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agroportal / project-management

Repository used to consolidate documentation about the AgroPortal project and track content related issues.
http://agroportal.lirmm.fr
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CO_336 can't parse #201

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_336

Result

fatal: Not a git repository (or any of the parent directories): .git
(LD) >> Using rdf store localhost:8081
(LD) >> Using term search server at http://localhost:8983/solr/term_search_core1
(LD) >> Using property search server at http://localhost:8983/solr/prop_search_core1
(LD) >> Using HTTP Redis instance at localhost:6380
(LD) >> Using Goo Redis instance at localhost:6381
DEPRECATION: Rsolr.new/connect option `read_timeout` is deprecated and will be removed in Rsolr 3. `timeout` is currently a synonym, use that instead.
DEPRECATION: Rsolr.new/connect option `read_timeout` is deprecated and will be removed in Rsolr 3. `timeout` is currently a synonym, use that instead.
fatal: Not a git repository (or any of the parent directories): .git
(AN) >> Using ANN Redis instance at localhost:6379
(CR) >> Using Redis instance at localhost:6379
Processing the following tasks: {:process_rdf=>true, :index_search=>true, :index_properties=>true, :run_metrics=>true, :process_annotator=>true, :diff=>true, :params=>nil} on ontologies: ["CO_336"]
Processing details are logged to STDOUT
I, [2022-02-04T17:54:45.598393 #897]  INFO -- : Logging parsing output to /srv/ontoportal/data/repository/CO_336/12/parsing.log
I, [2022-02-04T17:54:45.598538 #897]  INFO -- : ["Starting to process http://data.bioontology.org/ontologies/CO_336/submissions/12"]
I, [2022-02-04T17:54:45.703391 #897]  INFO -- : ["Starting to process CO_336/submissions/12"]
I, [2022-02-04T17:54:46.034515 #897]  INFO -- : ["deleting old owlapi.xrdf .."]
I, [2022-02-04T17:54:46.034955 #897]  INFO -- : ["deleted"]
I, [2022-02-04T17:54:46.046364 #897]  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_336/12/nt -o /srv/ontoportal/data/repository/CO_336/12 -r true]"]
I, [2022-02-04T17:54:47.395268 #897]  INFO -- : ["2022-02-04T17:54:46 [main] INFO  o.s.n.o.OntologyParserCommand - Parsing invocation with values: ParserInvocation [inputRepositoryFolder=null, outputRepositoryFolder=/srv/ontoportal/data/repository/CO_336/12, masterFileName=/srv/ontoportal/data/repository/CO_336/12/nt, invocationId=0, parserLog=, userReasoner= true]\n\n2022-02-04T17:54:46 [main] INFO  o.s.ncbo.oapiwrapper.OntologyParser - executor ...\n\n2022-02-04T17:54:46 [main] INFO  o.s.ncbo.oapiwrapper.OntologyParser - Input repository folder is null. Unique file being parsed.\n\n2022-02-04T17:54:47 [main] DEBUG o.e.rdf4j.rio.RDFParserRegistry - Registered service class org.eclipse.rdf4j.rio.binary.BinaryRDFParserFactory\n\n2022-02-04T17:54:47 [main] DEBUG o.e.rdf4j.rio.RDFParserRegistry - Registered service class org.eclipse.rdf4j.rio.n3.N3ParserFactory\n\n2022-02-04T17:54:47 [main] DEBUG o.e.rdf4j.rio.RDFParserRegistry - Registered service class org.eclipse.rdf4j.rio.nquads.NQuadsParserFactory\n\n2022-02-04T17:54:47 [main] DEBUG o.e.rdf4j.rio.RDFParserRegistry - Registered service class org.eclipse.rdf4j.rio.ntriples.NTriplesParserFactory\n\n2022-02-04T17:54:47 [main] DEBUG o.e.rdf4j.rio.RDFParserRegistry - Registered service class org.eclipse.rdf4j.rio.rdfjson.RDFJSONParserFactory\n\n2022-02-04T17:54:47 [main] DEBUG o.e.rdf4j.rio.RDFParserRegistry - Registered service class org.eclipse.rdf4j.rio.jsonld.JSONLDParserFactory\n\n2022-02-04T17:54:47 [main] DEBUG o.e.rdf4j.rio.RDFParserRegistry - Registered service class org.eclipse.rdf4j.rio.rdfxml.RDFXMLParserFactory\n\n2022-02-04T17:54:47 [main] DEBUG o.e.rdf4j.rio.RDFParserRegistry - Registered service class org.eclipse.rdf4j.rio.trix.TriXParserFactory\n\n2022-02-04T17:54:47 [main] DEBUG