mettre à jour les données des cirms

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

marked this issue as related to #66 (closed)

@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) :

taxa_index='17', strain_index='0', habitat_index='27,3,31,29,26'

pour CIRM BIA, seul le fichier change, les paramètres ne changent pas

created branch 71-mettre-a-jour-les-donnees-des-cirms to address this issue

mentioned in merge request !56 (merged)

assigned to @mandiayba

probléme avec les alias,

[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)
```

@robert.bossy l'erreur precedente est liée au param taxaDict de TabularProjector. Je n'ai vu ce param dans la doc, tu l'as ajouté récemment ?

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"/>

mentioned in commit 3f474f87

closed with merge request !56 (merged)

reopened

closed

reopened

closed