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ontology processing errors #219

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alexskr opened this issue Oct 9, 2024 · 9 comments · Fixed by ontoportal/goo#6
Closed

ontology processing errors #219

alexskr opened this issue Oct 9, 2024 · 9 comments · Fixed by ontoportal/goo#6
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@alexskr
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alexskr commented Oct 9, 2024 •
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We are encountering errors when processing some ontologies.
EFO:

E, [2024-10-09T10:24:23.594106 #365177] ERROR -- : ["Thread 1: NoMethodError: undefined method `map' for #<RDF::Literal::Decimal:0x819ee4(\"92.1\"^^<http://www.w3.org/2001/XMLSchema#decimal>)>\nDid you mean?  tap after retrying 10 times...\n/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/goo-74a012eebb94/lib/goo/base/resource.rb:250:in `block in map_attributes'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/goo-74a012eebb94/lib/goo/base/resource.rb:222:in `each'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/goo-74a012eebb94/lib/goo/base/resource.rb:222:in `map_attributes'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-8572cd25722c/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb:132:in `rescue in block (4 levels) in index'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-8572cd25722c/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb:118:in `block (4 levels) in index'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-8572cd25722c/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb:117:in `each'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-8572cd25722c/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb:117:in `block (3 levels) in index'"]
#<Thread:0x000055c56730a980 /srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-8572cd25722c/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb:56 run> terminated with exception (report_on_exception is true):
/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/goo-74a012eebb94/lib/goo/base/settings/settings.rb:300:in `block in shape_attribute': Attribute `synonym` is not loaded for http://www.ebi.ac.uk/efo/EFO_0022503. Loaded attributes: #<Set: {:submission, :label, :prefLabel}>. (Goo::Base::AttributeNotLoaded)
	from /srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-8572cd25722c/lib/ontologies_linked_data/utils/ontology_csv_writer.rb:44:in `write_class'
	from /srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-8572cd25722c/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb:148:in `block (5 levels) in index'
	from /srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-8572cd25722c/lib/ontologies_linked_data/models/ontology_submission.rb:90:in `synchronize'
	from /srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-8572cd25722c/lib/ontologies_linked_data/models/ontology_submission.rb:90:in `synchronize'
	from /srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-8572cd25722c/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb:147:in `block (4 levels) in index'
	from /srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-8572cd25722c/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb:117:in `each'
	from /srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-8572cd25722c/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb:117:in `block (3 levels) in index'

E, [2024-10-09T10:24:23.596405 #365177] ERROR -- : ["\n\nGoo::Base::AttributeNotLoaded: Attribute `synonym` is not loaded for http://www.ebi.ac.uk/efo/EFO_0022503. Loaded attributes: #<Set: {:submission, :label, :prefLabel}>.\n"]
E, [2024-10-09T10:24:23.596490 #365177] ERROR -- : [["/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/goo-74a012eebb94/lib/goo/base/settings/settings.rb:300:in `block in shape_attribute'", "/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-8572cd25722c/lib/ontologies_linked_data/utils/ontology_csv_writer.rb:44:in `write_class'", "/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-8572cd25722c/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb:148:in `block (5 levels) in index'", "/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-8572cd25722c/lib/ontologies_linked_data/models/ontology_submission.rb:90:in `synchronize'", "/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-8572cd25722c/lib/ontologies_linked_data/models/ontology_submission.rb:90:in `synchronize'", "/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-8572cd25722c/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb:147:in `block (4 levels) in index'", "/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-8572cd25722c/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb:117:in `each'", "/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-8572cd25722c/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb:117:in `block (3 levels) in index'"]]
E, [2024-10-09T10:24:23.597308 #365177] ERROR -- : ["Goo::Base::AttributeNotLoaded: Attribute `synonym` is not loaded for http://www.ebi.ac.uk/efo/EFO_0022503. Loaded attributes: #<Set: {:submission, :label, :prefLabel}>.\n/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/goo-74a012eebb94/lib/goo/base/settings/settings.rb:300:in `block in shape_attribute'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-8572cd25722c/lib/ontologies_linked_data/utils/ontology_csv_writer.rb:44:in `write_class'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-8572cd25722c/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb:148:in `block (5 levels) in index'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-8572cd25722c/lib/ontologies_linked_data/models/ontology_submission.rb:90:in `synchronize'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-8572cd25722c/lib/ontologies_linked_data/models/ontology_submission.rb:90:in `synchronize'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-8572cd25722c/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb:147:in `block (4 levels) in index'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-8572cd25722c/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb:117:in `each'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-8572cd25722c/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb:117:in `block (3 levels) in index'"]

