| Back to Long Tests report for BioC 3.19 |
This page was generated on 2024-05-11 23:55:01 -0400 (Sat, 11 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4751 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4485 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4515 |
| 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 7/33 | Hostname | OS / Arch | CHECK | |||||||
| biodbExpasy 1.8.0 (landing page) Pierrick Roger
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | |||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | ||||||||
|
To the developers/maintainers of the biodbExpasy 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: biodbExpasy |
| Version: 1.8.0 |
| Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbExpasy_1.8.0.tar.gz |
| StartedAt: 2024-05-11 16:04:36 -0400 (Sat, 11 May 2024) |
| EndedAt: 2024-05-11 16:05:20 -0400 (Sat, 11 May 2024) |
| EllapsedTime: 43.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: biodbExpasy.Rcheck |
| Warnings: 0 |
biodbExpasy.Rcheck/tests/testthat.Rout
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbExpasy)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbExpasy")
biodb.INFO [2024-05-11 16:05:12.816][biodb::testContext]
biodb.INFO [2024-05-11 16:05:12.819][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-11 16:05:12.820][biodb::testContext] Test context - Generic long tests
biodb.INFO [2024-05-11 16:05:12.821][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-11 16:05:12.822][biodb::testContext]
biodb.INFO [2024-05-11 16:05:12.829][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-05-11 16:05:12.831][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-05-11 16:05:12.838][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-11 16:05:12.840][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-11 16:05:12.841][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-11 16:05:12.842][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:12.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:12.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:12.845][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-11 16:05:12.865][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-11 16:05:12.866][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:12.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:12.867][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[2024-05-11 16:05:12.868][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-11 16:05:12.870][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-11 16:05:12.870][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:12.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:12.872][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:12.873][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-11 16:05:12.874][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-11 16:05:12.875][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-11 16:05:12.876][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:12.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:12.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:12.879][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-11 16:05:12.880][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-11 16:05:12.881][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-11 16:05:12.882][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:12.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:12.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:12.885][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-11 16:05:12.886][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-11 16:05:12.887][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:12.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:12.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:12.890][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-11 16:05:12.891][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-11 16:05:12.892][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-11 16:05:12.893][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:12.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:12.895][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:12.896][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-11 16:05:12.897][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-11 16:05:12.898][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:12.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:12.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:12.900][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-11 16:05:12.901][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-11 16:05:12.903][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-11 16:05:12.903][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:12.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:12.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:12.906][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-11 16:05:12.907][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-11 16:05:12.908][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-11 16:05:12.909][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-11 16:05:12.910][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-11 16:05:12.911][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-11 16:05:12.912][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:12.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:12.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:12.915][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-11 16:05:12.916][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-11 16:05:12.917][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:12.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:12.919][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:12.920][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-11 16:05:12.921][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-11 16:05:12.922][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:12.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:12.924][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[2024-05-11 16:05:12.925][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-11 16:05:12.926][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-11 16:05:12.927][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:12.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:12.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:12.930][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-11 16:05:12.931][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-11 16:05:12.932][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:12.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:12.933][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:12.934][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-11 16:05:12.935][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-11 16:05:12.936][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:12.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:12.938][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:12.939][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-11 16:05:12.940][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-11 16:05:12.944][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-11 16:05:12.945][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:12.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:12.947][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:12.948][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-11 16:05:12.949][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-11 16:05:12.950][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-11 16:05:12.951][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:12.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:12.952][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:12.957][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-11 16:05:12.993][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-11 16:05:13.016][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-05-11 16:05:13.017][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-11 16:05:13.018][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-11 16:05:13.019][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-11 16:05:13.019][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-11 16:05:13.020][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-11 16:05:13.021][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-11 16:05:13.022][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-11 16:05:13.023][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-11 16:05:13.024][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-11 16:05:13.025][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-11 16:05:13.026][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-11 16:05:13.027][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:05:13.027][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-11 16:05:13.028][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-11 16:05:13.028][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-11 16:05:13.028][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-11 16:05:13.028][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-11 16:05:13.028][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-11 16:05:13.029][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-11 16:05:13.030][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:05:13.031][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:05:13.032][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-11 16:05:13.033][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:05:13.034][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:05:13.034][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-11 16:05:13.035][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:05:13.036][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-11 16:05:13.037][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-11 16:05:13.038][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-11 16:05:13.039][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:05:13.040][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-11 16:05:13.041][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-11 16:05:13.042][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-11 16:05:13.043][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-11 16:05:13.044][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-11 16:05:13.045][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-11 16:05:13.046][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-11 16:05:13.047][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-11 16:05:13.048][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-11 16:05:13.049][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-11 16:05:13.050][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-11 16:05:13.050][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-11 16:05:13.051][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-11 16:05:13.052][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-11 16:05:13.053][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:05:13.054][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-11 16:05:13.055][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-11 16:05:13.055][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-11 16:05:13.055][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-11 16:05:13.055][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-11 16:05:13.055][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-11 16:05:13.056][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-11 16:05:13.057][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:05:13.058][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:05:13.058][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-11 16:05:13.059][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:05:13.060][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:05:13.061][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-11 16:05:13.062][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:05:13.063][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-11 16:05:13.064][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-11 16:05:13.064][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-11 16:05:13.065][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:05:13.066][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-11 16:05:13.068][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-11 16:05:13.069][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-05-11 16:05:13.070][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-11 16:05:13.071][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-11 16:05:13.072][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-11 16:05:13.072][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-11 16:05:13.073][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-11 16:05:13.074][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-11 16:05:13.075][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-11 16:05:13.076][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-11 16:05:13.077][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-11 16:05:13.078][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-11 16:05:13.079][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-11 16:05:13.080][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:05:13.081][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-11 16:05:13.081][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:05:13.082][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-11 16:05:13.083][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:05:13.084][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:05:13.085][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-11 16:05:13.086][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:05:13.087][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:05:13.087][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-11 16:05:13.088][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:05:13.089][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-11 16:05:13.090][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-11 16:05:13.091][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-11 16:05:13.092][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:05:13.093][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-11 16:05:13.095][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-11 16:05:13.095][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-11 16:05:13.096][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-11 16:05:13.097][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-11 16:05:13.098][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-11 16:05:13.099][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-11 16:05:13.100][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-11 16:05:13.101][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-11 16:05:13.102][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-11 16:05:13.103][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-11 16:05:13.104][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-11 16:05:13.105][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-11 16:05:13.105][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-11 16:05:13.106][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:05:13.107][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-11 16:05:13.108][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:05:13.109][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-11 16:05:13.110][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:05:13.111][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:05:13.112][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-11 16:05:13.112][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:05:13.113][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:05:13.114][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-11 16:05:13.115][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:05:13.116][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-11 16:05:13.117][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-11 16:05:13.118][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-11 16:05:13.118][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:05:13.122][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-11 16:05:13.123][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:13.124][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:13.125][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:13.