02.347][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:12:02.348][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:12:02.360][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:12:02.362][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:12:02.364][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:12:02.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-04 01:12:02.370][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:12:02.373][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:12:02.374][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:12:02.376][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:12:02.379][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:12:02.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:12:02.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:12:02.384][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:12:02.386][ef$get] Asked field names are: charge. biodb.TRACE[2024-05-04 01:12:02.388][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-05-04 01:12:02.390][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:12:02.392][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:12:02.394][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-04 01:12:02.396][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 01:12:02.398][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:12:02.400][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:12:02.402][ef$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 01:12:02.404][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 01:12:02.406][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:12:02.408][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:12:02.410][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 01:12:02.412][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 01:12:02.414][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:12:02.416][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:12:02.418][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-04 01:12:02.420][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-04 01:12:02.422][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:12:02.424][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:12:02.426][ef$get] Asked field names are: mass. biodb.TRACE[2024-05-04 01:12:02.440][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:12:02.442][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:12:02.444][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:12:02.447][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:12:02.449][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:12:02.451][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:12:02.452][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:12:02.455][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 01:12:02.457][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 01:12:02.459][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:12:02.460][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:12:02.463][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-05-04 01:12:02.465][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-05-04 01:12:02.467][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:12:02.468][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:12:02.471][ef$get] Asked field names are: smiles. biodb.TRACE[2024-05-04 01:12:02.473][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-04 01:12:02.475][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:12:02.476][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:12:02.479][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:12:02.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:12:02.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:12:02.484][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:12:02.486][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:12:02.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:12:02.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:12:02.492][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:12:02.494][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:12:02.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:12:02.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:12:02.500][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:12:02.502][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:12:02.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:12:02.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:12:02.508][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:12:02.510][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:12:02.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:12:02.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:12:02.517][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:12:02.520][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:12:02.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:12:02.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:12:02.527][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:12:02.529][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:12:02.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:12:02.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:12:02.536][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:12:02.538][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:12:02.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:12:02.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:12:02.544][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:12:02.546][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:12:02.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:12:02.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:12:02.552][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:12:02.554][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:12:02.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:12:02.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:12:02.560][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:12:02.562][self$createEntryFromContent] Accession numbers: . biodb.DEBUG[2024-05-04 01:12:02.564][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL. biodb.DEBUG[2024-05-04 01:12:02.566][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:12:02.568][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:12:02.570][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:12:02.581][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:12:02.584][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:12:02.586][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:12:02.587][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 01:12:02.590][private$loadEntries] Creating entries from ids [1]: "85084". biodb.DEBUG[2024-05-04 01:12:02.592][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-05-04 01:12:02.595][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084". biodb.TRACE[2024-05-04 01:12:02.598][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-05-04 01:12:02.600][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-05-04 01:12:02.603][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-05-04 01:12:02.605][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-05-04 01:12:02.607][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-05-04 01:12:02.609][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-05-04 01:12:02.614][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:12:02.615][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:12:02.617][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:12:02.629][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:12:02.631][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:12:02.633][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:12:02.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:12:02.637][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084". biodb.DEBUG[2024-05-04 01:12:02.640][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-04 01:12:02.642][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-04 01:12:02.651][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084". biodb.TRACE[2024-05-04 01:12:13.020][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 01:12:23.383][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-05-04 01:12:23.387][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content" biodb.TRACE[2024-05-04 01:12:23.394][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request" biodb.TRACE[2024-05-04 01:12:23.400][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml" biodb.DEBUG[2024-05-04 01:12:23.404][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-05-04 01:12:23.406][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-05-04 01:12:23.409][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-05-04 01:12:23.412][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:12:23.414][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:12:23.415][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:12:23.427][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:12:23.429][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:12:23.431][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:12:23.433][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-04 01:12:23.437][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:12:23.439][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:12:23.441][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:12:23.443][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:12:23.445][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:12:23.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:12:23.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:12:23.451][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:12:23.454][ef$get] Asked field names are: charge. biodb.TRACE[2024-05-04 01:12:23.456][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-05-04 01:12:23.458][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:12:23.460][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:12:23.462][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-04 01:12:23.464][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 01:12:23.466][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:12:23.468][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:12:23.471][ef$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 01:12:23.473][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 01:12:23.475][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:12:23.477][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:12:23.479][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 01:12:23.481][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 01:12:23.483][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:12:23.485][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:12:23.487][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-04 01:12:23.490][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-04 01:12:23.491][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:12:23.493][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:12:23.496][ef$get] Asked field names are: mass. biodb.TRACE[2024-05-04 01:12:23.498][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:12:23.500][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:12:23.502][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:12:23.504][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:12:23.506][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:12:23.508][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:12:23.510][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:12:23.513][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 01:12:23.515][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 01:12:23.517][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:12:23.519][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:12:23.521][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-05-04 01:12:23.523][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-05-04 01:12:23.525][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:12:23.527][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:12:23.530][ef$get] Asked field names are: smiles. biodb.TRACE[2024-05-04 01:12:23.532][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-04 01:12:23.534][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:12:23.535][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:12:23.538][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:12:23.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:12:23.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:12:23.544][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:12:23.546][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:12:23.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:12:23.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:12:23.551][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:12:23.553][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:12:23.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:12:23.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:12:23.559][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:12:23.562][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:12:23.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:12:23.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:12:23.568][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:12:23.570][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:12:23.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:12:23.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:12:23.576][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:12:23.578][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:12:23.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:12:23.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:12:23.594][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:12:23.596][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:12:23.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:12:23.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:12:23.602][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:12:23.605][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:12:23.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:12:23.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:12:23.610][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:12:23.612][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:12:23.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:12:23.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:12:23.618][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:12:23.620][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:12:23.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:12:23.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:12:23.625][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:12:23.627][self$createEntryFromContent] Accession numbers: . biodb.DEBUG[2024-05-04 01:12:23.629][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL. biodb.DEBUG[2024-05-04 01:12:23.631][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:12:23.632][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:12:23.634][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:12:23.645][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:12:23.647][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:12:23.649][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:12:23.651][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:12:23.653][private$loadEntries] Creating entries from ids [1]: "85086". biodb.DEBUG[2024-05-04 01:12:23.655][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-05-04 01:12:23.658][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086". biodb.TRACE[2024-05-04 01:12:23.661][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-05-04 01:12:23.663][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-05-04 01:12:23.665][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-05-04 01:12:23.667][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-05-04 01:12:23.669][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-05-04 01:12:23.671][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-05-04 01:12:23.675][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:12:23.677][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:12:23.679][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:12:23.690][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:12:23.692][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:12:23.694][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:12:23.696][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:12:23.699][scheduler$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 01:12:23.704][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-04 01:12:23.706][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-04 01:12:23.709][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086". biodb.TRACE[2024-05-04 01:12:35.505][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086). biodb.DEBUG[2024-05-04 01:13:03.687][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-05-04 01:13:03.692][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content" biodb.TRACE[2024-05-04 01:13:03.699][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request" biodb.TRACE[2024-05-04 01:13:03.706][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml" biodb.DEBUG[2024-05-04 01:13:03.710][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-05-04 01:13:03.713][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-05-04 01:13:03.715][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-05-04 01:13:03.719][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:13:03.721][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:13:03.723][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:13:03.735][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:13:03.737][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 01:13:03.739][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:13:03.741][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.TRACE[2024-05-04 01:13:03.745][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:13:03.747][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:13:03.750][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:03.752][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:03.754][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:13:03.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:13:03.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:03.760][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:03.762][ef$get] Asked field names are: charge. biodb.TRACE[2024-05-04 01:13:03.765][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-05-04 01:13:03.767][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:03.768][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:03.771][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-04 01:13:03.773][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 01:13:03.775][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:03.777][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:03.792][ef$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 01:13:03.795][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 01:13:03.797][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:03.799][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:03.802][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 01:13:03.804][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 01:13:03.810][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:03.813][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:03.815][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-04 01:13:03.817][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-04 01:13:03.819][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:03.822][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:03.824][ef$get] Asked field names are: mass. biodb.TRACE[2024-05-04 01:13:03.826][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:13:03.828][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:03.830][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:03.833][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:13:03.835][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:13:03.837][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:03.839][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:03.841][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 01:13:03.843][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 01:13:03.845][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:03.847][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:03.850][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-05-04 01:13:03.852][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-05-04 01:13:03.854][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:03.856][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:03.858][ef$get] Asked field names are: smiles. biodb.TRACE[2024-05-04 01:13:03.860][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-04 01:13:03.862][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:03.864][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:03.867][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:13:03.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:13:03.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:03.873][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:03.875][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:13:03.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:13:03.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:03.881][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:03.883][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:13:03.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:13:03.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:03.889][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:03.891][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:13:03.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:13:03.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:03.897][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:03.899][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:13:03.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:13:03.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:03.905][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:03.907][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:13:03.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:13:03.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:03.913][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:03.915][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:13:03.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:13:03.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:03.921][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:03.923][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:13:03.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:13:03.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:03.929][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:03.931][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:13:03.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:13:03.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:03.937][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:03.939][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:13:03.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:13:03.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:03.945][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:13:03.947][self$createEntryFromContent] Accession numbers: . biodb.DEBUG[2024-05-04 01:13:03.949][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL. biodb.DEBUG[2024-05-04 01:13:03.951][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:13:03.953][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:13:03.955][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:13:03.966][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:13:03.968][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:13:03.970][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:13:03.972][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 01:13:03.974][private$loadEntries] Creating entries from ids [1]: "88123". biodb.DEBUG[2024-05-04 01:13:03.976][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-05-04 01:13:03.980][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123". biodb.TRACE[2024-05-04 01:13:03.982][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-05-04 01:13:03.985][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-05-04 01:13:03.987][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-05-04 01:13:03.989][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-05-04 01:13:03.991][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-05-04 01:13:03.993][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-05-04 01:13:03.999][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:13:04.010][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:13:04.012][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:13:04.024][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:13:04.026][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 01:13:04.028][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:13:04.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:13:04.032][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123". biodb.DEBUG[2024-05-04 01:13:04.037][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-04 01:13:04.039][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-04 01:13:04.042][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123". biodb.TRACE[2024-05-04 01:13:14.416][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 01:13:35.517][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-05-04 01:13:35.522][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content" biodb.TRACE[2024-05-04 01:13:35.531][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request" biodb.TRACE[2024-05-04 01:13:35.537][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml" biodb.DEBUG[2024-05-04 01:13:35.541][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-05-04 01:13:35.544][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-05-04 01:13:35.547][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-05-04 01:13:35.549][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:13:35.551][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:13:35.553][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:13:35.565][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:13:35.567][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:13:35.568][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:13:35.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-04 01:13:35.573][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:13:35.574][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:13:35.575][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:35.576][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:35.578][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:13:35.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:13:35.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:35.583][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:35.584][ef$get] Asked field names are: charge. biodb.TRACE[2024-05-04 01:13:35.586][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-05-04 01:13:35.587][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:35.589][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:35.591][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-04 01:13:35.593][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 01:13:35.594][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:35.596][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:35.598][ef$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 01:13:35.600][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 01:13:35.601][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:35.603][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:35.605][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 01:13:35.606][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 01:13:35.608][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:35.609][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:35.611][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-04 01:13:35.613][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-04 01:13:35.614][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:35.616][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:35.617][ef$get] Asked field names are: mass. biodb.TRACE[2024-05-04 01:13:35.619][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:13:35.621][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:35.623][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:35.626][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:13:35.628][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:13:35.630][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:35.633][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:35.634][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 01:13:35.636][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 01:13:35.637][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:35.638][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:35.640][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-05-04 01:13:35.641][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-05-04 01:13:35.642][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:35.644][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:35.645][ef$get] Asked field names are: smiles. biodb.TRACE[2024-05-04 01:13:35.647][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-04 01:13:35.648][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:35.649][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:35.651][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:13:35.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:13:35.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:35.655][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:35.656][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:13:35.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:13:35.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:35.660][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:35.674][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:13:35.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:13:35.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:35.679][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:35.681][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:13:35.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:13:35.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:35.686][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:35.688][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:13:35.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:13:35.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:35.693][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:35.695][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:13:35.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:13:35.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:35.699][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:35.701][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:13:35.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:13:35.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:35.705][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:35.707][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:13:35.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:13:35.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:35.711][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:35.715][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:13:35.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:13:35.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:35.719][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:35.720][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:13:35.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:13:35.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:35.725][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:13:35.726][self$createEntryFromContent] Accession numbers: . biodb.DEBUG[2024-05-04 01:13:35.727][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL. biodb.DEBUG[2024-05-04 01:13:35.728][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:13:35.730][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:13:35.731][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:13:35.739][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:13:35.741][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:13:35.743][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:13:35.746][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:13:35.748][private$loadEntries] Creating entries from ids [1]: "134117". biodb.DEBUG[2024-05-04 01:13:35.750][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-05-04 01:13:35.754][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117". biodb.TRACE[2024-05-04 01:13:35.757][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-05-04 01:13:35.759][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-05-04 01:13:35.762][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-05-04 01:13:35.764][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-05-04 01:13:35.767][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-05-04 01:13:35.768][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-05-04 01:13:35.772][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:13:35.774][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:13:35.776][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:13:35.786][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:13:35.788][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:13:35.790][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:13:35.792][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:13:35.795][scheduler$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 01:13:35.800][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-04 01:13:35.803][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-04 01:13:35.806][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117". biodb.TRACE[2024-05-04 01:13:36.378][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117). biodb.DEBUG[2024-05-04 01:13:36.745][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-05-04 01:13:36.750][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content" biodb.TRACE[2024-05-04 01:13:36.757][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request" biodb.TRACE[2024-05-04 01:13:36.764][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml" biodb.DEBUG[2024-05-04 01:13:36.768][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-05-04 01:13:36.770][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-05-04 01:13:36.773][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-05-04 01:13:36.776][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:13:36.778][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:13:36.780][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:13:36.793][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:13:36.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:13:36.797][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:13:36.799][FUN] Functions in observer BiodbConfig: [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 01:13:36.803][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:13:36.813][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:13:36.815][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:36.816][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:36.818][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:13:36.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:13:36.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:36.822][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:36.824][ef$get] Asked field names are: charge. biodb.TRACE[2024-05-04 01:13:36.825][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-05-04 01:13:36.827][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:36.828][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:36.830][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-05-04 01:13:36.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-05-04 01:13:36.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:36.834][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:36.835][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-04 01:13:36.837][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 01:13:36.838][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:36.840][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:36.842][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 01:13:36.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 01:13:36.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:36.849][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:36.851][ef$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 01:13:36.853][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 01:13:36.855][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:36.857][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:36.860][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 01:13:36.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 01:13:36.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:36.866][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:36.868][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 01:13:36.870][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 01:13:36.872][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:36.874][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:36.877][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 01:13:36.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 01:13:36.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:36.883][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:36.886][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-04 01:13:36.888][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-04 01:13:36.890][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:36.892][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:36.894][ef$get] Asked field names are: mass. biodb.TRACE[2024-05-04 01:13:36.896][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:13:36.898][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:36.900][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:36.902][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-05-04 01:13:36.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:13:36.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:36.908][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:36.910][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:13:36.912][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:13:36.914][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:36.915][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:36.918][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:13:36.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:13:36.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:36.923][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:36.925][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 01:13:36.927][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 01:13:36.929][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:36.931][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:36.933][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 01:13:36.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 01:13:36.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:36.938][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:36.940][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-05-04 01:13:36.941][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-05-04 01:13:36.943][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:36.944][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:36.945][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-05-04 01:13:36.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-05-04 01:13:36.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:36.951][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:36.953][ef$get] Asked field names are: smiles. biodb.TRACE[2024-05-04 01:13:36.955][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-04 01:13:36.957][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:36.959][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:36.962][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-05-04 01:13:36.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-04 01:13:36.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:36.968][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:36.970][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:13:36.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:13:36.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:36.974][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:36.975][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:13:36.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:13:36.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:36.979][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:36.980][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:13:36.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:13:36.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:36.984][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:36.994][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:13:36.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:13:36.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:36.999][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:37.001][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:13:37.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:13:37.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:37.005][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:37.006][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:13:37.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:13:37.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:37.010][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:37.011][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:13:37.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:13:37.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:37.015][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:37.017][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:13:37.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:13:37.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:37.021][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:37.022][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:13:37.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:13:37.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:37.026][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:37.028][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:13:37.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:13:37.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:37.032][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:13:37.034][self$createEntryFromContent] Accession numbers: 134117. biodb.TRACE[2024-05-04 01:13:37.036][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:13:37.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:13:37.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:37.043][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:37.045][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:13:37.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:13:37.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:37.052][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:37.054][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:13:37.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:13:37.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:37.058][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:13:37.060][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:13:37.061][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:13:37.063][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:13:37.071][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:13:37.072][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:13:37.074][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:13:37.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:13:37.077][private$loadEntries] Creating entries from ids [1]: "138307". biodb.DEBUG[2024-05-04 01:13:37.078][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-05-04 01:13:37.080][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307". biodb.TRACE[2024-05-04 01:13:37.082][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-05-04 01:13:37.083][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-05-04 01:13:37.085][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-05-04 01:13:37.086][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-05-04 01:13:37.087][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-05-04 01:13:37.089][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-05-04 01:13:37.092][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:13:37.093][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:13:37.094][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:13:37.105][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:13:37.107][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:13:37.108][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:13:37.109][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:13:37.111][scheduler$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 01:13:37.114][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-04 01:13:37.115][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-04 01:13:37.117][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307". biodb.TRACE[2024-05-04 01:13:37.481][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307). biodb.DEBUG[2024-05-04 01:13:37.877][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-05-04 01:13:37.881][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content" biodb.TRACE[2024-05-04 01:13:37.889][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request" biodb.TRACE[2024-05-04 01:13:37.895][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml" biodb.DEBUG[2024-05-04 01:13:37.899][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-05-04 01:13:37.902][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-05-04 01:13:37.905][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-05-04 01:13:37.908][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:13:37.910][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:13:37.912][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:13:38.185][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:13:38.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:13:38.197][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:13:38.199][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.TRACE[2024-05-04 01:13:38.202][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:13:38.204][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:13:38.205][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:38.206][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:38.208][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:13:38.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:13:38.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:38.212][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:38.213][ef$get] Asked field names are: charge. biodb.TRACE[2024-05-04 01:13:38.216][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-05-04 01:13:38.217][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:38.219][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:38.222][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-05-04 01:13:38.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-05-04 01:13:38.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:38.228][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:38.231][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-04 01:13:38.233][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 01:13:38.235][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:38.237][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:38.239][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 01:13:38.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 01:13:38.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:38.244][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:38.246][ef$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 01:13:38.247][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 01:13:38.248][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:38.250][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:38.251][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 01:13:38.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 01:13:38.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:38.255][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:38.256][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 01:13:38.258][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 01:13:38.259][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:38.260][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:38.262][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 01:13:38.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 01:13:38.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:38.266][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:38.267][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-04 01:13:38.268][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-04 01:13:38.269][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:38.271][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:38.272][ef$get] Asked field names are: mass. biodb.TRACE[2024-05-04 01:13:38.274][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:13:38.275][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:38.277][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:38.280][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-05-04 01:13:38.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:13:38.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:38.286][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:38.289][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:13:38.291][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:13:38.293][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:38.295][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:38.298][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:13:38.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:13:38.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:38.304][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:38.306][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 01:13:38.308][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 01:13:38.310][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:38.312][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:38.315][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 01:13:38.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 01:13:38.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:38.322][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:38.324][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-05-04 01:13:38.326][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-05-04 01:13:38.328][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:38.330][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:38.333][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-05-04 01:13:38.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-05-04 01:13:38.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:38.339][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:38.342][ef$get] Asked field names are: smiles. biodb.TRACE[2024-05-04 01:13:38.344][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-04 01:13:38.346][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:38.348][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:38.350][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-05-04 01:13:38.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-04 01:13:38.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:38.357][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:38.359][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:13:38.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:13:38.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:38.366][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:38.368][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:13:38.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:13:38.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:38.374][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:38.377][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:13:38.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:13:38.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:38.392][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:38.395][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:13:38.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:13:38.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:38.402][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:38.404][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:13:38.