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ncbo / bioportal-project

Serves to consolidate (in Zenhub) all public issues in BioPortal
BSD 2-Clause "Simplified" License
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Diff is failing for AFO ontology #219

Closed jvendetti closed 2 years ago

jvendetti commented 2 years ago

Received a report from end user that AFO is displaying an "Error Diff" status on the summary page.

Stack trace from parsing log:

I, [2021-10-11T10:28:55.430441 #23475]  INFO -- : ["Java call [java -DentityExpansionLimit=1500000 -Xmx5120M -jar /srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.6.0/bundler/gems/ontologies_linked_data-c4562ccb355a/bin/bubastis.jar -ontology1 /srv/ncbo/repository/AFO/19/merged-without-qudt.ttl -ontology2 /srv/ncbo/repository/AFO/20/merged-without-qudt-and-inferred.ttl -output /srv/ncbo/repository/AFO/20/bubastis_diff.xml -format xml]"]
I, [2021-10-11T10:28:55.888639 #23475]  INFO -- : ["Bubastis diff finished OK."]
I, [2021-10-11T10:28:55.888695 #23475]  INFO -- : ["Performing diff failed.  Reason: null"]
I, [2021-10-11T10:28:55.888753 #23475]  INFO -- : ["ontology 1 is a file /srv/ncbo/repository/AFO/19/merged-without-qudt.ttl
ontology 2 is a file /srv/ncbo/repository/AFO/20/merged-without-qudt-and-inferred.ttl
trying load now"]
E, [2021-10-11T10:28:55.889135 #23475] ERROR -- : ["Bubastis diff for http://data.bioontology.org/ontologies/AFO/submissions/20 failed - LinkedData::Diff::BubastisDiffException: Bubastis diff command exited with status=0. Output file /srv/ncbo/repository/AFO/20/bubastis_diff.xml cannot be found."]
E, [2021-10-11T10:28:55.889293 #23475] ERROR -- : ["LinkedData::Diff::BubastisDiffException: Bubastis diff command exited with status=0. Output file /srv/ncbo/repository/AFO/20/bubastis_diff.xml cannot be found.
/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.6.0/bundler/gems/ontologies_linked_data-c4562ccb355a/lib/ontologies_linked_data/diff/bubastis_diff.rb:100:in `call_bubastis_java_cmd'
    /srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.6.0/bundler/gems/ontologies_linked_data-c4562ccb355a/lib/ontologies_linked_data/diff/bubastis_diff.rb:114:in `diff'
    /srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.6.0/bundler/gems/ontologies_linked_data-c4562ccb355a/lib/ontologies_linked_data/models/ontology_submission.rb:340:in `diff'
    /srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.6.0/bundler/gems/ontologies_linked_data-c4562ccb355a/lib/ontologies_linked_data/models/ontology_submission.rb:1090:in `process_submission'
    /srv/ncbo/ncbo_cron/lib/ncbo_cron/ontology_submission_parser.rb:177:in `process_submission'
    /srv/ncbo/ncbo_cron/lib/ncbo_cron/ontology_submission_parser.rb:47:in `block in process_queue_submissions'
    /srv/ncbo/ncbo_cron/lib/ncbo_cron/ontology_submission_parser.rb:41:in `each'
    /srv/ncbo/ncbo_cron/lib/ncbo_cron/ontology_submission_parser.rb:41:in `process_queue_submissions'
    /srv/ncbo/ncbo_cron/bin/ncbo_cron:246:in `block (3 levels) in <main>'
    /srv/ncbo/ncbo_cron/lib/ncbo_cron/scheduler.rb:65:in `block (3 levels) in scheduled_locking_job'
    /srv/ncbo/ncbo_cron/lib/ncbo_cron/scheduler.rb:51:in `fork'
    /srv/ncbo/ncbo_cron/lib/ncbo_cron/scheduler.rb:51:in `block (2 levels) in scheduled_locking_job'
    /srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.6.0/gems/mlanett-redis-lock-0.2.7/lib/redis-lock.rb:43:in `lock'
    /srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.6.0/gems/mlanett-redis-lock-0.2.7/lib/redis-lock.rb:234:in `lock'
    /srv/ncbo/ncbo_cron/lib/ncbo_cron/scheduler.rb:50:in `block in scheduled_locking_job'
    /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'
    /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'
    /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'"]
jvendetti commented 2 years ago

Performed the following: