| Back to Long Tests report for BioC 3.22 |
This page was generated on 2025-08-09 23:55 -0400 (Sat, 09 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4553 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4595 |
| 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 7/29 | Hostname | OS / Arch | CHECK | |||||||
Pierrick Roger
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | ERROR | |||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | ERROR | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | ERROR | ||||||||
|
To the developers/maintainers of the biodbNcbi 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. |
| Package: biodbNcbi |
| Version: 1.13.1 |
| Command: F:\biocbuild\bbs-3.22-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 biodbNcbi_1.13.1.tar.gz |
| StartedAt: 2025-08-09 16:02:49 -0400 (Sat, 09 Aug 2025) |
| EndedAt: 2025-08-09 16:03:50 -0400 (Sat, 09 Aug 2025) |
| EllapsedTime: 61.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: biodbNcbi.Rcheck |
| Warnings: NA |
biodbNcbi.Rcheck/tests/testthat.Rout.fail
R version 4.5.1 (2025-06-13 ucrt) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbNci)
Warning message:
In fun(libname, pkgname) :
Package 'biodbNci' is deprecated and will be removed from Bioconductor
version 3.23
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbNcbi")
Loading required package: biodbNcbi
biodb.INFO [2025-08-09 16:03:40.118][biodb::testContext]
biodb.INFO [2025-08-09 16:03:40.121][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-09 16:03:40.122][biodb::testContext] Test context - CCDS long tests
biodb.INFO [2025-08-09 16:03:40.124][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-09 16:03:40.125][biodb::testContext]
biodb.INFO [2025-08-09 16:03:40.131][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.1.
biodb.DEBUG[2025-08-09 16:03:40.133][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.22-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2025-08-09 16:03:40.141][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-09 16:03:40.142][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-08-09 16:03:40.143][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-08-09 16:03:40.144][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:40.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:40.147][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:40.148][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-08-09 16:03:40.165][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-08-09 16:03:40.166][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:40.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:40.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:40.169][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-08-09 16:03:40.171][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-08-09 16:03:40.172][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:40.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:40.174][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:40.175][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-08-09 16:03:40.177][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-08-09 16:03:40.178][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-08-09 16:03:40.179][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:40.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:40.181][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:40.182][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-08-09 16:03:40.184][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-08-09 16:03:40.185][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-08-09 16:03:40.186][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:40.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:40.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:40.189][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-08-09 16:03:40.191][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-08-09 16:03:40.192][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:40.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:40.194][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:40.195][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-08-09 16:03:40.197][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-08-09 16:03:40.198][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-08-09 16:03:40.199][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:40.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:40.201][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:40.202][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-08-09 16:03:40.204][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-08-09 16:03:40.205][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:40.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:40.207][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:40.208][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-08-09 16:03:40.209][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-08-09 16:03:40.211][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-08-09 16:03:40.212][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:40.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:40.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:40.215][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-08-09 16:03:40.216][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-08-09 16:03:40.218][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-08-09 16:03:40.219][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-08-09 16:03:40.220][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-08-09 16:03:40.221][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-08-09 16:03:40.223][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:40.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:40.225][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:40.226][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-08-09 16:03:40.227][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-08-09 16:03:40.228][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:40.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:40.231][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:40.232][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-08-09 16:03:40.239][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-08-09 16:03:40.240][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:40.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:40.242][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:40.243][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-08-09 16:03:40.244][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-08-09 16:03:40.245][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:40.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:40.248][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:40.249][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-08-09 16:03:40.250][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-08-09 16:03:40.251][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-08-09 16:03:40.252][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:40.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:40.255][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:40.256][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-08-09 16:03:40.257][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-08-09 16:03:40.261][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-08-09 16:03:40.262][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:40.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:40.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:40.265][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-08-09 16:03:40.266][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-08-09 16:03:40.268][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-08-09 16:03:40.269][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:40.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:40.271][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[2025-08-09 16:03:40.274][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-08-09 16:03:40.301][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:40.315][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-08-09 16:03:40.316][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:40.317][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-09 16:03:40.319][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:40.320][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-09 16:03:40.321][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:40.322][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-09 16:03:40.323][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-09 16:03:40.325][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-09 16:03:40.326][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:40.327][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-08-09 16:03:40.328][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-09 16:03:40.330][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:40.331][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:40.332][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-09 16:03:40.332][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-09 16:03:40.332][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-09 16:03:40.332][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-09 16:03:40.332][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-09 16:03:40.333][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-09 16:03:40.335][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:40.336][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:40.337][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-09 16:03:40.338][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:40.339][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:40.340][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-09 16:03:40.342][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:40.343][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-09 16:03:40.344][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-09 16:03:40.345][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:40.346][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:40.348][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-08-09 16:03:40.350][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:40.351][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-08-09 16:03:40.352][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:40.353][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-09 16:03:40.354][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:40.356][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-09 16:03:40.357][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:40.358][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-09 16:03:40.359][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-09 16:03:40.360][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-09 16:03:40.362][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:40.363][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-08-09 16:03:40.364][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-09 16:03:40.365][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:40.367][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:40.368][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-09 16:03:40.368][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-09 16:03:40.368][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-09 16:03:40.368][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-09 16:03:40.368][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-09 16:03:40.369][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-09 16:03:40.370][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:40.372][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:40.373][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-09 16:03:40.374][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:40.375][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:40.376][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-09 16:03:40.377][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:40.379][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-09 16:03:40.380][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-09 16:03:40.381][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:40.382][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:40.384][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-08-09 16:03:40.385][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:40.387][self$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[2025-08-09 16:03:40.388][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:40.389][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-09 16:03:40.390][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:40.392][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-09 16:03:40.393][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:40.394][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-09 16:03:40.395][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-09 16:03:40.396][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-09 16:03:40.398][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:40.399][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-08-09 16:03:40.400][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-09 16:03:40.401][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:40.403][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:40.404][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:40.405][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-09 16:03:40.406][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:40.408][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:40.409][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-09 16:03:40.410][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:40.411][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:40.412][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-09 16:03:40.413][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:40.415][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-09 16:03:40.416][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-09 16:03:40.417][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:40.418][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:40.425][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-08-09 16:03:40.427][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:40.428][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-08-09 16:03:40.429][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:40.430][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-09 16:03:40.432][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:40.433][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-09 16:03:40.434][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:40.435][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-09 16:03:40.436][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-09 16:03:40.438][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-09 16:03:40.439][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:40.440][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-08-09 16:03:40.441][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-09 16:03:40.443][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:40.444][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:40.445][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:40.446][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-09 16:03:40.448][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:40.449][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:40.450][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-09 16:03:40.451][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:40.452][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:40.453][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-09 16:03:40.455][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:40.456][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-09 16:03:40.457][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-09 16:03:40.458][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:40.459][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:40.463][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-09 16:03:40.464][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:40.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:40.466][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:40.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:40.468][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:40.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:40.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:40.472][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:40.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:40.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:40.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:40.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:40.477][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:40.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:40.479][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:40.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:40.482][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:40.483][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:40.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:40.485][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:40.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:40.487][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:40.488][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:40.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:40.490][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:40.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:40.493][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:40.494][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:40.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:40.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:40.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:40.498][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:40.499][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:40.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:40.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:40.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:40.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:40.505][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:40.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:40.507][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:40.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:40.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:40.510][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:40.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:40.512][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:40.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:40.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:40.516][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:40.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:40.518][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:40.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:40.520][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:40.522][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:40.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:40.524][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:40.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:40.526][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:40.527][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:40.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:40.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:40.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:40.531][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:40.533][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:40.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:40.535][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:40.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:40.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:40.538][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:40.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:40.540][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:40.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:40.543][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:40.544][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:40.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:40.546][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:40.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:40.548][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:40.549][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:40.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:40.552][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:40.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:40.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:40.555][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-08-09 16:03:40.559][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-08-09 16:03:40.561][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-08-09 16:03:40.562][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-08-09 16:03:40.564][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-09 16:03:40.566][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-08-09 16:03:40.567][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-08-09 16:03:40.569][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-08-09 16:03:40.570][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-08-09 16:03:40.572][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-08-09 16:03:40.574][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-09 16:03:40.575][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-08-09 16:03:40.577][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-08-09 16:03:40.578][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-08-09 16:03:40.580][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-08-09 16:03:40.581][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-08-09 16:03:40.583][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-08-09 16:03:40.585][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-08-09 16:03:40.586][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-09 16:03:40.588][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-08-09 16:03:40.590][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-08-09 16:03:40.591][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-08-09 16:03:40.593][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-08-09 16:03:40.594][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-08-09 16:03:40.596][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-08-09 16:03:40.598][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-08-09 16:03:40.599][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-08-09 16:03:40.601][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-08-09 16:03:40.602][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-08-09 16:03:40.604][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-08-09 16:03:40.606][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-08-09 16:03:40.607][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-08-09 16:03:40.609][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-08-09 16:03:40.610][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-08-09 16:03:40.612][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-08-09 16:03:40.614][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-08-09 16:03:40.615][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-08-09 16:03:40.617][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-08-09 16:03:40.619][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-08-09 16:03:40.620][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-08-09 16:03:40.627][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-08-09 16:03:40.629][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-08-09 16:03:40.631][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-08-09 16:03:40.632][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-08-09 16:03:40.634][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-08-09 16:03:40.635][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-08-09 16:03:40.637][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-08-09 16:03:40.639][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-08-09 16:03:40.640][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-08-09 16:03:40.642][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-08-09 16:03:40.643][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-08-09 16:03:40.645][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-08-09 16:03:40.647][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-08-09 16:03:40.648][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-08-09 16:03:40.650][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-08-09 16:03:40.652][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-08-09 16:03:40.653][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-08-09 16:03:40.655][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-08-09 16:03:40.656][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-08-09 16:03:40.658][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-08-09 16:03:40.660][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-08-09 16:03:40.661][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-08-09 16:03:40.663][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-08-09 16:03:40.664][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-08-09 16:03:40.666][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-08-09 16:03:40.668][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-08-09 16:03:40.669][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-09 16:03:40.671][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-09 16:03:40.672][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-08-09 16:03:40.674][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-08-09 16:03:40.675][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-08-09 16:03:40.677][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-08-09 16:03:40.679][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-08-09 16:03:40.680][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-08-09 16:03:40.682][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-08-09 16:03:40.683][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-08-09 16:03:40.685][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-08-09 16:03:40.687][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-08-09 16:03:40.688][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-08-09 16:03:40.690][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-08-09 16:03:40.691][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-08-09 16:03:40.693][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-08-09 16:03:40.695][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-08-09 16:03:40.734][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-08-09 16:03:40.737][initialize] This is biodb version 1.17.1.
biodb.DEBUG[2025-08-09 16:03:40.740][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-09 16:03:40.741][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:40.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:40.744][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:40.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:40.749][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:40.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:40.751][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:40.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:40.753][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:40.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:40.756][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:40.757][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:40.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:40.759][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:40.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:40.761][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:40.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:40.763][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:40.764][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:40.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:40.766][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:40.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:40.768][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:40.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:40.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:40.772][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:40.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:40.774][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:40.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:40.776][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:40.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:40.778][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:40.779][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:40.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:40.781][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:40.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:40.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:40.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:40.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:40.787][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:40.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:40.789][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:40.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:40.791][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:40.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:40.793][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:40.794][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:40.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:40.796][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:40.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:40.799][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:40.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:40.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:40.802][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:40.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:40.804][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:40.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:40.806][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:40.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:40.808][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:40.809][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:40.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:40.812][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:40.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:40.814][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:40.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:40.816][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:40.817][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:40.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:40.819][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:40.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:40.821][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:40.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:40.824][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:40.825][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:40.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:40.827][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:40.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:40.829][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:40.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:40.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:40.832][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:40.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:40.835][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:40.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:40.837][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:40.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:40.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:40.840][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:40.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:40.842][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:40.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:40.844][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:40.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:40.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:40.852][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:40.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:40.854][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:40.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:40.857][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:40.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:40.859][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:40.860][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:40.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:40.862][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:40.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:40.864][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:40.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:40.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:40.867][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:40.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:40.869][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:40.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:40.872][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:40.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:40.874][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:40.877][bdb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2025-08-09 16:03:40.887][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2025-08-09 16:03:40.889][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:40.890][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2025-08-09 16:03:40.891][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:40.892][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-09 16:03:40.893][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:40.895][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-09 16:03:40.896][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:40.897][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-09 16:03:40.898][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2025-08-09 16:03:40.899][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-09 16:03:40.900][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:40.902][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2025-08-09 16:03:40.903][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-09 16:03:40.904][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2025-08-09 16:03:40.904][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2025-08-09 16:03:40.905][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:40.906][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:40.908][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-08-09 16:03:40.909][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:40.910][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:40.911][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-09 16:03:40.912][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:40.913][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:40.914][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-09 16:03:40.916][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-08-09 16:03:40.916][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2025-08-09 16:03:40.917][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-09 16:03:40.918][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-09 16:03:40.919][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:40.920][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:40.922][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2025-08-09 16:03:40.924][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:40.925][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2025-08-09 16:03:40.926][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:40.927][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-09 16:03:40.928][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:40.930][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-09 16:03:40.931][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:40.932][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-09 16:03:40.933][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-08-09 16:03:40.934][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-09 16:03:40.936][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:40.937][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2025-08-09 16:03:40.938][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-09 16:03:40.939][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2025-08-09 16:03:40.939][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2025-08-09 16:03:40.939][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2025-08-09 16:03:40.939][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2025-08-09 16:03:40.939][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2025-08-09 16:03:40.939][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2025-08-09 16:03:40.940][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:40.942][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-09 16:03:40.943][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-08-09 16:03:40.944][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:40.945][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:40.946][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-09 16:03:40.947][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:40.948][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:40.950][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-09 16:03:40.951][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-08-09 16:03:40.951][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-08-09 16:03:40.952][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-09 16:03:40.953][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-09 16:03:40.954][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:40.955][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:40.957][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2025-08-09 16:03:40.959][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:40.960][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2025-08-09 16:03:40.961][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:40.962][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-09 16:03:40.964][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:40.965][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-09 16:03:40.966][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:40.967][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-09 16:03:40.968][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-08-09 16:03:40.969][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-09 16:03:40.971][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:40.972][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2025-08-09 16:03:40.973][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-09 16:03:40.974][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-08-09 16:03:40.974][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-08-09 16:03:40.974][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='CAS-like Style']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-08-09 16:03:40.974][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-08-09 16:03:40.974][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-08-09 16:03:40.974][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-08-09 16:03:40.974][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-08-09 16:03:40.974][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-08-09 16:03:40.974][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-08-09 16:03:40.974][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-08-09 16:03:40.974][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2025-08-09 16:03:40.974][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-08-09 16:03:40.974][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-08-09 16:03:40.974][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-08-09 16:03:40.976][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:40.977][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-09 16:03:40.977][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-09 16:03:40.977][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-09 16:03:40.978][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-08-09 16:03:40.979][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:40.980][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:40.982][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-09 16:03:40.983][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:40.984][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:40.985][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-09 16:03:40.986][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-08-09 16:03:40.986][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-08-09 16:03:40.986][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-08-09 16:03:40.987][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-09 16:03:40.988][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-09 16:03:40.989][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:40.991][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-08-09 16:03:40.992][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2025-08-09 16:03:40.994][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:40.995][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2025-08-09 16:03:40.997][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:40.998][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-09 16:03:40.999][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:41.000][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-09 16:03:41.001][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:41.002][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-09 16:03:41.004][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-08-09 16:03:41.005][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-09 16:03:41.006][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:41.007][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2025-08-09 16:03:41.008][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-09 16:03:41.010][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2025-08-09 16:03:41.010][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-08-09 16:03:41.011][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:41.012][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:41.013][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-08-09 16:03:41.014][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:41.015][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:41.017][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-09 16:03:41.018][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:41.019][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:41.020][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-09 16:03:41.021][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-08-09 16:03:41.021][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-08-09 16:03:41.021][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-08-09 16:03:41.022][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-09 16:03:41.023][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-09 16:03:41.025][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:41.026][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-08-09 16:03:41.031][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2025-08-09 16:03:41.033][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-08-09 16:03:41.035][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-08-09 16:03:41.041][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2025-08-09 16:03:41.043][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-08-09 16:03:41.044][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2025-08-09 16:03:41.064][initialize] Initialize connector ncbi.ccds.
biodb.DEBUG[2025-08-09 16:03:41.091][bdb$getFactory()$createConn] Creating new connector ncbi.ccds for database class ncbi.ccds .
biodb.INFO [2025-08-09 16:03:41.101][biodb::testThat]
biodb.INFO [2025-08-09 16:03:41.102][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2025-08-09 16:03:41.103][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-09 16:03:41.104][biodb::testThat]
biodb.TRACE[2025-08-09 16:03:41.110][loadFileContents] Loaded 1 files from cache: [1]: "F:/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.ccds-CCDS12227.1-content.html".
