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ncbo / ncbo_annotator

To automatically process a piece of data text to annotate it with relevant ontology concepts and return the annotations.
http://bioportal.bioontology.org/annotator
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annotator cache generation failure - Unsupported command argument type: RDF::URI #26

Closed alexskr closed 1 year ago

alexskr commented 1 year ago

Annotator fails to create cache for a number of ontologies with an error Unsupported command argument type: RDF::URI

According to the parsing logs the annotator cache was generated successfully in the past but started to fail consistently. This issue applies to both 4store (prod) and AG (stage) backends.

example ontologies: FOVT GSSO BMTO ONS PP PORO BSPO PLACES ECTO EDAMT VTO NeuroFMA NCI MMIRNAO DATASET MLTX PEAO ITO IOBC

E, [2023-01-18T10:02:09.765678 #11136] ERROR -- : ["Unsupported command argument type: RDF::URI\n/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.7.0/gems/redis-client-0.11.2/lib/redis_client/command_builder.rb:75:inblock in generate'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.7.0/gems/redis-client-0.11.2/lib/redis_client/command_builder.rb:68:in map!'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.7.0/gems/redis-client-0.11.2/lib/redis_client/command_builder.rb:68:ingenerate'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.7.0/gems/redis-client-0.11.2/lib/redis_client.rb:218:in call_v'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.7.0/gems/redis-5.0.5/lib/redis/client.rb:73:incall_v'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.7.0/gems/redis-5.0.5/lib/redis.rb:167:in block in send_command'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.7.0/gems/redis-5.0.5/lib/redis.rb:166:insynchronize'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.7.0/gems/redis-5.0.5/lib/redis.rb:166:in send_command'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.7.0/gems/redis-5.0.5/lib/redis/commands/hashes.rb:26:inhset'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.7.0/bundler/gems/ncbo_annotator-71d41e3afb35/lib/ncbo_annotator.rb:676:in create_term_entry'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.7.0/bundler/gems/ncbo_annotator-71d41e3afb35/lib/ncbo_annotator.rb:337:inblock (3 levels) in create_term_cache_for_submission'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.7.0/bundler/gems/ncbo_annotator-71d41e3afb35/lib/ncbo_annotator.rb:336:in each'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.7.0/bundler/gems/ncbo_annotator-71d41e3afb35/lib/ncbo_annotator.rb:336:inblock (2 levels) in create_term_cache_for_submission'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.7.0/bundler/gems/ncbo_annotator-71d41e3afb35/lib/ncbo_annotator.rb:292:in each'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.7.0/bundler/gems/ncbo_annotator-71d41e3afb35/lib/ncbo_annotator.rb:292:inblock in create_term_cache_for_submission'\n\t/usr/local/rbenv/versions/2.7.6/lib/ruby/2.7.0/benchmark.rb:308:in realtime'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.7.0/bundler/gems/ncbo_annotator-71d41e3afb35/lib/ncbo_annotator.rb:273:increate_term_cache_for_submission'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.7.0/bundler/gems/ncbo_annotator-71d41e3afb35/lib/ncbo_annotator.rb:190:in block in create_term_cache_from_ontologies'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.7.0/bundler/gems/ncbo_annotator-71d41e3afb35/lib/ncbo_annotator.rb:166:ineach_index'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.7.0/bundler/gems/ncbo_annotator-71d41e3afb35/lib/ncbo_annotator.rb:166:in create_term_cache_from_ontologies'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.7.0/bundler/gems/ncbo_annotator-71d41e3afb35/lib/ncbo_annotator.rb:106:increate_term_cache'\n\tbin/ncbo_ontology_annotate_generate_cache:113:in block in <top (required)>'\n\t/usr/local/rbenv/versions/2.7.6/lib/ruby/2.7.0/benchmark.rb:308:inrealtime'\n\tbin/ncbo_ontology_annotate_generate_cache:112:in <top (required)>'\n\t/usr/local/rbenv/versions/2.7.6/lib/ruby/gems/2.7.0/gems/bundler-2.3.13/lib/bundler/cli/exec.rb:58:inload'\n\t/usr/local/rbenv/versions/2.7.6/lib/ruby/gems/2.7.0/gems/bundler-2.3.13/lib/bundler/cli/exec.rb:58:in kernel_load'\n\t/usr/local/rbenv/versions/2.7.6/lib/ruby/gems/2.7.0/gems/bundler-2.3.13/lib/bundler/cli/exec.rb:23:inrun'\n\t/usr/local/rbenv/versions/2.7.6/lib/ruby/gems/2.7.0/gems/bundler-2.3.13/lib/bundler/cli.rb:483:in exec'\n\t/usr/local/rbenv/versions/2.7.6/lib/ruby/gems/2.7.0/gems/bundler-2.3.13/lib/bundler/vendor/thor/lib/thor/command.rb:27:inrun'\n\t/usr/local/rbenv/versions/2.7.6/lib/ruby/gems/2.7.0/gems/bundler-2.3.13/lib/bundler/vendor/thor/lib/thor/invocation.rb:127:in invoke_command'\n\t/usr/local/rbenv/versions/2.7.6/lib/ruby/gems/2.7.0/gems/bundler-2.3.13/lib/bundler/vendor/thor/lib/thor.rb:392:indispatch'\n\t/usr/local/rbenv/versions/2.7.6/lib/ruby/gems/2.7.0/gems/bundler-2.3.13/lib/bundler/cli.rb:31:in dispatch'\n\t/usr/local/rbenv/versions/2.7.6/lib/ruby/gems/2.7.0/gems/bundler-2.3.13/lib/bundler/vendor/thor/lib/thor/base.rb:485:instart'\n\t/usr/local/rbenv/versions/2.7.6/lib/ruby/gems/2.7.0/gems/bundler-2.3.13/lib/bundler/cli.rb:25:in start'\n\t/usr/local/rbenv/versions/2.7.6/lib/ruby/gems/2.7.0/gems/bundler-2.3.13/exe/bundle:48:inblock in <top (required)>'\n\t/usr/local/rbenv/versions/2.7.6/lib/ruby/gems/2.7.0/gems/bundler-2.3.13/lib/bundler/friendly_errors.rb:103:in with_friendly_errors'\n\t/usr/local/rbenv/versions/2.7.6/lib/ruby/gems/2.7.0/gems/bundler-2.3.13/exe/bundle:36:in<top (required)>'\n\t/usr/local/rbenv/versions/2.7.6/bin/bundle:23:in load'\n\t/usr/local/rbenv/versions/2.7.6/bin/bundle:23:in

'"] `

mdorf commented 1 year ago

I resolved this in the code; should go out in the next prod release.