Back to Long Tests report for BioC 3.19

This page was generated on 2024-05-04 23:55:02 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
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 12/33HostnameOS / ArchCHECK
biodbNci 1.8.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-05-04 09:55:02 -0400 (Sat, 04 May 2024)
git_url: https://git.bioconductor.org/packages/biodbNci
git_branch: RELEASE_3_19
git_last_commit: 0db4525
git_last_commit_date: 2024-04-30 11:41:04 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK  
palomino3Windows Server 2022 Datacenter / x64  ERROR  
lconwaymacOS 12.7.1 Monterey / x86_64  OK  

CHECK results for biodbNci on palomino3


To the developers/maintainers of the biodbNci package:
- 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.

raw results


Summary

Package: biodbNci
Version: 1.8.0
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.8.0.tar.gz
StartedAt: 2024-05-04 16:07:53 -0400 (Sat, 04 May 2024)
EndedAt: 2024-05-04 16:09:26 -0400 (Sat, 04 May 2024)
EllapsedTime: 93.5 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbNci.Rcheck
Warnings: NA

Tests output

biodbNci.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

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Type 'license()' or 'licence()' for distribution details.

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Type 'contributors()' for more information and
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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbNci)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbNci")
biodb.INFO [2024-05-04 16:09:22.925][biodb::testContext]
biodb.INFO [2024-05-04 16:09:22.928][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-04 16:09:22.929][biodb::testContext] Test context - Generic long tests
biodb.INFO [2024-05-04 16:09:22.930][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-04 16:09:22.931][biodb::testContext]
biodb.INFO [2024-05-04 16:09:22.938][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-05-04 16:09:22.940][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2024-05-04 16:09:22.948][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-04 16:09:22.949][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-04 16:09:22.950][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-04 16:09:22.951][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:22.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:22.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:22.955][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-04 16:09:22.971][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-04 16:09:22.972][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:22.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:22.974][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 16:09:22.975][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-04 16:09:22.976][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-04 16:09:22.978][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:22.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:22.980][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:22.981][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-04 16:09:22.982][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-04 16:09:22.983][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-04 16:09:22.984][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:22.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:22.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:22.988][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-04 16:09:22.989][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-04 16:09:22.990][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-04 16:09:22.991][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:22.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:22.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:22.995][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-04 16:09:22.996][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-04 16:09:22.997][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:22.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:22.999][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.DEBUG[2024-05-04 16:09:23.001][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-04 16:09:23.002][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-04 16:09:23.004][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-04 16:09:23.005][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:23.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:23.007][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:23.008][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-04 16:09:23.009][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-04 16:09:23.011][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:23.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:23.013][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:23.014][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-04 16:09:23.015][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-04 16:09:23.016][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-04 16:09:23.017][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:23.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:23.019][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:23.021][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-04 16:09:23.022][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-04 16:09:23.023][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-04 16:09:23.024][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-04 16:09:23.026][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-04 16:09:23.027][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-04 16:09:23.028][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:23.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:23.030][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 16:09:23.031][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-04 16:09:23.032][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-04 16:09:23.033][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:23.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:23.036][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:23.037][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-04 16:09:23.038][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-04 16:09:23.039][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:23.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:23.041][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:23.042][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-04 16:09:23.044][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-04 16:09:23.045][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:23.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:23.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:23.048][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-04 16:09:23.049][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-04 16:09:23.050][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:23.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:23.053][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.DEBUG[2024-05-04 16:09:23.054][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-04 16:09:23.055][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-04 16:09:23.056][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:23.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:23.058][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:23.059][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-04 16:09:23.061][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-04 16:09:23.064][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-04 16:09:23.065][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:23.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:23.068][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:23.069][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-04 16:09:23.070][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-04 16:09:23.071][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-04 16:09:23.072][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:23.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:23.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:23.078][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-04 16:09:23.113][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-04 16:09:23.127][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-05-04 16:09:23.129][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 16:09:23.130][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 16:09:23.131][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 16:09:23.132][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 16:09:23.133][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-04 16:09:23.135][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 16:09:23.136][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-04 16:09:23.137][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 16:09:23.138][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-04 16:09:23.139][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-04 16:09:23.141][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 16:09:23.142][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:09:23.143][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-04 16:09:23.144][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-04 16:09:23.144][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-04 16:09:23.144][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-04 16:09:23.144][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-04 16:09:23.144][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-04 16:09:23.145][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-04 16:09:23.147][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:09:23.148][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:09:23.149][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 16:09:23.150][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:09:23.151][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:09:23.152][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 16:09:23.153][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:09:23.154][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 16:09:23.156][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 16:09:23.157][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-04 16:09:23.158][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:09:23.159][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-04 16:09:23.161][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-04 16:09:23.162][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-04 16:09:23.164][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 16:09:23.165][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 16:09:23.166][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 16:09:23.167][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 16:09:23.168][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-04 16:09:23.169][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 16:09:23.171][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-04 16:09:23.172][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 16:09:23.173][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-04 16:09:23.174][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-04 16:09:23.175][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 16:09:23.177][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:09:23.178][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-04 16:09:23.179][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-04 16:09:23.179][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-04 16:09:23.179][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-04 16:09:23.179][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-04 16:09:23.179][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-04 16:09:23.180][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-04 16:09:23.181][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:09:23.182][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:09:23.184][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 16:09:23.185][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:09:23.186][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:09:23.187][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 16:09:23.188][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:09:23.189][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 16:09:23.190][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 16:09:23.192][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-04 16:09:23.193][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:09:23.194][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-04 16:09:23.196][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-04 16:09:23.197][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-05-04 16:09:23.198][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 16:09:23.200][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 16:09:23.201][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 16:09:23.202][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 16:09:23.203][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-04 16:09:23.204][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 16:09:23.205][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-04 16:09:23.207][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 16:09:23.208][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-04 16:09:23.209][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-04 16:09:23.210][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 16:09:23.211][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:09:23.213][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-04 16:09:23.214][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:09:23.215][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-04 16:09:23.216][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:09:23.217][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:09:23.218][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 16:09:23.220][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:09:23.221][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:09:23.222][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 16:09:23.223][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:09:23.224][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 16:09:23.225][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 16:09:23.226][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-04 16:09:23.227][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:09:23.229][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-04 16:09:23.231][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-04 16:09:23.232][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-04 16:09:23.233][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 16:09:23.234][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 16:09:23.236][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 16:09:23.237][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 16:09:23.238][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-04 16:09:23.239][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 16:09:23.240][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-04 16:09:23.242][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 16:09:23.243][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-04 16:09:23.244][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-04 16:09:23.245][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 16:09:23.246][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:09:23.248][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-04 16:09:23.249][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:09:23.250][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-04 16:09:23.251][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:09:23.252][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:09:23.253][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 16:09:23.255][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:09:23.256][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:09:23.257][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 16:09:23.258][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:09:23.259][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 16:09:23.260][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 16:09:23.261][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-04 16:09:23.263][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:09:23.266][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-04 16:09:23.267][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:23.268][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.DEBUG[2024-05-04 16:09:23.269][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:23.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:23.272][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:09:23.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:23.274][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:23.275][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:23.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:23.277][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:09:23.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:23.279][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 16:09:23.280][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:23.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:23.283][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:09:23.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:23.285][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 16:09:23.286][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:23.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:23.288][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:09:23.