St/queries to snakemake - #85
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Introduces new queries for airway and sputum/secretions data, and refactors the flow sheet query to consolidate multiple values into a wider format. A new README documents the overall data extraction goal and the current set of scripts.
…Claude Sonnet 5.0
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## dev #85 +/- ##
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+ Coverage 50.44% 56.52% +6.07%
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Files 14 15 +1
Lines 563 667 +104
Branches 47 54 +7
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+ Hits 284 377 +93
- Misses 263 269 +6
- Partials 16 21 +5 ☔ View full report in Codecov by Harness. 🚀 New features to boost your workflow:
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Transforms specific lab test results (e.g., CRP, WCC) from a long format into distinct columns using `MAX() FILTER`. This enables direct consumption of lab data in a wider format, simplifying downstream analysis. Additionally, the query is updated to use parameters for `hospital_visit_id` and to include date range filtering, improving its flexibility.
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This work in progress. Creating PR as I'll be off till monday in case anyone else wants to take some of it on.