Pierrick Roger
| Snapshot Date: 2025-01-27 13:40 -0500 (Mon, 27 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/biodb |
| git_branch: devel |
| git_last_commit: 9aceaac |
| git_last_commit_date: 2024-10-29 10:59:40 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-01-28 11:47 -0500 (Tue, 28 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4659 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" | 4454 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" | 4465 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4419 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4409 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 200/2286 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodb 1.15.0 (landing page) Pierrick Roger
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | TIMEOUT | ||||||||||
|
To the developers/maintainers of the biodb package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodb.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: biodb |
| Version: 1.15.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:biodb.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings biodb_1.15.0.tar.gz |
| StartedAt: 2025-01-28 03:55:09 -0000 (Tue, 28 Jan 2025) |
| EndedAt: 2025-01-28 08:39:55 -0000 (Tue, 28 Jan 2025) |
| EllapsedTime: 17086.7 seconds |
| RetCode: None |
| Status: TIMEOUT |
| CheckDir: biodb.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:biodb.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings biodb_1.15.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/biodb.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodb/DESCRIPTION’ ... OK
* this is package ‘biodb’ version ‘1.15.0’
* 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 ... NOTE
Found the following hidden files and directories:
.gitlab-ci.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodb’ can be installed ... WARNING
Found the following significant warnings:
closeMatchPpm.cpp:251:9: warning: ‘void free(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
See ‘/home/biocbuild/bbs-3.21-bioc/meat/biodb.Rcheck/00install.out’ for details.
* used C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
* checking installed package size ... INFO
installed size is 9.5Mb
sub-directories of 1Mb or more:
R 2.1Mb
libs 6.0Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
checkRd: (-1) BiodbMain.Rd:101: Lost braces
101 | Closes \\code{BiodbMain} instance. Call this method when you are done with
| ^
checkRd: (-1) BiodbMain.Rd:102: Lost braces
102 | your \\code{BiodbMain} instance.
| ^
checkRd: (-1) BiodbMain.Rd:124: Lost braces
124 | \\code{BiodbMain} (databases, fields or configuration keys).}
| ^
checkRd: (-1) BiodbMain.Rd:138: Lost braces
138 | Returns the single instance of the \\code{BiodbConfig} class.
| ^
checkRd: (-1) BiodbMain.Rd:144: Lost braces
144 | The instance of the \\code{BiodbConfig} class attached to
| ^
checkRd: (-1) BiodbMain.Rd:166: Lost braces
166 | Returns the single instance of the \\code{BiodbDbsInfo} class.
| ^
checkRd: (-1) BiodbMain.Rd:172: Lost braces
172 | The instance of the \\code{BiodbDbsInfo} class attached to
| ^
checkRd: (-1) BiodbMain.Rd:180: Lost braces
180 | Returns the single instance of the \\code{BiodbEntryFields} class.
| ^
checkRd: (-1) BiodbMain.Rd:186: Lost braces
186 | The instance of the \\code{BiodbEntryFields} class
| ^
checkRd: (-1) BiodbMain.Rd:194: Lost braces
194 | Returns the single instance of the \\code{BiodbFactory} class.
| ^
checkRd: (-1) BiodbMain.Rd:200: Lost braces
200 | The instance of the \\code{BiodbFactory} class attached to
| ^
checkRd: (-1) BiodbMain.Rd:208: Lost braces
208 | Returns the single instance of the \\code{BiodbRequestScheduler}
| ^
checkRd: (-1) BiodbMain.Rd:215: Lost braces
215 | The instance of the \\code{BiodbRequestScheduler} class
| ^
checkRd: (-1) BiodbMain.Rd:291: Lost braces
291 | \item{\code{entries}}{A list of \\code{BiodbEntry} instances.}
| ^
checkRd: (-1) BiodbMain.Rd:295: Lost braces
295 | \item{\code{flatten}}{If set to \\code{TRUE} and the field has a cardinality
| ^
checkRd: (-1) BiodbMain.Rd:299: Lost braces
299 | \item{\code{compute}}{If set to \\code{TRUE}, computable fields will be
| ^
checkRd: (-1) BiodbMain.Rd:312: Lost braces
312 | \\code{TRUE}, otherwise a list.
| ^
checkRd: (-1) BiodbMain.Rd:320: Lost braces
320 | (\\code{BiodbEntry} objects) into a data frame.
| ^
checkRd: (-1) BiodbMain.Rd:341: Lost braces
341 | \item{\code{entries}}{A list of \\code{BiodbEntry} instances or a list of list of
| ^
checkRd: (-1) BiodbMain.Rd:342: Lost braces
342 | \\code{BiodbEntry} instances.}
| ^
checkRd: (-1) BiodbMain.Rd:344: Lost braces
344 | \item{\code{only.atomic}}{If set to \\code{TRUE}, output only atomic fields, i.e.:
| ^
checkRd: (-1) BiodbMain.Rd:348: Lost braces
348 | \item{\code{null.to.na}}{If set to \\code{TRUE}, each \\code{NULL} entry in the
| ^
checkRd: (-1) BiodbMain.Rd:348: Lost braces
348 | \item{\code{null.to.na}}{If set to \\code{TRUE}, each \\code{NULL} entry in the
| ^
checkRd: (-1) BiodbMain.Rd:351: Lost braces
351 | \item{\code{compute}}{If set to \\code{TRUE}, computable fields will be output.}
| ^
checkRd: (-1) BiodbMain.Rd:360: Lost braces
360 | \item{\code{drop}}{If set to \\code{TRUE} and the resulting data frame has only one
| ^
checkRd: (-1) BiodbMain.Rd:365: Lost braces
365 | \item{\code{flatten}}{If set to \\code{TRUE}, then each field with a cardinality
| ^
checkRd: (-1) BiodbMain.Rd:467: Lost braces
467 | Converts a list of \\code{BiodbEntry} objects into JSON. Returns a vector of
| ^
checkRd: (-1) BiodbMain.Rd:476: Lost braces
476 | \item{\code{entries}}{A list of \\code{BiodbEntry} instances. It may contain NULL
| ^
checkRd: (-1) BiodbMain.Rd:479: Lost braces
479 | \item{\code{compute}}{If set to \\code{TRUE}, computable fields will added to JSON
| ^
checkRd: (-1) BiodbMain.Rd:595: Lost braces
595 | \item{\code{entries}}{A list of \\code{BiodbEntry} instances. It may contain NULL
| ^
checkRd: (-1) BiodbMain.Rd:617: Lost braces
617 | \item{\code{entries}}{A list of \\code{BiodbEntry} instances. It may contain NULL
| ^
checkRd: (-1) BiodbMain.Rd:623: Lost braces
623 | \item{\code{compute}}{If set to \\code{TRUE}, computable fields will be saved too.}
| ^
checkRd: (-1) BiodbMain.Rd:649: Lost braces
649 | \\code{NULL}, copy the whole database.}
| ^
checkRd: (-1) BiodbMain.Rd:675: Lost braces
675 | method is \\code{BiodbEntryField :isVector()}."
| ^
checkRd: (-1) BiodbPersistentCache.Rd:120: Lost braces
120 | \item{\code{conn}}{If not \\code{NULL}, checks if the cache system is readable for
| ^
checkRd: (-1) BiodbPersistentCache.Rd:126: Lost braces
126 | \\code{TRUE} if the cache system is readable,
| ^
checkRd: (-1) BiodbPersistentCache.Rd:127: Lost braces
127 | \\code{FALSE} otherwise.
| ^
checkRd: (-1) BiodbPersistentCache.Rd:142: Lost braces
142 | \item{\code{conn}}{If not \\code{NULL}, checks if the cache system is writable for
| ^
checkRd: (-1) BiodbPersistentCache.Rd:148: Lost braces
148 | \\code{TRUE} if the cache system is writable,
| ^
checkRd: (-1) BiodbPersistentCache.Rd:149: Lost braces
149 | \\code{FALSE} otherwise.
| ^
checkRd: (-1) BiodbPersistentCache.Rd:230: Lost braces
230 | A character vector, the same size as \\code{names},
| ^
checkRd: (-1) BiodbPersistentCache.Rd:276: Lost braces
276 | A logical vector, the same size as \\code{name}, with \\code{TRUE}
| ^
checkRd: (-1) BiodbPersistentCache.Rd:276: Lost braces
276 | A logical vector, the same size as \\code{name}, with \\code{TRUE}
| ^
checkRd: (-1) BiodbPersistentCache.Rd:277: Lost braces
277 | value if the file exists in the cache, or \\code{FALSE} otherwise.
| ^
checkRd: (-1) BiodbPersistentCache.Rd:302: Lost braces
302 | A logical vector, the same size as \\code{name}, with \\code{TRUE}
| ^
checkRd: (-1) BiodbPersistentCache.Rd:302: Lost braces
302 | A logical vector, the same size as \\code{name}, with \\code{TRUE}
| ^
checkRd: (-1) BiodbPersistentCache.Rd:303: Lost braces
303 | value if the file exists in the cache, or \\code{FALSE} otherwise.
| ^
checkRd: (-1) BiodbPersistentCache.Rd:325: Lost braces
325 | A logical vector, the same size as \\code{name}, with
| ^
checkRd: (-1) BiodbPersistentCache.Rd:326: Lost braces
326 | \\code{TRUE} value if the marker file exists in the cache, or \\code{FALSE}
| ^
checkRd: (-1) BiodbPersistentCache.Rd:326: Lost braces
326 | \\code{TRUE} value if the marker file exists in the cache, or \\code{FALSE}
| ^
checkRd: (-1) BiodbPersistentCache.Rd:351: Lost braces
351 | A logical vector, the same size as \\code{name}, with
| ^
checkRd: (-1) BiodbPersistentCache.Rd:352: Lost braces
352 | \\code{TRUE} value if the marker file exists in the cache, or \\code{FALSE}
| ^
checkRd: (-1) BiodbPersistentCache.Rd:352: Lost braces
352 | \\code{TRUE} value if the marker file exists in the cache, or \\code{FALSE}
| ^
checkRd: (-1) BiodbPersistentCache.Rd:428: Lost braces
428 | \item{\code{output.vector}}{If set to \\code{TRUE}, force output to be a
| ^
checkRd: (-1) BiodbPersistentCache.Rd:429: Lost braces
429 | \\code{vector} instead of a \\code{list}. Where the list contains a
| ^
checkRd: (-1) BiodbPersistentCache.Rd:429: Lost braces
429 | \\code{vector} instead of a \\code{list}. Where the list contains a
| ^
checkRd: (-1) BiodbPersistentCache.Rd:430: Lost braces
430 | \\code{NULL}, the \\code{vector} will contain an \\code{NA} value.}
| ^
checkRd: (-1) BiodbPersistentCache.Rd:430: Lost braces
430 | \\code{NULL}, the \\code{vector} will contain an \\code{NA} value.}
| ^
checkRd: (-1) BiodbPersistentCache.Rd:430: Lost braces
430 | \\code{NULL}, the \\code{vector} will contain an \\code{NA} value.}
| ^
checkRd: (-1) BiodbPersistentCache.Rd:435: Lost braces
435 | A list (or a vector if \\code{output.vector} is set to
| ^
checkRd: (-1) BiodbPersistentCache.Rd:436: Lost braces
436 | \\code{TRUE}), the same size as \\code{name}, containing the contents of the
| ^
checkRd: (-1) BiodbPersistentCache.Rd:436: Lost braces
436 | \\code{TRUE}), the same size as \\code{name}, containing the contents of the
| ^
checkRd: (-1) BiodbPersistentCache.Rd:437: Lost braces
437 | files. If some file does not exist, a \\code{NULL} value is inserted inside
| ^
checkRd: (-1) BiodbPersistentCache.Rd:454: Lost braces
454 | files. It must have the same length as \\code{name}.}
| ^
checkRd: (-1) BiodbPersistentCache.Rd:667: Lost braces
667 | \item{\code{extract.name}}{If set to \\code{TRUE}, instead of returning the file
| ^
checkRd: (-1) BiodbPersistentCache.Rd:671: Lost braces
671 | \item{\code{full.path}}{If set to \\code{TRUE}, returns full path for files.}
| ^
checkRd: (-1) BiodbPersistentCache.Rd:677: Lost braces
677 | \\code{extract.name} is set to \\code{TRUE}.
| ^
checkRd: (-1) BiodbPersistentCache.Rd:677: Lost braces
677 | \\code{extract.name} is set to \\code{TRUE}.
| ^
checkRd: (-1) BiodbPersistentCache.Rd:695: Lost braces
695 | \\code{BiodbConfig :isEnabled('cache.system')}.
| ^
checkRd: (-1) BiodbPersistentCache.Rd:706: Lost braces
706 | \\code{BiodbConfig :enable('cache.system')}.
| ^
checkRd: (-1) BiodbPersistentCache.Rd:717: Lost braces
717 | \\code{BiodbConfig :disable('cache.system')}.
| ^
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
biodb.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD INSTALL biodb
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘biodb’ ...
** using staged installation
** libs
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/testthat/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/testthat/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c closeMatchPpm.cpp -o closeMatchPpm.o
closeMatchPpm.cpp: In function ‘Rcpp::List closeMatchPpm(Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::IntegerVector, Rcpp::IntegerVector, int, double, double)’:
closeMatchPpm.cpp:251:9: warning: ‘void free(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
251 | free(pidxS);
| ~~~~^~~~~~~
closeMatchPpm.cpp:238:50: note: returned from ‘void* operator new [](std::size_t)’
238 | tIdxStruct *pidxS = new tIdxStruct[x.length()];
| ^
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/testthat/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c test-100-ms_matching.cpp -o test-100-ms_matching.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/testthat/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c test-runner.cpp -o test-runner.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o biodb.so RcppExports.o closeMatchPpm.o test-100-ms_matching.o test-runner.o -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/00LOCK-biodb/00new/biodb/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodb)
biodb.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # vi: fdm=marker
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodb)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodb")
Warning: program compiled against libxml 212 using older 211
biodb.INFO [2025-01-28 03:56:47.422][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-01-28 03:56:47.430][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-01-28 03:56:47.448][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-28 03:56:47.454][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-01-28 03:56:47.456][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-01-28 03:56:47.461][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:47.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:47.468][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:47.470][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-01-28 03:56:47.527][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-01-28 03:56:47.532][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:47.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:47.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:47.541][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-01-28 03:56:47.543][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-01-28 03:56:47.548][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:47.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:47.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:47.557][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-01-28 03:56:47.558][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-01-28 03:56:47.560][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-01-28 03:56:47.565][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:47.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:47.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:47.574][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-01-28 03:56:47.575][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-01-28 03:56:47.581][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-01-28 03:56:47.582][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:47.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:47.589][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:47.591][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-01-28 03:56:47.596][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-01-28 03:56:47.598][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:47.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:47.605][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[2025-01-28 03:56:47.606][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-01-28 03:56:47.608][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-01-28 03:56:47.614][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-01-28 03:56:47.615][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:47.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:47.622][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:47.623][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-01-28 03:56:47.629][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-01-28 03:56:47.630][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:47.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:47.637][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:47.639][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-01-28 03:56:47.644][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-01-28 03:56:47.646][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-01-28 03:56:47.647][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:47.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:47.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:47.656][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-01-28 03:56:47.661][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-01-28 03:56:47.663][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-01-28 03:56:47.669][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-01-28 03:56:47.670][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-01-28 03:56:47.672][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-01-28 03:56:47.677][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:47.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:47.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:47.686][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-01-28 03:56:47.687][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-01-28 03:56:47.693][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:47.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:47.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:47.701][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-01-28 03:56:47.703][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-01-28 03:56:47.704][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:47.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:47.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:47.716][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-01-28 03:56:47.718][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-01-28 03:56:47.719][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:47.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:47.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:47.728][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-01-28 03:56:47.733][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-01-28 03:56:47.735][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:47.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:47.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:47.743][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-01-28 03:56:47.749][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-01-28 03:56:47.750][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:47.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:47.757][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:47.759][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-01-28 03:56:47.765][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-01-28 03:56:47.838][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-01-28 03:56:47.839][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:47.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:47.842][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:47.843][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-01-28 03:56:47.845][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-01-28 03:56:47.846][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-01-28 03:56:47.848][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:47.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:47.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:47.864][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-01-28 03:56:48.011][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-28 03:56:48.073][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-01-28 03:56:48.075][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:48.081][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-28 03:56:48.083][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:48.089][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-28 03:56:48.090][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-28 03:56:48.096][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-28 03:56:48.098][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-28 03:56:48.100][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-28 03:56:48.106][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:48.107][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-01-28 03:56:48.113][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-28 03:56:48.115][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:48.121][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:48.123][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-28 03:56:48.123][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-28 03:56:48.123][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-28 03:56:48.123][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-28 03:56:48.123][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-28 03:56:48.129][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-28 03:56:48.130][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-28 03:56:48.132][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-28 03:56:48.138][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-28 03:56:48.139][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-28 03:56:48.145][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-28 03:56:48.147][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-28 03:56:48.153][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:48.154][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-28 03:56:48.156][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-28 03:56:48.162][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-28 03:56:48.164][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:48.170][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-01-28 03:56:48.177][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-28 03:56:48.179][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-01-28 03:56:48.185][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:48.187][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-28 03:56:48.192][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:48.194][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-28 03:56:48.196][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-28 03:56:48.202][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-28 03:56:48.203][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-28 03:56:48.209][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-28 03:56:48.211][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:48.217][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-01-28 03:56:48.219][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-28 03:56:48.225][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:48.227][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:48.232][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-28 03:56:48.232][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-28 03:56:48.232][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-28 03:56:48.232][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-28 03:56:48.232][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-28 03:56:48.234][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-28 03:56:48.240][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-28 03:56:48.242][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-28 03:56:48.244][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-28 03:56:48.250][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-28 03:56:48.251][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-28 03:56:48.257][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-28 03:56:48.259][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:48.265][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-28 03:56:48.267][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-28 03:56:48.272][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-28 03:56:48.274][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:48.281][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-01-28 03:56:48.284][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:48.290][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-01-28 03:56:48.292][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:48.298][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-28 03:56:48.300][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:48.306][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-28 03:56:48.307][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-28 03:56:48.313][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-28 03:56:48.315][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-28 03:56:48.321][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-28 03:56:48.323][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-28 03:56:48.329][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-01-28 03:56:48.331][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-28 03:56:48.337][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:48.339][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:48.345][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:48.347][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-28 03:56:48.353][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-28 03:56:48.354][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-28 03:56:48.356][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-28 03:56:48.362][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-28 03:56:48.364][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-28 03:56:48.370][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-28 03:56:48.371][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:48.377][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-28 03:56:48.379][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-28 03:56:48.385][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-28 03:56:48.387][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:48.393][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-01-28 03:56:48.400][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:48.402][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-01-28 03:56:48.408][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:48.410][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-28 03:56:48.416][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:48.418][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-28 03:56:48.424][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-28 03:56:48.426][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-28 03:56:48.432][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-28 03:56:48.434][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-28 03:56:48.441][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-28 03:56:48.443][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-01-28 03:56:48.449][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-28 03:56:48.451][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:48.457][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:48.458][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:48.464][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-28 03:56:48.466][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-28 03:56:48.468][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-28 03:56:48.474][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-28 03:56:48.476][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-28 03:56:48.481][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-28 03:56:48.483][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-28 03:56:48.489][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:48.491][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-28 03:56:48.497][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-28 03:56:48.505][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-28 03:56:48.507][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:48.517][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-28 03:56:48.519][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:48.525][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:48.526][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:48.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:48.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:48.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:48.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:48.543][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:48.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:48.575][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:48.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:48.582][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:48.584][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:48.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:48.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:48.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:48.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:48.605][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:48.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:48.613][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:48.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:48.621][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[2025-01-28 03:56:48.622][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:48.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:48.630][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:48.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:48.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:48.640][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:48.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:48.647][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:48.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:48.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:48.661][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:48.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:48.669][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:48.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:48.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:48.678][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:48.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:48.685][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:48.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:48.693][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:48.695][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:48.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:48.702][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:48.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:48.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:48.711][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:48.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:48.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:48.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:48.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:48.726][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:48.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:48.734][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:48.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:48.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:48.742][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:48.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:48.749][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:48.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:48.756][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:48.758][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:48.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:48.765][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:48.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:48.768][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:48.773][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:48.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:48.780][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:48.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:48.783][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:48.789][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:48.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:48.792][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:48.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:48.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:48.804][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:48.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:48.807][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:48.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:48.814][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:48.815][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:48.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:48.822][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:48.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:48.829][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:48.831][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-01-28 03:56:48.846][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-01-28 03:56:48.848][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-01-28 03:56:48.854][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-01-28 03:56:48.861][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-01-28 03:56:48.863][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-01-28 03:56:48.870][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-01-28 03:56:48.872][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-01-28 03:56:48.878][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-01-28 03:56:48.885][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-01-28 03:56:48.887][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-01-28 03:56:48.893][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-01-28 03:56:48.896][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-01-28 03:56:48.902][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-01-28 03:56:48.909][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-01-28 03:56:48.911][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-01-28 03:56:48.917][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-01-28 03:56:48.920][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-01-28 03:56:48.926][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-01-28 03:56:48.933][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-01-28 03:56:48.935][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-01-28 03:56:48.942][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-01-28 03:56:48.944][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-01-28 03:56:48.951][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-01-28 03:56:48.957][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-01-28 03:56:48.959][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-01-28 03:56:48.966][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-01-28 03:56:48.972][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-01-28 03:56:48.975][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-01-28 03:56:48.981][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-01-28 03:56:48.984][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-01-28 03:56:48.990][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-01-28 03:56:48.996][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-01-28 03:56:48.999][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-01-28 03:56:49.005][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-01-28 03:56:49.007][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-01-28 03:56:49.014][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-01-28 03:56:49.020][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-01-28 03:56:49.023][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-01-28 03:56:49.029][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-01-28 03:56:49.032][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-01-28 03:56:49.038][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-01-28 03:56:49.044][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-01-28 03:56:49.047][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-01-28 03:56:49.053][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-01-28 03:56:49.055][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-01-28 03:56:49.062][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-01-28 03:56:49.068][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-01-28 03:56:49.071][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-01-28 03:56:49.077][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-01-28 03:56:49.079][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-01-28 03:56:49.086][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-01-28 03:56:49.088][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-01-28 03:56:49.094][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-01-28 03:56:49.101][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-01-28 03:56:49.103][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-01-28 03:56:49.110][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-01-28 03:56:49.112][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-01-28 03:56:49.118][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-01-28 03:56:49.125][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-01-28 03:56:49.127][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-01-28 03:56:49.133][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-01-28 03:56:49.136][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-01-28 03:56:49.142][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-01-28 03:56:49.149][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-01-28 03:56:49.151][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-01-28 03:56:49.157][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-01-28 03:56:49.160][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-01-28 03:56:49.166][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-01-28 03:56:49.188][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-01-28 03:56:49.191][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-01-28 03:56:49.197][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-01-28 03:56:49.200][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-01-28 03:56:49.206][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-01-28 03:56:49.213][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-01-28 03:56:49.215][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-01-28 03:56:49.221][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-01-28 03:56:49.224][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-01-28 03:56:49.231][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-01-28 03:56:49.237][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-01-28 03:56:49.239][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-01-28 03:56:49.246][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-01-28 03:56:49.252][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-01-28 03:56:49.270][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-01-28 03:56:49.276][initialize] This is biodb version 1.15.0.
biodb.INFO [2025-01-28 03:56:49.278][biodb::testContext]
biodb.INFO [2025-01-28 03:56:49.280][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-28 03:56:49.285][biodb::testContext] Test context - Test abstract declaration.
biodb.INFO [2025-01-28 03:56:49.287][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-28 03:56:49.293][biodb::testContext]
biodb.INFO [2025-01-28 03:56:49.295][biodb::testThat]
biodb.INFO [2025-01-28 03:56:49.301][biodb::testThat] Running test function test.abstractClass.declaration (" An abstract class cannot be instantiated. ").
biodb.INFO [2025-01-28 03:56:49.303][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-28 03:56:49.308][biodb::testThat]
biodb.ERROR[2025-01-28 03:56:49.317][abstractClass] Class BiodbConnBase is abstract and thus cannot be instantiated.
biodb.INFO [2025-01-28 03:56:49.398][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-01-28 03:56:49.399][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-01-28 03:56:49.405][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:49.406][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:49.408][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:49.414][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.INFO [2025-01-28 03:56:49.430][biodb::testContext]
biodb.INFO [2025-01-28 03:56:49.432][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-28 03:56:49.434][biodb::testContext] Test context - Testing BiodbUrl.
biodb.INFO [2025-01-28 03:56:49.436][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-28 03:56:49.441][biodb::testContext]
biodb.INFO [2025-01-28 03:56:49.444][biodb::testThat]
biodb.INFO [2025-01-28 03:56:49.450][biodb::testThat] Running test function test_BiodbUrl (" BiodbUrl works fine. ").
biodb.INFO [2025-01-28 03:56:49.451][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-28 03:56:49.457][biodb::testThat]
biodb.INFO [2025-01-28 03:56:49.540][biodb::testThat]
biodb.INFO [2025-01-28 03:56:49.546][biodb::testThat] Running test function test_biodburl_encoding (" BiodbUrl encoding works correctly. ").
biodb.INFO [2025-01-28 03:56:49.547][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-28 03:56:49.553][biodb::testThat]
biodb.INFO [2025-01-28 03:56:49.688][biodb::testThat]
biodb.INFO [2025-01-28 03:56:49.690][biodb::testThat] Running test function test_getRCurlContent (" getRCurlContent() works fine. ").
biodb.INFO [2025-01-28 03:56:49.692][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-28 03:56:49.697][biodb::testThat]
biodb.INFO [2025-01-28 03:56:50.826][biodb::testContext]
biodb.INFO [2025-01-28 03:56:50.827][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-28 03:56:50.829][biodb::testContext] Test context - Testing Range class.
biodb.INFO [2025-01-28 03:56:50.830][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-28 03:56:50.832][biodb::testContext]
biodb.INFO [2025-01-28 03:56:50.838][biodb::testThat]
biodb.INFO [2025-01-28 03:56:50.840][biodb::testThat] Running test function test_range (" Range class works correctly. ").