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:23.290][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 16:09:23.291][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:23.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:23.293][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 16:09:23.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:23.296][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 16:09:23.297][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:23.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:23.304][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 16:09:23.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:23.306][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 16:09:23.307][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:23.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:23.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:09:23.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:23.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:23.313][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:23.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:23.315][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:09:23.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:23.317][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 16:09:23.318][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:23.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:23.320][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:09:23.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:23.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:23.323][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:23.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:23.326][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 16:09:23.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:23.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:23.329][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:23.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:23.331][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 16:09:23.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:23.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:23.334][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:23.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:23.336][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:09:23.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:23.339][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:23.340][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:23.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:23.342][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:09:23.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:23.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:23.345][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:23.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:23.347][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:09:23.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:23.349][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:23.351][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:23.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:23.353][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 16:09:23.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:23.355][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.DEBUG[2024-05-04 16:09:23.356][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:23.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:23.358][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:09:23.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:23.360][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 16:09:23.361][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:23.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:23.363][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:09:23.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:23.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:23.367][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-04 16:09:23.371][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-04 16:09:23.372][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-04 16:09:23.374][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-04 16:09:23.376][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-04 16:09:23.377][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-04 16:09:23.379][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-04 16:09:23.380][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-04 16:09:23.382][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-04 16:09:23.383][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-04 16:09:23.385][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-04 16:09:23.386][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-04 16:09:23.388][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-04 16:09:23.389][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-04 16:09:23.391][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-04 16:09:23.392][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-04 16:09:23.394][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-04 16:09:23.396][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-04 16:09:23.397][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-04 16:09:23.399][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-04 16:09:23.400][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-04 16:09:23.402][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-04 16:09:23.403][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-04 16:09:23.405][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-04 16:09:23.406][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-04 16:09:23.408][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-04 16:09:23.410][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-04 16:09:23.411][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-04 16:09:23.413][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-04 16:09:23.414][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-04 16:09:23.416][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-04 16:09:23.417][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-04 16:09:23.419][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-04 16:09:23.420][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-04 16:09:23.422][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-04 16:09:23.423][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-04 16:09:23.425][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-04 16:09:23.426][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-04 16:09:23.428][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-04 16:09:23.429][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-04 16:09:23.431][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-04 16:09:23.433][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-04 16:09:23.434][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-04 16:09:23.436][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-04 16:09:23.437][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-04 16:09:23.439][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-04 16:09:23.440][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-04 16:09:23.442][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-04 16:09:23.443][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-04 16:09:23.445][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-04 16:09:23.446][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-04 16:09:23.448][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-04 16:09:23.450][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-04 16:09:23.451][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-04 16:09:23.453][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-04 16:09:23.454][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-04 16:09:23.456][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-04 16:09:23.457][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-04 16:09:23.459][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-04 16:09:23.460][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-04 16:09:23.462][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-04 16:09:23.463][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-04 16:09:23.465][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-04 16:09:23.467][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-04 16:09:23.468][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-04 16:09:23.470][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-04 16:09:23.471][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-04 16:09:23.473][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-04 16:09:23.474][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-04 16:09:23.476][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-04 16:09:23.477][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-04 16:09:23.479][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-04 16:09:23.480][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-04 16:09:23.482][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-04 16:09:23.483][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-04 16:09:23.485][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-04 16:09:23.487][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-04 16:09:23.488][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-04 16:09:23.490][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-04 16:09:23.491][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-04 16:09:23.493][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-04 16:09:23.494][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-04 16:09:23.496][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-04 16:09:23.536][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-04 16:09:23.539][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-05-04 16:09:23.542][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-04 16:09:23.543][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:23.544][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:09:23.545][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:23.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:23.551][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:23.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:09:23.553][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:09:23.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:23.555][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:09:23.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:23.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:23.558][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:23.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:09:23.561][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:09:23.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:23.563][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:09:23.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:23.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:23.566][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:23.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:09:23.568][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:09:23.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:23.570][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:09:23.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:23.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:23.574][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:23.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:09:23.576][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:09:23.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:23.578][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:09:23.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:23.580][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:23.581][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:23.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:09:23.583][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:09:23.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:23.585][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:09:23.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:23.588][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 16:09:23.589][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:23.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:09:23.591][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:09:23.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:23.593][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:09:23.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:23.595][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:23.596][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:23.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:09:23.598][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:09:23.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:23.601][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:09:23.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:23.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:23.604][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:23.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:09:23.606][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:09:23.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:23.608][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:09:23.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:23.610][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:23.611][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:23.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:09:23.614][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:09:23.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:23.616][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:09:23.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:23.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:23.619][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:23.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:09:23.621][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:09:23.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:23.623][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 16:09:23.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:23.626][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 16:09:23.627][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:23.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:09:23.629][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:09:23.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:23.631][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 16:09:23.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:23.633][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:23.634][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:23.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:09:23.637][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:09:23.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:23.639][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:09:23.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:23.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:23.642][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:23.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:09:23.644][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:09:23.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:23.646][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:09:23.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:23.649][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:23.650][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:23.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:09:23.652][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:09:23.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:23.654][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:09:23.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:23.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:23.657][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:23.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:09:23.659][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:09:23.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:23.662][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:09:23.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:23.664][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:23.665][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:23.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:09:23.667][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:09:23.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:23.669][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:09:23.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:23.671][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 16:09:23.672][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:23.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:09:23.675][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:09:23.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:23.677][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:09:23.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:23.