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Missing file while deploying ontoportal with any ontology sets, e,g GO, STY, MEDDRA, etc #5

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nsimbi opened this issue Oct 18, 2024 · 0 comments

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nsimbi commented Oct 18, 2024

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 '

@nsimbi 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 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
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