E, [2024-10-09T12:05:38.508345 #369858] ERROR -- : [["Failed caching classes for EFO (http://data.bioontology.org/ontologies/EFO/submissions/268)"]]
E, [2024-10-09T12:05:38.509743 #369858] 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\tbin/ncbo_ontology_process:106:in `block in <top (required)>'\n\tbin/ncbo_ontology_process:89:in `each'\n\tbin/ncbo_ontology_process:89:in `<top (required)>'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/gems/bundler-2.5.20/lib/bundler/cli/exec.rb:58:in `load'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/gems/bundler-2.5.20/lib/bundler/cli/exec.rb:58:in `kernel_load'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/gems/bundler-2.5.20/lib/bundler/cli/exec.rb:23:in `run'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/gems/bundler-2.5.20/lib/bundler/cli.rb:455:in `exec'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/gems/bundler-2.5.20/lib/bundler/vendor/thor/lib/thor/command.rb:28:in `run'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/gems/bundler-2.5.20/lib/bundler/vendor/thor/lib/thor/invocation.rb:127:in `invoke_command'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/gems/bundler-2.5.20/lib/bundler/vendor/thor/lib/thor.rb:527:in `dispatch'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/gems/bundler-2.5.20/lib/bundler/cli.rb:35:in `dispatch'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/gems/bundler-2.5.20/lib/bundler/vendor/thor/lib/thor/base.rb:584:in `start'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/gems/bundler-2.5.20/lib/bundler/cli.rb:29:in `start'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/gems/bundler-2.5.20/exe/bundle:28:in `block in <top (required)>'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/gems/bundler-2.5.20/lib/bundler/friendly_errors.rb:117:in `with_friendly_errors'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/gems/bundler-2.5.20/exe/bundle:20:in `<top (required)>'\n\t/usr/local/rbenv/versions/3.0.6/bin/bundle:25:in `load'\n\t/usr/local/rbenv/versions/3.0.6/bin/bundle:25:in `<main>'"]]

FYPO:

I, [2024-10-09T13:30:40.046055 #380428]  INFO -- : ["Thread 1: Page 4 of 17 - 1000 ontology terms indexed in 45.203980855 sec."]
I, [2024-10-09T13:30:44.330454 #380428]  INFO -- : ["Thread 1: Page 5 of 17 - 1000 ontology terms retrieved in 9.737e-06 sec."]
E, [2024-10-09T13:30:44.772420 #380428] ERROR -- : ["Thread 1: Exception while mapping attributes for http://purl.obolibrary.org/obo/FYPO_0008033. Retrying 1 times..."]
E, [2024-10-09T13:30:46.773008 #380428] ERROR -- : ["Thread 1: Exception while mapping attributes for http://purl.obolibrary.org/obo/FYPO_0008033. Retrying 2 times..."]
E, [2024-10-09T13:30:48.773649 #380428] ERROR -- : ["Thread 1: Exception while mapping attributes for http://purl.obolibrary.org/obo/FYPO_0008033. Retrying 3 times..."]
E, [2024-10-09T13:30:50.774253 #380428] ERROR -- : ["Thread 1: Exception while mapping attributes for http://purl.obolibrary.org/obo/FYPO_0008033. Retrying 4 times..."]
E, [2024-10-09T13:30:52.774852 #380428] ERROR -- : ["Thread 1: Exception while mapping attributes for http://purl.obolibrary.org/obo/FYPO_0008033. Retrying 5 times..."]
E, [2024-10-09T13:30:54.775442 #380428] ERROR -- : ["Thread 1: Exception while mapping attributes for http://purl.obolibrary.org/obo/FYPO_0008033. Retrying 6 times..."]
E, [2024-10-09T13:30:56.776063 #380428] ERROR -- : ["Thread 1: Exception while mapping attributes for http://purl.obolibrary.org/obo/FYPO_0008033. Retrying 7 times..."]
E, [2024-10-09T13:30:58.776652 #380428] ERROR -- : ["Thread 1: Exception while mapping attributes for http://purl.obolibrary.org/obo/FYPO_0008033. Retrying 8 times..."]
E, [2024-10-09T13:31:00.777252 #380428] ERROR -- : ["Thread 1: Exception while mapping attributes for http://purl.obolibrary.org/obo/FYPO_0008033. Retrying 9 times..."]
E, [2024-10-09T13:31:02.777867 #380428] ERROR -- : ["Thread 1: Exception while mapping attributes for http://purl.obolibrary.org/obo/FYPO_0008033. Retrying 10 times..."]
E, [2024-10-09T13:31:04.778491 #380428] ERROR -- : ["Thread 1: Error mapping attributes for http://purl.obolibrary.org/obo/FYPO_0008033:"]
E, [2024-10-09T13:31:04.779553 #380428] ERROR -- : ["Thread 1: NoMethodError: undefined method `map' for #<RDF::Literal:0x24813c(\"A cell morphology phenotype in which a vegetative cell is elongated, has no septum, and contains one nucleus, and is arrested in mototic S-phase\"^^<http://www.w3.org/2001/XMLSchema#anyURI>)>\nDid you mean?  tap after retrying 10 times...\n/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/goo-f943ac33e87c/lib/goo/base/resource.rb:250:in `block in map_attributes'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/goo-f943ac33e87c/lib/goo/base/resource.rb:222:in `each'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/goo-f943ac33e87c/lib/goo/base/resource.rb:222:in `map_attributes'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-9ab4be437ed8/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb:132:in `rescue in block (4 levels) in index'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-9ab4be437ed8/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb:118:in `block (4 levels) in index'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-9ab4be437ed8/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb:117:in `each'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-9ab4be437ed8/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb:117:in `block (3 levels) in index'"]
#<Thread:0x000055997f310470 /srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-9ab4be437ed8/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb:56 run> terminated with exception (report_on_exception is true):
/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/goo-f943ac33e87c/lib/goo/base/settings/settings.rb:300:in `block in shape_attribute': Attribute `definition` is not loaded for http://purl.obolibrary.org/obo/FYPO_0008033. Loaded attributes: #<Set: {:submission, :label, :prefLabel, :synonym}>. (Goo::Base::AttributeNotLoaded)
	from /srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-9ab4be437ed8/lib/ontologies_linked_data/utils/ontology_csv_writer.rb:48:in `write_class'
	from /srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-9ab4be437ed8/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb:148:in `block (5 levels) in index'
	from /srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-9ab4be437ed8/lib/ontologies_linked_data/models/ontology_submission.rb:90:in `synchronize'
	from /srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-9ab4be437ed8/lib/ontologies_linked_data/models/ontology_submission.rb:90:in `synchronize'
	from /srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-9ab4be437ed8/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb:147:in `block (4 levels) in index'
	from /srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-9ab4be437ed8/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb:117:in `each'
	from /srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-9ab4be437ed8/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb:117:in `block (3 levels) in index'
E, [2024-10-09T13:31:04.781787 #380428] ERROR -- : ["\n\nGoo::Base::AttributeNotLoaded: Attribute `definition` is not loaded for http://purl.obolibrary.org/obo/FYPO_0008033. Loaded attributes: #<Set: {:submission, :label, :prefLabel, :synonym}>.\n"]
E, [2024-10-09T13:31:04.781867 #380428] ERROR -- : [["/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/goo-f943ac33e87c/lib/goo/base/settings/settings.rb:300:in `block in shape_attribute'", "/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-9ab4be437ed8/lib/ontologies_linked_data/utils/ontology_csv_writer.rb:48:in `write_class'", "/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-9ab4be437ed8/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb:148:in `block (5 levels) in index'", "/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-9ab4be437ed8/lib/ontologies_linked_data/models/ontology_submission.rb:90:in `synchronize'", "/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-9ab4be437ed8/lib/ontologies_linked_data/models/ontology_submission.rb:90:in `synchronize'", "/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-9ab4be437ed8/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb:147:in `block (4 levels) in index'", "/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-9ab4be437ed8/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb:117:in `each'", "/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-9ab4be437ed8/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb:117:in `block (3 levels) in index'"]]
E, [2024-10-09T13:31:04.782032 #380428] ERROR -- : ["Goo::Base::AttributeNotLoaded: Attribute `definition` is not loaded for http://purl.obolibrary.org/obo/FYPO_0008033. Loaded attributes: #<Set: {:submission, :label, :prefLabel, :synonym}>.\n/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/goo-f943ac33e87c/lib/goo/base/settings/settings.rb:300:in `block in shape_attribute'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-9ab4be437ed8/lib/ontologies_linked_data/utils/ontology_csv_writer.rb:48:in `write_class'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-9ab4be437ed8/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb:148:in `block (5 levels) in index'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-9ab4be437ed8/lib/ontologies_linked_data/models/ontology_submission.rb:90:in `synchronize'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-9ab4be437ed8/lib/ontologies_linked_data/models/ontology_submission.rb:90:in `synchronize'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-9ab4be437ed8/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb:147:in `block (4 levels) in index'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-9ab4be437ed8/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb:117:in `each'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-9ab4be437ed8/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb:117:in `block (3 levels) in index'"]

STATO:

I, [2024-07-19T18:17:01.374473 #1163655]  INFO -- : ["Removed ontology terms index (0.126251334s)"]
I, [2024-07-19T18:17:39.346740 #1163655]  INFO -- : ["Thread 1: Page 1 of 1 - 959 ontology terms retrieved in 1.4692e-05 sec."]
E, [2024-07-19T18:17:39.849696 #1163655] ERROR -- : ["Thread 1: Exception while mapping attributes for http://purl.obolibrary.org/obo/STATO_0000594. Retrying 1 times..."]
E, [2024-07-19T18:17:41.850354 #1163655] ERROR -- : ["Thread 1: Exception while mapping attributes for http://purl.obolibrary.org/obo/STATO_0000594. Retrying 2 times..."]
E, [2024-07-19T18:17:43.851010 #1163655] ERROR -- : ["Thread 1: Exception while mapping attributes for http://purl.obolibrary.org/obo/STATO_0000594. Retrying 3 times..."]
E, [2024-07-19T18:17:45.851675 #1163655] ERROR -- : ["Thread 1: Exception while mapping attributes for http://purl.obolibrary.org/obo/STATO_0000594. Retrying 4 times..."]
E, [2024-07-19T18:17:47.852278 #1163655] ERROR -- : ["Thread 1: Exception while mapping attributes for http://purl.obolibrary.org/obo/STATO_0000594. Retrying 5 times..."]
E, [2024-07-19T18:17:49.852885 #1163655] ERROR -- : ["Thread 1: Exception while mapping attributes for http://purl.obolibrary.org/obo/STATO_0000594. Retrying 6 times..."]
E, [2024-07-19T18:17:51.853452 #1163655] ERROR -- : ["Thread 1: Exception while mapping attributes for http://purl.obolibrary.org/obo/STATO_0000594. Retrying 7 times..."]
E, [2024-07-19T18:17:53.854119 #1163655] ERROR -- : ["Thread 1: Exception while mapping attributes for http://purl.obolibrary.org/obo/STATO_0000594. Retrying 8 times..."]
E, [2024-07-19T18:17:55.854794 #1163655] ERROR -- : ["Thread 1: Exception while mapping attributes for http://purl.obolibrary.org/obo/STATO_0000594. Retrying 9 times..."]
E, [2024-07-19T18:17:57.855411 #1163655] ERROR -- : ["Thread 1: Exception while mapping attributes for http://purl.obolibrary.org/obo/STATO_0000594. Retrying 10 times..."]
E, [2024-07-19T18:17:59.856065 #1163655] ERROR -- : ["Thread 1: Error mapping attributes for http://purl.obolibrary.org/obo/STATO_0000594:"]
E, [2024-07-19T18:17:59.856953 #1163655] ERROR -- : ["Thread 1: NoMethodError: undefined method `map' for #<RDF::URI:0x46bcc(http://purl.obolibrary.org/obo/IAO_0000122)>\nDid you mean?  tap after retrying 10 times...\n/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/2.7.0/bundler/gems/goo-2cec53c2d841/lib/goo/mixins/sparql_client.rb:62:in `method_missing'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/2.7.0/bundler/gems/goo-2cec53c2d841/lib/goo/base/resource.rb:265:in `block in map_attributes'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/2.7.0/bundler/gems/goo-2cec53c2d841/lib/goo/base/resource.rb:237:in `each'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/2.7.0/bundler/gems/goo-2cec53c2d841/lib/goo/base/resource.rb:237:in `map_attributes'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/2.7.0/bundler/gems/ontologies_linked_data-70fc2c8b377b/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb:132:in `rescue in block (4 levels) in index'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/2.7.0/bundler/gems/ontologies_linked_data-70fc2c8b377b/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb:118:in `block (4 levels) in index'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/2.7.0/bundler/gems/ontologies_linked_data-70fc2c8b377b/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb:117:in `each'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/2.7.0/bundler/gems/ontologies_linked_data-70fc2c8b377b/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb:117:in `block (3 levels) in index'"]
E, [2024-07-19T18:17:59.858948 #1163655] ERROR -- : ["\n\nGoo::Base::AttributeNotLoaded: Attribute `synonym` is not loaded for http://purl.obolibrary.org/obo/STATO_0000594. Loaded attributes: #<Set: {:submission, :label, :prefLabel}>.\n"]
E, [2024-07-19T18:17:59.859411 #1163655] ERROR -- : [["/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/2.7.0/bundler/gems/goo-2cec53c2d841/lib/goo/base/settings/settings.rb:283:in `block in shape_attribute'", "/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/2.7.0/bundler/gems/ontologies_linked_data-70fc2c8b377b/lib/ontologies_linked_data/utils/ontology_csv_writer.rb:44:in `write_class'", "/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/2.7.0/bundler/gems/ontologies_linked_data-70fc2c8b377b/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb:148:in `block (5 levels) in index'", "/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/2.7.0/bundler/gems/ontologies_linked_data-70fc2c8b377b/lib/ontologies_linked_data/models/ontology_submission.rb:90:in `synchronize'", "/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/2.7.0/bundler/gems/ontologies_linked_data-70fc2c8b377b/lib/ontologies_linked_data/models/ontology_submission.rb:90:in `synchronize'", "/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/2.7.0/bundler/gems/ontologies_linked_data-70fc2c8b377b/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb:147:in `block (4 levels) in index'", "/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/2.7.0/bundler/gems/ontologies_linked_data-70fc2c8b377b/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb:117:in `each'", "/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/2.7.0/bundler/gems/ontologies_linked_data-70fc2c8b377b/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb:117:in `block (3 levels) in index'"]]
E, [2024-07-19T18:17:59.860244 #1163655] ERROR -- : ["Goo::Base::AttributeNotLoaded: Attribute `synonym` is not loaded for http://purl.obolibrary.org/obo/STATO_0000594. Loaded attributes: #<Set: {:submission, :label, :prefLabel}>.\n/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/2.7.0/bundler/gems/goo-2cec53c2d841/lib/goo/base/settings/settings.rb:283:in `block in shape_attribute'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/2.7.0/bundler/gems/ontologies_linked_data-70fc2c8b377b/lib/ontologies_linked_data/utils/ontology_csv_writer.rb:44:in `write_class'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/2.7.0/bundler/gems/ontologies_linked_data-70fc2c8b377b/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb:148:in `block (5 levels) in index'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/2.7.0/bundler/gems/ontologies_linked_data-70fc2c8b377b/lib/ontologies_linked_data/models/ontology_submission.rb:90:in `synchronize'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/2.7.0/bundler/gems/ontologies_linked_data-70fc2c8b377b/lib/ontologies_linked_data/models/ontology_submission.rb:90:in `synchronize'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/2.7.0/bundler/gems/ontologies_linked_data-70fc2c8b377b/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb:147:in `block (4 levels) in index'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/2.7.0/bundler/gems/ontologies_linked_data-70fc2c8b377b/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb:117:in `each'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/2.7.0/bundler/gems/ontologies_linked_data-70fc2c8b377b/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb:117:in `block (3 levels) in index'"]

ECTO:

E, [2024-10-08T13:22:30.388995 #332024] ERROR -- : ["Thread 1: Exception while mapping attributes for http://purl.obolibrary.org/obo/FOODON_00001264. Retrying 1 times..."]
E, [2024-10-08T13:22:32.389652 #332024] ERROR -- : ["Thread 1: Exception while mapping attributes for http://purl.obolibrary.org/obo/FOODON_00001264. Retrying 2 times..."]
E, [2024-10-08T13:22:34.390256 #332024] ERROR -- : ["Thread 1: Exception while mapping attributes for http://purl.obolibrary.org/obo/FOODON_00001264. Retrying 3 times..."]
E, [2024-10-08T13:22:36.390788 #332024] ERROR -- : ["Thread 1: Exception while mapping attributes for http://purl.obolibrary.org/obo/FOODON_00001264. Retrying 4 times..."]
E, [2024-10-08T13:22:38.391335 #332024] ERROR -- : ["Thread 1: Exception while mapping attributes for http://purl.obolibrary.org/obo/FOODON_00001264. Retrying 5 times..."]
E, [2024-10-08T13:22:40.391908 #332024] ERROR -- : ["Thread 1: Exception while mapping attributes for http://purl.obolibrary.org/obo/FOODON_00001264. Retrying 6 times..."]
E, [2024-10-08T13:22:42.392698 #332024] ERROR -- : ["Thread 1: Exception while mapping attributes for http://purl.obolibrary.org/obo/FOODON_00001264. Retrying 7 times..."]
E, [2024-10-08T13:22:44.393286 #332024] ERROR -- : ["Thread 1: Exception while mapping attributes for http://purl.obolibrary.org/obo/FOODON_00001264. Retrying 8 times..."]
E, [2024-10-08T13:22:46.393928 #332024] ERROR -- : ["Thread 1: Exception while mapping attributes for http://purl.obolibrary.org/obo/FOODON_00001264. Retrying 9 times..."]
E, [2024-10-08T13:22:48.394574 #332024] ERROR -- : ["Thread 1: Exception while mapping attributes for http://purl.obolibrary.org/obo/FOODON_00001264. Retrying 10 times..."]
E, [2024-10-08T13:22:50.395662 #332024] ERROR -- : ["Thread 1: Error mapping attributes for http://purl.obolibrary.org/obo/FOODON_00001264:"]
E, [2024-10-08T13:22:50.399137 #332024] ERROR -- : ["Thread 1: NoMethodError: undefined method `map' for #<RDF::Literal:0x63ec(\"http://purl.obolibrary.org/obo/FOODON_03411254\"^^<http://www.w3.org/2001/XMLSchema#anyURI>)>\nDid you mean?  tap after retrying 10 times...\n/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/goo-f943ac33e87c/lib/goo/base/resource.rb:250:in `block in map_attributes'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/goo-f943ac33e87c/lib/goo/base/resource.rb:222:in `each'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/goo-f943ac33e87c/lib/goo/base/resource.rb:222:in `map_attributes'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-9ab4be437ed8/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb:132:in `rescue in block (4 levels) in index'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-9ab4be437ed8/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb:118:in `block (4 levels) in index'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-9ab4be437ed8/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb:117:in `each'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-9ab4be437ed8/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb:117:in `block (3 levels) in index'"]
E, [2024-10-08T13:22:50.401899 #332024] ERROR -- : ["\n\nGoo::Base::AttributeNotLoaded: Attribute `synonym` is not loaded for http://purl.obolibrary.org/obo/FOODON_00001264. Loaded attributes: #<Set: {:submission, :label, :prefLabel}>.\n"]
E, [2024-10-08T13:22:50.401992 #332024] ERROR -- : [["/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/goo-f943ac33e87c/lib/goo/base/settings/settings.rb:300:in `block in shape_attribute'", "/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-9ab4be437ed8/lib/ontologies_linked_data/utils/ontology_csv_writer.rb:44:in `write_class'", "/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-9ab4be437ed8/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb:148:in `block (5 levels) in index'", "/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-9ab4be437ed8/lib/ontologies_linked_data/models/ontology_submission.rb:90:in `synchronize'", "/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-9ab4be437ed8/lib/ontologies_linked_data/models/ontology_submission.rb:90:in `synchronize'", "/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-9ab4be437ed8/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb:147:in `block (4 levels) in index'", "/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-9ab4be437ed8/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb:117:in `each'", "/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-9ab4be437ed8/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb:117:in `block (3 levels) in index'"]]
E, [2024-10-08T13:22:50.402106 #332024] ERROR -- : ["Goo::Base::AttributeNotLoaded: Attribute `synonym` is not loaded for http://purl.obolibrary.org/obo/FOODON_00001264. Loaded attributes: #<Set: {:submission, :label, :prefLabel}>.\n/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/goo-f943ac33e87c/lib/goo/base/settings/settings.rb:300:in `block in shape_attribute'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-9ab4be437ed8/lib/ontologies_linked_data/utils/ontology_csv_writer.rb:44:in `write_class'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-9ab4be437ed8/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb:148:in `block (5 levels) in index'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-9ab4be437ed8/lib/ontologies_linked_data/models/ontology_submission.rb:90:in `synchronize'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-9ab4be437ed8/lib/ontologies_linked_data/models/ontology_submission.rb:90:in `synchronize'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-9ab4be437ed8/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb:147:in `block (4 levels) in index'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-9ab4be437ed8/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb:117:in `each'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-9ab4be437ed8/lib/ontologies_linked_data/services/submission_process/operations/submission_indexer.rb:117:in `block (3 levels) in index'"]
I, [2024-10-08T13:22:50.502357 #332024]  INFO -- : ["Submission processing of http://data.bioontology.org/ontologies/ECTO/submissions/10 completed successfully"]

