erreur avec une entrée de yatea durant le CI
Une erreur liée à un fichier d'entrée de yatea (/usr/local/share/perl5/Lingua/YaTeA/TestifiedTermSet.pm
).
alvisnlp -J-Xmx8g -cleanTmp -verbose -alias input ancillaries/BioNLP-OST+EnovFood-Phenotype.obo -alias output ancillaries/BioNLP-OST+EnovFood-Phenotype.tomap plans/phenotype_ontology_analyzer.plan'
Activating singularity image softwares/alvisnlp.sif
[2022-07-25 12:52:14.457][alvisnlp] build version: 0.7.0
[2022-07-25 12:52:14.461][alvisnlp] tag: 0.7.1 +0
[2022-07-25 12:52:14.461][alvisnlp] commit id: a3bf34d6e0c20a2e73c92cb272e53660c6d735f7
[2022-07-25 12:52:14.465][alvisnlp] commit time: Mon May 18 15:01:37 UTC 2020
[2022-07-25 12:52:14.466][alvisnlp] branch: a3bf34d6e0c20a2e73c92cb272e53660c6d735f7
[2022-07-25 12:52:14.466][alvisnlp] build host: runner-b5ef1728-project-1344-concurrent-0
[2022-07-25 12:52:14.466][alvisnlp] build time: Tue Jun 02 12:30:41 UTC 2020
[2022-07-25 12:52:14.469][alvisnlp] host: runner-lzguszxt-project-6407-concurrent-0
[2022-07-25 12:52:14.469][alvisnlp] class path: /alvisnlp/lib/*:
[2022-07-25 12:52:14.469][alvisnlp] java version: 1.8.0_252
[2022-07-25 12:52:14.532][alvisnlp] loading plan from plans/phenotype_ontology_analyzer.plan
[2022-07-25 12:52:14.605][alvisnlp] finished loading plans/phenotype_ontology_analyzer.plan
[2022-07-25 12:52:14.606][alvisnlp] setting input to 'ancillaries/BioNLP-OST+EnovFood-Phenotype.obo' in ontology-analyzer
[2022-07-25 12:52:14.607][alvisnlp] setting output to 'ancillaries/BioNLP-OST+EnovFood-Phenotype.tomap' in ontology-analyzer
[2022-07-25 12:52:14.620][alvisnlp] External resources
[2022-07-25 12:52:14.622][ontology-analyzer.genia] R: geniaDir = /alvisnlp/externalSoftDir/geniatagger-3.0.2
[2022-07-25 12:52:14.622][ontology-analyzer.genia] R: geniaTaggerExecutable = /builds/migale/text-mining-workflow/./geniatagger
[2022-07-25 12:52:14.623][ontology-analyzer.analyze] R: configDir = /builds/migale/text-mining-workflow/ancillaries/YaTeA/config-habitats
[2022-07-25 12:52:14.624][ontology-analyzer.analyze] R: localeDir = /builds/migale/text-mining-workflow/ancillaries/YaTeA/locale
[2022-07-25 12:52:14.624][ontology-analyzer.analyze] R: outFile = ancillaries/BioNLP-OST+EnovFood-Phenotype.tomap
[2022-07-25 12:52:14.624][ontology-analyzer.analyze] R: rcFile = ancillaries/YaTeA/yatea.rc
[2022-07-25 12:52:14.624][ontology-analyzer.analyze] R: workingDir = /builds/migale/text-mining-workflow/yatea-train
[2022-07-25 12:52:14.624][ontology-analyzer.analyze] R: yateaExecutable = /usr/local/bin/yatea
[2022-07-25 12:52:14.727][ontology-analyzer.analyze] WARNING this module is EXPERIMENTAL
[2022-07-25 12:52:14.730][ontology-analyzer.analyze] SEVERE workingDir is deprecated, use xmlTermsFile and termListFile to specify yatea output file
[2022-07-25 12:52:14.731][ontology-analyzer.analyze] SEVERE future versions may not support workingDir
[2022-07-25 12:52:14.749][alvisnlp] temporary directory: /tmp/alvisnlp8159763568214661014
[2022-07-25 12:52:14.754][alvisnlp] usage for section names
[2022-07-25 12:52:14.754][alvisnlp] section name: ontology-analyzer.read-obo
[2022-07-25 12:52:14.754][alvisnlp] WARNING section name used only once by ontology-analyzer.read-obo
[2022-07-25 12:52:14.754][alvisnlp] section synonym: ontology-analyzer.read-obo
[2022-07-25 12:52:14.754][alvisnlp] WARNING section synonym used only once by ontology-analyzer.read-obo
[2022-07-25 12:52:14.754][alvisnlp] section syno: ontology-analyzer.add-synonyms, ontology-analyzer.add-synonyms2, ontology-analyzer.add-synonyms3