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:13.126][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:13.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:13.128][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:13.133][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:13.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:13.135][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:13.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:13.137][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:13.138][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:13.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:13.140][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:13.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:13.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:13.143][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:13.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:13.144][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:13.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:13.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:13.147][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:13.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:13.149][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:13.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:13.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:13.152][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:13.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:13.153][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:13.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:13.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:13.156][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:13.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:13.158][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:13.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:13.160][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:13.160][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:13.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:13.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:13.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:13.164][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:13.165][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:13.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:13.167][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:13.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:13.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:13.169][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:13.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:13.171][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:13.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:13.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:13.174][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:13.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:13.176][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:13.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:13.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:13.178][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:13.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:13.180][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:13.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:13.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:13.183][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:13.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:13.184][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:13.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:13.186][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:13.187][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:13.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:13.189][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:13.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:13.191][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:13.191][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:13.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:13.193][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:13.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:13.195][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:13.196][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:13.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:13.198][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:13.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:13.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:13.200][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:13.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:13.202][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:13.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:13.204][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:13.205][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-11 16:05:13.211][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-11 16:05:13.212][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-11 16:05:13.214][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-11 16:05:13.215][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-11 16:05:13.216][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-11 16:05:13.218][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-11 16:05:13.219][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-11 16:05:13.220][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-11 16:05:13.222][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-11 16:05:13.223][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-11 16:05:13.225][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-11 16:05:13.226][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-11 16:05:13.227][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-11 16:05:13.229][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-11 16:05:13.230][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-11 16:05:13.232][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-11 16:05:13.233][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-11 16:05:13.234][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-11 16:05:13.236][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-11 16:05:13.237][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-11 16:05:13.238][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-11 16:05:13.240][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-11 16:05:13.241][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-11 16:05:13.243][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-11 16:05:13.244][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-11 16:05:13.245][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-11 16:05:13.247][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-11 16:05:13.248][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-11 16:05:13.249][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-11 16:05:13.251][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-11 16:05:13.252][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-11 16:05:13.254][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-11 16:05:13.255][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-11 16:05:13.256][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-11 16:05:13.258][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-11 16:05:13.259][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-11 16:05:13.273][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-11 16:05:13.274][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-11 16:05:13.276][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-11 16:05:13.277][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-11 16:05:13.279][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-11 16:05:13.280][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-11 16:05:13.281][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-11 16:05:13.283][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-11 16:05:13.284][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-11 16:05:13.286][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-11 16:05:13.287][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-11 16:05:13.288][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-11 16:05:13.290][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-11 16:05:13.291][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-11 16:05:13.293][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-11 16:05:13.294][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-11 16:05:13.295][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-11 16:05:13.297][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-11 16:05:13.298][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-11 16:05:13.300][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-11 16:05:13.301][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-11 16:05:13.302][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-11 16:05:13.304][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-11 16:05:13.305][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-11 16:05:13.307][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-11 16:05:13.308][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-11 16:05:13.309][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-11 16:05:13.311][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-11 16:05:13.312][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-11 16:05:13.313][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-11 16:05:13.315][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-11 16:05:13.316][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-11 16:05:13.318][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-11 16:05:13.319][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-11 16:05:13.320][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-11 16:05:13.322][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-11 16:05:13.323][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-11 16:05:13.324][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-11 16:05:13.326][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-11 16:05:13.327][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-11 16:05:13.328][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-11 16:05:13.330][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-11 16:05:13.331][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-11 16:05:13.333][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-11 16:05:13.334][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-11 16:05:13.335][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-11 16:05:13.341][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-11 16:05:13.343][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-05-11 16:05:13.346][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-11 16:05:13.347][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:13.348][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:13.349][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:13.350][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:13.355][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:13.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:05:13.356][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:05:13.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:13.358][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:13.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:13.360][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:13.361][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:13.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:05:13.363][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:05:13.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:13.364][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:13.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:13.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:13.367][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:13.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:05:13.369][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:05:13.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:13.370][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:13.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:13.372][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:13.373][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:13.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:05:13.375][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:05:13.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:13.377][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:13.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:13.378][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:13.379][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:13.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:05:13.381][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:05:13.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:13.383][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:13.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:13.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:13.385][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:13.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:05:13.387][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:05:13.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:13.389][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:13.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:13.390][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:13.391][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:13.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:05:13.393][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:05:13.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:13.395][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:13.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:13.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:13.397][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:13.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:05:13.399][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:05:13.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:13.400][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:13.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:13.402][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:13.403][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:13.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:05:13.404][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:05:13.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:13.406][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:13.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:13.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:13.408][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:13.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:05:13.410][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:05:13.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:13.412][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:13.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:13.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:13.414][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:13.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:05:13.416][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:05:13.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:13.417][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:13.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:13.419][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:13.420][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:13.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:05:13.421][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:05:13.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:13.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:13.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:13.424][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:13.425][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:13.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:05:13.427][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:05:13.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:13.429][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:13.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:13.430][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:13.431][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:13.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:05:13.433][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:05:13.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:13.434][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:13.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:13.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:13.437][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:13.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:05:13.438][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:05:13.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:13.440][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:13.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:13.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:13.442][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:13.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:05:13.444][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:05:13.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:13.446][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:13.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:13.447][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:13.448][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:13.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:05:13.450][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:05:13.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:13.451][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:13.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:13.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:13.454][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2024-05-11 16:05:13.463][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2024-05-11 16:05:13.465][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-11 16:05:13.466][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2024-05-11 16:05:13.467][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-11 16:05:13.468][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-11 16:05:13.469][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-11 16:05:13.469][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-11 16:05:13.470][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-11 16:05:13.471][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-11 16:05:13.472][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2024-05-11 16:05:13.473][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-11 16:05:13.474][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-11 16:05:13.475][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2024-05-11 16:05:13.476][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-11 16:05:13.477][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2024-05-11 16:05:13.477][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2024-05-11 16:05:13.477][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2024-05-11 16:05:13.477][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2024-05-11 16:05:13.478][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-11 16:05:13.479][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-11 16:05:13.479][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-05-11 16:05:13.480][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:05:13.481][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:05:13.482][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-11 16:05:13.483][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:05:13.484][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:05:13.485][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-11 16:05:13.485][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2024-05-11 16:05:13.486][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-11 16:05:13.487][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-11 16:05:13.488][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-11 16:05:13.489][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:05:13.494][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-11 16:05:13.520][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2024-05-11 16:05:13.522][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2024-05-11 16:05:13.525][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2024-05-11 16:05:13.529][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2024-05-11 16:05:13.533][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-11 16:05:13.534][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-11 16:05:13.535][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2024-05-11 16:05:13.544][biodb::testThat]
biodb.INFO [2024-05-11 16:05:13.545][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2024-05-11 16:05:13.546][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-11 16:05:13.547][biodb::testThat]
biodb.TRACE[2024-05-11 16:05:13.550][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.19-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.1-content.txt".
biodb.DEBUG[2024-05-11 16:05:13.552][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2024-05-11 16:05:13.555][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2024-05-11 16:05:13.564][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-11 16:05:13.565][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:05:13.565][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:05:13.577][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:13.578][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:13.579][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:13.580][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-11 16:05:13.591][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:05:13.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:05:13.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:13.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:13.618][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-11 16:05:13.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-11 16:05:13.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:13.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:13.632][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-05-11 16:05:13.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-11 16:05:13.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:13.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:13.636][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:05:13.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:05:13.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:13.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:13.640][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-05-11 16:05:13.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-11 16:05:13.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:13.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:13.644][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-05-11 16:05:13.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-11 16:05:13.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:13.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:13.647][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-05-11 16:05:13.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-11 16:05:13.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:13.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:13.651][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-05-11 16:05:13.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-11 16:05:13.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:13.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:13.655][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-05-11 16:05:13.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-11 16:05:13.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:13.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:13.674][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:05:13.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:05:13.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:13.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:13.677][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:05:13.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:05:13.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:13.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:13.711][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:05:13.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:05:13.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:13.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:13.715][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:05:13.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:05:13.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:13.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:13.718][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:05:13.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:05:13.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:13.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:13.722][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:05:13.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:05:13.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:13.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:13.726][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:05:13.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:05:13.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:13.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:13.730][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:05:13.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:05:13.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:13.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:13.733][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:05:13.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:05:13.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:13.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:13.737][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:05:13.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:05:13.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:13.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:13.748][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:05:13.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:05:13.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:13.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:13.752][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:05:13.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:05:13.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:13.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:13.756][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:05:13.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:05:13.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:13.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:13.759][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:05:13.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:05:13.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:13.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:13.763][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:05:13.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:05:13.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:13.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-11 16:05:13.766][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.1.
biodb.TRACE[2024-05-11 16:05:13.769][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-11 16:05:13.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-11 16:05:13.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:13.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:13.773][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-11 16:05:13.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-11 16:05:13.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:13.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:13.776][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-11 16:05:13.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-11 16:05:13.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:13.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:13.780][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-11 16:05:13.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-11 16:05:13.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:13.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:13.798][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:05:13.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:05:13.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:13.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:13.813][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:05:13.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:05:13.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:13.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:13.820][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:05:13.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:05:13.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:13.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:13.824][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:05:13.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:05:13.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:13.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:13.827][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:05:13.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:05:13.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:13.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:13.832][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:05:13.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:05:13.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:13.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:13.836][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:05:13.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:05:13.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:13.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:13.840][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:05:13.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:05:13.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:13.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:13.843][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:05:13.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:05:13.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:13.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:13.847][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:05:13.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:05:13.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:13.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:13.851][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:05:13.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:05:13.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:13.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:13.860][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:05:13.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:05:13.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:13.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:13.864][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:05:13.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:05:13.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:13.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:13.867][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:05:13.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:05:13.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:13.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:13.871][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:05:13.872][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:05:13.873][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:13.874][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:13.874][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:05:13.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:05:13.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:13.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:13.885][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:05:13.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:05:13.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:13.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:13.889][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:05:13.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:05:13.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:13.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:13.893][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:05:13.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:05:13.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:13.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:13.896][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:05:13.897][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:05:13.898][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:13.899][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:13.900][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:05:13.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:05:13.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:13.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:13.910][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-05-11 16:05:13.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-11 16:05:13.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:13.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:13.913][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-05-11 16:05:13.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-11 16:05:13.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:13.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:13.917][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-05-11 16:05:13.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-11 16:05:13.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:13.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:13.921][ef$get] Asked field names are: cofactor.
biodb.TRACE[2024-05-11 16:05:13.922][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-11 16:05:13.922][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:13.923][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:13.924][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-05-11 16:05:13.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-11 16:05:13.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:13.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:13.934][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-11 16:05:13.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-11 16:05:13.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:13.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:13.938][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-11 16:05:13.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-11 16:05:13.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:13.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:13.941][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-11 16:05:13.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-11 16:05:13.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:13.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:13.945][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-11 16:05:13.946][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-11 16:05:13.947][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:13.947][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:13.948][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-11 16:05:13.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-11 16:05:13.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:13.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:13.980][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:05:13.982][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:05:13.982][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:13.983][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:13.987][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-11 16:05:13.988][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-11 16:05:13.989][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:13.990][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:13.993][ef$get] Asked field names are: cofactor.
biodb.TRACE[2024-05-11 16:05:13.994][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-11 16:05:13.995][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:13.996][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.000][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:05:14.001][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:05:14.002][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.002][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.017][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.19-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.54-content.txt".
biodb.DEBUG[2024-05-11 16:05:14.049][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2024-05-11 16:05:14.050][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2024-05-11 16:05:14.052][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-11 16:05:14.053][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:05:14.054][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:05:14.058][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:14.058][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:14.059][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:14.060][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-11 16:05:14.062][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:05:14.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:05:14.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.066][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-11 16:05:14.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-11 16:05:14.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.070][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:05:14.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:05:14.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.074][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-05-11 16:05:14.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-11 16:05:14.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.078][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:05:14.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:05:14.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.081][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:05:14.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:05:14.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.085][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:05:14.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:05:14.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.088][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:05:14.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:05:14.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.092][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:05:14.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:05:14.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.096][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:05:14.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:05:14.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.099][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:05:14.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:05:14.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.103][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:05:14.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:05:14.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.106][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:05:14.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:05:14.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.110][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:05:14.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:05:14.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-11 16:05:14.114][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.54.
biodb.TRACE[2024-05-11 16:05:14.132][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-11 16:05:14.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-11 16:05:14.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.135][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-11 16:05:14.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-11 16:05:14.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.139][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-11 16:05:14.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-11 16:05:14.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.143][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-11 16:05:14.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-11 16:05:14.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.147][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:05:14.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:05:14.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.154][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:05:14.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:05:14.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.165][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:05:14.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:05:14.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.169][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:05:14.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:05:14.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.173][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:05:14.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:05:14.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.178][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:05:14.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:05:14.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.181][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:05:14.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:05:14.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.185][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:05:14.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:05:14.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.189][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:05:14.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:05:14.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.192][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:05:14.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:05:14.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.196][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:05:14.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:05:14.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.213][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:05:14.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:05:14.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.217][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:05:14.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:05:14.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.221][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:05:14.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:05:14.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.224][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:05:14.225][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:05:14.226][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.227][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.228][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:05:14.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:05:14.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.238][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:05:14.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:05:14.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.241][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:05:14.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:05:14.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.245][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:05:14.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:05:14.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.248][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:05:14.249][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:05:14.250][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.251][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.252][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:05:14.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:05:14.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.262][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-11 16:05:14.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-11 16:05:14.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.265][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-11 16:05:14.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-11 16:05:14.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.269][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-11 16:05:14.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-11 16:05:14.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.272][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-11 16:05:14.273][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-11 16:05:14.274][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.275][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.276][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-11 16:05:14.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-11 16:05:14.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.286][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:05:14.287][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:05:14.288][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.289][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.292][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-11 16:05:14.293][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-11 16:05:14.294][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.295][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.299][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:05:14.299][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:05:14.300][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.301][ef$get] fields variable is a list.
biodb.INFO [2024-05-11 16:05:14.307][biodb::testThat]
biodb.INFO [2024-05-11 16:05:14.308][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-05-11 16:05:14.309][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-11 16:05:14.310][biodb::testThat]
biodb.DEBUG[2024-05-11 16:05:14.312][private$loadEntries] Creating entries from ids [2]: "1.1.1.1, 1.1.1.54".