biodb.INFO [2025-01-28 03:56:50.846][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-28 03:56:50.847][biodb::testThat]
biodb.INFO [2025-01-28 03:56:50.907][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-01-28 03:56:50.910][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-01-28 03:56:50.920][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-28 03:56:50.926][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-01-28 03:56:50.928][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-01-28 03:56:50.934][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:50.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:50.941][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:50.943][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-01-28 03:56:50.950][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-01-28 03:56:50.951][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:50.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:50.962][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:50.964][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-01-28 03:56:50.974][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-01-28 03:56:50.975][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:50.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:50.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:50.989][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-01-28 03:56:50.991][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-01-28 03:56:50.997][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-01-28 03:56:50.998][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:51.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:51.005][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[2025-01-28 03:56:51.007][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-01-28 03:56:51.013][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-01-28 03:56:51.015][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-01-28 03:56:51.020][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:51.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:51.023][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:51.029][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-01-28 03:56:51.031][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-01-28 03:56:51.144][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:51.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:51.150][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:51.152][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-01-28 03:56:51.154][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-01-28 03:56:51.156][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-01-28 03:56:51.157][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:51.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:51.160][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:51.161][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-01-28 03:56:51.163][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-01-28 03:56:51.164][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:51.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:51.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:51.168][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-01-28 03:56:51.170][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-01-28 03:56:51.171][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-01-28 03:56:51.172][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:51.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:51.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:51.176][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-01-28 03:56:51.178][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-01-28 03:56:51.179][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-01-28 03:56:51.181][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-01-28 03:56:51.182][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-01-28 03:56:51.184][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-01-28 03:56:51.185][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:51.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:51.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:51.189][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-01-28 03:56:51.191][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-01-28 03:56:51.192][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:51.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:51.195][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:51.196][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-01-28 03:56:51.198][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-01-28 03:56:51.199][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:51.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:51.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:51.203][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-01-28 03:56:51.205][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-01-28 03:56:51.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:51.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:51.209][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:51.210][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-01-28 03:56:51.212][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-01-28 03:56:51.213][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:51.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:51.216][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:51.217][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-01-28 03:56:51.219][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-01-28 03:56:51.221][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:51.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:51.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:51.225][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-01-28 03:56:51.226][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-01-28 03:56:51.237][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-01-28 03:56:51.239][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:51.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:51.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:51.247][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-01-28 03:56:51.253][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-01-28 03:56:51.255][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-01-28 03:56:51.260][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:51.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:51.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:51.269][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-01-28 03:56:51.276][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-28 03:56:51.278][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-01-28 03:56:51.279][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:51.285][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-28 03:56:51.287][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:51.293][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-28 03:56:51.294][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-28 03:56:51.296][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-28 03:56:51.302][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-28 03:56:51.303][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-28 03:56:51.309][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:51.311][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-01-28 03:56:51.317][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-28 03:56:51.319][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:51.323][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:51.325][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-28 03:56:51.325][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-28 03:56:51.325][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-28 03:56:51.325][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-28 03:56:51.325][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-28 03:56:51.326][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-28 03:56:51.328][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-28 03:56:51.331][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-28 03:56:51.332][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-28 03:56:51.334][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-28 03:56:51.335][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-28 03:56:51.338][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-28 03:56:51.339][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:51.341][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-28 03:56:51.343][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-28 03:56:51.360][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-28 03:56:51.362][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:51.364][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-01-28 03:56:51.371][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-28 03:56:51.377][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-01-28 03:56:51.378][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:51.380][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-28 03:56:51.386][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:51.387][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-28 03:56:51.393][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-28 03:56:51.395][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-28 03:56:51.396][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-28 03:56:51.402][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-28 03:56:51.403][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:51.409][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-01-28 03:56:51.411][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-28 03:56:51.412][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:51.418][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:51.419][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-28 03:56:51.419][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-28 03:56:51.419][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-28 03:56:51.419][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-28 03:56:51.419][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-28 03:56:51.425][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-28 03:56:51.427][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-28 03:56:51.428][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-28 03:56:51.434][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-28 03:56:51.435][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-28 03:56:51.440][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-28 03:56:51.442][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-28 03:56:51.443][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:51.449][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-28 03:56:51.450][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-28 03:56:51.452][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-28 03:56:51.458][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:51.460][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-01-28 03:56:51.462][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:51.464][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-01-28 03:56:51.470][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:51.471][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-28 03:56:51.477][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:51.479][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-28 03:56:51.484][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-28 03:56:51.486][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-28 03:56:51.487][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-28 03:56:51.493][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-28 03:56:51.495][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-28 03:56:51.501][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-01-28 03:56:51.502][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-28 03:56:51.508][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:51.510][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:51.528][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:51.534][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-28 03:56:51.535][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-28 03:56:51.541][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-28 03:56:51.542][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-28 03:56:51.544][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-28 03:56:51.549][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-28 03:56:51.551][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-28 03:56:51.556][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:51.558][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-28 03:56:51.559][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-28 03:56:51.565][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-28 03:56:51.566][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:51.568][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-01-28 03:56:51.571][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:51.572][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-01-28 03:56:51.574][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:51.575][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-28 03:56:51.576][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:51.578][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-28 03:56:51.579][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-28 03:56:51.581][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-28 03:56:51.582][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-28 03:56:51.583][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-28 03:56:51.585][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-28 03:56:51.586][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-01-28 03:56:51.588][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-28 03:56:51.589][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:51.591][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:51.592][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:51.593][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-28 03:56:51.595][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-28 03:56:51.596][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-28 03:56:51.597][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-28 03:56:51.599][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-28 03:56:51.600][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-28 03:56:51.601][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-28 03:56:51.603][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:51.604][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-28 03:56:51.605][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-28 03:56:51.607][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-28 03:56:51.608][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:51.610][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-28 03:56:51.611][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:51.613][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:51.614][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:51.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:51.616][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:51.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:51.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:51.620][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:51.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:51.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:51.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:51.626][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[2025-01-28 03:56:51.627][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:51.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:51.629][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:51.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:51.632][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:51.633][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:51.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:51.636][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:51.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:51.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:51.640][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:51.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:51.642][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:51.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:51.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:51.646][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:51.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:51.649][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:51.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:51.651][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:51.653][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:51.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:51.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:51.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:51.658][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:51.659][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:51.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:51.662][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:51.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:51.664][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:51.666][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:51.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:51.668][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:51.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:51.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:51.672][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:51.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:51.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:51.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:51.677][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:51.679][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:51.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:51.681][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:51.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:51.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:51.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:51.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:51.688][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:51.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:51.691][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:51.692][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:51.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:51.695][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:51.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:51.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:51.699][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:51.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:51.702][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:51.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:51.704][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:51.706][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:51.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:51.708][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:51.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:51.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:51.712][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:51.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:51.715][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:51.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:51.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:51.719][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:51.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:51.721][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:51.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:51.724][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:51.725][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-01-28 03:56:51.727][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-01-28 03:56:51.730][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-01-28 03:56:51.732][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-01-28 03:56:51.734][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-01-28 03:56:51.736][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-01-28 03:56:51.738][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-01-28 03:56:51.740][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-01-28 03:56:51.742][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-01-28 03:56:51.744][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-01-28 03:56:51.747][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-01-28 03:56:51.756][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-01-28 03:56:51.759][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-01-28 03:56:51.761][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-01-28 03:56:51.763][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-01-28 03:56:51.766][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-01-28 03:56:51.768][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-01-28 03:56:51.770][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-01-28 03:56:51.772][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-01-28 03:56:51.774][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-01-28 03:56:51.777][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-01-28 03:56:51.779][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-01-28 03:56:51.781][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-01-28 03:56:51.783][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-01-28 03:56:51.785][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-01-28 03:56:51.788][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-01-28 03:56:51.790][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-01-28 03:56:51.792][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-01-28 03:56:51.794][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-01-28 03:56:51.796][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-01-28 03:56:51.798][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-01-28 03:56:51.800][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-01-28 03:56:51.803][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-01-28 03:56:51.805][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-01-28 03:56:51.807][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-01-28 03:56:51.809][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-01-28 03:56:51.811][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-01-28 03:56:51.813][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-01-28 03:56:51.816][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-01-28 03:56:51.818][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-01-28 03:56:51.820][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-01-28 03:56:51.822][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-01-28 03:56:51.824][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-01-28 03:56:51.826][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-01-28 03:56:51.828][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-01-28 03:56:51.831][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-01-28 03:56:51.833][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-01-28 03:56:51.835][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-01-28 03:56:51.837][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-01-28 03:56:51.839][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-01-28 03:56:51.842][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-01-28 03:56:51.844][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-01-28 03:56:51.846][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-01-28 03:56:51.848][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-01-28 03:56:51.850][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-01-28 03:56:51.852][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-01-28 03:56:51.854][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-01-28 03:56:51.856][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-01-28 03:56:51.859][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-01-28 03:56:51.861][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-01-28 03:56:51.863][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-01-28 03:56:51.865][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-01-28 03:56:51.867][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-01-28 03:56:51.869][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-01-28 03:56:51.872][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-01-28 03:56:51.874][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-01-28 03:56:51.876][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-01-28 03:56:51.878][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-01-28 03:56:51.880][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-01-28 03:56:51.883][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-01-28 03:56:51.885][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-01-28 03:56:51.887][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-01-28 03:56:51.889][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-01-28 03:56:51.891][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-01-28 03:56:51.894][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-01-28 03:56:51.896][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-01-28 03:56:51.898][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-01-28 03:56:51.900][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-01-28 03:56:51.902][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-01-28 03:56:51.904][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-01-28 03:56:51.907][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-01-28 03:56:51.909][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-01-28 03:56:51.911][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-01-28 03:56:51.913][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-01-28 03:56:51.915][initialize] This is biodb version 1.15.0.
biodb.INFO [2025-01-28 03:56:51.917][biodb::testContext]
biodb.INFO [2025-01-28 03:56:51.918][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-28 03:56:51.920][biodb::testContext] Test context - Test object printing.
biodb.INFO [2025-01-28 03:56:51.921][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-28 03:56:51.923][biodb::testContext]
biodb.INFO [2025-01-28 03:56:51.925][biodb::testThat]
biodb.INFO [2025-01-28 03:56:51.926][biodb::testThat] Running test function test.BiodbMain.print (" BiodbMain print method returns correct information. ").
biodb.INFO [2025-01-28 03:56:51.927][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-28 03:56:51.929][biodb::testThat]
biodb.INFO [2025-01-28 03:56:51.941][biodb::testThat]
biodb.INFO [2025-01-28 03:56:51.942][biodb::testThat] Running test function test.BiodbCache.print (" BiodbCache print method returns correct information. ").
biodb.INFO [2025-01-28 03:56:51.944][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-28 03:56:51.945][biodb::testThat]
biodb.INFO [2025-01-28 03:56:51.969][biodb::testThat]
biodb.INFO [2025-01-28 03:56:51.970][biodb::testThat] Running test function test.BiodbConfig.print (" BiodbConfig print method returns correct information. ").
biodb.INFO [2025-01-28 03:56:51.972][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-28 03:56:51.982][biodb::testThat]
biodb.INFO [2025-01-28 03:56:51.999][biodb::testThat]
biodb.INFO [2025-01-28 03:56:52.000][biodb::testThat] Running test function test.BiodbFactory.print (" BiodbFactory print method returns correct information. ").
biodb.INFO [2025-01-28 03:56:52.002][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-28 03:56:52.003][biodb::testThat]
biodb.INFO [2025-01-28 03:56:52.018][biodb::testThat]
biodb.INFO [2025-01-28 03:56:52.019][biodb::testThat] Running test function test.BiodbEntry.print (" BiodbEntry print method returns correct information. ").
biodb.INFO [2025-01-28 03:56:52.021][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-28 03:56:52.022][biodb::testThat]
biodb.DEBUG[2025-01-28 03:56:52.048][super$initialize] Initialize connector mass.csv.file.
biodb.DEBUG[2025-01-28 03:56:52.050][biodb$getFactory()$createConn] Creating new connector mass.csv.file for database class mass.csv.file .
biodb.DEBUG[2025-01-28 03:56:52.069][private$loadEntries] Creating entries from ids [1]: "C1".
biodb.DEBUG[2025-01-28 03:56:52.071][conn$getEntryContent] Get Mass spectra CSV File entry content(s) for 1 id(s)...
biodb.DEBUG[2025-01-28 03:56:52.073][conn$getEntryContent] 1 entry content(s) need to be fetched from Mass spectra CSV File database "NA".
biodb.DEBUG[2025-01-28 03:56:52.075][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-28 03:56:52.076][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-28 03:56:52.077][private$doGetEntryContentFromDb] Entry id: C1
biodb.DEBUG[2025-01-28 03:56:52.080][self$setField] Set field accession to column(s) accession.
biodb.TRACE[2025-01-28 03:56:52.081][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 03:56:52.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 03:56:52.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-28 03:56:52.106][self$setPropertyValue] Setting property "parsing.expr" to "accession".
biodb.DEBUG[2025-01-28 03:56:52.152][self$setField] Set field ms.mode to column(s) ms.mode.
biodb.TRACE[2025-01-28 03:56:52.154][self$getBiodb()$getEntryFields()$get] Asked field names are: ms.mode.
biodb.TRACE[2025-01-28 03:56:52.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ms.mode.
biodb.TRACE[2025-01-28 03:56:52.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-28 03:56:52.161][self$setPropertyValue] Setting property "parsing.expr" to "accession".
biodb.DEBUG[2025-01-28 03:56:52.161][self$setPropertyValue] Setting property "parsing.expr" to "ms.mode".
biodb.DEBUG[2025-01-28 03:56:52.163][self$setField] Set field peak.mztheo to column(s) peak.mztheo.
biodb.TRACE[2025-01-28 03:56:52.164][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-28 03:56:52.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-28 03:56:52.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-28 03:56:52.170][self$setPropertyValue] Setting property "parsing.expr" to "accession".
biodb.DEBUG[2025-01-28 03:56:52.170][self$setPropertyValue] Setting property "parsing.expr" to "ms.mode".
biodb.DEBUG[2025-01-28 03:56:52.170][self$setPropertyValue] Setting property "parsing.expr" to "peak.mztheo".
biodb.DEBUG[2025-01-28 03:56:52.172][self$setField] Set field peak.comp to column(s) peak.comp.
biodb.TRACE[2025-01-28 03:56:52.175][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.comp.
biodb.TRACE[2025-01-28 03:56:52.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.comp.
biodb.TRACE[2025-01-28 03:56:52.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-28 03:56:52.195][self$setPropertyValue] Setting property "parsing.expr" to "accession".
biodb.DEBUG[2025-01-28 03:56:52.195][self$setPropertyValue] Setting property "parsing.expr" to "ms.mode".
biodb.DEBUG[2025-01-28 03:56:52.195][self$setPropertyValue] Setting property "parsing.expr" to "peak.mztheo".
biodb.DEBUG[2025-01-28 03:56:52.195][self$setPropertyValue] Setting property "parsing.expr" to "peak.comp".
biodb.DEBUG[2025-01-28 03:56:52.197][self$setField] Set field peak.attr to column(s) peak.attr.
biodb.TRACE[2025-01-28 03:56:52.199][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr.
biodb.TRACE[2025-01-28 03:56:52.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr.
biodb.TRACE[2025-01-28 03:56:52.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-28 03:56:52.204][self$setPropertyValue] Setting property "parsing.expr" to "accession".
biodb.DEBUG[2025-01-28 03:56:52.204][self$setPropertyValue] Setting property "parsing.expr" to "ms.mode".
biodb.DEBUG[2025-01-28 03:56:52.204][self$setPropertyValue] Setting property "parsing.expr" to "peak.mztheo".
biodb.DEBUG[2025-01-28 03:56:52.204][self$setPropertyValue] Setting property "parsing.expr" to "peak.comp".
biodb.DEBUG[2025-01-28 03:56:52.204][self$setPropertyValue] Setting property "parsing.expr" to "peak.attr".
biodb.DEBUG[2025-01-28 03:56:52.206][self$setField] Set field formula to column(s) formula.
biodb.TRACE[2025-01-28 03:56:52.208][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-28 03:56:52.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-28 03:56:52.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-28 03:56:52.214][self$setPropertyValue] Setting property "parsing.expr" to "accession".
biodb.DEBUG[2025-01-28 03:56:52.214][self$setPropertyValue] Setting property "parsing.expr" to "ms.mode".
biodb.DEBUG[2025-01-28 03:56:52.214][self$setPropertyValue] Setting property "parsing.expr" to "peak.mztheo".
biodb.DEBUG[2025-01-28 03:56:52.214][self$setPropertyValue] Setting property "parsing.expr" to "peak.comp".
biodb.DEBUG[2025-01-28 03:56:52.214][self$setPropertyValue] Setting property "parsing.expr" to "peak.attr".
biodb.DEBUG[2025-01-28 03:56:52.214][self$setPropertyValue] Setting property "parsing.expr" to "formula".
biodb.DEBUG[2025-01-28 03:56:52.216][self$setField] Set field molecular.mass to column(s) molecular.mass.
biodb.TRACE[2025-01-28 03:56:52.217][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-28 03:56:52.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-28 03:56:52.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-28 03:56:52.223][self$setPropertyValue] Setting property "parsing.expr" to "accession".
biodb.DEBUG[2025-01-28 03:56:52.223][self$setPropertyValue] Setting property "parsing.expr" to "ms.mode".
biodb.DEBUG[2025-01-28 03:56:52.223][self$setPropertyValue] Setting property "parsing.expr" to "peak.mztheo".
biodb.DEBUG[2025-01-28 03:56:52.223][self$setPropertyValue] Setting property "parsing.expr" to "peak.comp".
biodb.DEBUG[2025-01-28 03:56:52.223][self$setPropertyValue] Setting property "parsing.expr" to "peak.attr".
biodb.DEBUG[2025-01-28 03:56:52.223][self$setPropertyValue] Setting property "parsing.expr" to "formula".
biodb.DEBUG[2025-01-28 03:56:52.223][self$setPropertyValue] Setting property "parsing.expr" to "molecular.mass".
biodb.DEBUG[2025-01-28 03:56:52.225][self$setField] Set field name to column(s) name.
biodb.TRACE[2025-01-28 03:56:52.227][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-28 03:56:52.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-28 03:56:52.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-28 03:56:52.232][self$setPropertyValue] Setting property "parsing.expr" to "accession".
biodb.DEBUG[2025-01-28 03:56:52.232][self$setPropertyValue] Setting property "parsing.expr" to "ms.mode".
biodb.DEBUG[2025-01-28 03:56:52.232][self$setPropertyValue] Setting property "parsing.expr" to "peak.mztheo".
biodb.DEBUG[2025-01-28 03:56:52.232][self$setPropertyValue] Setting property "parsing.expr" to "peak.comp".
biodb.DEBUG[2025-01-28 03:56:52.232][self$setPropertyValue] Setting property "parsing.expr" to "peak.attr".
biodb.DEBUG[2025-01-28 03:56:52.232][self$setPropertyValue] Setting property "parsing.expr" to "formula".
biodb.DEBUG[2025-01-28 03:56:52.232][self$setPropertyValue] Setting property "parsing.expr" to "molecular.mass".
biodb.DEBUG[2025-01-28 03:56:52.232][self$setPropertyValue] Setting property "parsing.expr" to "name".
biodb.DEBUG[2025-01-28 03:56:52.286][private$doGetEntryContentFromDb] Content of first entry: accession ms.mode peak.mztheo peak.comp peak.attr formula molecular.mass name
C1 pos 112.07569 P9Z6W410 O [(M+H)-(H2O)-(NH3)]+ J114L6M62O2 146.10553 Blablaine
biodb.DEBUG[2025-01-28 03:56:52.289][self$createEntryFromContent] Creating Mass spectra CSV File entries from 1 content(s).
biodb.DEBUG[2025-01-28 03:56:52.294][self$createEntryFromContent] Parsing 1 Mass spectra CSV File entries.
biodb.DEBUG[2025-01-28 03:56:52.305][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-28 03:56:52.306][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:52.307][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:52.308][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:52.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:52.324][self$setPropertyValue] Setting property "parsing.expr" to "accession".
biodb.DEBUG[2025-01-28 03:56:52.324][self$setPropertyValue] Setting property "parsing.expr" to "ms.mode".
biodb.DEBUG[2025-01-28 03:56:52.324][self$setPropertyValue] Setting property "parsing.expr" to "peak.mztheo".
biodb.DEBUG[2025-01-28 03:56:52.324][self$setPropertyValue] Setting property "parsing.expr" to "peak.comp".
biodb.DEBUG[2025-01-28 03:56:52.324][self$setPropertyValue] Setting property "parsing.expr" to "peak.attr".
biodb.DEBUG[2025-01-28 03:56:52.324][self$setPropertyValue] Setting property "parsing.expr" to "formula".
biodb.DEBUG[2025-01-28 03:56:52.324][self$setPropertyValue] Setting property "parsing.expr" to "molecular.mass".
biodb.DEBUG[2025-01-28 03:56:52.324][self$setPropertyValue] Setting property "parsing.expr" to "name".
biodb.DEBUG[2025-01-28 03:56:52.326][self$setPropertyValue] Setting property "parsing.expr" to "accession".
biodb.DEBUG[2025-01-28 03:56:52.326][self$setPropertyValue] Setting property "parsing.expr" to "ms.mode".
biodb.DEBUG[2025-01-28 03:56:52.326][self$setPropertyValue] Setting property "parsing.expr" to "peak.mztheo".
biodb.DEBUG[2025-01-28 03:56:52.326][self$setPropertyValue] Setting property "parsing.expr" to "peak.comp".
biodb.DEBUG[2025-01-28 03:56:52.326][self$setPropertyValue] Setting property "parsing.expr" to "peak.attr".
biodb.DEBUG[2025-01-28 03:56:52.326][self$setPropertyValue] Setting property "parsing.expr" to "formula".
biodb.DEBUG[2025-01-28 03:56:52.326][self$setPropertyValue] Setting property "parsing.expr" to "molecular.mass".
biodb.DEBUG[2025-01-28 03:56:52.326][self$setPropertyValue] Setting property "parsing.expr" to "name".
biodb.DEBUG[2025-01-28 03:56:52.328][self$setPropertyValue] Setting property "parsing.expr" to "accession".
biodb.DEBUG[2025-01-28 03:56:52.328][self$setPropertyValue] Setting property "parsing.expr" to "ms.mode".
biodb.DEBUG[2025-01-28 03:56:52.328][self$setPropertyValue] Setting property "parsing.expr" to "peak.mztheo".
biodb.DEBUG[2025-01-28 03:56:52.328][self$setPropertyValue] Setting property "parsing.expr" to "peak.comp".
biodb.DEBUG[2025-01-28 03:56:52.328][self$setPropertyValue] Setting property "parsing.expr" to "peak.attr".
biodb.DEBUG[2025-01-28 03:56:52.328][self$setPropertyValue] Setting property "parsing.expr" to "formula".
biodb.DEBUG[2025-01-28 03:56:52.328][self$setPropertyValue] Setting property "parsing.expr" to "molecular.mass".
biodb.DEBUG[2025-01-28 03:56:52.328][self$setPropertyValue] Setting property "parsing.expr" to "name".
biodb.DEBUG[2025-01-28 03:56:52.330][self$setPropertyValue] Setting property "parsing.expr" to "accession".
biodb.DEBUG[2025-01-28 03:56:52.330][self$setPropertyValue] Setting property "parsing.expr" to "ms.mode".
biodb.DEBUG[2025-01-28 03:56:52.330][self$setPropertyValue] Setting property "parsing.expr" to "peak.mztheo".
biodb.DEBUG[2025-01-28 03:56:52.330][self$setPropertyValue] Setting property "parsing.expr" to "peak.comp".
biodb.DEBUG[2025-01-28 03:56:52.330][self$setPropertyValue] Setting property "parsing.expr" to "peak.attr".
biodb.DEBUG[2025-01-28 03:56:52.330][self$setPropertyValue] Setting property "parsing.expr" to "formula".
biodb.DEBUG[2025-01-28 03:56:52.330][self$setPropertyValue] Setting property "parsing.expr" to "molecular.mass".
biodb.DEBUG[2025-01-28 03:56:52.330][self$setPropertyValue] Setting property "parsing.expr" to "name".
biodb.DEBUG[2025-01-28 03:56:52.331][self$setPropertyValue] Setting property "parsing.expr" to "accession".
biodb.DEBUG[2025-01-28 03:56:52.331][self$setPropertyValue] Setting property "parsing.expr" to "ms.mode".
biodb.DEBUG[2025-01-28 03:56:52.331][self$setPropertyValue] Setting property "parsing.expr" to "peak.mztheo".
biodb.DEBUG[2025-01-28 03:56:52.331][self$setPropertyValue] Setting property "parsing.expr" to "peak.comp".
biodb.DEBUG[2025-01-28 03:56:52.331][self$setPropertyValue] Setting property "parsing.expr" to "peak.attr".
biodb.DEBUG[2025-01-28 03:56:52.331][self$setPropertyValue] Setting property "parsing.expr" to "formula".
biodb.DEBUG[2025-01-28 03:56:52.331][self$setPropertyValue] Setting property "parsing.expr" to "molecular.mass".
biodb.DEBUG[2025-01-28 03:56:52.331][self$setPropertyValue] Setting property "parsing.expr" to "name".
biodb.DEBUG[2025-01-28 03:56:52.333][self$setPropertyValue] Setting property "parsing.expr" to "accession".
biodb.DEBUG[2025-01-28 03:56:52.333][self$setPropertyValue] Setting property "parsing.expr" to "ms.mode".
biodb.DEBUG[2025-01-28 03:56:52.333][self$setPropertyValue] Setting property "parsing.expr" to "peak.mztheo".
biodb.DEBUG[2025-01-28 03:56:52.333][self$setPropertyValue] Setting property "parsing.expr" to "peak.comp".
biodb.DEBUG[2025-01-28 03:56:52.333][self$setPropertyValue] Setting property "parsing.expr" to "peak.attr".
biodb.DEBUG[2025-01-28 03:56:52.333][self$setPropertyValue] Setting property "parsing.expr" to "formula".
biodb.DEBUG[2025-01-28 03:56:52.333][self$setPropertyValue] Setting property "parsing.expr" to "molecular.mass".
biodb.DEBUG[2025-01-28 03:56:52.333][self$setPropertyValue] Setting property "parsing.expr" to "name".
biodb.DEBUG[2025-01-28 03:56:52.335][self$setPropertyValue] Setting property "parsing.expr" to "accession".
biodb.DEBUG[2025-01-28 03:56:52.335][self$setPropertyValue] Setting property "parsing.expr" to "ms.mode".
biodb.DEBUG[2025-01-28 03:56:52.335][self$setPropertyValue] Setting property "parsing.expr" to "peak.mztheo".
biodb.DEBUG[2025-01-28 03:56:52.335][self$setPropertyValue] Setting property "parsing.expr" to "peak.comp".
biodb.DEBUG[2025-01-28 03:56:52.335][self$setPropertyValue] Setting property "parsing.expr" to "peak.attr".
biodb.DEBUG[2025-01-28 03:56:52.335][self$setPropertyValue] Setting property "parsing.expr" to "formula".
biodb.DEBUG[2025-01-28 03:56:52.335][self$setPropertyValue] Setting property "parsing.expr" to "molecular.mass".
biodb.DEBUG[2025-01-28 03:56:52.335][self$setPropertyValue] Setting property "parsing.expr" to "name".
biodb.DEBUG[2025-01-28 03:56:52.336][self$setPropertyValue] Setting property "parsing.expr" to "accession".
biodb.DEBUG[2025-01-28 03:56:52.336][self$setPropertyValue] Setting property "parsing.expr" to "ms.mode".
biodb.DEBUG[2025-01-28 03:56:52.336][self$setPropertyValue] Setting property "parsing.expr" to "peak.mztheo".
biodb.DEBUG[2025-01-28 03:56:52.336][self$setPropertyValue] Setting property "parsing.expr" to "peak.comp".
biodb.DEBUG[2025-01-28 03:56:52.336][self$setPropertyValue] Setting property "parsing.expr" to "peak.attr".
biodb.DEBUG[2025-01-28 03:56:52.336][self$setPropertyValue] Setting property "parsing.expr" to "formula".
biodb.DEBUG[2025-01-28 03:56:52.336][self$setPropertyValue] Setting property "parsing.expr" to "molecular.mass".
biodb.DEBUG[2025-01-28 03:56:52.336][self$setPropertyValue] Setting property "parsing.expr" to "name".
biodb.TRACE[2025-01-28 03:56:52.338][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 03:56:52.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 03:56:52.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:52.344][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 03:56:52.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 03:56:52.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:52.350][self$getBiodb()$getEntryFields()$get] Asked field names are: ms.mode.
biodb.TRACE[2025-01-28 03:56:52.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ms.mode.
biodb.TRACE[2025-01-28 03:56:52.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:52.423][self$getBiodb()$getEntryFields()$get] Asked field names are: ms.mode.
biodb.TRACE[2025-01-28 03:56:52.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ms.mode.
biodb.TRACE[2025-01-28 03:56:52.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:52.458][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-28 03:56:52.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-28 03:56:52.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:52.464][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-28 03:56:52.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-28 03:56:52.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:52.470][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.comp.
biodb.TRACE[2025-01-28 03:56:52.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.comp.
biodb.TRACE[2025-01-28 03:56:52.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:52.476][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.comp.
biodb.TRACE[2025-01-28 03:56:52.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.comp.
biodb.TRACE[2025-01-28 03:56:52.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:52.481][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr.
biodb.TRACE[2025-01-28 03:56:52.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr.
biodb.TRACE[2025-01-28 03:56:52.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:52.487][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr.
biodb.TRACE[2025-01-28 03:56:52.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr.
biodb.TRACE[2025-01-28 03:56:52.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:52.493][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-28 03:56:52.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-28 03:56:52.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:52.499][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-28 03:56:52.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-28 03:56:52.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:52.505][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-28 03:56:52.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-28 03:56:52.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:52.511][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-28 03:56:52.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-28 03:56:52.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:52.517][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-28 03:56:52.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-28 03:56:52.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:52.527][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-28 03:56:52.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-28 03:56:52.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:52.534][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-28 03:56:52.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-28 03:56:52.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:52.540][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-28 03:56:52.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-28 03:56:52.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:52.546][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-28 03:56:52.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-28 03:56:52.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:52.560][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-28 03:56:52.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-28 03:56:52.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:52.565][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-01-28 03:56:52.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-01-28 03:56:52.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:52.571][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-28 03:56:52.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-28 03:56:52.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:52.625][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-28 03:56:52.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-28 03:56:52.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:52.631][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-28 03:56:52.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-28 03:56:52.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:52.637][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-28 03:56:52.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-28 03:56:52.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:52.643][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-28 03:56:52.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-28 03:56:52.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:52.648][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-28 03:56:52.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-28 03:56:52.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:52.654][self$getBiodb()$getEntryFields()$get] Asked field names are: peaks.
biodb.TRACE[2025-01-28 03:56:52.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peaks.
biodb.TRACE[2025-01-28 03:56:52.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:52.660][self$getBiodb()$getEntryFields()$get] Asked field names are: peaks.
biodb.TRACE[2025-01-28 03:56:52.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peaks.
biodb.TRACE[2025-01-28 03:56:52.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:52.665][self$getBiodb()$getEntryFields()$get] Asked field names are: peaks.
biodb.TRACE[2025-01-28 03:56:52.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peaks.