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:23.682][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2024-05-04 16:09:23.691][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2024-05-04 16:09:23.693][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-04 16:09:23.694][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2024-05-04 16:09:23.696][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 16:09:23.697][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 16:09:23.698][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-05-04 16:09:23.699][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2024-05-04 16:09:23.700][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-04 16:09:23.701][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 16:09:23.703][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2024-05-04 16:09:23.704][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 16:09:23.705][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-04 16:09:23.706][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2024-05-04 16:09:23.707][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 16:09:23.709][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2024-05-04 16:09:23.709][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2024-05-04 16:09:23.709][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2024-05-04 16:09:23.709][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2024-05-04 16:09:23.709][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2024-05-04 16:09:23.709][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2024-05-04 16:09:23.709][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2024-05-04 16:09:23.710][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-04 16:09:23.711][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:09:23.712][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-05-04 16:09:23.713][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:09:23.715][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:09:23.716][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 16:09:23.717][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:09:23.718][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:09:23.719][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 16:09:23.720][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-05-04 16:09:23.720][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-05-04 16:09:23.720][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2024-05-04 16:09:23.720][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2024-05-04 16:09:23.722][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 16:09:23.723][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 16:09:23.724][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-04 16:09:23.725][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:09:23.731][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2024-05-04 16:09:23.779][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2024-05-04 16:09:23.780][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2024-05-04 16:09:23.784][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2024-05-04 16:09:23.788][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2024-05-04 16:09:23.791][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-04 16:09:23.792][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-04 16:09:23.794][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-05-04 16:09:23.796][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-05-04 16:09:23.797][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-05-04 16:09:23.798][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2024-05-04 16:09:23.808][biodb::testThat]
biodb.INFO [2024-05-04 16:09:23.809][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-05-04 16:09:23.810][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 16:09:23.811][biodb::testThat]
biodb.TRACE[2024-05-04 16:09:23.816][loadFileContents] Loaded 1 files from cache: [1]: "F:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2024-05-04 16:09:23.818][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2024-05-04 16:09:23.821][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2024-05-04 16:09:23.828][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 16:09:23.829][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:09:23.830][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:09:23.846][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:23.847][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 16:09:23.848][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:23.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:09:23.864][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:09:23.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:09:23.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:23.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:23.869][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:09:23.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:09:23.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:23.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:23.885][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:09:23.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:09:23.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:23.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:23.911][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:09:23.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:09:23.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:23.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:23.917][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:09:23.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:09:23.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:23.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:23.922][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:09:23.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:09:23.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:23.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:23.928][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:09:23.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:09:23.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:23.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:23.933][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:09:23.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:09:23.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:23.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:23.938][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:09:23.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:09:23.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:23.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:23.943][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:09:23.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:09:23.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:23.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:23.949][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-05-04 16:09:23.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-05-04 16:09:23.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:23.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:23.954][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-05-04 16:09:23.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-05-04 16:09:23.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:23.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:23.959][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:09:23.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:09:23.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:23.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:23.974][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-05-04 16:09:23.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-05-04 16:09:23.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:23.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:23.978][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:09:23.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:09:23.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:23.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:23.983][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:09:23.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:09:23.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:23.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:23.988][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:09:23.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:09:23.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:23.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.033][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:09:24.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:09:24.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.041][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:09:24.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:09:24.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.046][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:09:24.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:09:24.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 16:09:24.051][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2024-05-04 16:09:24.054][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-04 16:09:24.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-04 16:09:24.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.061][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-04 16:09:24.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-04 16:09:24.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.069][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-04 16:09:24.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-04 16:09:24.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.076][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-04 16:09:24.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-04 16:09:24.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.101][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:09:24.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:09:24.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.120][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-05-04 16:09:24.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-05-04 16:09:24.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.146][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:09:24.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:09:24.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.151][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:09:24.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:09:24.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.156][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:09:24.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:09:24.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.163][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:09:24.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:09:24.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.173][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:09:24.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:09:24.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.178][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:09:24.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:09:24.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.183][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-05-04 16:09:24.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-05-04 16:09:24.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.188][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-05-04 16:09:24.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-05-04 16:09:24.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.193][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-05-04 16:09:24.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-05-04 16:09:24.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.209][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:09:24.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:09:24.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.214][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:09:24.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:09:24.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.219][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:09:24.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:09:24.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.224][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:09:24.225][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:09:24.227][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.228][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.229][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:09:24.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:09:24.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.244][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:09:24.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:09:24.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.249][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:09:24.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:09:24.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.254][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:09:24.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:09:24.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.258][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:09:24.260][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:09:24.261][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.262][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.263][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:09:24.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:09:24.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.279][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:09:24.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:09:24.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.284][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:09:24.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:09:24.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.289][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:09:24.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:09:24.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.294][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:09:24.295][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:09:24.296][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.298][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.299][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:09:24.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:09:24.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.314][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:09:24.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:09:24.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.319][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:09:24.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:09:24.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.324][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:09:24.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:09:24.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.329][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:09:24.330][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:09:24.331][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.332][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.334][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:09:24.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:09:24.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.349][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:09:24.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:09:24.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.354][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:09:24.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:09:24.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.364][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:09:24.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:09:24.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.369][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:09:24.370][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:09:24.371][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.372][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.373][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:09:24.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:09:24.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.388][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:09:24.390][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:09:24.391][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.392][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.399][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:09:24.400][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:09:24.402][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.403][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.410][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:09:24.411][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:09:24.412][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.413][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.420][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:09:24.421][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:09:24.423][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.424][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.431][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:09:24.432][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:09:24.433][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.434][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.452][loadFileContents] Loaded 1 files from cache: [1]: "F:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2024-05-04 16:09:24.482][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2024-05-04 16:09:24.484][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2024-05-04 16:09:24.486][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 16:09:24.487][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:09:24.488][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:09:24.495][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:24.496][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 16:09:24.497][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:24.498][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 16:09:24.507][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:09:24.