biodb.DEBUG[2024-05-11 16:05:14.318][conn$getEntryContent] Get Expasy ENZYME database. entry content(s) for 2 id(s)...
biodb.TRACE[2024-05-11 16:05:14.323][cch$loadFileContent] Trying to load 2 files from cache: [2]: "1.1.1.1, 1.1.1.54".
biodb.TRACE[2024-05-11 16:05:14.324][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2024-05-11 16:05:14.326][loadFileContents] Loaded 2 files from cache: [2]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.1.txt, /home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.54.txt".
biodb.DEBUG[2024-05-11 16:05:14.327][conn$getEntryContent] 2 Expasy ENZYME database. entry content(s) loaded from cache.
biodb.DEBUG[2024-05-11 16:05:14.328][self$createEntryFromContent] Creating Expasy ENZYME database. entries from 2 content(s).
biodb.DEBUG[2024-05-11 16:05:14.329][self$createEntryFromContent] Parsing 2 Expasy ENZYME database. entries.
biodb.DEBUG[2024-05-11 16:05:14.331][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-11 16:05:14.331][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:05:14.332][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:05:14.336][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:14.337][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:14.338][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:14.339][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-11 16:05:14.341][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:05:14.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:05:14.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.345][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-11 16:05:14.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-11 16:05:14.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.349][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:05:14.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:05:14.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.353][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-05-11 16:05:14.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-11 16:05:14.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.357][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:05:14.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:05:14.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.360][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:05:14.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:05:14.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.364][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:05:14.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:05:14.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.372][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:05:14.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:05:14.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.376][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:05:14.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:05:14.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.380][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:05:14.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:05:14.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.383][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:05:14.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:05:14.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.387][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:05:14.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:05:14.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.391][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:05:14.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:05:14.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.394][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:05:14.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:05:14.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.398][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:05:14.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:05:14.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.402][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:05:14.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:05:14.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-11 16:05:14.405][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-11 16:05:14.406][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:05:14.407][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:05:14.411][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:14.412][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:14.413][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:14.414][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-11 16:05:14.416][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:05:14.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:05:14.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.419][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-11 16:05:14.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-11 16:05:14.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.423][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:05:14.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:05:14.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.427][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-05-11 16:05:14.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-11 16:05:14.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.431][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:05:14.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:05:14.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.434][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:05:14.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:05:14.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.438][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:05:14.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:05:14.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.441][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:05:14.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-11 16:05:14.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.445][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:05:14.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:05:14.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.449][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:05:14.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:05:14.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.452][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:05:14.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:05:14.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.456][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:05:14.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:05:14.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.460][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:05:14.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:05:14.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.463][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:05:14.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:05:14.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.467][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:05:14.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:05:14.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.471][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:05:14.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:05:14.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.474][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:05:14.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:05:14.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-11 16:05:14.478][self$createEntryFromContent] Accession numbers: 1.1.1.1, 1.1.1.54.
biodb.TRACE[2024-05-11 16:05:14.479][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-05-11 16:05:14.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-05-11 16:05:14.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.482][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-05-11 16:05:14.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-05-11 16:05:14.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.486][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-05-11 16:05:14.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-05-11 16:05:14.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.493][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-05-11 16:05:14.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-05-11 16:05:14.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.497][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-05-11 16:05:14.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-05-11 16:05:14.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.500][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-05-11 16:05:14.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-05-11 16:05:14.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-11 16:05:14.510][biodb::testThat]
biodb.INFO [2024-05-11 16:05:14.511][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2024-05-11 16:05:14.511][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-11 16:05:14.512][biodb::testThat]
biodb.TRACE[2024-05-11 16:05:14.515][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:05:14.516][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:05:14.517][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.518][ef$get] fields variable is a list.
biodb.DEBUG[2024-05-11 16:05:14.519][function(conn, opt)] Testing searchForEntries() with entry "1.1.1.1" and field "name".
biodb.TRACE[2024-05-11 16:05:14.541][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:05:14.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:05:14.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.544][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:05:14.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:05:14.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.548][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:05:14.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:05:14.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-11 16:05:14.554][function(conn, opt)] With value "alcohol dehydrogenase".
biodb.DEBUG[2024-05-11 16:05:14.558][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2024-05-11 16:05:14.581][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-11 16:05:14.596][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f603fa2a57aec59588edc37541c6f6d5".
biodb.TRACE[2024-05-11 16:05:14.597][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-11 16:05:14.599][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content".
biodb.DEBUG[2024-05-11 16:05:14.604][function(conn, opt)] With found IDs [1]: "1.1.1.1".
biodb.INFO [2024-05-11 16:05:14.617][biodb::testThat]
biodb.INFO [2024-05-11 16:05:14.617][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2024-05-11 16:05:14.618][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-11 16:05:14.619][biodb::testThat]
biodb.TRACE[2024-05-11 16:05:14.640][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:05:14.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:05:14.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.644][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:05:14.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:05:14.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.647][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:05:14.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:05:14.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-11 16:05:14.693][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2024-05-11 16:05:14.696][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-11 16:05:14.697][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f603fa2a57aec59588edc37541c6f6d5".
biodb.TRACE[2024-05-11 16:05:14.698][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-11 16:05:14.699][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content".