biodb.TRACE[2025-01-28 03:56:52.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:52.727][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-28 03:56:52.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-28 03:56:52.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:52.733][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-28 03:56:52.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-28 03:56:52.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:52.739][private$selectFields] Fields none
biodb.TRACE[2025-01-28 03:56:52.740][private$selectFields] Fields type: peak
biodb.TRACE[2025-01-28 03:56:52.742][private$selectFields] Fields is null: TRUE
biodb.TRACE[2025-01-28 03:56:52.743][private$selectFields] Fields.type is null: FALSE
biodb.TRACE[2025-01-28 03:56:52.745][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 03:56:52.746][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 03:56:52.748][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.749][ef$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:52.751][ef$get] Asked field names are: ms.mode.
biodb.TRACE[2025-01-28 03:56:52.752][ef$get] Realnames of fields are: ms.mode.
biodb.TRACE[2025-01-28 03:56:52.754][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.755][ef$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:52.757][ef$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-28 03:56:52.758][ef$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-28 03:56:52.760][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.761][ef$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:52.762][ef$get] Asked field names are: peak.comp.
biodb.TRACE[2025-01-28 03:56:52.764][ef$get] Realnames of fields are: peak.comp.
biodb.TRACE[2025-01-28 03:56:52.766][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.767][ef$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:52.768][ef$get] Asked field names are: peak.attr.
biodb.TRACE[2025-01-28 03:56:52.770][ef$get] Realnames of fields are: peak.attr.
biodb.TRACE[2025-01-28 03:56:52.771][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.773][ef$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:52.774][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-28 03:56:52.776][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-28 03:56:52.777][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.779][ef$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:52.780][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-28 03:56:52.782][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-28 03:56:52.783][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.785][ef$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:52.786][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-28 03:56:52.788][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-28 03:56:52.790][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.791][ef$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:52.792][ef$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-28 03:56:52.794][ef$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-28 03:56:52.795][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.797][ef$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:52.798][private$selectFields] Fields [4]: "peak.mztheo, peak.comp, peak.attr, peak.mz"
biodb.TRACE[2025-01-28 03:56:52.800][ef$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-28 03:56:52.801][ef$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-28 03:56:52.803][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.804][ef$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:52.806][ef$get] Asked field names are: peak.comp.
biodb.TRACE[2025-01-28 03:56:52.807][ef$get] Realnames of fields are: peak.comp.
biodb.TRACE[2025-01-28 03:56:52.809][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.811][ef$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:52.812][ef$get] Asked field names are: peak.attr.
biodb.TRACE[2025-01-28 03:56:52.814][ef$get] Realnames of fields are: peak.attr.
biodb.TRACE[2025-01-28 03:56:52.816][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.817][ef$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:52.819][ef$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-28 03:56:52.821][ef$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-28 03:56:52.823][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.824][ef$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:52.826][private$selectFields] Fields [4]: "peak.mztheo, peak.comp, peak.attr, peak.mz"
biodb.TRACE[2025-01-28 03:56:52.827][private$organizeFieldsByGroups] Fields [4]: "peak.mztheo, peak.comp, peak.attr, peak.mz"
biodb.TRACE[2025-01-28 03:56:52.829][ef$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-28 03:56:52.830][ef$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-28 03:56:52.832][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.833][ef$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:52.835][ef$get] Asked field names are: peak.comp.
biodb.TRACE[2025-01-28 03:56:52.836][ef$get] Realnames of fields are: peak.comp.
biodb.TRACE[2025-01-28 03:56:52.838][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.839][ef$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:52.840][ef$get] Asked field names are: peak.attr.
biodb.TRACE[2025-01-28 03:56:52.842][ef$get] Realnames of fields are: peak.attr.
biodb.TRACE[2025-01-28 03:56:52.844][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.845][ef$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:52.846][ef$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-28 03:56:52.848][ef$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-28 03:56:52.849][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.851][ef$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:52.852][private$organizeFieldsByGroups] Groups [2]: "character(0), list(peaks = c("peak.mztheo", "peak.comp", "peak.attr", "peak.mz"))"
biodb.TRACE[2025-01-28 03:56:52.854][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-28 03:56:52.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-28 03:56:52.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:52.860][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-28 03:56:52.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-28 03:56:52.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:52.874][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-28 03:56:52.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-28 03:56:52.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:52.880][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.comp.
biodb.TRACE[2025-01-28 03:56:52.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.comp.
biodb.TRACE[2025-01-28 03:56:52.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:52.886][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.comp.
biodb.TRACE[2025-01-28 03:56:52.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.comp.
biodb.TRACE[2025-01-28 03:56:52.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:52.892][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.comp.
biodb.TRACE[2025-01-28 03:56:52.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.comp.
biodb.TRACE[2025-01-28 03:56:52.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:52.898][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr.
biodb.TRACE[2025-01-28 03:56:52.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr.
biodb.TRACE[2025-01-28 03:56:52.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:52.904][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr.
biodb.TRACE[2025-01-28 03:56:52.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr.
biodb.TRACE[2025-01-28 03:56:52.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:52.911][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr.
biodb.TRACE[2025-01-28 03:56:52.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr.
biodb.TRACE[2025-01-28 03:56:52.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:52.917][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-28 03:56:52.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-28 03:56:52.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:52.923][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-28 03:56:52.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-28 03:56:52.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:52.929][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-28 03:56:52.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-28 03:56:52.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:52.949][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.col.name.
biodb.TRACE[2025-01-28 03:56:52.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.col.name.
biodb.TRACE[2025-01-28 03:56:52.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:52.955][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.col.name.
biodb.TRACE[2025-01-28 03:56:52.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.col.name.
biodb.TRACE[2025-01-28 03:56:52.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:52.961][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.col.id.
biodb.TRACE[2025-01-28 03:56:52.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.col.id.
biodb.TRACE[2025-01-28 03:56:52.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:52.967][self$getBiodb()$getEntryFields()$get] Asked field names are: msprecmz.
biodb.TRACE[2025-01-28 03:56:52.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: msprecmz.
biodb.TRACE[2025-01-28 03:56:52.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:52.973][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr.
biodb.TRACE[2025-01-28 03:56:52.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr.
biodb.TRACE[2025-01-28 03:56:52.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:52.979][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-28 03:56:52.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-28 03:56:52.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:52.985][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-28 03:56:52.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-28 03:56:52.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:52.991][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-28 03:56:52.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-28 03:56:52.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:52.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:52.997][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr.
biodb.TRACE[2025-01-28 03:56:52.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr.
biodb.TRACE[2025-01-28 03:56:53.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:53.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:53.003][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr.
biodb.TRACE[2025-01-28 03:56:53.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr.
biodb.TRACE[2025-01-28 03:56:53.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:53.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:53.009][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr.
biodb.TRACE[2025-01-28 03:56:53.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr.
biodb.TRACE[2025-01-28 03:56:53.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:53.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:53.015][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.csv.file.id.
biodb.TRACE[2025-01-28 03:56:53.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mass.csv.file.id.
biodb.TRACE[2025-01-28 03:56:53.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:53.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:53.021][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.csv.file.id.
biodb.TRACE[2025-01-28 03:56:53.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mass.csv.file.id.
biodb.TRACE[2025-01-28 03:56:53.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:53.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:53.027][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 03:56:53.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 03:56:53.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:53.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:53.040][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.csv.file.id.
biodb.TRACE[2025-01-28 03:56:53.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mass.csv.file.id.
biodb.TRACE[2025-01-28 03:56:53.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:53.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:53.047][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 03:56:53.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 03:56:53.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:53.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:53.053][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 03:56:53.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 03:56:53.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:53.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:53.059][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 03:56:53.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 03:56:53.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:53.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:53.065][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 03:56:53.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 03:56:53.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:53.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:53.071][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 03:56:53.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 03:56:53.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:53.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:53.077][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 03:56:53.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 03:56:53.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:53.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-28 03:56:53.083][self$createEntryFromContent] Accession numbers: C1.
biodb.INFO [2025-01-28 03:56:53.101][biodb$getFactory()$deleteConn] Connector "mass.csv.file" deleted.
biodb.INFO [2025-01-28 03:56:53.107][biodb::testThat]
biodb.INFO [2025-01-28 03:56:53.109][biodb::testThat] Running test function test.BiodbConn.print (" BiodbConn print method returns correct information. ").
biodb.INFO [2025-01-28 03:56:53.110][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-28 03:56:53.112][biodb::testThat]
biodb.DEBUG[2025-01-28 03:56:53.164][super$initialize] Initialize connector comp.csv.file.
biodb.DEBUG[2025-01-28 03:56:53.185][biodb$getFactory()$createConn] Creating new connector comp.csv.file for database class comp.csv.file , with base URL "/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/biodb/extdata/chebi_extract.tsv".
biodb.INFO [2025-01-28 03:56:53.286][biodb::testThat]
biodb.INFO [2025-01-28 03:56:53.287][biodb::testThat] Running test function test.BiodbDbsInfo.print (" BiodbDbsInfo print method returns correct information. ").
biodb.INFO [2025-01-28 03:56:53.293][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-28 03:56:53.294][biodb::testThat]
biodb.INFO [2025-01-28 03:56:53.318][biodb::testThat]
biodb.INFO [2025-01-28 03:56:53.319][biodb::testThat] Running test function test.BiodbEntryFields.print (" BiodbEntryFields print method returns correct information. ").
biodb.INFO [2025-01-28 03:56:53.325][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-28 03:56:53.326][biodb::testThat]
biodb.INFO [2025-01-28 03:56:53.349][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-01-28 03:56:53.351][self$deleteConn] Connector "comp.csv.file" deleted.
biodb.DEBUG[2025-01-28 03:56:53.352][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-01-28 03:56:53.354][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:53.355][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:53.360][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:53.362][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-01-28 03:56:53.374][biodb::testContext]
biodb.INFO [2025-01-28 03:56:53.376][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-28 03:56:53.377][biodb::testContext] Test context - Testing mass functions
biodb.INFO [2025-01-28 03:56:53.378][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-28 03:56:53.380][biodb::testContext]
biodb.INFO [2025-01-28 03:56:53.386][biodb::testThat]
biodb.INFO [2025-01-28 03:56:53.387][biodb::testThat] Running test function test_convertTolToRange (" Conversion from tolerance to range works correctly. ").
biodb.INFO [2025-01-28 03:56:53.393][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-28 03:56:53.395][biodb::testThat]
biodb.INFO [2025-01-28 03:56:53.490][biodb::testThat]
biodb.INFO [2025-01-28 03:56:53.491][biodb::testThat] Running test function test_closeMatchPpm (" closeMatchPpm() works correctly. ").
biodb.INFO [2025-01-28 03:56:53.497][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-28 03:56:53.498][biodb::testThat]
biodb.INFO [2025-01-28 03:56:53.566][biodb::testContext]
biodb.INFO [2025-01-28 03:56:53.567][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-28 03:56:53.569][biodb::testContext] Test context - Testing biodb functions
biodb.INFO [2025-01-28 03:56:53.570][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-28 03:56:53.571][biodb::testContext]
biodb.INFO [2025-01-28 03:56:53.577][biodb::testThat]
biodb.INFO [2025-01-28 03:56:53.579][biodb::testThat] Running test function test_connNameToClassPrefix (" We can convert a connector name into a class prefix. ").
biodb.INFO [2025-01-28 03:56:53.584][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-28 03:56:53.586][biodb::testThat]
biodb.INFO [2025-01-28 03:56:53.612][biodb::testThat]
biodb.INFO [2025-01-28 03:56:53.618][biodb::testThat] Running test function test_extractVersion (" We can extract the version number from a template file. ").
biodb.INFO [2025-01-28 03:56:53.619][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-28 03:56:53.625][biodb::testThat]
biodb.INFO [2025-01-28 03:56:53.661][biodb::testContext]
biodb.INFO [2025-01-28 03:56:53.663][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-28 03:56:53.665][biodb::testContext] Test context - Testing miscellaneous functions
biodb.INFO [2025-01-28 03:56:53.666][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-28 03:56:53.668][biodb::testContext]
biodb.INFO [2025-01-28 03:56:53.669][biodb::testThat]
biodb.INFO [2025-01-28 03:56:53.671][biodb::testThat] Running test function test_splitVersion (" We can split version string. ").
biodb.INFO [2025-01-28 03:56:53.673][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-28 03:56:53.674][biodb::testThat]
biodb.INFO [2025-01-28 03:56:53.693][biodb::testThat]
biodb.INFO [2025-01-28 03:56:53.694][biodb::testThat] Running test function test_compareVersions (" We can compare string versions. ").
biodb.INFO [2025-01-28 03:56:53.696][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-28 03:56:53.697][biodb::testThat]
biodb.INFO [2025-01-28 03:56:53.747][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-01-28 03:56:53.754][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-01-28 03:56:53.763][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-28 03:56:53.769][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-01-28 03:56:53.770][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-01-28 03:56:53.772][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:53.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:53.779][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:53.784][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-01-28 03:56:53.786][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-01-28 03:56:53.787][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:53.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:53.811][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:53.817][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-01-28 03:56:53.819][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-01-28 03:56:53.825][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:53.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:53.828][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:53.834][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-01-28 03:56:53.835][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-01-28 03:56:53.841][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-01-28 03:56:53.842][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:53.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:53.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:53.851][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-01-28 03:56:53.853][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-01-28 03:56:53.854][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-01-28 03:56:53.855][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:53.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:53.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:53.864][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-01-28 03:56:53.870][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-01-28 03:56:53.871][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:53.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:53.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:53.879][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-01-28 03:56:53.885][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-01-28 03:56:53.887][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-01-28 03:56:53.892][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:53.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:53.895][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:53.901][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-01-28 03:56:53.902][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-01-28 03:56:53.904][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:53.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:53.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:53.911][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-01-28 03:56:53.913][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-01-28 03:56:53.914][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-01-28 03:56:53.916][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:53.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:53.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:53.920][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-01-28 03:56:53.921][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-01-28 03:56:53.923][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-01-28 03:56:53.924][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-01-28 03:56:53.926][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-01-28 03:56:53.927][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-01-28 03:56:53.929][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:53.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:53.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:53.933][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-01-28 03:56:53.935][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-01-28 03:56:53.936][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:53.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:53.939][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:53.940][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-01-28 03:56:53.942][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-01-28 03:56:53.943][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:53.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:53.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:53.947][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-01-28 03:56:53.949][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-01-28 03:56:53.950][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:53.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:53.953][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:53.954][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-01-28 03:56:53.956][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-01-28 03:56:53.957][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:53.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:53.959][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:53.961][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-01-28 03:56:53.963][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-01-28 03:56:53.964][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:53.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:53.967][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:53.968][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-01-28 03:56:53.970][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-01-28 03:56:53.989][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-01-28 03:56:53.990][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:53.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:53.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:53.997][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-01-28 03:56:53.999][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-01-28 03:56:54.002][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-01-28 03:56:54.003][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:54.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:54.007][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:54.009][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-01-28 03:56:54.015][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-28 03:56:54.017][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-01-28 03:56:54.019][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:54.023][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-28 03:56:54.025][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:54.027][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-28 03:56:54.034][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-28 03:56:54.035][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-28 03:56:54.037][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-28 03:56:54.038][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-28 03:56:54.040][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:54.042][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-01-28 03:56:54.043][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-28 03:56:54.045][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:54.046][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:54.048][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-28 03:56:54.048][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-28 03:56:54.048][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-28 03:56:54.048][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-28 03:56:54.048][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-28 03:56:54.049][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-28 03:56:54.051][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-28 03:56:54.052][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-28 03:56:54.054][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-28 03:56:54.055][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-28 03:56:54.056][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-28 03:56:54.065][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-28 03:56:54.067][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:54.069][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-28 03:56:54.070][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-28 03:56:54.071][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-28 03:56:54.073][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:54.075][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-01-28 03:56:54.077][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-28 03:56:54.079][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-01-28 03:56:54.080][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:54.082][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-28 03:56:54.083][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:54.084][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-28 03:56:54.086][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-28 03:56:54.087][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-28 03:56:54.089][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-28 03:56:54.090][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-28 03:56:54.092][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:54.093][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-01-28 03:56:54.095][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-28 03:56:54.096][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:54.098][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:54.099][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-28 03:56:54.099][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-28 03:56:54.099][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-28 03:56:54.099][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-28 03:56:54.099][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-28 03:56:54.101][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-28 03:56:54.102][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-28 03:56:54.103][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-28 03:56:54.105][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-28 03:56:54.106][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-28 03:56:54.108][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-28 03:56:54.109][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-28 03:56:54.110][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:54.112][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-28 03:56:54.113][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-28 03:56:54.115][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-28 03:56:54.116][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:54.118][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-01-28 03:56:54.120][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:54.122][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-01-28 03:56:54.124][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:54.125][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-28 03:56:54.126][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:54.128][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-28 03:56:54.129][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-28 03:56:54.131][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-28 03:56:54.132][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-28 03:56:54.134][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-28 03:56:54.135][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-28 03:56:54.137][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-01-28 03:56:54.138][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-28 03:56:54.140][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:54.141][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:54.142][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:54.144][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-28 03:56:54.145][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-28 03:56:54.147][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-28 03:56:54.148][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-28 03:56:54.149][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-28 03:56:54.151][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-28 03:56:54.152][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-28 03:56:54.154][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:54.155][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-28 03:56:54.156][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-28 03:56:54.158][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-28 03:56:54.159][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:54.161][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-01-28 03:56:54.163][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:54.165][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-01-28 03:56:54.166][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:54.168][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-28 03:56:54.169][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:54.171][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-28 03:56:54.172][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-28 03:56:54.174][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-28 03:56:54.175][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-28 03:56:54.177][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-28 03:56:54.178][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-28 03:56:54.180][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-01-28 03:56:54.181][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-28 03:56:54.183][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:54.184][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:54.185][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:54.187][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-28 03:56:54.188][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-28 03:56:54.190][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-28 03:56:54.191][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-28 03:56:54.192][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-28 03:56:54.194][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-28 03:56:54.195][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-28 03:56:54.197][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:54.198][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-28 03:56:54.199][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-28 03:56:54.201][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-28 03:56:54.202][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:54.204][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-28 03:56:54.205][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:54.207][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:54.208][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:54.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:54.211][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:54.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:54.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:54.215][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:54.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:54.217][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:54.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:54.228][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:54.229][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:54.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:54.232][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:54.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:54.235][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:54.236][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:54.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:54.239][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:54.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:54.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:54.243][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:54.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:54.245][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:54.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:54.248][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:54.249][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:54.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:54.252][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:54.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:54.255][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:54.256][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:54.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:54.259][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:54.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:54.262][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:54.263][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:54.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:54.266][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:54.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:54.268][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:54.270][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:54.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:54.272][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:54.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:54.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:54.276][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:54.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:54.279][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:54.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:54.281][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:54.283][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:54.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:54.285][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:54.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:54.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:54.289][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:54.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:54.292][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:54.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:54.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:54.296][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:54.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:54.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:54.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:54.301][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:54.302][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:54.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:54.305][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:54.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:54.308][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:54.309][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:54.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:54.312][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:54.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:54.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:54.315][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:54.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:54.318][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:54.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:54.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:54.322][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:54.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:54.325][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:54.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:54.327][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:54.329][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-01-28 03:56:54.331][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-01-28 03:56:54.333][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-01-28 03:56:54.335][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-01-28 03:56:54.337][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-01-28 03:56:54.339][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-01-28 03:56:54.341][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-01-28 03:56:54.343][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-01-28 03:56:54.345][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-01-28 03:56:54.347][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-01-28 03:56:54.350][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-01-28 03:56:54.352][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-01-28 03:56:54.354][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-01-28 03:56:54.356][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-01-28 03:56:54.358][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-01-28 03:56:54.360][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-01-28 03:56:54.362][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-01-28 03:56:54.364][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-01-28 03:56:54.366][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-01-28 03:56:54.368][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-01-28 03:56:54.370][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-01-28 03:56:54.372][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-01-28 03:56:54.374][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-01-28 03:56:54.376][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-01-28 03:56:54.378][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-01-28 03:56:54.388][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-01-28 03:56:54.390][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-01-28 03:56:54.393][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-01-28 03:56:54.395][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-01-28 03:56:54.397][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-01-28 03:56:54.399][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-01-28 03:56:54.401][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-01-28 03:56:54.403][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-01-28 03:56:54.405][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-01-28 03:56:54.407][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-01-28 03:56:54.409][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-01-28 03:56:54.411][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-01-28 03:56:54.413][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-01-28 03:56:54.415][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-01-28 03:56:54.417][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-01-28 03:56:54.419][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-01-28 03:56:54.421][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-01-28 03:56:54.423][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-01-28 03:56:54.426][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-01-28 03:56:54.428][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-01-28 03:56:54.430][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-01-28 03:56:54.432][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-01-28 03:56:54.434][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-01-28 03:56:54.436][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-01-28 03:56:54.438][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-01-28 03:56:54.440][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-01-28 03:56:54.442][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-01-28 03:56:54.444][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-01-28 03:56:54.446][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-01-28 03:56:54.448][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-01-28 03:56:54.450][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-01-28 03:56:54.452][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-01-28 03:56:54.454][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-01-28 03:56:54.456][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-01-28 03:56:54.458][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-01-28 03:56:54.460][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-01-28 03:56:54.463][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-01-28 03:56:54.465][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-01-28 03:56:54.467][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-01-28 03:56:54.469][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-01-28 03:56:54.471][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-01-28 03:56:54.473][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-01-28 03:56:54.475][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-01-28 03:56:54.478][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-01-28 03:56:54.480][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-01-28 03:56:54.482][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-01-28 03:56:54.484][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-01-28 03:56:54.486][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-01-28 03:56:54.488][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-01-28 03:56:54.491][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-01-28 03:56:54.493][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-01-28 03:56:54.495][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-01-28 03:56:54.497][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-01-28 03:56:54.499][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-01-28 03:56:54.501][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-01-28 03:56:54.504][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-01-28 03:56:54.506][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-01-28 03:56:54.508][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-01-28 03:56:54.510][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-01-28 03:56:54.512][initialize] This is biodb version 1.15.0.
biodb.INFO [2025-01-28 03:56:54.514][biodb::testContext]
biodb.INFO [2025-01-28 03:56:54.516][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-28 03:56:54.517][biodb::testContext] Test context - Test messages.
biodb.INFO [2025-01-28 03:56:54.519][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-28 03:56:54.520][biodb::testContext]
biodb.INFO [2025-01-28 03:56:54.522][biodb::testThat]
biodb.INFO [2025-01-28 03:56:54.524][biodb::testThat] Running test function test.deprecatedMethods (" Deprecated methods send correct message. ").
biodb.INFO [2025-01-28 03:56:54.525][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-28 03:56:54.526][biodb::testThat]
biodb.DEBUG[2025-01-28 03:56:54.533][super$initialize] Initialize connector mass.csv.file.
biodb.DEBUG[2025-01-28 03:56:54.535][biodb$getFactory()$createConn] Creating new connector mass.csv.file for database class mass.csv.file .
biodb.DEBUG[2025-01-28 03:56:54.537][private$loadEntries] Creating entries from ids [1]: "C1".
biodb.DEBUG[2025-01-28 03:56:54.539][conn$getEntryContent] Get Mass spectra CSV File entry content(s) for 1 id(s)...
biodb.DEBUG[2025-01-28 03:56:54.551][conn$getEntryContent] 1 entry content(s) need to be fetched from Mass spectra CSV File database "NA".
biodb.DEBUG[2025-01-28 03:56:54.553][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-28 03:56:54.554][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-28 03:56:54.556][private$doGetEntryContentFromDb] Entry id: C1
biodb.DEBUG[2025-01-28 03:56:54.558][self$setField] Set field accession to column(s) accession.
biodb.TRACE[2025-01-28 03:56:54.560][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 03:56:54.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 03:56:54.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:54.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-28 03:56:54.566][self$setPropertyValue] Setting property "parsing.expr" to "accession".
biodb.DEBUG[2025-01-28 03:56:54.568][self$setField] Set field ms.mode to column(s) ms.mode.
biodb.TRACE[2025-01-28 03:56:54.570][self$getBiodb()$getEntryFields()$get] Asked field names are: ms.mode.
biodb.TRACE[2025-01-28 03:56:54.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ms.mode.
biodb.TRACE[2025-01-28 03:56:54.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:54.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-28 03:56:54.576][self$setPropertyValue] Setting property "parsing.expr" to "accession".
biodb.DEBUG[2025-01-28 03:56:54.576][self$setPropertyValue] Setting property "parsing.expr" to "ms.mode".
biodb.DEBUG[2025-01-28 03:56:54.578][self$setField] Set field peak.mztheo to column(s) peak.mztheo.
biodb.TRACE[2025-01-28 03:56:54.580][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-28 03:56:54.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-28 03:56:54.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:54.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-28 03:56:54.586][self$setPropertyValue] Setting property "parsing.expr" to "accession".
biodb.DEBUG[2025-01-28 03:56:54.586][self$setPropertyValue] Setting property "parsing.expr" to "ms.mode".
biodb.DEBUG[2025-01-28 03:56:54.586][self$setPropertyValue] Setting property "parsing.expr" to "peak.mztheo".
biodb.DEBUG[2025-01-28 03:56:54.589][self$setField] Set field peak.comp to column(s) peak.comp.
biodb.TRACE[2025-01-28 03:56:54.590][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.comp.
biodb.TRACE[2025-01-28 03:56:54.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.comp.
biodb.TRACE[2025-01-28 03:56:54.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:54.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-28 03:56:54.603][self$setPropertyValue] Setting property "parsing.expr" to "accession".
biodb.DEBUG[2025-01-28 03:56:54.603][self$setPropertyValue] Setting property "parsing.expr" to "ms.mode".
biodb.DEBUG[2025-01-28 03:56:54.603][self$setPropertyValue] Setting property "parsing.expr" to "peak.mztheo".
biodb.DEBUG[2025-01-28 03:56:54.603][self$setPropertyValue] Setting property "parsing.expr" to "peak.comp".
biodb.DEBUG[2025-01-28 03:56:54.606][self$setField] Set field peak.attr to column(s) peak.attr.
biodb.TRACE[2025-01-28 03:56:54.608][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr.
biodb.TRACE[2025-01-28 03:56:54.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr.
biodb.TRACE[2025-01-28 03:56:54.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:54.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-28 03:56:54.615][self$setPropertyValue] Setting property "parsing.expr" to "accession".
biodb.DEBUG[2025-01-28 03:56:54.615][self$setPropertyValue] Setting property "parsing.expr" to "ms.mode".
biodb.DEBUG[2025-01-28 03:56:54.615][self$setPropertyValue] Setting property "parsing.expr" to "peak.mztheo".
biodb.DEBUG[2025-01-28 03:56:54.615][self$setPropertyValue] Setting property "parsing.expr" to "peak.comp".
biodb.DEBUG[2025-01-28 03:56:54.615][self$setPropertyValue] Setting property "parsing.expr" to "peak.attr".
biodb.DEBUG[2025-01-28 03:56:54.617][self$setField] Set field formula to column(s) formula.
biodb.TRACE[2025-01-28 03:56:54.619][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-28 03:56:54.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-28 03:56:54.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:54.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-28 03:56:54.626][self$setPropertyValue] Setting property "parsing.expr" to "accession".
biodb.DEBUG[2025-01-28 03:56:54.626][self$setPropertyValue] Setting property "parsing.expr" to "ms.mode".
biodb.DEBUG[2025-01-28 03:56:54.626][self$setPropertyValue] Setting property "parsing.expr" to "peak.mztheo".
biodb.DEBUG[2025-01-28 03:56:54.626][self$setPropertyValue] Setting property "parsing.expr" to "peak.comp".
biodb.DEBUG[2025-01-28 03:56:54.626][self$setPropertyValue] Setting property "parsing.expr" to "peak.attr".
biodb.DEBUG[2025-01-28 03:56:54.626][self$setPropertyValue] Setting property "parsing.expr" to "formula".
biodb.DEBUG[2025-01-28 03:56:54.629][self$setField] Set field molecular.mass to column(s) molecular.mass.
biodb.TRACE[2025-01-28 03:56:54.631][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-28 03:56:54.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-28 03:56:54.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:54.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-28 03:56:54.638][self$setPropertyValue] Setting property "parsing.expr" to "accession".
biodb.DEBUG[2025-01-28 03:56:54.638][self$setPropertyValue] Setting property "parsing.expr" to "ms.mode".
biodb.DEBUG[2025-01-28 03:56:54.638][self$setPropertyValue] Setting property "parsing.expr" to "peak.mztheo".
biodb.DEBUG[2025-01-28 03:56:54.638][self$setPropertyValue] Setting property "parsing.expr" to "peak.comp".
biodb.DEBUG[2025-01-28 03:56:54.638][self$setPropertyValue] Setting property "parsing.expr" to "peak.attr".
biodb.DEBUG[2025-01-28 03:56:54.638][self$setPropertyValue] Setting property "parsing.expr" to "formula".
biodb.DEBUG[2025-01-28 03:56:54.638][self$setPropertyValue] Setting property "parsing.expr" to "molecular.mass".