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:09:24.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.517][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:09:24.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:09:24.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.538][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-04 16:09:24.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-04 16:09:24.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.543][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-04 16:09:24.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-04 16:09:24.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.549][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:09:24.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:09:24.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.554][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:09:24.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:09:24.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.559][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:09:24.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:09:24.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.564][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:09:24.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:09:24.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.569][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:09:24.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:09:24.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.574][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:09:24.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:09:24.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.579][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:09:24.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:09:24.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.584][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:09:24.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:09:24.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.589][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:09:24.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:09:24.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.594][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:09:24.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:09:24.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.599][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:09:24.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:09:24.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.604][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:09:24.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:09:24.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.609][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:09:24.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:09:24.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.615][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:09:24.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:09:24.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.619][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:09:24.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:09:24.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.625][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-05-04 16:09:24.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-05-04 16:09:24.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.630][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-05-04 16:09:24.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-05-04 16:09:24.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.635][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:09:24.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:09:24.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.640][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-05-04 16:09:24.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-05-04 16:09:24.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.644][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:09:24.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:09:24.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.649][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:09:24.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:09:24.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.654][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:09:24.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:09:24.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.659][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:09:24.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:09:24.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.664][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:09:24.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:09:24.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.669][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:09:24.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:09:24.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 16:09:24.674][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2024-05-04 16:09:24.697][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-04 16:09:24.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-04 16:09:24.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.702][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-04 16:09:24.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-04 16:09:24.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.707][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-04 16:09:24.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-04 16:09:24.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.711][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-04 16:09:24.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-04 16:09:24.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.718][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:09:24.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:09:24.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.728][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-05-04 16:09:24.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-05-04 16:09:24.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.739][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:09:24.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:09:24.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.744][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:09:24.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:09:24.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.749][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:09:24.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:09:24.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.755][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:09:24.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:09:24.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.760][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:09:24.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:09:24.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.765][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:09:24.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:09:24.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.770][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-05-04 16:09:24.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-05-04 16:09:24.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.775][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-05-04 16:09:24.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-05-04 16:09:24.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.780][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-05-04 16:09:24.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-05-04 16:09:24.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.804][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:09:24.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:09:24.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.809][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:09:24.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:09:24.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.814][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:09:24.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:09:24.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.819][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:09:24.820][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:09:24.821][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.822][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.823][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:09:24.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:09:24.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.838][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-04 16:09:24.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-04 16:09:24.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.843][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-04 16:09:24.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-04 16:09:24.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.853][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-04 16:09:24.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-04 16:09:24.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.858][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-04 16:09:24.860][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-04 16:09:24.861][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.862][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.863][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-04 16:09:24.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-04 16:09:24.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.878][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:09:24.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:09:24.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.883][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:09:24.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:09:24.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.888][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:09:24.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:09:24.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.893][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:09:24.894][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:09:24.895][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.896][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.898][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:09:24.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:09:24.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.913][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:09:24.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:09:24.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.918][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:09:24.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:09:24.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.922][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:09:24.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:09:24.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.927][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:09:24.929][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:09:24.930][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.931][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.932][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:09:24.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:09:24.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.947][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:09:24.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:09:24.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.952][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:09:24.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:09:24.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.957][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:09:24.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:09:24.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.962][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:09:24.963][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:09:24.964][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.966][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.967][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:09:24.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:09:24.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.982][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:09:24.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:09:24.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.987][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:09:24.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:09:24.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.991][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:09:24.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:09:24.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:24.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:24.996][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:09:24.998][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:09:24.999][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:25.000][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:25.001][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:09:25.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:09:25.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:25.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:25.018][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:09:25.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:09:25.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:25.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:25.023][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:09:25.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:09:25.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:25.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:25.028][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:09:25.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:09:25.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:25.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:25.038][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:09:25.039][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:09:25.041][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:25.042][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:25.043][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:09:25.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:09:25.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:25.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:25.058][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:09:25.059][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:09:25.061][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:25.062][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:25.069][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-04 16:09:25.070][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-04 16:09:25.071][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:25.073][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:25.079][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-04 16:09:25.081][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-04 16:09:25.082][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:25.083][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:25.090][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-04 16:09:25.091][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-04 16:09:25.092][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:25.094][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:25.100][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-04 16:09:25.102][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-04 16:09:25.103][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:25.104][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:25.111][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-04 16:09:25.112][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-04 16:09:25.113][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:25.114][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:09:25.121][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:09:25.123][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:09:25.124][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:09:25.125][ef$get] fields variable is a list.
biodb.INFO [2024-05-04 16:09:25.137][biodb::testThat]
biodb.INFO [2024-05-04 16:09:25.139][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-05-04 16:09:25.140][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 16:09:25.141][biodb::testThat]
biodb.DEBUG[2024-05-04 16:09:25.144][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2024-05-04 16:09:25.150][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.INFO [2024-05-04 16:09:25.156][self$getFolderPath] Create cache folder "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427" for "nci.cactus-8efc65070d01b214e760b1d4932ee427".
biodb.DEBUG[2024-05-04 16:09:25.159][self$isDownloaded] Database nci.cactus has not yet been downloaded.
biodb.INFO [2024-05-04 16:09:25.160][self$download] Downloading whole database of nci.cactus.
biodb.INFO [2024-05-04 16:09:25.161][private$doDownload] Downloading NCI CACTUS database at "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz" ...
biodb.DEBUG[2024-05-04 16:09:25.163][sched$downloadFile] Downloading file "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
trying URL 'https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz'
Content type 'application/x-gzip' length 206737123 bytes (197.2 MB)