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:13:38.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:38.411][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:38.413][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:13:38.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:13:38.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:38.419][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:38.421][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:13:38.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:13:38.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:38.428][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:38.430][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:13:38.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:13:38.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:38.437][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:38.439][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:13:38.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:13:38.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:38.445][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:38.447][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:13:38.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:13:38.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:38.454][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:13:38.456][self$createEntryFromContent] Accession numbers: 138307. biodb.TRACE[2024-05-04 01:13:38.458][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:13:38.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:13:38.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:38.465][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:38.467][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:13:38.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:13:38.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:38.473][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:38.475][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:13:38.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:13:38.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:38.482][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:13:38.484][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:13:38.486][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:13:38.488][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:13:38.500][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:13:38.502][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:13:38.504][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:13:38.506][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:13:38.508][private$loadEntries] Creating entries from ids [1]: "176803". biodb.DEBUG[2024-05-04 01:13:38.511][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-05-04 01:13:38.514][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803". biodb.TRACE[2024-05-04 01:13:38.517][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-05-04 01:13:38.519][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-05-04 01:13:38.522][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-05-04 01:13:38.524][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-05-04 01:13:38.526][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-05-04 01:13:38.529][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-05-04 01:13:38.533][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:13:38.536][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:13:38.538][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:13:38.550][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:13:38.552][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:13:38.554][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:13:38.556][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:13:38.558][scheduler$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 01:13:38.563][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-04 01:13:38.565][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-04 01:13:38.568][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803". biodb.TRACE[2024-05-04 01:13:38.944][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803). biodb.DEBUG[2024-05-04 01:13:39.322][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-05-04 01:13:39.327][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content" biodb.TRACE[2024-05-04 01:13:39.332][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request" biodb.TRACE[2024-05-04 01:13:39.337][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml" biodb.DEBUG[2024-05-04 01:13:39.340][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-05-04 01:13:39.342][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-05-04 01:13:39.344][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-05-04 01:13:39.346][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:13:39.347][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:13:39.349][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:13:39.366][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:13:39.368][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:13:39.369][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:13:39.371][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.TRACE[2024-05-04 01:13:39.373][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:13:39.375][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:13:39.376][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:39.378][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:39.379][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:13:39.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:13:39.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:39.383][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:39.385][ef$get] Asked field names are: charge. biodb.TRACE[2024-05-04 01:13:39.386][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-05-04 01:13:39.389][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:39.390][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:39.392][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-05-04 01:13:39.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-05-04 01:13:39.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:39.396][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:39.398][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-04 01:13:39.399][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 01:13:39.400][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:39.401][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:39.403][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 01:13:39.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 01:13:39.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:39.407][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:39.409][ef$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 01:13:39.410][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 01:13:39.411][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:39.413][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:39.414][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 01:13:39.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 01:13:39.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:39.418][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:39.420][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 01:13:39.421][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 01:13:39.422][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:39.424][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:39.425][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 01:13:39.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 01:13:39.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:39.429][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:39.431][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-04 01:13:39.432][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-04 01:13:39.433][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:39.435][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:39.436][ef$get] Asked field names are: mass. biodb.TRACE[2024-05-04 01:13:39.438][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:13:39.439][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:39.440][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:39.442][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-05-04 01:13:39.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:13:39.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:39.446][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:39.448][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:13:39.449][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:13:39.450][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:39.451][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:39.453][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:13:39.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:13:39.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:39.457][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:39.458][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 01:13:39.460][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 01:13:39.461][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:39.462][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:39.464][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 01:13:39.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 01:13:39.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:39.468][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:39.470][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-05-04 01:13:39.471][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-05-04 01:13:39.472][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:39.473][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:39.475][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-05-04 01:13:39.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-05-04 01:13:39.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:39.479][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:39.480][ef$get] Asked field names are: smiles. biodb.TRACE[2024-05-04 01:13:39.482][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-04 01:13:39.483][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:39.484][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:39.486][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-05-04 01:13:39.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-04 01:13:39.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:39.490][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:39.491][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:13:39.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:13:39.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:39.497][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:39.499][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:13:39.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:13:39.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:39.508][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:39.510][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:13:39.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:13:39.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:39.516][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:39.517][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:13:39.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:13:39.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:39.521][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:39.523][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:13:39.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:13:39.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:39.527][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:39.529][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:13:39.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:13:39.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:39.533][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:39.534][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:13:39.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:13:39.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:39.538][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:39.540][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:13:39.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:13:39.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:39.544][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:39.545][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:13:39.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:13:39.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:39.549][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:39.550][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:13:39.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:13:39.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:39.554][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:13:39.556][self$createEntryFromContent] Accession numbers: 176803. biodb.TRACE[2024-05-04 01:13:39.557][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:13:39.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:13:39.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:39.561][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:39.563][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:13:39.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:13:39.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:39.566][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:39.568][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:13:39.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:13:39.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:39.572][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:13:39.573][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:13:39.574][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:13:39.575][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:13:39.583][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:13:39.584][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:13:39.586][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:13:39.587][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:13:39.589][private$loadEntries] Creating entries from ids [1]: "176962". biodb.DEBUG[2024-05-04 01:13:39.590][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-05-04 01:13:39.592][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962". biodb.TRACE[2024-05-04 01:13:39.594][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-05-04 01:13:39.595][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-05-04 01:13:39.597][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-05-04 01:13:39.598][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-05-04 01:13:39.600][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-05-04 01:13:39.601][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-05-04 01:13:39.605][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:13:39.606][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:13:39.607][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:13:39.616][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:13:39.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:13:39.618][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:13:39.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:13:39.622][scheduler$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 01:13:39.625][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-04 01:13:39.626][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-04 01:13:39.628][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962". biodb.TRACE[2024-05-04 01:13:40.006][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962). biodb.DEBUG[2024-05-04 01:13:40.383][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-05-04 01:13:40.388][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content" biodb.TRACE[2024-05-04 01:13:40.395][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request" biodb.TRACE[2024-05-04 01:13:40.402][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml" biodb.DEBUG[2024-05-04 01:13:40.405][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-05-04 01:13:40.407][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-05-04 01:13:40.409][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-05-04 01:13:40.411][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:13:40.420][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:13:40.421][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:13:40.432][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:13:40.434][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:13:40.437][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:13:40.438][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.TRACE[2024-05-04 01:13:40.441][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:13:40.443][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:13:40.444][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:40.445][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:40.447][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:13:40.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:13:40.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:40.451][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:40.452][ef$get] Asked field names are: charge. biodb.TRACE[2024-05-04 01:13:40.453][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-05-04 01:13:40.455][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:40.456][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:40.458][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-05-04 01:13:40.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-05-04 01:13:40.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:40.462][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:40.464][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-04 01:13:40.466][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 01:13:40.467][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:40.468][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:40.470][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 01:13:40.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 01:13:40.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:40.474][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:40.476][ef$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 01:13:40.477][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 01:13:40.479][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:40.480][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:40.482][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 01:13:40.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 01:13:40.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:40.486][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:40.487][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 01:13:40.489][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 01:13:40.490][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:40.492][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:40.493][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 01:13:40.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 01:13:40.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:40.498][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:40.499][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-04 01:13:40.501][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-04 01:13:40.502][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:40.503][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:40.505][ef$get] Asked field names are: mass. biodb.TRACE[2024-05-04 01:13:40.507][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:13:40.509][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:40.510][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:40.512][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-05-04 01:13:40.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:13:40.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:40.517][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:40.519][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:13:40.521][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:13:40.523][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:40.524][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:40.526][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:13:40.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:13:40.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:40.531][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:40.533][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 01:13:40.535][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 01:13:40.536][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:40.538][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:40.541][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 01:13:40.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 01:13:40.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:40.546][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:40.548][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-05-04 01:13:40.550][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-05-04 01:13:40.551][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:40.553][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:40.555][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-05-04 01:13:40.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-05-04 01:13:40.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:40.559][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:40.560][ef$get] Asked field names are: smiles. biodb.TRACE[2024-05-04 01:13:40.562][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-04 01:13:40.563][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:40.564][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:40.566][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-05-04 01:13:40.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-04 01:13:40.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:40.571][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:40.572][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:13:40.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:13:40.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:40.583][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:40.585][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:13:40.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:13:40.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:40.590][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:40.591][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:13:40.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:13:40.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:40.595][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:40.597][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:13:40.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:13:40.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:40.601][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:40.603][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:13:40.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:13:40.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:40.607][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:40.608][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:13:40.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:13:40.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:40.613][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:40.614][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:13:40.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:13:40.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:40.618][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:40.620][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:13:40.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:13:40.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:40.624][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:40.626][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:13:40.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:13:40.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:40.630][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:40.631][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:13:40.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:13:40.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:40.635][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:13:40.637][self$createEntryFromContent] Accession numbers: 176962. biodb.TRACE[2024-05-04 01:13:40.638][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:13:40.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:13:40.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:40.643][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:40.644][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:13:40.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:13:40.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:40.648][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:40.650][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:13:40.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:13:40.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:40.654][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:13:40.656][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:13:40.657][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:13:40.658][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:13:40.669][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:13:40.671][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:13:40.673][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:13:40.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:13:40.678][private$loadEntries] Creating entries from ids [1]: "198655". biodb.DEBUG[2024-05-04 01:13:40.682][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-05-04 01:13:40.686][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655". biodb.TRACE[2024-05-04 01:13:40.690][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-05-04 01:13:40.693][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-05-04 01:13:40.696][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-05-04 01:13:40.699][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-05-04 01:13:40.701][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-05-04 01:13:40.704][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-05-04 01:13:40.709][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:13:40.712][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:13:40.714][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:13:40.723][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:13:40.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:13:40.726][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:13:40.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:13:40.730][scheduler$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 01:13:40.733][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-04 01:13:40.735][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-04 01:13:40.737][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655". biodb.TRACE[2024-05-04 01:13:41.109][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655). biodb.DEBUG[2024-05-04 01:13:53.298][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-05-04 01:13:53.301][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content" biodb.TRACE[2024-05-04 01:13:53.306][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request" biodb.TRACE[2024-05-04 01:13:53.310][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml" biodb.DEBUG[2024-05-04 01:13:53.313][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-05-04 01:13:53.323][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-05-04 01:13:53.325][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-05-04 01:13:53.327][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:13:53.329][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:13:53.330][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:13:53.939][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:13:53.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:13:53.942][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:13:53.943][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.TRACE[2024-05-04 01:13:53.947][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:13:53.949][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:13:53.951][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:53.953][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:53.955][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:13:53.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:13:53.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:53.961][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:53.964][ef$get] Asked field names are: charge. biodb.TRACE[2024-05-04 01:13:53.966][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-05-04 01:13:53.968][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:53.970][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:53.973][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-04 01:13:53.975][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 01:13:53.977][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:53.979][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:53.981][ef$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 01:13:53.984][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 01:13:53.986][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:53.987][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:53.990][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 01:13:53.992][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 01:13:53.994][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:53.996][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:53.998][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-04 01:13:54.001][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-04 01:13:54.002][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:54.004][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:54.007][ef$get] Asked field names are: mass. biodb.TRACE[2024-05-04 01:13:54.009][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:13:54.011][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:54.013][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:54.015][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:13:54.018][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:13:54.020][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:54.021][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:54.024][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 01:13:54.026][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 01:13:54.028][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:54.030][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:54.033][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-05-04 01:13:54.035][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-05-04 01:13:54.037][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:54.039][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:54.041][ef$get] Asked field names are: smiles. biodb.TRACE[2024-05-04 01:13:54.043][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-04 01:13:54.045][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:54.047][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:54.050][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:13:54.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:13:54.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:54.056][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:54.058][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:13:54.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:13:54.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:54.064][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:54.066][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:13:54.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:13:54.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:54.072][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:54.074][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:13:54.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:13:54.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:54.080][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:54.083][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:13:54.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:13:54.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:54.089][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:54.091][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:13:54.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:13:54.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:54.097][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:54.099][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:13:54.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:13:54.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:54.105][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:54.108][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:13:54.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:13:54.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:54.114][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:54.116][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:13:54.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:13:54.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:54.131][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:13:54.134][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:13:54.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:13:54.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:13:54.141][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:13:54.144][self$createEntryFromContent] Accession numbers: . biodb.DEBUG[2024-05-04 01:13:54.146][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL. biodb.DEBUG[2024-05-04 01:13:54.148][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:13:54.150][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:13:54.152][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:13:54.163][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:13:54.165][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:13:54.166][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:13:54.168][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 01:13:54.169][private$loadEntries] Creating entries from ids [1]: "215045". biodb.DEBUG[2024-05-04 01:13:54.171][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-05-04 01:13:54.173][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045". biodb.TRACE[2024-05-04 01:13:54.175][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-05-04 01:13:54.177][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-05-04 01:13:54.179][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-05-04 01:13:54.181][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-05-04 01:13:54.183][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-05-04 01:13:54.185][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-05-04 01:13:54.190][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:13:54.192][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:13:54.194][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:13:54.207][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:13:54.209][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 01:13:54.211][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:13:54.212][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 01:13:54.214][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045". biodb.DEBUG[2024-05-04 01:13:54.219][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-04 01:13:54.221][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-04 01:13:54.224][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045". biodb.TRACE[2024-05-04 01:14:13.124][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 01:14:13.488][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-05-04 01:14:13.493][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.content" biodb.TRACE[2024-05-04 01:14:13.500][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.request" biodb.TRACE[2024-05-04 01:14:13.506][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml" biodb.DEBUG[2024-05-04 01:14:13.511][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-05-04 01:14:13.513][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-05-04 01:14:13.516][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-05-04 01:14:13.519][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:13.521][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:13.523][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:15.460][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:15.463][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:15.465][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:15.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-04 01:14:15.471][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:14:15.473][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:14:15.474][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:15.475][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:15.477][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:14:15.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:14:15.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:15.481][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:15.482][ef$get] Asked field names are: charge. biodb.TRACE[2024-05-04 01:14:15.484][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-05-04 01:14:15.485][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:15.486][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:15.488][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-05-04 01:14:15.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-05-04 01:14:15.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:15.492][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:15.493][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-04 01:14:15.495][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 01:14:15.496][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:15.497][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:15.499][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 01:14:15.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 01:14:15.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:15.503][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:15.504][ef$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 01:14:15.506][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 01:14:15.507][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:15.508][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:15.516][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 01:14:15.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 01:14:15.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:15.523][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:15.525][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 01:14:15.527][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 01:14:15.528][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:15.529][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:15.531][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 01:14:15.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 01:14:15.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:15.535][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:15.536][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-04 01:14:15.537][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-04 01:14:15.539][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:15.540][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:15.541][ef$get] Asked field names are: mass. biodb.TRACE[2024-05-04 01:14:15.543][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:14:15.544][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:15.545][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:15.547][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-05-04 01:14:15.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:14:15.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:15.551][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:15.552][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:15.553][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:15.555][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:15.556][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:15.557][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:15.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:15.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:15.561][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:15.563][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 01:14:15.564][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 01:14:15.565][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:15.566][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:15.568][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 01:14:15.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 01:14:15.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:15.572][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:15.573][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-05-04 01:14:15.575][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-05-04 01:14:15.576][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:15.577][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:15.579][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-05-04 01:14:15.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-05-04 01:14:15.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:15.582][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:15.584][ef$get] Asked field names are: smiles. biodb.TRACE[2024-05-04 01:14:15.585][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-04 01:14:15.586][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:15.587][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:15.589][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-05-04 01:14:15.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-04 01:14:15.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:15.593][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:15.595][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:15.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:15.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:15.599][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:15.600][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:15.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:15.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:15.604][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:15.605][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:14:15.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:14:15.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:15.609][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:15.610][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:15.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:15.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:15.614][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:15.616][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:14:15.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:14:15.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:15.620][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:15.621][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:14:15.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:14:15.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:15.625][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:15.626][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:14:15.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:14:15.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:15.630][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:15.632][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:14:15.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:14:15.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:15.638][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:15.640][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:14:15.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:14:15.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:15.646][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:15.648][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:14:15.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:14:15.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:15.654][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:14:15.656][self$createEntryFromContent] Accession numbers: 215045. biodb.TRACE[2024-05-04 01:14:15.667][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:14:15.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:14:15.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:15.674][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:15.677][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:14:15.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:14:15.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:15.683][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:15.685][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:14:15.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:14:15.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:15.690][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:14:15.724][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 01:14:15.729][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-05-04 01:14:15.730][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2". biodb.TRACE[2024-05-04 01:14:15.732][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-05-04 01:14:15.745][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content". biodb.DEBUG[2024-05-04 01:14:15.749][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:15.750][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:15.752][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:15.762][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:15.764][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 01:14:15.766][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:15.769][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-04 01:14:15.771][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:14:15.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:14:15.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:15.778][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:15.780][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:14:15.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:14:15.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:15.786][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:15.788][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:14:15.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:14:15.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:15.791][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:14:15.793][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:15.794][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:15.795][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:15.805][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:15.807][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:15.809][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:15.811][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 01:14:15.813][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:15.815][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:15.817][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:15.829][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:15.831][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:15.833][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:15.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:14:15.838][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:15.840][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:15.842][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:15.851][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:15.852][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 01:14:15.854][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:15.855][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 01:14:15.856][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:15.857][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:15.858][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:15.866][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:15.867][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:15.869][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:15.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:14:15.877][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:15.879][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:15.881][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:15.890][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:15.892][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 01:14:15.894][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:15.895][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:14:15.897][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:15.898][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:15.900][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:15.911][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:15.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:15.915][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:15.917][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 01:14:15.918][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:15.920][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:15.921][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:15.929][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:15.931][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 01:14:15.932][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:15.933][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 01:14:15.935][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:15.936][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:15.937][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:15.947][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:15.949][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:15.951][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:15.953][FUN] Functions in observer BiodbConfig: [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 01:14:15.955][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:14:15.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:14:15.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:15.961][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:15.963][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:14:15.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:14:15.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:15.969][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:15.971][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:14:15.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:14:15.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:15.977][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:14:15.979][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:15.981][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:15.982][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:15.994][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:15.995][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 01:14:15.997][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:15.998][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.DEBUG[2024-05-04 01:14:16.000][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:16.002][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:16.004][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:16.016][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:16.018][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 01:14:16.020][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:16.022][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:14:16.024][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:16.026][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:16.028][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:16.038][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:16.040][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:16.041][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:16.042][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:14:16.044][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:16.045][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:16.047][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:16.056][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:16.058][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:16.060][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:16.