biodb.DEBUG[2025-01-28 03:56:54.640][self$setField] Set field name to column(s) name.
biodb.TRACE[2025-01-28 03:56:54.642][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-28 03:56:54.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-28 03:56:54.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:54.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-28 03:56:54.649][self$setPropertyValue] Setting property "parsing.expr" to "accession".
biodb.DEBUG[2025-01-28 03:56:54.649][self$setPropertyValue] Setting property "parsing.expr" to "ms.mode".
biodb.DEBUG[2025-01-28 03:56:54.649][self$setPropertyValue] Setting property "parsing.expr" to "peak.mztheo".
biodb.DEBUG[2025-01-28 03:56:54.649][self$setPropertyValue] Setting property "parsing.expr" to "peak.comp".
biodb.DEBUG[2025-01-28 03:56:54.649][self$setPropertyValue] Setting property "parsing.expr" to "peak.attr".
biodb.DEBUG[2025-01-28 03:56:54.649][self$setPropertyValue] Setting property "parsing.expr" to "formula".
biodb.DEBUG[2025-01-28 03:56:54.649][self$setPropertyValue] Setting property "parsing.expr" to "molecular.mass".
biodb.DEBUG[2025-01-28 03:56:54.649][self$setPropertyValue] Setting property "parsing.expr" to "name".
biodb.DEBUG[2025-01-28 03:56:54.656][private$doGetEntryContentFromDb] Content of first entry: accession ms.mode peak.mztheo peak.comp peak.attr formula molecular.mass name
C1 pos 112.07569 P9Z6W410 O [(M+H)-(H2O)-(NH3)]+ J114L6M62O2 146.10553 Blablaine
biodb.DEBUG[2025-01-28 03:56:54.659][self$createEntryFromContent] Creating Mass spectra CSV File entries from 1 content(s).
biodb.DEBUG[2025-01-28 03:56:54.662][self$createEntryFromContent] Parsing 1 Mass spectra CSV File entries.
biodb.DEBUG[2025-01-28 03:56:54.665][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-28 03:56:54.666][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:54.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:54.669][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:54.670][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:54.677][self$setPropertyValue] Setting property "parsing.expr" to "accession".
biodb.DEBUG[2025-01-28 03:56:54.677][self$setPropertyValue] Setting property "parsing.expr" to "ms.mode".
biodb.DEBUG[2025-01-28 03:56:54.677][self$setPropertyValue] Setting property "parsing.expr" to "peak.mztheo".
biodb.DEBUG[2025-01-28 03:56:54.677][self$setPropertyValue] Setting property "parsing.expr" to "peak.comp".
biodb.DEBUG[2025-01-28 03:56:54.677][self$setPropertyValue] Setting property "parsing.expr" to "peak.attr".
biodb.DEBUG[2025-01-28 03:56:54.677][self$setPropertyValue] Setting property "parsing.expr" to "formula".
biodb.DEBUG[2025-01-28 03:56:54.677][self$setPropertyValue] Setting property "parsing.expr" to "molecular.mass".
biodb.DEBUG[2025-01-28 03:56:54.677][self$setPropertyValue] Setting property "parsing.expr" to "name".
biodb.DEBUG[2025-01-28 03:56:54.679][self$setPropertyValue] Setting property "parsing.expr" to "accession".
biodb.DEBUG[2025-01-28 03:56:54.679][self$setPropertyValue] Setting property "parsing.expr" to "ms.mode".
biodb.DEBUG[2025-01-28 03:56:54.679][self$setPropertyValue] Setting property "parsing.expr" to "peak.mztheo".
biodb.DEBUG[2025-01-28 03:56:54.679][self$setPropertyValue] Setting property "parsing.expr" to "peak.comp".
biodb.DEBUG[2025-01-28 03:56:54.679][self$setPropertyValue] Setting property "parsing.expr" to "peak.attr".
biodb.DEBUG[2025-01-28 03:56:54.679][self$setPropertyValue] Setting property "parsing.expr" to "formula".
biodb.DEBUG[2025-01-28 03:56:54.679][self$setPropertyValue] Setting property "parsing.expr" to "molecular.mass".
biodb.DEBUG[2025-01-28 03:56:54.679][self$setPropertyValue] Setting property "parsing.expr" to "name".
biodb.DEBUG[2025-01-28 03:56:54.680][self$setPropertyValue] Setting property "parsing.expr" to "accession".
biodb.DEBUG[2025-01-28 03:56:54.680][self$setPropertyValue] Setting property "parsing.expr" to "ms.mode".
biodb.DEBUG[2025-01-28 03:56:54.680][self$setPropertyValue] Setting property "parsing.expr" to "peak.mztheo".
biodb.DEBUG[2025-01-28 03:56:54.680][self$setPropertyValue] Setting property "parsing.expr" to "peak.comp".
biodb.DEBUG[2025-01-28 03:56:54.680][self$setPropertyValue] Setting property "parsing.expr" to "peak.attr".
biodb.DEBUG[2025-01-28 03:56:54.680][self$setPropertyValue] Setting property "parsing.expr" to "formula".
biodb.DEBUG[2025-01-28 03:56:54.680][self$setPropertyValue] Setting property "parsing.expr" to "molecular.mass".
biodb.DEBUG[2025-01-28 03:56:54.680][self$setPropertyValue] Setting property "parsing.expr" to "name".
biodb.DEBUG[2025-01-28 03:56:54.682][self$setPropertyValue] Setting property "parsing.expr" to "accession".
biodb.DEBUG[2025-01-28 03:56:54.682][self$setPropertyValue] Setting property "parsing.expr" to "ms.mode".
biodb.DEBUG[2025-01-28 03:56:54.682][self$setPropertyValue] Setting property "parsing.expr" to "peak.mztheo".
biodb.DEBUG[2025-01-28 03:56:54.682][self$setPropertyValue] Setting property "parsing.expr" to "peak.comp".
biodb.DEBUG[2025-01-28 03:56:54.682][self$setPropertyValue] Setting property "parsing.expr" to "peak.attr".
biodb.DEBUG[2025-01-28 03:56:54.682][self$setPropertyValue] Setting property "parsing.expr" to "formula".
biodb.DEBUG[2025-01-28 03:56:54.682][self$setPropertyValue] Setting property "parsing.expr" to "molecular.mass".
biodb.DEBUG[2025-01-28 03:56:54.682][self$setPropertyValue] Setting property "parsing.expr" to "name".
biodb.DEBUG[2025-01-28 03:56:54.684][self$setPropertyValue] Setting property "parsing.expr" to "accession".
biodb.DEBUG[2025-01-28 03:56:54.684][self$setPropertyValue] Setting property "parsing.expr" to "ms.mode".
biodb.DEBUG[2025-01-28 03:56:54.684][self$setPropertyValue] Setting property "parsing.expr" to "peak.mztheo".
biodb.DEBUG[2025-01-28 03:56:54.684][self$setPropertyValue] Setting property "parsing.expr" to "peak.comp".
biodb.DEBUG[2025-01-28 03:56:54.684][self$setPropertyValue] Setting property "parsing.expr" to "peak.attr".
biodb.DEBUG[2025-01-28 03:56:54.684][self$setPropertyValue] Setting property "parsing.expr" to "formula".
biodb.DEBUG[2025-01-28 03:56:54.684][self$setPropertyValue] Setting property "parsing.expr" to "molecular.mass".
biodb.DEBUG[2025-01-28 03:56:54.684][self$setPropertyValue] Setting property "parsing.expr" to "name".
biodb.DEBUG[2025-01-28 03:56:54.686][self$setPropertyValue] Setting property "parsing.expr" to "accession".
biodb.DEBUG[2025-01-28 03:56:54.686][self$setPropertyValue] Setting property "parsing.expr" to "ms.mode".
biodb.DEBUG[2025-01-28 03:56:54.686][self$setPropertyValue] Setting property "parsing.expr" to "peak.mztheo".
biodb.DEBUG[2025-01-28 03:56:54.686][self$setPropertyValue] Setting property "parsing.expr" to "peak.comp".
biodb.DEBUG[2025-01-28 03:56:54.686][self$setPropertyValue] Setting property "parsing.expr" to "peak.attr".
biodb.DEBUG[2025-01-28 03:56:54.686][self$setPropertyValue] Setting property "parsing.expr" to "formula".
biodb.DEBUG[2025-01-28 03:56:54.686][self$setPropertyValue] Setting property "parsing.expr" to "molecular.mass".
biodb.DEBUG[2025-01-28 03:56:54.686][self$setPropertyValue] Setting property "parsing.expr" to "name".
biodb.DEBUG[2025-01-28 03:56:54.687][self$setPropertyValue] Setting property "parsing.expr" to "accession".
biodb.DEBUG[2025-01-28 03:56:54.687][self$setPropertyValue] Setting property "parsing.expr" to "ms.mode".
biodb.DEBUG[2025-01-28 03:56:54.687][self$setPropertyValue] Setting property "parsing.expr" to "peak.mztheo".
biodb.DEBUG[2025-01-28 03:56:54.687][self$setPropertyValue] Setting property "parsing.expr" to "peak.comp".
biodb.DEBUG[2025-01-28 03:56:54.687][self$setPropertyValue] Setting property "parsing.expr" to "peak.attr".
biodb.DEBUG[2025-01-28 03:56:54.687][self$setPropertyValue] Setting property "parsing.expr" to "formula".
biodb.DEBUG[2025-01-28 03:56:54.687][self$setPropertyValue] Setting property "parsing.expr" to "molecular.mass".
biodb.DEBUG[2025-01-28 03:56:54.687][self$setPropertyValue] Setting property "parsing.expr" to "name".
biodb.DEBUG[2025-01-28 03:56:54.689][self$setPropertyValue] Setting property "parsing.expr" to "accession".
biodb.DEBUG[2025-01-28 03:56:54.689][self$setPropertyValue] Setting property "parsing.expr" to "ms.mode".
biodb.DEBUG[2025-01-28 03:56:54.689][self$setPropertyValue] Setting property "parsing.expr" to "peak.mztheo".
biodb.DEBUG[2025-01-28 03:56:54.689][self$setPropertyValue] Setting property "parsing.expr" to "peak.comp".
biodb.DEBUG[2025-01-28 03:56:54.689][self$setPropertyValue] Setting property "parsing.expr" to "peak.attr".
biodb.DEBUG[2025-01-28 03:56:54.689][self$setPropertyValue] Setting property "parsing.expr" to "formula".
biodb.DEBUG[2025-01-28 03:56:54.689][self$setPropertyValue] Setting property "parsing.expr" to "molecular.mass".
biodb.DEBUG[2025-01-28 03:56:54.689][self$setPropertyValue] Setting property "parsing.expr" to "name".
biodb.TRACE[2025-01-28 03:56:54.691][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 03:56:54.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 03:56:54.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:54.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:54.698][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 03:56:54.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 03:56:54.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:54.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:54.705][self$getBiodb()$getEntryFields()$get] Asked field names are: ms.mode.
biodb.TRACE[2025-01-28 03:56:54.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ms.mode.
biodb.TRACE[2025-01-28 03:56:54.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:54.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:54.711][self$getBiodb()$getEntryFields()$get] Asked field names are: ms.mode.
biodb.TRACE[2025-01-28 03:56:54.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ms.mode.
biodb.TRACE[2025-01-28 03:56:54.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:54.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:54.718][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-28 03:56:54.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-28 03:56:54.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:54.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:54.724][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-28 03:56:54.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-28 03:56:54.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:54.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:54.730][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.comp.
biodb.TRACE[2025-01-28 03:56:54.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.comp.
biodb.TRACE[2025-01-28 03:56:54.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:54.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:54.752][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.comp.
biodb.TRACE[2025-01-28 03:56:54.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.comp.
biodb.TRACE[2025-01-28 03:56:54.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:54.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:54.759][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr.
biodb.TRACE[2025-01-28 03:56:54.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr.
biodb.TRACE[2025-01-28 03:56:54.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:54.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:54.765][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr.
biodb.TRACE[2025-01-28 03:56:54.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr.
biodb.TRACE[2025-01-28 03:56:54.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:54.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:54.771][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-28 03:56:54.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-28 03:56:54.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:54.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:54.778][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-28 03:56:54.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-28 03:56:54.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:54.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:54.784][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-28 03:56:54.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-28 03:56:54.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:54.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:54.790][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-28 03:56:54.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-28 03:56:54.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:54.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:54.796][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-28 03:56:54.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-28 03:56:54.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:54.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:54.802][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-28 03:56:54.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-28 03:56:54.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:54.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:54.808][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-28 03:56:54.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-28 03:56:54.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:54.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:54.813][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-28 03:56:54.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-28 03:56:54.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:54.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:54.819][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-28 03:56:54.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-28 03:56:54.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:54.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:54.824][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-28 03:56:54.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-28 03:56:54.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:54.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:54.830][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-01-28 03:56:54.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-01-28 03:56:54.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:54.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:54.835][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-28 03:56:54.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-28 03:56:54.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:54.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:54.841][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-28 03:56:54.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-28 03:56:54.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:54.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:54.847][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-28 03:56:54.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-28 03:56:54.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:54.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:54.852][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-28 03:56:54.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-28 03:56:54.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:54.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:54.858][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-28 03:56:54.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-28 03:56:54.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:54.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:54.864][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-28 03:56:54.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-28 03:56:54.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:54.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:54.870][self$getBiodb()$getEntryFields()$get] Asked field names are: peaks.
biodb.TRACE[2025-01-28 03:56:54.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peaks.
biodb.TRACE[2025-01-28 03:56:54.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:54.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:54.876][self$getBiodb()$getEntryFields()$get] Asked field names are: peaks.
biodb.TRACE[2025-01-28 03:56:54.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peaks.
biodb.TRACE[2025-01-28 03:56:54.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:54.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:54.881][self$getBiodb()$getEntryFields()$get] Asked field names are: peaks.
biodb.TRACE[2025-01-28 03:56:54.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peaks.
biodb.TRACE[2025-01-28 03:56:54.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:54.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:54.888][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-28 03:56:54.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-28 03:56:54.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:54.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:54.894][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-28 03:56:54.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-28 03:56:54.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:54.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:54.899][private$selectFields] Fields none
biodb.TRACE[2025-01-28 03:56:54.908][private$selectFields] Fields type: peak
biodb.TRACE[2025-01-28 03:56:54.910][private$selectFields] Fields is null: TRUE
biodb.TRACE[2025-01-28 03:56:54.911][private$selectFields] Fields.type is null: FALSE
biodb.TRACE[2025-01-28 03:56:54.913][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 03:56:54.914][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 03:56:54.916][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:54.917][ef$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:54.918][ef$get] Asked field names are: ms.mode.
biodb.TRACE[2025-01-28 03:56:54.920][ef$get] Realnames of fields are: ms.mode.
biodb.TRACE[2025-01-28 03:56:54.921][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:54.923][ef$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:54.924][ef$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-28 03:56:54.926][ef$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-28 03:56:54.927][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:54.928][ef$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:54.930][ef$get] Asked field names are: peak.comp.
biodb.TRACE[2025-01-28 03:56:54.931][ef$get] Realnames of fields are: peak.comp.
biodb.TRACE[2025-01-28 03:56:54.933][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:54.934][ef$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:54.936][ef$get] Asked field names are: peak.attr.
biodb.TRACE[2025-01-28 03:56:54.937][ef$get] Realnames of fields are: peak.attr.
biodb.TRACE[2025-01-28 03:56:54.939][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:54.940][ef$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:54.942][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-28 03:56:54.943][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-28 03:56:54.945][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:54.946][ef$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:54.948][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-28 03:56:54.949][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-28 03:56:54.951][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:54.952][ef$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:54.954][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-28 03:56:54.955][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-28 03:56:54.956][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:54.958][ef$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:54.959][ef$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-28 03:56:54.961][ef$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-28 03:56:54.962][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:54.964][ef$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:54.965][private$selectFields] Fields [4]: "peak.mztheo, peak.comp, peak.attr, peak.mz"
biodb.TRACE[2025-01-28 03:56:54.967][ef$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-28 03:56:54.968][ef$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-28 03:56:54.969][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:54.971][ef$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:54.972][ef$get] Asked field names are: peak.comp.
biodb.TRACE[2025-01-28 03:56:54.974][ef$get] Realnames of fields are: peak.comp.
biodb.TRACE[2025-01-28 03:56:54.975][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:54.977][ef$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:54.978][ef$get] Asked field names are: peak.attr.
biodb.TRACE[2025-01-28 03:56:54.980][ef$get] Realnames of fields are: peak.attr.
biodb.TRACE[2025-01-28 03:56:54.981][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:54.983][ef$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:54.984][ef$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-28 03:56:54.986][ef$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-28 03:56:54.987][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:54.989][ef$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:54.990][private$selectFields] Fields [4]: "peak.mztheo, peak.comp, peak.attr, peak.mz"
biodb.TRACE[2025-01-28 03:56:54.991][private$organizeFieldsByGroups] Fields [4]: "peak.mztheo, peak.comp, peak.attr, peak.mz"
biodb.TRACE[2025-01-28 03:56:54.993][ef$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-28 03:56:54.994][ef$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-28 03:56:54.996][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:54.997][ef$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:54.999][ef$get] Asked field names are: peak.comp.
biodb.TRACE[2025-01-28 03:56:55.000][ef$get] Realnames of fields are: peak.comp.
biodb.TRACE[2025-01-28 03:56:55.002][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:55.003][ef$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:55.004][ef$get] Asked field names are: peak.attr.
biodb.TRACE[2025-01-28 03:56:55.006][ef$get] Realnames of fields are: peak.attr.
biodb.TRACE[2025-01-28 03:56:55.007][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:55.009][ef$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:55.010][ef$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-28 03:56:55.012][ef$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-28 03:56:55.013][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:55.015][ef$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:55.016][private$organizeFieldsByGroups] Groups [2]: "character(0), list(peaks = c("peak.mztheo", "peak.comp", "peak.attr", "peak.mz"))"
biodb.TRACE[2025-01-28 03:56:55.018][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-28 03:56:55.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-28 03:56:55.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:55.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:55.024][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-28 03:56:55.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-28 03:56:55.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:55.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:55.031][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-28 03:56:55.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-28 03:56:55.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:55.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:55.040][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.comp.
biodb.TRACE[2025-01-28 03:56:55.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.comp.
biodb.TRACE[2025-01-28 03:56:55.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:55.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:55.047][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.comp.
biodb.TRACE[2025-01-28 03:56:55.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.comp.
biodb.TRACE[2025-01-28 03:56:55.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:55.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:55.053][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.comp.
biodb.TRACE[2025-01-28 03:56:55.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.comp.
biodb.TRACE[2025-01-28 03:56:55.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:55.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:55.059][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr.
biodb.TRACE[2025-01-28 03:56:55.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr.
biodb.TRACE[2025-01-28 03:56:55.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:55.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:55.066][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr.
biodb.TRACE[2025-01-28 03:56:55.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr.
biodb.TRACE[2025-01-28 03:56:55.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:55.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:55.090][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr.
biodb.TRACE[2025-01-28 03:56:55.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr.
biodb.TRACE[2025-01-28 03:56:55.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:55.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:55.096][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-28 03:56:55.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-28 03:56:55.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:55.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:55.102][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-28 03:56:55.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-28 03:56:55.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:55.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:55.108][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-28 03:56:55.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-28 03:56:55.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:55.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:55.114][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.col.name.
biodb.TRACE[2025-01-28 03:56:55.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.col.name.
biodb.TRACE[2025-01-28 03:56:55.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:55.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:55.124][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.col.name.
biodb.TRACE[2025-01-28 03:56:55.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.col.name.
biodb.TRACE[2025-01-28 03:56:55.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:55.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:55.143][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.col.id.
biodb.TRACE[2025-01-28 03:56:55.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.col.id.
biodb.TRACE[2025-01-28 03:56:55.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:55.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:55.157][self$getBiodb()$getEntryFields()$get] Asked field names are: msprecmz.
biodb.TRACE[2025-01-28 03:56:55.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: msprecmz.
biodb.TRACE[2025-01-28 03:56:55.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:55.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:55.168][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr.
biodb.TRACE[2025-01-28 03:56:55.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr.
biodb.TRACE[2025-01-28 03:56:55.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:55.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:55.182][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-28 03:56:55.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-28 03:56:55.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:55.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:55.197][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-28 03:56:55.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-28 03:56:55.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:55.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:55.208][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-28 03:56:55.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-28 03:56:55.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:55.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:55.223][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr.
biodb.TRACE[2025-01-28 03:56:55.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr.
biodb.TRACE[2025-01-28 03:56:55.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:55.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:55.237][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr.
biodb.TRACE[2025-01-28 03:56:55.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr.
biodb.TRACE[2025-01-28 03:56:55.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:55.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:55.248][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr.
biodb.TRACE[2025-01-28 03:56:55.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr.
biodb.TRACE[2025-01-28 03:56:55.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:55.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:55.262][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.csv.file.id.
biodb.TRACE[2025-01-28 03:56:55.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mass.csv.file.id.
biodb.TRACE[2025-01-28 03:56:55.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:55.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:55.277][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.csv.file.id.
biodb.TRACE[2025-01-28 03:56:55.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mass.csv.file.id.
biodb.TRACE[2025-01-28 03:56:55.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:55.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:55.288][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 03:56:55.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 03:56:55.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:55.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:55.302][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.csv.file.id.
biodb.TRACE[2025-01-28 03:56:55.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: mass.csv.file.id.
biodb.TRACE[2025-01-28 03:56:55.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:55.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:55.317][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 03:56:55.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 03:56:55.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:55.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:55.328][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 03:56:55.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 03:56:55.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:55.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:55.342][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 03:56:55.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 03:56:55.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:55.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:55.358][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 03:56:55.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 03:56:55.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:55.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:55.373][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 03:56:55.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 03:56:55.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:55.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:55.388][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 03:56:55.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 03:56:55.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:55.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-28 03:56:55.415][self$createEntryFromContent] Accession numbers: C1.
biodb.DEBUG[2025-01-28 03:56:55.618][self$setPropertyValue] Setting property "urls" to "https://foo/".
biodb.DEBUG[2025-01-28 03:56:55.620][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-28 03:56:55.622][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-28 03:56:55.750][self$setPropertyValue] Setting property "urls" to "https://foo/".
biodb.DEBUG[2025-01-28 03:56:55.750][self$setPropertyValue] Setting property "urls" to "https://foo/".
biodb.DEBUG[2025-01-28 03:56:55.752][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-28 03:56:55.753][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-28 03:56:55.861][self$setPropertyValue] Setting property "urls" to "https://foo/".
biodb.DEBUG[2025-01-28 03:56:55.861][self$setPropertyValue] Setting property "urls" to "https://foo/".
biodb.DEBUG[2025-01-28 03:56:55.865][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-28 03:56:55.866][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.WARN [2025-01-28 03:56:55.916][self$searchForEntries] This database is not searchable by field "name".
biodb.TRACE[2025-01-28 03:56:55.945][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-28 03:56:55.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-28 03:56:55.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:55.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:56:55.997][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-28 03:56:55.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-28 03:56:56.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:56.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-01-28 03:56:56.003][biodb$getFactory()$deleteConn] Connector "mass.csv.file" deleted.
biodb.INFO [2025-01-28 03:56:56.009][biodb::testThat]
biodb.INFO [2025-01-28 03:56:56.010][biodb::testThat] Running test function test.default.messages (" Test what messages are printed by default. ").
biodb.INFO [2025-01-28 03:56:56.012][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-28 03:56:56.013][biodb::testThat]
biodb.INFO [2025-01-28 03:56:56.096][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-01-28 03:56:56.098][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-01-28 03:56:56.099][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:56.100][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:56.101][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:56.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-01-28 03:56:56.134][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-01-28 03:56:56.140][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-01-28 03:56:56.150][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-28 03:56:56.151][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-01-28 03:56:56.157][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-01-28 03:56:56.159][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:56.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:56.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:56.167][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-01-28 03:56:56.173][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-01-28 03:56:56.174][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:56.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:56.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:56.179][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-01-28 03:56:56.180][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-01-28 03:56:56.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:56.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:56.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:56.186][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-01-28 03:56:56.187][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-01-28 03:56:56.189][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-01-28 03:56:56.190][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:56.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:56.193][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:56.194][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-01-28 03:56:56.196][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-01-28 03:56:56.206][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-01-28 03:56:56.207][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:56.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:56.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:56.215][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-01-28 03:56:56.221][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-01-28 03:56:56.223][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:56.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:56.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:56.231][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-01-28 03:56:56.237][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-01-28 03:56:56.239][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-01-28 03:56:56.244][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:56.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:56.247][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:56.252][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-01-28 03:56:56.254][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-01-28 03:56:56.256][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:56.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:56.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:56.268][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-01-28 03:56:56.270][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-01-28 03:56:56.271][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-01-28 03:56:56.277][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:56.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:56.280][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:56.285][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-01-28 03:56:56.287][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-01-28 03:56:56.292][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-01-28 03:56:56.294][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-01-28 03:56:56.296][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-01-28 03:56:56.301][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-01-28 03:56:56.303][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:56.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:56.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:56.311][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-01-28 03:56:56.317][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-01-28 03:56:56.318][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:56.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:56.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:56.327][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-01-28 03:56:56.332][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-01-28 03:56:56.334][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:56.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:56.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:56.342][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-01-28 03:56:56.344][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-01-28 03:56:56.349][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:56.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:56.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:56.358][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-01-28 03:56:56.359][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-01-28 03:56:56.376][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:56.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:56.379][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:56.385][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-01-28 03:56:56.387][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-01-28 03:56:56.393][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:56.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:56.395][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:56.401][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-01-28 03:56:56.419][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-01-28 03:56:56.439][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-01-28 03:56:56.440][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:56.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:56.443][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:56.453][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-01-28 03:56:56.455][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-01-28 03:56:56.460][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-01-28 03:56:56.462][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:56.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:56.469][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:56.471][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-01-28 03:56:56.478][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-28 03:56:56.479][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-01-28 03:56:56.485][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:56.487][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-28 03:56:56.492][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:56.494][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-28 03:56:56.495][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-28 03:56:56.501][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-28 03:56:56.503][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-28 03:56:56.504][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-28 03:56:56.510][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:56.511][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-01-28 03:56:56.517][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-28 03:56:56.519][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:56.524][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:56.526][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-28 03:56:56.526][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-28 03:56:56.526][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-28 03:56:56.526][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-28 03:56:56.526][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-28 03:56:56.527][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-28 03:56:56.533][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-28 03:56:56.535][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-28 03:56:56.536][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-28 03:56:56.542][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-28 03:56:56.543][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-28 03:56:56.549][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-28 03:56:56.550][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:56.552][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-28 03:56:56.557][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-28 03:56:56.559][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-28 03:56:56.564][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:56.566][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-01-28 03:56:56.573][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-28 03:56:56.575][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-01-28 03:56:56.580][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:56.582][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-28 03:56:56.584][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:56.589][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-28 03:56:56.591][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-28 03:56:56.596][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-28 03:56:56.598][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-28 03:56:56.599][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-28 03:56:56.605][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:56.607][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-01-28 03:56:56.612][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-28 03:56:56.614][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:56.615][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:56.621][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-28 03:56:56.621][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-28 03:56:56.621][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-28 03:56:56.621][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-28 03:56:56.621][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-28 03:56:56.623][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-28 03:56:56.629][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-28 03:56:56.630][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-28 03:56:56.632][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-28 03:56:56.637][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-28 03:56:56.639][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-28 03:56:56.644][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-28 03:56:56.646][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:56.648][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-28 03:56:56.653][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-28 03:56:56.655][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-28 03:56:56.661][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:56.663][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-01-28 03:56:56.670][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:56.671][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-01-28 03:56:56.677][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:56.679][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-28 03:56:56.684][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:56.686][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-28 03:56:56.688][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-28 03:56:56.693][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-28 03:56:56.695][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-28 03:56:56.700][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-28 03:56:56.702][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-28 03:56:56.703][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-01-28 03:56:56.709][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-28 03:56:56.711][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:56.716][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:56.718][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:56.720][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-28 03:56:56.725][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-28 03:56:56.727][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-28 03:56:56.732][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-28 03:56:56.734][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-28 03:56:56.735][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-28 03:56:56.741][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-28 03:56:56.743][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:56.749][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-28 03:56:56.750][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-28 03:56:56.768][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-28 03:56:56.774][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:56.776][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-01-28 03:56:56.783][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:56.789][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-01-28 03:56:56.791][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:56.796][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-28 03:56:56.798][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:56.800][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-28 03:56:56.805][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-28 03:56:56.807][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-28 03:56:56.813][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-28 03:56:56.814][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-28 03:56:56.816][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-28 03:56:56.822][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-01-28 03:56:56.823][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-28 03:56:56.829][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:56.831][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:56.836][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:56.838][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-28 03:56:56.839][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-28 03:56:56.845][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-28 03:56:56.847][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-28 03:56:56.852][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-28 03:56:56.854][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-28 03:56:56.855][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-28 03:56:56.861][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:56.862][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-28 03:56:56.864][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-28 03:56:56.870][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-28 03:56:56.871][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:56.877][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-28 03:56:56.879][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:56.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:56.886][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:56.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:56.893][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:56.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:56.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:56.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:56.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:56.909][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:56.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:56.912][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:56.917][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:56.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:56.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:56.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:56.927][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:56.933][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:56.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:56.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:56.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:56.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:56.944][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:56.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:56.951][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:56.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:56.958][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:56.960][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:56.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:56.967][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:56.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:56.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:56.976][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:56.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:56.983][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:56.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:56.990][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:56.996][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:56.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:56.999][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:57.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:57.007][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:57.012][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:57.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:57.015][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:57.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:57.022][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[2025-01-28 03:56:57.024][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:57.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:57.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:57.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:57.038][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:57.039][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:57.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:57.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:57.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:57.053][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:57.055][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:57.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:57.062][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:57.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:57.069][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:57.070][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:57.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:57.077][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:57.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:57.085][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:57.086][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:57.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:57.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:57.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:57.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:57.119][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:57.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:57.126][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:57.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:57.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:57.135][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:57.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:57.142][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:57.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:57.149][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:57.151][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:57.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:57.158][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:57.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:57.165][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:57.167][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-01-28 03:56:57.174][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-01-28 03:56:57.181][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-01-28 03:56:57.183][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-01-28 03:56:57.190][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-01-28 03:56:57.197][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-01-28 03:56:57.199][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-01-28 03:56:57.206][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-01-28 03:56:57.213][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-01-28 03:56:57.215][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-01-28 03:56:57.222][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-01-28 03:56:57.229][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-01-28 03:56:57.232][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-01-28 03:56:57.239][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-01-28 03:56:57.245][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-01-28 03:56:57.248][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-01-28 03:56:57.254][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-01-28 03:56:57.261][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-01-28 03:56:57.263][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-01-28 03:56:57.270][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-01-28 03:56:57.276][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-01-28 03:56:57.279][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-01-28 03:56:57.285][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-01-28 03:56:57.288][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-01-28 03:56:57.294][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-01-28 03:56:57.301][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-01-28 03:56:57.303][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-01-28 03:56:57.310][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-01-28 03:56:57.316][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-01-28 03:56:57.319][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-01-28 03:56:57.325][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-01-28 03:56:57.328][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-01-28 03:56:57.334][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-01-28 03:56:57.341][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-01-28 03:56:57.343][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-01-28 03:56:57.349][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-01-28 03:56:57.352][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-01-28 03:56:57.358][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-01-28 03:56:57.365][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-01-28 03:56:57.367][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-01-28 03:56:57.374][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-01-28 03:56:57.381][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-01-28 03:56:57.383][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-01-28 03:56:57.389][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-01-28 03:56:57.392][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-01-28 03:56:57.398][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-01-28 03:56:57.405][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-01-28 03:56:57.407][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-01-28 03:56:57.414][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-01-28 03:56:57.420][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-01-28 03:56:57.423][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-01-28 03:56:57.429][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-01-28 03:56:57.432][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-01-28 03:56:57.439][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-01-28 03:56:57.445][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-01-28 03:56:57.448][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-01-28 03:56:57.471][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-01-28 03:56:57.478][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-01-28 03:56:57.484][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-01-28 03:56:57.487][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-01-28 03:56:57.494][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-01-28 03:56:57.500][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-01-28 03:56:57.502][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-01-28 03:56:57.508][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-01-28 03:56:57.511][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-01-28 03:56:57.517][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-01-28 03:56:57.519][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-01-28 03:56:57.526][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-01-28 03:56:57.528][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-01-28 03:56:57.534][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-01-28 03:56:57.541][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-01-28 03:56:57.543][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-01-28 03:56:57.549][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-01-28 03:56:57.552][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-01-28 03:56:57.558][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-01-28 03:56:57.564][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-01-28 03:56:57.567][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-01-28 03:56:57.573][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-01-28 03:56:57.575][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-01-28 03:56:57.582][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-01-28 03:56:57.588][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-01-28 03:56:57.591][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-01-28 03:56:57.597][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-01-28 03:56:57.599][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-01-28 03:56:57.606][initialize] This is biodb version 1.15.0.