o.e.rdf4j.rio.RDFParserRegistry - Registered service class org.eclipse.rdf4j.rio.turtle.TurtleParserFactory\n\n2022-02-04T17:54:47 [main] DEBUG o.e.rdf4j.rio.RDFParserRegistry - Registered service class org.eclipse.rdf4j.rio.trig.TriGParserFactory\n\n2022-02-04T17:54:47 [main] DEBUG o.e.r.rio.DatatypeHandlerRegistry - Registered service class org.eclipse.rdf4j.rio.datatypes.XMLSchemaDatatypeHandler\n\n2022-02-04T17:54:47 [main] DEBUG o.e.r.rio.DatatypeHandlerRegistry - Registered service class org.eclipse.rdf4j.rio.datatypes.RDFDatatypeHandler\n\n2022-02-04T17:54:47 [main] DEBUG o.e.r.rio.DatatypeHandlerRegistry - Registered service class org.eclipse.rdf4j.rio.datatypes.DBPediaDatatypeHandler\n\n2022-02-04T17:54:47 [main] DEBUG o.e.r.rio.DatatypeHandlerRegistry - Registered service class org.eclipse.rdf4j.rio.datatypes.VirtuosoGeometryDatatypeHandler\n\n2022-02-04T17:54:47 [main] DEBUG o.e.r.rio.DatatypeHandlerRegistry - Registered service class org.eclipse.rdf4j.rio.datatypes.GeoSPARQLDatatypeHandler\n\n2022-02-04T17:54:47 [main] DEBUG o.e.r.rio.LanguageHandlerRegistry - Registered service class org.eclipse.rdf4j.rio.languages.RFC3066LanguageHandler\n\n2022-02-04T17:54:47 [main] DEBUG o.e.r.rio.LanguageHandlerRegistry - Registered service class org.eclipse.rdf4j.rio.languages.BCP47LanguageHandler\n\n2022-02-04T17:54:47 [main] INFO  o.s.ncbo.oapiwrapper.OntologyMetrics - Calculating metrics for /srv/ontoportal/data/repository/CO_336/12/nt\n\n2022-02-04T17:54:47 [main] INFO  o.s.ncbo.oapiwrapper.OntologyMetrics - Finished metrics calculation for /srv/ontoportal/data/repository/CO_336/12/nt in 1 milliseconds\n\n2022-02-04T17:54:47 [main] INFO  o.s.ncbo.oapiwrapper.OntologyMetrics - Generated metrics CSV file for /srv/ontoportal/data/repository/CO_336/12/nt\n\n2022-02-04T17:54:47 [main] INFO  o.s.ncbo.oapiwrapper.OntologyParser - Ontology document format: org.semanticweb.owlapi.formats.OBODocumentFormat\n\n2022-02-04T17:54:47 [main] INFO  o.s.ncbo.oapiwrapper.OntologyParser - isPrefixOWLOntologyFormat: false\n\n2022-02-04T17:54:47 [main] INFO  o.s.ncbo.oapiwrapper.OntologyParser - isOBO: true\n\n2022-02-04T17:54:47 [main] INFO  o.s.ncbo.oapiwrapper.OntologyParser - Serializing ontology in RDF ...\n\n2022-02-04T17:54:47 [main] INFO  o.s.ncbo.oapiwrapper.OntologyParser - Serialization done!\n\n2022-02-04T17:54:47 [main] INFO  o.s.n.o.OntologyParserCommand - Parse result: true\n\n2022-02-04T17:54:47 [main] INFO  o.s.n.o.OntologyParserCommand - Output triples in: {}/srv/ontoportal/data/repository/CO_336/12/owlapi.xrdf\n\n2022-02-04T17:54:47 [main] INFO  o.s.n.o.OntologyParserCommand - Finished parsing!\n"]
I, [2022-02-04T17:54:47.395622 #897]  INFO -- : ["OWLAPI Java command: parsing finished successfully."]
I, [2022-02-04T17:54:47.395784 #897]  INFO -- : ["Output size 5834 in `/srv/ontoportal/data/repository/CO_336/12/owlapi.xrdf`"]
E, [2022-02-04T17:54:47.495715 #897] ERROR -- : ["{}"]
E, [2022-02-04T17:54:47.495995 #897] ERROR -- : ["RestClient::BadRequest: 400 Bad Request\n/srv/ontoportal/ncbo_cron_deployments/shared/bundle/ruby/2.6.0/gems/rest-client-2.1.0/lib/restclient/abstract_response.rb:249:in `exception_with_response'\n\t/srv/ontoportal/ncbo_cron_deployments/shared/bundle/ruby/2.6.0/gems/rest-client-2.1.0/lib/restclient/abstract_response.rb:129:in `return!'