search

agroportal / project-management

Repository used to consolidate documentation about the AgroPortal project and track content related issues.
http://agroportal.lirmm.fr
7 stars 0 forks source link

CO_359 can't parse #203

Closed syphax-bouazzouni closed 2 years ago

syphax-bouazzouni commented 2 years ago

Try to parse

[ontoportal@agroportal 20220124143731]$ bin/ncbo_ontology_process -o CO_359

Result

It worked 

I, [2022-02-04T17:55:46.836230 #1189]  INFO -- : Logging parsing output to /srv/ontoportal/data/repository/CO_359/10/parsing.log
I, [2022-02-04T17:55:46.836365 #1189]  INFO -- : ["Starting to process http://data.bioontology.org/ontologies/CO_359/submissions/10"]
I, [2022-02-04T17:55:46.895219 #1189]  INFO -- : ["Starting to process CO_359/submissions/10"]
I, [2022-02-04T17:55:47.027974 #1189]  INFO -- : ["deleting old owlapi.xrdf .."]
I, [2022-02-04T17:55:47.030397 #1189]  INFO -- : ["deleted"]
I, [2022-02-04T17:55:47.045510 #1189]  INFO -- : ["Java call [java -DentityExpansionLimit=2500000 -Xmx10240M -jar /srv/ontoportal/ncbo_cron_deployments/shared/bundle/ruby/2.6.0/bundler/gems/ontologies_linked_data-db2377e860d7/bin/owlapi-wrapper.jar -m /srv/ontoportal/data/repository/CO_359/10/owl -o /srv/ontoportal/data/repository/CO_359/10 -r true]"]
I, [2022-02-04T17:55:48.996297 #1189]  INFO -- : ["2022-02-04T17:55:47 [main] INFO  o.s.n.o.OntologyParserCommand - Parsing invocation with values: ParserInvocation [inputRepositoryFolder=null, outputRepositoryFolder=/srv/ontoportal/data/repository/CO_359/10, masterFileName=/srv/ontoportal/data/repository/CO_359/10/owl, invocationId=0, parserLog=, userReasoner= true]\n\n2022-02-04T17:55:47 [main] INFO  o.s.ncbo.oapiwrapper.OntologyParser - executor ...\n\n2022-02-04T17:55:47 [main] INFO  o.s.ncbo.oapiwrapper.OntologyParser - Input repository folder is null. Unique file being parsed.\n\n2022-02-04T17:55:48 [main] INFO  o.s.ncbo.oapiwrapper.OntologyMetrics - Calculating metrics for /srv/ontoportal/data/repository/CO_359/10/owl\n\n2022-02-04T17:55:48 [main] INFO  o.s.ncbo.oapiwrapper.OntologyMetrics - Finished metrics calculation for /srv/ontoportal/data/repository/CO_359/10/owl in 2 milliseconds\n\n2022-02-04T17:55:48 [main] INFO  o.s.ncbo.oapiwrapper.OntologyMetrics - Generated metrics CSV file for /srv/ontoportal/data/repository/CO_359/10/owl\n\n2022-02-04T17:55:48 [main] INFO  o.s.ncbo.oapiwrapper.OntologyParser - Ontology document format: org.semanticweb.owlapi.formats.RDFXMLDocumentFormat\n\n2022-02-04T17:55:48 [main] INFO  o.s.ncbo.oapiwrapper.OntologyParser - isPrefixOWLOntologyFormat: true\n\n2022-02-04T17:55:48 [main] INFO  o.s.ncbo.oapiwrapper.OntologyParser - isOBO: false\n\n2022-02-04T17:55:48 [main] INFO  o.s.ncbo.oapiwrapper.OntologyParser - Serializing ontology in RDF ...\n\n2022-02-04T17:55:48 [main] INFO  o.s.ncbo.oapiwrapper.OntologyParser - Serialization done!\n\n2022-02-04T17:55:48 [main] INFO  o.s.n.o.OntologyParserCommand - Parse result: true\n\n2022-02-04T17:55:48 [main] INFO  o.s.n.o.OntologyParserCommand - Output triples in: {}/srv/ontoportal/data/repository/CO_359/10/owlapi.xrdf\n\n2022-02-04T17:55:48 [main] INFO  o.s.n.o.OntologyParserCommand - Finished parsing!\n"]
I, [2022-02-04T17:55:48.996544 #1189]  INFO -- : ["OWLAPI Java command: parsing finished successfully."]
....
I, [2022-02-04T18:13:03.531571 #1189]  INFO -- : Lemmatized dictionary generated successfully!
D, [2022-02-04T18:13:03.770413 #1189] DEBUG -- : ["Completed processing of http://data.bioontology.org/ontologies/CO_359/submissions/10 in 1037.61s"]
I, [2022-02-04T18:13:03.797235 #1189]  INFO -- : ["Running ontologies report for ontologies CO_359...\n"]
I, [2022-02-04T18:13:03.797421 #1189]  INFO -- : ["Processing report for CO_359 - 1 of 1 ontologies."]
I, [2022-02-04T18:13:07.039866 #1189]  INFO -- : ["Finished report for CO_359 in 3.242177540436387 sec."]
I, [2022-02-04T18:13:07.044874 #1189]  INFO -- : ["Finished updating report for ontologies