biodb.INFO [2025-01-28 03:56:57.608][biodb::testContext]
biodb.INFO [2025-01-28 03:56:57.613][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-28 03:56:57.615][biodb::testContext] Test context - Test config.
biodb.INFO [2025-01-28 03:56:57.620][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-28 03:56:57.622][biodb::testContext]
biodb.INFO [2025-01-28 03:56:57.624][biodb::testThat]
biodb.INFO [2025-01-28 03:56:57.630][biodb::testThat] Running test function test.listKeys (" Keys are listed correctly. ").
biodb.INFO [2025-01-28 03:56:57.631][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-28 03:56:57.637][biodb::testThat]
biodb.INFO [2025-01-28 03:56:57.701][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-01-28 03:56:57.737][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-01-28 03:56:57.738][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:57.740][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:57.745][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:57.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-01-28 03:56:57.764][biodb::testContext]
biodb.INFO [2025-01-28 03:56:57.765][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-28 03:56:57.767][biodb::testContext] Test context - Test persistent cache.
biodb.INFO [2025-01-28 03:56:57.768][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-28 03:56:57.774][biodb::testContext]
biodb.INFO [2025-01-28 03:56:57.779][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-01-28 03:56:57.781][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-01-28 03:56:57.794][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-28 03:56:57.796][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-01-28 03:56:57.797][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-01-28 03:56:57.799][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:57.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:57.803][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:57.805][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-01-28 03:56:57.806][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-01-28 03:56:57.816][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:57.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:57.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:57.824][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-01-28 03:56:57.826][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-01-28 03:56:57.828][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:57.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:57.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:57.833][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-01-28 03:56:57.834][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-01-28 03:56:57.836][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-01-28 03:56:57.837][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:57.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:57.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:57.841][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-01-28 03:56:57.843][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-01-28 03:56:57.847][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-01-28 03:56:57.848][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:57.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:57.851][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[2025-01-28 03:56:57.852][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-01-28 03:56:57.854][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-01-28 03:56:57.855][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:57.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:57.858][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:57.860][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-01-28 03:56:57.864][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-01-28 03:56:57.865][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-01-28 03:56:57.867][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:57.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:57.869][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:57.871][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-01-28 03:56:57.872][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-01-28 03:56:57.874][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:57.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:57.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:57.878][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-01-28 03:56:57.880][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-01-28 03:56:57.881][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-01-28 03:56:57.883][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:57.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:57.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:57.887][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-01-28 03:56:57.889][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-01-28 03:56:57.890][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-01-28 03:56:57.892][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-01-28 03:56:57.893][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-01-28 03:56:57.895][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-01-28 03:56:57.896][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:57.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:57.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:57.900][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-01-28 03:56:57.902][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-01-28 03:56:57.903][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:57.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:57.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:57.908][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-01-28 03:56:57.909][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-01-28 03:56:57.911][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:57.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:57.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:57.924][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-01-28 03:56:57.930][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-01-28 03:56:57.931][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:57.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:57.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:57.939][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-01-28 03:56:57.940][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-01-28 03:56:57.942][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:57.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:57.944][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:57.946][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-01-28 03:56:57.947][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-01-28 03:56:57.949][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:57.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:57.951][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:57.952][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-01-28 03:56:57.954][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-01-28 03:56:57.966][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-01-28 03:56:57.968][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:57.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:57.970][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:57.972][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-01-28 03:56:57.981][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-01-28 03:56:57.983][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-01-28 03:56:57.988][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:57.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:57.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:57.997][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-01-28 03:56:58.000][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-28 03:56:58.006][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-01-28 03:56:58.007][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:58.013][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-28 03:56:58.014][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:58.016][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-28 03:56:58.022][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-28 03:56:58.023][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-28 03:56:58.040][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-28 03:56:58.042][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-28 03:56:58.044][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:58.047][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-01-28 03:56:58.049][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-28 03:56:58.051][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:58.057][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:58.059][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-28 03:56:58.059][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-28 03:56:58.059][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-28 03:56:58.059][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-28 03:56:58.059][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-28 03:56:58.065][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-28 03:56:58.067][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-28 03:56:58.073][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-28 03:56:58.075][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-28 03:56:58.081][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-28 03:56:58.083][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-28 03:56:58.089][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-28 03:56:58.091][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:58.095][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-28 03:56:58.097][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-28 03:56:58.099][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-28 03:56:58.100][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:58.102][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-01-28 03:56:58.109][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-28 03:56:58.111][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-01-28 03:56:58.116][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:58.118][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-28 03:56:58.120][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:58.126][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-28 03:56:58.127][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-28 03:56:58.133][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-28 03:56:58.135][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-28 03:56:58.141][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-28 03:56:58.143][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:58.148][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-01-28 03:56:58.150][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-28 03:56:58.151][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:58.157][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:58.159][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-28 03:56:58.159][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-28 03:56:58.159][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-28 03:56:58.159][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-28 03:56:58.159][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-28 03:56:58.165][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-28 03:56:58.167][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-28 03:56:58.171][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-28 03:56:58.173][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-28 03:56:58.175][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-28 03:56:58.181][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-28 03:56:58.182][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-28 03:56:58.184][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:58.190][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-28 03:56:58.191][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-28 03:56:58.194][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-28 03:56:58.195][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:58.197][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-01-28 03:56:58.210][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:58.212][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-01-28 03:56:58.214][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:58.216][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-28 03:56:58.222][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:58.224][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-28 03:56:58.230][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-28 03:56:58.232][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-28 03:56:58.238][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-28 03:56:58.240][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-28 03:56:58.246][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-28 03:56:58.248][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-01-28 03:56:58.254][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-28 03:56:58.256][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:58.262][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:58.264][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:58.265][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-28 03:56:58.267][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-28 03:56:58.270][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-28 03:56:58.272][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-28 03:56:58.274][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-28 03:56:58.275][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-28 03:56:58.281][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-28 03:56:58.282][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:58.284][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-28 03:56:58.286][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-28 03:56:58.287][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-28 03:56:58.289][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:58.291][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-01-28 03:56:58.294][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:58.296][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-01-28 03:56:58.298][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:58.299][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-28 03:56:58.301][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:58.303][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-28 03:56:58.305][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-28 03:56:58.306][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-28 03:56:58.308][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-28 03:56:58.310][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-28 03:56:58.311][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-28 03:56:58.313][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-01-28 03:56:58.315][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-28 03:56:58.324][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:58.326][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-28 03:56:58.327][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:58.329][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-28 03:56:58.331][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-28 03:56:58.332][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-28 03:56:58.333][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-28 03:56:58.335][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-28 03:56:58.336][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-28 03:56:58.338][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-28 03:56:58.339][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:58.341][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-28 03:56:58.342][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-28 03:56:58.343][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-28 03:56:58.345][self$setPropertyValue]
biodb.DEBUG[2025-01-28 03:56:58.347][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-28 03:56:58.348][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:58.349][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:58.351][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:58.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:58.353][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:58.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:58.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:58.357][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:58.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:58.360][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:58.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:58.363][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:58.364][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:58.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:58.367][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:58.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:58.369][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:58.371][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:58.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:58.373][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:58.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:58.376][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:58.377][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:58.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:58.380][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:58.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:58.383][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:58.384][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:58.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:58.387][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:58.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:58.389][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:58.391][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:58.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:58.393][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:58.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:58.396][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[2025-01-28 03:56:58.397][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:58.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:58.400][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:58.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:58.402][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[2025-01-28 03:56:58.404][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:58.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:58.406][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:58.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:58.409][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:58.410][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:58.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:58.413][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:58.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:58.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:58.421][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:58.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:58.424][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:58.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:58.431][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:58.436][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:58.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:58.439][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:58.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:58.446][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:58.448][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:58.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:58.455][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:58.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:58.462][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:58.463][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:58.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:58.470][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:58.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:58.477][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:58.479][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:58.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:58.486][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:58.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:58.493][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:58.494][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:58.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:58.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:58.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:58.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:58.510][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:58.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:58.517][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:58.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:58.536][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:58.542][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-01-28 03:56:58.548][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-01-28 03:56:58.551][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-01-28 03:56:58.557][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-01-28 03:56:58.560][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-01-28 03:56:58.566][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-01-28 03:56:58.573][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-01-28 03:56:58.575][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-01-28 03:56:58.582][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-01-28 03:56:58.589][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-01-28 03:56:58.591][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-01-28 03:56:58.598][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-01-28 03:56:58.600][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-01-28 03:56:58.607][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-01-28 03:56:58.613][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-01-28 03:56:58.616][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-01-28 03:56:58.622][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-01-28 03:56:58.629][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-01-28 03:56:58.631][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-01-28 03:56:58.637][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-01-28 03:56:58.640][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-01-28 03:56:58.646][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-01-28 03:56:58.653][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-01-28 03:56:58.655][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-01-28 03:56:58.662][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-01-28 03:56:58.664][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-01-28 03:56:58.670][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-01-28 03:56:58.677][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-01-28 03:56:58.679][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-01-28 03:56:58.686][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-01-28 03:56:58.692][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-01-28 03:56:58.695][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-01-28 03:56:58.705][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-01-28 03:56:58.707][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-01-28 03:56:58.718][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-01-28 03:56:58.728][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-01-28 03:56:58.731][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-01-28 03:56:58.741][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-01-28 03:56:58.744][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-01-28 03:56:58.754][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-01-28 03:56:58.760][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-01-28 03:56:58.763][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-01-28 03:56:58.773][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-01-28 03:56:58.776][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-01-28 03:56:58.786][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-01-28 03:56:58.797][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-01-28 03:56:58.799][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-01-28 03:56:58.810][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-01-28 03:56:58.812][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-01-28 03:56:58.823][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-01-28 03:56:58.833][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-01-28 03:56:58.836][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-01-28 03:56:58.846][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-01-28 03:56:58.857][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-01-28 03:56:58.859][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-01-28 03:56:58.870][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-01-28 03:56:58.876][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-01-28 03:56:58.879][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-01-28 03:56:58.885][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-01-28 03:56:58.888][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-01-28 03:56:58.894][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-01-28 03:56:58.901][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-01-28 03:56:58.904][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-01-28 03:56:58.907][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-01-28 03:56:58.930][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-01-28 03:56:58.933][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-01-28 03:56:58.936][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-01-28 03:56:58.938][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-01-28 03:56:58.940][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-01-28 03:56:58.946][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-01-28 03:56:58.948][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-01-28 03:56:58.950][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-01-28 03:56:58.957][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-01-28 03:56:58.959][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-01-28 03:56:58.966][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-01-28 03:56:58.968][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-01-28 03:56:58.971][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-01-28 03:56:58.975][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-01-28 03:56:58.977][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-01-28 03:56:58.979][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-01-28 03:56:58.990][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-01-28 03:56:58.997][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-01-28 03:56:58.999][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-01-28 03:56:59.006][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-01-28 03:56:59.012][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-01-28 03:56:59.014][biodb$getConfig()$set] Set key use.cache.for.local.db to TRUE.
biodb.DEBUG[2025-01-28 03:56:59.016][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:59.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:59.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:59.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:59.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:56:59.028][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-01-28 03:56:59.033][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 03:56:59.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:56:59.040][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:56:59.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:56:59.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-01-28 03:56:59.076][biodb$getPersistentCache()$erase] Erasing cache "/home/biocbuild/.cache/R/biodb".
biodb.DEBUG[2025-01-28 03:56:59.675][super$initialize] Initialize connector comp.csv.file.
biodb.DEBUG[2025-01-28 03:56:59.681][biodb$getFactory()$createConn] Creating new connector comp.csv.file for database class comp.csv.file , with base URL "/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/biodb/extdata/chebi_extract.tsv".
biodb.INFO [2025-01-28 03:56:59.683][biodb::testThat]
biodb.INFO [2025-01-28 03:56:59.689][biodb::testThat] Running test function test_cacheFiles (" We can list cache files. ").
biodb.INFO [2025-01-28 03:56:59.690][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-28 03:56:59.692][biodb::testThat]
biodb.INFO [2025-01-28 03:56:59.699][private$initDb] Loading file database "/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/biodb/extdata/chebi_extract.tsv".
biodb.DEBUG[2025-01-28 03:56:59.706][self$setField] Set field accession to column(s) accession.
biodb.TRACE[2025-01-28 03:56:59.708][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 03:56:59.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 03:56:59.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:59.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-28 03:56:59.722][self$setPropertyValue] Setting property "parsing.expr" to "accession".
biodb.DEBUG[2025-01-28 03:56:59.728][self$setField] Set field formula to column(s) formula.
biodb.TRACE[2025-01-28 03:56:59.730][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-28 03:56:59.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-28 03:56:59.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:59.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-28 03:56:59.745][self$setPropertyValue] Setting property "parsing.expr" to "accession".
biodb.DEBUG[2025-01-28 03:56:59.745][self$setPropertyValue] Setting property "parsing.expr" to "formula".
biodb.DEBUG[2025-01-28 03:56:59.747][self$setField] Set field monoisotopic.mass to column(s) monoisotopic.mass.
biodb.TRACE[2025-01-28 03:56:59.753][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-28 03:56:59.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-28 03:56:59.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:59.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-28 03:56:59.763][self$setPropertyValue] Setting property "parsing.expr" to "accession".
biodb.DEBUG[2025-01-28 03:56:59.763][self$setPropertyValue] Setting property "parsing.expr" to "formula".
biodb.DEBUG[2025-01-28 03:56:59.763][self$setPropertyValue] Setting property "parsing.expr" to "monoisotopic.mass".
biodb.DEBUG[2025-01-28 03:56:59.769][self$setField] Set field molecular.mass to column(s) molecular.mass.
biodb.TRACE[2025-01-28 03:56:59.771][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-28 03:56:59.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-28 03:56:59.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:59.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-28 03:56:59.786][self$setPropertyValue] Setting property "parsing.expr" to "accession".
biodb.DEBUG[2025-01-28 03:56:59.786][self$setPropertyValue] Setting property "parsing.expr" to "formula".
biodb.DEBUG[2025-01-28 03:56:59.786][self$setPropertyValue] Setting property "parsing.expr" to "monoisotopic.mass".
biodb.DEBUG[2025-01-28 03:56:59.786][self$setPropertyValue] Setting property "parsing.expr" to "molecular.mass".
biodb.DEBUG[2025-01-28 03:56:59.792][self$setField] Set field kegg.compound.id to column(s) kegg.compound.id.
biodb.TRACE[2025-01-28 03:56:59.794][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-28 03:56:59.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-28 03:56:59.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:59.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-28 03:56:59.809][self$setPropertyValue] Setting property "parsing.expr" to "accession".
biodb.DEBUG[2025-01-28 03:56:59.809][self$setPropertyValue] Setting property "parsing.expr" to "formula".
biodb.DEBUG[2025-01-28 03:56:59.809][self$setPropertyValue] Setting property "parsing.expr" to "monoisotopic.mass".
biodb.DEBUG[2025-01-28 03:56:59.809][self$setPropertyValue] Setting property "parsing.expr" to "molecular.mass".
biodb.DEBUG[2025-01-28 03:56:59.809][self$setPropertyValue] Setting property "parsing.expr" to "kegg.compound.id".
biodb.DEBUG[2025-01-28 03:56:59.811][self$setField] Set field name to column(s) name.
biodb.TRACE[2025-01-28 03:56:59.817][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-28 03:56:59.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-28 03:56:59.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:59.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-28 03:56:59.828][self$setPropertyValue] Setting property "parsing.expr" to "accession".
biodb.DEBUG[2025-01-28 03:56:59.828][self$setPropertyValue] Setting property "parsing.expr" to "formula".
biodb.DEBUG[2025-01-28 03:56:59.828][self$setPropertyValue] Setting property "parsing.expr" to "monoisotopic.mass".
biodb.DEBUG[2025-01-28 03:56:59.828][self$setPropertyValue] Setting property "parsing.expr" to "molecular.mass".
biodb.DEBUG[2025-01-28 03:56:59.828][self$setPropertyValue] Setting property "parsing.expr" to "kegg.compound.id".
biodb.DEBUG[2025-01-28 03:56:59.828][self$setPropertyValue] Setting property "parsing.expr" to "name".
biodb.DEBUG[2025-01-28 03:56:59.834][self$setField] Set field smiles to column(s) smiles.
biodb.TRACE[2025-01-28 03:56:59.857][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-28 03:56:59.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-28 03:56:59.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:59.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-28 03:56:59.868][self$setPropertyValue] Setting property "parsing.expr" to "accession".
biodb.DEBUG[2025-01-28 03:56:59.868][self$setPropertyValue] Setting property "parsing.expr" to "formula".
biodb.DEBUG[2025-01-28 03:56:59.868][self$setPropertyValue] Setting property "parsing.expr" to "monoisotopic.mass".
biodb.DEBUG[2025-01-28 03:56:59.868][self$setPropertyValue] Setting property "parsing.expr" to "molecular.mass".
biodb.DEBUG[2025-01-28 03:56:59.868][self$setPropertyValue] Setting property "parsing.expr" to "kegg.compound.id".
biodb.DEBUG[2025-01-28 03:56:59.868][self$setPropertyValue] Setting property "parsing.expr" to "name".
biodb.DEBUG[2025-01-28 03:56:59.868][self$setPropertyValue] Setting property "parsing.expr" to "smiles".
biodb.DEBUG[2025-01-28 03:56:59.874][self$setField] Set field description to column(s) description.
biodb.TRACE[2025-01-28 03:56:59.876][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-28 03:56:59.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-28 03:56:59.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:56:59.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-28 03:56:59.891][self$setPropertyValue] Setting property "parsing.expr" to "accession".
biodb.DEBUG[2025-01-28 03:56:59.891][self$setPropertyValue] Setting property "parsing.expr" to "formula".
biodb.DEBUG[2025-01-28 03:56:59.891][self$setPropertyValue] Setting property "parsing.expr" to "monoisotopic.mass".
biodb.DEBUG[2025-01-28 03:56:59.891][self$setPropertyValue] Setting property "parsing.expr" to "molecular.mass".
biodb.DEBUG[2025-01-28 03:56:59.891][self$setPropertyValue] Setting property "parsing.expr" to "kegg.compound.id".
biodb.DEBUG[2025-01-28 03:56:59.891][self$setPropertyValue] Setting property "parsing.expr" to "name".
biodb.DEBUG[2025-01-28 03:56:59.891][self$setPropertyValue] Setting property "parsing.expr" to "smiles".
biodb.DEBUG[2025-01-28 03:56:59.891][self$setPropertyValue] Setting property "parsing.expr" to "description".
biodb.INFO [2025-01-28 03:56:59.919][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/comp.csv.file-a49c5db9408932a2c8454375877bd673" for "comp.csv.file-a49c5db9408932a2c8454375877bd673".
biodb.DEBUG[2025-01-28 03:56:59.921][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/comp.csv.file-a49c5db9408932a2c8454375877bd673 using pattern ^.*\.tsv$.
biodb.DEBUG[2025-01-28 03:56:59.931][private$loadEntries] Creating entries from ids [3]: "1018, 1390, 1456".
biodb.DEBUG[2025-01-28 03:56:59.937][conn$getEntryContent] Get Compound CSV File entry content(s) for 3 id(s)...
biodb.TRACE[2025-01-28 03:56:59.939][cch$loadFileContent] Trying to load 3 files from cache: [3]: "1018, 1390, 1456".
biodb.TRACE[2025-01-28 03:56:59.945][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2025-01-28 03:56:59.947][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-28 03:56:59.953][conn$getEntryContent] 0 Compound CSV File entry content(s) loaded from cache.
biodb.DEBUG[2025-01-28 03:56:59.955][conn$getEntryContent] 3 entry content(s) need to be fetched from Compound CSV File database "/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/biodb/extdata/chebi_extract.tsv".
biodb.DEBUG[2025-01-28 03:56:59.961][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-28 03:56:59.963][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-28 03:56:59.968][private$doGetEntryContentFromDb] Entry id: 1018, 1390, 1456
biodb.DEBUG[2025-01-28 03:56:59.986][private$doGetEntryContentFromDb] Content of first entry: accession formula monoisotopic.mass molecular.mass kegg.compound.id name smiles description
1018 C2H8AsNO3 168.97201 169.012 C07279 2-Aminoethylarsonate NCC[As](O)(O)=O
biodb.TRACE[2025-01-28 03:57:00.091][private$doSaveContentToFile] Saving to cache [3]: "/home/biocbuild/.cache/R/biodb/comp.csv.file-a49c5db9408932a2c8454375877bd673/1018.tsv, /home/biocbuild/.cache/R/biodb/comp.csv.file-a49c5db9408932a2c8454375877bd673/1390.tsv, /home/biocbuild/.cache/R/biodb/comp.csv.file-a49c5db9408932a2c8454375877bd673/1456.tsv"
biodb.DEBUG[2025-01-28 03:57:00.102][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-28 03:57:00.113][self$createEntryFromContent] Creating Compound CSV File entries from 3 content(s).
biodb.DEBUG[2025-01-28 03:57:00.126][self$createEntryFromContent] Parsing 3 Compound CSV File entries.
biodb.DEBUG[2025-01-28 03:57:00.137][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-28 03:57:00.138][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:57:00.139][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:57:00.149][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:57:00.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 03:57:00.173][self$setPropertyValue] Setting property "parsing.expr" to "accession".
biodb.DEBUG[2025-01-28 03:57:00.173][self$setPropertyValue] Setting property "parsing.expr" to "formula".
biodb.DEBUG[2025-01-28 03:57:00.173][self$setPropertyValue] Setting property "parsing.expr" to "monoisotopic.mass".
biodb.DEBUG[2025-01-28 03:57:00.173][self$setPropertyValue] Setting property "parsing.expr" to "molecular.mass".
biodb.DEBUG[2025-01-28 03:57:00.173][self$setPropertyValue] Setting property "parsing.expr" to "kegg.compound.id".
biodb.DEBUG[2025-01-28 03:57:00.173][self$setPropertyValue] Setting property "parsing.expr" to "name".
biodb.DEBUG[2025-01-28 03:57:00.173][self$setPropertyValue] Setting property "parsing.expr" to "smiles".
biodb.DEBUG[2025-01-28 03:57:00.173][self$setPropertyValue] Setting property "parsing.expr" to "description".
biodb.DEBUG[2025-01-28 03:57:00.174][self$setPropertyValue] Setting property "parsing.expr" to "accession".
biodb.DEBUG[2025-01-28 03:57:00.174][self$setPropertyValue] Setting property "parsing.expr" to "formula".
biodb.DEBUG[2025-01-28 03:57:00.174][self$setPropertyValue] Setting property "parsing.expr" to "monoisotopic.mass".
biodb.DEBUG[2025-01-28 03:57:00.174][self$setPropertyValue] Setting property "parsing.expr" to "molecular.mass".
biodb.DEBUG[2025-01-28 03:57:00.174][self$setPropertyValue] Setting property "parsing.expr" to "kegg.compound.id".
biodb.DEBUG[2025-01-28 03:57:00.174][self$setPropertyValue] Setting property "parsing.expr" to "name".
biodb.DEBUG[2025-01-28 03:57:00.174][self$setPropertyValue] Setting property "parsing.expr" to "smiles".
biodb.DEBUG[2025-01-28 03:57:00.174][self$setPropertyValue] Setting property "parsing.expr" to "description".
biodb.DEBUG[2025-01-28 03:57:00.184][self$setPropertyValue] Setting property "parsing.expr" to "accession".
biodb.DEBUG[2025-01-28 03:57:00.184][self$setPropertyValue] Setting property "parsing.expr" to "formula".
biodb.DEBUG[2025-01-28 03:57:00.184][self$setPropertyValue] Setting property "parsing.expr" to "monoisotopic.mass".
biodb.DEBUG[2025-01-28 03:57:00.184][self$setPropertyValue] Setting property "parsing.expr" to "molecular.mass".
biodb.DEBUG[2025-01-28 03:57:00.184][self$setPropertyValue] Setting property "parsing.expr" to "kegg.compound.id".
biodb.DEBUG[2025-01-28 03:57:00.184][self$setPropertyValue] Setting property "parsing.expr" to "name".
biodb.DEBUG[2025-01-28 03:57:00.184][self$setPropertyValue] Setting property "parsing.expr" to "smiles".
biodb.DEBUG[2025-01-28 03:57:00.184][self$setPropertyValue] Setting property "parsing.expr" to "description".
biodb.DEBUG[2025-01-28 03:57:00.186][self$setPropertyValue] Setting property "parsing.expr" to "accession".
biodb.DEBUG[2025-01-28 03:57:00.186][self$setPropertyValue] Setting property "parsing.expr" to "formula".
biodb.DEBUG[2025-01-28 03:57:00.186][self$setPropertyValue] Setting property "parsing.expr" to "monoisotopic.mass".