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:14:16.063][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:16.064][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:16.065][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:16.073][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:16.080][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:16.081][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:16.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:14:16.085][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:16.086][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:16.087][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:16.095][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:16.096][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 01:14:16.097][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:16.098][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.TRACE[2024-05-04 01:14:16.100][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:14:16.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:14:16.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:16.106][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:16.108][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:14:16.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:14:16.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:16.114][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:16.117][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:14:16.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:14:16.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:16.123][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:14:16.125][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:16.127][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:16.129][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:16.141][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:16.143][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 01:14:16.145][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:16.147][FUN] Functions in observer BiodbConfig: [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 01:14:16.150][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:14:16.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:14:16.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:16.156][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:16.159][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:14:16.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:14:16.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:16.165][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:16.167][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:14:16.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:14:16.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:16.174][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:14:16.176][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:16.178][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:16.180][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:16.191][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:16.193][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 01:14:16.195][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:16.197][FUN] Functions in observer BiodbConfig: [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 01:14:16.199][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:14:16.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:14:16.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:16.205][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:16.207][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:14:16.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:14:16.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:16.213][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:16.215][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:14:16.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:14:16.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:16.221][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:14:16.223][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:16.225][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:16.227][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:16.238][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:16.240][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:16.242][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:16.244][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.TRACE[2024-05-04 01:14:16.246][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:14:16.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:14:16.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:16.252][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:16.254][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:14:16.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:14:16.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:16.260][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:16.262][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:14:16.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:14:16.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:16.268][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:14:16.270][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:16.271][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:16.273][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:16.284][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:16.286][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 01:14:16.296][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:16.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:14:16.301][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:16.303][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:16.306][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:16.314][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:16.316][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 01:14:16.317][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:16.319][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.TRACE[2024-05-04 01:14:16.320][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:14:16.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:14:16.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:16.325][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:16.326][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:14:16.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:14:16.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:16.331][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:16.332][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:14:16.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:14:16.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:16.337][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:16.375][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:16.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:16.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:16.382][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:16.384][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:16.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:16.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:16.390][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:16.392][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:16.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:16.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:16.398][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:16.400][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:16.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:16.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:16.406][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:16.408][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:16.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:16.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:16.414][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:14:16.459][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 01:14:16.465][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-04 01:14:16.467][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-04 01:14:16.471][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL". biodb.TRACE[2024-05-04 01:14:16.836][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL). biodb.DEBUG[2024-05-04 01:14:17.209][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-05-04 01:14:17.213][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content" biodb.TRACE[2024-05-04 01:14:17.219][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request" biodb.DEBUG[2024-05-04 01:14:17.224][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-05-04 01:14:17.228][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-04 01:14:17.229][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-04 01:14:17.232][private$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 01:14:17.600][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 01:14:17.979][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-05-04 01:14:17.982][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content" biodb.TRACE[2024-05-04 01:14:17.988][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request" biodb.DEBUG[2024-05-04 01:14:17.993][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:17.994][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:17.996][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:18.008][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:18.010][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 01:14:18.012][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:18.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:14:18.016][private$loadEntries] Creating entries from ids [1]: "4648". biodb.DEBUG[2024-05-04 01:14:18.018][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-05-04 01:14:18.022][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648". biodb.TRACE[2024-05-04 01:14:18.025][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-05-04 01:14:18.027][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-05-04 01:14:18.029][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-05-04 01:14:18.031][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-05-04 01:14:18.034][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-05-04 01:14:18.036][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-05-04 01:14:18.041][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:18.042][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:18.044][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:18.056][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:18.058][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:18.060][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:18.062][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.DEBUG[2024-05-04 01:14:18.065][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648". biodb.DEBUG[2024-05-04 01:14:18.070][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-04 01:14:18.072][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-04 01:14:18.075][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648". biodb.TRACE[2024-05-04 01:14:18.486][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 01:14:18.913][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-05-04 01:14:18.917][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content" biodb.TRACE[2024-05-04 01:14:18.925][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request" biodb.TRACE[2024-05-04 01:14:18.931][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml" biodb.DEBUG[2024-05-04 01:14:18.935][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-05-04 01:14:18.938][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-05-04 01:14:18.941][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-05-04 01:14:18.944][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:18.946][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:18.947][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:20.720][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:20.722][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:20.724][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:20.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-04 01:14:20.730][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:14:20.733][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:14:20.735][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:20.737][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:20.739][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:14:20.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:14:20.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:20.746][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:20.749][ef$get] Asked field names are: charge. biodb.TRACE[2024-05-04 01:14:20.763][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-05-04 01:14:20.765][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:20.767][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:20.770][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-05-04 01:14:20.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-05-04 01:14:20.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:20.776][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:20.778][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-04 01:14:20.781][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 01:14:20.782][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:20.784][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:20.787][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 01:14:20.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 01:14:20.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:20.793][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:20.795][ef$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 01:14:20.797][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 01:14:20.799][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:20.800][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:20.803][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 01:14:20.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 01:14:20.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:20.809][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:20.811][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 01:14:20.813][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 01:14:20.815][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:20.816][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:20.819][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 01:14:20.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 01:14:20.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:20.825][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:20.827][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-04 01:14:20.829][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-04 01:14:20.830][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:20.832][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:20.835][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-04 01:14:20.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-04 01:14:20.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:20.840][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:20.843][ef$get] Asked field names are: mass. biodb.TRACE[2024-05-04 01:14:20.845][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:14:20.846][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:20.848][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:20.850][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-05-04 01:14:20.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:14:20.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:20.856][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:20.858][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:20.860][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:20.862][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:20.864][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:20.866][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:20.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:20.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:20.872][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:20.873][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 01:14:20.875][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 01:14:20.876][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:20.877][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:20.879][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 01:14:20.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 01:14:20.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:20.885][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:20.887][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-05-04 01:14:20.890][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-05-04 01:14:20.892][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:20.894][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:20.897][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-05-04 01:14:20.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-05-04 01:14:20.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:20.903][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:20.906][ef$get] Asked field names are: smiles. biodb.TRACE[2024-05-04 01:14:20.908][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-04 01:14:20.910][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:20.912][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:20.914][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-05-04 01:14:20.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-04 01:14:20.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:20.920][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:20.922][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:20.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:20.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:20.927][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:20.929][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:20.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:20.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:20.935][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:20.937][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:14:20.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:14:20.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:20.942][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:20.944][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:20.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:20.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:20.950][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:20.962][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:14:20.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:14:20.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:20.970][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:20.973][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:14:20.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:14:20.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:20.979][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:20.981][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:14:20.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:14:20.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:20.985][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:20.986][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:14:20.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:14:20.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:20.991][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:20.993][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:14:20.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:14:20.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:21.000][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:21.002][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:14:21.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:14:21.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:21.008][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:14:21.010][self$createEntryFromContent] Accession numbers: 4648. biodb.TRACE[2024-05-04 01:14:21.015][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:21.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:21.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:21.021][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:21.022][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:21.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:21.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:21.027][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:21.029][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:21.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:21.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:21.033][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:14:21.035][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:21.036][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:21.037][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:21.047][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:21.049][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:21.051][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:21.053][FUN] Functions in observer BiodbConfig: [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 01:14:21.056][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:21.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:21.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:21.062][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:21.064][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:21.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:21.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:21.070][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:21.071][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:21.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:21.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:21.075][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:14:21.076][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:21.077][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:21.078][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:21.086][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:21.087][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:21.091][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:21.092][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 01:14:21.094][private$loadEntries] Creating entries from ids [1]: "62447". biodb.DEBUG[2024-05-04 01:14:21.095][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-05-04 01:14:21.098][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447". biodb.TRACE[2024-05-04 01:14:21.100][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-05-04 01:14:21.101][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-05-04 01:14:21.103][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-05-04 01:14:21.105][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-05-04 01:14:21.106][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-05-04 01:14:21.107][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-05-04 01:14:21.111][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:21.112][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:21.114][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:21.122][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:21.123][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 01:14:21.124][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:21.125][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 01:14:21.127][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447". biodb.DEBUG[2024-05-04 01:14:21.130][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-04 01:14:21.132][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-04 01:14:21.134][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447". biodb.TRACE[2024-05-04 01:14:21.507][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 01:14:21.891][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-05-04 01:14:21.895][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content" biodb.TRACE[2024-05-04 01:14:21.903][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request" biodb.TRACE[2024-05-04 01:14:21.908][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml" biodb.DEBUG[2024-05-04 01:14:21.911][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-05-04 01:14:21.914][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-05-04 01:14:21.917][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-05-04 01:14:21.919][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:21.921][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:21.923][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:21.934][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:21.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:21.938][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:21.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-04 01:14:21.944][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:14:21.946][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:14:21.948][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:21.950][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:21.952][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:14:21.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:14:21.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:21.958][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:21.960][ef$get] Asked field names are: charge. biodb.TRACE[2024-05-04 01:14:21.962][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-05-04 01:14:21.964][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:21.966][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:21.968][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-05-04 01:14:21.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-05-04 01:14:21.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:21.974][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:21.976][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-04 01:14:21.978][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 01:14:21.980][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:21.981][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:21.984][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 01:14:21.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 01:14:21.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:21.989][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:21.992][ef$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 01:14:21.994][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 01:14:21.995][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:21.997][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:21.999][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 01:14:22.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 01:14:22.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:22.005][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:22.007][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 01:14:22.008][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 01:14:22.009][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:22.011][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:22.012][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 01:14:22.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 01:14:22.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:22.016][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:22.018][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-04 01:14:22.019][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-04 01:14:22.021][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:22.022][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:22.024][ef$get] Asked field names are: mass. biodb.TRACE[2024-05-04 01:14:22.026][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:14:22.027][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:22.028][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:22.030][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-05-04 01:14:22.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:14:22.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:22.034][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:22.036][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:22.037][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:22.038][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:22.040][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:22.041][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:22.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:22.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:22.045][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:22.047][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 01:14:22.048][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 01:14:22.049][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:22.051][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:22.053][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 01:14:22.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 01:14:22.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:22.057][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:22.058][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-05-04 01:14:22.060][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-05-04 01:14:22.061][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:22.069][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:22.072][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-05-04 01:14:22.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-05-04 01:14:22.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:22.078][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:22.080][ef$get] Asked field names are: smiles. biodb.TRACE[2024-05-04 01:14:22.081][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-04 01:14:22.082][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:22.084][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:22.085][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-05-04 01:14:22.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-04 01:14:22.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:22.089][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:22.090][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:22.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:22.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:22.094][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:22.096][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:22.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:22.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:22.099][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:22.101][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:14:22.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:14:22.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:22.105][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:22.106][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:22.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:22.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:22.110][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:22.111][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:14:22.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:14:22.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:22.115][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:22.116][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:14:22.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:14:22.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:22.121][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:22.122][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:14:22.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:14:22.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:22.128][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:22.130][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:14:22.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:14:22.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:22.135][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:22.137][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:14:22.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:14:22.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:22.140][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:22.142][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:14:22.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:14:22.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:22.146][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:14:22.147][self$createEntryFromContent] Accession numbers: 62447. biodb.TRACE[2024-05-04 01:14:22.148][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:22.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:22.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:22.152][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:22.153][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:22.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:22.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:22.157][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:22.159][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:22.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:22.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:22.162][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:14:22.192][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 01:14:22.196][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-05-04 01:14:22.198][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2". biodb.TRACE[2024-05-04 01:14:22.200][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-05-04 01:14:22.203][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content". biodb.DEBUG[2024-05-04 01:14:22.206][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:22.208][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:22.209][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:22.228][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:22.231][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:22.233][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:22.235][FUN] Functions in observer BiodbConfig: [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 01:14:22.238][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:22.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:22.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:22.243][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:22.244][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:22.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:22.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:22.248][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:22.249][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:22.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:22.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:22.254][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:14:22.255][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:22.256][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:22.258][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:22.266][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:22.267][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:22.268][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:22.270][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.DEBUG[2024-05-04 01:14:22.271][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:22.272][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:22.273][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:22.281][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:22.282][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:22.283][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:22.285][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:14:22.286][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:22.287][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:22.288][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:22.297][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:22.298][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 01:14:22.299][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:22.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:14:22.302][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:22.303][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:22.304][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:22.314][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:22.316][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 01:14:22.318][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:22.319][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 01:14:22.320][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:22.321][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:22.323][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:22.333][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:22.335][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:22.337][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:22.338][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:14:22.341][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:22.342][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:22.344][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:22.354][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:22.356][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:22.358][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:22.360][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:14:22.362][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:22.364][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:22.366][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:22.378][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:22.380][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 01:14:22.382][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:22.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:14:22.387][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:22.389][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:22.390][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:22.403][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:22.405][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:22.407][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:22.409][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.TRACE[2024-05-04 01:14:22.412][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:22.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:22.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:22.429][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:22.431][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:22.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:22.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:22.439][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:22.441][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:22.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:22.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:22.448][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:14:22.451][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:22.453][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:22.454][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:22.464][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:22.465][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 01:14:22.467][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:22.468][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 01:14:22.469][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:22.470][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:22.471][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:22.481][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:22.483][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 01:14:22.484][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:22.485][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 01:14:22.487][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:22.488][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:22.489][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:22.497][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:22.499][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:22.500][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:22.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:14:22.502][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:22.504][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:22.505][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:22.514][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:22.516][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:22.517][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:22.518][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 01:14:22.520][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:22.522][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:22.523][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:22.534][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:22.536][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:22.538][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:22.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:14:22.543][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:22.545][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:22.548][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:22.560][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:22.562][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:22.564][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:22.566][FUN] Functions in observer BiodbConfig: [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 01:14:22.569][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:22.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:22.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:22.576][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:22.579][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:22.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:22.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:22.586][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:22.589][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:22.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:22.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:22.595][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:14:22.597][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:22.598][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:22.599][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:22.609][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:22.611][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:22.612][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:22.614][FUN] Functions in observer BiodbConfig: [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 01:14:22.616][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:22.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:22.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:22.620][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:22.621][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:22.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:22.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:22.850][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:22.852][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:22.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:22.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:22.855][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:14:22.857][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:22.858][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:22.860][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:22.870][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:22.872][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:22.873][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:22.875][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 01:14:22.878][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:22.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:22.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:22.884][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:22.886][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:22.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:22.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:22.892][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:22.894][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:22.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:22.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:22.900][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:14:22.902][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:22.904][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:22.906][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:22.919][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:22.921][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:22.923][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:22.925][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.TRACE[2024-05-04 01:14:22.927][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:22.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:22.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:22.933][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:22.935][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:22.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:22.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:22.941][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:22.943][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:22.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:22.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:22.949][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:14:22.951][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:22.953][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:22.955][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:22.966][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:22.968][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:22.970][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:22.971][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 01:14:22.974][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:22.975][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:22.977][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:22.989][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:22.991][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:22.993][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:22.995][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 01:14:22.997][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:22.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:23.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:23.003][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:23.005][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:23.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:23.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:23.011][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:23.013][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:23.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:23.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:23.018][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:14:23.049][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 01:14:23.054][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-05-04 01:14:23.056][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2". biodb.TRACE[2024-05-04 01:14:23.058][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-05-04 01:14:23.060][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content". biodb.DEBUG[2024-05-04 01:14:23.064][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:23.066][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:23.067][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:23.076][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:23.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:23.079][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:23.081][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.TRACE[2024-05-04 01:14:23.082][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:23.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:23.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:23.087][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:23.089][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:23.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:23.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:23.094][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:23.096][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:23.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:23.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:23.101][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:14:23.102][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:23.104][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:23.105][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:23.116][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:23.117][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:23.119][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:23.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:14:23.123][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:23.124][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:23.125][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:23.134][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:23.136][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 01:14:23.137][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:23.138][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 01:14:23.140][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:23.142][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:23.143][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:23.153][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:23.154][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 01:14:23.156][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:23.157][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:14:23.159][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:23.160][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:23.162][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:23.171][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:23.172][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 01:14:23.174][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:23.175][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 01:14:23.177][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:23.178][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:23.179][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:23.189][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:23.190][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:23.192][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:23.193][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 01:14:23.195][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:23.196][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:23.198][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:23.206][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:23.207][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 01:14:23.209][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:23.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:14:23.212][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:23.214][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:23.215][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:23.227][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:23.229][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 01:14:23.231][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:23.233][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:14:23.234][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:23.236][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:23.238][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:23.247][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:23.248][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:23.250][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:23.251][FUN] Functions in observer BiodbConfig: [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 01:14:23.253][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:23.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:23.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:23.257][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:23.259][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:23.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:23.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:23.263][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:23.265][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:23.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:23.