\n\t/srv/ontoportal/ncbo_cron_deployments/shared/bundle/ruby/2.6.0/gems/rest-client-2.1.0/lib/restclient/request.rb:836:in `process_result'\n\t/srv/ontoportal/ncbo_cron_deployments/shared/bundle/ruby/2.6.0/gems/rest-client-2.1.0/lib/restclient/request.rb:743:in `block in transmit'\n\t/usr/local/rbenv/versions/2.6.9/lib/ruby/2.6.0/net/http.rb:920:in `start'\n\t/srv/ontoportal/ncbo_cron_deployments/shared/bundle/ruby/2.6.0/gems/rest-client-2.1.0/lib/restclient/request.rb:727:in `transmit'\n\t/srv/ontoportal/ncbo_cron_deployments/shared/bundle/ruby/2.6.0/gems/rest-client-2.1.0/lib/restclient/request.rb:163:in `execute'\n\t/srv/ontoportal/ncbo_cron_deployments/shared/bundle/ruby/2.6.0/gems/rest-client-2.1.0/lib/restclient/request.rb:63:in `execute'\n\t/srv/ontoportal/ncbo_cron_deployments/shared/bundle/ruby/2.6.0/bundler/gems/goo-89a8f665f706/lib/goo/sparql/client.rb:116:in `append_triples_no_bnodes'\n\t/srv/ontoportal/ncbo_cron_deployments/shared/bundle/ruby/2.6.0/bundler/gems/goo-89a8f665f706/lib/goo/sparql/client.rb:141:in `put_triples'\n\t/srv/ontoportal/ncbo_cron_deployments/shared/bundle/ruby/2.6.0/bundler/gems/ontologies_linked_data-db2377e860d7/lib/ontologies_linked_data/models/ontology_submission.rb:2358:in `delete_and_append'\n\t/srv/ontoportal/ncbo_cron_deployments/shared/bundle/ruby/2.6.0/bundler/gems/ontologies_linked_data-db2377e860d7/lib/ontologies_linked_data/models/ontology_submission.rb:915:in `generate_rdf'\n\t/srv/ontoportal/ncbo_cron_deployments/shared/bundle/ruby/2.6.0/bundler/gems/ontologies_linked_data-db2377e860d7/lib/ontologies_linked_data/models/ontology_submission.rb:1779:in `process_submission'\n\t/srv/ontoportal/ncbo_cron_deployments/releases/20220124143731/lib/ncbo_cron/ontology_submission_parser.rb:193:in `process_submission'\n\tbin/ncbo_ontology_process:98:in `block in <main>'\n\tbin/ncbo_ontology_process:81:in `each'\n\tbin/ncbo_ontology_process:81:in `<main>'"]
E, [2022-02-04T17:54:47.648296 #897] ERROR -- : Failed, exception: RestClient::BadRequest: 400 Bad Request
/srv/ontoportal/ncbo_cron_deployments/shared/bundle/ruby/2.6.0/gems/rest-client-2.1.0/lib/restclient/abstract_response.rb:249:in `exception_with_response'
/srv/ontoportal/ncbo_cron_deployments/shared/bundle/ruby/2.6.0/gems/rest-client-2.1.0/lib/restclient/abstract_response.rb:129:in `return!'
/srv/ontoportal/ncbo_cron_deployments/shared/bundle/ruby/2.6.0/gems/rest-client-2.1.0/lib/restclient/request.rb:836:in `process_result'
/srv/ontoportal/ncbo_cron_deployments/shared/bundle/ruby/2.6.0/gems/rest-client-2.1.0/lib/restclient/request.rb:743:in `block in transmit'
/usr/local/rbenv/versions/2.6.9/lib/ruby/2.6.0/net/http.rb:920:in `start'
/srv/ontoportal/ncbo_cron_deployments/shared/bundle/ruby/2.6.0/gems/rest-client-2.1.0/lib/restclient/request.rb:727:in `transmit'
/srv/ontoportal/ncbo_cron_deployments/shared/bundle/ruby/2.6.0/gems/rest-client-2.1.0/lib/restclient/request.rb:163:in `execute'
/srv/ontoportal/ncbo_cron_deployments/shared/bundle/ruby/2.6.0/gems/rest-client-2.1.0/lib/restclient/request.rb:63:in `execute'
/srv/ontoportal/ncbo_cron_deployments/shared/bundle/ruby/2.6.0/bundler/gems/goo-89a8f665f706/lib/goo/sparql/client.rb:116:in `append_triples_no_bnodes'
/srv/ontoportal/ncbo_cron_deployments/shared/bundle/ruby/2.6.0/bundler/gems/goo-89a8f665f706/lib/goo/sparql/client.rb:141:in `put_triples'
/srv/ontoportal/ncbo_cron_deployments/shared/bundle/ruby/2.6.0/bundler/gems/ontologies_linked_data-db2377e860d7/lib/ontologies_linked_data/models/ontology_submission.rb:2358:in `delete_and_append'
/srv/ontoportal/ncbo_cron_deployments/shared/bundle/ruby/2.6.0/bundler/gems/ontologies_linked_data-db2377e860d7/lib/ontologies_linked_data/models/ontology_submission.rb:915:in `generate_rdf'
/srv/ontoportal/ncbo_cron_deployments/shared/bundle/ruby/2.6.0/bundler/gems/ontologies_linked_data-db2377e860d7/lib/ontologies_linked_data/models/ontology_submission.rb:1779:in `process_submission'
/srv/ontoportal/ncbo_cron_deployments/releases/20220124143731/lib/ncbo_cron/ontology_submission_parser.rb:193:in `process_submission'
bin/ncbo_ontology_process:98:in `block in <main>'
bin/ncbo_ontology_process:81:in `each'
bin/ncbo_ontology_process:81:in `<main>'
jonquet commented 2 years ago

Just tried to load another rdf file downloaded from https://cropontology.org/ontology/CO_357/rdf The file opens in Protégé. Will see.

syphax-bouazzouni commented 2 years ago

Worked

image