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

@nsimbi

Description

@nsimbi

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 '

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