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:23.270][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:14:23.272][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:23.273][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:23.274][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:23.283][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:23.284][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:23.286][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:23.287][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:14:23.289][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:23.291][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:23.292][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:23.302][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:23.303][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:23.305][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:23.307][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:14:23.309][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:23.310][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:23.312][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:23.322][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:23.325][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 01:14:23.327][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:23.329][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:14:23.332][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:23.334][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:23.336][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:23.349][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:23.350][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:23.352][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:23.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:14:23.355][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:23.356][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:23.358][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:23.366][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:23.367][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 01:14:23.369][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:23.370][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 01:14:23.372][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:23.373][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:23.374][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:23.383][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:23.384][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 01:14:23.385][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:23.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-04 01:14:23.388][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:23.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:23.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:23.393][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:23.394][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:23.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:23.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:23.398][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:23.400][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:23.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:23.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:23.404][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:14:23.406][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:23.407][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:23.408][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:23.417][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:23.419][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 01:14:23.420][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:23.422][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.TRACE[2024-05-04 01:14:23.423][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:23.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:23.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:23.428][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:23.430][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:23.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:23.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:23.435][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:23.436][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:23.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:23.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:23.441][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:14:23.442][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:23.444][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:23.445][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:23.455][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:23.458][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:23.460][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:23.462][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-04 01:14:23.464][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:23.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:23.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:23.468][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:23.470][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:23.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:23.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:23.475][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:23.477][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:23.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:23.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:23.481][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:14:23.483][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:23.485][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:23.486][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:23.495][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:23.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:23.504][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:23.505][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 01:14:23.507][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:23.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:23.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:23.511][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:23.513][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:23.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:23.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:23.517][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:23.518][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:23.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:23.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:23.522][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:14:23.524][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:23.525][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:23.526][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:23.534][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:23.535][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:23.537][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:23.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:14:23.539][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:23.540][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:23.541][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:23.549][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:23.550][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:23.551][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:23.552][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.TRACE[2024-05-04 01:14:23.554][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:23.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:23.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:23.558][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:23.559][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:23.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:23.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:23.563][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:23.565][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:23.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:23.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:23.568][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:23.602][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass. biodb.TRACE[2024-05-04 01:14:23.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass. biodb.TRACE[2024-05-04 01:14:23.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:23.606][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.INFO [2024-05-04 01:14:23.622][biodb::testThat] biodb.INFO [2024-05-04 01:14:23.624][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. "). biodb.INFO [2024-05-04 01:14:23.626][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 01:14:23.627][biodb::testThat] biodb.TRACE[2024-05-04 01:14:23.631][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-05-04 01:14:23.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-05-04 01:14:23.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:23.635][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:23.636][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:14:23.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:14:23.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:23.641][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:23.643][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:14:23.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:14:23.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:23.647][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:23.649][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:14:23.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:14:23.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:23.653][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:23.654][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:14:23.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:14:23.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:23.658][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:14:23.663][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:23.664][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:23.665][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:23.673][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:23.674][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:23.675][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:23.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:14:23.680][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 01:14:23.684][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-05-04 01:14:23.685][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1". biodb.TRACE[2024-05-04 01:14:23.688][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-05-04 01:14:23.700][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content". biodb.DEBUG[2024-05-04 01:14:23.704][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:23.707][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:23.708][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:23.716][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:23.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:23.719][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:23.721][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 01:14:23.725][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 01:14:23.728][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-05-04 01:14:23.730][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6". biodb.TRACE[2024-05-04 01:14:23.732][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-05-04 01:14:23.746][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content". biodb.DEBUG[2024-05-04 01:14:23.749][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:23.750][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:23.752][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:23.760][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:23.761][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:23.762][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:23.763][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 01:14:23.765][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:14:23.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:14:23.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:23.769][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:23.770][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:14:23.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:14:23.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:23.774][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:23.775][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:14:23.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:14:23.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:23.780][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:14:23.781][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:23.783][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:23.784][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:23.792][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:23.793][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:23.795][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:23.796][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 01:14:23.797][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:23.799][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:23.800][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:23.807][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:23.809][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 01:14:23.810][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:23.811][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 01:14:23.813][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 01:14:23.818][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-05-04 01:14:23.819][cch$loadFileContent] Trying to load 1 files from cache: [1]: "94c7655c8f372fb2982c15119402bcba". biodb.TRACE[2024-05-04 01:14:23.821][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-05-04 01:14:23.833][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.content". biodb.DEBUG[2024-05-04 01:14:23.836][private$bdb$entriesToDataframe] 1 entrie(s) to convert in data frame. biodb.DEBUG[2024-05-04 01:14:23.838][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:23.839][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:23.841][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:23.849][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:23.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:23.851][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:23.853][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.TRACE[2024-05-04 01:14:23.854][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:23.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:23.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:23.858][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:23.860][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:23.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:23.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:23.864][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:23.865][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-05-04 01:14:23.866][private$selectFields] biodb.TRACE[2024-05-04 01:14:23.868][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-05-04 01:14:23.869][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-05-04 01:14:23.870][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-05-04 01:14:23.871][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:23.873][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:23.874][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:23.875][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:23.876][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:23.878][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:23.879][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:23.880][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:23.881][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-05-04 01:14:23.883][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-05-04 01:14:23.884][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:23.885][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:23.886][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:23.888][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:23.889][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-05-04 01:14:23.890][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:23.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:23.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:23.895][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:23.897][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:23.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:23.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:23.901][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:23.903][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:23.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:23.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:23.909][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:23.919][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440]. biodb.DEBUG[2024-05-04 01:14:23.921][private$entriesToListOfDataframes] Converted 1 entry/ies to data frame(s). biodb.DEBUG[2024-05-04 01:14:23.922][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.TRACE[2024-05-04 01:14:23.938][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:23.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:23.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:23.943][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:23.944][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:23.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:23.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:23.948][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:23.949][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:23.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:23.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:23.953][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:23.954][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:23.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:23.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:23.959][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:14:24.014][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:24.015][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:24.017][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:24.028][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:24.030][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:24.032][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:24.034][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:14:24.039][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 01:14:24.046][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-04 01:14:24.048][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-04 01:14:24.053][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL". biodb.TRACE[2024-05-04 01:14:24.475][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL). biodb.DEBUG[2024-05-04 01:14:24.942][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-05-04 01:14:24.947][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content" biodb.TRACE[2024-05-04 01:14:24.954][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request" biodb.DEBUG[2024-05-04 01:14:24.960][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-05-04 01:14:24.964][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-04 01:14:24.966][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-04 01:14:24.968][private$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 01:14:25.327][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 01:14:25.694][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-05-04 01:14:25.698][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content" biodb.TRACE[2024-05-04 01:14:25.707][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request" biodb.DEBUG[2024-05-04 01:14:25.713][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:25.715][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:25.717][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:25.729][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:25.731][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 01:14:25.733][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:25.735][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-04 01:14:25.737][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:25.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:25.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:25.743][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:25.745][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:25.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:25.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:25.751][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:25.753][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:25.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:25.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:25.759][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:14:25.761][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:25.763][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:25.765][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:25.776][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:25.778][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 01:14:25.779][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:25.780][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.TRACE[2024-05-04 01:14:25.782][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:25.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:25.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:25.785][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:25.787][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:25.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:25.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:25.790][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:25.792][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:25.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:25.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:25.795][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:14:25.797][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:25.798][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:25.799][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:25.807][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:25.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:25.809][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:25.810][FUN] Functions in observer BiodbConfig: [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 01:14:25.812][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:25.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:25.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:25.816][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:25.817][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:25.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:25.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:25.821][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:25.822][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:25.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:25.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:25.826][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:14:25.853][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-05-04 01:14:25.893][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:25.899][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:25.902][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:25.913][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:25.915][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:25.917][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:25.918][FUN] Functions in observer BiodbConfig: [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 01:14:25.921][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:25.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:25.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:25.926][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:25.928][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:25.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:25.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:25.934][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:25.936][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-05-04 01:14:25.937][private$selectFields] biodb.TRACE[2024-05-04 01:14:25.939][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-05-04 01:14:25.941][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-05-04 01:14:25.943][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-05-04 01:14:25.945][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:25.947][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:25.949][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:25.951][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:25.953][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:25.955][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:25.956][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:25.958][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:25.960][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-05-04 01:14:25.962][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-05-04 01:14:25.964][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:25.966][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:25.967][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:25.969][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:25.971][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-05-04 01:14:25.973][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:25.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:25.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:25.979][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:25.981][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:25.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:25.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:25.986][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:25.987][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:25.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:25.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:25.991][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:25.993][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648]. biodb.DEBUG[2024-05-04 01:14:25.995][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:25.996][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:25.997][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:26.006][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:26.007][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:26.009][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:26.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-04 01:14:26.023][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.028][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:26.029][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.033][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:26.053][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-05-04 01:14:26.055][private$selectFields] biodb.TRACE[2024-05-04 01:14:26.056][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-05-04 01:14:26.057][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-05-04 01:14:26.059][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-05-04 01:14:26.060][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.061][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.063][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.064][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:26.065][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.067][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.068][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.069][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:26.070][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-05-04 01:14:26.080][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-05-04 01:14:26.082][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.083][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.084][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.086][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:26.087][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-05-04 01:14:26.088][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.092][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:26.093][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.097][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:26.098][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.102][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:26.104][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440]. biodb.DEBUG[2024-05-04 01:14:26.105][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:26.106][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:26.108][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:26.116][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:26.124][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:26.128][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:26.129][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.TRACE[2024-05-04 01:14:26.131][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.134][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:26.136][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.139][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:26.141][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-05-04 01:14:26.142][private$selectFields] biodb.TRACE[2024-05-04 01:14:26.143][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-05-04 01:14:26.144][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-05-04 01:14:26.145][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-05-04 01:14:26.147][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.148][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.149][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.150][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:26.152][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.153][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.154][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.155][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:26.156][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-05-04 01:14:26.158][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-05-04 01:14:26.159][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.160][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.161][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.162][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:26.164][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-05-04 01:14:26.165][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.169][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:26.170][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.174][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:26.175][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.180][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:26.183][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447]. biodb.DEBUG[2024-05-04 01:14:26.185][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-05-04 01:14:26.186][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.TRACE[2024-05-04 01:14:26.201][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass. biodb.TRACE[2024-05-04 01:14:26.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass. biodb.TRACE[2024-05-04 01:14:26.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.207][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.INFO [2024-05-04 01:14:26.216][biodb::testThat] biodb.INFO [2024-05-04 01:14:26.218][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() "). biodb.INFO [2024-05-04 01:14:26.219][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 01:14:26.220][biodb::testThat] biodb.TRACE[2024-05-04 01:14:26.224][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-05-04 01:14:26.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-05-04 01:14:26.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.228][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:26.229][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:14:26.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:14:26.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.233][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:26.234][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:14:26.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:14:26.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.238][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:26.239][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:14:26.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:14:26.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.243][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:26.244][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:14:26.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:14:26.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.248][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:14:26.252][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:26.253][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:26.254][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:26.261][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:26.263][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:26.264][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:26.265][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:14:26.268][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 01:14:26.272][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-05-04 01:14:26.274][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1". biodb.TRACE[2024-05-04 01:14:26.276][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-05-04 01:14:26.278][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content". biodb.DEBUG[2024-05-04 01:14:26.282][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:26.284][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:26.286][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:26.295][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:26.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:26.297][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:26.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:14:26.302][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 01:14:26.308][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-05-04 01:14:26.310][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6". biodb.TRACE[2024-05-04 01:14:26.311][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-05-04 01:14:26.313][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content". biodb.DEBUG[2024-05-04 01:14:26.316][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:26.317][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:26.319][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:26.329][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:26.331][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:26.332][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:26.334][FUN] Functions in observer BiodbConfig: [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 01:14:26.336][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:14:26.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:14:26.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.342][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:26.343][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:14:26.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:14:26.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.347][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:26.350][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:14:26.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:14:26.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.356][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:14:26.357][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:26.358][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:26.359][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:26.367][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:26.368][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:26.369][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:26.371][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 01:14:26.372][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:26.373][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:26.374][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:26.382][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:26.383][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:26.384][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:26.385][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:14:26.388][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 01:14:26.391][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-05-04 01:14:26.393][cch$loadFileContent] Trying to load 1 files from cache: [1]: "94c7655c8f372fb2982c15119402bcba". biodb.TRACE[2024-05-04 01:14:26.395][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-05-04 01:14:26.397][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.content". biodb.DEBUG[2024-05-04 01:14:26.400][private$bdb$entriesToDataframe] 1 entrie(s) to convert in data frame. biodb.DEBUG[2024-05-04 01:14:26.402][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:26.403][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:26.404][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:26.411][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:26.413][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 01:14:26.414][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:26.415][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.TRACE[2024-05-04 01:14:26.416][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.420][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:26.421][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.425][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:26.426][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-05-04 01:14:26.427][private$selectFields] biodb.TRACE[2024-05-04 01:14:26.429][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-05-04 01:14:26.430][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-05-04 01:14:26.431][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-05-04 01:14:26.432][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.434][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.435][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.436][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:26.437][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.439][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.440][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.441][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:26.442][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-05-04 01:14:26.443][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-05-04 01:14:26.445][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.446][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.447][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.448][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:26.450][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-05-04 01:14:26.451][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.455][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:26.456][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.459][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:26.461][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.464][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:26.466][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440]. biodb.DEBUG[2024-05-04 01:14:26.467][private$entriesToListOfDataframes] Converted 1 entry/ies to data frame(s). biodb.DEBUG[2024-05-04 01:14:26.468][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.TRACE[2024-05-04 01:14:26.480][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:26.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:26.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.484][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:26.485][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:26.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:26.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.489][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:26.490][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:26.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:26.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.494][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:26.495][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:26.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:26.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.499][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:14:26.503][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:26.504][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:26.505][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:26.513][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:26.514][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 01:14:26.515][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:26.517][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.DEBUG[2024-05-04 01:14:26.520][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 01:14:26.524][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-05-04 01:14:26.525][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386". biodb.TRACE[2024-05-04 01:14:26.527][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-05-04 01:14:26.529][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content". biodb.DEBUG[2024-05-04 01:14:26.534][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 01:14:26.540][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-05-04 01:14:26.543][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f". biodb.TRACE[2024-05-04 01:14:26.546][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-05-04 01:14:26.552][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content". biodb.DEBUG[2024-05-04 01:14:26.557][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:26.559][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:26.561][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:26.572][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:26.574][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 01:14:26.576][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:26.578][FUN] Functions in observer BiodbConfig: [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 01:14:26.581][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:26.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:26.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.586][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:26.588][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:26.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:26.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.594][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:26.596][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:26.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:26.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.601][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:14:26.603][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:26.605][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:26.606][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:26.617][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:26.619][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:26.621][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:26.623][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-04 01:14:26.625][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:26.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:26.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.630][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:26.632][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:26.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:26.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.638][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:26.640][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:26.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:26.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.646][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:14:26.648][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:26.649][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:26.651][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:26.662][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:26.664][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:26.665][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:26.667][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.TRACE[2024-05-04 01:14:26.669][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:26.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:26.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.684][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:26.686][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:26.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:26.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.691][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:26.693][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:26.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:26.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.699][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:14:26.701][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-05-04 01:14:26.703][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:26.705][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:26.706][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:26.713][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:26.714][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:26.715][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:26.716][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.TRACE[2024-05-04 01:14:26.718][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.722][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:26.723][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.727][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:26.728][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-05-04 01:14:26.729][private$selectFields] biodb.TRACE[2024-05-04 01:14:26.730][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-05-04 01:14:26.731][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-05-04 01:14:26.732][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-05-04 01:14:26.734][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.735][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.736][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.737][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:26.739][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.740][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.741][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.742][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:26.744][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-05-04 01:14:26.745][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-05-04 01:14:26.746][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.747][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.748][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.750][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:26.751][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-05-04 01:14:26.752][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.756][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:26.757][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.761][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:26.762][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.768][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:26.770][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648]. biodb.DEBUG[2024-05-04 01:14:26.772][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:26.774][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:26.776][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:26.787][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:26.789][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:26.791][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:26.793][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-04 01:14:26.796][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.802][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:26.804][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.809][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:26.810][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-05-04 01:14:26.811][private$selectFields] biodb.TRACE[2024-05-04 01:14:26.812][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-05-04 01:14:26.813][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-05-04 01:14:26.815][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-05-04 01:14:26.816][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.817][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.818][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.819][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:26.821][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.822][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.823][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.824][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:26.826][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-05-04 01:14:26.827][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-05-04 01:14:26.828][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.829][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.830][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.832][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:26.833][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-05-04 01:14:26.834][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.838][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:26.839][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.843][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:26.844][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.848][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:26.849][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440]. biodb.DEBUG[2024-05-04 01:14:26.851][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:26.852][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:26.853][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:26.861][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:26.862][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:26.863][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:26.864][FUN] Functions in observer BiodbConfig: [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 01:14:26.866][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.869][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:26.871][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.874][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:26.876][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-05-04 01:14:26.877][private$selectFields] biodb.TRACE[2024-05-04 01:14:26.878][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-05-04 01:14:26.879][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-05-04 01:14:26.880][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-05-04 01:14:26.882][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.883][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.884][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.885][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:26.887][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.888][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.889][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.890][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:26.892][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-05-04 01:14:26.894][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-05-04 01:14:26.895][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.897][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.899][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.901][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:26.903][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-05-04 01:14:26.905][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.910][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:26.911][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.915][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:26.916][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:26.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.920][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:26.922][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447]. biodb.DEBUG[2024-05-04 01:14:26.923][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-05-04 01:14:26.924][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.TRACE[2024-05-04 01:14:26.936][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass. biodb.TRACE[2024-05-04 01:14:26.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass. biodb.TRACE[2024-05-04 01:14:26.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.940][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.INFO [2024-05-04 01:14:26.948][biodb::testThat] biodb.INFO [2024-05-04 01:14:26.949][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() "). biodb.INFO [2024-05-04 01:14:26.950][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 01:14:26.951][biodb::testThat] biodb.TRACE[2024-05-04 01:14:26.955][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-05-04 01:14:26.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-05-04 01:14:26.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.959][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:26.960][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:14:26.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:14:26.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.964][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:26.965][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:14:26.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:14:26.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.969][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:26.970][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:14:26.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:14:26.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.974][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:26.975][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:14:26.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:14:26.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:26.979][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:14:26.985][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:26.986][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:26.987][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:26.994][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:26.996][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:26.997][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:26.998][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.DEBUG[2024-05-04 01:14:27.001][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 01:14:27.005][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-05-04 01:14:27.007][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1". biodb.TRACE[2024-05-04 01:14:27.008][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-05-04 01:14:27.010][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content". biodb.DEBUG[2024-05-04 01:14:27.013][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:27.014][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:27.015][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:27.023][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:27.024][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:27.025][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:27.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:14:27.029][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 01:14:27.033][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-05-04 01:14:27.034][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6". biodb.TRACE[2024-05-04 01:14:27.036][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-05-04 01:14:27.038][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content". biodb.DEBUG[2024-05-04 01:14:27.041][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:27.042][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:27.043][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:27.051][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:27.052][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:27.053][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:27.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-04 01:14:27.056][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:14:27.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:14:27.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:27.060][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:27.061][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:14:27.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:14:27.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:27.065][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:27.066][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 01:14:27.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:14:27.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:27.070][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:14:27.071][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:27.072][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:27.073][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:27.081][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:27.082][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 01:14:27.083][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:27.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:14:27.086][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:27.087][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:27.088][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:27.095][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:27.097][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:27.098][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:27.099][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 01:14:27.101][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 01:14:27.105][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-05-04 01:14:27.107][cch$loadFileContent] Trying to load 1 files from cache: [1]: "94c7655c8f372fb2982c15119402bcba". biodb.TRACE[2024-05-04 01:14:27.108][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-05-04 01:14:27.111][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.content". biodb.DEBUG[2024-05-04 01:14:27.114][private$bdb$entriesToDataframe] 1 entrie(s) to convert in data frame. biodb.DEBUG[2024-05-04 01:14:27.116][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:27.117][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:27.118][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:27.126][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:27.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:27.129][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:27.130][FUN] Functions in observer BiodbConfig: [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 01:14:27.131][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:27.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:27.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:27.135][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:27.136][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:27.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:27.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:27.140][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:27.141][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-05-04 01:14:27.143][private$selectFields] biodb.TRACE[2024-05-04 01:14:27.144][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-05-04 01:14:27.145][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-05-04 01:14:27.146][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-05-04 01:14:27.147][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:27.149][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:27.150][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:27.151][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:27.152][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:27.154][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:27.155][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:27.156][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:27.157][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-05-04 01:14:27.159][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-05-04 01:14:27.160][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:27.161][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:27.162][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:27.163][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:27.165][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-05-04 01:14:27.166][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:27.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:27.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:27.175][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:27.177][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:27.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:27.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:27.180][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:27.182][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:27.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:27.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:27.185][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:27.187][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440]. biodb.DEBUG[2024-05-04 01:14:27.188][private$entriesToListOfDataframes] Converted 1 entry/ies to data frame(s). biodb.DEBUG[2024-05-04 01:14:27.189][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.TRACE[2024-05-04 01:14:27.217][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:27.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:27.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:27.221][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:27.222][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:27.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:27.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:27.226][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:27.227][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:27.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:27.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:27.231][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:27.232][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:27.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:27.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:27.236][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:14:27.241][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:27.242][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:27.243][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:27.251][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:27.252][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:27.253][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:27.254][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:14:27.257][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 01:14:27.261][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-05-04 01:14:27.263][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386". biodb.TRACE[2024-05-04 01:14:27.264][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-05-04 01:14:27.266][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content". biodb.DEBUG[2024-05-04 01:14:27.270][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 01:14:27.274][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-05-04 01:14:27.275][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f". biodb.TRACE[2024-05-04 01:14:27.277][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-05-04 01:14:27.279][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content". biodb.DEBUG[2024-05-04 01:14:27.282][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:27.283][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:27.284][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:27.291][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:27.293][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 01:14:27.294][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:27.295][FUN] Functions in observer BiodbConfig: [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 01:14:27.296][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:27.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:27.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:27.300][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:27.301][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:27.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:27.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:27.305][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:27.306][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:27.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:27.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:27.310][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:14:27.311][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:27.312][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:27.314][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:27.321][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:27.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:27.324][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:27.325][FUN] Functions in observer BiodbConfig: [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 01:14:27.327][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:27.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:27.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:27.330][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:27.332][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:27.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:27.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:27.335][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:27.337][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:27.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:27.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:27.340][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:14:27.342][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:27.343][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:27.344][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:27.351][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:27.353][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:27.354][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:27.355][FUN] Functions in observer BiodbConfig: [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 01:14:27.356][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:27.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:27.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:27.360][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:27.361][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:27.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:27.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:27.365][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:27.366][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:27.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:27.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:27.370][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:14:27.372][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-05-04 01:14:27.373][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:27.374][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:27.376][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:27.383][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:27.384][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 01:14:27.386][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:27.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-04 01:14:27.388][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:27.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:27.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:27.392][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:27.393][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:27.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:27.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:27.397][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:27.398][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-05-04 01:14:27.399][private$selectFields] biodb.TRACE[2024-05-04 01:14:27.401][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-05-04 01:14:27.402][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-05-04 01:14:27.403][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-05-04 01:14:27.404][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:27.405][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:27.407][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:27.408][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:27.409][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:27.410][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:27.412][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:27.413][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:27.414][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-05-04 01:14:27.415][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-05-04 01:14:27.416][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:27.418][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:27.419][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:27.420][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:27.421][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-05-04 01:14:27.423][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:27.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:27.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:27.426][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:27.428][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:27.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:27.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:27.431][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:27.433][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:27.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:27.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:27.436][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:27.438][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648]. biodb.DEBUG[2024-05-04 01:14:27.439][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:27.440][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:27.441][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:27.449][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:27.450][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:27.451][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:27.452][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-04 01:14:27.454][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:27.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:27.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:27.458][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:27.459][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:27.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:27.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:27.463][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:27.464][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-05-04 01:14:27.465][private$selectFields] biodb.TRACE[2024-05-04 01:14:27.466][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-05-04 01:14:27.467][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-05-04 01:14:27.469][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-05-04 01:14:27.470][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:27.471][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:27.472][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:27.473][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:27.475][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:27.476][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:27.477][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:27.478][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:27.480][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-05-04 01:14:27.481][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-05-04 01:14:27.482][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:27.483][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:27.484][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:27.486][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:27.487][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-05-04 01:14:27.488][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:27.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:27.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:27.492][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:27.493][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:27.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:27.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:27.497][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:27.498][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:27.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:27.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:27.502][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:27.504][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440]. biodb.DEBUG[2024-05-04 01:14:27.505][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:27.506][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:27.508][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:27.521][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:27.524][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 01:14:27.526][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:27.528][FUN] Functions in observer BiodbConfig: [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 01:14:27.530][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:27.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:27.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:27.537][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:27.539][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:27.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:27.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:27.545][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:27.547][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-05-04 01:14:27.549][private$selectFields] biodb.TRACE[2024-05-04 01:14:27.551][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-05-04 01:14:27.553][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-05-04 01:14:27.555][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-05-04 01:14:27.557][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:27.559][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:27.561][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:27.563][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:27.565][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:27.567][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:27.569][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:27.571][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:27.573][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-05-04 01:14:27.575][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-05-04 01:14:27.577][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:27.579][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:27.581][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:27.583][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:27.585][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-05-04 01:14:27.587][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:27.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:27.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:27.593][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:27.595][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:27.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:27.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:27.601][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:27.603][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:27.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:27.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:27.609][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:27.611][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447]. biodb.DEBUG[2024-05-04 01:14:27.613][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-05-04 01:14:27.615][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.TRACE[2024-05-04 01:14:27.661][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass. biodb.TRACE[2024-05-04 01:14:27.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass. biodb.TRACE[2024-05-04 01:14:27.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:27.667][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.INFO [2024-05-04 01:14:27.679][biodb::testThat] biodb.INFO [2024-05-04 01:14:27.681][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL "). biodb.INFO [2024-05-04 01:14:27.683][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 01:14:27.685][biodb::testThat] biodb.DEBUG[2024-05-04 01:14:27.689][private$loadEntries] Creating entries from ids [1]: "WRONGA". biodb.DEBUG[2024-05-04 01:14:27.691][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-05-04 01:14:27.694][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA". biodb.TRACE[2024-05-04 01:14:27.697][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-05-04 01:14:27.699][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-05-04 01:14:27.701][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-05-04 01:14:27.703][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-05-04 01:14:27.705][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-05-04 01:14:27.707][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-05-04 01:14:27.712][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:27.722][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:27.724][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:27.735][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:27.737][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 01:14:27.739][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:27.741][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 01:14:27.744][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA". biodb.DEBUG[2024-05-04 01:14:27.749][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-04 01:14:27.751][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-04 01:14:27.754][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA". biodb.TRACE[2024-05-04 01:14:28.116][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 01:14:28.474][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-05-04 01:14:28.478][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content" biodb.TRACE[2024-05-04 01:14:28.486][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request" biodb.TRACE[2024-05-04 01:14:28.492][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml" biodb.DEBUG[2024-05-04 01:14:28.495][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-05-04 01:14:28.498][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-05-04 01:14:28.501][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-05-04 01:14:28.504][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:28.506][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:28.508][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:28.520][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:28.522][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:28.524][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:28.526][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-04 01:14:28.530][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:14:28.532][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:14:28.534][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:28.536][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:28.538][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:14:28.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:14:28.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:28.544][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:28.547][ef$get] Asked field names are: charge. biodb.TRACE[2024-05-04 01:14:28.549][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-05-04 01:14:28.551][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:28.553][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:28.555][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-04 01:14:28.557][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 01:14:28.559][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:28.561][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:28.564][ef$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 01:14:28.566][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 01:14:28.568][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:28.570][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:28.572][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 01:14:28.574][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 01:14:28.576][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:28.578][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:28.581][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-04 01:14:28.583][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-04 01:14:28.584][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:28.586][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:28.589][ef$get] Asked field names are: mass. biodb.TRACE[2024-05-04 01:14:28.591][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:14:28.593][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:28.595][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:28.598][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:28.599][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:14:28.602][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:28.604][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:28.605][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 01:14:28.606][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 01:14:28.608][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:28.609][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:28.610][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-05-04 01:14:28.612][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-05-04 01:14:28.613][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:28.614][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:28.616][ef$get] Asked field names are: smiles. biodb.TRACE[2024-05-04 01:14:28.617][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-04 01:14:28.618][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:28.620][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:28.621][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:28.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:28.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:28.625][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:28.628][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:28.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:28.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:28.632][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:28.634][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:14:28.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:14:28.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:28.638][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:28.639][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:14:28.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:14:28.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:28.644][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:28.645][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:14:28.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:14:28.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:28.649][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:28.651][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:14:28.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:14:28.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:28.657][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:28.659][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:14:28.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:14:28.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:28.664][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:28.665][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:14:28.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:14:28.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:28.670][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:28.671][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:14:28.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:14:28.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:28.675][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:14:28.676][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:14:28.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:14:28.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:14:28.680][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:14:28.681][self$createEntryFromContent] Accession numbers: . biodb.DEBUG[2024-05-04 01:14:28.682][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL. biodb.INFO [2024-05-04 01:14:28.696][biodb::testThat] biodb.INFO [2024-05-04 01:14:28.698][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones "). biodb.INFO [2024-05-04 01:14:28.699][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 01:14:28.700][biodb::testThat] biodb.DEBUG[2024-05-04 01:14:28.760][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799" biodb.DEBUG[2024-05-04 01:14:28.762][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799". biodb.DEBUG[2024-05-04 01:14:28.763][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)... biodb.TRACE[2024-05-04 01:14:28.766][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799". biodb.TRACE[2024-05-04 01:14:28.768][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE". biodb.TRACE[2024-05-04 01:14:28.769][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-05-04 01:14:28.771][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-05-04 01:14:28.772][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-05-04 01:14:28.774][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-05-04 01:14:28.775][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-05-04 01:14:28.780][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:28.781][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:28.782][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:28.790][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:28.791][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:28.793][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:28.794][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:14:28.795][scheduler$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 01:14:28.799][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-04 01:14:28.800][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-04 01:14:28.802][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB". biodb.TRACE[2024-05-04 01:14:29.159][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB). biodb.DEBUG[2024-05-04 01:14:29.514][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-05-04 01:14:29.518][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content" biodb.TRACE[2024-05-04 01:14:29.525][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request" biodb.DEBUG[2024-05-04 01:14:29.528][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:29.531][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:29.533][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:29.545][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:29.547][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:29.549][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:29.550][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:14:29.553][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528". biodb.DEBUG[2024-05-04 01:14:29.558][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-04 01:14:29.560][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-04 01:14:29.563][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528". biodb.TRACE[2024-05-04 01:14:39.931][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 01:14:50.391][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-05-04 01:14:50.396][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.content" biodb.TRACE[2024-05-04 01:14:50.403][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.request" biodb.DEBUG[2024-05-04 01:14:50.407][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:14:50.409][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:14:50.411][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:14:50.423][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:14:50.425][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:14:50.427][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:14:50.429][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:14:50.432][scheduler$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 01:14:50.437][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-04 01:14:50.439][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-04 01:14:50.442][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799". biodb.TRACE[2024-05-04 01:15:10.216][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799). biodb.DEBUG[2024-05-04 01:15:20.591][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-05-04 01:15:20.596][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content" biodb.TRACE[2024-05-04 01:15:20.604][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request" biodb.TRACE[2024-05-04 01:15:20.610][private$doSaveContentToFile] Saving to cache [3]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml" biodb.DEBUG[2024-05-04 01:15:20.616][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-05-04 01:15:20.621][self$createEntryFromContent] Creating ChEBI entries from 3 content(s). biodb.DEBUG[2024-05-04 01:15:20.624][self$createEntryFromContent] Parsing 3 ChEBI entries. biodb.DEBUG[2024-05-04 01:15:20.628][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:15:20.630][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:15:20.632][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:15:20.642][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:20.644][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:15:20.645][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:20.647][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.TRACE[2024-05-04 01:15:20.650][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:15:20.651][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:15:20.653][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:15:20.654][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:15:20.656][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:15:20.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:15:20.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:15:20.660][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:15:20.662][ef$get] Asked field names are: charge. biodb.TRACE[2024-05-04 01:15:20.663][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-05-04 01:15:20.664][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:15:20.666][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:15:20.668][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-04 01:15:20.669][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 01:15:20.671][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:15:20.672][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:15:20.674][ef$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 01:15:20.675][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 01:15:20.677][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:15:20.678][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:15:20.680][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 01:15:20.682][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 01:15:20.683][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:15:20.685][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:15:20.687][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-04 01:15:20.689][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-04 01:15:20.691][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:15:20.693][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:15:20.694][ef$get] Asked field names are: mass. biodb.TRACE[2024-05-04 01:15:20.696][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:15:20.698][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:15:20.699][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:15:20.701][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:15:20.702][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:15:20.703][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:15:20.705][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:15:20.707][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 01:15:20.709][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 01:15:20.710][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:15:20.711][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:15:20.713][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-05-04 01:15:20.715][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-05-04 01:15:20.716][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:15:20.718][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:15:20.719][ef$get] Asked field names are: smiles. biodb.TRACE[2024-05-04 01:15:20.721][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-04 01:15:20.722][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:15:20.724][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:15:20.726][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:15:20.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:15:20.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:15:20.731][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:15:20.732][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:15:20.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:15:20.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:15:20.737][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:15:20.739][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:15:20.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:15:20.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:15:20.743][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:15:20.744][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:15:20.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:15:20.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:15:20.749][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:15:20.750][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:15:20.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:15:20.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:15:20.754][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:15:20.756][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:15:20.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:15:20.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:15:20.760][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:15:20.762][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:15:20.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:15:20.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:15:20.766][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:15:20.768][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:15:20.769][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:15:20.770][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:15:20.778][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:20.786][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 01:15:20.792][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:20.793][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.TRACE[2024-05-04 01:15:20.796][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:15:20.797][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:15:20.799][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:15:20.800][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:15:20.801][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:15:20.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:15:20.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:15:20.805][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:15:20.806][ef$get] Asked field names are: charge. biodb.TRACE[2024-05-04 01:15:20.808][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-05-04 01:15:20.809][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:15:20.810][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:15:20.812][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-04 01:15:20.813][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 01:15:20.814][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:15:20.815][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:15:20.817][ef$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 01:15:20.818][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 01:15:20.819][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:15:20.821][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:15:20.822][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 01:15:20.823][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 01:15:20.825][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:15:20.826][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:15:20.827][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-04 01:15:20.829][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-04 01:15:20.832][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:15:20.833][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:15:20.834][ef$get] Asked field names are: mass. biodb.TRACE[2024-05-04 01:15:20.836][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:15:20.837][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:15:20.838][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:15:20.840][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:15:20.841][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:15:20.843][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:15:20.844][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:15:20.846][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 01:15:20.847][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 01:15:20.848][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:15:20.850][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:15:20.852][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-05-04 01:15:20.853][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-05-04 01:15:20.854][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:15:20.856][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:15:20.858][ef$get] Asked field names are: smiles. biodb.TRACE[2024-05-04 01:15:20.859][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-04 01:15:20.861][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:15:20.862][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:15:20.863][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:15:20.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:15:20.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:15:20.867][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:15:20.869][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:15:20.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:15:20.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:15:20.873][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:15:20.874][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:15:20.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:15:20.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:15:20.878][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:15:20.879][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:15:20.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:15:20.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:15:20.884][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:15:20.885][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:15:20.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:15:20.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:15:20.889][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:15:20.891][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:15:20.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:15:20.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:15:20.895][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:15:20.897][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:15:20.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:15:20.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:15:20.903][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:15:20.905][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:15:20.907][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:15:20.908][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:15:20.918][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:20.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:15:20.921][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:20.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-04 01:15:20.926][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:15:20.928][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:15:20.930][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:15:20.931][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:15:20.934][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:15:20.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:15:20.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:15:20.939][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:15:20.942][ef$get] Asked field names are: charge. biodb.TRACE[2024-05-04 01:15:20.944][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-05-04 01:15:20.945][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:15:20.947][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:15:20.949][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-04 01:15:20.951][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 01:15:20.953][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:15:20.955][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:15:20.957][ef$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 01:15:20.958][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 01:15:20.959][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:15:20.960][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:15:20.962][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 01:15:20.963][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 01:15:20.965][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:15:20.966][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:15:20.967][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-04 01:15:20.969][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-04 01:15:20.970][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:15:20.971][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:15:20.973][ef$get] Asked field names are: mass. biodb.TRACE[2024-05-04 01:15:20.974][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:15:20.975][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:15:20.976][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:15:20.978][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:15:20.979][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:15:20.980][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:15:20.981][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:15:20.983][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 01:15:20.984][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 01:15:20.986][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:15:20.987][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:15:20.988][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-05-04 01:15:20.990][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-05-04 01:15:20.991][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:15:20.992][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:15:20.994][ef$get] Asked field names are: smiles. biodb.TRACE[2024-05-04 01:15:20.995][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-04 01:15:20.996][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:15:20.998][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:15:20.999][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:15:21.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:15:21.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:15:21.003][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:15:21.005][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:15:21.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:15:21.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:15:21.009][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:15:21.010][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:15:21.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:15:21.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:15:21.014][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:15:21.015][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:15:21.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:15:21.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:15:21.019][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:15:21.021][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:15:21.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:15:21.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:15:21.024][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:15:21.026][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:15:21.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:15:21.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:15:21.029][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:15:21.031][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:15:21.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:15:21.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:15:21.034][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:15:21.036][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:15:21.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:15:21.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:15:21.040][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:15:21.041][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:15:21.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:15:21.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:15:21.046][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:15:21.048][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:15:21.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:15:21.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:15:21.052][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:15:21.053][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:15:21.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:15:21.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:15:21.057][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:15:21.059][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:15:21.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:15:21.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:15:21.062][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:15:21.064][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:15:21.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:15:21.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:15:21.067][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:15:21.069][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:15:21.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:15:21.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:15:21.073][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:15:21.074][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:15:21.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:15:21.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:15:21.078][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:15:21.080][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:15:21.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:15:21.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:15:21.086][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:15:21.088][self$createEntryFromContent] Accession numbers: , , . biodb.DEBUG[2024-05-04 01:15:21.090][self$createEntryFromContent] Found 3 entry/ies without an accession number. Set it/them to NULL. biodb.DEBUG[2024-05-04 01:15:21.092][function(conn, opt)] Entries: [4]: "NULL, <environment>, NULL, NULL" biodb.INFO [2024-05-04 01:15:21.405][biodb::testThat] biodb.INFO [2024-05-04 01:15:21.407][biodb::testThat] Running test function test.peak.table (" The peak table is correct. "). biodb.INFO [2024-05-04 01:15:21.409][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 01:15:21.411][biodb::testThat] biodb.INFO [2024-05-04 01:15:21.497][biodb::testThat] biodb.INFO [2024-05-04 01:15:21.499][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. "). biodb.INFO [2024-05-04 01:15:21.500][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 01:15:21.503][biodb::testThat] biodb.INFO [2024-05-04 01:15:21.519][biodb::testThat] biodb.INFO [2024-05-04 01:15:21.520][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. "). biodb.INFO [2024-05-04 01:15:21.522][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 01:15:21.523][biodb::testThat] biodb.DEBUG[2024-05-04 01:15:21.526][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 01:15:21.530][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-04 01:15:21.532][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-04 01:15:21.535][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL". biodb.TRACE[2024-05-04 01:15:21.949][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL). biodb.DEBUG[2024-05-04 01:15:22.441][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-05-04 01:15:22.444][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content" biodb.TRACE[2024-05-04 01:15:22.450][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request" biodb.TRACE[2024-05-04 01:15:22.475][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 01:15:22.477][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 01:15:22.479][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:15:22.481][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:15:22.483][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:15:22.485][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:15:22.487][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:15:22.489][ef$get] fields variable is a list. biodb.INFO [2024-05-04 01:15:22.492][biodb::testThat] biodb.INFO [2024-05-04 01:15:22.494][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. "). biodb.INFO [2024-05-04 01:15:22.496][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 01:15:22.497][biodb::testThat] biodb.ERROR[2024-05-04 01:15:22.524][conn$annotateMzValues] No column named "mz" was found inside data frame. biodb.ERROR[2024-05-04 01:15:22.551][ef$checkIsDefined] Field(s) "foo" is/are not defined. biodb.INFO [2024-05-04 01:15:22.577][biodb$terminate] Closing BiodbMain instance... biodb.DEBUG[2024-05-04 01:15:22.580][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler biodb.INFO [2024-05-04 01:15:22.582][self$deleteConn] Connector "chebi" deleted. biodb.DEBUG[2024-05-04 01:15:22.584][notifyObservers] Notify observers for terminate. biodb.DEBUG[2024-05-04 01:15:22.586][FUN] Trying to call function terminate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:15:22.587][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:15:22.589][FUN] Trying to call function terminate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:22.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:15:22.593][FUN] Trying to call function terminate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:22.595][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.INFO [2024-05-04 01:15:22.625][biodb::testContext] biodb.INFO [2024-05-04 01:15:22.627][biodb::testContext] ******************************************************************************** biodb.INFO [2024-05-04 01:15:22.629][biodb::testContext] Test context - Test conversions biodb.INFO [2024-05-04 01:15:22.631][biodb::testContext] ******************************************************************************** biodb.INFO [2024-05-04 01:15:22.634][biodb::testContext] biodb.INFO [2024-05-04 01:15:22.638][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0. biodb.DEBUG[2024-05-04 01:15:22.642][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc/R/library/biodb/definitions.yml". biodb.DEBUG[2024-05-04 01:15:22.648][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-05-04 01:15:22.650][self$getConfig()$define] Define config key allow.huge.downloads. biodb.DEBUG[2024-05-04 01:15:22.652][self$set] Set key allow.huge.downloads to TRUE. biodb.DEBUG[2024-05-04 01:15:22.654][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:22.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:22.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:22.658][self$getConfig()$define] Define config key autoload.extra.pkgs. biodb.DEBUG[2024-05-04 01:15:22.660][self$set] Set key autoload.extra.pkgs to TRUE. biodb.DEBUG[2024-05-04 01:15:22.661][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:22.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:22.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:22.665][self$getConfig()$define] Define config key cache.all.requests. biodb.DEBUG[2024-05-04 01:15:22.666][self$set] Set key cache.all.requests to TRUE. biodb.DEBUG[2024-05-04 01:15:22.668][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:22.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:22.670][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 01:15:22.671][self$getConfig()$define] Define config key cache.directory. biodb.DEBUG[2024-05-04 01:15:22.673][self$getConfig()$define] Define config key cache.read.only. biodb.DEBUG[2024-05-04 01:15:22.674][self$set] Set key cache.read.only to FALSE. biodb.DEBUG[2024-05-04 01:15:22.675][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:22.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:22.678][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:22.679][self$getConfig()$define] Define config key cache.subfolders. biodb.DEBUG[2024-05-04 01:15:22.680][self$getConfig()$define] Define config key cache.system. biodb.DEBUG[2024-05-04 01:15:22.682][self$set] Set key cache.system to TRUE. biodb.DEBUG[2024-05-04 01:15:22.683][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:22.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:22.685][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 01:15:22.687][self$getConfig()$define] Define config key use.cache.for.local.db. biodb.DEBUG[2024-05-04 01:15:22.688][self$set] Set key use.cache.for.local.db to FALSE. biodb.DEBUG[2024-05-04 01:15:22.689][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:22.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:22.691][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:22.693][self$getConfig()$define] Define config key dwnld.chunk.size. biodb.DEBUG[2024-05-04 01:15:22.694][self$getConfig()$define] Define config key dwnld.timeout. biodb.DEBUG[2024-05-04 01:15:22.695][self$set] Set key dwnld.timeout to 3600. biodb.DEBUG[2024-05-04 01:15:22.696][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:22.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:22.699][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:22.700][self$getConfig()$define] Define config key compute.fields. biodb.DEBUG[2024-05-04 01:15:22.701][self$set] Set key compute.fields to TRUE. biodb.DEBUG[2024-05-04 01:15:22.702][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:22.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:22.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:22.706][self$getConfig()$define] Define config key factory.cache. biodb.DEBUG[2024-05-04 01:15:22.707][self$getConfig()$define] Define config key force.locale. biodb.DEBUG[2024-05-04 01:15:22.708][self$set] Set key force.locale to TRUE. biodb.DEBUG[2024-05-04 01:15:22.710][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:22.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:22.712][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.DEBUG[2024-05-04 01:15:22.713][self$getConfig()$define] Define config key longterm.cache.subfolder. biodb.DEBUG[2024-05-04 01:15:22.714][self$getConfig()$define] Define config key msg.caution.lvl. biodb.DEBUG[2024-05-04 01:15:22.716][self$getConfig()$define] Define config key msg.debug.lvl. biodb.DEBUG[2024-05-04 01:15:22.717][self$getConfig()$define] Define config key msg.info.lvl. biodb.DEBUG[2024-05-04 01:15:22.718][self$getConfig()$define] Define config key multival.field.sep. biodb.DEBUG[2024-05-04 01:15:22.719][self$set] Set key multival.field.sep to ";". biodb.DEBUG[2024-05-04 01:15:22.721][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:22.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:22.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:22.724][self$getConfig()$define] Define config key intra.field.name.sep. biodb.DEBUG[2024-05-04 01:15:22.725][self$set] Set key intra.field.name.sep to ".". biodb.DEBUG[2024-05-04 01:15:22.727][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:22.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:22.729][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:22.730][self$getConfig()$define] Define config key entries.sep. biodb.DEBUG[2024-05-04 01:15:22.731][self$set] Set key entries.sep to "|". biodb.DEBUG[2024-05-04 01:15:22.733][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:22.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:22.735][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:22.736][self$getConfig()$define] Define config key offline. biodb.DEBUG[2024-05-04 01:15:22.738][self$set] Set key offline to FALSE. biodb.DEBUG[2024-05-04 01:15:22.739][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:22.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:22.741][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 01:15:22.742][self$getConfig()$define] Define config key persistent.cache.impl. biodb.DEBUG[2024-05-04 01:15:22.743][self$set] Set key persistent.cache.impl to "custom". biodb.DEBUG[2024-05-04 01:15:22.745][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:22.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:22.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:22.748][self$getConfig()$define] Define config key proton.mass. biodb.DEBUG[2024-05-04 01:15:22.749][self$set] Set key proton.mass to 1.0072765. biodb.DEBUG[2024-05-04 01:15:22.750][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:22.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:22.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:22.754][self$getConfig()$define] Define config key shortterm.cache.subfolder. biodb.DEBUG[2024-05-04 01:15:22.755][self$getConfig()$define] Define config key svn.binary.path. biodb.DEBUG[2024-05-04 01:15:22.759][self$set] Set key svn.binary.path to "". biodb.DEBUG[2024-05-04 01:15:22.761][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:22.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:22.763][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:22.764][self$getConfig()$define] Define config key test.functions. biodb.DEBUG[2024-05-04 01:15:22.765][self$getConfig()$define] Define config key useragent. biodb.DEBUG[2024-05-04 01:15:22.767][self$set] Set key useragent to "R Bioconductor biodb library.". biodb.DEBUG[2024-05-04 01:15:22.768][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:22.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:22.770][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 01:15:22.772][self$getDbsInfo()$define] Define connector comp.csv.file. biodb.DEBUG[2024-05-04 01:15:22.774][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-05-04 01:15:22.800][self$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 01:15:22.803][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 01:15:22.805][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 01:15:22.807][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 01:15:22.809][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 01:15:22.811][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-04 01:15:22.814][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 01:15:22.816][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2024-05-04 01:15:22.818][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 01:15:22.820][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-05-04 01:15:22.822][self$setPropertyValue] Setting property "name" to "Compound CSV File". biodb.DEBUG[2024-05-04 01:15:22.824][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 01:15:22.826][self$setPropertyValue] biodb.DEBUG[2024-05-04 01:15:22.828][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-04 01:15:22.830][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-05-04 01:15:22.830][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-05-04 01:15:22.830][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2024-05-04 01:15:22.830][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2024-05-04 01:15:22.830][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2024-05-04 01:15:22.832][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 01:15:22.835][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 01:15:22.848][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 01:15:22.851][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 01:15:22.853][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 01:15:22.855][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 01:15:22.857][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 01:15:22.860][self$setPropertyValue] biodb.DEBUG[2024-05-04 01:15:22.862][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 01:15:22.864][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 01:15:22.865][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-04 01:15:22.867][self$setPropertyValue] biodb.DEBUG[2024-05-04 01:15:22.868][self$getDbsInfo()$define] Define connector comp.sqlite. biodb.DEBUG[2024-05-04 01:15:22.870][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-05-04 01:15:22.871][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.". biodb.DEBUG[2024-05-04 01:15:22.873][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 01:15:22.874][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 01:15:22.875][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 01:15:22.876][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 01:15:22.878][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-04 01:15:22.879][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 01:15:22.880][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2024-05-04 01:15:22.881][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 01:15:22.882][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-05-04 01:15:22.884][self$setPropertyValue] Setting property "name" to "Compound SQLite". biodb.DEBUG[2024-05-04 01:15:22.885][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 01:15:22.886][self$setPropertyValue] biodb.DEBUG[2024-05-04 01:15:22.887][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-04 01:15:22.888][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-05-04 01:15:22.888][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-05-04 01:15:22.888][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2024-05-04 01:15:22.888][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2024-05-04 01:15:22.888][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2024-05-04 01:15:22.890][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 01:15:22.891][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 01:15:22.893][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 01:15:22.894][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 01:15:22.896][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 01:15:22.898][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 01:15:22.899][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 01:15:22.901][self$setPropertyValue] biodb.DEBUG[2024-05-04 01:15:22.903][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 01:15:22.905][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 01:15:22.907][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-04 01:15:22.908][self$setPropertyValue] biodb.DEBUG[2024-05-04 01:15:22.910][self$getDbsInfo()$define] Define connector mass.csv.file. biodb.DEBUG[2024-05-04 01:15:22.912][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2024-05-04 01:15:22.913][self$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 01:15:22.915][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 01:15:22.916][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 01:15:22.917][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 01:15:22.918][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 01:15:22.920][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-04 01:15:22.921][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 01:15:22.922][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2024-05-04 01:15:22.923][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 01:15:22.925][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2024-05-04 01:15:22.926][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File". biodb.DEBUG[2024-05-04 01:15:22.927][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 01:15:22.928][self$setPropertyValue] biodb.DEBUG[2024-05-04 01:15:22.929][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-04 01:15:22.931][self$setPropertyValue] biodb.DEBUG[2024-05-04 01:15:22.932][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 01:15:22.933][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 01:15:22.934][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 01:15:22.935][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 01:15:22.937][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 01:15:22.938][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 01:15:22.939][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 01:15:22.940][self$setPropertyValue] biodb.DEBUG[2024-05-04 01:15:22.942][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 01:15:22.943][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 01:15:22.945][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-04 01:15:22.946][self$setPropertyValue] biodb.DEBUG[2024-05-04 01:15:22.948][self$getDbsInfo()$define] Define connector mass.sqlite. biodb.DEBUG[2024-05-04 01:15:22.950][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2024-05-04 01:15:22.951][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.". biodb.DEBUG[2024-05-04 01:15:22.952][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 01:15:22.953][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 01:15:22.955][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 01:15:22.956][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 01:15:22.957][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-04 01:15:22.958][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 01:15:22.959][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2024-05-04 01:15:22.961][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 01:15:22.962][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2024-05-04 01:15:22.963][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite". biodb.DEBUG[2024-05-04 01:15:22.964][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 01:15:22.966][self$setPropertyValue] biodb.DEBUG[2024-05-04 01:15:22.967][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-04 01:15:22.968][self$setPropertyValue] biodb.DEBUG[2024-05-04 01:15:22.969][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 01:15:22.970][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 01:15:22.972][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 01:15:22.973][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 01:15:22.974][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 01:15:22.975][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 01:15:22.976][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 01:15:22.977][self$setPropertyValue] biodb.DEBUG[2024-05-04 01:15:22.979][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 01:15:22.980][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 01:15:22.981][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-04 01:15:22.982][self$setPropertyValue] biodb.DEBUG[2024-05-04 01:15:22.984][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-05-04 01:15:22.985][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:22.986][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:22.987][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:22.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:22.989][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 01:15:22.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:22.992][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:22.993][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:22.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:22.995][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 01:15:22.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:22.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:22.999][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:23.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:23.001][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 01:15:23.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:23.003][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:23.004][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:23.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:23.007][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:15:23.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:23.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:23.010][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:23.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:23.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:15:23.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:23.015][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:23.016][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:23.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:23.018][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 01:15:23.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:23.020][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 01:15:23.021][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:23.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:23.024][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:15:23.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:23.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:23.027][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:23.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:23.030][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:15:23.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:23.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:23.033][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:23.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:23.036][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:15:23.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:23.038][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:23.039][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:23.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:23.041][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:15:23.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:23.044][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 01:15:23.045][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:23.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:23.047][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 01:15:23.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:23.050][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 01:15:23.051][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:23.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:23.053][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:15:23.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:23.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:23.056][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:23.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:23.058][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:15:23.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:23.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:23.062][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:23.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:23.064][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:15:23.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:23.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:23.068][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:23.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:23.070][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:15:23.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:23.072][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:23.073][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:23.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:23.075][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:15:23.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:23.078][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:23.079][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:23.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:23.081][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:15:23.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:23.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:23.085][self$getEntryFields()$define] Define field accession. biodb.DEBUG[2024-05-04 01:15:23.086][self$getEntryFields()$define] Define field description. biodb.DEBUG[2024-05-04 01:15:23.088][self$getEntryFields()$define] Define field name. biodb.DEBUG[2024-05-04 01:15:23.090][self$getEntryFields()$define] Define field cas.id. biodb.DEBUG[2024-05-04 01:15:23.091][self$getEntryFields()$define] Define field chebi.id. biodb.DEBUG[2024-05-04 01:15:23.093][self$getEntryFields()$define] Define field chemspider.id. biodb.DEBUG[2024-05-04 01:15:23.095][self$getEntryFields()$define] Define field comp.csv.file.id. biodb.DEBUG[2024-05-04 01:15:23.096][self$getEntryFields()$define] Define field comp.sqlite.id. biodb.DEBUG[2024-05-04 01:15:23.098][self$getEntryFields()$define] Define field expasy.enzyme.id. biodb.DEBUG[2024-05-04 01:15:23.099][self$getEntryFields()$define] Define field hmdb.metabolites.id. biodb.DEBUG[2024-05-04 01:15:23.101][self$getEntryFields()$define] Define field kegg.compound.id. biodb.DEBUG[2024-05-04 01:15:23.103][self$getEntryFields()$define] Define field kegg.genes.id. biodb.DEBUG[2024-05-04 01:15:23.104][self$getEntryFields()$define] Define field mass.csv.file.id. biodb.DEBUG[2024-05-04 01:15:23.106][self$getEntryFields()$define] Define field mass.sqlite.id. biodb.DEBUG[2024-05-04 01:15:23.107][self$getEntryFields()$define] Define field ncbi.gene.id. biodb.DEBUG[2024-05-04 01:15:23.109][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id. biodb.DEBUG[2024-05-04 01:15:23.111][self$getEntryFields()$define] Define field compound.id. biodb.DEBUG[2024-05-04 01:15:23.112][self$getEntryFields()$define] Define field average.mass. biodb.DEBUG[2024-05-04 01:15:23.114][self$getEntryFields()$define] Define field molecular.mass. biodb.DEBUG[2024-05-04 01:15:23.116][self$getEntryFields()$define] Define field monoisotopic.mass. biodb.DEBUG[2024-05-04 01:15:23.117][self$getEntryFields()$define] Define field nominal.mass. biodb.DEBUG[2024-05-04 01:15:23.119][self$getEntryFields()$define] Define field peak.attr. biodb.DEBUG[2024-05-04 01:15:23.120][self$getEntryFields()$define] Define field peak.comp. biodb.DEBUG[2024-05-04 01:15:23.122][self$getEntryFields()$define] Define field peak.error.ppm. biodb.DEBUG[2024-05-04 01:15:23.124][self$getEntryFields()$define] Define field peak.formula. biodb.DEBUG[2024-05-04 01:15:23.125][self$getEntryFields()$define] Define field peak.intensity. biodb.DEBUG[2024-05-04 01:15:23.127][self$getEntryFields()$define] Define field peak.mass. biodb.DEBUG[2024-05-04 01:15:23.129][self$getEntryFields()$define] Define field peak.mztheo. biodb.DEBUG[2024-05-04 01:15:23.130][self$getEntryFields()$define] Define field peak.mzexp. biodb.DEBUG[2024-05-04 01:15:23.132][self$getEntryFields()$define] Define field peak.mz. biodb.DEBUG[2024-05-04 01:15:23.134][self$getEntryFields()$define] Define field peak.relative.intensity. biodb.DEBUG[2024-05-04 01:15:23.135][self$getEntryFields()$define] Define field peaks. biodb.DEBUG[2024-05-04 01:15:23.137][self$getEntryFields()$define] Define field chrom.col.constructor. biodb.DEBUG[2024-05-04 01:15:23.138][self$getEntryFields()$define] Define field chrom.col.diameter. biodb.DEBUG[2024-05-04 01:15:23.140][self$getEntryFields()$define] Define field chrom.col.id. biodb.DEBUG[2024-05-04 01:15:23.142][self$getEntryFields()$define] Define field chrom.col.length. biodb.DEBUG[2024-05-04 01:15:23.143][self$getEntryFields()$define] Define field chrom.col.method.protocol. biodb.DEBUG[2024-05-04 01:15:23.145][self$getEntryFields()$define] Define field chrom.col.name. biodb.DEBUG[2024-05-04 01:15:23.147][self$getEntryFields()$define] Define field chrom.flow.gradient. biodb.DEBUG[2024-05-04 01:15:23.148][self$getEntryFields()$define] Define field chrom.flow.rate. biodb.DEBUG[2024-05-04 01:15:23.150][self$getEntryFields()$define] Define field chrom.rt. biodb.DEBUG[2024-05-04 01:15:23.152][self$getEntryFields()$define] Define field chrom.rt.max. biodb.DEBUG[2024-05-04 01:15:23.153][self$getEntryFields()$define] Define field chrom.rt.min. biodb.DEBUG[2024-05-04 01:15:23.155][self$getEntryFields()$define] Define field chrom.rt.unit. biodb.DEBUG[2024-05-04 01:15:23.157][self$getEntryFields()$define] Define field chrom.solvent. biodb.DEBUG[2024-05-04 01:15:23.158][self$getEntryFields()$define] Define field aa.seq. biodb.DEBUG[2024-05-04 01:15:23.160][self$getEntryFields()$define] Define field aa.seq.length. biodb.DEBUG[2024-05-04 01:15:23.162][self$getEntryFields()$define] Define field aa.seq.location. biodb.DEBUG[2024-05-04 01:15:23.163][self$getEntryFields()$define] Define field nt.seq. biodb.DEBUG[2024-05-04 01:15:23.165][self$getEntryFields()$define] Define field nt.seq.length. biodb.DEBUG[2024-05-04 01:15:23.166][self$getEntryFields()$define] Define field ec. biodb.DEBUG[2024-05-04 01:15:23.168][self$getEntryFields()$define] Define field organism. biodb.DEBUG[2024-05-04 01:15:23.170][self$getEntryFields()$define] Define field pathway.class. biodb.DEBUG[2024-05-04 01:15:23.171][self$getEntryFields()$define] Define field catalytic.activity. biodb.DEBUG[2024-05-04 01:15:23.173][self$getEntryFields()$define] Define field cofactor. biodb.DEBUG[2024-05-04 01:15:23.175][self$getEntryFields()$define] Define field gene.symbol. biodb.DEBUG[2024-05-04 01:15:23.176][self$getEntryFields()$define] Define field charge. biodb.DEBUG[2024-05-04 01:15:23.178][self$getEntryFields()$define] Define field comp.iupac.name.allowed. biodb.DEBUG[2024-05-04 01:15:23.180][self$getEntryFields()$define] Define field comp.iupac.name.cas. biodb.DEBUG[2024-05-04 01:15:23.181][self$getEntryFields()$define] Define field comp.iupac.name.pref. biodb.DEBUG[2024-05-04 01:15:23.183][self$getEntryFields()$define] Define field comp.iupac.name.syst. biodb.DEBUG[2024-05-04 01:15:23.184][self$getEntryFields()$define] Define field comp.iupac.name.trad. biodb.DEBUG[2024-05-04 01:15:23.186][self$getEntryFields()$define] Define field comp.super.class. biodb.DEBUG[2024-05-04 01:15:23.188][self$getEntryFields()$define] Define field equation. biodb.DEBUG[2024-05-04 01:15:23.189][self$getEntryFields()$define] Define field formula. biodb.DEBUG[2024-05-04 01:15:23.191][self$getEntryFields()$define] Define field composition. biodb.DEBUG[2024-05-04 01:15:23.193][self$getEntryFields()$define] Define field inchi. biodb.DEBUG[2024-05-04 01:15:23.194][self$getEntryFields()$define] Define field inchikey. biodb.DEBUG[2024-05-04 01:15:23.196][self$getEntryFields()$define] Define field logp. biodb.DEBUG[2024-05-04 01:15:23.198][self$getEntryFields()$define] Define field ms.level. biodb.DEBUG[2024-05-04 01:15:23.199][self$getEntryFields()$define] Define field ms.mode. biodb.DEBUG[2024-05-04 01:15:23.201][self$getEntryFields()$define] Define field msdev. biodb.DEBUG[2024-05-04 01:15:23.203][self$getEntryFields()$define] Define field msdevtype. biodb.DEBUG[2024-05-04 01:15:23.204][self$getEntryFields()$define] Define field msprecannot. biodb.DEBUG[2024-05-04 01:15:23.206][self$getEntryFields()$define] Define field msprecmz. biodb.DEBUG[2024-05-04 01:15:23.208][self$getEntryFields()$define] Define field mstype. biodb.DEBUG[2024-05-04 01:15:23.209][self$getEntryFields()$define] Define field nb.compounds. biodb.DEBUG[2024-05-04 01:15:23.212][self$getEntryFields()$define] Define field nb.peaks. biodb.DEBUG[2024-05-04 01:15:23.215][self$getEntryFields()$define] Define field products. biodb.DEBUG[2024-05-04 01:15:23.217][self$getEntryFields()$define] Define field smiles. biodb.DEBUG[2024-05-04 01:15:23.227][self$getEntryFields()$define] Define field smiles.canonical. biodb.DEBUG[2024-05-04 01:15:23.229][self$getEntryFields()$define] Define field smiles.isomeric. biodb.DEBUG[2024-05-04 01:15:23.230][self$getEntryFields()$define] Define field substrates. biodb.DEBUG[2024-05-04 01:15:23.232][initialize] Created successfully new BiodbMain instance. biodb.DEBUG[2024-05-04 01:15:23.235][initialize] This is biodb version 1.12.0. biodb.DEBUG[2024-05-04 01:15:23.236][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-05-04 01:15:23.237][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:23.238][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 01:15:23.240][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:23.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:23.242][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:23.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:15:23.244][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:15:23.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:23.246][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:15:23.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:23.249][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 01:15:23.250][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:23.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:15:23.252][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:15:23.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:23.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:15:23.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:23.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:23.258][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:23.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:15:23.260][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:15:23.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:23.263][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:15:23.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:23.265][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:23.266][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:23.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:15:23.269][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:15:23.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:23.271][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:15:23.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:23.273][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:23.274][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:23.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:15:23.277][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:15:23.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:23.280][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 01:15:23.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:23.283][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 01:15:23.285][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:23.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:15:23.287][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:15:23.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:23.289][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 01:15:23.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:23.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:23.292][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:23.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:15:23.294][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:15:23.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:23.297][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:15:23.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:23.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:23.300][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:23.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:15:23.303][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:15:23.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:23.306][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:15:23.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:23.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:23.310][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:23.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:15:23.312][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:15:23.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:23.314][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:15:23.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:23.317][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:23.318][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:23.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:15:23.320][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:15:23.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:23.322][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:15:23.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:23.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:23.326][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:23.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:15:23.328][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:15:23.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:23.330][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:15:23.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:23.332][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:23.334][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:23.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:15:23.336][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:15:23.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:23.338][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:15:23.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:23.340][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:23.341][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:23.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:15:23.343][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:15:23.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:23.346][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 01:15:23.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:23.348][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:23.349][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:23.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:15:23.351][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:15:23.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:23.354][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:15:23.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:23.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:23.357][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:23.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:15:23.359][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:15:23.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:23.362][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:15:23.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:23.364][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:23.365][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:23.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:15:23.367][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:15:23.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:23.370][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 01:15:23.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:23.372][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:23.373][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:23.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:15:23.375][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:15:23.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:23.378][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:15:23.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:23.380][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:23.383][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc/R/library/biodbChebi/definitions.yml". biodb.DEBUG[2024-05-04 01:15:23.394][self$getDbsInfo()$define] Define connector chebi. biodb.DEBUG[2024-05-04 01:15:23.397][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-05-04 01:15:23.399][self$setPropertyValue] Setting property "description" to "NA". biodb.DEBUG[2024-05-04 01:15:23.400][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 01:15:23.401][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 01:15:23.402][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 01:15:23.404][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 01:15:23.405][self$setPropertyValue] Setting property "editable" to "FALSE". biodb.DEBUG[2024-05-04 01:15:23.406][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8". biodb.DEBUG[2024-05-04 01:15:23.408][self$setPropertyValue] Setting property "entry.content.type" to "xml". biodb.DEBUG[2024-05-04 01:15:23.409][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 01:15:23.410][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-05-04 01:15:23.411][self$setPropertyValue] Setting property "name" to "ChEBI". biodb.DEBUG[2024-05-04 01:15:23.413][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 01:15:23.414][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')". biodb.DEBUG[2024-05-04 01:15:23.414][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge". biodb.DEBUG[2024-05-04 01:15:23.414][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")". biodb.DEBUG[2024-05-04 01:15:23.414][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi". biodb.DEBUG[2024-05-04 01:15:23.414][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey". biodb.DEBUG[2024-05-04 01:15:23.414][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data". biodb.DEBUG[2024-05-04 01:15:23.414][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass". biodb.DEBUG[2024-05-04 01:15:23.414][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass". biodb.DEBUG[2024-05-04 01:15:23.414][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")". biodb.DEBUG[2024-05-04 01:15:23.414][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar". biodb.DEBUG[2024-05-04 01:15:23.414][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles". biodb.DEBUG[2024-05-04 01:15:23.416][self$setPropertyValue] Setting property "remote" to "TRUE". biodb.DEBUG[2024-05-04 01:15:23.417][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-05-04 01:15:23.417][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-05-04 01:15:23.417][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2024-05-04 01:15:23.418][self$setPropertyValue] Setting property "scheduler.n" to "3". biodb.DEBUG[2024-05-04 01:15:23.419][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 01:15:23.421][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 01:15:23.422][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 01:15:23.423][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 01:15:23.424][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 01:15:23.425][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 01:15:23.427][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-05-04 01:15:23.427][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/". biodb.DEBUG[2024-05-04 01:15:23.428][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 01:15:23.429][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 01:15:23.430][self$setPropertyValue] Setting property "writable" to "FALSE". biodb.DEBUG[2024-05-04 01:15:23.432][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi". biodb.DEBUG[2024-05-04 01:15:23.432][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema". biodb.DEBUG[2024-05-04 01:15:23.433][self$getEntryFields()$define] Define field chebi.id. biodb.DEBUG[2024-05-04 01:15:23.435][self$getEntryFields()$define] Define field kegg.compound.id. biodb.DEBUG[2024-05-04 01:15:23.437][self$getEntryFields()$define] Define field n_stars. biodb.DEBUG[2024-05-04 01:15:23.439][self$getEntryFields()$define] Define field molecular.mass. biodb.DEBUG[2024-05-04 01:15:23.441][self$getEntryFields()$define] Define field inchi. biodb.DEBUG[2024-05-04 01:15:23.443][self$getEntryFields()$define] Define field inchikey. biodb.DEBUG[2024-05-04 01:15:23.449][super$initialize] Initialize connector chebi. biodb.DEBUG[2024-05-04 01:15:23.451][super$initialize] Register connector chebi with the request scheduler biodb.DEBUG[2024-05-04 01:15:23.452][private$bdb$getRequestScheduler()$re ...] Register connector chebi. biodb.DEBUG[2024-05-04 01:15:23.454][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi". biodb.DEBUG[2024-05-04 01:15:23.456][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2024-05-04 01:15:23.457][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2024-05-04 01:15:23.459][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk". biodb.DEBUG[2024-05-04 01:15:23.460][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi . biodb.INFO [2024-05-04 01:15:23.463][biodb::testThat] biodb.INFO [2024-05-04 01:15:23.464][biodb::testThat] Running test function test_chebi_convCasToChebi (" convCasToChebi() works. "). biodb.INFO [2024-05-04 01:15:23.465][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 01:15:23.467][biodb::testThat] biodb.DEBUG[2024-05-04 01:15:23.472][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl". biodb.DEBUG[2024-05-04 01:15:23.478][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-04 01:15:23.479][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-04 01:15:23.481][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl". biodb.TRACE[2024-05-04 01:15:23.832][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl). biodb.DEBUG[2024-05-04 01:15:24.262][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-05-04 01:15:24.266][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content" biodb.TRACE[2024-05-04 01:15:24.275][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request" biodb.DEBUG[2024-05-04 01:15:24.284][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 01:15:24.290][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-04 01:15:24.293][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-04 01:15:24.295][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL". biodb.TRACE[2024-05-04 01:15:24.648][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL). biodb.DEBUG[2024-05-04 01:15:24.998][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-05-04 01:15:25.002][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content" biodb.TRACE[2024-05-04 01:15:25.008][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request" biodb.DEBUG[2024-05-04 01:15:25.012][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:15:25.013][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:15:25.014][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:15:25.025][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:25.027][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:15:25.029][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:25.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:25.035][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL". biodb.DEBUG[2024-05-04 01:15:25.042][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-04 01:15:25.044][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-04 01:15:25.048][private$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 01:15:25.410][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 01:15:25.758][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-05-04 01:15:25.762][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content" biodb.TRACE[2024-05-04 01:15:25.770][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request" biodb.DEBUG[2024-05-04 01:15:25.775][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:15:25.777][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:15:25.779][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:15:25.790][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:25.792][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:15:25.794][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:25.796][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 01:15:25.822][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:15:25.824][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:15:25.826][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:15:25.837][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:25.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:15:25.841][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:25.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:25.852][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 01:15:25.857][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-05-04 01:15:25.860][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3". biodb.TRACE[2024-05-04 01:15:25.863][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-05-04 01:15:25.866][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content". biodb.DEBUG[2024-05-04 01:15:25.869][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:15:25.871][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:15:25.873][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:15:25.898][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:25.900][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:15:25.902][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:25.