biodb.DEBUG[2025-08-09 16:03:41.112][biodb$getFactory()$createEntryFromCo ...] Creating NCBI CCDS entries from 1 content(s).
biodb.DEBUG[2025-08-09 16:03:41.116][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI CCDS entries.
biodb.DEBUG[2025-08-09 16:03:41.122][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-09 16:03:41.124][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:41.125][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:41.140][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:41.142][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:41.143][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:41.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-09 16:03:41.171][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:41.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:41.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.176][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-08-09 16:03:41.187][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-08-09 16:03:41.189][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.190][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.213][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-08-09 16:03:41.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-08-09 16:03:41.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.219][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-08-09 16:03:41.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-08-09 16:03:41.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.224][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-08-09 16:03:41.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-08-09 16:03:41.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.229][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:41.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:41.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.234][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-08-09 16:03:41.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-08-09 16:03:41.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.238][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:41.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:41.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.255][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:41.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:41.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.260][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:41.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:41.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.292][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:41.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:41.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.297][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:41.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:41.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.302][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:41.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:41.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-09 16:03:41.307][biodb$getFactory()$createEntryFromCo ...] Accession numbers: CCDS12227.1.
biodb.TRACE[2025-08-09 16:03:41.310][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-08-09 16:03:41.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-08-09 16:03:41.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.315][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-08-09 16:03:41.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-08-09 16:03:41.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.338][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-09 16:03:41.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-09 16:03:41.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.343][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-09 16:03:41.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-09 16:03:41.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.348][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-08-09 16:03:41.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-08-09 16:03:41.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.353][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-08-09 16:03:41.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-08-09 16:03:41.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.359][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:41.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:41.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.382][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-08-09 16:03:41.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-08-09 16:03:41.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.393][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:41.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:41.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.398][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:41.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:41.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.403][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:41.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:41.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.410][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:41.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:41.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.415][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:41.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:41.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.419][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:41.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:41.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.424][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-08-09 16:03:41.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-08-09 16:03:41.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.429][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-08-09 16:03:41.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-08-09 16:03:41.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.434][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-08-09 16:03:41.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-08-09 16:03:41.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.447][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:41.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:41.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.452][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:41.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:41.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.457][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:41.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:41.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.462][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:41.463][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:41.464][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.465][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.466][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:41.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:41.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.481][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-08-09 16:03:41.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-08-09 16:03:41.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.486][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-08-09 16:03:41.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-08-09 16:03:41.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.491][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-08-09 16:03:41.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-08-09 16:03:41.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.495][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-08-09 16:03:41.497][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-08-09 16:03:41.498][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.499][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.500][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-08-09 16:03:41.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-08-09 16:03:41.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.514][ef$get] Asked field names are: aa.seq.
biodb.TRACE[2025-08-09 16:03:41.516][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-08-09 16:03:41.517][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.518][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.524][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:41.525][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:41.527][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.528][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.586][loadFileContents] Loaded 1 files from cache: [1]: "F:/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.ccds-CCDS43240.1-content.html".
biodb.DEBUG[2025-08-09 16:03:41.615][biodb$getFactory()$createEntryFromCo ...] Creating NCBI CCDS entries from 1 content(s).
biodb.DEBUG[2025-08-09 16:03:41.617][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI CCDS entries.
biodb.DEBUG[2025-08-09 16:03:41.619][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-09 16:03:41.620][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:41.621][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:41.628][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:41.629][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:41.630][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:41.631][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-09 16:03:41.645][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:41.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:41.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.664][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-08-09 16:03:41.666][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-08-09 16:03:41.667][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.668][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.670][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-08-09 16:03:41.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-08-09 16:03:41.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.675][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-08-09 16:03:41.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-08-09 16:03:41.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.680][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-08-09 16:03:41.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-08-09 16:03:41.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.684][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:41.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:41.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.694][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-08-09 16:03:41.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-08-09 16:03:41.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.699][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:41.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:41.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.704][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:41.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:41.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.709][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:41.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:41.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.714][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:41.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:41.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.719][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:41.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:41.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.724][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:41.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:41.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-09 16:03:41.729][biodb$getFactory()$createEntryFromCo ...] Accession numbers: CCDS43240.1.
biodb.TRACE[2025-08-09 16:03:41.747][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-08-09 16:03:41.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-08-09 16:03:41.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.752][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-08-09 16:03:41.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-08-09 16:03:41.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.757][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-09 16:03:41.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-09 16:03:41.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.761][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-09 16:03:41.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-09 16:03:41.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.766][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-08-09 16:03:41.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-08-09 16:03:41.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.771][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-08-09 16:03:41.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-08-09 16:03:41.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.777][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:41.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:41.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.787][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-08-09 16:03:41.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-08-09 16:03:41.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.797][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:41.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:41.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.802][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:41.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:41.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.807][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:41.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:41.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.814][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:41.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:41.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.819][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:41.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:41.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.823][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:41.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:41.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.828][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-08-09 16:03:41.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-08-09 16:03:41.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.833][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-08-09 16:03:41.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-08-09 16:03:41.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.843][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-08-09 16:03:41.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-08-09 16:03:41.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.865][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:41.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:41.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.870][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:41.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:41.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.875][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:41.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:41.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.880][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:41.881][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:41.882][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.884][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.885][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:41.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:41.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.899][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-08-09 16:03:41.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-08-09 16:03:41.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.904][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-08-09 16:03:41.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-08-09 16:03:41.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.909][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-08-09 16:03:41.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-08-09 16:03:41.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.914][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-08-09 16:03:41.915][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-08-09 16:03:41.916][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.917][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.919][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-08-09 16:03:41.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-08-09 16:03:41.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.933][ef$get] Asked field names are: aa.seq.
biodb.TRACE[2025-08-09 16:03:41.934][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-08-09 16:03:41.935][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.937][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:41.943][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:41.944][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:41.945][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:41.947][ef$get] fields variable is a list.
biodb.INFO [2025-08-09 16:03:41.958][biodb::testThat]
biodb.INFO [2025-08-09 16:03:41.959][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-08-09 16:03:41.961][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-09 16:03:41.962][biodb::testThat]
biodb.DEBUG[2025-08-09 16:03:41.965][private$loadEntries] Creating entries from ids [2]: "CCDS12227.1, CCDS43240.1".
biodb.DEBUG[2025-08-09 16:03:41.984][conn$getEntryContent] Get NCBI CCDS entry content(s) for 2 id(s)...
fscache.INFO [2025-08-09 16:03:41.988][cch$loadContents] Load 2 contents, from C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704.
biodb.DEBUG[2025-08-09 16:03:41.990][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2025-08-09 16:03:41.991][conn$getEntryContent] 2 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-08-09 16:03:41.992][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-09 16:03:41.994][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-08-09 16:03:42.042][biodb::testThat]
biodb.INFO [2025-08-09 16:03:42.043][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2025-08-09 16:03:42.044][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-09 16:03:42.046][biodb::testThat]
biodb.INFO [2025-08-09 16:03:42.054][biodb::testThat]
biodb.INFO [2025-08-09 16:03:42.055][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2025-08-09 16:03:42.056][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-09 16:03:42.058][biodb::testThat]
biodb.WARN [2025-08-09 16:03:42.075][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-08-09 16:03:42.091][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-08-09 16:03:42.103][biodb::testThat]
biodb.INFO [2025-08-09 16:03:42.104][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2025-08-09 16:03:42.105][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-09 16:03:42.106][biodb::testThat]
biodb.DEBUG[2025-08-09 16:03:42.122][private$loadEntries] Creating entries from ids [1]: "CCDS12227.1".
biodb.DEBUG[2025-08-09 16:03:42.168][conn$getEntryContent] Get NCBI CCDS entry content(s) for 1 id(s)...
fscache.INFO [2025-08-09 16:03:42.193][cch$loadContents] Load 1 contents, from C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704.
biodb.DEBUG[2025-08-09 16:03:42.195][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2025-08-09 16:03:42.196][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-08-09 16:03:42.197][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-09 16:03:42.199][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-08-09 16:03:42.238][biodb::testThat]
biodb.INFO [2025-08-09 16:03:42.239][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-08-09 16:03:42.240][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-09 16:03:42.241][biodb::testThat]
biodb.INFO [2025-08-09 16:03:42.257][biodb::testThat]
biodb.INFO [2025-08-09 16:03:42.259][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-08-09 16:03:42.260][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-09 16:03:42.261][biodb::testThat]
biodb.INFO [2025-08-09 16:03:42.271][biodb::testThat]
biodb.INFO [2025-08-09 16:03:42.272][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2025-08-09 16:03:42.274][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-09 16:03:42.275][biodb::testThat]
biodb.INFO [2025-08-09 16:03:42.290][biodb::testThat]
biodb.INFO [2025-08-09 16:03:42.291][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2025-08-09 16:03:42.293][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-09 16:03:42.294][biodb::testThat]
biodb.INFO [2025-08-09 16:03:42.302][bdb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-08-09 16:03:42.303][self$deleteConn] Connector "ncbi.ccds" deleted.
biodb.DEBUG[2025-08-09 16:03:42.304][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-08-09 16:03:42.306][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:42.307][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:42.308][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:42.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:42.310][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:42.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-08-09 16:03:42.321][biodb::testContext]
biodb.INFO [2025-08-09 16:03:42.323][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-09 16:03:42.324][biodb::testContext] Test context - Gene long tests
biodb.INFO [2025-08-09 16:03:42.325][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-09 16:03:42.326][biodb::testContext]
biodb.INFO [2025-08-09 16:03:42.329][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.1.
biodb.DEBUG[2025-08-09 16:03:42.331][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.22-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2025-08-09 16:03:42.336][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-09 16:03:42.338][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-08-09 16:03:42.339][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-08-09 16:03:42.340][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:42.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:42.342][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:42.343][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-08-09 16:03:42.345][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-08-09 16:03:42.346][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:42.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:42.348][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:42.349][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-08-09 16:03:42.350][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-08-09 16:03:42.351][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:42.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:42.354][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:42.355][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-08-09 16:03:42.356][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-08-09 16:03:42.357][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-08-09 16:03:42.358][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:42.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:42.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:42.362][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-08-09 16:03:42.363][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-08-09 16:03:42.364][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-08-09 16:03:42.365][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:42.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:42.373][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:42.374][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-08-09 16:03:42.375][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-08-09 16:03:42.376][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:42.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:42.378][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:42.380][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-08-09 16:03:42.381][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-08-09 16:03:42.382][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-08-09 16:03:42.383][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:42.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:42.385][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:42.387][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-08-09 16:03:42.388][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-08-09 16:03:42.389][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:42.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:42.391][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:42.392][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-08-09 16:03:42.394][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-08-09 16:03:42.395][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-08-09 16:03:42.396][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:42.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:42.398][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:42.399][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-08-09 16:03:42.400][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-08-09 16:03:42.402][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-08-09 16:03:42.403][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-08-09 16:03:42.404][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-08-09 16:03:42.405][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-08-09 16:03:42.406][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:42.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:42.409][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:42.410][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-08-09 16:03:42.411][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-08-09 16:03:42.412][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:42.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:42.414][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:42.415][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-08-09 16:03:42.417][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-08-09 16:03:42.418][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:42.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:42.420][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:42.421][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-08-09 16:03:42.422][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-08-09 16:03:42.423][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:42.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:42.426][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:42.427][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-08-09 16:03:42.428][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-08-09 16:03:42.429][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-08-09 16:03:42.430][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:42.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:42.432][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:42.434][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-08-09 16:03:42.435][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-08-09 16:03:42.438][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-08-09 16:03:42.439][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:42.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:42.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:42.443][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-08-09 16:03:42.444][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-08-09 16:03:42.445][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-08-09 16:03:42.446][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:42.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:42.449][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:42.450][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-08-09 16:03:42.452][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:42.466][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-08-09 16:03:42.467][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:42.468][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-09 16:03:42.470][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:42.471][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-09 16:03:42.472][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:42.473][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-09 16:03:42.474][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-09 16:03:42.476][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-09 16:03:42.477][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:42.478][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-08-09 16:03:42.479][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-09 16:03:42.481][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:42.482][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:42.483][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-09 16:03:42.483][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-09 16:03:42.483][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-09 16:03:42.483][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-09 16:03:42.483][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-09 16:03:42.484][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-09 16:03:42.485][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:42.487][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:42.488][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-09 16:03:42.489][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:42.490][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:42.491][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-09 16:03:42.492][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:42.494][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-09 16:03:42.495][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-09 16:03:42.496][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:42.497][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:42.499][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-08-09 16:03:42.501][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:42.502][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-08-09 16:03:42.503][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:42.504][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-09 16:03:42.506][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:42.512][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-09 16:03:42.513][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:42.514][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-09 16:03:42.515][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-09 16:03:42.516][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-09 16:03:42.518][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:42.519][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-08-09 16:03:42.520][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-09 16:03:42.521][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:42.523][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:42.524][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-09 16:03:42.524][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-09 16:03:42.524][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-09 16:03:42.524][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-09 16:03:42.524][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-09 16:03:42.525][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-09 16:03:42.526][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:42.527][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:42.529][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-09 16:03:42.530][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:42.531][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:42.532][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-09 16:03:42.533][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:42.535][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-09 16:03:42.536][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-09 16:03:42.537][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:42.538][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:42.539][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-08-09 16:03:42.541][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:42.543][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-08-09 16:03:42.544][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:42.545][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-09 16:03:42.546][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:42.547][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-09 16:03:42.549][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:42.550][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-09 16:03:42.551][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-09 16:03:42.552][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-09 16:03:42.554][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:42.555][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-08-09 16:03:42.556][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-09 16:03:42.557][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:42.558][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:42.560][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:42.561][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-09 16:03:42.562][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:42.563][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:42.564][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-09 16:03:42.565][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:42.567][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:42.568][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-09 16:03:42.569][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:42.570][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-09 16:03:42.571][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-09 16:03:42.572][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:42.574][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:42.575][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-08-09 16:03:42.577][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:42.578][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-08-09 16:03:42.579][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:42.581][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-09 16:03:42.582][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:42.583][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-09 16:03:42.584][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:42.585][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-09 16:03:42.587][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-09 16:03:42.588][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-09 16:03:42.589][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:42.590][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-08-09 16:03:42.591][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-09 16:03:42.593][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:42.594][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:42.595][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:42.596][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-09 16:03:42.598][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:42.599][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:42.600][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-09 16:03:42.601][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:42.602][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:42.603][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-09 16:03:42.605][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:42.606][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-09 16:03:42.607][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-09 16:03:42.608][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:42.609][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:42.611][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-09 16:03:42.612][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:42.613][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:42.614][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:42.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:42.616][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:42.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:42.618][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[2025-08-09 16:03:42.620][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:42.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:42.622][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:42.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:42.624][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:42.625][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:42.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:42.627][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:42.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:42.629][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:42.631][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:42.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:42.633][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:42.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:42.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:42.636][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:42.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:42.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:42.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:42.641][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[2025-08-09 16:03:42.642][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:42.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:42.644][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:42.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:42.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:42.647][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:42.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:42.650][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:42.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:42.652][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:42.657][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:42.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:42.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:42.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:42.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:42.663][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:42.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:42.665][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:42.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:42.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:42.669][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:42.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:42.671][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:42.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:42.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:42.674][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:42.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:42.677][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:42.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:42.679][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[2025-08-09 16:03:42.680][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:42.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:42.682][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:42.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:42.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:42.685][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:42.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:42.688][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:42.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:42.690][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:42.691][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:42.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:42.693][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:42.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:42.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:42.697][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:42.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:42.699][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:42.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:42.701][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:42.702][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:42.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:42.705][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:42.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:42.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:42.708][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-08-09 16:03:42.710][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-08-09 16:03:42.711][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-08-09 16:03:42.713][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-08-09 16:03:42.715][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-09 16:03:42.716][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-08-09 16:03:42.718][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-08-09 16:03:42.719][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-08-09 16:03:42.721][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-08-09 16:03:42.722][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-08-09 16:03:42.724][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-09 16:03:42.725][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-08-09 16:03:42.727][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-08-09 16:03:42.729][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-08-09 16:03:42.730][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-08-09 16:03:42.732][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-08-09 16:03:42.733][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-08-09 16:03:42.735][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-08-09 16:03:42.736][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-09 16:03:42.738][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-08-09 16:03:42.740][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-08-09 16:03:42.741][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-08-09 16:03:42.743][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-08-09 16:03:42.744][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-08-09 16:03:42.746][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-08-09 16:03:42.747][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-08-09 16:03:42.749][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-08-09 16:03:42.750][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-08-09 16:03:42.752][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-08-09 16:03:42.754][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-08-09 16:03:42.755][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-08-09 16:03:42.757][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-08-09 16:03:42.758][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-08-09 16:03:42.760][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-08-09 16:03:42.761][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-08-09 16:03:42.763][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-08-09 16:03:42.764][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-08-09 16:03:42.766][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-08-09 16:03:42.768][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-08-09 16:03:42.769][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-08-09 16:03:42.771][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-08-09 16:03:42.772][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-08-09 16:03:42.774][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-08-09 16:03:42.776][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-08-09 16:03:42.777][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-08-09 16:03:42.779][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-08-09 16:03:42.780][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-08-09 16:03:42.782][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-08-09 16:03:42.783][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-08-09 16:03:42.785][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-08-09 16:03:42.787][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-08-09 16:03:42.788][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-08-09 16:03:42.790][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-08-09 16:03:42.796][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-08-09 16:03:42.798][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-08-09 16:03:42.800][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-08-09 16:03:42.801][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-08-09 16:03:42.803][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-08-09 16:03:42.804][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-08-09 16:03:42.806][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-08-09 16:03:42.808][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-08-09 16:03:42.809][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-08-09 16:03:42.811][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-08-09 16:03:42.812][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-08-09 16:03:42.814][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-08-09 16:03:42.815][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-08-09 16:03:42.817][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-09 16:03:42.819][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-09 16:03:42.820][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-08-09 16:03:42.822][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-08-09 16:03:42.823][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-08-09 16:03:42.825][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-08-09 16:03:42.826][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-08-09 16:03:42.828][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-08-09 16:03:42.830][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-08-09 16:03:42.831][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-08-09 16:03:42.833][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-08-09 16:03:42.834][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-08-09 16:03:42.836][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-08-09 16:03:42.838][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-08-09 16:03:42.839][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-08-09 16:03:42.841][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-08-09 16:03:42.842][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-08-09 16:03:42.844][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-08-09 16:03:42.846][initialize] This is biodb version 1.17.1.