downloaded 0 bytes

biodb.INFO [2024-05-04 16:09:25.311][biodb::testThat]
biodb.INFO [2024-05-04 16:09:25.313][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-05-04 16:09:25.314][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 16:09:25.315][biodb::testThat]
biodb.INFO [2024-05-04 16:09:25.324][biodb::testThat]
biodb.INFO [2024-05-04 16:09:25.326][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-05-04 16:09:25.327][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 16:09:25.328][biodb::testThat]
biodb.WARN [2024-05-04 16:09:25.353][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2024-05-04 16:09:25.370][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2024-05-04 16:09:25.383][biodb::testThat]
biodb.INFO [2024-05-04 16:09:25.384][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-05-04 16:09:25.385][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 16:09:25.386][biodb::testThat]
biodb.DEBUG[2024-05-04 16:09:25.403][private$loadEntries] Creating entries from ids [1]: "749674".
biodb.DEBUG[2024-05-04 16:09:25.449][conn$getEntryContent] Get NCI CACTUS entry content(s) for 1 id(s)...
biodb.DEBUG[2024-05-04 16:09:25.451][self$isDownloaded] Database nci.cactus has not yet been downloaded.
biodb.INFO [2024-05-04 16:09:25.452][self$download] Downloading whole database of nci.cactus.
biodb.INFO [2024-05-04 16:09:25.453][private$doDownload] Downloading NCI CACTUS database at "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz" ...
biodb.DEBUG[2024-05-04 16:09:25.468][sched$downloadFile] Downloading file "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.TRACE[2024-05-04 16:09:25.494][cch$addFilesToCache] Moving files to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/tmp\nci.cactus7fd02919ea9gz".
biodb.TRACE[2024-05-04 16:09:25.495][private$doAddFilesToCache] Destination files are [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/download.gz".
biodb.DEBUG[2024-05-04 16:09:25.508][cch$addFilesToCache] Done adding files.
biodb.DEBUG[2024-05-04 16:09:25.510][self$getDownloadPath] Download path of nci.cactus is "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/download.gz".
biodb.DEBUG[2024-05-04 16:09:25.512][self$getDownloadPath] Download path of nci.cactus is "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/download.gz".
biodb.ERROR[2024-05-04 16:09:25.513][self$download] File C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/download.gz does not exists. Downloading went wrong.
biodb.INFO [2024-05-04 16:09:25.540][biodb::testThat]
biodb.INFO [2024-05-04 16:09:25.541][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-05-04 16:09:25.542][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 16:09:25.543][biodb::testThat]
biodb.INFO [2024-05-04 16:09:25.554][biodb::testThat]
biodb.INFO [2024-05-04 16:09:25.556][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-05-04 16:09:25.557][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 16:09:25.558][biodb::testThat]
biodb.INFO [2024-05-04 16:09:25.569][biodb::testThat]
biodb.INFO [2024-05-04 16:09:25.570][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-05-04 16:09:25.571][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 16:09:25.572][biodb::testThat]
biodb.INFO [2024-05-04 16:09:25.584][biodb::testThat]
biodb.INFO [2024-05-04 16:09:25.586][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-05-04 16:09:25.588][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 16:09:25.589][biodb::testThat]
biodb.INFO [2024-05-04 16:09:25.599][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-04 16:09:25.600][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2024-05-04 16:09:25.607][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2024-05-04 16:09:25.608][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-04 16:09:25.609][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:09:25.610][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:09:25.611][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:25.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:09:25.613][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:25.614][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.INFO [2024-05-04 16:09:25.625][biodb::testContext]
biodb.INFO [2024-05-04 16:09:25.626][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-04 16:09:25.627][biodb::testContext] Test context - Example long tests
biodb.INFO [2024-05-04 16:09:25.628][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-04 16:09:25.629][biodb::testContext]
biodb.INFO [2024-05-04 16:09:25.632][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-05-04 16:09:25.634][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2024-05-04 16:09:25.640][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-04 16:09:25.641][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-04 16:09:25.642][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-04 16:09:25.643][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:25.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:25.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:25.647][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-04 16:09:25.648][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-04 16:09:25.649][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:25.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:25.651][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 16:09:25.652][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-04 16:09:25.654][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-04 16:09:25.655][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:25.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:25.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:25.658][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-04 16:09:25.659][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-04 16:09:25.661][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-04 16:09:25.662][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:25.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:25.664][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:25.665][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-04 16:09:25.666][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-04 16:09:25.667][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-04 16:09:25.668][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:25.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:25.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:25.672][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-04 16:09:25.673][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-04 16:09:25.674][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:25.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:25.676][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 16:09:25.677][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-04 16:09:25.679][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-04 16:09:25.680][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-04 16:09:25.681][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:25.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:25.683][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:25.684][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-04 16:09:25.686][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-04 16:09:25.687][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:25.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:25.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:25.690][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-04 16:09:25.691][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-04 16:09:25.692][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-04 16:09:25.694][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:25.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:25.696][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:25.697][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-04 16:09:25.698][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-04 16:09:25.699][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-04 16:09:25.700][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-04 16:09:25.702][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-04 16:09:25.703][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-04 16:09:25.704][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:25.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:25.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:25.707][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-04 16:09:25.709][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-04 16:09:25.710][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:25.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:25.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:25.713][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-04 16:09:25.714][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-04 16:09:25.715][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:25.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:25.718][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:25.719][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-04 16:09:25.720][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-04 16:09:25.721][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:25.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:25.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:25.724][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-04 16:09:25.726][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-04 16:09:25.727][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:25.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:25.729][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 16:09:25.730][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-04 16:09:25.731][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-04 16:09:25.733][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:25.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:25.735][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:25.736][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-04 16:09:25.737][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-04 16:09:25.741][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-04 16:09:25.742][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:25.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:25.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:25.745][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-04 16:09:25.746][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-04 16:09:25.748][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-04 16:09:25.749][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:25.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:25.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:25.752][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-04 16:09:25.754][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-04 16:09:25.756][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-05-04 16:09:25.757][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 16:09:25.758][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 16:09:25.759][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 16:09:25.760][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 16:09:25.762][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-04 16:09:25.763][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 16:09:25.764][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-04 16:09:25.765][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 16:09:25.767][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-04 16:09:25.773][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-04 16:09:25.774][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 16:09:25.775][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:09:25.777][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-04 16:09:25.778][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-04 16:09:25.778][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-04 16:09:25.778][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-04 16:09:25.778][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-04 16:09:25.778][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-04 16:09:25.779][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-04 16:09:25.780][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:09:25.781][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:09:25.783][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 16:09:25.784][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:09:25.785][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:09:25.786][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 16:09:25.787][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:09:25.788][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 16:09:25.789][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 16:09:25.791][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-04 16:09:25.792][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:09:25.793][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-04 16:09:25.795][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-04 16:09:25.796][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-04 16:09:25.798][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 16:09:25.799][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 16:09:25.800][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 16:09:25.801][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 16:09:25.803][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-04 16:09:25.804][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 16:09:25.805][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-04 16:09:25.806][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 16:09:25.807][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-04 16:09:25.809][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-04 16:09:25.810][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 16:09:25.811][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:09:25.812][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-04 16:09:25.813][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-04 16:09:25.813][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-04 16:09:25.813][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-04 16:09:25.813][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-04 16:09:25.813][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-04 16:09:25.815][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-04 