Il faudra bien prendre en compte les dernières données des CIRM (BIA et CFBP a minima ; peut-être Levures si on a des nouvelles de Michel-Yves d'ici là).
données dans /save_projet/omnicrobe_data/CIRM/*/2022
@Ba Pour les CIRM CFBP, il faudra mettre les paramètres suivants dans les règles get_cirm_cfbp_taxa_habitats et format_cirm_cfbp_results (snakefile process_CIRM_corpus) :
[2022-04-11 16:05:15.814][alvisnlp] loading plan from plans/map_microorganisms.plan[2022-04-11 16:05:15.829][alvisnlp] loading plan from /work_projet/omnicrobe_data/tm_workflow/text-mining-workflow/plans/taxa.plan[2022-04-11 16:05:15.866][alvisnlp] loading plan from /work_projet/omnicrobe_data/tm_workflow/text-mining-workflow/plans/strains-1.plan[2022-04-11 16:05:15.872][alvisnlp] finished loading /work_projet/omnicrobe_data/tm_workflow/text-mining-workflow/plans/strains-1.plan[2022-04-11 16:05:15.872][alvisnlp] finished loading /work_projet/omnicrobe_data/tm_workflow/text-mining-workflow/plans/taxa.plan[2022-04-11 16:05:15.873][alvisnlp] loading plan from /work_projet/omnicrobe_data/tm_workflow/text-mining-workflow/plans/syntax.plan[2022-04-11 16:05:15.876][alvisnlp] loading plan from /work_projet/omnicrobe_data/tm_workflow/text-mining-workflow/plans/segmentation.plan[2022-04-11 16:05:15.880][alvisnlp] loading plan from fr/inra/maiage/bibliome/alvisnlp/bibliomefactory/resources/number-and-dates.plan[2022-04-11 16:05:15.885][alvisnlp] finished loading fr/inra/maiage/bibliome/alvisnlp/bibliomefactory/resources/number-and-dates.plan[2022-04-11 16:05:15.894][alvisnlp] finished loading /work_projet/omnicrobe_data/tm_workflow/text-mining-workflow/plans/segmentation.plan[2022-04-11 16:05:15.898][alvisnlp] finished loading /work_projet/omnicrobe_data/tm_workflow/text-mining-workflow/plans/syntax.plan[2022-04-11 16:05:15.899][alvisnlp] loading plan from /work_projet/omnicrobe_data/tm_workflow/text-mining-workflow/plans/strains-2.plan[2022-04-11 16:05:15.922][alvisnlp] finished loading /work_projet/omnicrobe_data/tm_workflow/text-mining-workflow/plans/strains-2.plan[2022-04-11 16:05:15.928][alvisnlp] SEVERE unrecoverable error### error type:### fr.inra.maiage.bibliome.alvisnlp.core.module.UnexpectedParameterException###### error message:### parameter taxaDict is not recognized by map-microorganisms.taxa.dict###### stack trace:### fr.inra.maiage.bibliome.alvisnlp.core.module.lib.ModuleBase.getParamHandler(ModuleBase.java:186)### fr.inra.maiage.bibliome.alvisnlp.core.module.Sequence$CompositeParamHandler.addParamHandler(Sequence.java:127)### fr.inra.maiage.bibliome.alvisnlp.core.plan.PlanLoader.setAliasParam(PlanLoader.java:416)### fr.inra.maiage.bibliome.alvisnlp.core.plan.PlanLoader.loadSequence(PlanLoader.java:400)### fr.inra.maiage.bibliome.alvisnlp.core.plan.PlanLoader.loadDocument(PlanLoader.java:247)### fr.inra.maiage.bibliome.alvisnlp.core.app.cli.AbstractAlvisNLP.buildMainModule(AbstractAlvisNLP.java:974)### fr.inra.maiage.bibliome.alvisnlp.core.app.cli.AbstractAlvisNLP.process(AbstractAlvisNLP.java:1106)### fr.inra.maiage.bibliome.alvisnlp.core.app.cli.AbstractAlvisNLP.run(AbstractAlvisNLP.java:1221)### fr.inra.maiage.bibliome.alvisnlp.core.app.cli.AlvisNLP.main(AlvisNLP.java:85)```
problème semble lié au passage de param entre plans, ça passe si je remplace <alias module="taxa.dict" param="taxaDict"/> par <alias module="taxa" param="taxaDict"/>