biodb.DEBUG[2025-01-28 03:57:00.186][self$setPropertyValue] Setting property "parsing.expr" to "molecular.mass".
biodb.DEBUG[2025-01-28 03:57:00.186][self$setPropertyValue] Setting property "parsing.expr" to "kegg.compound.id".
biodb.DEBUG[2025-01-28 03:57:00.186][self$setPropertyValue] Setting property "parsing.expr" to "name".
biodb.DEBUG[2025-01-28 03:57:00.186][self$setPropertyValue] Setting property "parsing.expr" to "smiles".
biodb.DEBUG[2025-01-28 03:57:00.186][self$setPropertyValue] Setting property "parsing.expr" to "description".
biodb.DEBUG[2025-01-28 03:57:00.188][self$setPropertyValue] Setting property "parsing.expr" to "accession".
biodb.DEBUG[2025-01-28 03:57:00.188][self$setPropertyValue] Setting property "parsing.expr" to "formula".
biodb.DEBUG[2025-01-28 03:57:00.188][self$setPropertyValue] Setting property "parsing.expr" to "monoisotopic.mass".
biodb.DEBUG[2025-01-28 03:57:00.188][self$setPropertyValue] Setting property "parsing.expr" to "molecular.mass".
biodb.DEBUG[2025-01-28 03:57:00.188][self$setPropertyValue] Setting property "parsing.expr" to "kegg.compound.id".
biodb.DEBUG[2025-01-28 03:57:00.188][self$setPropertyValue] Setting property "parsing.expr" to "name".
biodb.DEBUG[2025-01-28 03:57:00.188][self$setPropertyValue] Setting property "parsing.expr" to "smiles".
biodb.DEBUG[2025-01-28 03:57:00.188][self$setPropertyValue] Setting property "parsing.expr" to "description".
biodb.DEBUG[2025-01-28 03:57:00.198][self$setPropertyValue] Setting property "parsing.expr" to "accession".
biodb.DEBUG[2025-01-28 03:57:00.198][self$setPropertyValue] Setting property "parsing.expr" to "formula".
biodb.DEBUG[2025-01-28 03:57:00.198][self$setPropertyValue] Setting property "parsing.expr" to "monoisotopic.mass".
biodb.DEBUG[2025-01-28 03:57:00.198][self$setPropertyValue] Setting property "parsing.expr" to "molecular.mass".
biodb.DEBUG[2025-01-28 03:57:00.198][self$setPropertyValue] Setting property "parsing.expr" to "kegg.compound.id".
biodb.DEBUG[2025-01-28 03:57:00.198][self$setPropertyValue] Setting property "parsing.expr" to "name".
biodb.DEBUG[2025-01-28 03:57:00.198][self$setPropertyValue] Setting property "parsing.expr" to "smiles".
biodb.DEBUG[2025-01-28 03:57:00.198][self$setPropertyValue] Setting property "parsing.expr" to "description".
biodb.DEBUG[2025-01-28 03:57:00.200][self$setPropertyValue] Setting property "parsing.expr" to "accession".
biodb.DEBUG[2025-01-28 03:57:00.200][self$setPropertyValue] Setting property "parsing.expr" to "formula".
biodb.DEBUG[2025-01-28 03:57:00.200][self$setPropertyValue] Setting property "parsing.expr" to "monoisotopic.mass".
biodb.DEBUG[2025-01-28 03:57:00.200][self$setPropertyValue] Setting property "parsing.expr" to "molecular.mass".
biodb.DEBUG[2025-01-28 03:57:00.200][self$setPropertyValue] Setting property "parsing.expr" to "kegg.compound.id".
biodb.DEBUG[2025-01-28 03:57:00.200][self$setPropertyValue] Setting property "parsing.expr" to "name".
biodb.DEBUG[2025-01-28 03:57:00.200][self$setPropertyValue] Setting property "parsing.expr" to "smiles".
biodb.DEBUG[2025-01-28 03:57:00.200][self$setPropertyValue] Setting property "parsing.expr" to "description".
biodb.DEBUG[2025-01-28 03:57:00.210][self$setPropertyValue] Setting property "parsing.expr" to "accession".
biodb.DEBUG[2025-01-28 03:57:00.210][self$setPropertyValue] Setting property "parsing.expr" to "formula".
biodb.DEBUG[2025-01-28 03:57:00.210][self$setPropertyValue] Setting property "parsing.expr" to "monoisotopic.mass".
biodb.DEBUG[2025-01-28 03:57:00.210][self$setPropertyValue] Setting property "parsing.expr" to "molecular.mass".
biodb.DEBUG[2025-01-28 03:57:00.210][self$setPropertyValue] Setting property "parsing.expr" to "kegg.compound.id".
biodb.DEBUG[2025-01-28 03:57:00.210][self$setPropertyValue] Setting property "parsing.expr" to "name".
biodb.DEBUG[2025-01-28 03:57:00.210][self$setPropertyValue] Setting property "parsing.expr" to "smiles".
biodb.DEBUG[2025-01-28 03:57:00.210][self$setPropertyValue] Setting property "parsing.expr" to "description".
biodb.TRACE[2025-01-28 03:57:00.212][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 03:57:00.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 03:57:00.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:00.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:00.234][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 03:57:00.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 03:57:00.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:00.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:00.257][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-28 03:57:00.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-28 03:57:00.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:00.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:00.272][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-28 03:57:00.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-28 03:57:00.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:00.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:00.295][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-28 03:57:00.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-28 03:57:00.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:00.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:00.345][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-28 03:57:00.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-28 03:57:00.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:00.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:00.360][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-28 03:57:00.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-28 03:57:00.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:00.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:00.371][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-28 03:57:00.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-28 03:57:00.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:00.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:00.386][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-28 03:57:00.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-28 03:57:00.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:00.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:00.401][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-28 03:57:00.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-28 03:57:00.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:00.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:00.412][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-28 03:57:00.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-28 03:57:00.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:00.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:00.426][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-28 03:57:00.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-28 03:57:00.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:00.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:00.441][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-28 03:57:00.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-28 03:57:00.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:00.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:00.452][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-28 03:57:00.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-28 03:57:00.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:00.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:00.467][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-28 03:57:00.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-28 03:57:00.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:00.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:00.481][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-28 03:57:00.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-28 03:57:00.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:00.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:00.492][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.csv.file.id.
biodb.TRACE[2025-01-28 03:57:00.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.csv.file.id.
biodb.TRACE[2025-01-28 03:57:00.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:00.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:00.506][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.csv.file.id.
biodb.TRACE[2025-01-28 03:57:00.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.csv.file.id.
biodb.TRACE[2025-01-28 03:57:00.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:00.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:00.521][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 03:57:00.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 03:57:00.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:00.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:00.531][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.csv.file.id.
biodb.TRACE[2025-01-28 03:57:00.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.csv.file.id.
biodb.TRACE[2025-01-28 03:57:00.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:00.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:00.545][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 03:57:00.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 03:57:00.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:00.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:00.556][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 03:57:00.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 03:57:00.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:00.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:00.570][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 03:57:00.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 03:57:00.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:00.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-28 03:57:00.585][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-28 03:57:00.587][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:57:00.588][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:57:00.594][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:57:00.595][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-28 03:57:00.619][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 03:57:00.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 03:57:00.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:00.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:00.674][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 03:57:00.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 03:57:00.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:00.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:00.690][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-28 03:57:00.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-28 03:57:00.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:00.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:00.704][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-28 03:57:00.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-28 03:57:00.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:00.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:00.715][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-28 03:57:00.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-28 03:57:00.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:00.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:00.730][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-28 03:57:00.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-28 03:57:00.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:00.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:00.745][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-28 03:57:00.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-28 03:57:00.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:00.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:00.759][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-28 03:57:00.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-28 03:57:00.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:00.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:00.782][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-28 03:57:00.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-28 03:57:00.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:00.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:00.805][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-28 03:57:00.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-28 03:57:00.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:00.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:00.820][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-28 03:57:00.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-28 03:57:00.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:00.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:00.835][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-28 03:57:00.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-28 03:57:00.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:00.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:00.850][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-28 03:57:00.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-28 03:57:00.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:00.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:00.864][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-28 03:57:00.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-28 03:57:00.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:00.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:00.875][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-28 03:57:00.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-28 03:57:00.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:00.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:00.890][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-28 03:57:00.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-28 03:57:00.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:00.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:00.905][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.csv.file.id.
biodb.TRACE[2025-01-28 03:57:00.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.csv.file.id.
biodb.TRACE[2025-01-28 03:57:00.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:00.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:00.915][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.csv.file.id.
biodb.TRACE[2025-01-28 03:57:00.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.csv.file.id.
biodb.TRACE[2025-01-28 03:57:00.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:00.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:00.930][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 03:57:00.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 03:57:00.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:00.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:00.936][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.csv.file.id.
biodb.TRACE[2025-01-28 03:57:00.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.csv.file.id.
biodb.TRACE[2025-01-28 03:57:00.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:00.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:00.942][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 03:57:00.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 03:57:00.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:00.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:00.947][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 03:57:00.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 03:57:00.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:00.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:00.953][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 03:57:00.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 03:57:00.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:00.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-28 03:57:00.967][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-28 03:57:00.969][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:57:00.970][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:57:00.972][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:57:00.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-28 03:57:00.978][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 03:57:00.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 03:57:00.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:00.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:00.984][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 03:57:00.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 03:57:00.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:00.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:00.991][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-28 03:57:00.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-28 03:57:00.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:00.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:00.997][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-28 03:57:00.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-28 03:57:01.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:01.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:01.003][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-28 03:57:01.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-28 03:57:01.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:01.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:01.009][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-28 03:57:01.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-28 03:57:01.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:01.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:01.016][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-28 03:57:01.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-28 03:57:01.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:01.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:01.022][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-28 03:57:01.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-28 03:57:01.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:01.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:01.028][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-28 03:57:01.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-28 03:57:01.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:01.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:01.035][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-28 03:57:01.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-28 03:57:01.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:01.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:01.041][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-28 03:57:01.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-28 03:57:01.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:01.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:01.047][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-28 03:57:01.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-28 03:57:01.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:01.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:01.053][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-28 03:57:01.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-28 03:57:01.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:01.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:01.059][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-28 03:57:01.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-28 03:57:01.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:01.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:01.065][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-28 03:57:01.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-28 03:57:01.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:01.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:01.071][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-28 03:57:01.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-28 03:57:01.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:01.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:01.077][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.csv.file.id.
biodb.TRACE[2025-01-28 03:57:01.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.csv.file.id.
biodb.TRACE[2025-01-28 03:57:01.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:01.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:01.083][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.csv.file.id.
biodb.TRACE[2025-01-28 03:57:01.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.csv.file.id.
biodb.TRACE[2025-01-28 03:57:01.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:01.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:01.089][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 03:57:01.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 03:57:01.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:01.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:01.095][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.csv.file.id.
biodb.TRACE[2025-01-28 03:57:01.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.csv.file.id.
biodb.TRACE[2025-01-28 03:57:01.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:01.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:01.101][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 03:57:01.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 03:57:01.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:01.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:01.116][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 03:57:01.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 03:57:01.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:01.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:01.123][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 03:57:01.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 03:57:01.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:01.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:01.130][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 03:57:01.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 03:57:01.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:01.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:01.136][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 03:57:01.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 03:57:01.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:01.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:01.142][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 03:57:01.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 03:57:01.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:01.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:01.148][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 03:57:01.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 03:57:01.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:01.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:01.155][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 03:57:01.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 03:57:01.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:01.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:01.161][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 03:57:01.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 03:57:01.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:01.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:01.167][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 03:57:01.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 03:57:01.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:01.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:01.173][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 03:57:01.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 03:57:01.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:01.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:01.179][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 03:57:01.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 03:57:01.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:01.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-28 03:57:01.193][self$createEntryFromContent] Accession numbers: 1018, 1390, 1456.
biodb.DEBUG[2025-01-28 03:57:01.218][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/comp.csv.file-a49c5db9408932a2c8454375877bd673 using pattern ^.*\.tsv$.
biodb.DEBUG[2025-01-28 03:57:01.490][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/comp.csv.file-a49c5db9408932a2c8454375877bd673 using pattern ^.*\.tsv$.
biodb.DEBUG[2025-01-28 03:57:01.500][cache$listFiles] Extracting accession number from file names associated with comp.csv.file-a49c5db9408932a2c8454375877bd673 using pattern ^(.*)\.tsv$
biodb.DEBUG[2025-01-28 03:57:01.502][cache$listFiles] files = 1018.tsv, 1390.tsv, 1456.tsv
biodb.INFO [2025-01-28 03:57:01.542][biodb::testThat]
biodb.INFO [2025-01-28 03:57:01.544][biodb::testThat] Running test function test_deleteFilesForWrongCacheId (" We got a warning if we try to delete files for a cache.id that has no associated folder. ").
biodb.INFO [2025-01-28 03:57:01.553][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-28 03:57:01.555][biodb::testThat]
biodb.WARN [2025-01-28 03:57:01.566][self$getFolderPath] No cache folder "/home/biocbuild/.cache/R/biodb/foo-1234567890abcdef01234" exists for "foo-1234567890abcdef01234".
biodb.INFO [2025-01-28 03:57:01.587][biodb::testThat]
biodb.INFO [2025-01-28 03:57:01.614][biodb::testThat] Running test function test_filesExistForConn (" We detect if cache files exist for a connector ").
biodb.INFO [2025-01-28 03:57:01.616][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-28 03:57:01.618][biodb::testThat]
biodb.INFO [2025-01-28 03:57:01.639][cache$deleteAllFiles] Erasing all files in "/home/biocbuild/.cache/R/biodb/comp.csv.file-a49c5db9408932a2c8454375877bd673".
biodb.INFO [2025-01-28 03:57:01.646][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/comp.csv.file-a49c5db9408932a2c8454375877bd673" for "comp.csv.file-a49c5db9408932a2c8454375877bd673".
biodb.INFO [2025-01-28 03:57:01.676][biodb::testThat]
biodb.INFO [2025-01-28 03:57:01.678][biodb::testThat] Running test function test_noFilesExist (" No cache files exist for unknown cache ID. ").
biodb.INFO [2025-01-28 03:57:01.680][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-28 03:57:01.685][biodb::testThat]
biodb.INFO [2025-01-28 03:57:01.690][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/foo-1234567890abcdef01234" for "foo-1234567890abcdef01234".
biodb.INFO [2025-01-28 03:57:01.714][biodb::testThat]
biodb.INFO [2025-01-28 03:57:01.715][biodb::testThat] Running test function test_usedCacheIds (" We can a list of used cache IDs ").
biodb.INFO [2025-01-28 03:57:01.721][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-28 03:57:01.723][biodb::testThat]
biodb.DEBUG[2025-01-28 03:57:01.822][private$loadEntries] Creating entries from ids [3]: "1018, 1390, 1456".
biodb.DEBUG[2025-01-28 03:57:01.984][conn$getEntryContent] Get Compound CSV File entry content(s) for 3 id(s)...
biodb.TRACE[2025-01-28 03:57:02.012][cch$loadFileContent] Trying to load 3 files from cache: [3]: "1018, 1390, 1456".
biodb.TRACE[2025-01-28 03:57:02.014][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2025-01-28 03:57:02.016][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-28 03:57:02.018][conn$getEntryContent] 0 Compound CSV File entry content(s) loaded from cache.
biodb.DEBUG[2025-01-28 03:57:02.019][conn$getEntryContent] 3 entry content(s) need to be fetched from Compound CSV File database "/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/biodb/extdata/chebi_extract.tsv".
biodb.DEBUG[2025-01-28 03:57:02.022][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-28 03:57:02.024][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-28 03:57:02.026][private$doGetEntryContentFromDb] Entry id: 1018, 1390, 1456
biodb.DEBUG[2025-01-28 03:57:02.035][private$doGetEntryContentFromDb] Content of first entry: accession formula monoisotopic.mass molecular.mass kegg.compound.id name smiles description
1018 C2H8AsNO3 168.97201 169.012 C07279 2-Aminoethylarsonate NCC[As](O)(O)=O
biodb.TRACE[2025-01-28 03:57:02.059][private$doSaveContentToFile] Saving to cache [3]: "/home/biocbuild/.cache/R/biodb/comp.csv.file-a49c5db9408932a2c8454375877bd673/1018.tsv, /home/biocbuild/.cache/R/biodb/comp.csv.file-a49c5db9408932a2c8454375877bd673/1390.tsv, /home/biocbuild/.cache/R/biodb/comp.csv.file-a49c5db9408932a2c8454375877bd673/1456.tsv"
biodb.DEBUG[2025-01-28 03:57:02.062][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-28 03:57:02.115][self$createEntryFromContent] Creating Compound CSV File entries from 3 content(s).
biodb.DEBUG[2025-01-28 03:57:02.117][self$createEntryFromContent] Parsing 3 Compound CSV File entries.
biodb.DEBUG[2025-01-28 03:57:02.120][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-28 03:57:02.122][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:57:02.124][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:57:02.125][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:57:02.127][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-28 03:57:02.132][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 03:57:02.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 03:57:02.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:02.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:02.140][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 03:57:02.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 03:57:02.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:02.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:02.148][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-28 03:57:02.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-28 03:57:02.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:02.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:02.192][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-28 03:57:02.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-28 03:57:02.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:02.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:02.207][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-28 03:57:02.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-28 03:57:02.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:02.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:02.217][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-28 03:57:02.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-28 03:57:02.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:02.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:02.224][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-28 03:57:02.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-28 03:57:02.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:02.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:02.231][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-28 03:57:02.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-28 03:57:02.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:02.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:02.238][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-28 03:57:02.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-28 03:57:02.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:02.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:02.245][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-28 03:57:02.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-28 03:57:02.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:02.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:02.251][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-28 03:57:02.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-28 03:57:02.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:02.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:02.258][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-28 03:57:02.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-28 03:57:02.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:02.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:02.266][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-28 03:57:02.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-28 03:57:02.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:02.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:02.273][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-28 03:57:02.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-28 03:57:02.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:02.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:02.289][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-28 03:57:02.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-28 03:57:02.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:02.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:02.297][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-28 03:57:02.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-28 03:57:02.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:02.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:02.304][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.csv.file.id.
biodb.TRACE[2025-01-28 03:57:02.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.csv.file.id.
biodb.TRACE[2025-01-28 03:57:02.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:02.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:02.310][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.csv.file.id.
biodb.TRACE[2025-01-28 03:57:02.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.csv.file.id.
biodb.TRACE[2025-01-28 03:57:02.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:02.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:02.317][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 03:57:02.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 03:57:02.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:02.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:02.323][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.csv.file.id.
biodb.TRACE[2025-01-28 03:57:02.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.csv.file.id.
biodb.TRACE[2025-01-28 03:57:02.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:02.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:02.330][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 03:57:02.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 03:57:02.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:02.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:02.337][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 03:57:02.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 03:57:02.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:02.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:02.344][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 03:57:02.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 03:57:02.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:02.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-28 03:57:02.351][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-28 03:57:02.352][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:57:02.354][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:57:02.355][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:57:02.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-28 03:57:02.363][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 03:57:02.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 03:57:02.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:02.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:02.370][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 03:57:02.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 03:57:02.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:02.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:02.377][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-28 03:57:02.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-28 03:57:02.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:02.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:02.385][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-28 03:57:02.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-28 03:57:02.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:02.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:02.391][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-28 03:57:02.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-28 03:57:02.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:02.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:02.398][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-28 03:57:02.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-28 03:57:02.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:02.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:02.405][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-28 03:57:02.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-28 03:57:02.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:02.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:02.412][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-28 03:57:02.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-28 03:57:02.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:02.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:02.420][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-28 03:57:02.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-28 03:57:02.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:02.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:02.454][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-28 03:57:02.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-28 03:57:02.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:02.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:02.467][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-28 03:57:02.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-28 03:57:02.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:02.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:03.078][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-28 03:57:03.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-28 03:57:03.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:03.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:03.092][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-28 03:57:03.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-28 03:57:03.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:03.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:03.099][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-28 03:57:03.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-28 03:57:03.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:03.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:03.104][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-28 03:57:03.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-28 03:57:03.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:03.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:03.110][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-28 03:57:03.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-28 03:57:03.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:03.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:03.116][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.csv.file.id.
biodb.TRACE[2025-01-28 03:57:03.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.csv.file.id.
biodb.TRACE[2025-01-28 03:57:03.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:03.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:03.122][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.csv.file.id.
biodb.TRACE[2025-01-28 03:57:03.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.csv.file.id.
biodb.TRACE[2025-01-28 03:57:03.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:03.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:03.127][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 03:57:03.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 03:57:03.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:03.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:03.133][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.csv.file.id.
biodb.TRACE[2025-01-28 03:57:03.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.csv.file.id.
biodb.TRACE[2025-01-28 03:57:03.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:03.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:03.139][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 03:57:03.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 03:57:03.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:03.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:03.144][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 03:57:03.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 03:57:03.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:03.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:03.150][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 03:57:03.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 03:57:03.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:03.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-28 03:57:03.156][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-28 03:57:03.157][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 03:57:03.158][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 03:57:03.159][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-28 03:57:03.161][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-28 03:57:03.198][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 03:57:03.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 03:57:03.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:03.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:03.204][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 03:57:03.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 03:57:03.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:03.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:03.210][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-28 03:57:03.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-28 03:57:03.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:03.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:03.216][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-28 03:57:03.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-28 03:57:03.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:03.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:03.222][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-28 03:57:03.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-28 03:57:03.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:03.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:03.227][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-28 03:57:03.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-28 03:57:03.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:03.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:03.233][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-28 03:57:03.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-28 03:57:03.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:03.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:03.239][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-28 03:57:03.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-28 03:57:03.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:03.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:03.245][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-28 03:57:03.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-28 03:57:03.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:03.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:03.250][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-28 03:57:03.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-28 03:57:03.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:03.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:03.256][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-28 03:57:03.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-28 03:57:03.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:03.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:03.262][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-28 03:57:03.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-28 03:57:03.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:03.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:03.268][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-28 03:57:03.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-28 03:57:03.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:03.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:03.274][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-28 03:57:03.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-28 03:57:03.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:03.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:03.280][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-28 03:57:03.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-28 03:57:03.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 03:57:03.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 03:57:03.286][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-28 03:57:19.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-28 05:59:57.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 06:00:19.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:01:39.345][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.csv.file.id.
biodb.TRACE[2025-01-28 08:28:44.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.csv.file.id.
biodb.TRACE[2025-01-28 08:28:44.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:28:44.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:28:44.273][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.csv.file.id.
biodb.TRACE[2025-01-28 08:28:44.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.csv.file.id.
biodb.TRACE[2025-01-28 08:28:44.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:28:44.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:28:44.283][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:28:44.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:28:44.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:28:44.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:28:44.289][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.csv.file.id.
biodb.TRACE[2025-01-28 08:28:44.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.csv.file.id.
biodb.TRACE[2025-01-28 08:28:44.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:28:44.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:28:44.296][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:28:44.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:28:44.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:28:44.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:28:44.302][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:28:44.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:28:44.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:28:44.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:28:44.308][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:28:44.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:28:44.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:28:44.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:28:44.315][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:28:44.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:28:44.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:28:44.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:28:44.321][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:28:44.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:28:44.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:28:44.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:28:44.327][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:28:44.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:28:44.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:28:44.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:28:44.333][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:28:44.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:28:44.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:28:44.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:28:44.339][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:28:44.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:28:44.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:28:44.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:28:44.346][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:28:44.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:28:44.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:28:44.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:28:44.352][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:28:44.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:28:44.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:28:44.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:28:44.359][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:28:44.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:28:44.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:28:44.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:28:44.365][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:28:44.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:28:44.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:28:44.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-28 08:28:44.372][self$createEntryFromContent] Accession numbers: 1018, 1390, 1456.
biodb.INFO [2025-01-28 08:28:44.504][cache$deleteAllFiles] Erasing all files in "/home/biocbuild/.cache/R/biodb/comp.csv.file-a49c5db9408932a2c8454375877bd673".
biodb.INFO [2025-01-28 08:28:44.544][biodb::testThat]
biodb.INFO [2025-01-28 08:28:44.545][biodb::testThat] Running test function test_deleteAllFiles (" We can delete all cache files for a connector ").
biodb.INFO [2025-01-28 08:28:44.547][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-28 08:28:44.548][biodb::testThat]
biodb.DEBUG[2025-01-28 08:28:44.554][private$loadEntries] Creating entries from ids [3]: "1018, 1390, 1456".
biodb.DEBUG[2025-01-28 08:28:44.556][conn$getEntryContent] Get Compound CSV File entry content(s) for 3 id(s)...
biodb.TRACE[2025-01-28 08:28:44.559][cch$loadFileContent] Trying to load 3 files from cache: [3]: "1018, 1390, 1456".
biodb.INFO [2025-01-28 08:28:44.560][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/comp.csv.file-a49c5db9408932a2c8454375877bd673" for "comp.csv.file-a49c5db9408932a2c8454375877bd673".
biodb.TRACE[2025-01-28 08:28:44.562][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2025-01-28 08:28:44.564][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-28 08:28:44.566][conn$getEntryContent] 0 Compound CSV File entry content(s) loaded from cache.
biodb.DEBUG[2025-01-28 08:28:44.567][conn$getEntryContent] 3 entry content(s) need to be fetched from Compound CSV File database "/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/biodb/extdata/chebi_extract.tsv".
biodb.DEBUG[2025-01-28 08:28:44.569][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-28 08:28:44.570][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-28 08:28:44.572][private$doGetEntryContentFromDb] Entry id: 1018, 1390, 1456
biodb.DEBUG[2025-01-28 08:28:44.591][private$doGetEntryContentFromDb] Content of first entry: accession formula monoisotopic.mass molecular.mass kegg.compound.id name smiles description
1018 C2H8AsNO3 168.97201 169.012 C07279 2-Aminoethylarsonate NCC[As](O)(O)=O
biodb.TRACE[2025-01-28 08:28:44.603][private$doSaveContentToFile] Saving to cache [3]: "/home/biocbuild/.cache/R/biodb/comp.csv.file-a49c5db9408932a2c8454375877bd673/1018.tsv, /home/biocbuild/.cache/R/biodb/comp.csv.file-a49c5db9408932a2c8454375877bd673/1390.tsv, /home/biocbuild/.cache/R/biodb/comp.csv.file-a49c5db9408932a2c8454375877bd673/1456.tsv"
biodb.DEBUG[2025-01-28 08:28:44.610][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-28 08:28:44.616][self$createEntryFromContent] Creating Compound CSV File entries from 3 content(s).
biodb.DEBUG[2025-01-28 08:28:44.619][self$createEntryFromContent] Parsing 3 Compound CSV File entries.
biodb.DEBUG[2025-01-28 08:28:44.658][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-28 08:28:44.659][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 08:28:44.665][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 08:28:44.667][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-28 08:28:44.672][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-28 08:28:44.716][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:28:44.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:28:44.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:28:44.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:28:44.804][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:28:44.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:28:44.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:58.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:58.609][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-28 08:29:58.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-28 08:29:58.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:58.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:58.618][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-28 08:29:58.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-28 08:29:58.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:58.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:58.624][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-28 08:29:58.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-28 08:29:58.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:58.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:58.633][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-28 08:29:58.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-28 08:29:58.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:58.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:58.643][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-28 08:29:58.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-28 08:29:58.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:58.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:58.659][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-28 08:29:58.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-28 08:29:58.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:58.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:58.678][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-28 08:29:58.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-28 08:29:58.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:58.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:58.697][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-28 08:29:58.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-28 08:29:58.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:58.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:58.707][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-28 08:29:58.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-28 08:29:58.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:58.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:58.713][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-28 08:29:58.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-28 08:29:58.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:58.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:58.719][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-28 08:29:58.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-28 08:29:58.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:58.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:58.726][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-28 08:29:58.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-28 08:29:58.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:58.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:58.735][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-28 08:29:58.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-28 08:29:58.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:58.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:58.741][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-28 08:29:58.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-28 08:29:58.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:58.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:58.747][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.csv.file.id.
biodb.TRACE[2025-01-28 08:29:58.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.csv.file.id.
biodb.TRACE[2025-01-28 08:29:58.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:58.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:58.753][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.csv.file.id.
biodb.TRACE[2025-01-28 08:29:58.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.csv.file.id.
biodb.TRACE[2025-01-28 08:29:58.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:58.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:58.761][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:29:58.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:29:58.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:58.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:58.767][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.csv.file.id.
biodb.TRACE[2025-01-28 08:29:58.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.csv.file.id.
