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ontology processing error: undefined method `casecmp' for 0.921e2:BigDecimal #37

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alexskr opened this issue Nov 15, 2024 · 0 comments · Fixed by #41
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ontology processing error: undefined method `casecmp' for 0.921e2:BigDecimal #37

alexskr opened this issue Nov 15, 2024 · 0 comments · Fixed by #41
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alexskr commented Nov 15, 2024

errors when processing EFO, CCONT and other ontologies:

E, [2024-11-15T10:35:27.059812 #3481217] ERROR -- : [["Failed caching classes for EFO (http://data.bioontology.org/ontologies/EFO/submissions/269)"]]
E, [2024-11-15T10:35:27.061057 #3481217] ERROR -- : [["undefined method `casecmp' for 0.921e2:BigDecimal\n/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ncbo_annotator-b2731c98bfef/lib/ncbo_annotator.rb:343:in `block (3 levels) in create_term_cache_for_submission'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ncbo_annotator-b2731c98bfef/lib/ncbo_annotator.rb:336:in `each'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ncbo_annotator-b2731c98bfef/lib/ncbo_annotator.rb:336:in `block (2 levels) in create_term_cache_for_submission'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ncbo_annotator-b2731c98bfef/lib/ncbo_annotator.rb:292:in `each'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ncbo_annotator-b2731c98bfef/lib/ncbo_annotator.rb:292:in `block in create_term_cache_for_submission'\n\t/usr/local/rbenv/versions/3.0.6/lib/ruby/3.0.0/benchmark.rb:308:in `realtime'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ncbo_annotator-b2731c98bfef/lib/ncbo_annotator.rb:273:in `create_term_cache_for_submission'\n\t/srv/ontoportal/ncbo_cron/lib/ncbo_cron/ontology_submission_parser.rb:219:in `process_annotator'\n\t/srv/ontoportal/ncbo_cron/lib/ncbo_cron/ontology_submission_parser.rb:176:in `process_submission'\n\t./bin/ncbo_ontology_process:106:in `block in <main>'\n\t./bin/ncbo_ontology_process:89:in `each'\n\t./bin/ncbo_ontology_process:89:in `<main>'"]]

related to ncbo/ontologies_linked_data#219

@alexskr alexskr added the bug label Nov 15, 2024
@alexskr alexskr self-assigned this Nov 15, 2024
alexskr added a commit that referenced this issue Nov 18, 2024
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