[2022-07-25 12:52:14.754][alvisnlp] usage for layer names
[2022-07-25 12:52:14.754][alvisnlp] layer words: ontology-analyzer.words, ontology-analyzer.sentences, ontology-analyzer.words2, ontology-analyzer.sentences2, ontology-analyzer.genia, ontology-analyzer.adapt-hyphens, ontology-analyzer.adapt-affix, ontology-analyzer.POS-tag-correction-1, ontology-analyzer.POS-tag-correction, ontology-analyzer.lemma-correction, ontology-analyzer.lemma-correction-2, ontology-analyzer.specific-POS-tag-correction, ontology-analyzer.POS-tag-correction2-1, ontology-analyzer.POS-tag-correction2, ontology-analyzer.POS-tag-correction2-2, ontology-analyzer.POS-tag-correction5-1, ontology-analyzer.POS-tag-correction5-2, ontology-analyzer.POS-tag-correction3-1, ontology-analyzer.POS-tag-correction3, ontology-analyzer.POS-tag-correction4, ontology-analyzer.analyze
[2022-07-25 12:52:14.755][alvisnlp] layer sentences: ontology-analyzer.sentences, ontology-analyzer.add-synonyms, ontology-analyzer.add-synonyms2, ontology-analyzer.add-synonyms3, ontology-analyzer.sentences2, ontology-analyzer.genia, ontology-analyzer.POS-tag-correction2, ontology-analyzer.POS-tag-correction5-2, ontology-analyzer.analyze
[2022-07-25 12:52:14.755][alvisnlp] no usage for relation names
[2022-07-25 12:52:14.755][alvisnlp] no usage for argument names
[2022-07-25 12:52:14.755][alvisnlp] usage for feature names
[2022-07-25 12:52:14.755][alvisnlp] feature is_a: ontology-analyzer.read-obo
[2022-07-25 12:52:14.755][alvisnlp] WARNING feature is_a used only once by ontology-analyzer.read-obo
[2022-07-25 12:52:14.755][alvisnlp] feature path: ontology-analyzer.read-obo
[2022-07-25 12:52:14.759][alvisnlp] WARNING feature path used only once by ontology-analyzer.read-obo
[2022-07-25 12:52:14.759][alvisnlp] feature wordType: ontology-analyzer.words, ontology-analyzer.sentences, ontology-analyzer.words2, ontology-analyzer.sentences2
[2022-07-25 12:52:14.759][alvisnlp] feature eos: ontology-analyzer.sentences, ontology-analyzer.sentences2
[2022-07-25 12:52:14.759][alvisnlp] feature syno: ontology-analyzer.add-synonyms, ontology-analyzer.add-synonyms2, ontology-analyzer.add-synonyms3, ontology-analyzer.words2, ontology-analyzer.sentences2
[2022-07-25 12:52:14.759][alvisnlp] feature lemma: ontology-analyzer.genia, ontology-analyzer.POS-tag-correction-1, ontology-analyzer.lemma-correction, ontology-analyzer.lemma-correction-2, ontology-analyzer.POS-tag-correction2-1, ontology-analyzer.POS-tag-correction5-1, ontology-analyzer.POS-tag-correction3-1, ontology-analyzer.analyze
[2022-07-25 12:52:14.759][alvisnlp] feature pos: ontology-analyzer.genia, ontology-analyzer.adapt-hyphens, ontology-analyzer.adapt-affix, ontology-analyzer.POS-tag-correction-1, ontology-analyzer.POS-tag-correction, ontology-analyzer.lemma-correction, ontology-analyzer.lemma-correction-2, ontology-analyzer.specific-POS-tag-correction, ontology-analyzer.POS-tag-correction2-1, ontology-analyzer.POS-tag-correction2, ontology-analyzer.POS-tag-correction2-2, ontology-analyzer.POS-tag-correction5-1, ontology-analyzer.POS-tag-correction5-2, ontology-analyzer.POS-tag-correction3-1, ontology-analyzer.POS-tag-correction3, ontology-analyzer.POS-tag-correction4, ontology-analyzer.analyze
[2022-07-25 12:52:14.760][alvisnlp] start
[2022-07-25 12:52:14.761][ontology-analyzer] processing
[2022-07-25 12:52:14.762][ontology-analyzer.read-obo] processing