16:09:25.816][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:09:25.817][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:09:25.818][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 16:09:25.819][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:09:25.820][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:09:25.821][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 16:09:25.823][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:09:25.824][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 16:09:25.825][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 16:09:25.826][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-04 16:09:25.827][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:09:25.829][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-04 16:09:25.831][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-04 16:09:25.832][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-05-04 16:09:25.833][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 16:09:25.834][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 16:09:25.835][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 16:09:25.837][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 16:09:25.838][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-04 16:09:25.839][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 16:09:25.840][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-04 16:09:25.841][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 16:09:25.843][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-04 16:09:25.844][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-04 16:09:25.845][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 16:09:25.846][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:09:25.847][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-04 16:09:25.848][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:09:25.850][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-04 16:09:25.851][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:09:25.852][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:09:25.853][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 16:09:25.854][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:09:25.855][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:09:25.856][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 16:09:25.858][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:09:25.859][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 16:09:25.860][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 16:09:25.861][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-04 16:09:25.862][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:09:25.864][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-04 16:09:25.866][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-04 16:09:25.867][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-04 16:09:25.868][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 16:09:25.869][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 16:09:25.870][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 16:09:25.872][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 16:09:25.873][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-04 16:09:25.874][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 16:09:25.875][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-04 16:09:25.876][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 16:09:25.878][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-04 16:09:25.879][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-04 16:09:25.880][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 16:09:25.881][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:09:25.882][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-04 16:09:25.884][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:09:25.885][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-04 16:09:25.886][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:09:25.887][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:09:25.888][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 16:09:25.889][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:09:25.891][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:09:25.892][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 16:09:25.893][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:09:25.894][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 16:09:25.895][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 16:09:25.896][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-04 16:09:25.898][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:09:25.899][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-04 16:09:25.900][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:25.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:25.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:25.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:25.905][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:09:25.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:25.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:25.908][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:25.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:25.910][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:09:25.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:25.912][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:25.913][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:25.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:25.915][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 16:09:25.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:25.918][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.DEBUG[2024-05-04 16:09:25.919][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:25.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:25.921][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 16:09:25.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:25.923][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:25.924][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:25.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:25.926][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:09:25.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:25.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:25.935][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:25.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:25.937][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:09:25.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:25.939][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:25.940][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:25.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:25.942][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:09:25.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:25.944][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:25.945][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:25.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:25.948][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 16:09:25.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:25.950][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:25.951][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:25.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:25.953][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:09:25.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:25.955][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:25.956][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:25.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:25.959][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:09:25.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:25.961][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:25.962][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:25.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:25.964][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 16:09:25.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:25.966][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 16:09:25.967][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:25.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:25.970][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:09:25.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:25.972][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 16:09:25.973][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:25.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:25.975][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:09:25.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:25.977][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:25.978][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:25.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:25.980][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 16:09:25.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:25.983][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 16:09:25.984][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:25.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:25.986][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:09:25.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:25.988][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:25.989][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:25.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:25.991][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 16:09:25.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:25.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:25.995][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:25.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:25.997][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:09:25.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:25.999][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.DEBUG[2024-05-04 16:09:26.000][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-04 16:09:26.002][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-04 16:09:26.004][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-04 16:09:26.006][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-04 16:09:26.007][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-04 16:09:26.009][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-04 16:09:26.011][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-04 16:09:26.012][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-04 16:09:26.014][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-04 16:09:26.015][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-04 16:09:26.017][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-04 16:09:26.018][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-04 16:09:26.020][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-04 16:09:26.021][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-04 16:09:26.023][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-04 16:09:26.024][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-04 16:09:26.026][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-04 16:09:26.028][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-04 16:09:26.029][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-04 16:09:26.031][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-04 16:09:26.032][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-04 16:09:26.034][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-04 16:09:26.035][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-04 16:09:26.037][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-04 16:09:26.039][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-04 16:09:26.040][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-04 16:09:26.042][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-04 16:09:26.043][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-04 16:09:26.045][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-04 16:09:26.046][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-04 16:09:26.048][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-04 16:09:26.050][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-04 16:09:26.051][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-04 16:09:26.053][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-04 16:09:26.054][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-04 16:09:26.056][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-04 16:09:26.057][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-04 16:09:26.059][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-04 16:09:26.060][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-04 16:09:26.062][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-04 16:09:26.063][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-04 16:09:26.065][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-04 16:09:26.067][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-04 16:09:26.068][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-04 16:09:26.070][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-04 16:09:26.071][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-04 16:09:26.073][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-04 16:09:26.074][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-04 16:09:26.076][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-04 16:09:26.078][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-04 16:09:26.079][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-04 16:09:26.081][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-04 16:09:26.087][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-04 16:09:26.089][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-04 16:09:26.091][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-04 16:09:26.092][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-04 16:09:26.094][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-04 16:09:26.095][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-04 16:09:26.097][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-04 16:09:26.098][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-04 16:09:26.100][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-04 16:09:26.102][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-04 16:09:26.103][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-04 16:09:26.105][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-04 16:09:26.106][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-04 16:09:26.108][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-04 16:09:26.109][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-04 16:09:26.111][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-04 16:09:26.113][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-04 16:09:26.114][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-04 16:09:26.116][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-04 16:09:26.117][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-04 16:09:26.119][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-04 16:09:26.120][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-04 16:09:26.122][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-04 16:09:26.123][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-04 16:09:26.125][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-04 16:09:26.127][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-04 16:09:26.128][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-04 16:09:26.130][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-04 16:09:26.131][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-04 16:09:26.133][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-04 16:09:26.134][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-04 16:09:26.136][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-04 16:09:26.138][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-05-04 16:09:26.140][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-04 16:09:26.141][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:26.142][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:09:26.143][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:26.