biodb.INFO [2024-05-11 16:05:14.713][biodb::testThat]
biodb.INFO [2024-05-11 16:05:14.714][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2024-05-11 16:05:14.715][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-11 16:05:14.716][biodb::testThat]
biodb.TRACE[2024-05-11 16:05:14.724][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-11 16:05:14.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-11 16:05:14.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.728][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-11 16:05:14.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-11 16:05:14.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.732][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-11 16:05:14.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-11 16:05:14.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.735][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-11 16:05:14.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-11 16:05:14.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.774][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-11 16:05:14.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-11 16:05:14.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.778][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-11 16:05:14.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-11 16:05:14.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.781][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-11 16:05:14.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-11 16:05:14.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:14.785][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-11 16:05:14.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-11 16:05:14.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:14.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-11 16:05:14.793][biodb::testThat]
biodb.INFO [2024-05-11 16:05:14.794][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-05-11 16:05:14.795][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-11 16:05:14.796][biodb::testThat]
biodb.INFO [2024-05-11 16:05:14.803][biodb::testThat]
biodb.INFO [2024-05-11 16:05:14.804][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-05-11 16:05:14.805][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-11 16:05:14.806][biodb::testThat]
biodb.INFO [2024-05-11 16:05:14.812][biodb::testThat]
biodb.INFO [2024-05-11 16:05:14.813][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2024-05-11 16:05:14.814][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-11 16:05:14.815][biodb::testThat]
biodb.DEBUG[2024-05-11 16:05:14.827][function(conn, opt)] Trying to download "https://enzyme.expasy.org/cgi-bin/enzyme/enzyme-search-ec?field1=1&field2=1&field3=1&field4=1".
biodb.DEBUG[2024-05-11 16:05:15.786][getUrlContent] Use RCurl for downloading content of URL https://enzyme.expasy.org/cgi-bin/enzyme/enzyme-search-ec?field1=1&field2=1&field3=1&field4=1.
biodb.INFO [2024-05-11 16:05:16.551][biodb::testThat]
biodb.INFO [2024-05-11 16:05:16.553][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2024-05-11 16:05:16.555][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-11 16:05:16.557][biodb::testThat]
biodb.DEBUG[2024-05-11 16:05:18.124][getUrlContent] Use RCurl for downloading content of URL https://enzyme.expasy.org/images/1.1.1.1/image.png.
biodb.TRACE[2024-05-11 16:05:18.523][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:05:18.526][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:05:18.528][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:18.531][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:05:18.533][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:05:18.536][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:05:18.539][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:05:18.541][ef$get] fields variable is a list.
biodb.INFO [2024-05-11 16:05:18.544][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-11 16:05:18.547][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2024-05-11 16:05:18.550][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2024-05-11 16:05:18.552][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-11 16:05:18.554][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:05:18.556][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:05:18.558][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:18.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:18.562][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:18.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-05-11 16:05:18.580][biodb::testContext]
biodb.INFO [2024-05-11 16:05:18.582][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-11 16:05:18.583][biodb::testContext] Test context - Example long tests
biodb.INFO [2024-05-11 16:05:18.584][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-11 16:05:18.585][biodb::testContext]
biodb.INFO [2024-05-11 16:05:18.588][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-05-11 16:05:18.591][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-05-11 16:05:18.595][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-11 16:05:18.596][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-11 16:05:18.598][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-11 16:05:18.598][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:18.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:18.600][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:18.601][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-11 16:05:18.603][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-11 16:05:18.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:18.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:18.605][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:18.606][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-11 16:05:18.607][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-11 16:05:18.608][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:18.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:18.610][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:18.611][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-11 16:05:18.612][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-11 16:05:18.613][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-11 16:05:18.614][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:18.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:18.616][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:18.617][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-11 16:05:18.618][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-11 16:05:18.619][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-11 16:05:18.619][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:18.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:18.621][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:18.622][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-11 16:05:18.623][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-11 16:05:18.624][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:18.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:18.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:18.627][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-11 16:05:18.628][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-11 16:05:18.629][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-11 16:05:18.630][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:18.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:18.631][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:18.632][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-11 16:05:18.633][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-11 16:05:18.634][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:18.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:18.636][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:18.637][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-11 16:05:18.638][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-11 16:05:18.639][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-11 16:05:18.640][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:18.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:18.642][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:18.643][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-11 16:05:18.644][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-11 16:05:18.645][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-11 16:05:18.646][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-11 16:05:18.647][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-11 16:05:18.648][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-11 16:05:18.649][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:18.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:18.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:18.651][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-11 16:05:18.652][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-11 16:05:18.653][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:18.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:18.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:18.656][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-11 16:05:18.657][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-11 16:05:18.658][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:18.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:18.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:18.661][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-11 16:05:18.662][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-11 16:05:18.663][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:18.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:18.665][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:18.665][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-11 16:05:18.667][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-11 16:05:18.667][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:18.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:18.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:18.670][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-11 16:05:18.671][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-11 16:05:18.672][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:18.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:18.674][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:18.675][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-11 16:05:18.676][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-11 16:05:18.679][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-11 16:05:18.680][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:18.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:18.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:18.683][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-11 16:05:18.683][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-11 16:05:18.685][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-11 16:05:18.685][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:18.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:18.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:18.688][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-11 16:05:18.690][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-11 16:05:18.691][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-05-11 16:05:18.692][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-11 16:05:18.693][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-11 16:05:18.694][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-11 16:05:18.695][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-11 16:05:18.696][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-11 16:05:18.697][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-11 16:05:18.698][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-11 16:05:18.699][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-11 16:05:18.700][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-11 16:05:18.701][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-11 16:05:18.702][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-11 16:05:18.703][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:05:18.704][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-11 16:05:18.705][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-11 16:05:18.705][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-11 16:05:18.705][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-11 16:05:18.705][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-11 16:05:18.705][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-11 16:05:18.706][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-11 16:05:18.707][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:05:18.708][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:05:18.709][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-11 16:05:18.710][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:05:18.711][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:05:18.712][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-11 16:05:18.713][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:05:18.714][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-11 16:05:18.715][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-11 16:05:18.716][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-11 16:05:18.717][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:05:18.718][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-11 16:05:18.720][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-11 16:05:18.721][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-11 16:05:18.722][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-11 16:05:18.723][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-11 16:05:18.724][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-11 16:05:18.725][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-11 16:05:18.726][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-11 16:05:18.726][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-11 16:05:18.727][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-11 16:05:18.742][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-11 16:05:18.743][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-11 