[2022-07-25 12:52:14.830][ontology-analyzer.read-obo] done in 67 ms
[2022-07-25 12:52:14.830][ontology-analyzer.words] processing
[2022-07-25 12:52:14.832][ontology-analyzer.words] created 0 word annotations
[2022-07-25 12:52:14.832][ontology-analyzer.words] done in 1 ms
[2022-07-25 12:52:14.832][ontology-analyzer.sentences] processing
[2022-07-25 12:52:14.832][ontology-analyzer.sentences] created 0 sentence annotations
[2022-07-25 12:52:14.832][ontology-analyzer.sentences] done in 0 ms
[2022-07-25 12:52:14.833][ontology-analyzer.add-synonyms] processing
[2022-07-25 12:52:14.841][ontology-analyzer.add-synonyms] WARNING no targets visited
[2022-07-25 12:52:14.841][ontology-analyzer.add-synonyms] done in 8 ms
[2022-07-25 12:52:14.841][ontology-analyzer.add-synonyms2] processing
[2022-07-25 12:52:14.842][ontology-analyzer.add-synonyms2] WARNING no targets visited
[2022-07-25 12:52:14.842][ontology-analyzer.add-synonyms2] done in 1 ms
[2022-07-25 12:52:14.843][ontology-analyzer.add-synonyms3] processing
[2022-07-25 12:52:14.844][ontology-analyzer.add-synonyms3] WARNING no targets visited
[2022-07-25 12:52:14.844][ontology-analyzer.add-synonyms3] done in 1 ms
[2022-07-25 12:52:14.844][ontology-analyzer.words2] processing
[2022-07-25 12:52:14.844][ontology-analyzer.words2] created 0 word annotations
[2022-07-25 12:52:14.844][ontology-analyzer.words2] done in 0 ms
[2022-07-25 12:52:14.844][ontology-analyzer.sentences2] processing
[2022-07-25 12:52:14.844][ontology-analyzer.sentences2] created 0 sentence annotations
[2022-07-25 12:52:14.844][ontology-analyzer.sentences2] done in 0 ms
[2022-07-25 12:52:14.844][ontology-analyzer.genia] processing
[2022-07-25 12:52:14.845][ontology-analyzer.genia] alvisnlp-to-genia
[2022-07-25 12:52:14.846][ontology-analyzer.genia] genia (stderr)
[2022-07-25 12:52:15.122][ontology-analyzer.genia] loading morphdic...done.
[2022-07-25 12:52:19.143][ontology-analyzer.genia] loading pos_models................done.
[2022-07-25 12:52:20.025][ontology-analyzer.genia] loading chunk_models....done.
[2022-07-25 12:52:21.338][ontology-analyzer.genia] loading named_entity_models..done.
[2022-07-25 12:52:22.218][ontology-analyzer.genia] genia-to-alvisnlp
[2022-07-25 12:52:22.220][ontology-analyzer.genia] done in 7375 ms
[2022-07-25 12:52:22.220][ontology-analyzer.adapt-hyphens] processing
[2022-07-25 12:52:22.224][ontology-analyzer.adapt-hyphens] WARNING no targets visited
[2022-07-25 12:52:22.224][ontology-analyzer.adapt-hyphens] done in 3 ms
[2022-07-25 12:52:22.225][ontology-analyzer.adapt-affix] processing
[2022-07-25 12:52:22.227][ontology-analyzer.adapt-affix] WARNING no targets visited
[2022-07-25 12:52:22.227][ontology-analyzer.adapt-affix] done in 1 ms
[2022-07-25 12:52:22.227][ontology-analyzer.POS-tag-correction-1] processing
[2022-07-25 12:52:22.229][ontology-analyzer.POS-tag-correction-1] WARNING no targets visited
[2022-07-25 12:52:22.229][ontology-analyzer.POS-tag-correction-1] done in 1 ms
[2022-07-25 12:52:22.229][ontology-analyzer.POS-tag-correction] processing
[2022-07-25 12:52:22.231][ontology-analyzer.POS-tag-correction] WARNING no targets visited
[2022-07-25 12:52:22.231][ontology-analyzer.POS-tag-correction] done in 1 ms
[2022-07-25 12:52:22.232][ontology-analyzer.lemma-correction] processing
[2022-07-25 12:52:22.233][ontology-analyzer.lemma-correction] WARNING no targets visited
[2022-07-25 12:52:22.234][ontology-analyzer.lemma-correction] done in 1 ms
[2022-07-25 12:52:22.234][ontology-analyzer.lemma-correction-2] processing