biodb.DEBUG[2025-08-09 16:03:42.847][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-09 16:03:42.848][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:42.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:42.851][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:42.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:42.853][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:42.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:42.855][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:42.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:42.857][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:42.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:42.859][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:42.860][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:42.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:42.863][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:42.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:42.865][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:42.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:42.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:42.868][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:42.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:42.870][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:42.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:42.872][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:42.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:42.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:42.876][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:42.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:42.878][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:42.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:42.880][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:42.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:42.882][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:42.883][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:42.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:42.885][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:42.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:42.887][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:42.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:42.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:42.891][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:42.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:42.893][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:42.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:42.895][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:42.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:42.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:42.898][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:42.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:42.900][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:42.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:42.903][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:42.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:42.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:42.906][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:42.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:42.908][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:42.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:42.910][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:42.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:42.912][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[2025-08-09 16:03:42.913][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:42.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:42.916][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:42.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:42.918][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:42.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:42.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:42.921][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:42.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:42.923][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:42.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:42.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:42.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:42.928][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:42.929][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:42.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:42.931][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:42.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:42.938][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:42.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:42.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:42.941][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:42.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:42.944][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:42.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:42.946][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:42.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:42.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:42.949][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:42.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:42.951][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:42.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:42.954][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:42.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:42.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:42.957][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:42.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:42.959][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:42.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:42.961][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:42.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:42.963][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:42.964][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:42.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:42.967][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:42.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:42.969][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:42.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:42.971][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:42.972][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:42.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:42.974][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:42.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:42.976][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:42.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:42.979][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:42.982][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2025-08-09 16:03:42.984][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2025-08-09 16:03:42.986][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:42.987][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2025-08-09 16:03:42.989][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:42.990][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-09 16:03:42.991][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:42.992][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-09 16:03:42.993][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:42.995][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-09 16:03:42.997][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2025-08-09 16:03:42.998][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-09 16:03:42.999][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:43.000][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2025-08-09 16:03:43.002][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-09 16:03:43.003][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2025-08-09 16:03:43.003][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2025-08-09 16:03:43.004][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:43.005][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:43.006][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-08-09 16:03:43.008][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:43.009][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:43.010][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-09 16:03:43.011][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:43.012][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:43.013][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-09 16:03:43.015][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-08-09 16:03:43.015][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2025-08-09 16:03:43.016][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-09 16:03:43.017][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-09 16:03:43.018][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:43.019][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:43.021][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2025-08-09 16:03:43.023][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:43.024][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2025-08-09 16:03:43.025][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:43.026][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-09 16:03:43.028][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:43.029][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-09 16:03:43.030][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:43.031][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-09 16:03:43.033][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-08-09 16:03:43.034][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-09 16:03:43.035][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:43.036][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2025-08-09 16:03:43.037][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-09 16:03:43.039][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2025-08-09 16:03:43.039][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2025-08-09 16:03:43.039][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2025-08-09 16:03:43.039][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2025-08-09 16:03:43.039][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2025-08-09 16:03:43.039][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2025-08-09 16:03:43.040][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:43.041][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-09 16:03:43.042][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-08-09 16:03:43.043][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:43.045][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:43.046][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-09 16:03:43.047][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:43.048][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:43.049][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-09 16:03:43.050][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-08-09 16:03:43.050][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-08-09 16:03:43.052][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-09 16:03:43.053][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-09 16:03:43.054][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:43.055][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:43.057][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2025-08-09 16:03:43.059][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:43.060][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2025-08-09 16:03:43.061][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:43.062][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-09 16:03:43.064][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:43.065][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-09 16:03:43.066][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:43.067][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-09 16:03:43.069][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-08-09 16:03:43.070][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-09 16:03:43.071][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:43.072][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2025-08-09 16:03:43.073][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-09 16:03:43.075][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-08-09 16:03:43.075][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-08-09 16:03:43.075][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='CAS-like Style']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-08-09 16:03:43.075][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-08-09 16:03:43.075][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-08-09 16:03:43.075][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-08-09 16:03:43.075][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-08-09 16:03:43.075][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-08-09 16:03:43.075][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-08-09 16:03:43.075][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-08-09 16:03:43.075][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2025-08-09 16:03:43.075][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-08-09 16:03:43.075][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-08-09 16:03:43.075][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-08-09 16:03:43.076][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:43.077][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-09 16:03:43.077][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-09 16:03:43.077][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-09 16:03:43.083][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-08-09 16:03:43.085][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:43.086][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:43.087][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-09 16:03:43.088][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:43.089][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:43.090][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-09 16:03:43.092][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-08-09 16:03:43.092][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-08-09 16:03:43.092][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-08-09 16:03:43.093][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-09 16:03:43.094][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-09 16:03:43.095][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:43.096][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-08-09 16:03:43.098][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2025-08-09 16:03:43.100][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:43.101][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2025-08-09 16:03:43.102][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:43.104][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-09 16:03:43.105][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:43.106][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-09 16:03:43.107][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:43.109][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-09 16:03:43.110][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-08-09 16:03:43.111][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-09 16:03:43.112][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:43.113][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2025-08-09 16:03:43.115][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-09 16:03:43.116][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2025-08-09 16:03:43.116][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-08-09 16:03:43.117][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:43.118][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:43.119][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-08-09 16:03:43.121][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:43.122][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:43.123][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-09 16:03:43.124][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:43.125][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:43.126][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-09 16:03:43.127][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-08-09 16:03:43.127][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-08-09 16:03:43.127][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-08-09 16:03:43.129][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-09 16:03:43.130][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-09 16:03:43.131][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:43.132][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-08-09 16:03:43.134][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2025-08-09 16:03:43.135][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-08-09 16:03:43.137][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-08-09 16:03:43.139][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2025-08-09 16:03:43.140][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-08-09 16:03:43.142][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2025-08-09 16:03:43.149][super$initialize] Initialize connector ncbi.gene.
biodb.DEBUG[2025-08-09 16:03:43.246][biodb$getFactory()$createConn] Creating new connector ncbi.gene for database class ncbi.gene .
biodb.INFO [2025-08-09 16:03:43.252][biodb::testThat]
biodb.INFO [2025-08-09 16:03:43.253][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2025-08-09 16:03:43.254][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-09 16:03:43.255][biodb::testThat]
biodb.TRACE[2025-08-09 16:03:43.269][loadFileContents] Loaded 1 files from cache: [1]: "F:/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.gene-2833-content.xml".
biodb.DEBUG[2025-08-09 16:03:43.270][biodb$getFactory()$createEntryFromCo ...] Creating NCBI Gene entries from 1 content(s).
biodb.DEBUG[2025-08-09 16:03:43.274][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI Gene entries.
biodb.DEBUG[2025-08-09 16:03:43.276][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-09 16:03:43.277][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:43.278][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:43.284][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:43.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:43.287][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:43.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-09 16:03:43.301][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:43.302][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:43.304][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:43.305][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:43.307][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:43.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:43.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:43.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:43.312][ef$get] Asked field names are: description.
biodb.TRACE[2025-08-09 16:03:43.313][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-08-09 16:03:43.314][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:43.316][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:43.318][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-08-09 16:03:43.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-08-09 16:03:43.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:43.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:43.323][ef$get] Asked field names are: location.
biodb.TRACE[2025-08-09 16:03:43.324][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-08-09 16:03:43.325][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:43.326][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:43.329][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-08-09 16:03:43.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-08-09 16:03:43.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:43.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:43.334][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-08-09 16:03:43.335][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-08-09 16:03:43.336][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:43.337][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:43.339][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-08-09 16:03:43.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-08-09 16:03:43.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:43.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:43.344][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-08-09 16:03:43.346][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-09 16:03:43.347][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:43.348][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:43.350][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-08-09 16:03:43.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-09 16:03:43.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:43.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:43.355][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-08-09 16:03:43.357][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-08-09 16:03:43.358][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:43.359][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:43.368][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-08-09 16:03:43.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-08-09 16:03:43.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:43.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:43.377][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-08-09 16:03:43.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-08-09 16:03:43.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:43.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:43.382][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-08-09 16:03:43.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-08-09 16:03:43.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:43.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:43.387][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-08-09 16:03:43.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-08-09 16:03:43.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:43.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:43.392][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:43.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:43.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:43.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:43.396][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-08-09 16:03:43.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-08-09 16:03:43.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:43.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:43.401][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:43.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:43.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:43.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:43.406][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:43.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:43.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:43.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:43.411][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:43.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:43.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:43.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:43.416][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:43.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:43.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:43.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:43.421][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:43.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:43.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:43.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:43.426][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:43.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:43.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:43.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-09 16:03:43.431][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 2833.
biodb.TRACE[2025-08-09 16:03:43.433][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-08-09 16:03:43.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-08-09 16:03:43.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:43.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:43.438][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-08-09 16:03:43.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-08-09 16:03:43.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:43.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:43.443][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-08-09 16:03:43.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-08-09 16:03:43.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:43.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:43.448][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-08-09 16:03:43.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-08-09 16:03:43.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:43.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:43.453][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-08-09 16:03:43.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-08-09 16:03:43.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:43.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-09 16:03:43.458][private$computeField] Compute value for field "aa.seq".
biodb.DEBUG[2025-08-09 16:03:43.488][initialize] Initialize connector ncbi.ccds.
biodb.DEBUG[2025-08-09 16:03:43.501][self$createConn] Creating new connector ncbi.ccds for database class ncbi.ccds .
biodb.DEBUG[2025-08-09 16:03:43.503][private$loadEntries] Creating entries from ids [1]: "CCDS14416.1".
biodb.DEBUG[2025-08-09 16:03:43.523][conn$getEntryContent] Get NCBI CCDS entry content(s) for 1 id(s)...
fscache.INFO [2025-08-09 16:03:43.525][cch$loadContents] Load 1 contents, from C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704.
biodb.DEBUG[2025-08-09 16:03:43.526][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2025-08-09 16:03:43.527][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-08-09 16:03:43.529][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-09 16:03:43.530][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-08-09 16:03:43.546][biodb::testThat]
biodb.INFO [2025-08-09 16:03:43.547][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-08-09 16:03:43.548][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-09 16:03:43.549][biodb::testThat]
biodb.DEBUG[2025-08-09 16:03:43.552][private$loadEntries] Creating entries from ids [8]: "2833, 3002, 3627, 4316, 50943, 5551, 916, 9606".
biodb.DEBUG[2025-08-09 16:03:43.554][conn$getEntryContent] Get NCBI Gene entry content(s) for 8 id(s)...
fscache.INFO [2025-08-09 16:03:43.579][cch$loadContents] Load 8 contents, from C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2025-08-09 16:03:43.581][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2025-08-09 16:03:43.583][conn$getEntryContent] 8 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-08-09 16:03:43.584][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-09 16:03:43.585][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-08-09 16:03:43.586][private$retrieveContents] Get entry content(s) for 8 id(s)...
biodb.INFO [2025-08-09 16:03:43.611][biodb::testThat]
biodb.INFO [2025-08-09 16:03:43.612][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2025-08-09 16:03:43.614][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-09 16:03:43.615][biodb::testThat]
biodb.TRACE[2025-08-09 16:03:43.618][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-09 16:03:43.620][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-09 16:03:43.621][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:43.622][ef$get] fields variable is a list.
biodb.DEBUG[2025-08-09 16:03:43.624][function(conn, opt)] Testing searchForEntries() with entry "2833" and field "name".
biodb.DEBUG[2025-08-09 16:03:43.636][private$loadEntries] Creating entries from ids [1]: "2833".
biodb.DEBUG[2025-08-09 16:03:43.637][conn$getEntryContent] Get NCBI Gene entry content(s) for 1 id(s)...
fscache.INFO [2025-08-09 16:03:43.639][cch$loadContents] Load 1 contents, from C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2025-08-09 16:03:43.641][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2025-08-09 16:03:43.642][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-08-09 16:03:43.643][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-09 16:03:43.644][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-08-09 16:03:43.660][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.INFO [2025-08-09 16:03:43.691][biodb::testThat]
biodb.INFO [2025-08-09 16:03:43.692][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2025-08-09 16:03:43.693][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-09 16:03:43.695][biodb::testThat]
biodb.DEBUG[2025-08-09 16:03:43.712][private$loadEntries] Creating entries from ids [1]: "2833".
biodb.DEBUG[2025-08-09 16:03:43.714][conn$getEntryContent] Get NCBI Gene entry content(s) for 1 id(s)...
fscache.INFO [2025-08-09 16:03:43.716][cch$loadContents] Load 1 contents, from C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2025-08-09 16:03:43.717][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2025-08-09 16:03:43.718][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-08-09 16:03:43.719][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-09 16:03:43.721][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-08-09 16:03:43.722][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.INFO [2025-08-09 16:03:43.739][biodb::testThat]
biodb.INFO [2025-08-09 16:03:43.740][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2025-08-09 16:03:43.741][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-09 16:03:43.742][biodb::testThat]
biodb.DEBUG[2025-08-09 16:03:43.748][private$loadEntries] Creating entries from ids [1]: "2833".
biodb.DEBUG[2025-08-09 16:03:43.749][conn$getEntryContent] Get NCBI Gene entry content(s) for 1 id(s)...
fscache.INFO [2025-08-09 16:03:43.751][cch$loadContents] Load 1 contents, from C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2025-08-09 16:03:43.752][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2025-08-09 16:03:43.753][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-08-09 16:03:43.755][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-09 16:03:43.756][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-08-09 16:03:43.757][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.INFO [2025-08-09 16:03:43.776][biodb::testThat]
biodb.INFO [2025-08-09 16:03:43.777][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-08-09 16:03:43.779][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-09 16:03:43.780][biodb::testThat]
biodb.INFO [2025-08-09 16:03:43.796][biodb::testThat]
biodb.INFO [2025-08-09 16:03:43.798][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-08-09 16:03:43.799][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-09 16:03:43.800][biodb::testThat]
biodb.INFO [2025-08-09 16:03:43.811][biodb::testThat]
biodb.INFO [2025-08-09 16:03:43.812][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2025-08-09 16:03:43.813][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-09 16:03:43.814][biodb::testThat]
biodb.INFO [2025-08-09 16:03:43.831][biodb::testThat]
biodb.INFO [2025-08-09 16:03:43.832][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2025-08-09 16:03:43.838][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-09 16:03:43.840][biodb::testThat]
biodb.INFO [2025-08-09 16:03:43.848][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-08-09 16:03:43.850][self$deleteConn] Connector "ncbi.gene" deleted.
biodb.INFO [2025-08-09 16:03:43.851][self$deleteConn] Connector "ncbi.ccds" deleted.