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:25.907][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL". biodb.DEBUG[2024-05-04 01:15:25.913][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-05-04 01:15:25.935][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744". biodb.TRACE[2024-05-04 01:15:25.938][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-05-04 01:15:25.942][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content". biodb.DEBUG[2024-05-04 01:15:25.945][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:15:25.947][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:15:25.948][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:15:25.958][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:25.960][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:15:25.961][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:25.963][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:25.964][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:15:25.965][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:15:25.967][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:15:25.975][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:25.976][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:15:25.977][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:25.979][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:25.983][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 01:15:25.987][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-05-04 01:15:25.989][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3". biodb.TRACE[2024-05-04 01:15:25.991][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-05-04 01:15:25.993][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content". biodb.DEBUG[2024-05-04 01:15:25.995][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:15:25.996][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:15:25.997][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:15:26.006][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:26.008][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 01:15:26.010][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:26.011][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:26.014][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 01:15:26.020][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-05-04 01:15:26.023][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744". biodb.TRACE[2024-05-04 01:15:26.026][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-05-04 01:15:26.029][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content". biodb.DEBUG[2024-05-04 01:15:26.033][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:15:26.035][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:15:26.037][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:15:26.046][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:26.047][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 01:15:26.049][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:26.050][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 01:15:26.052][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 01:15:26.056][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-04 01:15:26.058][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-04 01:15:26.060][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL". biodb.TRACE[2024-05-04 01:15:26.411][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL). biodb.DEBUG[2024-05-04 01:15:27.371][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-05-04 01:15:27.376][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content" biodb.TRACE[2024-05-04 01:15:27.386][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request" biodb.DEBUG[2024-05-04 01:15:27.392][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:15:27.395][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:15:27.397][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:15:27.410][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:27.411][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:15:27.413][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:27.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.INFO [2024-05-04 01:15:27.433][biodb::testThat] biodb.INFO [2024-05-04 01:15:27.438][biodb::testThat] Running test function test_chebi_convInchiToChebi (" convInchiToChebi() works. "). biodb.INFO [2024-05-04 01:15:27.441][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 01:15:27.443][biodb::testThat] biodb.DEBUG[2024-05-04 01:15:27.449][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11?,12?,13?,14?,15-/m0/s1&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL". biodb.DEBUG[2024-05-04 01:15:27.456][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-04 01:15:27.459][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-04 01:15:27.463][private$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 01:15:30.270][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 01:15:36.804][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-05-04 01:15:36.809][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content" biodb.TRACE[2024-05-04 01:15:36.817][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request" biodb.DEBUG[2024-05-04 01:15:36.822][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:15:36.824][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:15:36.827][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:15:36.836][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:36.838][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:15:36.839][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:36.840][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 01:15:36.845][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 01:15:36.849][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-04 01:15:36.851][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-04 01:15:36.855][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL". biodb.TRACE[2024-05-04 01:15:55.356][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL). biodb.DEBUG[2024-05-04 01:15:55.939][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-05-04 01:15:55.944][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content" biodb.TRACE[2024-05-04 01:15:55.977][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request" biodb.DEBUG[2024-05-04 01:15:55.982][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:15:55.984][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:15:55.986][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:15:55.998][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:56.000][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:15:56.002][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:56.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.INFO [2024-05-04 01:15:56.018][biodb$terminate] Closing BiodbMain instance... biodb.DEBUG[2024-05-04 01:15:56.021][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler biodb.INFO [2024-05-04 01:15:56.023][self$deleteConn] Connector "chebi" deleted. biodb.DEBUG[2024-05-04 01:15:56.025][notifyObservers] Notify observers for terminate. biodb.DEBUG[2024-05-04 01:15:56.027][FUN] Trying to call function terminate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:15:56.029][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:15:56.031][FUN] Trying to call function terminate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:56.033][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:15:56.035][FUN] Trying to call function terminate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:56.037][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.INFO [2024-05-04 01:15:56.057][biodb::testContext] biodb.INFO [2024-05-04 01:15:56.059][biodb::testContext] ******************************************************************************** biodb.INFO [2024-05-04 01:15:56.061][biodb::testContext] Test context - Test web services biodb.INFO [2024-05-04 01:15:56.062][biodb::testContext] ******************************************************************************** biodb.INFO [2024-05-04 01:15:56.064][biodb::testContext] biodb.INFO [2024-05-04 01:15:56.067][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0. biodb.DEBUG[2024-05-04 01:15:56.070][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc/R/library/biodb/definitions.yml". biodb.DEBUG[2024-05-04 01:15:56.077][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-05-04 01:15:56.079][self$getConfig()$define] Define config key allow.huge.downloads. biodb.DEBUG[2024-05-04 01:15:56.080][self$set] Set key allow.huge.downloads to TRUE. biodb.DEBUG[2024-05-04 01:15:56.082][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:56.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:56.085][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 01:15:56.087][self$getConfig()$define] Define config key autoload.extra.pkgs. biodb.DEBUG[2024-05-04 01:15:56.089][self$set] Set key autoload.extra.pkgs to TRUE. biodb.DEBUG[2024-05-04 01:15:56.090][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:56.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:56.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:56.094][self$getConfig()$define] Define config key cache.all.requests. biodb.DEBUG[2024-05-04 01:15:56.096][self$set] Set key cache.all.requests to TRUE. biodb.DEBUG[2024-05-04 01:15:56.098][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:56.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:56.101][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:56.104][self$getConfig()$define] Define config key cache.directory. biodb.DEBUG[2024-05-04 01:15:56.106][self$getConfig()$define] Define config key cache.read.only. biodb.DEBUG[2024-05-04 01:15:56.108][self$set] Set key cache.read.only to FALSE. biodb.DEBUG[2024-05-04 01:15:56.110][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:56.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:56.114][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:56.116][self$getConfig()$define] Define config key cache.subfolders. biodb.DEBUG[2024-05-04 01:15:56.118][self$getConfig()$define] Define config key cache.system. biodb.DEBUG[2024-05-04 01:15:56.120][self$set] Set key cache.system to TRUE. biodb.DEBUG[2024-05-04 01:15:56.122][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:56.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:56.126][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:56.127][self$getConfig()$define] Define config key use.cache.for.local.db. biodb.DEBUG[2024-05-04 01:15:56.129][self$set] Set key use.cache.for.local.db to FALSE. biodb.DEBUG[2024-05-04 01:15:56.130][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:56.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:56.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:56.136][self$getConfig()$define] Define config key dwnld.chunk.size. biodb.DEBUG[2024-05-04 01:15:56.138][self$getConfig()$define] Define config key dwnld.timeout. biodb.DEBUG[2024-05-04 01:15:56.140][self$set] Set key dwnld.timeout to 3600. biodb.DEBUG[2024-05-04 01:15:56.142][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:56.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:56.145][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 01:15:56.146][self$getConfig()$define] Define config key compute.fields. biodb.DEBUG[2024-05-04 01:15:56.147][self$set] Set key compute.fields to TRUE. biodb.DEBUG[2024-05-04 01:15:56.149][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:56.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:56.152][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:56.153][self$getConfig()$define] Define config key factory.cache. biodb.DEBUG[2024-05-04 01:15:56.155][self$getConfig()$define] Define config key force.locale. biodb.DEBUG[2024-05-04 01:15:56.156][self$set] Set key force.locale to TRUE. biodb.DEBUG[2024-05-04 01:15:56.157][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:56.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:56.160][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 01:15:56.161][self$getConfig()$define] Define config key longterm.cache.subfolder. biodb.DEBUG[2024-05-04 01:15:56.163][self$getConfig()$define] Define config key msg.caution.lvl. biodb.DEBUG[2024-05-04 01:15:56.164][self$getConfig()$define] Define config key msg.debug.lvl. biodb.DEBUG[2024-05-04 01:15:56.166][self$getConfig()$define] Define config key msg.info.lvl. biodb.DEBUG[2024-05-04 01:15:56.167][self$getConfig()$define] Define config key multival.field.sep. biodb.DEBUG[2024-05-04 01:15:56.168][self$set] Set key multival.field.sep to ";". biodb.DEBUG[2024-05-04 01:15:56.170][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:56.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:56.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:56.173][self$getConfig()$define] Define config key intra.field.name.sep. biodb.DEBUG[2024-05-04 01:15:56.175][self$set] Set key intra.field.name.sep to ".". biodb.DEBUG[2024-05-04 01:15:56.176][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:56.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:56.178][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 01:15:56.180][self$getConfig()$define] Define config key entries.sep. biodb.DEBUG[2024-05-04 01:15:56.181][self$set] Set key entries.sep to "|". biodb.DEBUG[2024-05-04 01:15:56.183][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:56.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:56.185][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:56.186][self$getConfig()$define] Define config key offline. biodb.DEBUG[2024-05-04 01:15:56.188][self$set] Set key offline to FALSE. biodb.DEBUG[2024-05-04 01:15:56.189][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:56.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:56.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:56.193][self$getConfig()$define] Define config key persistent.cache.impl. biodb.DEBUG[2024-05-04 01:15:56.194][self$set] Set key persistent.cache.impl to "custom". biodb.DEBUG[2024-05-04 01:15:56.195][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:56.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:56.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:56.201][self$getConfig()$define] Define config key proton.mass. biodb.DEBUG[2024-05-04 01:15:56.203][self$set] Set key proton.mass to 1.0072765. biodb.DEBUG[2024-05-04 01:15:56.204][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:56.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:56.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:56.208][self$getConfig()$define] Define config key shortterm.cache.subfolder. biodb.DEBUG[2024-05-04 01:15:56.209][self$getConfig()$define] Define config key svn.binary.path. biodb.DEBUG[2024-05-04 01:15:56.214][self$set] Set key svn.binary.path to "". biodb.DEBUG[2024-05-04 01:15:56.222][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:56.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:56.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:56.231][self$getConfig()$define] Define config key test.functions. biodb.DEBUG[2024-05-04 01:15:56.232][self$getConfig()$define] Define config key useragent. biodb.DEBUG[2024-05-04 01:15:56.234][self$set] Set key useragent to "R Bioconductor biodb library.". biodb.DEBUG[2024-05-04 01:15:56.235][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:56.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:56.237][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.DEBUG[2024-05-04 01:15:56.239][self$getDbsInfo()$define] Define connector comp.csv.file. biodb.DEBUG[2024-05-04 01:15:56.242][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-05-04 01:15:56.259][self$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 01:15:56.261][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 01:15:56.263][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 01:15:56.264][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 01:15:56.265][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 01:15:56.267][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-04 01:15:56.268][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 01:15:56.269][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2024-05-04 01:15:56.271][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 01:15:56.272][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-05-04 01:15:56.273][self$setPropertyValue] Setting property "name" to "Compound CSV File". biodb.DEBUG[2024-05-04 01:15:56.274][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 01:15:56.276][self$setPropertyValue] biodb.DEBUG[2024-05-04 01:15:56.277][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-04 01:15:56.279][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-05-04 01:15:56.279][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-05-04 01:15:56.279][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2024-05-04 01:15:56.279][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2024-05-04 01:15:56.279][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2024-05-04 01:15:56.281][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 01:15:56.282][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 01:15:56.283][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 01:15:56.284][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 01:15:56.285][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 01:15:56.287][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 01:15:56.288][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 01:15:56.289][self$setPropertyValue] biodb.DEBUG[2024-05-04 01:15:56.290][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 01:15:56.291][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 01:15:56.293][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-04 01:15:56.294][self$setPropertyValue] biodb.DEBUG[2024-05-04 01:15:56.295][self$getDbsInfo()$define] Define connector comp.sqlite. biodb.DEBUG[2024-05-04 01:15:56.299][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-05-04 01:15:56.300][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.". biodb.DEBUG[2024-05-04 01:15:56.301][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 01:15:56.303][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 01:15:56.304][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 01:15:56.306][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 01:15:56.308][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-04 01:15:56.309][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 01:15:56.311][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2024-05-04 01:15:56.313][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 01:15:56.315][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-05-04 01:15:56.317][self$setPropertyValue] Setting property "name" to "Compound SQLite". biodb.DEBUG[2024-05-04 01:15:56.319][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 01:15:56.321][self$setPropertyValue] biodb.DEBUG[2024-05-04 01:15:56.323][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-04 01:15:56.324][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-05-04 01:15:56.324][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-05-04 01:15:56.324][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2024-05-04 01:15:56.324][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2024-05-04 01:15:56.324][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2024-05-04 01:15:56.326][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 01:15:56.327][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 01:15:56.328][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 01:15:56.330][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 01:15:56.331][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 01:15:56.332][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 01:15:56.333][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 01:15:56.334][self$setPropertyValue] biodb.DEBUG[2024-05-04 01:15:56.336][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 01:15:56.337][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 01:15:56.338][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-04 01:15:56.340][self$setPropertyValue] biodb.DEBUG[2024-05-04 01:15:56.341][self$getDbsInfo()$define] Define connector mass.csv.file. biodb.DEBUG[2024-05-04 01:15:56.343][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2024-05-04 01:15:56.345][self$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 01:15:56.346][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 01:15:56.347][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 01:15:56.348][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 01:15:56.349][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 01:15:56.351][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-04 01:15:56.352][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 01:15:56.353][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2024-05-04 01:15:56.355][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 01:15:56.356][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2024-05-04 01:15:56.357][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File". biodb.DEBUG[2024-05-04 01:15:56.358][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 01:15:56.360][self$setPropertyValue] biodb.DEBUG[2024-05-04 01:15:56.361][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-04 01:15:56.363][self$setPropertyValue] biodb.DEBUG[2024-05-04 01:15:56.364][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 01:15:56.366][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 01:15:56.368][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 01:15:56.370][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 01:15:56.371][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 01:15:56.372][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 01:15:56.374][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 01:15:56.376][self$setPropertyValue] biodb.DEBUG[2024-05-04 01:15:56.378][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 01:15:56.380][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 01:15:56.381][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-04 01:15:56.383][self$setPropertyValue] biodb.DEBUG[2024-05-04 01:15:56.385][self$getDbsInfo()$define] Define connector mass.sqlite. biodb.DEBUG[2024-05-04 01:15:56.387][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2024-05-04 01:15:56.388][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.". biodb.DEBUG[2024-05-04 01:15:56.389][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 01:15:56.391][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 01:15:56.392][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 01:15:56.394][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 01:15:56.396][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-04 01:15:56.399][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 01:15:56.401][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2024-05-04 01:15:56.402][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 01:15:56.404][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2024-05-04 01:15:56.406][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite". biodb.DEBUG[2024-05-04 01:15:56.408][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 01:15:56.409][self$setPropertyValue] biodb.DEBUG[2024-05-04 01:15:56.411][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-04 01:15:56.413][self$setPropertyValue] biodb.DEBUG[2024-05-04 01:15:56.414][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 01:15:56.416][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 01:15:56.418][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 01:15:56.420][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 01:15:56.422][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 01:15:56.423][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 01:15:56.425][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 01:15:56.426][self$setPropertyValue] biodb.DEBUG[2024-05-04 01:15:56.427][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 01:15:56.429][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 01:15:56.430][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-04 01:15:56.431][self$setPropertyValue] biodb.DEBUG[2024-05-04 01:15:56.434][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-05-04 01:15:56.436][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:56.438][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 01:15:56.439][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:56.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:56.441][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:15:56.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:56.445][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 01:15:56.447][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:56.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:56.449][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 01:15:56.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:56.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:56.454][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:56.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:56.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:15:56.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:56.461][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 01:15:56.462][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:56.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:56.466][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:15:56.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:56.469][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:56.471][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:56.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:56.473][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 01:15:56.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:56.475][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 01:15:56.476][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:56.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:56.479][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:15:56.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:56.482][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:56.483][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:56.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:56.486][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 01:15:56.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:56.489][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:56.491][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:56.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:56.494][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:15:56.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:56.497][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 01:15:56.498][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:56.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:56.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:15:56.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:56.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:56.505][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:56.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:56.507][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 01:15:56.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:56.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:56.513][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:56.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:56.516][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:15:56.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:56.519][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 01:15:56.521][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:56.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:56.524][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 01:15:56.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:56.528][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:56.529][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:56.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:56.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:15:56.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:56.536][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:56.537][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:56.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:56.539][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:15:56.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:56.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:56.543][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:56.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:56.546][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:15:56.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:56.548][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:56.549][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:56.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:56.552][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:15:56.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:56.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:56.555][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:56.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:56.558][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 01:15:56.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:56.561][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:56.563][self$getEntryFields()$define] Define field accession. biodb.DEBUG[2024-05-04 01:15:56.565][self$getEntryFields()$define] Define field description. biodb.DEBUG[2024-05-04 01:15:56.567][self$getEntryFields()$define] Define field name. biodb.DEBUG[2024-05-04 01:15:56.568][self$getEntryFields()$define] Define field cas.id. biodb.DEBUG[2024-05-04 01:15:56.570][self$getEntryFields()$define] Define field chebi.id. biodb.DEBUG[2024-05-04 01:15:56.572][self$getEntryFields()$define] Define field chemspider.id. biodb.DEBUG[2024-05-04 01:15:56.574][self$getEntryFields()$define] Define field comp.csv.file.id. biodb.DEBUG[2024-05-04 01:15:56.575][self$getEntryFields()$define] Define field comp.sqlite.id. biodb.DEBUG[2024-05-04 01:15:56.577][self$getEntryFields()$define] Define field expasy.enzyme.id. biodb.DEBUG[2024-05-04 01:15:56.579][self$getEntryFields()$define] Define field hmdb.metabolites.id. biodb.DEBUG[2024-05-04 01:15:56.580][self$getEntryFields()$define] Define field kegg.compound.id. biodb.DEBUG[2024-05-04 01:15:56.582][self$getEntryFields()$define] Define field kegg.genes.id. biodb.DEBUG[2024-05-04 01:15:56.584][self$getEntryFields()$define] Define field mass.csv.file.id. biodb.DEBUG[2024-05-04 01:15:56.586][self$getEntryFields()$define] Define field mass.sqlite.id. biodb.DEBUG[2024-05-04 01:15:56.587][self$getEntryFields()$define] Define field ncbi.gene.id. biodb.DEBUG[2024-05-04 01:15:56.589][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id. biodb.DEBUG[2024-05-04 01:15:56.591][self$getEntryFields()$define] Define field compound.id. biodb.DEBUG[2024-05-04 01:15:56.593][self$getEntryFields()$define] Define field average.mass. biodb.DEBUG[2024-05-04 01:15:56.595][self$getEntryFields()$define] Define field molecular.mass. biodb.DEBUG[2024-05-04 01:15:56.596][self$getEntryFields()$define] Define field monoisotopic.mass. biodb.DEBUG[2024-05-04 01:15:56.598][self$getEntryFields()$define] Define field nominal.mass. biodb.DEBUG[2024-05-04 01:15:56.600][self$getEntryFields()$define] Define field peak.attr. biodb.DEBUG[2024-05-04 01:15:56.602][self$getEntryFields()$define] Define field peak.comp. biodb.DEBUG[2024-05-04 01:15:56.604][self$getEntryFields()$define] Define field peak.error.ppm. biodb.DEBUG[2024-05-04 01:15:56.606][self$getEntryFields()$define] Define field peak.formula. biodb.DEBUG[2024-05-04 01:15:56.608][self$getEntryFields()$define] Define field peak.intensity. biodb.DEBUG[2024-05-04 01:15:56.609][self$getEntryFields()$define] Define field peak.mass. biodb.DEBUG[2024-05-04 01:15:56.611][self$getEntryFields()$define] Define field peak.mztheo. biodb.DEBUG[2024-05-04 01:15:56.613][self$getEntryFields()$define] Define field peak.mzexp. biodb.DEBUG[2024-05-04 01:15:56.615][self$getEntryFields()$define] Define field peak.mz. biodb.DEBUG[2024-05-04 01:15:56.616][self$getEntryFields()$define] Define field peak.relative.intensity. biodb.DEBUG[2024-05-04 01:15:56.618][self$getEntryFields()$define] Define field peaks. biodb.DEBUG[2024-05-04 01:15:56.620][self$getEntryFields()$define] Define field chrom.col.constructor. biodb.DEBUG[2024-05-04 01:15:56.622][self$getEntryFields()$define] Define field chrom.col.diameter. biodb.DEBUG[2024-05-04 01:15:56.624][self$getEntryFields()$define] Define field chrom.col.id. biodb.DEBUG[2024-05-04 01:15:56.626][self$getEntryFields()$define] Define field chrom.col.length. biodb.DEBUG[2024-05-04 01:15:56.628][self$getEntryFields()$define] Define field chrom.col.method.protocol. biodb.DEBUG[2024-05-04 01:15:56.631][self$getEntryFields()$define] Define field chrom.col.name. biodb.DEBUG[2024-05-04 01:15:56.633][self$getEntryFields()$define] Define field chrom.flow.gradient. biodb.DEBUG[2024-05-04 01:15:56.635][self$getEntryFields()$define] Define field chrom.flow.rate. biodb.DEBUG[2024-05-04 01:15:56.637][self$getEntryFields()$define] Define field chrom.rt. biodb.DEBUG[2024-05-04 01:15:56.639][self$getEntryFields()$define] Define field chrom.rt.max. biodb.DEBUG[2024-05-04 01:15:56.641][self$getEntryFields()$define] Define field chrom.rt.min. biodb.DEBUG[2024-05-04 01:15:56.644][self$getEntryFields()$define] Define field chrom.rt.unit. biodb.DEBUG[2024-05-04 01:15:56.654][self$getEntryFields()$define] Define field chrom.solvent. biodb.DEBUG[2024-05-04 01:15:56.657][self$getEntryFields()$define] Define field aa.seq. biodb.DEBUG[2024-05-04 01:15:56.660][self$getEntryFields()$define] Define field aa.seq.length. biodb.DEBUG[2024-05-04 01:15:56.663][self$getEntryFields()$define] Define field aa.seq.location. biodb.DEBUG[2024-05-04 01:15:56.666][self$getEntryFields()$define] Define field nt.seq. biodb.DEBUG[2024-05-04 01:15:56.668][self$getEntryFields()$define] Define field nt.seq.length. biodb.DEBUG[2024-05-04 01:15:56.671][self$getEntryFields()$define] Define field ec. biodb.DEBUG[2024-05-04 01:15:56.674][self$getEntryFields()$define] Define field organism. biodb.DEBUG[2024-05-04 01:15:56.676][self$getEntryFields()$define] Define field pathway.class. biodb.DEBUG[2024-05-04 01:15:56.679][self$getEntryFields()$define] Define field catalytic.activity. biodb.DEBUG[2024-05-04 01:15:56.681][self$getEntryFields()$define] Define field cofactor. biodb.DEBUG[2024-05-04 01:15:56.684][self$getEntryFields()$define] Define field gene.symbol. biodb.DEBUG[2024-05-04 01:15:56.686][self$getEntryFields()$define] Define field charge. biodb.DEBUG[2024-05-04 01:15:56.689][self$getEntryFields()$define] Define field comp.iupac.name.allowed. biodb.DEBUG[2024-05-04 01:15:56.691][self$getEntryFields()$define] Define field comp.iupac.name.cas. biodb.DEBUG[2024-05-04 01:15:56.694][self$getEntryFields()$define] Define field comp.iupac.name.pref. biodb.DEBUG[2024-05-04 01:15:56.696][self$getEntryFields()$define] Define field comp.iupac.name.syst. biodb.DEBUG[2024-05-04 01:15:56.699][self$getEntryFields()$define] Define field comp.iupac.name.trad. biodb.DEBUG[2024-05-04 01:15:56.701][self$getEntryFields()$define] Define field comp.super.class. biodb.DEBUG[2024-05-04 01:15:56.704][self$getEntryFields()$define] Define field equation. biodb.DEBUG[2024-05-04 01:15:56.706][self$getEntryFields()$define] Define field formula. biodb.DEBUG[2024-05-04 01:15:56.709][self$getEntryFields()$define] Define field composition. biodb.DEBUG[2024-05-04 01:15:56.711][self$getEntryFields()$define] Define field inchi. biodb.DEBUG[2024-05-04 01:15:56.714][self$getEntryFields()$define] Define field inchikey. biodb.DEBUG[2024-05-04 01:15:56.716][self$getEntryFields()$define] Define field logp. biodb.DEBUG[2024-05-04 01:15:56.719][self$getEntryFields()$define] Define field ms.level. biodb.DEBUG[2024-05-04 01:15:56.721][self$getEntryFields()$define] Define field ms.mode. biodb.DEBUG[2024-05-04 01:15:56.724][self$getEntryFields()$define] Define field msdev. biodb.DEBUG[2024-05-04 01:15:56.726][self$getEntryFields()$define] Define field msdevtype. biodb.DEBUG[2024-05-04 01:15:56.729][self$getEntryFields()$define] Define field msprecannot. biodb.DEBUG[2024-05-04 01:15:56.731][self$getEntryFields()$define] Define field msprecmz. biodb.DEBUG[2024-05-04 01:15:56.734][self$getEntryFields()$define] Define field mstype. biodb.DEBUG[2024-05-04 01:15:56.736][self$getEntryFields()$define] Define field nb.compounds. biodb.DEBUG[2024-05-04 01:15:56.739][self$getEntryFields()$define] Define field nb.peaks. biodb.DEBUG[2024-05-04 01:15:56.741][self$getEntryFields()$define] Define field products. biodb.DEBUG[2024-05-04 01:15:56.744][self$getEntryFields()$define] Define field smiles. biodb.DEBUG[2024-05-04 01:15:56.747][self$getEntryFields()$define] Define field smiles.canonical. biodb.DEBUG[2024-05-04 01:15:56.749][self$getEntryFields()$define] Define field smiles.isomeric. biodb.DEBUG[2024-05-04 01:15:56.752][self$getEntryFields()$define] Define field substrates. biodb.DEBUG[2024-05-04 01:15:56.754][initialize] Created successfully new BiodbMain instance. biodb.DEBUG[2024-05-04 01:15:56.758][initialize] This is biodb version 1.12.0. biodb.DEBUG[2024-05-04 01:15:56.760][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-05-04 01:15:56.762][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:56.763][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 01:15:56.765][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:56.767][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.DEBUG[2024-05-04 01:15:56.769][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:56.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:15:56.772][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:15:56.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:56.776][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 01:15:56.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:56.779][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 01:15:56.781][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:56.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:15:56.784][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:15:56.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:56.788][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:15:56.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:56.791][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:56.793][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:56.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:15:56.797][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:15:56.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:56.800][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 01:15:56.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:56.804][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 01:15:56.805][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:56.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:15:56.809][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:15:56.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:56.812][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:15:56.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:56.816][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 01:15:56.818][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:56.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:15:56.821][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:15:56.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:56.825][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:15:56.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:56.828][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 01:15:56.832][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:56.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:15:56.836][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:15:56.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:56.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:15:56.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:56.845][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:56.846][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:56.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:15:56.848][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:15:56.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:56.851][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:15:56.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:56.853][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 01:15:56.854][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:56.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:15:56.857][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:15:56.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:56.861][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:15:56.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:56.865][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:56.867][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:56.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:15:56.871][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:15:56.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:56.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:15:56.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:56.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:56.879][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:56.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:15:56.883][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:15:56.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:56.886][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:15:56.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:56.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:56.892][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:56.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:15:56.895][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:15:56.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:56.898][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:15:56.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:56.902][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 01:15:56.904][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:56.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:15:56.909][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:15:56.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:56.912][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:15:56.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:56.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:56.916][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:56.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:15:56.919][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:15:56.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:56.923][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 01:15:56.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:56.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:56.927][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:56.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:15:56.930][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:15:56.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:56.934][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:15:56.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:56.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:56.941][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:56.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:15:56.944][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:15:56.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:56.948][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 01:15:56.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:56.951][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 01:15:56.953][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:56.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:15:56.957][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:15:56.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:56.960][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:15:56.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:56.964][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:56.965][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:15:56.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:15:56.969][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:15:56.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:15:56.972][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:15:56.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:15:56.976][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:15:56.980][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc/R/library/biodbChebi/definitions.yml". biodb.DEBUG[2024-05-04 01:15:56.983][self$getDbsInfo()$define] Define connector chebi. biodb.DEBUG[2024-05-04 01:15:56.986][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-05-04 01:15:56.988][self$setPropertyValue] Setting property "description" to "NA". biodb.DEBUG[2024-05-04 01:15:56.990][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 01:15:56.992][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 01:15:56.994][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 01:15:56.996][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 01:15:56.998][self$setPropertyValue] Setting property "editable" to "FALSE". biodb.DEBUG[2024-05-04 01:15:56.999][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8". biodb.DEBUG[2024-05-04 01:15:57.002][self$setPropertyValue] Setting property "entry.content.type" to "xml". biodb.DEBUG[2024-05-04 01:15:57.003][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 01:15:57.005][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-05-04 01:15:57.007][self$setPropertyValue] Setting property "name" to "ChEBI". biodb.DEBUG[2024-05-04 01:15:57.009][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 01:15:57.011][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')". biodb.DEBUG[2024-05-04 01:15:57.011][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge". biodb.DEBUG[2024-05-04 01:15:57.011][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")". biodb.DEBUG[2024-05-04 01:15:57.011][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi". biodb.DEBUG[2024-05-04 01:15:57.011][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey". biodb.DEBUG[2024-05-04 01:15:57.011][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data". biodb.DEBUG[2024-05-04 01:15:57.011][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass". biodb.DEBUG[2024-05-04 01:15:57.011][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass". biodb.DEBUG[2024-05-04 01:15:57.011][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")". biodb.DEBUG[2024-05-04 01:15:57.011][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar". biodb.DEBUG[2024-05-04 01:15:57.011][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles". biodb.DEBUG[2024-05-04 01:15:57.013][self$setPropertyValue] Setting property "remote" to "TRUE". biodb.DEBUG[2024-05-04 01:15:57.015][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-05-04 01:15:57.015][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-05-04 01:15:57.015][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2024-05-04 01:15:57.018][self$setPropertyValue] Setting property "scheduler.n" to "3". biodb.DEBUG[2024-05-04 01:15:57.019][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 01:15:57.021][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 01:15:57.023][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 01:15:57.025][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 01:15:57.027][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 01:15:57.028][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 01:15:57.030][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-05-04 01:15:57.030][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/". biodb.DEBUG[2024-05-04 01:15:57.033][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 01:15:57.034][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 01:15:57.036][self$setPropertyValue] Setting property "writable" to "FALSE". biodb.DEBUG[2024-05-04 01:15:57.038][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi". biodb.DEBUG[2024-05-04 01:15:57.038][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema". biodb.DEBUG[2024-05-04 01:15:57.041][self$getEntryFields()$define] Define field chebi.id. biodb.DEBUG[2024-05-04 01:15:57.044][self$getEntryFields()$define] Define field kegg.compound.id. biodb.DEBUG[2024-05-04 01:15:57.047][self$getEntryFields()$define] Define field n_stars. biodb.DEBUG[2024-05-04 01:15:57.051][self$getEntryFields()$define] Define field molecular.mass. biodb.DEBUG[2024-05-04 01:15:57.054][self$getEntryFields()$define] Define field inchi. biodb.DEBUG[2024-05-04 01:15:57.056][self$getEntryFields()$define] Define field inchikey. biodb.DEBUG[2024-05-04 01:15:57.061][super$initialize] Initialize connector chebi. biodb.DEBUG[2024-05-04 01:15:57.062][super$initialize] Register connector chebi with the request scheduler biodb.DEBUG[2024-05-04 01:15:57.065][private$bdb$getRequestScheduler()$re ...] Register connector chebi. biodb.DEBUG[2024-05-04 01:15:57.068][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi". biodb.DEBUG[2024-05-04 01:15:57.071][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2024-05-04 01:15:57.073][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2024-05-04 01:15:57.075][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk". biodb.DEBUG[2024-05-04 01:15:57.076][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi . biodb.INFO [2024-05-04 01:15:57.079][biodb::testThat] biodb.INFO [2024-05-04 01:15:57.082][biodb::testThat] Running test function test.chebi.wsGetLiteEntity (" Web service getLiteEntity works fine. "). biodb.INFO [2024-05-04 01:15:57.084][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 01:15:57.085][biodb::testThat] biodb.DEBUG[2024-05-04 01:15:57.091][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl". biodb.DEBUG[2024-05-04 01:15:57.099][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-05-04 01:15:57.102][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05". biodb.TRACE[2024-05-04 01:15:57.104][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-05-04 01:15:57.108][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content". biodb.DEBUG[2024-05-04 01:15:57.113][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL". biodb.DEBUG[2024-05-04 01:15:57.119][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-04 01:15:57.121][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-04 01:15:57.124][private$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 01:16:03.252][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 01:16:06.361][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-05-04 01:16:06.365][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content" biodb.TRACE[2024-05-04 01:16:06.373][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request" biodb.INFO [2024-05-04 01:16:06.391][biodb$terminate] Closing BiodbMain instance... biodb.DEBUG[2024-05-04 01:16:06.394][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler biodb.INFO [2024-05-04 01:16:06.396][self$deleteConn] Connector "chebi" deleted. biodb.DEBUG[2024-05-04 01:16:06.398][notifyObservers] Notify observers for terminate. biodb.DEBUG[2024-05-04 01:16:06.400][FUN] Trying to call function terminate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:16:06.401][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:16:06.403][FUN] Trying to call function terminate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:16:06.405][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:16:06.406][FUN] Trying to call function terminate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:16:06.408][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.INFO [2024-05-04 01:16:06.429][biodb::testContext] biodb.INFO [2024-05-04 01:16:06.438][biodb::testContext] ******************************************************************************** biodb.INFO [2024-05-04 01:16:06.440][biodb::testContext] Test context - Non regression tests biodb.INFO [2024-05-04 01:16:06.441][biodb::testContext] ******************************************************************************** biodb.INFO [2024-05-04 01:16:06.442][biodb::testContext] biodb.INFO [2024-05-04 01:16:06.446][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0. biodb.DEBUG[2024-05-04 01:16:06.448][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc/R/library/biodb/definitions.yml". biodb.DEBUG[2024-05-04 01:16:06.456][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-05-04 01:16:06.457][self$getConfig()$define] Define config key allow.huge.downloads. biodb.DEBUG[2024-05-04 01:16:06.460][self$set] Set key allow.huge.downloads to TRUE. biodb.DEBUG[2024-05-04 01:16:06.462][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:16:06.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:16:06.464][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:16:06.466][self$getConfig()$define] Define config key autoload.extra.pkgs. biodb.DEBUG[2024-05-04 01:16:06.468][self$set] Set key autoload.extra.pkgs to TRUE. biodb.DEBUG[2024-05-04 01:16:06.470][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:16:06.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:16:06.482][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:16:06.484][self$getConfig()$define] Define config key cache.all.requests. biodb.DEBUG[2024-05-04 01:16:06.485][self$set] Set key cache.all.requests to TRUE. biodb.DEBUG[2024-05-04 01:16:06.486][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:16:06.