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:26.145][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:26.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:09:26.147][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:09:26.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:26.149][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:09:26.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:26.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:26.153][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:26.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:09:26.155][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:09:26.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:26.157][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:09:26.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:26.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:26.160][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:26.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:09:26.162][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:09:26.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:26.164][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:09:26.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:26.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:26.168][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:26.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:09:26.170][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:09:26.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:26.172][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 16:09:26.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:26.174][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:26.175][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:26.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:09:26.178][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:09:26.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:26.180][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:09:26.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:26.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:26.183][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:26.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:09:26.185][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:09:26.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:26.187][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:09:26.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:26.190][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:26.191][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:26.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:09:26.193][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:09:26.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:26.195][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:09:26.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:26.197][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.DEBUG[2024-05-04 16:09:26.198][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:26.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:09:26.201][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:09:26.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:26.203][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:09:26.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:26.205][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:26.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:26.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:09:26.208][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:09:26.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:26.210][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 16:09:26.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:26.213][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 16:09:26.214][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:26.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:09:26.216][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:09:26.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:26.218][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 16:09:26.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:26.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:26.221][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:26.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:09:26.223][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:09:26.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:26.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:09:26.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:26.228][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:26.229][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:26.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:09:26.231][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:09:26.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:26.233][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:09:26.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:26.235][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 16:09:26.236][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:26.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:09:26.244][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:09:26.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:26.246][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 16:09:26.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:26.248][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 16:09:26.249][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:26.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:09:26.251][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:09:26.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:26.254][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 16:09:26.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:26.256][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 16:09:26.257][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:26.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:09:26.259][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:09:26.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:26.261][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:09:26.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:26.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:26.265][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:26.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:09:26.267][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:09:26.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:26.269][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:09:26.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:26.271][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:09:26.272][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:09:26.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:09:26.275][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:09:26.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:26.277][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:09:26.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:26.279][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 16:09:26.282][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2024-05-04 16:09:26.284][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2024-05-04 16:09:26.286][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-04 16:09:26.287][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2024-05-04 16:09:26.288][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 16:09:26.290][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 16:09:26.291][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-05-04 16:09:26.292][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2024-05-04 16:09:26.293][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-04 16:09:26.294][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 16:09:26.296][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2024-05-04 16:09:26.297][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 16:09:26.298][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-04 16:09:26.299][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2024-05-04 16:09:26.301][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 16:09:26.302][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2024-05-04 16:09:26.302][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2024-05-04 16:09:26.302][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2024-05-04 16:09:26.302][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2024-05-04 16:09:26.302][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2024-05-04 16:09:26.302][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2024-05-04 16:09:26.302][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2024-05-04 16:09:26.303][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-04 16:09:26.304][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:09:26.305][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-05-04 16:09:26.307][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:09:26.308][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:09:26.309][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 16:09:26.310][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:09:26.311][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:09:26.312][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 16:09:26.314][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-05-04 16:09:26.314][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-05-04 16:09:26.314][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2024-05-04 16:09:26.314][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2024-05-04 16:09:26.315][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 16:09:26.316][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 16:09:26.317][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-04 16:09:26.318][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:09:26.320][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2024-05-04 16:09:26.323][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2024-05-04 16:09:26.324][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2024-05-04 16:09:26.326][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2024-05-04 16:09:26.328][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2024-05-04 16:09:26.329][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-04 16:09:26.330][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-04 16:09:26.332][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-05-04 16:09:26.334][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-05-04 16:09:26.335][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-05-04 16:09:26.336][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2024-05-04 16:09:26.338][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-04 16:09:26.339][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2024-05-04 16:09:26.340][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2024-05-04 16:09:26.341][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-04 16:09:26.342][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:09:26.343][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:09:26.345][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:09:26.346][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 16:09:26.347][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:09:26.348][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".
[ FAIL 2 | WARN 5 | SKIP 0 | PASS 85 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_long_100_generic.R:37:1'): RT unit is defined when there is an RT value. ──
Error in `utils::download.file(url = url, destfile = dest.file, mode = "wb", 
    method = "auto", cacheOK = FALSE, quiet = FALSE)`: download from 'https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz' failed
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcCctsCn>`, opt = `<named list>`)
 3.   └─conn$getBiodb()$getFactory()$getEntry(...)
 4.     └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
 5.       └─conn$getEntryContent(ids)
 6.         └─self$download()
 7.           └─private$doDownload()
 8.             └─sched$downloadFile(url = gz.url, dest.file = tmpFile)
 9.               └─utils::download.file(...)
── Error ('test_long_100_generic.R:37:1'): We can load an entry from the database. ──
Error in `error("File %s does not exists. Downloading went wrong.", self$getDownloadPath())`: File C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/download.gz does not exists. Downloading went wrong.
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcCctsCn>`, opt = `<named list>`)
 3.   └─opt$refEntries$getRealEntry(id)
 4.     └─self$getRealEntries(ids = id)
 5.       └─private$bdb$getFactory()$getEntry(...)
 6.         └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
 7.           └─conn$getEntryContent(ids)
 8.             └─self$download()
 9.               └─biodb::error(...)