16:05:18.744][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-11 16:05:18.745][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-11 16:05:18.746][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:05:18.747][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-11 16:05:18.748][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-11 16:05:18.748][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-11 16:05:18.748][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-11 16:05:18.748][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-11 16:05:18.748][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-11 16:05:18.749][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-11 16:05:18.750][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:05:18.751][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:05:18.752][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-11 16:05:18.753][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:05:18.753][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:05:18.754][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-11 16:05:18.755][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:05:18.756][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-11 16:05:18.757][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-11 16:05:18.758][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-11 16:05:18.758][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:05:18.760][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-11 16:05:18.761][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-11 16:05:18.762][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-05-11 16:05:18.763][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-11 16:05:18.764][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-11 16:05:18.765][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-11 16:05:18.766][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-11 16:05:18.767][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-11 16:05:18.768][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-11 16:05:18.768][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-11 16:05:18.769][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-11 16:05:18.770][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-11 16:05:18.771][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-11 16:05:18.772][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-11 16:05:18.773][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:05:18.774][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-11 16:05:18.775][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:05:18.776][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-11 16:05:18.777][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:05:18.777][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:05:18.778][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-11 16:05:18.779][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:05:18.780][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:05:18.781][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-11 16:05:18.782][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:05:18.783][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-11 16:05:18.783][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-11 16:05:18.784][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-11 16:05:18.785][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:05:18.786][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-11 16:05:18.788][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-11 16:05:18.789][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-11 16:05:18.790][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-11 16:05:18.791][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-11 16:05:18.791][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-11 16:05:18.792][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-11 16:05:18.793][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-11 16:05:18.794][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-11 16:05:18.795][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-11 16:05:18.796][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-11 16:05:18.797][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-11 16:05:18.798][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-11 16:05:18.799][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-11 16:05:18.800][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:05:18.801][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-11 16:05:18.801][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:05:18.802][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-11 16:05:18.803][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:05:18.804][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:05:18.805][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-11 16:05:18.806][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:05:18.807][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:05:18.807][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-11 16:05:18.808][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:05:18.809][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-11 16:05:18.810][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-11 16:05:18.811][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-11 16:05:18.812][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:05:18.813][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-11 16:05:18.814][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:18.815][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:18.815][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:18.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:18.817][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:18.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:18.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:18.820][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:18.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:18.821][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:18.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:18.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:18.824][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:18.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:18.825][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:18.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:18.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:18.828][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:18.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:18.829][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:18.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:18.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:18.832][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:18.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:18.833][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:18.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:18.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:18.836][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:18.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:18.837][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:18.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:18.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:18.840][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:18.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:18.841][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:18.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:18.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:18.844][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:18.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:18.846][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:18.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:18.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:18.848][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:18.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:18.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:18.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:18.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:18.852][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:18.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:18.854][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:18.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:18.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:18.856][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:18.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:18.858][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:18.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:18.859][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:18.860][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:18.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:18.862][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:18.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:18.863][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:18.864][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:18.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:18.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:18.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:18.867][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[2024-05-11 16:05:18.868][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:18.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:18.870][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:18.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:18.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:18.872][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:18.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:18.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:18.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:18.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:18.876][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:18.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:18.878][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:18.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:18.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:18.880][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:18.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:18.882][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:18.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:18.884][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[2024-05-11 16:05:18.885][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-11 16:05:18.886][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-11 16:05:18.887][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-11 16:05:18.888][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-11 16:05:18.890][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-11 16:05:18.891][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-11 16:05:18.892][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-11 16:05:18.894][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-11 16:05:18.895][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-11 16:05:18.896][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-11 16:05:18.897][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-11 16:05:18.899][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-11 16:05:18.900][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-11 16:05:18.901][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-11 16:05:18.902][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-11 16:05:18.904][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-11 16:05:18.905][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-11 16:05:18.910][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-11 16:05:18.911][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-11 16:05:18.913][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-11 16:05:18.914][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-11 16:05:18.915][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-11 16:05:18.916][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-11 16:05:18.918][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-11 16:05:18.919][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-11 16:05:18.920][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-11 16:05:18.921][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-11 16:05:18.923][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-11 16:05:18.924][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-11 16:05:18.925][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-11 16:05:18.926][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-11 16:05:18.928][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-11 16:05:18.929][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-11 16:05:18.930][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-11 16:05:18.931][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-11 16:05:18.933][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-11 16:05:18.934][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-11 16:05:18.935][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-11 16:05:18.936][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-11 16:05:18.938][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-11 16:05:18.939][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-11 16:05:18.940][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-11 16:05:18.941][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-11 16:05:18.943][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-11 16:05:18.944][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-11 16:05:18.945][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-11 16:05:18.947][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-11 16:05:18.948][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-11 16:05:18.949][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-11 16:05:18.950][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-11 16:05:18.952][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-11 16:05:18.953][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-11 