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Serves to consolidate (in Zenhub) all public issues in BioPortal
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AG: Error during ontologies report paging - ArgumentError: Not supported case for embed #254

Closed alexskr closed 12 months ago

alexskr commented 2 years ago

getting Error during ontologies report paging - ArgumentError: Not supported case for embed when processing with AllegroGraph backend for the following ontologies:

CIDIT_V1 CLO ORDO_OBO UPHENO BIOMODELS MHCRO CCS_DIFF_CON_ANC CHEAR LION ZP XREF-FUNDER-REG CCONT RH-MESH WB-BT GO HOIP OGG CIDIO_AUX I2B2-LOINC

tracestack:

E, [2022-08-25T00:33:22.524952 #4829] ERROR -- : ["Error during ontologies report paging - ArgumentError: Not supported case for embed\n/srv/ncbo/ncbo_cron_ag/vendor/bundle/ruby/2.7.0/bundler/gems/goo-562826ba21f7/lib/goo/sparql/queries.rb:426:in `model_load_sliced'\n/srv/ncbo/ncbo_cron_ag/vendor/bundle/ruby/2.7.0/bundler/gems/goo-562826ba21f7/lib/goo/sparql/queries.rb:265:in `block in model_load'\n/srv/ncbo/ncbo_cron_ag/vendor/bundle/ruby/2.7.0/bundler/gems/goo-562826ba21f7/lib/goo/sparql/queries.rb:260:in `each'\n/srv/ncbo/ncbo_cron_ag/vendor/bundle/ruby/2.7.0/bundler/gems/goo-562826ba21f7/lib/goo/sparql/queries.rb:260:in `each_slice'\n/srv/ncbo/ncbo_cron_ag/vendor/bundle/ruby/2.7.0/bundler/gems/goo-562826ba21f7/lib/goo/sparql/queries.rb:260:in `model_load'\n/srv/ncbo/ncbo_cron_ag/vendor/bundle/ruby/2.7.0/bundler/gems/goo-562826ba21f7/lib/goo/base/where.rb:214:in `process_query_intl'\n/srv/ncbo/ncbo_cron_ag/vendor/bundle/ruby/2.7.0/bundler/gems/goo-562826ba21f7/lib/goo/base/where.rb:131:in `process_query'\n/srv/ncbo/ncbo_cron_ag/vendor/bundle/ruby/2.7.0/bundler/gems/goo-562826ba21f7/lib/goo/base/where.rb:282:in `all'\n/srv/ncbo/ncbo_cron_ag/lib/ncbo_cron/ontologies_report.rb:357:in `good_classes'\n/srv/ncbo/ncbo_cron_ag/lib/ncbo_cron/ontologies_report.rb:295:in `generate_single_ontology_report'\n/srv/ncbo/ncbo_cron_ag/lib/ncbo_cron/ontologies_report.rb:76:in `block (2 levels) in refresh_report'\n/usr/local/rbenv/versions/2.7.6/lib/ruby/2.7.0/benchmark.rb:308:in `realtime'\n/srv/ncbo/ncbo_cron_ag/lib/ncbo_cron/ontologies_report.rb:75:in `block in refresh_report'\n/srv/ncbo/ncbo_cron_ag/lib/ncbo_cron/ontologies_report.rb:72:in `each'\n/srv/ncbo/ncbo_cron_ag/lib/ncbo_cron/ontologies_report.rb:72:in `refresh_report'\n/srv/ncbo/ncbo_cron_ag/lib/ncbo_cron/ontology_submission_parser.rb:187:in `process_submission'\nbin/ncbo_ontology_process:98:in `block in <top (required)>'\nbin/ncbo_ontology_process:81:in `each'\nbin/ncbo_ontology_process:81:in `<top (required)>'\n/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 `load'\n/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/usr/local/rbenv/versions/2.7.6/lib/ruby/gems/2.7.0/gems/bundler-2.3.13/lib/bundler/cli/exec.rb:23:in `run'\n/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/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:in `run'\n/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/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:in `dispatch'\n/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/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:in `start'\n/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/usr/local/rbenv/versions/2.7.6/lib/ruby/gems/2.7.0/gems/bundler-2.3.13/exe/bundle:48:in `block in <top (required)>'\n/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/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/usr/local/rbenv/versions/2.7.6/bin/bundle:23:in `load'\n/usr/local/rbenv/versions/2.7.6/bin/bundle:23:in `<main>'"]
mdorf commented 2 years ago

I am unable to reproduce this error.

syphax-bouazzouni commented 2 years ago

Hi, My following remark is maybe not directly related to the issue

In this line

 paging = LinkedData::Models::Class.in(submission).include(:prefLabel, :synonym, metrics: :classes).page(page_num, page_size)

We include the embedded metrics attribute for the model Class, although it doesn't have it. It's the ÒntologySubmission that provides it. This means that the previous request need to be like this 

 paging = LinkedData::Models::Class.in(submission).include(:prefLabel, :synonym, submission: [metrics: [:classes]]).page(page_num, page_size)
mdorf commented 2 years ago

Hi, My following remark is maybe not directly related to the issue

In this line

 paging = LinkedData::Models::Class.in(submission).include(:prefLabel, :synonym, metrics: :classes).page(page_num, page_size)

We include the embedded metrics attribute for the model Class, although it doesn't have it. It's the ÒntologySubmission that provides it. This means that the previous request need to be like this

 paging = LinkedData::Models::Class.in(submission).include(:prefLabel, :synonym, submission: [metrics: [:classes]]).page(page_num, page_size)

Good catch, I'll fix this in the code.