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:16:06.489][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:16:06.490][self$getConfig()$define] Define config key cache.directory. biodb.DEBUG[2024-05-04 01:16:06.491][self$getConfig()$define] Define config key cache.read.only. biodb.DEBUG[2024-05-04 01:16:06.492][self$set] Set key cache.read.only to FALSE. biodb.DEBUG[2024-05-04 01:16:06.493][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:16:06.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:16:06.496][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:16:06.497][self$getConfig()$define] Define config key cache.subfolders. biodb.DEBUG[2024-05-04 01:16:06.498][self$getConfig()$define] Define config key cache.system. biodb.DEBUG[2024-05-04 01:16:06.499][self$set] Set key cache.system to TRUE. biodb.DEBUG[2024-05-04 01:16:06.500][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:16:06.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:16:06.502][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:16:06.504][self$getConfig()$define] Define config key use.cache.for.local.db. biodb.DEBUG[2024-05-04 01:16:06.505][self$set] Set key use.cache.for.local.db to FALSE. biodb.DEBUG[2024-05-04 01:16:06.506][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:16:06.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:16:06.508][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:16:06.510][self$getConfig()$define] Define config key dwnld.chunk.size. biodb.DEBUG[2024-05-04 01:16:06.511][self$getConfig()$define] Define config key dwnld.timeout. biodb.DEBUG[2024-05-04 01:16:06.513][self$set] Set key dwnld.timeout to 3600. biodb.DEBUG[2024-05-04 01:16:06.514][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:16:06.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:16:06.517][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:16:06.519][self$getConfig()$define] Define config key compute.fields. biodb.DEBUG[2024-05-04 01:16:06.521][self$set] Set key compute.fields to TRUE. biodb.DEBUG[2024-05-04 01:16:06.523][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:16:06.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:16:06.527][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:16:06.529][self$getConfig()$define] Define config key factory.cache. biodb.DEBUG[2024-05-04 01:16:06.531][self$getConfig()$define] Define config key force.locale. biodb.DEBUG[2024-05-04 01:16:06.533][self$set] Set key force.locale to TRUE. biodb.DEBUG[2024-05-04 01:16:06.535][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:16:06.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:16:06.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:16:06.540][self$getConfig()$define] Define config key longterm.cache.subfolder. biodb.DEBUG[2024-05-04 01:16:06.542][self$getConfig()$define] Define config key msg.caution.lvl. biodb.DEBUG[2024-05-04 01:16:06.544][self$getConfig()$define] Define config key msg.debug.lvl. biodb.DEBUG[2024-05-04 01:16:06.546][self$getConfig()$define] Define config key msg.info.lvl. biodb.DEBUG[2024-05-04 01:16:06.548][self$getConfig()$define] Define config key multival.field.sep. biodb.DEBUG[2024-05-04 01:16:06.550][self$set] Set key multival.field.sep to ";". biodb.DEBUG[2024-05-04 01:16:06.552][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:16:06.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:16:06.556][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:16:06.559][self$getConfig()$define] Define config key intra.field.name.sep. biodb.DEBUG[2024-05-04 01:16:06.561][self$set] Set key intra.field.name.sep to ".". biodb.DEBUG[2024-05-04 01:16:06.563][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:16:06.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:16:06.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:16:06.569][self$getConfig()$define] Define config key entries.sep. biodb.DEBUG[2024-05-04 01:16:06.572][self$set] Set key entries.sep to "|". biodb.DEBUG[2024-05-04 01:16:06.574][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:16:06.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:16:06.578][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:16:06.580][self$getConfig()$define] Define config key offline. biodb.DEBUG[2024-05-04 01:16:06.582][self$set] Set key offline to FALSE. biodb.DEBUG[2024-05-04 01:16:06.584][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:16:06.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:16:06.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:16:06.590][self$getConfig()$define] Define config key persistent.cache.impl. biodb.DEBUG[2024-05-04 01:16:06.592][self$set] Set key persistent.cache.impl to "custom". biodb.DEBUG[2024-05-04 01:16:06.594][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:16:06.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:16:06.598][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 01:16:06.600][self$getConfig()$define] Define config key proton.mass. biodb.DEBUG[2024-05-04 01:16:06.603][self$set] Set key proton.mass to 1.0072765. biodb.DEBUG[2024-05-04 01:16:06.605][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:16:06.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:16:06.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:16:06.611][self$getConfig()$define] Define config key shortterm.cache.subfolder. biodb.DEBUG[2024-05-04 01:16:06.613][self$getConfig()$define] Define config key svn.binary.path. biodb.DEBUG[2024-05-04 01:16:06.619][self$set] Set key svn.binary.path to "". biodb.DEBUG[2024-05-04 01:16:06.621][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:16:06.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:16:06.625][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 01:16:06.628][self$getConfig()$define] Define config key test.functions. biodb.DEBUG[2024-05-04 01:16:06.630][self$getConfig()$define] Define config key useragent. biodb.DEBUG[2024-05-04 01:16:06.632][self$set] Set key useragent to "R Bioconductor biodb library.". biodb.DEBUG[2024-05-04 01:16:06.634][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:16:06.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:16:06.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:16:06.640][self$getDbsInfo()$define] Define connector comp.csv.file. biodb.DEBUG[2024-05-04 01:16:06.643][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-05-04 01:16:06.646][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.". biodb.DEBUG[2024-05-04 01:16:06.648][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 01:16:06.650][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 01:16:06.652][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 01:16:06.654][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 01:16:06.656][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-04 01:16:06.658][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 01:16:06.660][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2024-05-04 01:16:06.662][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 01:16:06.665][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-05-04 01:16:06.667][self$setPropertyValue] Setting property "name" to "Compound CSV File". biodb.DEBUG[2024-05-04 01:16:06.669][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 01:16:06.671][self$setPropertyValue] biodb.DEBUG[2024-05-04 01:16:06.673][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-04 01:16:06.675][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-05-04 01:16:06.675][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-05-04 01:16:06.675][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2024-05-04 01:16:06.675][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2024-05-04 01:16:06.675][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2024-05-04 01:16:06.677][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 01:16:06.679][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 01:16:06.681][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 01:16:06.683][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 01:16:06.685][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 01:16:06.686][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 01:16:06.687][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 01:16:06.689][self$setPropertyValue] biodb.DEBUG[2024-05-04 01:16:06.690][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 01:16:06.691][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 01:16:06.692][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-04 01:16:06.693][self$setPropertyValue] biodb.DEBUG[2024-05-04 01:16:06.695][self$getDbsInfo()$define] Define connector comp.sqlite. biodb.DEBUG[2024-05-04 01:16:06.697][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-05-04 01:16:06.698][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.". biodb.DEBUG[2024-05-04 01:16:06.699][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 01:16:06.701][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 01:16:06.703][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 01:16:06.705][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 01:16:06.706][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-04 01:16:06.707][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 01:16:06.708][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2024-05-04 01:16:06.710][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 01:16:06.711][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-05-04 01:16:06.712][self$setPropertyValue] Setting property "name" to "Compound SQLite". biodb.DEBUG[2024-05-04 01:16:06.714][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 01:16:06.715][self$setPropertyValue] biodb.DEBUG[2024-05-04 01:16:06.716][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-04 01:16:06.717][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-05-04 01:16:06.717][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-05-04 01:16:06.717][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2024-05-04 01:16:06.717][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2024-05-04 01:16:06.717][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2024-05-04 01:16:06.719][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 01:16:06.720][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 01:16:06.722][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 01:16:06.723][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 01:16:06.724][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 01:16:06.725][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 01:16:06.726][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 01:16:06.728][self$setPropertyValue] biodb.DEBUG[2024-05-04 01:16:06.729][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 01:16:06.730][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 01:16:06.731][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-04 01:16:06.733][self$setPropertyValue] biodb.DEBUG[2024-05-04 01:16:06.734][self$getDbsInfo()$define] Define connector mass.csv.file. biodb.DEBUG[2024-05-04 01:16:06.736][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2024-05-04 01:16:06.737][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..". biodb.DEBUG[2024-05-04 01:16:06.739][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 01:16:06.740][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 01:16:06.741][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 01:16:06.743][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 01:16:06.744][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-04 01:16:06.745][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 01:16:06.747][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2024-05-04 01:16:06.748][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 01:16:06.749][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2024-05-04 01:16:06.751][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File". biodb.DEBUG[2024-05-04 01:16:06.753][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 01:16:06.754][self$setPropertyValue] biodb.DEBUG[2024-05-04 01:16:06.755][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-04 01:16:06.757][self$setPropertyValue] biodb.DEBUG[2024-05-04 01:16:06.759][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 01:16:06.761][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 01:16:06.763][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 01:16:06.764][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 01:16:06.766][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 01:16:06.767][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 01:16:06.768][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 01:16:06.769][self$setPropertyValue] biodb.DEBUG[2024-05-04 01:16:06.770][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 01:16:06.772][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 01:16:06.773][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-04 01:16:06.774][self$setPropertyValue] biodb.DEBUG[2024-05-04 01:16:06.776][self$getDbsInfo()$define] Define connector mass.sqlite. biodb.DEBUG[2024-05-04 01:16:06.778][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2024-05-04 01:16:06.779][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.". biodb.DEBUG[2024-05-04 01:16:06.780][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 01:16:06.781][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 01:16:06.783][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 01:16:06.784][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 01:16:06.785][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-04 01:16:06.786][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 01:16:06.788][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2024-05-04 01:16:06.789][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 01:16:06.790][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2024-05-04 01:16:06.792][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite". biodb.DEBUG[2024-05-04 01:16:06.793][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 01:16:06.794][self$setPropertyValue] biodb.DEBUG[2024-05-04 01:16:06.796][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-04 01:16:06.797][self$setPropertyValue] biodb.DEBUG[2024-05-04 01:16:06.798][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 01:16:06.800][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 01:16:06.801][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 01:16:06.802][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 01:16:06.803][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 01:16:06.804][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 01:16:06.806][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 01:16:06.807][self$setPropertyValue] biodb.DEBUG[2024-05-04 01:16:06.809][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 01:16:06.810][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 01:16:06.811][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-04 01:16:06.812][self$setPropertyValue] biodb.DEBUG[2024-05-04 01:16:06.814][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-05-04 01:16:06.815][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:16:06.816][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 01:16:06.818][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:16:06.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:16:06.820][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:16:06.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:16:06.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:16:06.824][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:16:06.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:16:06.826][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 01:16:06.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:16:06.828][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 01:16:06.830][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:16:06.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:16:06.832][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:16:06.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:16:06.834][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:16:06.836][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:16:06.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:16:06.838][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:16:06.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:16:06.840][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 01:16:06.842][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:16:06.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:16:06.844][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:16:06.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:16:06.846][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 01:16:06.848][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:16:06.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:16:06.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:16:06.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:16:06.853][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 01:16:06.854][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:16:06.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:16:06.856][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:16:06.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:16:06.859][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:16:06.860][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:16:06.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:16:06.862][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:16:06.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:16:06.865][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:16:06.866][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:16:06.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:16:06.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:16:06.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:16:06.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:16:06.872][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:16:06.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:16:06.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:16:06.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:16:06.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:16:06.877][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:16:06.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:16:06.879][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:16:06.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:16:06.882][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:16:06.883][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:16:06.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:16:06.885][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:16:06.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:16:06.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:16:06.889][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:16:06.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:16:06.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:16:06.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:16:06.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:16:06.895][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:16:06.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:16:06.897][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:16:06.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:16:06.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:16:06.901][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:16:06.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:16:06.903][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:16:06.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:16:06.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:16:06.908][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:16:06.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:16:06.912][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:16:06.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:16:06.916][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:16:06.917][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:16:06.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:16:06.922][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:16:06.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:16:06.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:16:06.928][self$getEntryFields()$define] Define field accession. biodb.DEBUG[2024-05-04 01:16:06.931][self$getEntryFields()$define] Define field description. biodb.DEBUG[2024-05-04 01:16:06.934][self$getEntryFields()$define] Define field name. biodb.DEBUG[2024-05-04 01:16:06.937][self$getEntryFields()$define] Define field cas.id. biodb.DEBUG[2024-05-04 01:16:06.940][self$getEntryFields()$define] Define field chebi.id. biodb.DEBUG[2024-05-04 01:16:06.953][self$getEntryFields()$define] Define field chemspider.id. biodb.DEBUG[2024-05-04 01:16:06.956][self$getEntryFields()$define] Define field comp.csv.file.id. biodb.DEBUG[2024-05-04 01:16:06.960][self$getEntryFields()$define] Define field comp.sqlite.id. biodb.DEBUG[2024-05-04 01:16:06.963][self$getEntryFields()$define] Define field expasy.enzyme.id. biodb.DEBUG[2024-05-04 01:16:06.966][self$getEntryFields()$define] Define field hmdb.metabolites.id. biodb.DEBUG[2024-05-04 01:16:06.969][self$getEntryFields()$define] Define field kegg.compound.id. biodb.DEBUG[2024-05-04 01:16:06.971][self$getEntryFields()$define] Define field kegg.genes.id. biodb.DEBUG[2024-05-04 01:16:06.974][self$getEntryFields()$define] Define field mass.csv.file.id. biodb.DEBUG[2024-05-04 01:16:06.977][self$getEntryFields()$define] Define field mass.sqlite.id. biodb.DEBUG[2024-05-04 01:16:06.979][self$getEntryFields()$define] Define field ncbi.gene.id. biodb.DEBUG[2024-05-04 01:16:06.982][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id. biodb.DEBUG[2024-05-04 01:16:06.985][self$getEntryFields()$define] Define field compound.id. biodb.DEBUG[2024-05-04 01:16:06.987][self$getEntryFields()$define] Define field average.mass. biodb.DEBUG[2024-05-04 01:16:06.990][self$getEntryFields()$define] Define field molecular.mass. biodb.DEBUG[2024-05-04 01:16:06.993][self$getEntryFields()$define] Define field monoisotopic.mass. biodb.DEBUG[2024-05-04 01:16:06.996][self$getEntryFields()$define] Define field nominal.mass. biodb.DEBUG[2024-05-04 01:16:06.998][self$getEntryFields()$define] Define field peak.attr. biodb.DEBUG[2024-05-04 01:16:07.001][self$getEntryFields()$define] Define field peak.comp. biodb.DEBUG[2024-05-04 01:16:07.004][self$getEntryFields()$define] Define field peak.error.ppm. biodb.DEBUG[2024-05-04 01:16:07.006][self$getEntryFields()$define] Define field peak.formula. biodb.DEBUG[2024-05-04 01:16:07.009][self$getEntryFields()$define] Define field peak.intensity. biodb.DEBUG[2024-05-04 01:16:07.012][self$getEntryFields()$define] Define field peak.mass. biodb.DEBUG[2024-05-04 01:16:07.014][self$getEntryFields()$define] Define field peak.mztheo. biodb.DEBUG[2024-05-04 01:16:07.017][self$getEntryFields()$define] Define field peak.mzexp. biodb.DEBUG[2024-05-04 01:16:07.020][self$getEntryFields()$define] Define field peak.mz. biodb.DEBUG[2024-05-04 01:16:07.022][self$getEntryFields()$define] Define field peak.relative.intensity. biodb.DEBUG[2024-05-04 01:16:07.025][self$getEntryFields()$define] Define field peaks. biodb.DEBUG[2024-05-04 01:16:07.028][self$getEntryFields()$define] Define field chrom.col.constructor. biodb.DEBUG[2024-05-04 01:16:07.030][self$getEntryFields()$define] Define field chrom.col.diameter. biodb.DEBUG[2024-05-04 01:16:07.033][self$getEntryFields()$define] Define field chrom.col.id. biodb.DEBUG[2024-05-04 01:16:07.035][self$getEntryFields()$define] Define field chrom.col.length. biodb.DEBUG[2024-05-04 01:16:07.038][self$getEntryFields()$define] Define field chrom.col.method.protocol. biodb.DEBUG[2024-05-04 01:16:07.041][self$getEntryFields()$define] Define field chrom.col.name. biodb.DEBUG[2024-05-04 01:16:07.043][self$getEntryFields()$define] Define field chrom.flow.gradient. biodb.DEBUG[2024-05-04 01:16:07.046][self$getEntryFields()$define] Define field chrom.flow.rate. biodb.DEBUG[2024-05-04 01:16:07.048][self$getEntryFields()$define] Define field chrom.rt. biodb.DEBUG[2024-05-04 01:16:07.051][self$getEntryFields()$define] Define field chrom.rt.max. biodb.DEBUG[2024-05-04 01:16:07.054][self$getEntryFields()$define] Define field chrom.rt.min. biodb.DEBUG[2024-05-04 01:16:07.056][self$getEntryFields()$define] Define field chrom.rt.unit. biodb.DEBUG[2024-05-04 01:16:07.059][self$getEntryFields()$define] Define field chrom.solvent. biodb.DEBUG[2024-05-04 01:16:07.062][self$getEntryFields()$define] Define field aa.seq. biodb.DEBUG[2024-05-04 01:16:07.065][self$getEntryFields()$define] Define field aa.seq.length. biodb.DEBUG[2024-05-04 01:16:07.069][self$getEntryFields()$define] Define field aa.seq.location. biodb.DEBUG[2024-05-04 01:16:07.072][self$getEntryFields()$define] Define field nt.seq. biodb.DEBUG[2024-05-04 01:16:07.075][self$getEntryFields()$define] Define field nt.seq.length. biodb.DEBUG[2024-05-04 01:16:07.079][self$getEntryFields()$define] Define field ec. biodb.DEBUG[2024-05-04 01:16:07.081][self$getEntryFields()$define] Define field organism. biodb.DEBUG[2024-05-04 01:16:07.084][self$getEntryFields()$define] Define field pathway.class. biodb.DEBUG[2024-05-04 01:16:07.087][self$getEntryFields()$define] Define field catalytic.activity. biodb.DEBUG[2024-05-04 01:16:07.090][self$getEntryFields()$define] Define field cofactor. biodb.DEBUG[2024-05-04 01:16:07.096][self$getEntryFields()$define] Define field gene.symbol. biodb.DEBUG[2024-05-04 01:16:07.099][self$getEntryFields()$define] Define field charge. biodb.DEBUG[2024-05-04 01:16:07.102][self$getEntryFields()$define] Define field comp.iupac.name.allowed. biodb.DEBUG[2024-05-04 01:16:07.105][self$getEntryFields()$define] Define field comp.iupac.name.cas. biodb.DEBUG[2024-05-04 01:16:07.108][self$getEntryFields()$define] Define field comp.iupac.name.pref. biodb.DEBUG[2024-05-04 01:16:07.111][self$getEntryFields()$define] Define field comp.iupac.name.syst. biodb.DEBUG[2024-05-04 01:16:07.113][self$getEntryFields()$define] Define field comp.iupac.name.trad. biodb.DEBUG[2024-05-04 01:16:07.120][self$getEntryFields()$define] Define field comp.super.class. biodb.DEBUG[2024-05-04 01:16:07.121][self$getEntryFields()$define] Define field equation. biodb.DEBUG[2024-05-04 01:16:07.124][self$getEntryFields()$define] Define field formula. biodb.DEBUG[2024-05-04 01:16:07.126][self$getEntryFields()$define] Define field composition. biodb.DEBUG[2024-05-04 01:16:07.127][self$getEntryFields()$define] Define field inchi. biodb.DEBUG[2024-05-04 01:16:07.129][self$getEntryFields()$define] Define field inchikey. biodb.DEBUG[2024-05-04 01:16:07.131][self$getEntryFields()$define] Define field logp. biodb.DEBUG[2024-05-04 01:16:07.133][self$getEntryFields()$define] Define field ms.level. biodb.DEBUG[2024-05-04 01:16:07.134][self$getEntryFields()$define] Define field ms.mode. biodb.DEBUG[2024-05-04 01:16:07.136][self$getEntryFields()$define] Define field msdev. biodb.DEBUG[2024-05-04 01:16:07.138][self$getEntryFields()$define] Define field msdevtype. biodb.DEBUG[2024-05-04 01:16:07.139][self$getEntryFields()$define] Define field msprecannot. biodb.DEBUG[2024-05-04 01:16:07.142][self$getEntryFields()$define] Define field msprecmz. biodb.DEBUG[2024-05-04 01:16:07.143][self$getEntryFields()$define] Define field mstype. biodb.DEBUG[2024-05-04 01:16:07.145][self$getEntryFields()$define] Define field nb.compounds. biodb.DEBUG[2024-05-04 01:16:07.147][self$getEntryFields()$define] Define field nb.peaks. biodb.DEBUG[2024-05-04 01:16:07.149][self$getEntryFields()$define] Define field products. biodb.DEBUG[2024-05-04 01:16:07.152][self$getEntryFields()$define] Define field smiles. biodb.DEBUG[2024-05-04 01:16:07.155][self$getEntryFields()$define] Define field smiles.canonical. biodb.DEBUG[2024-05-04 01:16:07.157][self$getEntryFields()$define] Define field smiles.isomeric. biodb.DEBUG[2024-05-04 01:16:07.159][self$getEntryFields()$define] Define field substrates. biodb.DEBUG[2024-05-04 01:16:07.161][initialize] Created successfully new BiodbMain instance. biodb.DEBUG[2024-05-04 01:16:07.163][initialize] This is biodb version 1.12.0. biodb.DEBUG[2024-05-04 01:16:07.165][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-05-04 01:16:07.166][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:16:07.167][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:16:07.168][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:16:07.169][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 01:16:07.171][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:16:07.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:16:07.173][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:16:07.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:16:07.175][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:16:07.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:16:07.178][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 01:16:07.179][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:16:07.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:16:07.182][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:16:07.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:16:07.184][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:16:07.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:16:07.186][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 01:16:07.188][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:16:07.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:16:07.190][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:16:07.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:16:07.193][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 01:16:07.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:16:07.195][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 01:16:07.196][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:16:07.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:16:07.199][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:16:07.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:16:07.201][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:16:07.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:16:07.204][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 01:16:07.205][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:16:07.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:16:07.207][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:16:07.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:16:07.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:16:07.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:16:07.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:16:07.214][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:16:07.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:16:07.216][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:16:07.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:16:07.218][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:16:07.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:16:07.221][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 01:16:07.222][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:16:07.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:16:07.225][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:16:07.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:16:07.227][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:16:07.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:16:07.229][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:16:07.230][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:16:07.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:16:07.233][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:16:07.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:16:07.236][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 01:16:07.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:16:07.238][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:16:07.239][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:16:07.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:16:07.243][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:16:07.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:16:07.245][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:16:07.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:16:07.248][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:16:07.249][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:16:07.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:16:07.252][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:16:07.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:16:07.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:16:07.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:16:07.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:16:07.258][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:16:07.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:16:07.260][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:16:07.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:16:07.263][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:16:07.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:16:07.265][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:16:07.266][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:16:07.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:16:07.268][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:16:07.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:16:07.271][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:16:07.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:16:07.273][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:16:07.274][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:16:07.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:16:07.276][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:16:07.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:16:07.279][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:16:07.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:16:07.281][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:16:07.283][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:16:07.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:16:07.285][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:16:07.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:16:07.287][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:16:07.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:16:07.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:16:07.291][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:16:07.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:16:07.293][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:16:07.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:16:07.295][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:16:07.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:16:07.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:16:07.299][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:16:07.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:16:07.301][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:16:07.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:16:07.304][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:16:07.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:16:07.306][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 01:16:07.307][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 01:16:07.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:16:07.310][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:16:07.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:16:07.312][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 01:16:07.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:16:07.314][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 01:16:07.318][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc/R/library/biodbChebi/definitions.yml". biodb.DEBUG[2024-05-04 01:16:07.320][self$getDbsInfo()$define] Define connector chebi. biodb.DEBUG[2024-05-04 01:16:07.323][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-05-04 01:16:07.324][self$setPropertyValue] Setting property "description" to "NA". biodb.DEBUG[2024-05-04 01:16:07.325][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 01:16:07.327][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 01:16:07.328][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 01:16:07.329][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 01:16:07.331][self$setPropertyValue] Setting property "editable" to "FALSE". biodb.DEBUG[2024-05-04 01:16:07.332][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8". biodb.DEBUG[2024-05-04 01:16:07.334][self$setPropertyValue] Setting property "entry.content.type" to "xml". biodb.DEBUG[2024-05-04 01:16:07.335][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 01:16:07.336][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-05-04 01:16:07.337][self$setPropertyValue] Setting property "name" to "ChEBI". biodb.DEBUG[2024-05-04 01:16:07.339][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 01:16:07.340][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')". biodb.DEBUG[2024-05-04 01:16:07.340][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge". biodb.DEBUG[2024-05-04 01:16:07.340][self$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 01:16:07.340][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi". biodb.DEBUG[2024-05-04 01:16:07.340][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey". biodb.DEBUG[2024-05-04 01:16:07.340][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data". biodb.DEBUG[2024-05-04 01:16:07.340][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass". biodb.DEBUG[2024-05-04 01:16:07.340][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass". biodb.DEBUG[2024-05-04 01:16:07.340][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")". biodb.DEBUG[2024-05-04 01:16:07.340][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar". biodb.DEBUG[2024-05-04 01:16:07.340][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles". biodb.DEBUG[2024-05-04 01:16:07.341][self$setPropertyValue] Setting property "remote" to "TRUE". biodb.DEBUG[2024-05-04 01:16:07.343][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-05-04 01:16:07.343][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-05-04 01:16:07.343][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2024-05-04 01:16:07.345][self$setPropertyValue] Setting property "scheduler.n" to "3". biodb.DEBUG[2024-05-04 01:16:07.346][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 01:16:07.347][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 01:16:07.348][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 01:16:07.350][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 01:16:07.351][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 01:16:07.352][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 01:16:07.353][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-05-04 01:16:07.353][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/". biodb.DEBUG[2024-05-04 01:16:07.354][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 01:16:07.356][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 01:16:07.357][self$setPropertyValue] Setting property "writable" to "FALSE". biodb.DEBUG[2024-05-04 01:16:07.358][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi". biodb.DEBUG[2024-05-04 01:16:07.358][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema". biodb.DEBUG[2024-05-04 01:16:07.360][self$getEntryFields()$define] Define field chebi.id. biodb.DEBUG[2024-05-04 01:16:07.361][self$getEntryFields()$define] Define field kegg.compound.id. biodb.DEBUG[2024-05-04 01:16:07.364][self$getEntryFields()$define] Define field n_stars. biodb.DEBUG[2024-05-04 01:16:07.366][self$getEntryFields()$define] Define field molecular.mass. biodb.DEBUG[2024-05-04 01:16:07.367][self$getEntryFields()$define] Define field inchi. biodb.DEBUG[2024-05-04 01:16:07.370][self$getEntryFields()$define] Define field inchikey. biodb.DEBUG[2024-05-04 01:16:07.373][super$initialize] Initialize connector chebi. biodb.DEBUG[2024-05-04 01:16:07.374][super$initialize] Register connector chebi with the request scheduler biodb.DEBUG[2024-05-04 01:16:07.376][private$bdb$getRequestScheduler()$re ...] Register connector chebi. biodb.DEBUG[2024-05-04 01:16:07.378][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi". biodb.DEBUG[2024-05-04 01:16:07.380][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2024-05-04 01:16:07.381][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2024-05-04 01:16:07.383][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk". biodb.DEBUG[2024-05-04 01:16:07.384][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi . biodb.INFO [2024-05-04 01:16:07.386][biodb::testThat] biodb.INFO [2024-05-04 01:16:07.388][biodb::testThat] Running test function test.chebi.encoding.issue.in.xml (" ChEBI encoding issue in XML is handled. "). biodb.INFO [2024-05-04 01:16:07.389][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 01:16:07.390][biodb::testThat] biodb.DEBUG[2024-05-04 01:16:07.394][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 01:16:07.406][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-05-04 01:16:07.408][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05". biodb.TRACE[2024-05-04 01:16:07.410][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-05-04 01:16:07.413][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content". biodb.DEBUG[2024-05-04 01:16:07.417][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 01:16:07.421][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-05-04 01:16:07.437][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e". biodb.TRACE[2024-05-04 01:16:07.439][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-05-04 01:16:07.441][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content". biodb.DEBUG[2024-05-04 01:16:07.446][private$loadEntries] Creating entries from ids [1]: "2571". biodb.DEBUG[2024-05-04 01:16:07.448][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-05-04 01:16:07.450][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571". biodb.TRACE[2024-05-04 01:16:07.451][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-05-04 01:16:07.453][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-05-04 01:16:07.454][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-05-04 01:16:07.456][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-05-04 01:16:07.457][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-05-04 01:16:07.459][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-05-04 01:16:07.463][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:16:07.464][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:16:07.465][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:16:07.473][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:16:07.475][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 01:16:07.476][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:16:07.477][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 01:16:07.479][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571". biodb.DEBUG[2024-05-04 01:16:07.482][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-04 01:16:07.483][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-04 01:16:07.485][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571". biodb.TRACE[2024-05-04 01:16:22.590][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 01:16:30.476][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-05-04 01:16:30.480][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content" biodb.TRACE[2024-05-04 01:16:30.489][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request" biodb.TRACE[2024-05-04 01:16:30.496][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml" biodb.DEBUG[2024-05-04 01:16:30.502][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-05-04 01:16:30.504][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-05-04 01:16:30.507][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-05-04 01:16:30.510][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 01:16:30.512][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:16:30.514][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:16:30.524][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:16:30.526][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 01:16:30.527][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:16:30.528][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-04 01:16:30.536][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:16:30.539][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:16:30.540][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:16:30.542][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:16:30.545][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:16:30.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:16:30.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:16:30.552][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:16:30.554][ef$get] Asked field names are: charge. biodb.TRACE[2024-05-04 01:16:30.556][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-05-04 01:16:30.557][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:16:30.558][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:16:30.560][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-05-04 01:16:30.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-05-04 01:16:30.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:16:30.564][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:16:30.566][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-04 01:16:30.567][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 01:16:30.569][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:16:30.570][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:16:30.572][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 01:16:30.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 01:16:30.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:16:30.576][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:16:30.577][ef$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 01:16:30.579][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 01:16:30.580][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:16:30.581][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:16:30.584][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 01:16:30.586][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 01:16:30.588][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:16:30.590][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:16:30.592][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-04 01:16:30.594][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-04 01:16:30.596][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:16:30.598][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:16:30.601][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-04 01:16:30.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-04 01:16:30.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:16:30.606][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:16:30.608][ef$get] Asked field names are: mass. biodb.TRACE[2024-05-04 01:16:30.610][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:16:30.612][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:16:30.614][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:16:30.617][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-05-04 01:16:30.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 01:16:30.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:16:30.622][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:16:30.624][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:16:30.626][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:16:30.628][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:16:30.630][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:16:30.633][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:16:30.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 01:16:30.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:16:30.638][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:16:30.640][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 01:16:30.643][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 01:16:30.644][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:16:30.646][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:16:30.650][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 01:16:30.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 01:16:30.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:16:30.655][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:16:30.657][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-05-04 01:16:30.659][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-05-04 01:16:30.661][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:16:30.663][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:16:30.666][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-05-04 01:16:30.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-05-04 01:16:30.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:16:30.672][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:16:30.674][ef$get] Asked field names are: smiles. biodb.TRACE[2024-05-04 01:16:30.676][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-04 01:16:30.678][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:16:30.679][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 01:16:30.682][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-05-04 01:16:30.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-04 01:16:30.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:16:30.688][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:16:30.690][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:16:30.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:16:30.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:16:30.696][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:16:30.698][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:16:30.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:16:30.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:16:30.703][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:16:30.705][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:16:30.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:16:30.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:16:30.711][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:16:30.713][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 01:16:30.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 01:16:30.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:16:30.718][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:16:30.720][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:16:30.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:16:30.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:16:30.726][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:16:30.728][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:16:30.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:16:30.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:16:30.734][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:16:30.736][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:16:30.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:16:30.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:16:30.741][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:16:30.743][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:16:30.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:16:30.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:16:30.749][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:16:30.751][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:16:30.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:16:30.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:16:30.755][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 01:16:30.756][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 01:16:30.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 01:16:30.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 01:16:30.760][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 01:16:30.762][self$createEntryFromContent] Accession numbers: 2571. biodb.INFO [2024-05-04 01:16:30.769][biodb$terminate] Closing BiodbMain instance... biodb.DEBUG[2024-05-04 01:16:30.771][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler biodb.INFO [2024-05-04 01:16:30.772][self$deleteConn] Connector "chebi" deleted. biodb.DEBUG[2024-05-04 01:16:30.773][notifyObservers] Notify observers for terminate. biodb.DEBUG[2024-05-04 01:16:30.775][FUN] Trying to call function terminate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 01:16:30.776][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 01:16:30.777][FUN] Trying to call function terminate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 01:16:30.778][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 01:16:30.780][FUN] Trying to call function terminate on observer BiodbConfig. biodb.DEBUG[2024-05-04 01:16:30.781][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". [ FAIL 2 | WARN 0 | SKIP 0 | PASS 384 ] ══ 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 384 ] Error: Test failures Execution halted
biodbChebi.Rcheck/biodbChebi-Ex.timings
name | user | system | elapsed | |
ChebiConn | 3.72 | 2.39 | 94.37 | |
ChebiEntry | 0.77 | 0.05 | 0.81 | |