biodb.DEBUG[2025-08-09 16:03:43.852][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-08-09 16:03:43.853][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:43.854][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:43.855][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:43.857][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:43.858][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:43.859][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-08-09 16:03:43.864][biodb::testContext]
biodb.INFO [2025-08-09 16:03:43.865][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-09 16:03:43.866][biodb::testContext] Test context - Pubchem comp long tests
biodb.INFO [2025-08-09 16:03:43.867][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-09 16:03:43.868][biodb::testContext]
biodb.INFO [2025-08-09 16:03:43.871][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.1.
biodb.DEBUG[2025-08-09 16:03:43.874][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.22-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2025-08-09 16:03:43.879][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-09 16:03:43.880][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-08-09 16:03:43.881][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-08-09 16:03:43.882][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:43.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:43.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:43.886][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-08-09 16:03:43.887][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-08-09 16:03:43.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:43.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:43.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:43.892][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-08-09 16:03:43.893][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-08-09 16:03:43.894][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:43.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:43.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:43.897][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-08-09 16:03:43.898][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-08-09 16:03:43.900][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-08-09 16:03:43.901][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:43.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:43.903][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:43.904][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-08-09 16:03:43.905][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-08-09 16:03:43.907][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-08-09 16:03:43.908][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:43.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:43.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:43.911][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-08-09 16:03:43.912][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-08-09 16:03:43.913][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:43.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:43.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:43.917][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-08-09 16:03:43.918][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-08-09 16:03:43.919][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-08-09 16:03:43.920][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:43.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:43.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:43.924][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-08-09 16:03:43.925][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-08-09 16:03:43.926][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:43.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:43.928][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:43.929][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-08-09 16:03:43.930][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-08-09 16:03:43.932][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-08-09 16:03:43.933][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:43.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:43.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:43.936][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-08-09 16:03:43.937][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-08-09 16:03:43.938][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-08-09 16:03:43.940][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-08-09 16:03:43.941][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-08-09 16:03:43.942][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-08-09 16:03:43.943][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:43.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:43.945][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:43.947][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-08-09 16:03:43.948][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-08-09 16:03:43.949][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:43.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:43.951][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:43.952][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-08-09 16:03:43.954][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-08-09 16:03:43.955][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:43.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:43.957][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:43.958][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-08-09 16:03:43.959][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-08-09 16:03:43.960][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:43.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:43.963][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:43.964][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-08-09 16:03:43.965][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-08-09 16:03:43.966][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-08-09 16:03:43.967][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:43.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:43.975][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:43.976][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-08-09 16:03:43.977][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-08-09 16:03:43.981][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-08-09 16:03:43.982][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:43.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:43.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:43.986][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-08-09 16:03:43.987][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-08-09 16:03:43.988][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-08-09 16:03:43.989][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:43.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:43.992][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:43.993][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-08-09 16:03:43.995][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:44.009][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-08-09 16:03:44.011][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:44.012][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-09 16:03:44.013][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:44.014][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-09 16:03:44.015][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:44.017][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-09 16:03:44.018][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-09 16:03:44.019][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-09 16:03:44.020][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:44.022][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-08-09 16:03:44.023][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-09 16:03:44.024][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:44.025][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:44.026][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-09 16:03:44.026][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-09 16:03:44.026][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-09 16:03:44.026][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-09 16:03:44.026][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-09 16:03:44.028][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-09 16:03:44.029][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:44.030][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:44.031][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-09 16:03:44.032][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:44.033][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:44.035][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-09 16:03:44.036][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:44.037][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-09 16:03:44.038][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-09 16:03:44.039][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:44.041][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:44.042][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-08-09 16:03:44.044][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:44.045][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-08-09 16:03:44.046][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:44.048][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-09 16:03:44.049][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:44.050][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-09 16:03:44.051][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:44.052][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-09 16:03:44.054][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-09 16:03:44.055][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-09 16:03:44.056][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:44.057][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-08-09 16:03:44.058][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-09 16:03:44.060][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:44.061][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:44.062][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-09 16:03:44.062][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-09 16:03:44.062][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-09 16:03:44.062][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-09 16:03:44.062][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-09 16:03:44.063][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-09 16:03:44.065][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:44.066][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:44.067][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-09 16:03:44.068][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:44.069][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:44.070][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-09 16:03:44.072][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:44.073][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-09 16:03:44.074][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-09 16:03:44.075][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:44.076][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:44.078][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-08-09 16:03:44.080][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:44.081][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-08-09 16:03:44.082][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:44.083][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-09 16:03:44.085][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:44.086][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-09 16:03:44.087][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:44.088][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-09 16:03:44.089][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-09 16:03:44.096][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-09 16:03:44.097][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:44.098][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-08-09 16:03:44.099][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-09 16:03:44.101][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:44.102][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:44.103][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:44.104][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-09 16:03:44.105][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:44.107][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:44.108][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-09 16:03:44.109][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:44.110][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:44.111][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-09 16:03:44.113][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:44.114][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-09 16:03:44.115][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-09 16:03:44.116][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:44.117][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:44.119][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-08-09 16:03:44.121][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:44.122][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-08-09 16:03:44.123][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:44.124][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-09 16:03:44.125][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:44.127][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-09 16:03:44.128][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:44.129][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-09 16:03:44.130][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-09 16:03:44.132][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-09 16:03:44.133][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:44.134][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-08-09 16:03:44.135][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-09 16:03:44.136][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:44.138][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:44.139][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:44.140][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-09 16:03:44.141][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:44.142][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:44.144][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-09 16:03:44.145][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:44.146][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:44.147][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-09 16:03:44.148][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:44.149][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-09 16:03:44.151][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-09 16:03:44.152][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:44.153][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:44.155][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-09 16:03:44.156][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:44.157][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:44.158][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:44.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:44.160][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:44.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:44.162][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:44.164][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:44.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:44.166][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:44.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:44.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:44.169][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:44.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:44.171][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:44.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:44.174][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[2025-08-09 16:03:44.175][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:44.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:44.177][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:44.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:44.179][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:44.180][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:44.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:44.182][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:44.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:44.185][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:44.186][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:44.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:44.188][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:44.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:44.190][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[2025-08-09 16:03:44.191][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:44.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:44.193][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:44.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:44.196][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:44.197][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:44.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:44.199][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:44.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:44.201][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:44.202][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:44.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:44.205][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:44.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:44.207][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:44.208][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:44.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:44.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:44.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:44.212][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:44.213][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:44.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:44.216][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:44.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:44.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:44.224][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:44.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:44.227][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:44.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:44.229][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:44.230][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:44.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:44.232][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:44.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:44.235][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[2025-08-09 16:03:44.236][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:44.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:44.238][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:44.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:44.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:44.241][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:44.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:44.244][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:44.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:44.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:44.247][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:44.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:44.249][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:44.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:44.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:44.253][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-08-09 16:03:44.254][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-08-09 16:03:44.256][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-08-09 16:03:44.258][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-08-09 16:03:44.259][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-09 16:03:44.261][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-08-09 16:03:44.263][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-08-09 16:03:44.264][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-08-09 16:03:44.266][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-08-09 16:03:44.267][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-08-09 16:03:44.269][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-09 16:03:44.270][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-08-09 16:03:44.272][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-08-09 16:03:44.274][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-08-09 16:03:44.275][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-08-09 16:03:44.277][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-08-09 16:03:44.278][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-08-09 16:03:44.280][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-08-09 16:03:44.282][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-09 16:03:44.283][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-08-09 16:03:44.285][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-08-09 16:03:44.286][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-08-09 16:03:44.288][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-08-09 16:03:44.289][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-08-09 16:03:44.291][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-08-09 16:03:44.293][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-08-09 16:03:44.294][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-08-09 16:03:44.296][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-08-09 16:03:44.297][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-08-09 16:03:44.299][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-08-09 16:03:44.300][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-08-09 16:03:44.302][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-08-09 16:03:44.304][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-08-09 16:03:44.305][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-08-09 16:03:44.307][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-08-09 16:03:44.308][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-08-09 16:03:44.310][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-08-09 16:03:44.311][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-08-09 16:03:44.313][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-08-09 16:03:44.315][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-08-09 16:03:44.316][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-08-09 16:03:44.318][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-08-09 16:03:44.319][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-08-09 16:03:44.321][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-08-09 16:03:44.322][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-08-09 16:03:44.324][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-08-09 16:03:44.326][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-08-09 16:03:44.327][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-08-09 16:03:44.329][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-08-09 16:03:44.330][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-08-09 16:03:44.332][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-08-09 16:03:44.334][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-08-09 16:03:44.335][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-08-09 16:03:44.337][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-08-09 16:03:44.338][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-08-09 16:03:44.360][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-08-09 16:03:44.362][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-08-09 16:03:44.364][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-08-09 16:03:44.365][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-08-09 16:03:44.367][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-08-09 16:03:44.368][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-08-09 16:03:44.370][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-08-09 16:03:44.372][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-08-09 16:03:44.373][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-08-09 16:03:44.375][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-08-09 16:03:44.376][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-08-09 16:03:44.378][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-09 16:03:44.379][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-09 16:03:44.381][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-08-09 16:03:44.383][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-08-09 16:03:44.384][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-08-09 16:03:44.386][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-08-09 16:03:44.387][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-08-09 16:03:44.389][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-08-09 16:03:44.391][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-08-09 16:03:44.392][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-08-09 16:03:44.394][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-08-09 16:03:44.395][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-08-09 16:03:44.397][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-08-09 16:03:44.398][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-08-09 16:03:44.400][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-08-09 16:03:44.402][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-08-09 16:03:44.403][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-08-09 16:03:44.405][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-08-09 16:03:44.407][initialize] This is biodb version 1.17.1.
biodb.DEBUG[2025-08-09 16:03:44.409][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-09 16:03:44.410][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:44.411][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:44.412][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:44.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:44.414][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:44.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:44.416][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:44.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:44.418][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:44.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:44.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:44.422][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:44.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:44.424][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:44.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:44.426][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:44.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:44.428][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:44.429][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:44.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:44.431][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:44.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:44.434][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:44.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:44.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:44.437][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:44.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:44.439][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:44.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:44.441][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:44.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:44.444][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:44.445][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:44.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:44.447][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:44.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:44.449][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:44.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:44.451][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:44.452][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:44.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:44.454][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:44.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:44.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:44.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:44.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:44.460][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:44.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:44.462][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:44.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:44.464][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:44.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:44.466][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:44.468][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:44.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:44.470][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:44.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:44.472][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:44.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:44.474][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:44.475][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:44.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:44.477][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:44.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:44.479][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:44.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:44.487][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:44.488][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:44.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:44.491][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:44.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:44.493][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:44.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:44.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:44.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:44.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:44.499][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:44.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:44.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:44.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:44.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:44.504][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:44.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:44.506][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:44.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:44.509][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:44.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:44.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:44.512][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:44.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:44.514][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:44.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:44.516][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:44.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:44.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:44.520][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:44.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:44.522][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:44.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:44.524][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:44.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:44.526][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:44.527][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:44.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:44.529][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:44.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:44.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:44.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:44.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:44.535][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:44.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:44.537][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:44.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:44.539][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:44.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:44.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:44.545][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2025-08-09 16:03:44.547][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2025-08-09 16:03:44.549][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:44.550][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2025-08-09 16:03:44.552][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:44.553][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-09 16:03:44.554][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:44.555][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-09 16:03:44.556][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:44.558][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-09 16:03:44.559][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2025-08-09 16:03:44.560][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-09 16:03:44.561][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:44.562][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2025-08-09 16:03:44.564][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-09 16:03:44.565][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2025-08-09 16:03:44.565][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2025-08-09 16:03:44.566][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:44.567][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:44.568][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-08-09 16:03:44.570][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:44.571][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:44.572][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-09 16:03:44.573][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:44.574][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:44.575][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-09 16:03:44.576][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-08-09 16:03:44.576][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2025-08-09 16:03:44.578][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-09 16:03:44.579][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-09 16:03:44.580][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:44.581][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:44.583][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2025-08-09 16:03:44.585][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:44.586][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2025-08-09 16:03:44.587][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:44.588][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-09 16:03:44.589][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:44.591][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-09 16:03:44.592][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:44.593][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-09 16:03:44.594][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-08-09 16:03:44.596][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-09 16:03:44.597][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:44.598][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2025-08-09 16:03:44.599][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-09 16:03:44.600][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2025-08-09 16:03:44.600][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2025-08-09 16:03:44.600][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2025-08-09 16:03:44.600][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2025-08-09 16:03:44.600][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2025-08-09 16:03:44.600][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2025-08-09 16:03:44.602][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:44.603][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-09 16:03:44.604][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-08-09 16:03:44.605][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:44.606][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:44.608][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-09 16:03:44.609][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:44.610][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:44.611][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-09 16:03:44.617][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-08-09 16:03:44.617][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-08-09 16:03:44.619][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-09 16:03:44.620][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-09 16:03:44.621][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:44.623][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:44.624][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2025-08-09 16:03:44.626][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:44.627][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2025-08-09 16:03:44.629][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:44.630][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-09 16:03:44.631][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:44.632][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-09 16:03:44.633][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:44.635][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-09 16:03:44.636][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-08-09 16:03:44.637][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-09 16:03:44.638][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:44.640][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2025-08-09 16:03:44.641][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-09 16:03:44.642][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-08-09 16:03:44.642][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-08-09 16:03:44.642][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='CAS-like Style']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-08-09 16:03:44.642][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-08-09 16:03:44.642][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-08-09 16:03:44.642][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-08-09 16:03:44.642][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-08-09 16:03:44.642][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-08-09 16:03:44.642][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-08-09 16:03:44.642][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-08-09 16:03:44.642][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2025-08-09 16:03:44.642][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-08-09 16:03:44.642][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-08-09 16:03:44.642][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-08-09 16:03:44.643][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:44.645][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-09 16:03:44.645][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-09 16:03:44.645][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-09 16:03:44.646][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-08-09 16:03:44.647][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:44.648][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:44.649][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-09 16:03:44.651][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:44.652][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:44.653][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-09 16:03:44.654][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-08-09 16:03:44.654][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-08-09 16:03:44.654][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-08-09 16:03:44.655][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-09 16:03:44.656][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-09 16:03:44.658][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:44.659][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-08-09 16:03:44.660][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2025-08-09 16:03:44.662][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:44.664][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2025-08-09 16:03:44.665][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:44.666][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-09 16:03:44.667][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:44.668][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-09 16:03:44.670][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:44.671][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-09 16:03:44.672][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-08-09 16:03:44.673][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-09 16:03:44.674][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:44.676][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2025-08-09 16:03:44.677][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-09 16:03:44.678][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2025-08-09 16:03:44.678][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-08-09 16:03:44.679][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:44.680][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:44.682][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-08-09 16:03:44.683][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:44.684][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:44.685][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-09 16:03:44.686][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:44.687][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:44.688][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-09 16:03:44.690][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-08-09 16:03:44.690][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-08-09 16:03:44.690][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-08-09 16:03:44.691][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-09 16:03:44.692][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-09 16:03:44.693][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:44.694][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-08-09 16:03:44.696][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2025-08-09 16:03:44.698][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-08-09 16:03:44.700][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-08-09 16:03:44.703][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2025-08-09 16:03:44.704][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-08-09 16:03:44.706][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2025-08-09 16:03:44.713][super$initialize] Initialize connector ncbi.pubchem.comp.
biodb.DEBUG[2025-08-09 16:03:44.735][biodb$getFactory()$createConn] Creating new connector ncbi.pubchem.comp for database class ncbi.pubchem.comp .
biodb.INFO [2025-08-09 16:03:44.740][biodb::testThat]
biodb.INFO [2025-08-09 16:03:44.742][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2025-08-09 16:03:44.743][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-09 16:03:44.744][biodb::testThat]
biodb.TRACE[2025-08-09 16:03:44.749][loadFileContents] Loaded 1 files from cache: [1]: "F:/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.pubchem.comp-2-content.xml".
biodb.DEBUG[2025-08-09 16:03:44.750][biodb$getFactory()$createEntryFromCo ...] Creating PubChem Compound entries from 1 content(s).
biodb.DEBUG[2025-08-09 16:03:44.754][biodb$getFactory()$createEntryFromCo ...] Parsing 1 PubChem Compound entries.
