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AG: Error during ontologies report paging - ArgumentError: Not supported case for embed #254

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alexskr opened this issue Aug 25, 2022 · 3 comments
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AG: Error during ontologies report paging - ArgumentError: Not supported case for embed #254

alexskr opened this issue Aug 25, 2022 · 3 comments
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@alexskr @mdorf

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@alexskr
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alexskr commented Aug 25, 2022

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>'"]
@alexskr alexskr self-assigned this Aug 25, 2022
@mdorf mdorf self-assigned this Oct 24, 2022
@mdorf
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mdorf commented Oct 24, 2022

I am unable to reproduce this error.

@syphax-bouazzouni
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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
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mdorf commented Oct 28, 2022

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.

mdorf added a commit to ncbo/ncbo_cron that referenced this issue Nov 3, 2022
@mdorf
fixed an API call mentioned by @syphax-bouazzouni in ncbo/bioportal-p…
0fe50fd 
…roject#254
mdorf added a commit to ncbo/ncbo_cron that referenced this issue Nov 3, 2022
@mdorf
fixed an API call mentioned by @syphax-bouazzouni in ncbo/bioportal-p…
4d409a9 
…roject#254
@alexskr alexskr closed this as completed Nov 20, 2023
syphax-bouazzouni added a commit to ontoportal/ncbo_cron that referenced this issue Jan 16, 2024
@syphax-bouazzouni @jvendetti
@mdorf @alexskr
Sync: bring OntoPortal up-to-date with BioPortal releases 5.26.0 and …
bc68802 
…onward (#2)

* add a script to eradicate (delete data+ files) submissions of an ontology

* Auto stash before merge of "development" and "master"

* omit logs link file

* update the eradicator to support the eradication of not archived submissions if wanted

* fix the delete submission files to not let behind empty directories

* not remove the submission directory beaucse it's already done by the submission.delete

* Update Gemfile.lock

* Reset branch specifier to develop

* extract do_ontology_pull function

* some simple code refactor in the ontology_pull

* simple code refactor of test_ontology_pull

* add a script to do a ontology pull on an ontology on demand

* set the name of the new script in $0

* extract new_file_exists? method from do_ontology_pull

* save the submission in the RemoteFileException

* some automatic code refactor/lint

* use the new do_ontology_pull in the old  do_remote_ontology_pull

* fixed an API call mentioned by @syphax-bouazzouni in ncbo/bioportal-project#254

* fixed an API call mentioned by @syphax-bouazzouni in ncbo/bioportal-project#254

* Gemfile.lock update

* bump up version of actions/checkout from v2->v3

* Gemfile.lock update

* Merge branch 'develop'

* remove forgot variables

* GH Actions unit test workflow refactor

- add ruby versioning via docker-compose.yml file
- bump up ruby v2.6 -> v2.7
- add AllegroGraph backend
- add code coverage

* Remove extra space

* fix for #61

- create contact instance if it doesn't exist
- changed --from-api to --from-apikey
- minor linting

* Restore branch specifier to develop

* Optimization - remove repeated query

* Gemfile.lock update

* Gemfile.lock update

* Gemfile.lock update

* Gemfile had references to develop branch

* implemented #64 - ability to generate labels independently of RDF processing (and vise versa)

* Gemfile.lock update

* fixed a bug in #64

* Relocate docker-compose file and update default configs

* Add GH workflow for publishing docker images

* use ruby native method for listing files instead of a git function

Resolves warning messages when we exclude .git directory from docker image

* remove comment

* capitalize argument in order to be consistent with other scripts

* add arm/64 platform

* additional error handling for SPAM deletion script, #60

* additional error handling for SPAM deletion script, #60

* implemented #67 - improved corrupt data and error handling

* Gemfile.lock update

* exclude test/data/dictionary.txt from git commits

* update version of solr-ut

* Gemfile.lock update

* Restore branch specifier to master

* fixed configuration for the analytics module

* Gemfile.lock update

* implemented #69 - scheduled annotator dictionary file generation should be a configurable option instead of the default

* Gemfile.lock update

* gem update

* create new rake taks for updating purls for all ontologies

moved from ontologies_api/fix_purls.rb

* initial implementation of #70 - Google Analytics v4 Update Compatibility Issue

* added the /data folder to ignore

* update gems

* Gemfile.lock update

* Gemfile.lock update

* Gemfile.lock update

* use patched version of agraph v7.3.1

* unpin faraday gem

* A chnage to reference Analytics Redis from LinkedData block

* Gemfile.lock update

* Gemfile.lock update

* Gemfile.lock update

* Gemfile.lock update

* use assert_operator instead of assert

minitest style guide adherence.
encountered an intermittent unit test failure so assert_operator will provide
better failure feedback than assert

* fixed ncbo_ontology_archive_old_submissions error output

* Gemfile.lock update

* Gemfile.lock update

* Gemfile update

* Gemfile update

* fixes to the analytics script and a new script to generate UA analytics for documentation

* Gemfile.lock update

* Gemfile.lock update

* implemented the first pass at bmir-radx/radx-project#37

* implemented the first pass at bmir-radx/radx-project#37

* set bundler version to be comptatible with ruby 2.7

+ AG v8

* Gemfile.lock update

* Gemfile.lock update

---------

Co-authored-by: Jennifer Vendetti <vendetti@stanford.edu>
Co-authored-by: mdorf <mdorf@stanford.edu>
Co-authored-by: Alex Skrenchuk <alexskr@stanford.edu>
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