[2022-07-25 12:52:22.235][ontology-analyzer.lemma-correction-2] WARNING no targets visited
[2022-07-25 12:52:22.235][ontology-analyzer.lemma-correction-2] done in 1 ms
[2022-07-25 12:52:22.235][ontology-analyzer.specific-POS-tag-correction] processing
[2022-07-25 12:52:22.236][ontology-analyzer.specific-POS-tag-correction] WARNING no targets visited
[2022-07-25 12:52:22.236][ontology-analyzer.specific-POS-tag-correction] done in 1 ms
[2022-07-25 12:52:22.237][ontology-analyzer.POS-tag-correction2-1] processing
[2022-07-25 12:52:22.238][ontology-analyzer.POS-tag-correction2-1] WARNING no targets visited
[2022-07-25 12:52:22.238][ontology-analyzer.POS-tag-correction2-1] done in 1 ms
[2022-07-25 12:52:22.238][ontology-analyzer.POS-tag-correction2] processing
[2022-07-25 12:52:22.239][ontology-analyzer.POS-tag-correction2] WARNING no targets visited
[2022-07-25 12:52:22.239][ontology-analyzer.POS-tag-correction2] done in 0 ms
[2022-07-25 12:52:22.239][ontology-analyzer.POS-tag-correction2-2] processing
[2022-07-25 12:52:22.240][ontology-analyzer.POS-tag-correction2-2] WARNING no targets visited
[2022-07-25 12:52:22.240][ontology-analyzer.POS-tag-correction2-2] done in 1 ms
[2022-07-25 12:52:22.240][ontology-analyzer.POS-tag-correction5-1] processing
[2022-07-25 12:52:22.241][ontology-analyzer.POS-tag-correction5-1] WARNING no targets visited
[2022-07-25 12:52:22.242][ontology-analyzer.POS-tag-correction5-1] done in 1 ms
[2022-07-25 12:52:22.242][ontology-analyzer.POS-tag-correction5-2] processing
[2022-07-25 12:52:22.243][ontology-analyzer.POS-tag-correction5-2] WARNING no targets visited
[2022-07-25 12:52:22.243][ontology-analyzer.POS-tag-correction5-2] done in 0 ms
[2022-07-25 12:52:22.243][ontology-analyzer.POS-tag-correction3-1] processing
[2022-07-25 12:52:22.244][ontology-analyzer.POS-tag-correction3-1] WARNING no targets visited
[2022-07-25 12:52:22.244][ontology-analyzer.POS-tag-correction3-1] done in 1 ms
[2022-07-25 12:52:22.244][ontology-analyzer.POS-tag-correction3] processing
[2022-07-25 12:52:22.245][ontology-analyzer.POS-tag-correction3] WARNING no targets visited
[2022-07-25 12:52:22.245][ontology-analyzer.POS-tag-correction3] done in 1 ms
[2022-07-25 12:52:22.245][ontology-analyzer.POS-tag-correction4] processing
[2022-07-25 12:52:22.246][ontology-analyzer.POS-tag-correction4] WARNING no targets visited
[2022-07-25 12:52:22.246][ontology-analyzer.POS-tag-correction4] done in 0 ms
[2022-07-25 12:52:22.246][ontology-analyzer.analyze] processing
[2022-07-25 12:52:22.248][ontology-analyzer.analyze] create-input
[2022-07-25 12:52:22.260][ontology-analyzer.analyze] owner.getOutputDir() = null
[2022-07-25 12:52:22.260][ontology-analyzer.analyze] options = {monolexical-included=0, TT-for-BioLG=0, debug=1, printChunking=0, output-path=., match-type=, monolexical-all=1, termino=/tmp/alvisnlp8159763568214661014/ontology-analyzer/analyze/corpus.ttg, termList=multi, language=EN, TC-for-BioLG=0, xmlout=1, MESSAGE_DISPLAY=EN, XML-corpus-for-BioLG=0, TTG-style-term-candidates=multi, suffix=default, annotate-only=0}
[2022-07-25 12:52:22.260][ontology-analyzer.analyze] defaultConfig = {LOCALE_DIR=/builds/migale/text-mining-workflow/ancillaries/YaTeA/locale, CONFIG_DIR=/builds/migale/text-mining-workflow/ancillaries/YaTeA/config-habitats, RESULT_DIR=$PWD/RESULTS}
[2022-07-25 12:52:22.261][ontology-analyzer.analyze] yatea (stderr and stdout)
[2022-07-25 12:52:22.348][ontology-analyzer.analyze] perl: warning: Setting locale failed.