biodb.DEBUG[2025-08-09 16:03:44.755][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-09 16:03:44.757][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:44.758][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:44.771][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:44.772][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:44.773][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:44.775][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-09 16:03:44.779][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:44.781][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:44.782][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:44.783][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:44.785][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:44.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:44.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:44.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:44.790][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-08-09 16:03:44.791][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-08-09 16:03:44.792][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:44.793][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:44.795][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-08-09 16:03:44.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-08-09 16:03:44.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:44.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:44.800][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-08-09 16:03:44.801][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-08-09 16:03:44.802][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:44.804][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:44.805][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-08-09 16:03:44.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-08-09 16:03:44.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:44.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:44.810][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-08-09 16:03:44.811][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-08-09 16:03:44.813][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:44.814][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:44.815][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-08-09 16:03:44.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-08-09 16:03:44.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:44.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:44.820][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-09 16:03:44.822][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-09 16:03:44.823][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:44.824][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:44.826][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-09 16:03:44.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-09 16:03:44.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:44.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:44.831][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-09 16:03:44.832][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-09 16:03:44.833][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:44.834][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:44.836][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-09 16:03:44.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-09 16:03:44.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:44.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:44.841][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2025-08-09 16:03:44.842][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-09 16:03:44.843][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:44.844][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:44.846][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-08-09 16:03:44.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-09 16:03:44.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:44.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:44.851][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-09 16:03:44.852][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-09 16:03:44.853][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:44.855][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:44.856][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-09 16:03:44.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-09 16:03:44.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:44.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:44.861][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-09 16:03:44.862][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-09 16:03:44.864][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:44.865][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:44.866][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-09 16:03:44.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-09 16:03:44.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:44.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:44.871][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-09 16:03:44.873][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-09 16:03:44.874][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:44.875][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:44.876][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-09 16:03:44.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-09 16:03:44.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:44.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:44.881][ef$get] Asked field names are: logp.
biodb.TRACE[2025-08-09 16:03:44.883][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-08-09 16:03:44.884][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:44.885][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:44.887][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-08-09 16:03:44.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-08-09 16:03:44.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:44.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:44.897][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-08-09 16:03:44.899][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-09 16:03:44.900][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:44.901][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:44.903][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-08-09 16:03:44.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-09 16:03:44.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:44.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:44.908][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-08-09 16:03:44.909][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-08-09 16:03:44.910][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:44.912][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:44.913][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-08-09 16:03:44.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-08-09 16:03:44.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:44.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:44.918][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-08-09 16:03:44.919][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-08-09 16:03:44.921][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:44.922][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:44.923][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-08-09 16:03:44.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-08-09 16:03:44.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:44.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:44.928][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2025-08-09 16:03:44.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-08-09 16:03:44.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:44.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:44.933][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-08-09 16:03:44.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-08-09 16:03:44.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:44.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:44.938][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-08-09 16:03:44.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-08-09 16:03:44.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:44.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:44.943][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2025-08-09 16:03:44.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-08-09 16:03:44.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:44.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:44.948][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-08-09 16:03:44.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-08-09 16:03:44.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:44.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:44.953][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-08-09 16:03:44.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-08-09 16:03:44.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:44.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:44.958][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2025-08-09 16:03:44.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-09 16:03:44.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:44.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:44.963][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-09 16:03:44.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-09 16:03:44.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:44.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:44.968][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-09 16:03:44.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-09 16:03:44.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:44.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:44.972][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2025-08-09 16:03:44.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-09 16:03:44.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:44.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:44.977][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-09 16:03:44.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-09 16:03:44.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:44.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:44.982][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-09 16:03:44.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-09 16:03:44.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:44.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:44.987][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2025-08-09 16:03:44.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-08-09 16:03:44.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:44.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:44.992][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-08-09 16:03:44.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-08-09 16:03:44.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:44.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:44.997][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-08-09 16:03:44.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-08-09 16:03:44.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.002][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-09 16:03:45.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-09 16:03:45.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.007][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-09 16:03:45.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-09 16:03:45.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.012][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-09 16:03:45.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-09 16:03:45.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.022][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:45.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:45.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.027][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-09 16:03:45.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-09 16:03:45.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.032][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:45.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:45.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.037][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:45.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:45.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.042][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:45.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:45.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.047][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:45.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:45.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.052][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:45.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:45.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.056][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:45.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:45.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-09 16:03:45.061][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 2.
biodb.TRACE[2025-08-09 16:03:45.064][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-08-09 16:03:45.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-08-09 16:03:45.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.069][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-08-09 16:03:45.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-08-09 16:03:45.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.075][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-08-09 16:03:45.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-08-09 16:03:45.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.080][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-09 16:03:45.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-09 16:03:45.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.085][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-09 16:03:45.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-09 16:03:45.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.089][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-08-09 16:03:45.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-08-09 16:03:45.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.094][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-08-09 16:03:45.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-08-09 16:03:45.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.101][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:45.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:45.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.111][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-09 16:03:45.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-09 16:03:45.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.121][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:45.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:45.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.126][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:45.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:45.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.131][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:45.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:45.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.137][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:45.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:45.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.147][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:45.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:45.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.153][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:45.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:45.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.158][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-09 16:03:45.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-09 16:03:45.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.163][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-09 16:03:45.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-09 16:03:45.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.168][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-09 16:03:45.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-09 16:03:45.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.181][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:45.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:45.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.186][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:45.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:45.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.190][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:45.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:45.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.195][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:45.197][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:45.198][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.199][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.200][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:45.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:45.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.215][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-08-09 16:03:45.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-09 16:03:45.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.220][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-09 16:03:45.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-09 16:03:45.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.225][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-09 16:03:45.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-09 16:03:45.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.230][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2025-08-09 16:03:45.231][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-09 16:03:45.232][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.233][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.235][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-08-09 16:03:45.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-09 16:03:45.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.249][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-08-09 16:03:45.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-09 16:03:45.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.254][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-09 16:03:45.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-09 16:03:45.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.259][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-09 16:03:45.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-09 16:03:45.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.264][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-08-09 16:03:45.265][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-09 16:03:45.266][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.272][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.274][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-08-09 16:03:45.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-09 16:03:45.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.289][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-09 16:03:45.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-09 16:03:45.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.294][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-09 16:03:45.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-09 16:03:45.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.299][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-09 16:03:45.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-09 16:03:45.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.304][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-09 16:03:45.306][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-09 16:03:45.307][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.308][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.309][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-09 16:03:45.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-09 16:03:45.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.323][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-08-09 16:03:45.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-08-09 16:03:45.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.328][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-08-09 16:03:45.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-08-09 16:03:45.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.333][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-08-09 16:03:45.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-08-09 16:03:45.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.338][ef$get] Asked field names are: logp.
biodb.TRACE[2025-08-09 16:03:45.340][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-08-09 16:03:45.341][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.342][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.343][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-08-09 16:03:45.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-08-09 16:03:45.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.357][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-08-09 16:03:45.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-08-09 16:03:45.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.362][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-08-09 16:03:45.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-08-09 16:03:45.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.367][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-08-09 16:03:45.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-08-09 16:03:45.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.372][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-08-09 16:03:45.373][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-08-09 16:03:45.375][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.376][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.377][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-08-09 16:03:45.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-08-09 16:03:45.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.392][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-08-09 16:03:45.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-08-09 16:03:45.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.402][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-08-09 16:03:45.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-08-09 16:03:45.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.408][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-08-09 16:03:45.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-08-09 16:03:45.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.413][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-08-09 16:03:45.414][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-08-09 16:03:45.415][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.417][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.418][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-08-09 16:03:45.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-08-09 16:03:45.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.432][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-08-09 16:03:45.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-08-09 16:03:45.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.437][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-08-09 16:03:45.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-08-09 16:03:45.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.442][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-08-09 16:03:45.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-08-09 16:03:45.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.447][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-08-09 16:03:45.448][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-08-09 16:03:45.449][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.450][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.452][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-08-09 16:03:45.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-08-09 16:03:45.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.466][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-08-09 16:03:45.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-08-09 16:03:45.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.471][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-08-09 16:03:45.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-08-09 16:03:45.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.476][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-08-09 16:03:45.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-08-09 16:03:45.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.481][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-08-09 16:03:45.482][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-08-09 16:03:45.483][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.484][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.485][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-08-09 16:03:45.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-08-09 16:03:45.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.500][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-08-09 16:03:45.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-08-09 16:03:45.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.505][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-08-09 16:03:45.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-08-09 16:03:45.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.510][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-08-09 16:03:45.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-08-09 16:03:45.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.515][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-08-09 16:03:45.516][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-08-09 16:03:45.517][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.518][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.519][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-08-09 16:03:45.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-08-09 16:03:45.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.539][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-09 16:03:45.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-09 16:03:45.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.545][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-09 16:03:45.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-09 16:03:45.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.549][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-09 16:03:45.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-09 16:03:45.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.554][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-09 16:03:45.556][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-09 16:03:45.557][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.558][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.559][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-09 16:03:45.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-09 16:03:45.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.574][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-09 16:03:45.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-09 16:03:45.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.579][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-09 16:03:45.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-09 16:03:45.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.584][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-09 16:03:45.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-09 16:03:45.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.589][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-09 16:03:45.590][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-09 16:03:45.591][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.592][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.593][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-09 16:03:45.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-09 16:03:45.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.608][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-09 16:03:45.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-09 16:03:45.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.613][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-09 16:03:45.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-09 16:03:45.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.617][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-09 16:03:45.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-09 16:03:45.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.622][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-09 16:03:45.624][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-09 16:03:45.625][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.626][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.627][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-09 16:03:45.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-09 16:03:45.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.642][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-09 16:03:45.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-09 16:03:45.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.652][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-09 16:03:45.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-09 16:03:45.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.657][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-09 16:03:45.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-09 16:03:45.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.662][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-09 16:03:45.663][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-09 16:03:45.665][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.666][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.667][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-09 16:03:45.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-09 16:03:45.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.681][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-09 16:03:45.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-09 16:03:45.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.686][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-09 16:03:45.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-09 16:03:45.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.691][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-09 16:03:45.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-09 16:03:45.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.696][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-09 16:03:45.698][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-09 16:03:45.699][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.700][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.702][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-09 16:03:45.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-09 16:03:45.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.718][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:45.719][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:45.720][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.721][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.728][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-08-09 16:03:45.729][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-08-09 16:03:45.730][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.732][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.738][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-08-09 16:03:45.739][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-08-09 16:03:45.740][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.742][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.748][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-08-09 16:03:45.749][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-08-09 16:03:45.750][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.752][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.758][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-09 16:03:45.759][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-09 16:03:45.760][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.762][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.769][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-09 16:03:45.770][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-09 16:03:45.771][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.773][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.779][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-09 16:03:45.786][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-09 16:03:45.787][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.788][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.795][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-09 16:03:45.797][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-09 16:03:45.798][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.799][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.806][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-09 16:03:45.807][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-09 16:03:45.808][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.809][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.816][ef$get] Asked field names are: logp.
biodb.TRACE[2025-08-09 16:03:45.817][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-08-09 16:03:45.818][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.819][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.826][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-09 16:03:45.827][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-09 16:03:45.828][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.829][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.836][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-09 16:03:45.837][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-09 16:03:45.838][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.839][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.845][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-09 16:03:45.847][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-09 16:03:45.848][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.849][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.855][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-08-09 16:03:45.857][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-08-09 16:03:45.858][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.859][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.865][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-08-09 16:03:45.866][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-08-09 16:03:45.868][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.869][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.877][loadFileContents] Loaded 1 files from cache: [1]: "F:/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.pubchem.comp-65124-content.xml".
biodb.DEBUG[2025-08-09 16:03:45.878][biodb$getFactory()$createEntryFromCo ...] Creating PubChem Compound entries from 1 content(s).
biodb.DEBUG[2025-08-09 16:03:45.880][biodb$getFactory()$createEntryFromCo ...] Parsing 1 PubChem Compound entries.
biodb.DEBUG[2025-08-09 16:03:45.882][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-09 16:03:45.883][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:45.884][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:45.890][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:45.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:45.892][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:45.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-09 16:03:45.896][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:45.898][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:45.899][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.900][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.902][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:45.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:45.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.907][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-08-09 16:03:45.908][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-08-09 16:03:45.909][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.910][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.912][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-08-09 16:03:45.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-08-09 16:03:45.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.922][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-08-09 16:03:45.924][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-08-09 16:03:45.925][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.926][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.928][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-08-09 16:03:45.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-08-09 16:03:45.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.933][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-08-09 16:03:45.934][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-08-09 16:03:45.936][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.937][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.938][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-08-09 16:03:45.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-08-09 16:03:45.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.944][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-09 16:03:45.945][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-09 16:03:45.946][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.947][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.949][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-09 16:03:45.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-09 16:03:45.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.954][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-09 16:03:45.955][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-09 16:03:45.956][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.957][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.959][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-09 16:03:45.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-09 16:03:45.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.964][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2025-08-09 16:03:45.965][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-09 16:03:45.966][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.968][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.969][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-08-09 16:03:45.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-09 16:03:45.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.974][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-09 16:03:45.976][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-09 16:03:45.977][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.978][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.979][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-09 16:03:45.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-09 16:03:45.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.984][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-09 16:03:45.986][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-09 16:03:45.987][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.988][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.990][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-09 16:03:45.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-09 16:03:45.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:45.995][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-09 16:03:45.996][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-09 16:03:45.997][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:45.998][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.000][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-09 16:03:46.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-09 16:03:46.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.005][ef$get] Asked field names are: logp.
biodb.TRACE[2025-08-09 16:03:46.006][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-08-09 16:03:46.007][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.008][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.010][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-08-09 16:03:46.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-08-09 16:03:46.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.015][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-08-09 16:03:46.016][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-09 16:03:46.017][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.019][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.020][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-08-09 16:03:46.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-09 16:03:46.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.025][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-08-09 16:03:46.027][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-08-09 16:03:46.028][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.029][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.030][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-08-09 16:03:46.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-08-09 16:03:46.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.036][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-08-09 16:03:46.037][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-08-09 16:03:46.038][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.039][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.041][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-08-09 16:03:46.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-08-09 16:03:46.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.052][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2025-08-09 16:03:46.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-08-09 16:03:46.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.057][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-08-09 16:03:46.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-08-09 16:03:46.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.062][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-08-09 16:03:46.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-08-09 16:03:46.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.067][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2025-08-09 16:03:46.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-08-09 16:03:46.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.072][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-08-09 16:03:46.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-08-09 16:03:46.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.077][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-08-09 16:03:46.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-08-09 16:03:46.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.082][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2025-08-09 16:03:46.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-09 16:03:46.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.087][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-09 16:03:46.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-09 16:03:46.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.092][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-09 16:03:46.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-09 16:03:46.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.096][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2025-08-09 16:03:46.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-09 16:03:46.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.101][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-09 16:03:46.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-09 16:03:46.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.106][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-09 16:03:46.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-09 16:03:46.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.111][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2025-08-09 16:03:46.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-08-09 16:03:46.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.116][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-08-09 16:03:46.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-08-09 16:03:46.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.121][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-08-09 16:03:46.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-08-09 16:03:46.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.126][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-09 16:03:46.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-09 16:03:46.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.131][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-09 16:03:46.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-09 16:03:46.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.135][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-09 16:03:46.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-09 16:03:46.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.140][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:46.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:46.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.145][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-09 16:03:46.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-09 16:03:46.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.150][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:46.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:46.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.155][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:46.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:46.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.160][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:46.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:46.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.170][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:46.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:46.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.175][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:46.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:46.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.180][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:46.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:46.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-09 16:03:46.185][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 65124.
biodb.TRACE[2025-08-09 16:03:46.188][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-08-09 16:03:46.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-08-09 16:03:46.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.193][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-08-09 16:03:46.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-08-09 16:03:46.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.197][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-08-09 16:03:46.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-08-09 16:03:46.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.202][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-09 16:03:46.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-09 16:03:46.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.207][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-09 16:03:46.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-09 16:03:46.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.212][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-08-09 16:03:46.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-08-09 16:03:46.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.217][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-08-09 16:03:46.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-08-09 16:03:46.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.223][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:46.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:46.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.233][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-09 16:03:46.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-09 16:03:46.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.244][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:46.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:46.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.249][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:46.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:46.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.254][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:46.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:46.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.260][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:46.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:46.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.265][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:46.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:46.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.270][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:46.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:46.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.275][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-09 16:03:46.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-09 16:03:46.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.280][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-09 16:03:46.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-09 16:03:46.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.285][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-09 16:03:46.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-09 16:03:46.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.304][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:46.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:46.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.309][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:46.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:46.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.314][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:46.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:46.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.319][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:46.320][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:46.321][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.322][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.323][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:46.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:46.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.338][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-09 16:03:46.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-09 16:03:46.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.343][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-09 16:03:46.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-09 16:03:46.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.348][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-09 16:03:46.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-09 16:03:46.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.353][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-09 16:03:46.354][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-09 16:03:46.355][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.356][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.357][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-09 16:03:46.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-09 16:03:46.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.372][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-09 16:03:46.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-09 16:03:46.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.377][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-09 16:03:46.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-09 16:03:46.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.382][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-09 16:03:46.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-09 16:03:46.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.386][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-09 16:03:46.388][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-09 16:03:46.389][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.390][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.391][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-09 16:03:46.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-09 16:03:46.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.406][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-09 16:03:46.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-09 16:03:46.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.411][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-09 16:03:46.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-09 16:03:46.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.421][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-09 16:03:46.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-09 16:03:46.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.427][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-09 16:03:46.428][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-09 16:03:46.429][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.430][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.432][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-09 16:03:46.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-09 16:03:46.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.446][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-08-09 16:03:46.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-08-09 16:03:46.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.451][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-08-09 16:03:46.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-08-09 16:03:46.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.456][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-08-09 16:03:46.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-08-09 16:03:46.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.461][ef$get] Asked field names are: logp.