also: NGBO, DDSS
@alexskr alexskr changed the title Indexing errors with goo v5.33.0 Indexing errors Oct 9, 2024
@alexskr alexskr changed the title Indexing errors ontology processing errors Oct 9, 2024
@alexskr
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alexskr commented Oct 9, 2024

relates to ncbo/bioportal_web_ui#335
and ncbo/bioportal-project#327

@mdorf
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mdorf commented Oct 9, 2024 •
edited
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@syphax-bouazzouni, The error happens in resource.rb (GOO) on line 250 because of a conflict introduced by the multilingual code:

              if include_languages && [RDF::URI, Hash].all?{|c| object.map(&:class).include?(c)}
                object = object.reduce({})  do |all, new_v|
                  new_v =  { none: [new_v] } if new_v.is_a?(RDF::URI)
                  all.merge(new_v) {|_, a, b| a + b }
                end
              elsif include_languages
=>              object = object.first
              end

The elsif condition turns the object from an Array to an Object. However, later in the code, there's no handling for when the object is NOT an Array. The method map is being called in the else block, which is a method of an Array:

            if object.is_a?(Hash)
              object = object.transform_values{|values| Array(values).map{|o|o.is_a?(RDF::URI) ? o : o.object}}
            else
=>            object = object.map {|o| o.is_a?(RDF::URI) ? o : o.object}
            end

@alexskr
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alexskr commented Oct 9, 2024

How do we reproduce this error so that we can catch it in our unit tests?

