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ERROR -- : Failed, exception: ArgumentError: File path not found
, [2024-10-18T09:15:31.761146 #7] INFO -- : ["properties finished"]
I, [2024-10-18T09:15:31.761623 #7] INFO -- : ["generation of metrics file finished"]
I, [2024-10-18T09:15:32.032008 #7] INFO -- : ["Java call [java -DentityExpansionLimit=1500000 -Xmx10240M -jar /srv/ontoportal/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-9ab4be437ed8/bin/bubastis.jar -ontology1 /srv/ontoportal/ncbo_cron -ontology2 /srv/ontoportal/data/repository/GO/1826/go.obo -output /srv/ontoportal/data/repository/GO/1826/bubastis_diff.xml -format xml]"]
I, [2024-10-18T09:15:32.382838 #7] INFO -- : ["Bubastis diff finished OK."]
I, [2024-10-18T09:15:32.383003 #7] INFO -- : ["Performing diff failed. Reason: null\n"]
I, [2024-10-18T09:15:32.383089 #7] INFO -- : ["ontology 1 is a file /srv/ontoportal/ncbo_cron\nontology 2 is a file /srv/ontoportal/data/repository/GO/1826/go.obo\ntrying load now\n"]
E, [2024-10-18T09:15:32.383454 #7] ERROR -- : ["LinkedData::Diff::BubastisDiffException: Bubastis diff command exited with status=0. Output file /srv/ontoportal/data/repository/GO/1826/bubastis_diff.xml cannot be found.\n/srv/ontoportal/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-9ab4be437ed8/lib/ontologies_linked_data/diff/bubastis_diff.rb:119:in call_bubastis_java_cmd'\n\t/srv/ontoportal/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-9ab4be437ed8/lib/ontologies_linked_data/diff/bubastis_diff.rb:56:in diff'\n\t/srv/ontoportal/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-9ab4be437ed8/lib/ontologies_linked_data/services/submission_process/operations/submission_diff_generator.rb:72:in generate_diff'\n\t/srv/ontoportal/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-9ab4be437ed8/lib/ontologies_linked_data/services/submission_process/operations/submission_diff_generator.rb:10:in diff'\n\t/srv/ontoportal/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-9ab4be437ed8/lib/ontologies_linked_data/services/submission_process/operations/submission_diff_generator.rb:48:in process_diff'\n\t/srv/ontoportal/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-9ab4be437ed8/lib/ontologies_linked_data/services/submission_process/operations/submission_diff_generator.rb:6:in process'\n\t/srv/ontoportal/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-9ab4be437ed8/lib/ontologies_linked_data/models/concerns/submission_process.rb:14:in generate_diff'\n\t/srv/ontoportal/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-9ab4be437ed8/lib/ontologies_linked_data/services/submission_process/submission_processor.rb:67:in process_submission'\n\t/srv/ontoportal/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-9ab4be437ed8/lib/ontologies_linked_data/services/submission_process/submission_processor.rb:18:in process'\n\t/srv/ontoportal/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-9ab4be437ed8/lib/ontologies_linked_data/models/concerns/submission_process.rb:6:in process_submission'\n\t/srv/ontoportal/ncbo_cron/lib/ncbo_cron/ontology_submission_parser.rb:171:in process_submission'\n\tbin/ncbo_ontology_process:106:in block in
'\n\tbin/ncbo_ontology_process:89:in each'\n\tbin/ncbo_ontology_process:89:in '"]
I, [2024-10-18T09:15:32.468079 #7] INFO -- : ["Submission processing of http://data.bioontology.org/ontologies/GO/submissions/1826 completed successfully"]
D, [2024-10-18T09:15:32.509572 #7] DEBUG -- : ["Archiving submissions previous to http://data.bioontology.org/ontologies/GO/submissions/1826..."]
I, [2024-10-18T09:15:32.661419 #7] INFO -- : ["Starting to process GO/submissions/1825"]
E, [2024-10-18T09:15:32.698081 #7] ERROR -- : Failed, exception: ArgumentError: File path not found
/srv/ontoportal/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-9ab4be437ed8/lib/ontologies_linked_data/utils/file.rb:21:in zip?' /srv/ontoportal/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-9ab4be437ed8/lib/ontologies_linked_data/models/ontology_submission.rb:280:in zipped?'
/srv/ontoportal/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-9ab4be437ed8/lib/ontologies_linked_data/services/submission_process/operations/submission_archiver.rb:38:in zip_submission_uploaded_file' /srv/ontoportal/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-9ab4be437ed8/lib/ontologies_linked_data/services/submission_process/operations/submission_archiver.rb:33:in archive_submission'
/srv/ontoportal/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-9ab4be437ed8/lib/ontologies_linked_data/services/submission_process/operations/submission_archiver.rb:10:in process' /srv/ontoportal/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-9ab4be437ed8/lib/ontologies_linked_data/models/concerns/submission_process.rb:26:inarchive'
/srv/ontoportal/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-9ab4be437ed8/lib/ontologies_linked_data/services/submission_process/submission_processor.rb:37:in process_submission' /srv/ontoportal/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-9ab4be437ed8/lib/ontologies_linked_data/services/submission_process/submission_processor.rb:18:in process'
/srv/ontoportal/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-9ab4be437ed8/lib/ontologies_linked_data/models/concerns/submission_process.rb:6:in process_submission' /srv/ontoportal/ncbo_cron/lib/ncbo_cron/ontology_submission_parser.rb:208:in block in archive_old_submissions'
/srv/ontoportal/ncbo_cron/lib/ncbo_cron/ontology_submission_parser.rb:205:in each' /srv/ontoportal/ncbo_cron/lib/ncbo_cron/ontology_submission_parser.rb:205:in archive_old_submissions'
/srv/ontoportal/ncbo_cron/lib/ncbo_cron/ontology_submission_parser.rb:175:in process_submission' bin/ncbo_ontology_process:106:in block in '
bin/ncbo_ontology_process:89:in each' bin/ncbo_ontology_process:89:in '
The text was updated successfully, but these errors were encountered:
nsimbi
changed the title
Missing file while deploying Ontoportal using any ontologiess, e,g GO, STY, MEDDRA, etc
Missing file while deploying ontoportal using any ontology sets, e,g GO, STY, MEDDRA, etc
Oct 18, 2024
nsimbi
changed the title
Missing file while deploying ontoportal using any ontology sets, e,g GO, STY, MEDDRA, etc
Missing file while deploying ontoportal with any ontology sets, e,g GO, STY, MEDDRA, etc
Oct 18, 2024
ERROR -- : Failed, exception: ArgumentError: File path not found
The text was updated successfully, but these errors were encountered: