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Feature: Extend YARRRML generator with CSV/TSV source support #2937

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Merged
merged 3 commits into from
Oct 16, 2025
Merged

Feature: Extend YARRRML generator with CSV/TSV source support #2937

merged 3 commits into from
Oct 16, 2025
+169 −7

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@lapkinvladimir
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This PR extends the YARRRML generator to support CSV/TSV sources.

What it does

Adds CSV/TSV as data sources in generated YARRRML
For CSV/TSV, emits sources as list-of-list: - ['path~csv'] (no iterator)
Infers ~csv / ~jsonpath for --source by file extension
Keeps JSON behavior unchanged

Tests

End-to-end tests covering:

  • CSV source generation and mapping
  • TSV source generation
  • Automatic suffix detection (file.csv to ~csv)
  • Existing JSON cases stay the same (all passing, one expected xfail)

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codecov bot commented Oct 12, 2025 •
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Codecov Report

❌ Patch coverage is 57.14286% with 6 lines in your changes missing coverage. Please review.
✅ Project coverage is 83.84%. Comparing base (551d2da) to head (4d9fe47).
⚠️ Report is 4 commits behind head on main.

Files with missing lines Patch % Lines
linkml/generators/yarrrmlgen.py 57.14% 3 Missing and 3 partials ⚠️
Additional details and impacted files 
@@            Coverage Diff             @@
##             main    #2937      +/-   ##
==========================================
+ Coverage   80.16%   83.84%   +3.68%     
==========================================
  Files         141      141              
  Lines       15807    15818      +11     
  Branches     3205     3209       +4     
==========================================
+ Hits        12671    13262     +591     
+ Misses       2469     1840     -629     
- Partials      667      716      +49

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amc-corey-cox
amc-corey-cox approved these changes Oct 16, 2025
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This looks good to me.

@amc-corey-cox amc-corey-cox merged commit 9157106 into linkml:main Oct 16, 2025
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@amc-corey-cox amc-corey-cox amc-corey-cox approved these changes

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2 participants

@lapkinvladimir @amc-corey-cox