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[bioontology-support] Error Uploading Latest Version of HHEAR Ontology

John Graybeal jgraybeal at stanford.edu
Fri Mar 11 15:59:42 PST 2022


Hello James,

Because we are relatively short staffed, we are unable to quickly review cases like yours ourselves. I can point you to a potentially useful resource from our OntoPortal Administration guide:
  https://ontoportal.github.io/administration/ontologies/troubleshooting_submissions/#check-the-ontology-ways-to-pre-validate-an-ontology

With this information, the following information from the log file may be useful. (Sorry for the ugly formatting!)  It looks like the problem may be that this is not a recognizable ontology format:
  2022-03-10T18:43:57 [main] ERROR o.s.ncbo.oapiwrapper.OntologyParser - Could not find an appropriate factory to load ontology from ontology document: <urn:x-evn-master:dublin_core_terms_ontology>

Without looking at the ontology, I might guess that there is an ontology identifier (for the Dublin Core ontology) that the parse can't find, since the identifier is a non-resolvable URN.

You can likely confirm that following one of the suggestions in the OntoPortal Administration guide link above. If not, let us know and eventually we, or someone else on the list, will find time to help.

John

# Logfile created on 2022-03-10 18:43:40 -0800 by logger.rb/v1.5.0
I, [2022-03-10T18:43:40.327999 #20987]  INFO -- : ["Starting to process http://data.bioontology.org/ontologies/HHEAR/submissions/9"]
I, [2022-03-10T18:43:40.767469 #20987]  INFO -- : ["Starting to process HHEAR/submissions/9"]
I, [2022-03-10T18:43:41.445991 #20987]  INFO -- : ["Java call [java -DentityExpansionLimit=2500000 -Xmx10240M -jar /srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.6.0/bundler/gems/ontologies_linked_data-f3532d2c8bab/bin/owlapi-wrapper-1.3.8.jar -m /srv/ncbo/repository/HHEAR/9/hhear-ontology-1.6.rdf -o /srv/ncbo/repository/HHEAR/9 -r true]"]
I, [2022-03-10T18:43:57.183604 #20987]  INFO -- : ["2022-03-10T18:43:41 [main] INFO  o.s.n.o.OntologyParserCommand - Parsing invocation with values: ParserInvocation [inputRepositoryFolder=null, outputRepositoryFolder=/srv/ncbo/repository/HHEAR/9, masterFileName=/srv/ncbo/repository/HHEAR/9/hhear-ontology-1.6.rdf, invocationId=0, parserLog=, userReasoner= true]\n\n2022-03-10T18:43:41 [main] INFO  o.s.ncbo.oapiwrapper.OntologyParser - executor ...\n\n2022-03-10T18:43:42 [main] INFO  o.s.ncbo.oapiwrapper.OntologyParser - Input repository folder is null. Unique file being parsed.\n\n2022-03-10T18:43:53 [main] DEBUG o.e.rdf4j.rio.RDFParserRegistry - Registered service class org.eclipse.rdf4j.rio.binary.BinaryRDFParserFactory\n\n2022-03-10T18:43:53 [main] DEBUG o.e.rdf4j.rio.RDFParserRegistry - Registered service class org.eclipse.rdf4j.rio.n3.N3ParserFactory\n\n2022-03-10T18:43:53 [main] DEBUG o.e.rdf4j.rio.RDFParserRegistry - Registered service class org.eclipse.rdf4j.rio.nquads.NQuadsParserFactory\n\n2022-03-10T18:43:53 [main] DEBUG o.e.rdf4j.rio.RDFParserRegistry - Registered service class org.eclipse.rdf4j.rio.ntriples.NTriplesParserFactory\n\n2022-03-10T18:43:53 [main] DEBUG o.e.rdf4j.rio.RDFParserRegistry - Registered service class org.eclipse.rdf4j.rio.rdfjson.RDFJSONParserFactory\n\n2022-03-10T18:43:53 [main] DEBUG o.e.rdf4j.rio.RDFParserRegistry - Registered service class org.eclipse.rdf4j.rio.jsonld.JSONLDParserFactory\n\n2022-03-10T18:43:53 [main] DEBUG o.e.rdf4j.rio.RDFParserRegistry - Registered service class org.eclipse.rdf4j.rio.rdfxml.RDFXMLParserFactory\n\n2022-03-10T18:43:53 [main] DEBUG o.e.rdf4j.rio.RDFParserRegistry - Registered service class org.eclipse.rdf4j.rio.trix.TriXParserFactory\n\n2022-03-10T18:43:53 [main] DEBUG o.e.rdf4j.rio.RDFParserRegistry - Registered service class org.eclipse.rdf4j.rio.turtle.TurtleParserFactory\n\n2022-03-10T18:43:53 [main] DEBUG o.e.rdf4j.rio.RDFParserRegistry - Registered service class org.eclipse.rdf4j.rio.trig.TriGParserFactory\n\n2022-03-10T18:43:53 [main] DEBUG o.e.r.rio.DatatypeHandlerRegistry - Registered service class org.eclipse.rdf4j.rio.datatypes.XMLSchemaDatatypeHandler\n\n2022-03-10T18:43:53 [main] DEBUG o.e.r.rio.DatatypeHandlerRegistry - Registered service class org.eclipse.rdf4j.rio.datatypes.RDFDatatypeHandler\n\n2022-03-10T18:43:53 [main] DEBUG o.e.r.rio.DatatypeHandlerRegistry - Registered service class org.eclipse.rdf4j.rio.datatypes.DBPediaDatatypeHandler\n\n2022-03-10T18:43:53 [main] DEBUG o.e.r.rio.DatatypeHandlerRegistry - Registered service class org.eclipse.rdf4j.rio.datatypes.VirtuosoGeometryDatatypeHandler\n\n2022-03-10T18:43:53 [main] DEBUG o.e.r.rio.DatatypeHandlerRegistry - Registered service class org.eclipse.rdf4j.rio.datatypes.GeoSPARQLDatatypeHandler\n\n2022-03-10T18:43:53 [main] DEBUG o.e.r.rio.LanguageHandlerRegistry - Registered service class org.eclipse.rdf4j.rio.languages.RFC3066LanguageHandler\n\n2022-03-10T18:43:53 [main] DEBUG o.e.r.rio.LanguageHandlerRegistry - Registered service class org.eclipse.rdf4j.rio.languages.BCP47LanguageHandler\n\n2022-03-10T18:43:57 [main] ERROR o.s.ncbo.oapiwrapper.OntologyParser - Could not find an appropriate factory to load ontology from ontology document: <urn:x-evn-master:dublin_core_terms_ontology>\n\n2022-03-10T18:43:57 [main] INFO  o.s.n.o.OntologyParserCommand - Parse result: false\n\n2022-03-10T18:43:57 [main] INFO  o.s.n.o.OntologyParserCommand - Output triples in: {}/srv/ncbo/repository/HHEAR/9/owlapi.xrdf\n\n2022-03-10T18:43:57 [main] INFO  o.s.n.o.OntologyParserCommand - Finished parsing!\n"]
I, [2022-03-10T18:43:57.184029 #20987]  INFO -- : ["OWLAPI Java command: parsing finished successfully."]
E, [2022-03-10T18:43:57.184321 #20987] ERROR -- : ["LinkedData::Parser::OWLAPIParserException: OWLAPI java command exited with  0. Output file /srv/ncbo/repository/HHEAR/9/owlapi.xrdf cannot be found.\n/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.6.0/bundler/gems/ontologies_linked_data-f3532d2c8bab/lib/ontologies_linked_data/parser/owlapi.rb:125:in `block in call_owlapi_java_command'\n\t/usr/local/rbenv/versions/2.6.8/lib/ruby/2.6.0/open3.rb:219:in `popen_run'\n\t/usr/local/rbenv/versions/2.6.8/lib/ruby/2.6.0/open3.rb:101:in `popen3'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.6.0/bundler/gems/ontologies_linked_data-f3532d2c8bab/lib/ontologies_linked_data/parser/owlapi.rb:76:in `call_owlapi_java_command'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.6.0/bundler/gems/ontologies_linked_data-f3532d2c8bab/lib/ontologies_linked_data/parser/owlapi.rb:153:in `parse'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.6.0/bundler/gems/ontologies_linked_data-f3532d2c8bab/lib/ontologies_linked_data/models/ontology_submission.rb:462:in `generate_rdf'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.6.0/bundler/gems/ontologies_linked_data-f3532d2c8bab/lib/ontologies_linked_data/models/ontology_submission.rb:973:in `process_submission'\n\t/srv/ncbo/ncbo_cron/lib/ncbo_cron/ontology_submission_parser.rb:177:in `process_submission'\n\t/srv/ncbo/ncbo_cron/lib/ncbo_cron/ontology_submission_parser.rb:47:in `block in process_queue_submissions'\n\t/srv/ncbo/ncbo_cron/lib/ncbo_cron/ontology_submission_parser.rb:41:in `each'\n\t/srv/ncbo/ncbo_cron/lib/ncbo_cron/ontology_submission_parser.rb:41:in `process_queue_submissions'\n\t/srv/ncbo/ncbo_cron/bin/ncbo_cron:246:in `block (3 levels) in <main>'\n\t/srv/ncbo/ncbo_cron/lib/ncbo_cron/scheduler.rb:65:in `block (3 levels) in scheduled_locking_job'\n\t/srv/ncbo/ncbo_cron/lib/ncbo_cron/scheduler.rb:51:in `fork'\n\t/srv/ncbo/ncbo_cron/lib/ncbo_cron/scheduler.rb:51:in `block (2 levels) in scheduled_locking_job'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.6.0/gems/mlanett-redis-lock-0.2.7/lib/redis-lock.rb:43:in `lock'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.6.0/gems/mlanett-redis-lock-0.2.7/lib/redis-lock.rb:234:in `lock'\n\t/srv/ncbo/ncbo_cron/lib/ncbo_cron/scheduler.rb:50:in `block in scheduled_locking_job'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.6.0/gems/rufus-scheduler-2.0.24/lib/rufus/sc/jobs.rb:230:in `trigger_block'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.6.0/gems/rufus-scheduler-2.0.24/lib/rufus/sc/jobs.rb:204:in `block in trigger'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.6.0/gems/rufus-scheduler-2.0.24/lib/rufus/sc/scheduler.rb:430:in `block in trigger_job'"]

On Mar 11, 2022, at 2:00 PM, Masters, James <James.Masters at mssm.edu<mailto:James.Masters at mssm.edu>> wrote:

Hello,

I am the primary curator of the HHEAR ontology, and I tried to upload our latest release (1.6) to Bioportal yesterday. I see on the Submissions list that this submission failed with an error:

1.6 (Uploaded, Error Rdf)
03/10/2022
03/10/2022
OWL<https://data.bioontology.org/ontologies/HHEAR/submissions/9/download?apikey=840ae862-3a0a-4a6d-8118-2304b98e1e29>


However, I do not know or see how to inspect the error that was found in order to fix it and resubmit. Can you please provide me with an error log or details of how I can retrieve the error from the website, if possible?

Thank you,

James “Chip” Masters, PhD (he/him)
Director, Semantic Technology and HHEAR Data Repository
Scientific Computing and Data
Icahn School of Medicine at Mount Sinai
150 E 42nd St
New York, NY 10017
United States

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========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632  | ORCID  0000-0001-6875-5360



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