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INS-1712: DCEG cohorts Sept 2026 - #55
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- Also reorder integer handling to prevent unintended conversion from int to float - Add tests for new function and integer handling
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🟡 Changes recommended
Dataset identity changes and invalid PubMed identifier fields remain unresolved.
Review effort: Balanced
Findings: 1
Open (3)
What changed in this PR
Updates the DCEG Cohorts catalog for INS with September 2026 curated data and improves TSV packaging for Excel-edited files.
Changes:
- Expands the catalog from 15 to 39 records and refreshes metadata.
- Adds UTF-8/CP1252 encoding fallback for curated files.
- Preserves nullable integer formatting and adds regression tests.
| File | Description |
|---|---|
tests/test_package_output_data.py |
Tests encoding fallback and integer serialization. |
modules/package_output_data.py |
Updates curated-file reading and integer conversion order. |
data/02_output/dceg_cohorts/2026-09-28/dceg_datasets_curated_clean.tsv |
Adds the refreshed clean catalog. |
data/02_output/dceg_cohorts/2026-02-03/dceg_datasets_curated_clean.tsv |
Removes the previous clean catalog. |
data/01_intermediate/dceg_cohorts/2026-09-28/dceg_datasets_curated.tsv |
Adds updated curated source records. |
data/01_intermediate/dceg_cohorts/2026-02-03/dceg_datasets_curated.tsv |
Removes the previous curated source. |
config.py |
Selects the September 2026 catalog version. |
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- Move publication URLs to study_links for two datasets and unpack PMIDs - Add filler text for CCSS PMIDs pointing to Related Links - Fix minor typo "and and"
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Update curated input of DCEG Cohorts for INS and processed output after minor standardization and formatting. This PR also includes a minor update to the output TSV packaging steps to better handle artifacts from Excel-curated files.