@mdorf
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mdorf commented Oct 10, 2024 •
edited
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@syphax-bouazzouni, some additional findings to help troubleshoot the issue:

When generating labels, for some reason the language information is NOT included in the unmapped property of each class:

@unmapped=
  {#<RDF::URI:0x238c(http://www.w3.org/2000/01/rdf-schema#label)>=>[#<RDF::Literal:0x23a0("Energy Metabolism"@en)>],
   #<RDF::URI:0x23b4(http://www.w3.org/2000/01/rdf-schema#comment)>=>
    [#<RDF::Literal:0x23c8("A set of metabolic pathways that are involved in the generation and use of energy within an organism, typically through processes like cellular
respiration and photosynthesis."@en)>],

However, when indexing, the language information IS included in unmapped of each class:

@unmapped=
  {#<RDF::URI:0x4fc4(http://www.w3.org/2000/01/rdf-schema#label)>=>{:en=>[#<RDF::Literal:0x4fd8("Energy Metabolism"@en)>]},
   #<RDF::URI:0x4fec(http://www.w3.org/2000/01/rdf-schema#comment)>=>
    {:en=>
      [#<RDF::Literal:0x5000("A set of metabolic pathways that are involved in the generation and use of energy within an organism, typically through processes like cellula
r respiration and photosynthesis."@en)>]},

@jvendetti jvendetti added the bug label Oct 11, 2024
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mdorf commented Oct 15, 2024

This has been fixed in #220

@alexskr alexskr mentioned this issue Oct 21, 2024
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alexskr commented Oct 25, 2024 •
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Processing of STATO ontology chokes on the http://purl.obolibrary.org/obo/STATO_0000594 class. If that class is removed, then processing completes successfully

    <!-- http://purl.obolibrary.org/obo/STATO_0000594 -->

    <owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000594">
        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000642"/>
        <rdfs:subClassOf>
            <owl:Class>
                <owl:intersectionOf rdf:parseType="Collection">
                    <owl:Restriction>
                        <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
                        <owl:qualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:qualifiedCardinality>
                        <owl:onClass rdf:resource="http://purl.obolibrary.org/obo/STATO_0000090"/>
                    </owl:Restriction>
                    <owl:Restriction>
                        <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
                        <owl:qualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:qualifiedCardinality>
                        <owl:onClass>
                            <owl:Class>
                                <owl:intersectionOf rdf:parseType="Collection">
                                    <rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000252"/>
                                    <owl:Restriction>
                                        <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0001927"/>
                                        <owl:qualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">2</owl:qualifiedCardinality>
                                        <owl:onClass rdf:resource="http://purl.obolibrary.org/obo/IAO_0000027"/>
                                    </owl:Restriction>
                                </owl:intersectionOf>
                            </owl:Class>
                        </owl:onClass>
                    </owl:Restriction>
                </owl:intersectionOf>
            </owl:Class>
        </rdfs:subClassOf>
        <obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
        <obo:IAO_0000115 xml:lang="en">a confusion matrix is a 2 by 2 contingency table used to evaluate the performance of a classifier, often a machine-learning classifier and  that allows visualization of the performance of an algorithm, typically a supervised learning one. It defines two dimensions (&quot;actual&quot; and &quot;predicted&quot;), and identical sets of &quot;classes&quot; in both dimensions (each combination of dimension and class is a variable in the contingency table).</obo:IAO_0000115>
        <obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
        <obo:IAO_0000118 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
        <obo:IAO_0000119 xml:lang="en">adapted from wikipedia:
https://en.wikipedia.org/wiki/Confusion_matrix
last accessed: 22.10.2019</obo:IAO_0000119>
        <obo:STATO_0000032 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
        <obo:STATO_0000041 xml:lang="en">https://www.rdocumentation.org/packages/caret/versions/3.45/topics/confusionMatrix
from:
https://www.rdocumentation.org/packages/caret/versions/3.45/topics/confusionMatrix</obo:STATO_0000041>
        <rdfs:label xml:lang="en">confusion matrix</rdfs:label>
    </owl:Class>

in FYPO ontology, the problematic class is http://purl.obolibrary.org/obo/FYPO_0008034

  <!-- http://purl.obolibrary.org/obo/FYPO_0008034 -->

    <owl:Class rdf:about="http://purl.obolibrary.org/obo/FYPO_0008034">
        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/FYPO_0000776"/>
        <obo:IAO_0000115>A cellular process phenotype observed in the vegetative growth phase of the life cycle in which the phosphorylation of the serine residue at position 7 within one or more copies of the heptapeptide repeat (YSPTSPS) of the C-terminal domain of RNA polymerase II normal (i.e. indistinguishable from wild type).</obo:IAO_0000115>
        <oboInOwl:created_by>vw</oboInOwl:created_by>
        <oboInOwl:creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2022-11-29T17:22:41Z</oboInOwl:creation_date>
        <rdfs:label xml:lang="en">normal phosphorylation of RNA polymerase II C-terminal domain serine 7 residues during vegetative growth</rdfs:label>
    </owl:Class>
    <owl:Axiom>
        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/FYPO_0008034"/>
        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
        <owl:annotatedTarget>A cellular process phenotype observed in the vegetative growth phase of the life cycle in which the phosphorylation of the serine residue at position 7 within one or more copies of the heptapeptide repeat (YSPTSPS) of the C-terminal domain of RNA polymerase II normal (i.e. indistinguishable from wild type).</owl:annotatedTarget>
        <oboInOwl:hasDbXref>PMID:32282918</oboInOwl:hasDbXref>
    </owl:Axiom>

