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Subclass Sync - Direct in source, indirect in Mondo #714

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@joeflack4 joeflack4 commented Dec 1, 2024

Resolves #708

Overview

Added code to implement Subclass Sync "case 2": Direct in source, indirect in Mondo.

Pre-merge checklist

Documentation

Was the documentation added/updated under docs/?

  • Yes
  • No, updates to the docs were not necessary after careful consideration

QC

Was the full pipeline run before submitting this PR using sh run.sh make build-mondo-ingest on this branch (after
docker pull obolibrary/odkfull:dev), and no errors occurred?

  • Yes
  • No, there are no functional (code-related) changes to the pipeline in the PR, so no re-run is necessary

Mini build:

New Packages

Were any new Python packages added?

Were any other non-Python packages added?

PR Review and Conversations Resolved

Has the PR been sufficiently reviewed by at least 1 team member of the Mondo Technical team and all threads resolved?

  • Yes

Additional info

I ran output and observed that the case in #708 appeared as expected!:

subject_mondo_id subject_mondo_label object_mondo_id subject_source_id object_source_id object_mondo_label
ID SC % >A oboInOwl:source
MONDO:0000248 dengue shock syndrome MONDO:0005502 DOID:0050125 DOID:12205 dengue disease

See: Google Sheets:

@joeflack4 joeflack4 self-assigned this Dec 1, 2024
@joeflack4 joeflack4 added the enhancement New feature or request label Dec 1, 2024
@joeflack4 joeflack4 force-pushed the subclass-sync-direct-source-indirect-mondo branch from 66141ce to 7a1411b Compare December 1, 2024 01:07
- Update: Added Python code to implement this case
- Update: Includes some refactoring around common '-confirmed' cases and in general
@joeflack4 joeflack4 force-pushed the subclass-sync-direct-source-indirect-mondo branch from 7a1411b to 2055a00 Compare December 1, 2024 01:07
- Update: Formalized new output *confirmed-direct-source-indirect-mondo.robot.tsv
@joeflack4 joeflack4 force-pushed the subclass-sync-direct-source-indirect-mondo branch from 4d366d4 to cf5cf23 Compare December 3, 2024 00:07
- Needed to fix an inconsistent named param
- Added some previously missing make prereqs
- Removed a todo
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Bug in Subclass Sync: Missing evidence in "confirmed" table
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