biodb.TRACE[2025-08-09 16:03:46.462][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-08-09 16:03:46.463][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.464][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.465][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-08-09 16:03:46.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-08-09 16:03:46.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.479][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-08-09 16:03:46.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-08-09 16:03:46.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.484][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-08-09 16:03:46.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-08-09 16:03:46.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.489][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-08-09 16:03:46.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-08-09 16:03:46.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.494][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-08-09 16:03:46.495][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-08-09 16:03:46.496][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.498][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.499][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-08-09 16:03:46.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-08-09 16:03:46.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.513][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-08-09 16:03:46.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-08-09 16:03:46.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.518][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-08-09 16:03:46.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-08-09 16:03:46.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.523][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-08-09 16:03:46.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-08-09 16:03:46.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.528][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-08-09 16:03:46.530][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-08-09 16:03:46.531][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.532][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.533][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-08-09 16:03:46.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-08-09 16:03:46.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.554][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-09 16:03:46.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-09 16:03:46.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.559][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-09 16:03:46.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-09 16:03:46.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.564][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-09 16:03:46.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-09 16:03:46.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.569][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-09 16:03:46.570][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-09 16:03:46.571][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.572][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.573][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-09 16:03:46.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-09 16:03:46.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.588][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-09 16:03:46.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-09 16:03:46.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.593][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-09 16:03:46.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-09 16:03:46.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.598][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-09 16:03:46.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-09 16:03:46.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.603][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-09 16:03:46.604][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-09 16:03:46.605][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.606][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.608][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-09 16:03:46.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-09 16:03:46.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.622][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-08-09 16:03:46.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-08-09 16:03:46.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.627][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-08-09 16:03:46.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-08-09 16:03:46.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.632][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-08-09 16:03:46.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-08-09 16:03:46.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.637][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-08-09 16:03:46.638][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-08-09 16:03:46.640][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.641][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.642][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-08-09 16:03:46.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-08-09 16:03:46.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.657][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-08-09 16:03:46.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-08-09 16:03:46.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.662][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-08-09 16:03:46.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-08-09 16:03:46.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.672][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-08-09 16:03:46.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-08-09 16:03:46.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.678][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-08-09 16:03:46.679][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-08-09 16:03:46.680][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.681][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.683][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-08-09 16:03:46.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-08-09 16:03:46.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.697][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-08-09 16:03:46.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-08-09 16:03:46.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.703][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-08-09 16:03:46.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-08-09 16:03:46.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.709][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-08-09 16:03:46.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-08-09 16:03:46.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.714][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-08-09 16:03:46.715][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-08-09 16:03:46.717][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.718][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.719][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-08-09 16:03:46.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-08-09 16:03:46.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.734][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-09 16:03:46.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-09 16:03:46.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.739][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-09 16:03:46.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-09 16:03:46.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.744][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-09 16:03:46.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-09 16:03:46.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.749][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-09 16:03:46.750][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-09 16:03:46.751][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.752][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.754][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-09 16:03:46.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-09 16:03:46.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.768][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-09 16:03:46.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-09 16:03:46.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.773][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-09 16:03:46.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-09 16:03:46.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.778][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-09 16:03:46.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-09 16:03:46.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.783][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-09 16:03:46.784][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-09 16:03:46.785][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.787][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.788][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-09 16:03:46.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-09 16:03:46.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.808][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-09 16:03:46.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-09 16:03:46.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.813][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-09 16:03:46.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-09 16:03:46.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.818][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-09 16:03:46.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-09 16:03:46.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.823][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-09 16:03:46.824][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-09 16:03:46.826][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.827][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.828][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-09 16:03:46.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-09 16:03:46.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.842][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:46.844][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:46.845][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.846][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.853][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-08-09 16:03:46.854][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-08-09 16:03:46.855][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.856][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.863][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-08-09 16:03:46.864][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-08-09 16:03:46.865][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.866][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.873][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-08-09 16:03:46.874][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-08-09 16:03:46.875][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.876][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.883][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-09 16:03:46.884][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-09 16:03:46.885][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.886][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.893][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-09 16:03:46.894][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-09 16:03:46.895][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.896][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.903][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-09 16:03:46.904][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-09 16:03:46.905][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.906][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.913][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-09 16:03:46.915][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-09 16:03:46.916][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.918][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.924][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-09 16:03:46.925][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-09 16:03:46.932][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.933][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.940][ef$get] Asked field names are: logp.
biodb.TRACE[2025-08-09 16:03:46.941][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-08-09 16:03:46.942][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.944][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.950][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-09 16:03:46.952][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-09 16:03:46.953][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.954][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.960][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-09 16:03:46.962][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-09 16:03:46.963][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.964][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.970][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-09 16:03:46.972][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-09 16:03:46.973][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.974][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.980][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-08-09 16:03:46.982][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-08-09 16:03:46.983][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.984][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:46.990][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-08-09 16:03:46.992][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-08-09 16:03:46.993][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:46.994][ef$get] fields variable is a list.
biodb.INFO [2025-08-09 16:03:47.005][biodb::testThat]
biodb.INFO [2025-08-09 16:03:47.006][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-08-09 16:03:47.008][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-09 16:03:47.009][biodb::testThat]
biodb.DEBUG[2025-08-09 16:03:47.012][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2025-08-09 16:03:47.031][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2025-08-09 16:03:47.033][cch$loadContents] Load 2 contents, from C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-08-09 16:03:47.035][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-08-09 16:03:47.036][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-08-09 16:03:47.038][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-09 16:03:47.039][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-08-09 16:03:47.040][private$retrieveContents] Get entry content(s) for 2 id(s)...
biodb.INFO [2025-08-09 16:03:47.055][biodb::testThat]
biodb.INFO [2025-08-09 16:03:47.056][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2025-08-09 16:03:47.058][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-09 16:03:47.059][biodb::testThat]
biodb.TRACE[2025-08-09 16:03:47.062][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-09 16:03:47.064][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-09 16:03:47.065][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:47.066][ef$get] fields variable is a list.
biodb.DEBUG[2025-08-09 16:03:47.068][function(conn, opt)] Testing searchForEntries() with entry "2" and field "name".
biodb.DEBUG[2025-08-09 16:03:47.090][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2025-08-09 16:03:47.092][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2025-08-09 16:03:47.110][cch$loadContents] Load 1 contents, from C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-08-09 16:03:47.111][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-08-09 16:03:47.113][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-08-09 16:03:47.114][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-09 16:03:47.115][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-08-09 16:03:47.117][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.INFO [2025-08-09 16:03:47.132][biodb::testThat]
biodb.INFO [2025-08-09 16:03:47.133][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2025-08-09 16:03:47.134][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-09 16:03:47.135][biodb::testThat]
biodb.DEBUG[2025-08-09 16:03:47.145][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2025-08-09 16:03:47.146][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2025-08-09 16:03:47.148][cch$loadContents] Load 1 contents, from C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-08-09 16:03:47.149][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-08-09 16:03:47.151][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-08-09 16:03:47.152][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-09 16:03:47.153][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-08-09 16:03:47.154][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.INFO [2025-08-09 16:03:47.169][biodb::testThat]
biodb.INFO [2025-08-09 16:03:47.170][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2025-08-09 16:03:47.172][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-09 16:03:47.173][biodb::testThat]
biodb.DEBUG[2025-08-09 16:03:47.178][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2025-08-09 16:03:47.179][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2025-08-09 16:03:47.181][cch$loadContents] Load 1 contents, from C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-08-09 16:03:47.182][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-08-09 16:03:47.183][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-08-09 16:03:47.185][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-09 16:03:47.186][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-08-09 16:03:47.187][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.INFO [2025-08-09 16:03:47.209][biodb::testThat]
biodb.INFO [2025-08-09 16:03:47.210][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-08-09 16:03:47.211][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-09 16:03:47.213][biodb::testThat]
biodb.INFO [2025-08-09 16:03:47.229][biodb::testThat]
biodb.INFO [2025-08-09 16:03:47.230][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-08-09 16:03:47.232][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-09 16:03:47.233][biodb::testThat]
biodb.INFO [2025-08-09 16:03:47.249][biodb::testThat]
biodb.INFO [2025-08-09 16:03:47.250][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2025-08-09 16:03:47.251][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-09 16:03:47.252][biodb::testThat]
biodb.INFO [2025-08-09 16:03:47.268][biodb::testThat]
biodb.INFO [2025-08-09 16:03:47.270][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2025-08-09 16:03:47.271][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-09 16:03:47.272][biodb::testThat]
biodb.TRACE[2025-08-09 16:03:47.294][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-09 16:03:47.296][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-09 16:03:47.297][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:47.298][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:47.305][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-09 16:03:47.306][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-09 16:03:47.308][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:47.309][ef$get] fields variable is a list.
biodb.INFO [2025-08-09 16:03:47.312][biodb::testThat]
biodb.INFO [2025-08-09 16:03:47.313][biodb::testThat] Running test function test.searchCompound (" We can search for a compound ").
biodb.INFO [2025-08-09 16:03:47.315][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-09 16:03:47.316][biodb::testThat]
biodb.DEBUG[2025-08-09 16:03:47.326][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2025-08-09 16:03:47.327][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2025-08-09 16:03:47.329][cch$loadContents] Load 1 contents, from C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-08-09 16:03:47.330][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-08-09 16:03:47.332][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-08-09 16:03:47.333][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-09 16:03:47.334][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-08-09 16:03:47.335][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.INFO [2025-08-09 16:03:47.351][biodb::testThat]
biodb.INFO [2025-08-09 16:03:47.352][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2025-08-09 16:03:47.354][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-09 16:03:47.355][biodb::testThat]
biodb.DEBUG[2025-08-09 16:03:47.359][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2025-08-09 16:03:47.360][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2025-08-09 16:03:47.362][cch$loadContents] Load 2 contents, from C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-08-09 16:03:47.363][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-08-09 16:03:47.365][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-08-09 16:03:47.366][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-09 16:03:47.367][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-08-09 16:03:47.368][private$retrieveContents] Get entry content(s) for 2 id(s)...
biodb.INFO [2025-08-09 16:03:47.383][biodb::testThat]
biodb.INFO [2025-08-09 16:03:47.385][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2025-08-09 16:03:47.386][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-09 16:03:47.387][biodb::testThat]
biodb.DEBUG[2025-08-09 16:03:47.391][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2025-08-09 16:03:47.392][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2025-08-09 16:03:47.394][cch$loadContents] Load 2 contents, from C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-08-09 16:03:47.395][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-08-09 16:03:47.397][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-08-09 16:03:47.398][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-09 16:03:47.399][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-08-09 16:03:47.401][private$retrieveContents] Get entry content(s) for 2 id(s)...
biodb.INFO [2025-08-09 16:03:47.416][biodb::testThat]
biodb.INFO [2025-08-09 16:03:47.417][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2025-08-09 16:03:47.418][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-09 16:03:47.420][biodb::testThat]
biodb.DEBUG[2025-08-09 16:03:47.429][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2025-08-09 16:03:47.430][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2025-08-09 16:03:47.432][cch$loadContents] Load 2 contents, from C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-08-09 16:03:47.434][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-08-09 16:03:47.435][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-08-09 16:03:47.437][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-09 16:03:47.438][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-08-09 16:03:47.439][private$retrieveContents] Get entry content(s) for 2 id(s)...
biodb.TRACE[2025-08-09 16:03:47.454][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-09 16:03:47.455][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-09 16:03:47.456][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:47.457][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:47.459][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-09 16:03:47.460][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-09 16:03:47.461][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:47.462][ef$get] fields variable is a list.
biodb.INFO [2025-08-09 16:03:47.464][biodb::testThat]
biodb.INFO [2025-08-09 16:03:47.466][biodb::testThat] Running test function test.annotateMzValues_real_values (" annotateMzValues() works correctly with real values. ").
biodb.INFO [2025-08-09 16:03:47.467][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-09 16:03:47.468][biodb::testThat]
biodb.DEBUG[2025-08-09 16:03:47.472][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2025-08-09 16:03:47.473][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2025-08-09 16:03:47.475][cch$loadContents] Load 2 contents, from C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-08-09 16:03:47.476][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-08-09 16:03:47.478][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-08-09 16:03:47.479][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-09 16:03:47.480][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-08-09 16:03:47.481][private$retrieveContents] Get entry content(s) for 2 id(s)...
biodb.INFO [2025-08-09 16:03:47.496][biodb::testThat]
biodb.INFO [2025-08-09 16:03:47.498][biodb::testThat] Running test function test_annotateMzValues_additional_fields (" Additional fields are accepted in annotateMzValues() ").
biodb.INFO [2025-08-09 16:03:47.499][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-09 16:03:47.500][biodb::testThat]
biodb.DEBUG[2025-08-09 16:03:47.504][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2025-08-09 16:03:47.505][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2025-08-09 16:03:47.507][cch$loadContents] Load 2 contents, from C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-08-09 16:03:47.508][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-08-09 16:03:47.510][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-08-09 16:03:47.511][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-09 16:03:47.512][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-08-09 16:03:47.513][private$retrieveContents] Get entry content(s) for 2 id(s)...
biodb.INFO [2025-08-09 16:03:47.527][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-08-09 16:03:47.529][self$deleteConn] Connector "ncbi.pubchem.comp" deleted.
biodb.DEBUG[2025-08-09 16:03:47.530][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-08-09 16:03:47.531][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:47.532][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:47.533][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:47.534][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:47.536][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:47.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-08-09 16:03:47.547][biodb::testContext]
biodb.INFO [2025-08-09 16:03:47.549][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-09 16:03:47.550][biodb::testContext] Test context - Pubchem Subst long tests
biodb.INFO [2025-08-09 16:03:47.552][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-09 16:03:47.553][biodb::testContext]
biodb.INFO [2025-08-09 16:03:47.556][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.1.