[2022-07-25 12:52:22.349][ontology-analyzer.analyze] perl: warning: Please check that your locale settings:
[2022-07-25 12:52:22.349][ontology-analyzer.analyze] LANGUAGE = (unset),
[2022-07-25 12:52:22.349][ontology-analyzer.analyze] LC_ALL = (unset),
[2022-07-25 12:52:22.349][ontology-analyzer.analyze] LC_CTYPE = "C.UTF-8",
[2022-07-25 12:52:22.349][ontology-analyzer.analyze] LANG = (unset)
[2022-07-25 12:52:22.349][ontology-analyzer.analyze] are supported and installed on your system.
[2022-07-25 12:52:22.349][ontology-analyzer.analyze] perl: warning: Falling back to the standard locale ("C").
[2022-07-25 12:52:22.567][ontology-analyzer.analyze]
[2022-07-25 12:52:22.567][ontology-analyzer.analyze]
[2022-07-25 12:52:22.567][ontology-analyzer.analyze]
[2022-07-25 12:52:22.567][ontology-analyzer.analyze]
[2022-07-25 12:52:22.567][ontology-analyzer.analyze] # # # ######### ####### #
[2022-07-25 12:52:22.567][ontology-analyzer.analyze] # # # # # # # #
[2022-07-25 12:52:22.567][ontology-analyzer.analyze] # # # # # # # #
[2022-07-25 12:52:22.567][ontology-analyzer.analyze] # # # # ##### # #
[2022-07-25 12:52:22.567][ontology-analyzer.analyze] # ####### # # #######
[2022-07-25 12:52:22.568][ontology-analyzer.analyze] # # # # # # #
[2022-07-25 12:52:22.568][ontology-analyzer.analyze] # # # # ####### # #
[2022-07-25 12:52:22.568][ontology-analyzer.analyze]
[2022-07-25 12:52:22.568][ontology-analyzer.analyze]
[2022-07-25 12:52:22.568][ontology-analyzer.analyze] Data will be loaded from: /builds/migale/text-mining-workflow/ancillaries/YaTeA/config-habitats/EN
[2022-07-25 12:52:22.575][ontology-analyzer.analyze] Data will be loaded from: /builds/migale/text-mining-workflow/ancillaries/YaTeA/locale/
[2022-07-25 12:52:22.630][ontology-analyzer.analyze] This repository is created: ./corpus/default/
[2022-07-25 12:52:22.630][ontology-analyzer.analyze]
[2022-07-25 12:52:22.631][ontology-analyzer.analyze] 1) Loading testified terms from
[2022-07-25 12:52:22.631][ontology-analyzer.analyze] check /tmp/alvisnlp8159763568214661014/ontology-analyzer/analyze/corpus.ttg
[2022-07-25 12:52:22.631][ontology-analyzer.analyze] undefined terminology input format at /usr/local/share/perl5/Lingua/YaTeA/TestifiedTermSet.pm line 65.
[2022-07-25 12:52:22.634][alvisnlp] SEVERE unrecoverable error
### error type:
### fr.inra.maiage.bibliome.alvisnlp.core.module.ProcessingException
###
### error message:
### external program returned 255
###
### stack trace:
### fr.inra.maiage.bibliome.alvisnlp.core.module.lib.ExternalHandler.doExec(ExternalHandler.java:129)
### fr.inra.maiage.bibliome.alvisnlp.core.module.lib.ExternalHandler.start(ExternalHandler.java:98)
### fr.inra.maiage.bibliome.alvisnlp.core.module.lib.ExternalHandler.start(ExternalHandler.java:105)
### fr.inra.maiage.bibliome.alvisnlp.bibliomefactory.modules.tomap.TomapTrain.process(TomapTrain.java:104)
### fr.inra.maiage.bibliome.alvisnlp.bibliomefactory.modules.tomap.TomapTrain.process(TomapTrain.java:69)
### fr.inra.maiage.bibliome.alvisnlp.core.app.cli.CommandLineProcessingContext.processCorpus(CommandLineProcessingContext.java:128)
### fr.inra.maiage.bibliome.alvisnlp.bibliomefactory.modules.Sequence_Impl.process(Sequence_Impl.java:112)
### fr.inra.maiage.bibliome.alvisnlp.bibliomefactory.modules.Sequence_Impl.process(Sequence_Impl.java:45)
### fr.inra.maiage.bibliome.alvisnlp.core.app.cli.CommandLineProcessingContext.processCorpus(CommandLineProcessingContext.java:128)
### fr.inra.maiage.bibliome.alvisnlp.core.app.cli.AbstractAlvisNLP.process(AbstractAlvisNLP.java:1100)
### fr.inra.maiage.bibliome.alvisnlp.core.app.cli.AbstractAlvisNLP.run(AbstractAlvisNLP.java:1207)
### fr.inra.maiage.bibliome.alvisnlp.core.app.cli.AlvisNLP.main(AlvisNLP.java:85)