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improve error handling in ncbo_ontology_archive_old_submissions script #67

Closed alexskr closed 1 year ago

alexskr commented 1 year ago

bin/ncbo_ontology_archive_old_submissions script quits when it encounters an ontology submission with bad metadata (missing required attributes). Ideally, it should log broken ontology submissions and move on. 

ARO: found un-archived old submission with ID 2.
ARO: found un-archived old submission with ID 3.
bundler: failed to load command: bin/ncbo_ontology_archive_old_submissions (bin/ncbo_ontology_archive_old_submissions)
Traceback (most recent call last):
    23: from /usr/local/rbenv/versions/2.7.7/bin/bundle:23:in `<main>'
    22: from /usr/local/rbenv/versions/2.7.7/bin/bundle:23:in `load'
    21: from /usr/local/rbenv/versions/2.7.7/lib/ruby/gems/2.7.0/gems/bundler-2.4.0/exe/bundle:33:in `<top (required)>'
    20: from /usr/local/rbenv/versions/2.7.7/lib/ruby/gems/2.7.0/gems/bundler-2.4.0/lib/bundler/friendly_errors.rb:117:in `with_friendly_errors'
    19: from /usr/local/rbenv/versions/2.7.7/lib/ruby/gems/2.7.0/gems/bundler-2.4.0/exe/bundle:45:in `block in <top (required)>'
    18: from /usr/local/rbenv/versions/2.7.7/lib/ruby/gems/2.7.0/gems/bundler-2.4.0/lib/bundler/cli.rb:28:in `start'
    17: from /usr/local/rbenv/versions/2.7.7/lib/ruby/gems/2.7.0/gems/bundler-2.4.0/lib/bundler/vendor/thor/lib/thor/base.rb:485:in `start'
    16: from /usr/local/rbenv/versions/2.7.7/lib/ruby/gems/2.7.0/gems/bundler-2.4.0/lib/bundler/cli.rb:34:in `dispatch'
    15: from /usr/local/rbenv/versions/2.7.7/lib/ruby/gems/2.7.0/gems/bundler-2.4.0/lib/bundler/vendor/thor/lib/thor.rb:392:in `dispatch'
    14: from /usr/local/rbenv/versions/2.7.7/lib/ruby/gems/2.7.0/gems/bundler-2.4.0/lib/bundler/vendor/thor/lib/thor/invocation.rb:127:in `invoke_command'
    13: from /usr/local/rbenv/versions/2.7.7/lib/ruby/gems/2.7.0/gems/bundler-2.4.0/lib/bundler/vendor/thor/lib/thor/command.rb:27:in `run'
    12: from /usr/local/rbenv/versions/2.7.7/lib/ruby/gems/2.7.0/gems/bundler-2.4.0/lib/bundler/cli.rb:491:in `exec'
    11: from /usr/local/rbenv/versions/2.7.7/lib/ruby/gems/2.7.0/gems/bundler-2.4.0/lib/bundler/cli/exec.rb:23:in `run'
    10: from /usr/local/rbenv/versions/2.7.7/lib/ruby/gems/2.7.0/gems/bundler-2.4.0/lib/bundler/cli/exec.rb:58:in `kernel_load'
     9: from /usr/local/rbenv/versions/2.7.7/lib/ruby/gems/2.7.0/gems/bundler-2.4.0/lib/bundler/cli/exec.rb:58:in `load'
     8: from bin/ncbo_ontology_archive_old_submissions:24:in `<top (required)>'
     7: from bin/ncbo_ontology_archive_old_submissions:24:in `each'
     6: from bin/ncbo_ontology_archive_old_submissions:31:in `block in <top (required)>'
     5: from bin/ncbo_ontology_archive_old_submissions:31:in `each'
     4: from bin/ncbo_ontology_archive_old_submissions:36:in `block (2 levels) in <top (required)>'
     3: from /srv/ncbo/ncbo_cron/lib/ncbo_cron/ontology_submission_parser.rb:178:in `process_submission'
     2: from /srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.7.0/bundler/gems/ontologies_linked_data-79527b94fbb5/lib/ontologies_linked_data/models/ontology_submission.rb:1160:in `process_submission'
     1: from /srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.7.0/bundler/gems/ontologies_linked_data-79527b94fbb5/lib/ontologies_linked_data/models/base.rb:13:in `save'
/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.7.0/bundler/gems/goo-b8c7867450ec/lib/goo/base/resource.rb:333:in `save': Object is not valid. Check errors. (Goo::Base::NotValidException)