16:05:18.954][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-11 16:05:18.955][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-11 16:05:18.957][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-11 16:05:18.958][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-11 16:05:18.959][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-11 16:05:18.960][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-11 16:05:18.962][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-11 16:05:18.963][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-11 16:05:18.964][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-11 16:05:18.966][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-11 16:05:18.967][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-11 16:05:18.968][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-11 16:05:18.969][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-11 16:05:18.971][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-11 16:05:18.972][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-11 16:05:18.973][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-11 16:05:18.974][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-11 16:05:18.976][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-11 16:05:18.977][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-11 16:05:18.978][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-11 16:05:18.979][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-11 16:05:18.981][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-11 16:05:18.982][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-11 16:05:18.983][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-11 16:05:18.984][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-11 16:05:18.986][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-11 16:05:18.987][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-11 16:05:18.988][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-11 16:05:18.990][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-11 16:05:18.991][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-11 16:05:18.992][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-11 16:05:18.993][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-11 16:05:18.995][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-05-11 16:05:18.996][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-11 16:05:18.997][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:18.997][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:18.998][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:18.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:19.000][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:19.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:05:19.001][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:05:19.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:19.003][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:19.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:19.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:19.006][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:19.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:05:19.007][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:05:19.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:19.009][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:19.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:19.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:19.011][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:19.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:05:19.013][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:05:19.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:19.014][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:19.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:19.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:19.017][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:19.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:05:19.018][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:05:19.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:19.020][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:19.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:19.022][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:19.022][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:19.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:05:19.024][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:05:19.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:19.026][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:19.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:19.027][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:19.028][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:19.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:05:19.030][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:05:19.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:19.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:19.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:19.033][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:19.034][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:19.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:05:19.035][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:05:19.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:19.037][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:19.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:19.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:19.039][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:19.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:05:19.041][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:05:19.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:19.043][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:19.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:19.044][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:19.045][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:19.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:05:19.047][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:05:19.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:19.048][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:19.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:19.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:19.051][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:19.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:05:19.052][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:05:19.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:19.054][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:19.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:19.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:19.056][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:19.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:05:19.058][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:05:19.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:19.060][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:19.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:19.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:19.062][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:19.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:05:19.064][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:05:19.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:19.065][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:19.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:19.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:19.068][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:19.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:05:19.069][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:05:19.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:19.075][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:19.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:19.077][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:19.078][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:19.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:05:19.079][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:05:19.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:19.081][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:19.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:19.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:19.083][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:19.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:05:19.085][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:05:19.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:19.087][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:19.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:19.088][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:19.089][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:19.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:05:19.091][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:05:19.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:19.092][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:19.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:19.094][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[2024-05-11 16:05:19.095][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:05:19.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:05:19.096][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:05:19.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:19.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:19.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:19.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:05:19.101][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2024-05-11 16:05:19.102][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2024-05-11 16:05:19.104][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-11 16:05:19.105][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2024-05-11 16:05:19.106][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-11 16:05:19.107][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-11 16:05:19.108][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-11 16:05:19.109][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-11 16:05:19.109][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-11 16:05:19.110][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-11 16:05:19.111][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2024-05-11 16:05:19.112][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-11 16:05:19.113][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-11 16:05:19.114][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2024-05-11 16:05:19.115][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-11 16:05:19.116][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2024-05-11 16:05:19.116][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2024-05-11 16:05:19.116][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2024-05-11 16:05:19.116][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2024-05-11 16:05:19.117][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-11 16:05:19.118][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-11 16:05:19.119][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-05-11 16:05:19.120][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:05:19.120][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:05:19.121][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-11 16:05:19.122][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:05:19.123][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:05:19.124][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-11 16:05:19.125][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2024-05-11 16:05:19.126][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-11 16:05:19.126][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-11 16:05:19.127][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-11 16:05:19.128][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:05:19.129][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-11 16:05:19.132][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2024-05-11 16:05:19.133][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2024-05-11 16:05:19.134][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2024-05-11 16:05:19.136][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2024-05-11 16:05:19.137][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-11 16:05:19.138][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-11 16:05:19.139][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2024-05-11 16:05:19.140][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-11 16:05:19.141][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2024-05-11 16:05:19.142][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2024-05-11 16:05:19.142][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-11 16:05:19.143][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:05:19.144][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:05:19.145][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:05:19.146][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:05:19.146][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:05:19.147][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".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 84 ]
>
> proc.time()
user system elapsed
4.678 0.262 8.051
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbExpasy_1.8.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc-longtests/meat/biodbExpasy.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbExpasy/DESCRIPTION’ ... OK
* this is package ‘biodbExpasy’ version ‘1.8.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbExpasy’ can be installed ... OK
* checking installed package size ... OK
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... 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’ ... OK
* checking tests in ‘longtests’ ...
Running ‘testthat.R’
OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.19-bioc-longtests/meat/biodbExpasy.Rcheck/00check.log’
for details.
biodbExpasy.Rcheck/00install.out
* installing *source* package ‘biodbExpasy’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (biodbExpasy)