biodb.DEBUG[2025-08-09 16:03:47.558][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.22-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2025-08-09 16:03:47.563][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-09 16:03:47.565][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-08-09 16:03:47.566][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-08-09 16:03:47.567][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:47.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:47.569][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:47.571][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-08-09 16:03:47.572][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-08-09 16:03:47.573][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:47.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:47.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:47.576][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-08-09 16:03:47.578][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-08-09 16:03:47.579][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:47.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:47.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:47.582][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-08-09 16:03:47.583][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-08-09 16:03:47.585][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-08-09 16:03:47.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:47.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:47.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:47.589][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-08-09 16:03:47.590][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-08-09 16:03:47.592][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-08-09 16:03:47.593][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:47.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:47.595][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[2025-08-09 16:03:47.596][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-08-09 16:03:47.597][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-08-09 16:03:47.598][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:47.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:47.601][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:47.602][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-08-09 16:03:47.603][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-08-09 16:03:47.604][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-08-09 16:03:47.605][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:47.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:47.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:47.609][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-08-09 16:03:47.610][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-08-09 16:03:47.611][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:47.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:47.613][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:47.615][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-08-09 16:03:47.616][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-08-09 16:03:47.617][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-08-09 16:03:47.618][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:47.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:47.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:47.621][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-08-09 16:03:47.623][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-08-09 16:03:47.624][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-08-09 16:03:47.625][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-08-09 16:03:47.626][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-08-09 16:03:47.628][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-08-09 16:03:47.629][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:47.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:47.631][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:47.632][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-08-09 16:03:47.633][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-08-09 16:03:47.634][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:47.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:47.637][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:47.638][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-08-09 16:03:47.639][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-08-09 16:03:47.640][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:47.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:47.642][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:47.644][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-08-09 16:03:47.645][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-08-09 16:03:47.646][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:47.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:47.648][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:47.649][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-08-09 16:03:47.651][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-08-09 16:03:47.652][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-08-09 16:03:47.653][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:47.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:47.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:47.656][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-08-09 16:03:47.658][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-08-09 16:03:47.661][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-08-09 16:03:47.662][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:47.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:47.665][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:47.666][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-08-09 16:03:47.672][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-08-09 16:03:47.674][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-08-09 16:03:47.675][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:47.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:47.678][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:47.679][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-08-09 16:03:47.681][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:47.696][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-08-09 16:03:47.697][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:47.699][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-09 16:03:47.700][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:47.701][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-09 16:03:47.702][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:47.704][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-09 16:03:47.706][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-09 16:03:47.707][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-09 16:03:47.709][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:47.711][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-08-09 16:03:47.712][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-09 16:03:47.714][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:47.715][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:47.716][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-09 16:03:47.716][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-09 16:03:47.716][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-09 16:03:47.716][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-09 16:03:47.716][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-09 16:03:47.717][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-09 16:03:47.719][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:47.720][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:47.721][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-09 16:03:47.722][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:47.723][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:47.724][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-09 16:03:47.726][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:47.727][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-09 16:03:47.728][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-09 16:03:47.729][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:47.730][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:47.732][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-08-09 16:03:47.734][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:47.735][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-08-09 16:03:47.736][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:47.737][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-09 16:03:47.739][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:47.740][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-09 16:03:47.741][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:47.742][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-09 16:03:47.744][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-09 16:03:47.745][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-09 16:03:47.746][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:47.747][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-08-09 16:03:47.749][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-09 16:03:47.750][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:47.751][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:47.752][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-09 16:03:47.752][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-09 16:03:47.752][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-09 16:03:47.752][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-09 16:03:47.752][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-09 16:03:47.753][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-09 16:03:47.755][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:47.756][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:47.757][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-09 16:03:47.758][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:47.759][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:47.761][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-09 16:03:47.762][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:47.763][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-09 16:03:47.764][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-09 16:03:47.765][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:47.766][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:47.768][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-08-09 16:03:47.770][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:47.771][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-08-09 16:03:47.772][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:47.774][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-09 16:03:47.775][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:47.776][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-09 16:03:47.777][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:47.784][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-09 16:03:47.785][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-09 16:03:47.787][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-09 16:03:47.788][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:47.790][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-08-09 16:03:47.791][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-09 16:03:47.792][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:47.793][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:47.795][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:47.797][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-09 16:03:47.798][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:47.799][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:47.800][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-09 16:03:47.802][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:47.803][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:47.804][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-09 16:03:47.805][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:47.806][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-09 16:03:47.807][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-09 16:03:47.809][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:47.810][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:47.811][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-08-09 16:03:47.813][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:47.814][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-08-09 16:03:47.816][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:47.817][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-09 16:03:47.818][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:47.819][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-09 16:03:47.821][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:47.822][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-09 16:03:47.823][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-09 16:03:47.824][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-09 16:03:47.826][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:47.827][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-08-09 16:03:47.828][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-09 16:03:47.829][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:47.831][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:47.832][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:47.833][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-09 16:03:47.834][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:47.835][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:47.836][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-09 16:03:47.838][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:47.839][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:47.840][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-09 16:03:47.841][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:47.842][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-09 16:03:47.844][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-09 16:03:47.845][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:47.846][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:47.848][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-09 16:03:47.849][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:47.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:47.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:47.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:47.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:47.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:47.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:47.857][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:47.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:47.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:47.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:47.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:47.862][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:47.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:47.864][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:47.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:47.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:47.868][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:47.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:47.870][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:47.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:47.872][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:47.874][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:47.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:47.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:47.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:47.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:47.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:47.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:47.881][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:47.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:47.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:47.885][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:47.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:47.887][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:47.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:47.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:47.891][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:47.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:47.893][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:47.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:47.895][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:47.896][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:47.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:47.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:47.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:47.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:47.907][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:47.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:47.910][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:47.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:47.912][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[2025-08-09 16:03:47.914][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:47.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:47.916][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:47.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:47.918][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[2025-08-09 16:03:47.919][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:47.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:47.921][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:47.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:47.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:47.925][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:47.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:47.927][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:47.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:47.929][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[2025-08-09 16:03:47.930][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:47.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:47.933][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:47.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:47.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:47.936][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:47.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:47.938][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:47.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:47.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:47.942][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:47.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:47.944][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:47.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:47.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:47.947][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-08-09 16:03:47.949][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-08-09 16:03:47.951][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-08-09 16:03:47.952][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-08-09 16:03:47.954][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-09 16:03:47.955][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-08-09 16:03:47.957][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-08-09 16:03:47.959][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-08-09 16:03:47.960][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-08-09 16:03:47.962][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-08-09 16:03:47.963][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-09 16:03:47.965][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-08-09 16:03:47.967][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-08-09 16:03:47.968][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-08-09 16:03:47.970][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-08-09 16:03:47.971][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-08-09 16:03:47.973][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-08-09 16:03:47.974][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-08-09 16:03:47.976][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-09 16:03:47.978][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-08-09 16:03:47.979][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-08-09 16:03:47.981][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-08-09 16:03:47.983][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-08-09 16:03:47.984][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-08-09 16:03:47.986][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-08-09 16:03:47.987][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-08-09 16:03:47.989][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-08-09 16:03:47.990][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-08-09 16:03:47.992][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-08-09 16:03:47.994][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-08-09 16:03:47.995][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-08-09 16:03:47.997][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-08-09 16:03:47.999][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-08-09 16:03:48.000][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-08-09 16:03:48.002][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-08-09 16:03:48.003][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-08-09 16:03:48.005][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-08-09 16:03:48.007][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-08-09 16:03:48.008][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-08-09 16:03:48.010][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-08-09 16:03:48.011][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-08-09 16:03:48.018][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-08-09 16:03:48.020][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-08-09 16:03:48.022][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-08-09 16:03:48.024][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-08-09 16:03:48.026][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-08-09 16:03:48.027][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-08-09 16:03:48.029][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-08-09 16:03:48.030][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-08-09 16:03:48.032][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-08-09 16:03:48.034][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-08-09 16:03:48.035][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-08-09 16:03:48.037][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-08-09 16:03:48.038][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-08-09 16:03:48.040][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-08-09 16:03:48.042][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-08-09 16:03:48.043][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-08-09 16:03:48.045][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-08-09 16:03:48.047][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-08-09 16:03:48.048][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-08-09 16:03:48.050][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-08-09 16:03:48.051][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-08-09 16:03:48.053][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-08-09 16:03:48.054][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-08-09 16:03:48.056][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-08-09 16:03:48.058][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-08-09 16:03:48.059][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-09 16:03:48.061][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-09 16:03:48.062][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-08-09 16:03:48.064][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-08-09 16:03:48.066][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-08-09 16:03:48.067][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-08-09 16:03:48.069][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-08-09 16:03:48.070][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-08-09 16:03:48.072][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-08-09 16:03:48.073][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-08-09 16:03:48.075][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-08-09 16:03:48.077][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-08-09 16:03:48.078][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-08-09 16:03:48.080][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-08-09 16:03:48.081][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-08-09 16:03:48.083][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-08-09 16:03:48.085][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-08-09 16:03:48.086][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-08-09 16:03:48.089][initialize] This is biodb version 1.17.1.
biodb.DEBUG[2025-08-09 16:03:48.090][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-09 16:03:48.091][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:48.092][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:48.093][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:48.094][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:48.095][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:48.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:48.098][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:48.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:48.100][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:48.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:48.102][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:48.103][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:48.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:48.105][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:48.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:48.107][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:48.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:48.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:48.111][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:48.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:48.113][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:48.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:48.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:48.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:48.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:48.118][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:48.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:48.121][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:48.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:48.123][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:48.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:48.131][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:48.132][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:48.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:48.135][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:48.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:48.137][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:48.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:48.139][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:48.140][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:48.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:48.143][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:48.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:48.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:48.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:48.147][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:48.148][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:48.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:48.150][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:48.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:48.152][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:48.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:48.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:48.156][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:48.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:48.158][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:48.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:48.160][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:48.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:48.162][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:48.164][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:48.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:48.166][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:48.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:48.168][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:48.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:48.170][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:48.171][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:48.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:48.173][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:48.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:48.176][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:48.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:48.178][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:48.179][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:48.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:48.181][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:48.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:48.183][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:48.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:48.185][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:48.187][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:48.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:48.189][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:48.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:48.191][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:48.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:48.193][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:48.194][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:48.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:48.196][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:48.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:48.199][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:48.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:48.201][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:48.202][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:48.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:48.204][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:48.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:48.206][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:48.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:48.208][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:48.210][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:48.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:48.212][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:48.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:48.214][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:48.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:48.216][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:48.217][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:48.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:48.219][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:48.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:48.221][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:48.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:48.224][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:48.227][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2025-08-09 16:03:48.229][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2025-08-09 16:03:48.231][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:48.233][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2025-08-09 16:03:48.234][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:48.235][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-09 16:03:48.236][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:48.238][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-09 16:03:48.239][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:48.240][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-09 16:03:48.246][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2025-08-09 16:03:48.248][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-09 16:03:48.249][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:48.251][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2025-08-09 16:03:48.252][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-09 16:03:48.254][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2025-08-09 16:03:48.254][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2025-08-09 16:03:48.255][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:48.256][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:48.258][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-08-09 16:03:48.259][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:48.260][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:48.261][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-09 16:03:48.262][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:48.263][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:48.265][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-09 16:03:48.266][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-08-09 16:03:48.266][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2025-08-09 16:03:48.267][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-09 16:03:48.268][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-09 16:03:48.269][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:48.270][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:48.272][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2025-08-09 16:03:48.274][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:48.275][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2025-08-09 16:03:48.276][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:48.278][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-09 16:03:48.279][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:48.280][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-09 16:03:48.281][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:48.282][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-09 16:03:48.284][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-08-09 16:03:48.285][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-09 16:03:48.286][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:48.287][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2025-08-09 16:03:48.288][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-09 16:03:48.290][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2025-08-09 16:03:48.290][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2025-08-09 16:03:48.290][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2025-08-09 16:03:48.290][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2025-08-09 16:03:48.290][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2025-08-09 16:03:48.290][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2025-08-09 16:03:48.291][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:48.292][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-09 16:03:48.293][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-08-09 16:03:48.295][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:48.296][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:48.297][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-09 16:03:48.298][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:48.299][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:48.300][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-09 16:03:48.301][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-08-09 16:03:48.301][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-08-09 16:03:48.303][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-09 16:03:48.304][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-09 16:03:48.305][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:48.306][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:48.308][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2025-08-09 16:03:48.310][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:48.311][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2025-08-09 16:03:48.312][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:48.313][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-09 16:03:48.315][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:48.316][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-09 16:03:48.317][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:48.318][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-09 16:03:48.319][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-08-09 16:03:48.321][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-09 16:03:48.322][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:48.323][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2025-08-09 16:03:48.324][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-09 16:03:48.325][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-08-09 16:03:48.325][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-08-09 16:03:48.325][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='CAS-like Style']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-08-09 16:03:48.325][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-08-09 16:03:48.325][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-08-09 16:03:48.325][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-08-09 16:03:48.325][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-08-09 16:03:48.325][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-08-09 16:03:48.325][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-08-09 16:03:48.325][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-08-09 16:03:48.325][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2025-08-09 16:03:48.325][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-08-09 16:03:48.325][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-08-09 16:03:48.325][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-08-09 16:03:48.327][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:48.328][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-09 16:03:48.328][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-09 16:03:48.328][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-09 16:03:48.329][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-08-09 16:03:48.331][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:48.332][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:48.333][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-09 16:03:48.334][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:48.335][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:48.336][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-09 16:03:48.337][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-08-09 16:03:48.337][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-08-09 16:03:48.337][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-08-09 16:03:48.339][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-09 16:03:48.340][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-09 16:03:48.341][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:48.342][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-08-09 16:03:48.344][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2025-08-09 16:03:48.346][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:48.347][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2025-08-09 16:03:48.348][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:48.349][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-09 16:03:48.351][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:48.352][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-09 16:03:48.353][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:48.354][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-09 16:03:48.356][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-08-09 16:03:48.362][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-09 16:03:48.363][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:48.365][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2025-08-09 16:03:48.366][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-09 16:03:48.368][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2025-08-09 16:03:48.368][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-08-09 16:03:48.369][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:48.370][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:48.371][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-08-09 16:03:48.373][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:48.374][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:48.375][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-09 16:03:48.376][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:48.377][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:48.378][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-09 16:03:48.380][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-08-09 16:03:48.380][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-08-09 16:03:48.380][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-08-09 16:03:48.381][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-09 16:03:48.382][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-09 16:03:48.383][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:48.384][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-08-09 16:03:48.386][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2025-08-09 16:03:48.388][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-08-09 16:03:48.389][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-08-09 16:03:48.391][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2025-08-09 16:03:48.393][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-08-09 16:03:48.394][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2025-08-09 16:03:48.400][super$initialize] Initialize connector ncbi.pubchem.subst.
biodb.DEBUG[2025-08-09 16:03:48.421][biodb$getFactory()$createConn] Creating new connector ncbi.pubchem.subst for database class ncbi.pubchem.subst .
biodb.INFO [2025-08-09 16:03:48.427][biodb::testThat]
biodb.INFO [2025-08-09 16:03:48.428][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2025-08-09 16:03:48.429][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-09 16:03:48.431][biodb::testThat]
biodb.TRACE[2025-08-09 16:03:48.435][loadFileContents] Loaded 1 files from cache: [1]: "F:/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.pubchem.subst-3-content.xml".
biodb.DEBUG[2025-08-09 16:03:48.436][biodb$getFactory()$createEntryFromCo ...] Creating PubChem Substance entries from 1 content(s).
biodb.DEBUG[2025-08-09 16:03:48.440][biodb$getFactory()$createEntryFromCo ...] Parsing 1 PubChem Substance entries.
biodb.DEBUG[2025-08-09 16:03:48.442][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-09 16:03:48.443][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:48.444][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:48.451][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:48.452][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:48.453][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:48.454][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-09 16:03:48.457][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:48.459][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:48.460][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:48.461][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:48.463][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:48.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:48.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:48.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:48.468][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-09 16:03:48.469][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-09 16:03:48.470][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:48.471][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:48.473][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-09 16:03:48.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-09 16:03:48.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:48.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:48.478][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-08-09 16:03:48.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-08-09 16:03:48.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:48.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:48.483][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-08-09 16:03:48.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-08-09 16:03:48.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:48.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:48.488][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:48.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:48.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:48.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:48.499][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-08-09 16:03:48.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-08-09 16:03:48.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:48.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:48.505][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:48.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:48.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:48.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:48.510][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:48.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:48.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:48.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:48.515][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:48.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:48.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:48.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:48.520][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:48.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:48.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:48.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:48.525][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:48.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:48.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:48.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:48.530][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:48.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:48.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:48.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-09 16:03:48.535][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 3.
biodb.TRACE[2025-08-09 16:03:48.537][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-08-09 16:03:48.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-08-09 16:03:48.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:48.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:48.542][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-08-09 16:03:48.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-08-09 16:03:48.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:48.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:48.547][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-08-09 16:03:48.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-08-09 16:03:48.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:48.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:48.552][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-09 16:03:48.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-09 16:03:48.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:48.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:48.557][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-09 16:03:48.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-09 16:03:48.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:48.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:48.562][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-08-09 16:03:48.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-08-09 16:03:48.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:48.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:48.567][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-08-09 16:03:48.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-08-09 16:03:48.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:48.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:48.574][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:48.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:48.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:48.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:48.584][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-08-09 16:03:48.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-08-09 16:03:48.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:48.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:48.596][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:48.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:48.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:48.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:48.601][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:48.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:48.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:48.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:48.606][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:48.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:48.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:48.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:48.618][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:48.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:48.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:48.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:48.624][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:48.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:48.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:48.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:48.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:48.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:48.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:48.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:48.634][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-08-09 16:03:48.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-08-09 16:03:48.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:48.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:48.639][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-08-09 16:03:48.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-08-09 16:03:48.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:48.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:48.644][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-08-09 16:03:48.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-08-09 16:03:48.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:48.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:48.657][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:48.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:48.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:48.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:48.662][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:48.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:48.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:48.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:48.667][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:48.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:48.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:48.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:48.671][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:48.673][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:48.674][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:48.675][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:48.676][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:48.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:48.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:48.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:48.690][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-09 16:03:48.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-09 16:03:48.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:48.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:48.696][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-09 16:03:48.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-09 16:03:48.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:48.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:48.700][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-09 16:03:48.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-09 16:03:48.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:48.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:48.705][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-09 16:03:48.707][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-09 16:03:48.708][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:48.709][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:48.710][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-09 16:03:48.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-09 16:03:48.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:48.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:48.727][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:48.728][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:48.729][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:48.730][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:48.743][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-09 16:03:48.744][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-09 16:03:48.746][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:48.747][ef$get] fields variable is a list.
biodb.INFO [2025-08-09 16:03:48.759][biodb::testThat]
biodb.INFO [2025-08-09 16:03:48.760][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-08-09 16:03:48.761][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-09 16:03:48.762][biodb::testThat]
biodb.DEBUG[2025-08-09 16:03:48.765][private$loadEntries] Creating entries from ids [1]: "3".
biodb.DEBUG[2025-08-09 16:03:48.785][conn$getEntryContent] Get PubChem Substance entry content(s) for 1 id(s)...