biodb.TRACE[2025-01-28 08:29:58.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:58.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:58.774][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:29:58.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:29:58.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:58.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:58.780][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:29:58.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:29:58.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:58.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:58.787][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:29:58.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:29:58.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:58.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-28 08:29:58.794][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-28 08:29:58.795][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 08:29:58.797][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 08:29:58.798][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-28 08:29:58.800][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-28 08:29:58.828][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:29:58.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:29:58.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:58.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:58.834][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:29:58.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:29:58.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:58.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:58.840][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-28 08:29:58.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-28 08:29:58.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:58.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:58.847][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-28 08:29:58.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-28 08:29:58.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:58.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:58.861][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-28 08:29:58.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-28 08:29:58.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:58.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:58.869][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-28 08:29:58.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-28 08:29:58.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:58.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:58.875][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-28 08:29:58.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-28 08:29:58.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:58.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:58.881][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-28 08:29:58.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-28 08:29:58.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:58.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:58.891][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-28 08:29:58.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-28 08:29:58.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:58.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:58.897][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-28 08:29:58.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-28 08:29:58.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:58.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:58.903][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-28 08:29:58.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-28 08:29:58.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:58.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:58.909][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-28 08:29:58.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-28 08:29:58.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:58.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:58.915][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-28 08:29:58.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-28 08:29:58.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:58.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:58.923][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-28 08:29:58.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-28 08:29:58.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:58.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:58.929][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-28 08:29:58.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-28 08:29:58.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:58.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:58.935][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-28 08:29:58.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-28 08:29:58.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:58.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:58.941][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.csv.file.id.
biodb.TRACE[2025-01-28 08:29:58.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.csv.file.id.
biodb.TRACE[2025-01-28 08:29:58.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:58.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:58.947][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.csv.file.id.
biodb.TRACE[2025-01-28 08:29:58.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.csv.file.id.
biodb.TRACE[2025-01-28 08:29:58.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:58.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:58.953][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:29:58.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:29:58.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:58.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:58.959][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.csv.file.id.
biodb.TRACE[2025-01-28 08:29:58.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.csv.file.id.
biodb.TRACE[2025-01-28 08:29:58.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:58.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:58.965][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:29:58.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:29:58.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:58.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:58.970][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:29:58.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:29:58.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:58.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:58.976][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:29:58.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:29:58.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:58.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-28 08:29:58.982][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-28 08:29:58.984][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 08:29:58.985][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 08:29:58.986][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-28 08:29:58.988][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-28 08:29:58.993][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:29:58.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:29:58.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:58.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:58.999][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:29:59.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:29:59.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:59.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:59.006][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-28 08:29:59.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-28 08:29:59.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:59.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:59.012][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-28 08:29:59.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-28 08:29:59.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:59.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:59.018][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-28 08:29:59.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-28 08:29:59.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:59.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:59.025][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-28 08:29:59.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-28 08:29:59.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:59.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:59.032][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-28 08:29:59.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-28 08:29:59.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:59.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:59.038][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-28 08:29:59.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-28 08:29:59.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:59.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:59.044][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-28 08:29:59.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-28 08:29:59.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:59.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:59.050][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-28 08:29:59.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-28 08:29:59.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:59.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:59.056][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-28 08:29:59.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-28 08:29:59.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:59.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:59.062][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-28 08:29:59.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-28 08:29:59.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:59.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:59.069][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-28 08:29:59.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-28 08:29:59.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:59.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:59.075][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-28 08:29:59.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-28 08:29:59.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:59.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:59.081][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-28 08:29:59.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-28 08:29:59.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:59.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:59.087][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-28 08:29:59.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-28 08:29:59.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:59.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:59.093][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.csv.file.id.
biodb.TRACE[2025-01-28 08:29:59.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.csv.file.id.
biodb.TRACE[2025-01-28 08:29:59.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:59.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:59.100][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.csv.file.id.
biodb.TRACE[2025-01-28 08:29:59.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.csv.file.id.
biodb.TRACE[2025-01-28 08:29:59.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:59.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:59.689][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:29:59.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:29:59.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:59.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:59.696][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.csv.file.id.
biodb.TRACE[2025-01-28 08:29:59.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.csv.file.id.
biodb.TRACE[2025-01-28 08:29:59.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:59.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:59.711][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:29:59.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:29:59.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:59.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:59.726][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:29:59.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:29:59.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:59.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:59.741][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:29:59.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:29:59.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:59.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:59.752][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:29:59.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:29:59.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:59.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:59.767][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:29:59.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:29:59.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:59.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:59.782][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:29:59.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:29:59.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:59.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:59.797][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:29:59.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:29:59.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:59.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:59.808][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:29:59.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:29:59.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:59.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:59.823][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:29:59.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:29:59.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:59.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:59.838][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:29:59.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:29:59.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:59.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:59.853][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:29:59.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:29:59.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:59.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:29:59.864][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:29:59.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:29:59.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:29:59.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-28 08:29:59.895][self$createEntryFromContent] Accession numbers: 1018, 1390, 1456.
biodb.INFO [2025-01-28 08:30:00.056][cache$deleteAllFiles] Erasing all files in "/home/biocbuild/.cache/R/biodb/comp.csv.file-a49c5db9408932a2c8454375877bd673".
biodb.INFO [2025-01-28 08:30:00.087][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/comp.csv.file-a49c5db9408932a2c8454375877bd673" for "comp.csv.file-a49c5db9408932a2c8454375877bd673".
biodb.DEBUG[2025-01-28 08:30:00.104][private$loadEntries] Creating entries from ids [3]: "1018, 1390, 1456".
biodb.DEBUG[2025-01-28 08:30:00.110][conn$getEntryContent] Get Compound CSV File entry content(s) for 3 id(s)...
biodb.TRACE[2025-01-28 08:30:00.117][cch$loadFileContent] Trying to load 3 files from cache: [3]: "1018, 1390, 1456".
biodb.TRACE[2025-01-28 08:30:00.119][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2025-01-28 08:30:00.125][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-28 08:30:00.127][conn$getEntryContent] 0 Compound CSV File entry content(s) loaded from cache.
biodb.DEBUG[2025-01-28 08:30:00.133][conn$getEntryContent] 3 entry content(s) need to be fetched from Compound CSV File database "/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/biodb/extdata/chebi_extract.tsv".
biodb.DEBUG[2025-01-28 08:30:00.135][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-28 08:30:00.140][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-28 08:30:00.142][private$doGetEntryContentFromDb] Entry id: 1018, 1390, 1456
biodb.DEBUG[2025-01-28 08:30:00.165][private$doGetEntryContentFromDb] Content of first entry: accession formula monoisotopic.mass molecular.mass kegg.compound.id name smiles description
1018 C2H8AsNO3 168.97201 169.012 C07279 2-Aminoethylarsonate NCC[As](O)(O)=O
biodb.TRACE[2025-01-28 08:30:00.173][private$doSaveContentToFile] Saving to cache [3]: "/home/biocbuild/.cache/R/biodb/comp.csv.file-a49c5db9408932a2c8454375877bd673/1018.tsv, /home/biocbuild/.cache/R/biodb/comp.csv.file-a49c5db9408932a2c8454375877bd673/1390.tsv, /home/biocbuild/.cache/R/biodb/comp.csv.file-a49c5db9408932a2c8454375877bd673/1456.tsv"
biodb.DEBUG[2025-01-28 08:30:00.180][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-28 08:30:00.183][self$createEntryFromContent] Creating Compound CSV File entries from 3 content(s).
biodb.DEBUG[2025-01-28 08:30:00.189][self$createEntryFromContent] Parsing 3 Compound CSV File entries.
biodb.DEBUG[2025-01-28 08:30:00.192][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-28 08:30:00.198][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 08:30:00.199][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 08:30:00.205][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-28 08:30:00.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-28 08:30:00.221][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:30:00.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:30:00.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.236][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:30:00.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:30:00.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.252][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-28 08:30:00.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-28 08:30:00.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.264][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-28 08:30:00.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-28 08:30:00.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.280][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-28 08:30:00.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-28 08:30:00.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.295][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-28 08:30:00.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-28 08:30:00.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.306][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-28 08:30:00.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-28 08:30:00.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.312][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-28 08:30:00.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-28 08:30:00.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.319][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-28 08:30:00.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-28 08:30:00.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.325][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-28 08:30:00.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-28 08:30:00.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.335][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-28 08:30:00.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-28 08:30:00.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.351][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-28 08:30:00.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-28 08:30:00.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.366][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-28 08:30:00.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-28 08:30:00.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.381][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-28 08:30:00.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-28 08:30:00.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.396][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-28 08:30:00.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-28 08:30:00.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.407][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-28 08:30:00.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-28 08:30:00.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.433][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.csv.file.id.
biodb.TRACE[2025-01-28 08:30:00.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.csv.file.id.
biodb.TRACE[2025-01-28 08:30:00.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.448][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.csv.file.id.
biodb.TRACE[2025-01-28 08:30:00.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.csv.file.id.
biodb.TRACE[2025-01-28 08:30:00.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.463][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:30:00.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:30:00.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.509][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.csv.file.id.
biodb.TRACE[2025-01-28 08:30:00.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.csv.file.id.
biodb.TRACE[2025-01-28 08:30:00.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.520][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:30:00.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:30:00.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.531][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:30:00.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:30:00.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.546][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:30:00.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:30:00.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-28 08:30:00.565][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-28 08:30:00.567][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 08:30:00.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 08:30:00.574][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-28 08:30:00.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-28 08:30:00.593][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:30:00.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:30:00.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.600][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:30:00.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:30:00.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.615][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-28 08:30:00.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-28 08:30:00.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.631][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-28 08:30:00.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-28 08:30:00.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.647][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-28 08:30:00.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-28 08:30:00.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.659][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-28 08:30:00.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-28 08:30:00.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.666][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-28 08:30:00.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-28 08:30:00.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.674][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-28 08:30:00.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-28 08:30:00.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.681][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-28 08:30:00.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-28 08:30:00.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.688][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-28 08:30:00.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-28 08:30:00.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.697][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-28 08:30:00.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-28 08:30:00.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.706][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-28 08:30:00.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-28 08:30:00.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.717][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-28 08:30:00.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-28 08:30:00.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.724][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-28 08:30:00.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-28 08:30:00.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.732][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-28 08:30:00.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-28 08:30:00.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.739][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-28 08:30:00.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-28 08:30:00.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.746][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.csv.file.id.
biodb.TRACE[2025-01-28 08:30:00.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.csv.file.id.
biodb.TRACE[2025-01-28 08:30:00.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.753][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.csv.file.id.
biodb.TRACE[2025-01-28 08:30:00.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.csv.file.id.
biodb.TRACE[2025-01-28 08:30:00.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.760][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:30:00.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:30:00.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.767][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.csv.file.id.
biodb.TRACE[2025-01-28 08:30:00.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.csv.file.id.
biodb.TRACE[2025-01-28 08:30:00.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.774][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:30:00.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:30:00.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.783][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:30:00.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:30:00.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.790][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:30:00.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:30:00.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-28 08:30:00.797][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-28 08:30:00.801][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 08:30:00.803][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 08:30:00.804][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-28 08:30:00.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-28 08:30:00.811][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:30:00.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:30:00.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.820][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:30:00.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:30:00.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.828][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-28 08:30:00.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-28 08:30:00.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.835][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-28 08:30:00.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-28 08:30:00.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.842][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-28 08:30:00.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-28 08:30:00.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.849][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-28 08:30:00.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-28 08:30:00.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.856][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-28 08:30:00.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-28 08:30:00.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.863][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-28 08:30:00.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-28 08:30:00.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.870][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-28 08:30:00.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-28 08:30:00.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.878][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-28 08:30:00.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-28 08:30:00.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.884][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-28 08:30:00.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-28 08:30:00.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.891][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-28 08:30:00.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-28 08:30:00.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.898][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-28 08:30:00.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-28 08:30:00.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.905][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-28 08:30:00.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-28 08:30:00.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.912][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-28 08:30:00.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-28 08:30:00.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.919][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-28 08:30:00.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-28 08:30:00.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.926][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.csv.file.id.
biodb.TRACE[2025-01-28 08:30:00.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.csv.file.id.
biodb.TRACE[2025-01-28 08:30:00.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.933][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.csv.file.id.
biodb.TRACE[2025-01-28 08:30:00.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.csv.file.id.
biodb.TRACE[2025-01-28 08:30:00.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.942][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:30:00.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:30:00.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.948][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.csv.file.id.
biodb.TRACE[2025-01-28 08:30:00.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.csv.file.id.
biodb.TRACE[2025-01-28 08:30:00.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.954][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:30:00.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:30:00.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.960][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:30:00.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:30:00.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.966][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:30:00.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:30:00.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.973][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:30:00.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:30:00.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.980][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:30:00.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:30:00.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.986][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:30:00.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:30:00.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.992][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:30:00.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:30:00.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:00.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:00.998][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:30:00.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:30:01.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:01.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:01.003][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:30:01.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:30:01.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:01.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:01.009][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:30:01.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:30:01.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:01.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:01.015][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:30:01.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:30:01.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:01.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:01.023][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:30:01.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:30:01.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:01.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-28 08:30:01.029][self$createEntryFromContent] Accession numbers: 1018, 1390, 1456.
biodb.INFO [2025-01-28 08:30:01.163][cache$deleteAllFiles] Erasing all files in "/home/biocbuild/.cache/R/biodb/comp.csv.file-a49c5db9408932a2c8454375877bd673".
biodb.INFO [2025-01-28 08:30:01.165][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/comp.csv.file-a49c5db9408932a2c8454375877bd673" for "comp.csv.file-a49c5db9408932a2c8454375877bd673".
biodb.INFO [2025-01-28 08:30:01.188][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-01-28 08:30:01.190][self$deleteConn] Connector "comp.csv.file" deleted.
biodb.DEBUG[2025-01-28 08:30:01.191][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-01-28 08:30:01.192][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 08:30:01.194][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 08:30:01.195][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 08:30:01.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-01-28 08:30:01.245][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-01-28 08:30:01.281][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-01-28 08:30:01.315][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-28 08:30:01.325][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-01-28 08:30:01.327][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-01-28 08:30:01.337][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 08:30:01.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 08:30:01.340][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 08:30:01.346][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-01-28 08:30:01.348][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-01-28 08:30:01.357][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 08:30:01.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 08:30:01.360][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[2025-01-28 08:30:01.362][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-01-28 08:30:01.364][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-01-28 08:30:01.366][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 08:30:01.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 08:30:01.369][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 08:30:01.370][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-01-28 08:30:01.372][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-01-28 08:30:01.374][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-01-28 08:30:01.375][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 08:30:01.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 08:30:01.378][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 08:30:01.380][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-01-28 08:30:01.381][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-01-28 08:30:01.383][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-01-28 08:30:01.385][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 08:30:01.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 08:30:01.388][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 08:30:01.390][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-01-28 08:30:01.391][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-01-28 08:30:01.394][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 08:30:01.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 08:30:01.397][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 08:30:01.399][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-01-28 08:30:01.402][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-01-28 08:30:01.404][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-01-28 08:30:01.405][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 08:30:01.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 08:30:01.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 08:30:01.410][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-01-28 08:30:01.412][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-01-28 08:30:01.413][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 08:30:01.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 08:30:01.425][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 08:30:01.426][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-01-28 08:30:01.428][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-01-28 08:30:01.430][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-01-28 08:30:01.431][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 08:30:01.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 08:30:01.434][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 08:30:01.436][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-01-28 08:30:01.437][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-01-28 08:30:01.439][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-01-28 08:30:01.441][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-01-28 08:30:01.442][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-01-28 08:30:01.444][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-01-28 08:30:01.445][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 08:30:01.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 08:30:01.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 08:30:01.450][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-01-28 08:30:01.451][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-01-28 08:30:01.453][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 08:30:01.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 08:30:01.455][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 08:30:01.457][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-01-28 08:30:01.458][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-01-28 08:30:01.460][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 08:30:01.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 08:30:01.462][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 08:30:01.464][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-01-28 08:30:01.465][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-01-28 08:30:01.466][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 08:30:01.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 08:30:01.469][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 08:30:01.470][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-01-28 08:30:01.472][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-01-28 08:30:01.473][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 08:30:01.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 08:30:01.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 08:30:01.477][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-01-28 08:30:01.478][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-01-28 08:30:01.480][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 08:30:01.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 08:30:01.482][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 08:30:01.484][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-01-28 08:30:01.485][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-01-28 08:30:01.676][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-01-28 08:30:01.678][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 08:30:01.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 08:30:01.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 08:30:01.686][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-01-28 08:30:01.696][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-01-28 08:30:01.698][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-01-28 08:30:01.700][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 08:30:01.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 08:30:01.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 08:30:01.722][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-01-28 08:30:01.733][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-28 08:30:01.735][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-01-28 08:30:01.745][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-28 08:30:01.747][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-28 08:30:01.757][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-28 08:30:01.759][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-28 08:30:01.769][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-28 08:30:01.771][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-28 08:30:01.781][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-28 08:30:01.783][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-28 08:30:01.793][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-28 08:30:01.795][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-01-28 08:30:01.805][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-28 08:30:01.807][self$setPropertyValue]
biodb.DEBUG[2025-01-28 08:30:01.817][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-28 08:30:01.819][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-28 08:30:01.819][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-28 08:30:01.819][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-28 08:30:01.819][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-28 08:30:01.819][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-28 08:30:01.829][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-28 08:30:01.831][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-28 08:30:01.841][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-28 08:30:01.843][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-28 08:30:01.853][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-28 08:30:01.854][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-28 08:30:01.860][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-28 08:30:01.862][self$setPropertyValue]
biodb.DEBUG[2025-01-28 08:30:01.868][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-28 08:30:01.870][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-28 08:30:01.872][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-28 08:30:01.878][self$setPropertyValue]
biodb.DEBUG[2025-01-28 08:30:01.884][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-01-28 08:30:01.888][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-28 08:30:01.894][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-01-28 08:30:01.895][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-28 08:30:01.901][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-28 08:30:01.903][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-28 08:30:01.909][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-28 08:30:01.911][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-28 08:30:01.916][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-28 08:30:01.918][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-28 08:30:01.920][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-28 08:30:01.926][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-28 08:30:01.928][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-01-28 08:30:01.934][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-28 08:30:01.935][self$setPropertyValue]
biodb.DEBUG[2025-01-28 08:30:01.941][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-28 08:30:01.943][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-28 08:30:01.943][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-28 08:30:01.943][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-28 08:30:01.943][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-28 08:30:01.943][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-28 08:30:01.949][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-28 08:30:01.951][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-28 08:30:01.957][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-28 08:30:01.958][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-28 08:30:01.960][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-28 08:30:01.966][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-28 08:30:01.968][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-28 08:30:01.974][self$setPropertyValue]
biodb.DEBUG[2025-01-28 08:30:01.975][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-28 08:30:01.981][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-28 08:30:01.983][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-28 08:30:01.989][self$setPropertyValue]
biodb.DEBUG[2025-01-28 08:30:01.991][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-01-28 08:30:01.999][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-28 08:30:02.005][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-01-28 08:30:02.007][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-28 08:30:02.013][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-28 08:30:02.015][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-28 08:30:02.021][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-28 08:30:02.023][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-28 08:30:02.029][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-28 08:30:02.031][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-28 08:30:02.037][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-28 08:30:02.039][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-28 08:30:02.045][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-01-28 08:30:02.047][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-28 08:30:02.053][self$setPropertyValue]
biodb.DEBUG[2025-01-28 08:30:02.054][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-28 08:30:02.060][self$setPropertyValue]
biodb.DEBUG[2025-01-28 08:30:02.062][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-28 08:30:02.068][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-28 08:30:02.070][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-28 08:30:02.072][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-28 08:30:02.078][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-28 08:30:02.079][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-28 08:30:02.085][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-28 08:30:02.087][self$setPropertyValue]
biodb.DEBUG[2025-01-28 08:30:02.093][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-28 08:30:02.095][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-28 08:30:02.101][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-28 08:30:02.103][self$setPropertyValue]
biodb.DEBUG[2025-01-28 08:30:02.109][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-01-28 08:30:02.116][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-28 08:30:02.118][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-01-28 08:30:02.120][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-28 08:30:02.126][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-28 08:30:02.128][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-28 08:30:02.134][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-28 08:30:02.135][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-28 08:30:02.141][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-28 08:30:02.143][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-28 08:30:02.150][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-28 08:30:02.151][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-28 08:30:02.158][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-01-28 08:30:02.160][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-28 08:30:02.166][self$setPropertyValue]
biodb.DEBUG[2025-01-28 08:30:02.168][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-28 08:30:02.174][self$setPropertyValue]
biodb.DEBUG[2025-01-28 08:30:02.176][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-28 08:30:02.182][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-28 08:30:02.183][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-28 08:30:02.189][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-28 08:30:02.191][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-28 08:30:02.197][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-28 08:30:02.199][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-28 08:30:02.204][self$setPropertyValue]
biodb.DEBUG[2025-01-28 08:30:02.206][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-28 08:30:02.208][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-28 08:30:02.213][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-28 08:30:02.215][self$setPropertyValue]
biodb.DEBUG[2025-01-28 08:30:02.221][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-28 08:30:02.223][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-28 08:30:02.228][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 08:30:02.230][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 08:30:02.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 08:30:02.237][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 08:30:02.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 08:30:02.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 08:30:02.245][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 08:30:02.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 08:30:02.252][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 08:30:02.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 08:30:02.255][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 08:30:02.261][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 08:30:02.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 08:30:02.264][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 08:30:02.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 08:30:02.271][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 08:30:02.277][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 08:30:02.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 08:30:02.279][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 08:30:02.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 08:30:02.287][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 08:30:02.288][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 08:30:02.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 08:30:02.295][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 08:30:02.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 08:30:02.302][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 08:30:02.303][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 08:30:02.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 08:30:02.311][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 08:30:02.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 08:30:02.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 08:30:02.319][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 08:30:02.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 08:30:02.326][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 08:30:02.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 08:30:02.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 08:30:02.335][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 08:30:02.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 08:30:02.342][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 08:30:02.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 08:30:02.349][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 08:30:02.351][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 08:30:02.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 08:30:02.358][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 08:30:02.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 08:30:02.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 08:30:02.366][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 08:30:02.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 08:30:02.374][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 08:30:02.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 08:30:02.381][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 08:30:02.382][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 08:30:02.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 08:30:02.389][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 08:30:02.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 08:30:02.396][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[2025-01-28 08:30:02.398][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 08:30:02.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 08:30:02.405][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 08:30:02.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 08:30:02.408][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[2025-01-28 08:30:02.414][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 08:30:02.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 08:30:02.421][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 08:30:02.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 08:30:02.424][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[2025-01-28 08:30:02.429][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 08:30:02.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 08:30:02.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 08:30:02.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 08:30:02.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 08:30:02.445][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 08:30:02.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 08:30:02.448][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 08:30:02.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 08:30:02.455][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 08:30:02.461][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 08:30:02.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 08:30:02.464][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 08:30:02.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 08:30:02.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 08:30:02.477][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 08:30:02.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 08:30:02.480][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 08:30:02.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 08:30:02.487][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 08:30:02.493][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-01-28 08:30:02.495][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-01-28 08:30:02.502][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-01-28 08:30:02.509][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-01-28 08:30:02.511][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-01-28 08:30:02.518][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-01-28 08:30:02.520][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-01-28 08:30:02.526][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-01-28 08:30:02.533][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-01-28 08:30:02.535][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-01-28 08:30:02.542][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-01-28 08:30:02.548][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-01-28 08:30:02.551][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-01-28 08:30:02.557][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-01-28 08:30:02.560][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-01-28 08:30:02.566][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-01-28 08:30:02.573][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-01-28 08:30:02.575][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-01-28 08:30:02.581][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-01-28 08:30:02.584][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-01-28 08:30:02.590][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-01-28 08:30:02.597][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-01-28 08:30:02.599][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-01-28 08:30:02.605][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-01-28 08:30:02.608][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-01-28 08:30:02.614][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-01-28 08:30:02.621][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-01-28 08:30:02.623][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-01-28 08:30:02.629][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-01-28 08:30:02.632][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-01-28 08:30:02.639][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-01-28 08:30:02.645][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-01-28 08:30:02.648][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-01-28 08:30:02.655][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-01-28 08:30:02.661][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-01-28 08:30:02.664][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-01-28 08:30:02.671][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-01-28 08:30:02.677][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-01-28 08:30:02.680][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-01-28 08:30:02.686][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-01-28 08:30:02.693][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-01-28 08:30:02.696][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-01-28 08:30:02.702][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-01-28 08:30:02.709][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-01-28 08:30:02.711][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-01-28 08:30:02.718][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-01-28 08:30:02.724][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-01-28 08:30:02.727][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-01-28 08:30:02.734][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-01-28 08:30:02.740][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-01-28 08:30:02.743][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-01-28 08:30:02.749][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-01-28 08:30:02.751][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-01-28 08:30:02.758][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-01-28 08:30:02.764][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-01-28 08:30:02.767][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-01-28 08:30:02.773][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-01-28 08:30:02.776][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-01-28 08:30:02.782][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-01-28 08:30:02.789][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-01-28 08:30:02.792][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-01-28 08:30:02.815][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-01-28 08:30:02.822][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-01-28 08:30:02.829][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-01-28 08:30:02.831][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-01-28 08:30:02.838][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-01-28 08:30:02.844][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-01-28 08:30:02.847][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-01-28 08:30:02.853][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-01-28 08:30:02.855][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-01-28 08:30:02.862][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-01-28 08:30:02.864][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-01-28 08:30:02.870][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-01-28 08:30:02.877][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-01-28 08:30:02.879][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-01-28 08:30:02.886][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-01-28 08:30:02.888][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-01-28 08:30:02.894][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-01-28 08:30:02.901][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-01-28 08:30:02.903][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-01-28 08:30:02.910][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-01-28 08:30:02.912][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-01-28 08:30:02.918][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-01-28 08:30:02.925][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-01-28 08:30:02.927][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-01-28 08:30:02.933][biodb$getConfig()$set] Set key use.cache.for.local.db to TRUE.
biodb.DEBUG[2025-01-28 08:30:02.934][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 08:30:02.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 08:30:02.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 08:30:02.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 08:30:02.944][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 08:30:02.950][biodb$getConfig()$set] Set key persistent.cache.impl to "bioc".
biodb.DEBUG[2025-01-28 08:30:02.951][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-28 08:30:02.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 08:30:02.958][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 08:30:02.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-28 08:30:02.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-01-28 08:30:02.980][biodb$getPersistentCache()$erase] Erasing cache "/home/biocbuild/.cache/R/biodb".
biodb.DEBUG[2025-01-28 08:30:03.024][super$initialize] Initialize connector comp.csv.file.
biodb.DEBUG[2025-01-28 08:30:03.026][biodb$getFactory()$createConn] Creating new connector comp.csv.file for database class comp.csv.file , with base URL "/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/biodb/extdata/chebi_extract.tsv".
biodb.INFO [2025-01-28 08:30:03.032][biodb::testThat]
biodb.INFO [2025-01-28 08:30:03.034][biodb::testThat] Running test function test_cacheFiles (" We can list cache files. ").
biodb.INFO [2025-01-28 08:30:03.035][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-28 08:30:03.041][biodb::testThat]
biodb.INFO [2025-01-28 08:30:03.097][private$initDb] Loading file database "/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/biodb/extdata/chebi_extract.tsv".
biodb.DEBUG[2025-01-28 08:30:03.106][self$setField] Set field accession to column(s) accession.
biodb.TRACE[2025-01-28 08:30:03.108][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:30:03.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:30:03.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:03.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-28 08:30:03.118][self$setPropertyValue] Setting property "parsing.expr" to "accession".
biodb.DEBUG[2025-01-28 08:30:03.125][self$setField] Set field formula to column(s) formula.
biodb.TRACE[2025-01-28 08:30:03.127][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-28 08:30:03.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-28 08:30:03.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:03.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-28 08:30:03.142][self$setPropertyValue] Setting property "parsing.expr" to "accession".
biodb.DEBUG[2025-01-28 08:30:03.142][self$setPropertyValue] Setting property "parsing.expr" to "formula".
biodb.DEBUG[2025-01-28 08:30:03.144][self$setField] Set field monoisotopic.mass to column(s) monoisotopic.mass.
biodb.TRACE[2025-01-28 08:30:03.150][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-28 08:30:03.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-28 08:30:03.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:03.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-28 08:30:03.165][self$setPropertyValue] Setting property "parsing.expr" to "accession".
biodb.DEBUG[2025-01-28 08:30:03.165][self$setPropertyValue] Setting property "parsing.expr" to "formula".
biodb.DEBUG[2025-01-28 08:30:03.165][self$setPropertyValue] Setting property "parsing.expr" to "monoisotopic.mass".
biodb.DEBUG[2025-01-28 08:30:03.167][self$setField] Set field molecular.mass to column(s) molecular.mass.
biodb.TRACE[2025-01-28 08:30:03.173][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-28 08:30:03.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-28 08:30:03.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:03.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-28 08:30:03.184][self$setPropertyValue] Setting property "parsing.expr" to "accession".
biodb.DEBUG[2025-01-28 08:30:03.184][self$setPropertyValue] Setting property "parsing.expr" to "formula".
biodb.DEBUG[2025-01-28 08:30:03.184][self$setPropertyValue] Setting property "parsing.expr" to "monoisotopic.mass".
biodb.DEBUG[2025-01-28 08:30:03.184][self$setPropertyValue] Setting property "parsing.expr" to "molecular.mass".
biodb.DEBUG[2025-01-28 08:30:03.190][self$setField] Set field kegg.compound.id to column(s) kegg.compound.id.
biodb.TRACE[2025-01-28 08:30:03.191][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-28 08:30:03.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-28 08:30:03.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:03.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-28 08:30:03.206][self$setPropertyValue] Setting property "parsing.expr" to "accession".
biodb.DEBUG[2025-01-28 08:30:03.206][self$setPropertyValue] Setting property "parsing.expr" to "formula".
biodb.DEBUG[2025-01-28 08:30:03.206][self$setPropertyValue] Setting property "parsing.expr" to "monoisotopic.mass".
biodb.DEBUG[2025-01-28 08:30:03.206][self$setPropertyValue] Setting property "parsing.expr" to "molecular.mass".
biodb.DEBUG[2025-01-28 08:30:03.206][self$setPropertyValue] Setting property "parsing.expr" to "kegg.compound.id".
biodb.DEBUG[2025-01-28 08:30:03.212][self$setField] Set field name to column(s) name.
biodb.TRACE[2025-01-28 08:30:03.214][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-28 08:30:03.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-28 08:30:03.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:03.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-28 08:30:03.229][self$setPropertyValue] Setting property "parsing.expr" to "accession".
biodb.DEBUG[2025-01-28 08:30:03.229][self$setPropertyValue] Setting property "parsing.expr" to "formula".
biodb.DEBUG[2025-01-28 08:30:03.229][self$setPropertyValue] Setting property "parsing.expr" to "monoisotopic.mass".
biodb.DEBUG[2025-01-28 08:30:03.229][self$setPropertyValue] Setting property "parsing.expr" to "molecular.mass".
biodb.DEBUG[2025-01-28 08:30:03.229][self$setPropertyValue] Setting property "parsing.expr" to "kegg.compound.id".
biodb.DEBUG[2025-01-28 08:30:03.229][self$setPropertyValue] Setting property "parsing.expr" to "name".
biodb.DEBUG[2025-01-28 08:30:03.231][self$setField] Set field smiles to column(s) smiles.
biodb.TRACE[2025-01-28 08:30:03.237][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-28 08:30:03.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-28 08:30:03.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:03.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-28 08:30:03.247][self$setPropertyValue] Setting property "parsing.expr" to "accession".
biodb.DEBUG[2025-01-28 08:30:03.247][self$setPropertyValue] Setting property "parsing.expr" to "formula".
biodb.DEBUG[2025-01-28 08:30:03.247][self$setPropertyValue] Setting property "parsing.expr" to "monoisotopic.mass".
biodb.DEBUG[2025-01-28 08:30:03.247][self$setPropertyValue] Setting property "parsing.expr" to "molecular.mass".
biodb.DEBUG[2025-01-28 08:30:03.247][self$setPropertyValue] Setting property "parsing.expr" to "kegg.compound.id".
biodb.DEBUG[2025-01-28 08:30:03.247][self$setPropertyValue] Setting property "parsing.expr" to "name".
biodb.DEBUG[2025-01-28 08:30:03.247][self$setPropertyValue] Setting property "parsing.expr" to "smiles".
biodb.DEBUG[2025-01-28 08:30:03.253][self$setField] Set field description to column(s) description.
biodb.TRACE[2025-01-28 08:30:03.255][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-28 08:30:03.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-28 08:30:03.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:03.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-28 08:30:03.270][self$setPropertyValue] Setting property "parsing.expr" to "accession".
biodb.DEBUG[2025-01-28 08:30:03.270][self$setPropertyValue] Setting property "parsing.expr" to "formula".
biodb.DEBUG[2025-01-28 08:30:03.270][self$setPropertyValue] Setting property "parsing.expr" to "monoisotopic.mass".
biodb.DEBUG[2025-01-28 08:30:03.270][self$setPropertyValue] Setting property "parsing.expr" to "molecular.mass".
biodb.DEBUG[2025-01-28 08:30:03.270][self$setPropertyValue] Setting property "parsing.expr" to "kegg.compound.id".
biodb.DEBUG[2025-01-28 08:30:03.270][self$setPropertyValue] Setting property "parsing.expr" to "name".
biodb.DEBUG[2025-01-28 08:30:03.270][self$setPropertyValue] Setting property "parsing.expr" to "smiles".
biodb.DEBUG[2025-01-28 08:30:03.270][self$setPropertyValue] Setting property "parsing.expr" to "description".
biodb.DEBUG[2025-01-28 08:30:03.296][private$loadEntries] Creating entries from ids [3]: "1018, 1390, 1456".
biodb.DEBUG[2025-01-28 08:30:03.302][conn$getEntryContent] Get Compound CSV File entry content(s) for 3 id(s)...
biodb.TRACE[2025-01-28 08:30:03.308][cch$loadFileContent] Trying to load 3 files from cache: [3]: "1018, 1390, 1456".
biodb.TRACE[2025-01-28 08:30:03.310][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2025-01-28 08:30:03.312][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-28 08:30:03.318][conn$getEntryContent] 0 Compound CSV File entry content(s) loaded from cache.
biodb.DEBUG[2025-01-28 08:30:03.320][conn$getEntryContent] 3 entry content(s) need to be fetched from Compound CSV File database "/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/biodb/extdata/chebi_extract.tsv".
biodb.DEBUG[2025-01-28 08:30:03.325][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-28 08:30:03.327][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-28 08:30:03.332][private$doGetEntryContentFromDb] Entry id: 1018, 1390, 1456
biodb.DEBUG[2025-01-28 08:30:03.349][private$doGetEntryContentFromDb] Content of first entry: accession formula monoisotopic.mass molecular.mass kegg.compound.id name smiles description
1018 C2H8AsNO3 168.97201 169.012 C07279 2-Aminoethylarsonate NCC[As](O)(O)=O
biodb.INFO [2025-01-28 08:30:03.352][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/comp.csv.file-a49c5db9408932a2c8454375877bd673" for "comp.csv.file-a49c5db9408932a2c8454375877bd673".
biodb.DEBUG[2025-01-28 08:30:05.004][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-28 08:30:05.598][self$createEntryFromContent] Creating Compound CSV File entries from 3 content(s).
biodb.DEBUG[2025-01-28 08:30:17.976][self$createEntryFromContent] Parsing 3 Compound CSV File entries.
biodb.DEBUG[2025-01-28 08:30:17.979][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-28 08:30:17.981][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 08:30:17.982][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 08:30:17.985][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-28 08:30:17.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-28 08:30:18.002][self$setPropertyValue] Setting property "parsing.expr" to "accession".
biodb.DEBUG[2025-01-28 08:30:18.002][self$setPropertyValue] Setting property "parsing.expr" to "formula".
biodb.DEBUG[2025-01-28 08:30:18.002][self$setPropertyValue] Setting property "parsing.expr" to "monoisotopic.mass".
biodb.DEBUG[2025-01-28 08:30:18.002][self$setPropertyValue] Setting property "parsing.expr" to "molecular.mass".
biodb.DEBUG[2025-01-28 08:30:18.002][self$setPropertyValue] Setting property "parsing.expr" to "kegg.compound.id".
biodb.DEBUG[2025-01-28 08:30:18.002][self$setPropertyValue] Setting property "parsing.expr" to "name".
biodb.DEBUG[2025-01-28 08:30:18.002][self$setPropertyValue] Setting property "parsing.expr" to "smiles".
biodb.DEBUG[2025-01-28 08:30:18.002][self$setPropertyValue] Setting property "parsing.expr" to "description".
biodb.DEBUG[2025-01-28 08:30:18.005][self$setPropertyValue] Setting property "parsing.expr" to "accession".
biodb.DEBUG[2025-01-28 08:30:18.005][self$setPropertyValue] Setting property "parsing.expr" to "formula".
biodb.DEBUG[2025-01-28 08:30:18.005][self$setPropertyValue] Setting property "parsing.expr" to "monoisotopic.mass".
biodb.DEBUG[2025-01-28 08:30:18.005][self$setPropertyValue] Setting property "parsing.expr" to "molecular.mass".
biodb.DEBUG[2025-01-28 08:30:18.005][self$setPropertyValue] Setting property "parsing.expr" to "kegg.compound.id".
biodb.DEBUG[2025-01-28 08:30:18.005][self$setPropertyValue] Setting property "parsing.expr" to "name".
biodb.DEBUG[2025-01-28 08:30:18.005][self$setPropertyValue] Setting property "parsing.expr" to "smiles".
biodb.DEBUG[2025-01-28 08:30:18.005][self$setPropertyValue] Setting property "parsing.expr" to "description".
biodb.DEBUG[2025-01-28 08:30:18.006][self$setPropertyValue] Setting property "parsing.expr" to "accession".
biodb.DEBUG[2025-01-28 08:30:18.006][self$setPropertyValue] Setting property "parsing.expr" to "formula".
biodb.DEBUG[2025-01-28 08:30:18.006][self$setPropertyValue] Setting property "parsing.expr" to "monoisotopic.mass".
biodb.DEBUG[2025-01-28 08:30:18.006][self$setPropertyValue] Setting property "parsing.expr" to "molecular.mass".
biodb.DEBUG[2025-01-28 08:30:18.006][self$setPropertyValue] Setting property "parsing.expr" to "kegg.compound.id".
biodb.DEBUG[2025-01-28 08:30:18.006][self$setPropertyValue] Setting property "parsing.expr" to "name".
biodb.DEBUG[2025-01-28 08:30:18.006][self$setPropertyValue] Setting property "parsing.expr" to "smiles".
biodb.DEBUG[2025-01-28 08:30:18.006][self$setPropertyValue] Setting property "parsing.expr" to "description".
biodb.DEBUG[2025-01-28 08:30:18.009][self$setPropertyValue] Setting property "parsing.expr" to "accession".
biodb.DEBUG[2025-01-28 08:30:18.009][self$setPropertyValue] Setting property "parsing.expr" to "formula".
biodb.DEBUG[2025-01-28 08:30:18.009][self$setPropertyValue] Setting property "parsing.expr" to "monoisotopic.mass".
biodb.DEBUG[2025-01-28 08:30:18.009][self$setPropertyValue] Setting property "parsing.expr" to "molecular.mass".
biodb.DEBUG[2025-01-28 08:30:18.009][self$setPropertyValue] Setting property "parsing.expr" to "kegg.compound.id".
biodb.DEBUG[2025-01-28 08:30:18.009][self$setPropertyValue] Setting property "parsing.expr" to "name".
biodb.DEBUG[2025-01-28 08:30:18.009][self$setPropertyValue] Setting property "parsing.expr" to "smiles".
biodb.DEBUG[2025-01-28 08:30:18.009][self$setPropertyValue] Setting property "parsing.expr" to "description".
biodb.DEBUG[2025-01-28 08:30:18.011][self$setPropertyValue] Setting property "parsing.expr" to "accession".
biodb.DEBUG[2025-01-28 08:30:18.011][self$setPropertyValue] Setting property "parsing.expr" to "formula".
biodb.DEBUG[2025-01-28 08:30:18.011][self$setPropertyValue] Setting property "parsing.expr" to "monoisotopic.mass".
biodb.DEBUG[2025-01-28 08:30:18.011][self$setPropertyValue] Setting property "parsing.expr" to "molecular.mass".
biodb.DEBUG[2025-01-28 08:30:18.011][self$setPropertyValue] Setting property "parsing.expr" to "kegg.compound.id".
biodb.DEBUG[2025-01-28 08:30:18.011][self$setPropertyValue] Setting property "parsing.expr" to "name".
biodb.DEBUG[2025-01-28 08:30:18.011][self$setPropertyValue] Setting property "parsing.expr" to "smiles".
biodb.DEBUG[2025-01-28 08:30:18.011][self$setPropertyValue] Setting property "parsing.expr" to "description".
biodb.DEBUG[2025-01-28 08:30:18.013][self$setPropertyValue] Setting property "parsing.expr" to "accession".
biodb.DEBUG[2025-01-28 08:30:18.013][self$setPropertyValue] Setting property "parsing.expr" to "formula".
biodb.DEBUG[2025-01-28 08:30:18.013][self$setPropertyValue] Setting property "parsing.expr" to "monoisotopic.mass".
biodb.DEBUG[2025-01-28 08:30:18.013][self$setPropertyValue] Setting property "parsing.expr" to "molecular.mass".
biodb.DEBUG[2025-01-28 08:30:18.013][self$setPropertyValue] Setting property "parsing.expr" to "kegg.compound.id".
biodb.DEBUG[2025-01-28 08:30:18.013][self$setPropertyValue] Setting property "parsing.expr" to "name".
biodb.DEBUG[2025-01-28 08:30:18.013][self$setPropertyValue] Setting property "parsing.expr" to "smiles".
biodb.DEBUG[2025-01-28 08:30:18.013][self$setPropertyValue] Setting property "parsing.expr" to "description".
biodb.DEBUG[2025-01-28 08:30:18.015][self$setPropertyValue] Setting property "parsing.expr" to "accession".
biodb.DEBUG[2025-01-28 08:30:18.015][self$setPropertyValue] Setting property "parsing.expr" to "formula".
biodb.DEBUG[2025-01-28 08:30:18.015][self$setPropertyValue] Setting property "parsing.expr" to "monoisotopic.mass".
biodb.DEBUG[2025-01-28 08:30:18.015][self$setPropertyValue] Setting property "parsing.expr" to "molecular.mass".
biodb.DEBUG[2025-01-28 08:30:18.015][self$setPropertyValue] Setting property "parsing.expr" to "kegg.compound.id".
biodb.DEBUG[2025-01-28 08:30:18.015][self$setPropertyValue] Setting property "parsing.expr" to "name".
biodb.DEBUG[2025-01-28 08:30:18.015][self$setPropertyValue] Setting property "parsing.expr" to "smiles".
biodb.DEBUG[2025-01-28 08:30:18.015][self$setPropertyValue] Setting property "parsing.expr" to "description".
biodb.DEBUG[2025-01-28 08:30:18.018][self$setPropertyValue] Setting property "parsing.expr" to "accession".
biodb.DEBUG[2025-01-28 08:30:18.018][self$setPropertyValue] Setting property "parsing.expr" to "formula".
biodb.DEBUG[2025-01-28 08:30:18.018][self$setPropertyValue] Setting property "parsing.expr" to "monoisotopic.mass".
biodb.DEBUG[2025-01-28 08:30:18.018][self$setPropertyValue] Setting property "parsing.expr" to "molecular.mass".
biodb.DEBUG[2025-01-28 08:30:18.018][self$setPropertyValue] Setting property "parsing.expr" to "kegg.compound.id".
biodb.DEBUG[2025-01-28 08:30:18.018][self$setPropertyValue] Setting property "parsing.expr" to "name".
biodb.DEBUG[2025-01-28 08:30:18.018][self$setPropertyValue] Setting property "parsing.expr" to "smiles".
biodb.DEBUG[2025-01-28 08:30:18.018][self$setPropertyValue] Setting property "parsing.expr" to "description".
biodb.TRACE[2025-01-28 08:30:18.020][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:30:18.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:30:18.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:18.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:18.028][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:30:18.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:30:18.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:18.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:18.034][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-28 08:30:18.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-28 08:30:18.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:18.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:18.043][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-28 08:30:18.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-28 08:30:18.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:18.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:18.071][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-28 08:30:18.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-28 08:30:18.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:18.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:18.091][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-28 08:30:18.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-28 08:30:18.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:18.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:18.106][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-28 08:30:18.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-28 08:30:18.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:18.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:18.122][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-28 08:30:18.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-28 08:30:18.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:18.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:18.144][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-28 08:30:18.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-28 08:30:18.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:18.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:18.168][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-28 08:30:18.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-28 08:30:18.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:18.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:18.186][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-28 08:30:18.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-28 08:30:18.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:18.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:18.201][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-28 08:30:18.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-28 08:30:18.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:18.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:18.217][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-28 08:30:18.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-28 08:30:18.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:18.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:18.226][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-28 08:30:18.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-28 08:30:18.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:18.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:18.232][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-28 08:30:18.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-28 08:30:18.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:18.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:18.239][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-28 08:30:18.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-28 08:30:18.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:18.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:18.245][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.csv.file.id.
biodb.TRACE[2025-01-28 08:30:18.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.csv.file.id.
biodb.TRACE[2025-01-28 08:30:18.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:18.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:18.252][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.csv.file.id.
biodb.TRACE[2025-01-28 08:30:18.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.csv.file.id.
biodb.TRACE[2025-01-28 08:30:18.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:18.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:18.259][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:30:18.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:30:18.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:18.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:18.265][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.csv.file.id.
biodb.TRACE[2025-01-28 08:30:18.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.csv.file.id.
biodb.TRACE[2025-01-28 08:30:18.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:18.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:18.271][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:30:18.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:30:18.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:18.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:18.278][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:30:18.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:30:18.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:18.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:18.284][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:30:18.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:30:18.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:18.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-28 08:30:18.290][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-28 08:30:18.291][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 08:30:18.293][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 08:30:18.294][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-28 08:30:18.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-28 08:30:18.300][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:30:18.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:30:18.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:18.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:18.307][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:30:18.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:30:18.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:18.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:18.314][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-28 08:30:18.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-28 08:30:18.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:18.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:18.320][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-28 08:30:18.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-28 08:30:18.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:18.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:18.327][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-28 08:30:18.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-28 08:30:18.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:18.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:18.333][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-28 08:30:18.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-28 08:30:18.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:18.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:18.340][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-28 08:30:18.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-28 08:30:18.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:18.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:18.346][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-28 08:30:18.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-28 08:30:18.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:18.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:18.353][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-28 08:30:18.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-28 08:30:18.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:18.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:18.359][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-28 08:30:18.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-28 08:30:18.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:18.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:18.366][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-28 08:30:18.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-28 08:30:18.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:18.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:18.372][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-28 08:30:18.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-28 08:30:18.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:18.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:18.379][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-28 08:30:18.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-28 08:30:18.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:18.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:18.385][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-28 08:30:18.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-28 08:30:18.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:18.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:18.391][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-28 08:30:18.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-28 08:30:18.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:18.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:18.398][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-28 08:30:18.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-28 08:30:18.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:18.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:18.404][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.csv.file.id.
biodb.TRACE[2025-01-28 08:30:18.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.csv.file.id.
biodb.TRACE[2025-01-28 08:30:18.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:18.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:18.410][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.csv.file.id.
biodb.TRACE[2025-01-28 08:30:18.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.csv.file.id.
biodb.TRACE[2025-01-28 08:30:18.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:18.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:18.416][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:30:18.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:30:18.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:18.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:18.423][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.csv.file.id.
biodb.TRACE[2025-01-28 08:30:18.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.csv.file.id.
biodb.TRACE[2025-01-28 08:30:18.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:18.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:18.429][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:30:18.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:30:18.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:18.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:18.435][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:30:18.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:30:18.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:18.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:18.442][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:30:18.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:30:18.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:18.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-28 08:30:18.448][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-28 08:30:18.449][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-28 08:30:18.451][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-28 08:30:18.452][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-28 08:30:18.454][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-28 08:30:18.459][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:30:18.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:30:18.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:18.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:18.465][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:30:18.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:30:18.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:18.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:18.471][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-28 08:30:18.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-28 08:30:18.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:18.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:18.478][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-28 08:30:18.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-28 08:30:18.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:18.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:18.485][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-28 08:30:18.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-28 08:30:18.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:18.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:18.491][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-28 08:30:18.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-28 08:30:18.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:18.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:18.497][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-28 08:30:18.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-28 08:30:18.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:18.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:18.504][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-28 08:30:18.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-28 08:30:18.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:18.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:18.510][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-28 08:30:18.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-28 08:30:18.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:18.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:18.517][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-28 08:30:18.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-28 08:30:18.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:18.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:18.523][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-28 08:30:18.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-28 08:30:18.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:18.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:18.529][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-28 08:30:18.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-28 08:30:18.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:18.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:18.535][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-28 08:30:18.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-28 08:30:18.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:18.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:18.542][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-28 08:30:18.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-28 08:30:18.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:18.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:18.548][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-28 08:30:18.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-28 08:30:18.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:18.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:18.554][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-28 08:30:18.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-28 08:30:18.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:18.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:18.560][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.csv.file.id.
biodb.TRACE[2025-01-28 08:30:18.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.csv.file.id.
biodb.TRACE[2025-01-28 08:30:18.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:18.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:18.567][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.csv.file.id.
biodb.TRACE[2025-01-28 08:30:18.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.csv.file.id.
biodb.TRACE[2025-01-28 08:30:18.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:18.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:18.573][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:30:18.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:30:18.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:18.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:18.579][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.csv.file.id.
biodb.TRACE[2025-01-28 08:30:18.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.csv.file.id.
biodb.TRACE[2025-01-28 08:30:18.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:18.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:18.585][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:30:18.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:30:18.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:18.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:18.591][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:30:18.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:30:18.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:30:18.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:30:18.597][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:30:18.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:31:25.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:31:25.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:31:25.259][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:31:25.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:31:25.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:31:25.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:31:25.269][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:31:25.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:31:25.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:31:25.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:31:25.284][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:31:25.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:31:25.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:31:25.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:31:25.294][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:31:25.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:31:25.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:31:25.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:31:25.301][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:31:25.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:31:25.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:31:25.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:31:25.307][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:31:25.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:31:25.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:31:25.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:31:25.313][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:31:25.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:31:25.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:31:25.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:31:25.320][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:31:25.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:31:25.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:31:25.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-28 08:31:25.326][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-28 08:31:25.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-28 08:31:25.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-28 08:31:25.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-28 08:31:25.332][self$createEntryFromContent] Accession numbers: 1018, 1390, 1456.
biodb.DEBUG[2025-01-28 08:39:55.724][cache$listFiles] Extracting accession number from file names associated with comp.csv.file-a49c5db9408932a2c8454375877bd673 using pattern ^(.*)\.tsv$
biodb.DEBUG[2025-01-28 08:39:55.727][cache$listFiles] files = 1018.tsv, 1390.tsv, 1456.tsv
biodb.INFO [2025-01-28 08:39:55.739][biodb::testThat]
biodb.INFO [2025-01-28 08:39:55.741][biodb::testThat] Running test function test_deleteFilesForWrongCacheId (" We got a warning if we try to delete files for a cache.id that has no associated folder. ").
biodb.INFO [2025-01-28 08:39:55.746][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-28 08:39:55.747][biodb::testThat]
biodb.WARN [2025-01-28 08:39:55.758][self$getFolderPath] No cache folder "/home/biocbuild/.cache/R/biodb/foo-1234567890abcdef01234" exists for "foo-1234567890abcdef01234".
biodb.INFO [2025-01-28 08:39:55.773][biodb::testThat]
biodb.INFO [2025-01-28 08:39:55.774][biodb::testThat] Running test function test_filesExistForConn (" We detect if cache files exist for a connector ").
biodb.INFO [2025-01-28 08:39:55.776][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-28 08:39:55.777][biodb::testThat]
biodb.Rcheck/biodb-Ex.timings
| name | user | system | elapsed | |
| BiodbConfig | 0.628 | 0.040 | 1.342 | |
| BiodbConn | 0.337 | 0.012 | 0.705 | |
| BiodbConnBase | 0.160 | 0.000 | 0.327 | |
| BiodbCsvEntry | 0.002 | 0.000 | 0.006 | |
| BiodbDbInfo | 0.153 | 0.001 | 0.304 | |
| BiodbDbsInfo | 0.156 | 0.000 | 0.317 | |
| BiodbEntry | 0.515 | 0.024 | 1.092 | |
| BiodbEntryField | 0.157 | 0.001 | 0.312 | |
| BiodbEntryFields | 0.156 | 0.000 | 0.315 | |
| BiodbFactory | 0.255 | 0.000 | 0.511 | |
| BiodbHtmlEntry | 0.001 | 0.000 | 0.000 | |
| BiodbJsonEntry | 0.001 | 0.000 | 0.001 | |
| BiodbListEntry | 0 | 0 | 0 | |
| BiodbMain | 0.153 | 0.004 | 0.320 | |
| BiodbPersistentCache | 0.613 | 0.000 | 1.226 | |
| BiodbRequest | 0.460 | 0.032 | 2.828 | |
| BiodbRequestScheduler | 0.253 | 0.029 | 1.874 | |
| BiodbSdfEntry | 0.001 | 0.000 | 0.000 | |
| BiodbTestMsgAck | 0.173 | 0.006 | 0.206 | |
| BiodbTxtEntry | 0.001 | 0.000 | 0.001 | |
| BiodbUrl | 0.002 | 0.000 | 0.002 | |
| BiodbXmlEntry | 0.001 | 0.000 | 0.001 | |
| CompCsvFileConn | 0.200 | 0.008 | 0.230 | |
| CompCsvFileEntry | 0.186 | 0.001 | 0.187 | |
| CompSqliteConn | 0.207 | 0.001 | 0.208 | |
| CompSqliteEntry | 0.234 | 0.011 | 0.348 | |
| CsvFileConn | 0.207 | 0.024 | 0.350 | |
| ExtConnClass | 0.177 | 0.000 | 0.302 | |
| ExtCpp | 0.041 | 0.004 | 0.097 | |
| ExtDefinitions | 0.028 | 0.000 | 0.057 | |
| ExtDescriptionFile | 0.013 | 0.000 | 0.028 | |
| ExtEntryClass | 0.018 | 0.001 | 0.036 | |
| ExtFileGenerator | 0.018 | 0.000 | 0.034 | |
| ExtGenerator | 0.273 | 0.021 | 0.589 | |
| ExtGitignore | 0.008 | 0.000 | 0.009 | |
| ExtLicense | 0.036 | 0.000 | 0.037 | |
| ExtMakefile | 0.019 | 0.000 | 0.027 | |
| ExtPackage | 0.251 | 0.016 | 0.268 | |
| ExtPackageFile | 0.008 | 0.000 | 0.008 | |
| ExtRbuildignore | 0.008 | 0.000 | 0.007 | |
| ExtReadme | 0.008 | 0.000 | 0.008 | |
| ExtTests | 0.072 | 0.007 | 0.081 | |
| ExtTravisFile | 0.010 | 0.000 | 0.011 | |
| ExtVignette | 0.01 | 0.00 | 0.01 | |
| MassCsvFileConn | 0.335 | 0.001 | 0.344 | |
| MassCsvFileEntry | 0.281 | 0.002 | 0.503 | |
| MassSqliteConn | 0.166 | 0.028 | 0.195 | |
| MassSqliteEntry | 0.188 | 0.011 | 0.357 | |
| Progress | 0.007 | 0.000 | 0.011 | |
| Range | 0.006 | 0.000 | 0.014 | |
| SqliteConn | 0.186 | 0.000 | 0.378 | |
| TestRefEntries | 0.024 | 0.000 | 0.046 | |
| checkDeprecatedCacheFolders | 0.000 | 0.000 | 0.001 | |
| createBiodbTestInstance | 0.150 | 0.000 | 0.299 | |
| df2str | 0.002 | 0.001 | 0.002 | |
| error | 0.003 | 0.000 | 0.002 | |
| error0 | 0.002 | 0.000 | 0.002 | |
| genNewExtPkg | 0.282 | 0.012 | 0.588 | |
| getConnClassName | 0.000 | 0.000 | 0.001 | |
| getConnTypes | 0 | 0 | 0 | |
| getDefaultCacheDir | 0.001 | 0.000 | 0.000 | |
| getEntryClassName | 0.000 | 0.000 | 0.001 | |
| getEntryTypes | 0.000 | 0.000 | 0.005 | |
| getLicenses | 0.000 | 0.000 | 0.001 | |
| getLogger | 0.014 | 0.000 | 0.026 | |
| getPkgName | 0 | 0 | 0 | |
| getReposName | 0.000 | 0.000 | 0.001 | |
| getTestOutputDir | 0 | 0 | 0 | |
| listTestRefEntries | 0.093 | 0.000 | 0.189 | |
| logDebug | 0.000 | 0.000 | 0.001 | |
| logDebug0 | 0 | 0 | 0 | |
| logInfo | 0.002 | 0.000 | 0.006 | |
| logInfo0 | 0.002 | 0.000 | 0.002 | |
| logTrace | 0.000 | 0.000 | 0.001 | |
| logTrace0 | 0.000 | 0.000 | 0.001 | |
| lst2str | 0 | 0 | 0 | |
| newInst | 0.217 | 0.004 | 0.341 | |
| runGenericTests | 0.172 | 0.000 | 0.355 | |
| testContext | 0.794 | 0.010 | 1.215 | |
| testThat | 0.350 | 0.006 | 0.712 | |
| upgradeExtPkg | 0.349 | 0.004 | 0.697 | |
| warn | 0.003 | 0.000 | 0.006 | |
| warn0 | 0.002 | 0.000 | 0.006 | |