fix: ontology_bump skip to support '||' separator.

[Bento007]

Reason for Change

This pull request enhances the handling of ontology term IDs in the ontology bump dry run script and improves the associated test coverage. The main improvements are the ability to support both comma- and double-pipe-delimited ontology term IDs, and a refactored, parameterized test to ensure both cases are properly handled.

Ontology term ID parsing improvements:

• Updated map_deprecated_terms in ontology_bump_dry_run.py to support both comma (,) and double-pipe (||) delimiters when splitting ontology_term_id values, ensuring robust parsing of multiple term IDs.

Testing enhancements:

• Refactored the test for multi-delimited ontology term IDs in test_ontology_bump_dry_run.py to use pytest.mark.parametrize, covering both comma and double-pipe delimiters and generalizing the expected output file selection.

[Copilot]

Pull Request Overview

This PR enhances the ontology bump dry run script to support both comma (,) and double-pipe (||) delimiters when parsing ontology term IDs, improving robustness for different data formats.

• Added conditional logic to handle both , and || separators in ontology term ID parsing
• Refactored tests to use parameterized testing for both delimiter types
• Added proper whitespace trimming for parsed term IDs

Reviewed Changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 1 comment.

File	Description
ontology_bump_dry_run.py	Enhanced map_deprecated_terms function to support both comma and double-pipe delimited ontology term IDs
test_ontology_bump_dry_run.py	Refactored test to use pytest parametrize for testing both delimiter types

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[Copilot]

The conditional logic will fail for strings containing both ',' and '||' delimiters. If a string contains both separators, only the comma logic will execute, potentially leaving '||' separators unparsed. Consider defining a priority order or handling mixed delimiters explicitly.

[nayib-jose-gloria]

I think the proper delimiter here is " || ", per the schema. Else we'll have leading + trailing whitespaces. Verify that assumption and update here and in the tests

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 89.33%. Comparing base (1d262b2) to head (68d8465).
⚠️ Report is 1 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1467      +/-   ##
==========================================
+ Coverage   89.22%   89.33%   +0.10%     
==========================================
  Files          23       23              
  Lines        2738     2756      +18     
==========================================
+ Hits         2443     2462      +19     
+ Misses        295      294       -1     

Components	Coverage Δ
cellxgene_schema_cli	89.79% <ø> (+0.04%)	⬆️
migration_assistant	91.26% <ø> (ø)
schema_bump_dry_run_genes	79.74% <ø> (ø)
schema_bump_dry_run_ontologies	99.55% <100.00%> (+0.03%)	⬆️

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