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feat: add MIMIC-IV OMOP test support (closes #13)#24

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tompollard merged 1 commit intomainfrom
feat/add-mimic-omop-test
Nov 23, 2025
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feat: add MIMIC-IV OMOP test support (closes #13)#24
tompollard merged 1 commit intomainfrom
feat/add-mimic-omop-test

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@rafiattrach
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feat: Add MIMIC-IV OMOP test support and validation

This PR adds the MIMIC-IV OMOP demo dataset to the test suite and verifies that croissant-maker correctly generates metadata for it "out of the box".

Changes

  • Added MIMIC-IV OMOP demo dataset (v0.9) to tests/data/input/.
  • Added new end-to-end test case test_mimiciv_demo_omop_generation in tests/test_end_to_end.py.

Results

The existing CSVHandler successfully processed all 22 CSV files in the OMOP export without requiring any code changes.

  • Correctly identified file structure, row counts, and columns.
  • Properly handled and skipped empty files (e.g., provider.csv, note.csv) to avoid creating empty RecordSets.
  • Generated valid Croissant JSON-LD that fully complies with the v1.0 spec.

Related

Closes #13

@rafiattrach rafiattrach added enhancement New feature or request and removed enhancement New feature or request labels Nov 23, 2025
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Very cool, thanks @rafiattrach!

@tompollard tompollard merged commit e7f9a5c into main Nov 23, 2025
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@tompollard tompollard deleted the feat/add-mimic-omop-test branch November 23, 2025 22:09
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Add Next Dataset Support (FHIR/OMOP/DICOM)

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