[ FAIL 2 | WARN 5 | SKIP 0 | PASS 85 ]
Error: Test failures
Execution halted

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.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 options '--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error'
* checking for file 'biodbNci/DESCRIPTION' ... OK
* this is package 'biodbNci' version '1.8.0'
* 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 'biodbNci' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
* 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 ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in 'vignettes' ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in 'longtests' ... OK
* checking tests in 'longtests' ...
  Running 'testthat.R'
 ERROR
Running the tests in 'longtests/testthat.R' failed.
Last 13 lines of output:
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<NcCctsCn>`, opt = `<named list>`)
   3.   └─opt$refEntries$getRealEntry(id)
   4.     └─self$getRealEntries(ids = id)
   5.       └─private$bdb$getFactory()$getEntry(...)
   6.         └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
   7.           └─conn$getEntryContent(ids)
   8.             └─self$download()
   9.               └─biodb::error(...)
  
  [ FAIL 2 | WARN 5 | SKIP 0 | PASS 85 ]
  Error: Test failures
  Execution halted
* DONE

Status: 1 ERROR
See
  'F:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck/00check.log'
for details.


Installation output

biodbNci.Rcheck/00install.out

* installing *source* package 'biodbNci' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c extractEntries.cpp -o extractEntries.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c test-100-example.cpp -o test-100-example.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c test-runner.cpp -o test-runner.o
g++ -std=gnu++17 -shared -s -static-libgcc -o biodbNci.dll tmp.def RcppExports.o extractEntries.o test-100-example.o test-runner.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck/00LOCK-biodbNci/00new/biodbNci/libs/x64
** 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 (biodbNci)