fscache.INFO [2025-08-09 16:03:48.787][cch$loadContents] Load 1 contents, from C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.subst-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-08-09 16:03:48.788][conn$getEntryContent] 0 PubChem Substance entry content(s) loaded from cache.
biodb.DEBUG[2025-08-09 16:03:48.789][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Substance database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-08-09 16:03:48.791][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-09 16:03:48.792][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-08-09 16:03:48.793][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.INFO [2025-08-09 16:03:48.808][biodb::testThat]
biodb.INFO [2025-08-09 16:03:48.809][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2025-08-09 16:03:48.811][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-09 16:03:48.812][biodb::testThat]
biodb.INFO [2025-08-09 16:03:48.821][biodb::testThat]
biodb.INFO [2025-08-09 16:03:48.822][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2025-08-09 16:03:48.823][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-09 16:03:48.824][biodb::testThat]
biodb.WARN [2025-08-09 16:03:48.828][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-08-09 16:03:48.832][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-08-09 16:03:48.843][biodb::testThat]
biodb.INFO [2025-08-09 16:03:48.845][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2025-08-09 16:03:48.846][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-09 16:03:48.847][biodb::testThat]
biodb.DEBUG[2025-08-09 16:03:48.852][private$loadEntries] Creating entries from ids [1]: "3".
biodb.DEBUG[2025-08-09 16:03:48.853][conn$getEntryContent] Get PubChem Substance entry content(s) for 1 id(s)...
fscache.INFO [2025-08-09 16:03:48.876][cch$loadContents] Load 1 contents, from C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/ncbi.pubchem.subst-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-08-09 16:03:48.878][conn$getEntryContent] 0 PubChem Substance entry content(s) loaded from cache.
biodb.DEBUG[2025-08-09 16:03:48.880][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Substance database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-08-09 16:03:48.881][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-09 16:03:48.882][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-08-09 16:03:48.883][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.INFO [2025-08-09 16:03:48.898][biodb::testThat]
biodb.INFO [2025-08-09 16:03:48.900][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-08-09 16:03:48.901][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-09 16:03:48.902][biodb::testThat]
biodb.INFO [2025-08-09 16:03:48.918][biodb::testThat]
biodb.INFO [2025-08-09 16:03:48.919][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-08-09 16:03:48.920][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-09 16:03:48.921][biodb::testThat]
biodb.INFO [2025-08-09 16:03:48.937][biodb::testThat]
biodb.INFO [2025-08-09 16:03:48.938][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2025-08-09 16:03:48.939][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-09 16:03:48.941][biodb::testThat]
biodb.INFO [2025-08-09 16:03:48.957][biodb::testThat]
biodb.INFO [2025-08-09 16:03:48.958][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2025-08-09 16:03:48.959][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-09 16:03:48.960][biodb::testThat]
biodb.INFO [2025-08-09 16:03:48.982][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-08-09 16:03:48.983][self$deleteConn] Connector "ncbi.pubchem.subst" deleted.
biodb.DEBUG[2025-08-09 16:03:48.984][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-08-09 16:03:48.985][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:48.987][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:48.988][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:48.989][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:48.990][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:48.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 31 | WARN 1 | SKIP 0 | PASS 247 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_long_100_ccds.R:37:1'): RT unit is defined when there is an RT value. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<NcbCcdsC>`, opt = `<named list>`)
3. └─conn$getBiodb()$getFactory()$getEntry(...)
4. └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
5. └─conn$getEntryContent(ids)
6. └─self$getEntryContentFromDb(ch.missing.ids)
7. └─private$doGetEntryContentFromDb(entry.id)
8. └─private$doGetEntryContentOneByOne(id)
9. └─self$getEntryContentRequest(entry.id, concatenate = FALSE)
10. └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
11. └─self$getEntryPageUrl(id)
12. └─private$doGetEntryPageUrl(entry.id)
13. └─base::vapply(id, fct, FUN.VALUE = "")
14. └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_100_ccds.R:37:1'): We can load an entry from the database. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<NcbCcdsC>`, 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$getEntryContent(ids)
8. └─self$getEntryContentFromDb(ch.missing.ids)
9. └─private$doGetEntryContentFromDb(entry.id)
10. └─private$doGetEntryContentOneByOne(id)
11. └─self$getEntryContentRequest(entry.id, concatenate = FALSE)
12. └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
13. └─self$getEntryPageUrl(id)
14. └─private$doGetEntryPageUrl(entry.id)
15. └─base::vapply(id, fct, FUN.VALUE = "")
16. └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_100_ccds.R:37:1'): We can get a URL pointing to the entry page. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<NcbCcdsC>`, opt = `<named list>`)
3. └─conn$getEntryPageUrl(ref.ids)
4. └─private$doGetEntryPageUrl(entry.id)
5. └─base::vapply(id, fct, FUN.VALUE = "")
6. └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_100_ccds.R:37:1'): The entry page URL can be downloaded. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<NcbCcdsC>`, opt = `<named list>`)
3. └─conn$getEntryPageUrl(ref.ids[[1]])
4. └─private$doGetEntryPageUrl(entry.id)
5. └─base::vapply(id, fct, FUN.VALUE = "")
6. └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_200_gene.R:37:1'): Entry fields have a correct value ──────
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
3. └─opt$refEntries$saveEntriesAsJson(id, list(e))
4. └─private$bdb$saveEntriesAsJson(entries, json.files)
5. └─entries[[i]]$getFieldsAsJson(compute = compute)
6. └─self$computeFields()
7. └─private$computeField(f)
8. └─self$getBiodb()$getFactory()$getEntry(db, id = db.id)
9. └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
10. └─conn$getEntryContent(ids)
11. └─self$getEntryContentFromDb(ch.missing.ids)
12. └─private$doGetEntryContentFromDb(entry.id)
13. └─private$doGetEntryContentOneByOne(id)
14. └─self$getEntryContentRequest(entry.id, concatenate = FALSE)
15. └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
16. └─self$getEntryPageUrl(id)
17. └─private$doGetEntryPageUrl(entry.id)
18. └─base::vapply(id, fct, FUN.VALUE = "")
19. └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_200_gene.R:37:1'): RT unit is defined when there is an RT value. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
3. └─conn$getBiodb()$getFactory()$getEntry(...)
4. └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
5. └─conn$getEntryContent(ids)
6. └─self$getEntryContentFromDb(ch.missing.ids)
7. └─private$doGetEntryContentFromDb(entry.id)
8. └─private$retrieveContents(...)
9. └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
10. └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
11. └─self$wsEfetch(id, retmode = "xml", retfmt = "request")
── Error ('test_long_200_gene.R:37:1'): We can search for an entry by searchable field ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
3. └─conn$getEntry(id, drop = TRUE)
4. └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
5. └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
6. └─conn$getEntryContent(ids)
7. └─self$getEntryContentFromDb(ch.missing.ids)
8. └─private$doGetEntryContentFromDb(entry.id)
9. └─private$retrieveContents(...)
10. └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
11. └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
12. └─self$wsEfetch(id, retmode = "xml", retfmt = "request")
── Error ('test_long_200_gene.R:37:1'): We can search for an entry by name. ────
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
3. └─conn$getEntry(id, drop = TRUE)
4. └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
5. └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
6. └─conn$getEntryContent(ids)
7. └─self$getEntryContentFromDb(ch.missing.ids)
8. └─private$doGetEntryContentFromDb(entry.id)
9. └─private$retrieveContents(...)
10. └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
11. └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
12. └─self$wsEfetch(id, retmode = "xml", retfmt = "request")
── Error ('test_long_200_gene.R:37:1'): We can load an entry from the database. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, 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$getEntryContent(ids)
8. └─self$getEntryContentFromDb(ch.missing.ids)
9. └─private$doGetEntryContentFromDb(entry.id)
10. └─private$retrieveContents(...)
11. └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
12. └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
13. └─self$wsEfetch(id, retmode = "xml", retfmt = "request")
── Error ('test_long_200_gene.R:37:1'): We can get a URL pointing to the entry page. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
3. └─conn$getEntryPageUrl(ref.ids)
4. └─private$doGetEntryPageUrl(entry.id)
5. └─base::vapply(id, fct, FUN.VALUE = "")
6. └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_200_gene.R:37:1'): The entry page URL can be downloaded. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
3. └─conn$getEntryPageUrl(ref.ids[[1]])
4. └─private$doGetEntryPageUrl(entry.id)
5. └─base::vapply(id, fct, FUN.VALUE = "")
6. └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_300_pubchem.comp.R:37:1'): RT unit is defined when there is an RT value. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
3. └─conn$getBiodb()$getFactory()$getEntry(...)
4. └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
5. └─conn$getEntryContent(ids)
6. └─self$getEntryContentFromDb(ch.missing.ids)
7. └─private$doGetEntryContentFromDb(entry.id)
8. └─private$retrieveContents(...)
9. └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
10. └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): We can search for an entry by searchable field ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
3. └─conn$getEntry(id, drop = TRUE)
4. └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
5. └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
6. └─conn$getEntryContent(ids)
7. └─self$getEntryContentFromDb(ch.missing.ids)
8. └─private$doGetEntryContentFromDb(entry.id)
9. └─private$retrieveContents(...)
10. └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
11. └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): We can search for an entry by name. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
3. └─conn$getEntry(id, drop = TRUE)
4. └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
5. └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
6. └─conn$getEntryContent(ids)
7. └─self$getEntryContentFromDb(ch.missing.ids)
8. └─private$doGetEntryContentFromDb(entry.id)
9. └─private$retrieveContents(...)
10. └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
11. └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): We can load an entry from the database. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, 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$getEntryContent(ids)
8. └─self$getEntryContentFromDb(ch.missing.ids)
9. └─private$doGetEntryContentFromDb(entry.id)
10. └─private$retrieveContents(...)
11. └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
12. └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): We can get a URL pointing to the entry page. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
3. └─conn$getEntryPageUrl(ref.ids)
4. └─private$doGetEntryPageUrl(entry.id)
5. └─base::vapply(id, fct, FUN.VALUE = "")
6. └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_300_pubchem.comp.R:37:1'): We can get a URL pointing to the entry image. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
3. └─conn$getEntryImageUrl(ref.ids)
4. └─private$doGetEntryImageUrl(entry.id)
── Error ('test_long_300_pubchem.comp.R:37:1'): The entry page URL can be downloaded. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
3. └─conn$getEntryPageUrl(ref.ids[[1]])
4. └─private$doGetEntryPageUrl(entry.id)
5. └─base::vapply(id, fct, FUN.VALUE = "")
6. └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_300_pubchem.comp.R:37:1'): The entry image URL can be downloaded. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
3. └─conn$getEntryImageUrl(ref.ids[[1]])
4. └─private$doGetEntryImageUrl(entry.id)
── Error ('test_long_300_pubchem.comp.R:37:1'): We can search for a compound ───
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(db = `<NcbPbcCC>`, opt = `<named list>`)
3. └─db$getEntry(id, drop = TRUE)
4. └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
5. └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
6. └─conn$getEntryContent(ids)
7. └─self$getEntryContentFromDb(ch.missing.ids)
8. └─private$doGetEntryContentFromDb(entry.id)
9. └─private$retrieveContents(...)
10. └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
11. └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): annotateMzValues() accepts a single vector. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
3. └─conn$getEntry(ids, drop = FALSE)
4. └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
5. └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
6. └─conn$getEntryContent(ids)
7. └─self$getEntryContentFromDb(ch.missing.ids)
8. └─private$doGetEntryContentFromDb(entry.id)
9. └─private$retrieveContents(...)
10. └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
11. └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): ppm tolerance works in annotateMzValues() ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
3. └─conn$getEntry(ids, drop = FALSE)
4. └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
5. └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
6. └─conn$getEntryContent(ids)
7. └─self$getEntryContentFromDb(ch.missing.ids)
8. └─private$doGetEntryContentFromDb(entry.id)
9. └─private$retrieveContents(...)
10. └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
11. └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): Input data frame is not modified by annotateMzValues() ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
3. └─conn$getEntry(ids, drop = FALSE)
4. └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
5. └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
6. └─conn$getEntryContent(ids)
7. └─self$getEntryContentFromDb(ch.missing.ids)
8. └─private$doGetEntryContentFromDb(entry.id)
9. └─private$retrieveContents(...)
10. └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
11. └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): annotateMzValues() works correctly with real values. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
3. └─conn$getEntry(ids, drop = FALSE)
4. └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
5. └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
6. └─conn$getEntryContent(ids)
7. └─self$getEntryContentFromDb(ch.missing.ids)
8. └─private$doGetEntryContentFromDb(entry.id)
9. └─private$retrieveContents(...)
10. └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
11. └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): Additional fields are accepted in annotateMzValues() ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
3. └─conn$getEntry(ids, drop = FALSE)
4. └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
5. └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
6. └─conn$getEntryContent(ids)
7. └─self$getEntryContentFromDb(ch.missing.ids)
8. └─private$doGetEntryContentFromDb(entry.id)
9. └─private$retrieveContents(...)
10. └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
11. └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_400_pubchem.subst.R:37:1'): RT unit is defined when there is an RT value. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
3. └─conn$getBiodb()$getFactory()$getEntry(...)
4. └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
5. └─conn$getEntryContent(ids)
6. └─self$getEntryContentFromDb(ch.missing.ids)
7. └─private$doGetEntryContentFromDb(entry.id)
8. └─private$retrieveContents(...)
9. └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
10. └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_400_pubchem.subst.R:37:1'): We can load an entry from the database. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
3. └─opt$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$getEntryContentFromDb(ch.missing.ids)
9. └─private$doGetEntryContentFromDb(entry.id)
10. └─private$retrieveContents(...)
11. └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
12. └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_400_pubchem.subst.R:37:1'): We can get a URL pointing to the entry page. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
3. └─conn$getEntryPageUrl(ref.ids)
4. └─private$doGetEntryPageUrl(entry.id)
5. └─base::vapply(id, fct, FUN.VALUE = "")
6. └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_400_pubchem.subst.R:37:1'): We can get a URL pointing to the entry image. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
3. └─conn$getEntryImageUrl(ref.ids)
4. └─private$doGetEntryImageUrl(entry.id)
── Error ('test_long_400_pubchem.subst.R:37:1'): The entry page URL can be downloaded. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
3. └─conn$getEntryPageUrl(ref.ids[[1]])
4. └─private$doGetEntryPageUrl(entry.id)
5. └─base::vapply(id, fct, FUN.VALUE = "")
6. └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_400_pubchem.subst.R:37:1'): The entry image URL can be downloaded. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
3. └─conn$getEntryImageUrl(ref.ids[[1]])
4. └─private$doGetEntryImageUrl(entry.id)
[ FAIL 31 | WARN 1 | SKIP 0 | PASS 247 ]
Error: Test failures
In addition: Warning message:
In fun(libname, pkgname) :
Package 'biodbNcbi' is deprecated and will be removed from Bioconductor
version 3.23
Execution halted
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.22-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 biodbNcbi_1.13.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* 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 'biodbNcbi/DESCRIPTION' ... OK
* this is package 'biodbNcbi' version '1.13.1'
* 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 'biodbNcbi' can be installed ... OK
* checking installed package size ... INFO
installed size is 8.1Mb
sub-directories of 1Mb or more:
testref 7.6Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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 whether startup messages can be suppressed ... 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
NcbiCcdsConn.Rd: BiodbFactory, BiodbConn
NcbiCcdsEntry.Rd: BiodbHtmlEntry
NcbiEntrezConn.Rd: BiodbConn
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 files in 'vignettes' ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in 'longtests' ... WARNING
'library' or 'require' call not declared from: 'biodbNci'
* checking tests in 'longtests' ...
Running 'testthat.R'
ERROR
Running the tests in 'longtests/testthat.R' failed.
Last 13 lines of output:
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
3. └─conn$getEntryImageUrl(ref.ids[[1]])
4. └─private$doGetEntryImageUrl(entry.id)
[ FAIL 31 | WARN 1 | SKIP 0 | PASS 247 ]
Error: Test failures
In addition: Warning message:
In fun(libname, pkgname) :
Package 'biodbNcbi' is deprecated and will be removed from Bioconductor
version 3.23
Execution halted
* DONE
Status: 1 ERROR, 1 WARNING, 2 NOTEs
See
'F:/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/00check.log'
for details.
biodbNcbi.Rcheck/00install.out
* installing *source* package 'biodbNcbi' ... ** this is package 'biodbNcbi' version '1.13.1' ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning in fun(libname, pkgname) : Package 'biodbNcbi' is deprecated and will be removed from Bioconductor version 3.23 ** testing if installed package can be loaded from final location Warning in fun(libname, pkgname) : Package 'biodbNcbi' is deprecated and will be removed from Bioconductor version 3.23 ** testing if installed package keeps a record of temporary installation path * DONE (biodbNcbi)