ECTO:

    <!-- http://purl.obolibrary.org/obo/FOODON_00001264 -->

    <owl:Class rdf:about="http://purl.obolibrary.org/obo/FOODON_00001264">
        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/FOODON_00001262"/>
        <obo:IAO_0000115>A one-celled fruit (pod) usually dehiscing down both sutures, and having the seed attached along a ventral suture. (Roubik 1995)</obo:IAO_0000115>
        <obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://www.fao.org/pollination/resources/glossary/en/</obo:IAO_0000119>
        <oboInOwl:hasExactSynonym xml:lang="en">legume</oboInOwl:hasExactSynonym>
        <oboInOwl:hasNarrowSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://purl.obolibrary.org/obo/FOODON_03411254</oboInOwl:hasNarrowSynonym>
        <oboInOwl:hasNarrowSynonym xml:lang="en">http://purl.obolibrary.org/obo/FOODON_03411338</oboInOwl:hasNarrowSynonym>
        <rdfs:label xml:lang="en">legume food product</rdfs:label>
    </owl:Class>

mdorf added a commit to ncbo/goo that referenced this issue Nov 13, 2024
@mdorf
implemented a fix for ncbo/ontologies_linked_data#219 - ontology proc…
3572185 
…essing errors
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alexskr commented Nov 14, 2024 •
edited
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fix 3572185
resolved issues with FYPO, NGBO and STATO ontologies.

EFO has a new 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

ECTO:

ERROR -- : ["NoMethodError: undefined method `keys' for [\"flavanone\"]:Array\n/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-a65341b714f2/lib/ontologies_linked_data/services/submission_process/operations/submission_rdf_generator.rb:199:in `generate_missing_labels_each'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-a65341b714f2/lib/ontologies_linked_data/services/submission_process/operations/submission_rdf_generator.rb:144:in `call'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-a65341b714f2/lib/ontologies_linked_data/services/submission_process/operations/submission_rdf_generator.rb:144:in `block (3 levels) in loop_classes'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-a65341b714f2/lib/ontologies_linked_data/services/submission_process/operations/submission_rdf_generator.rb:39:in `block in process_callbacks'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-a65341b714f2/lib/ontologies_linked_data/services/submission_process/operations/submission_rdf_generator.rb:35:in `delete_if'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-a65341b714f2/lib/ontologies_linked_data/services/submission_process/operations/submission_rdf_generator.rb:35:in `process_callbacks'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-a65341b714f2/lib/ontologies_linked_data/services/submission_process/operations/submission_rdf_generator.rb:143:in `block (2 levels) in loop_classes'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-a65341b714f2/lib/ontologies_linked_data/services/submission_process/operations/submission_rdf_generator.rb:142:in `each'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-a65341b714f2/lib/ontologies_linked_data/services/submission_process/operations/submission_rdf_generator.rb:142:in `block in loop_classes'\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/ontologies_linked_data-a65341b714f2/lib/ontologies_linked_data/services/submission_process/operations/submission_rdf_generator.rb:70:in `loop_classes'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-a65341b714f2/lib/ontologies_linked_data/services/submission_process/operations/submission_rdf_generator.rb:31:in `handle_missing_labels'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-a65341b714f2/lib/ontologies_linked_data/services/submission_process/operations/submission_rdf_generator.rb:7:in `process'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-a65341b714f2/lib/ontologies_linked_data/services/submission_process/operations/submission_rdf_generator.rb:330:in `process_rdf'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-a65341b714f2/lib/ontologies_linked_data/services/submission_process/operations/submission_rdf_generator.rb:292:in `process'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-a65341b714f2/lib/ontologies_linked_data/models/concerns/submission_process.rb:30:in `generate_rdf'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-a65341b714f2/lib/ontologies_linked_data/services/submission_process/submission_processor.rb:39:in `process_submission'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-a65341b714f2/lib/ontologies_linked_data/services/submission_process/submission_processor.rb:18:in `process'\n\t/srv/ontoportal/ncbo_cron/vendor/bundle/ruby/3.0.0/bundler/gems/ontologies_linked_data-a65341b714f2/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 <main>'\n\tbin/ncbo_ontology_process:89:in `each'\n\tbin/ncbo_ontology_process:89:in `<main>'"]
E, [2024-11-13T16:04:42.452996 #1241043] ERROR -- : Failed, exception: NoMethodError: undefined method `keys' for ["flavanone"]:Array

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alexskr commented Nov 14, 2024

ECTO is fixed after merging 55bcd74

This was referenced Nov 14, 2024
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alexskr commented Nov 19, 2024

resolved

@alexskr alexskr closed this as completed Nov 19, 2024
@alexskr alexskr mentioned this issue Nov 25, 2024
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Sync: ncbo v5.33.4 release ncbo/goo
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