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EHR queries - #103
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EHR queries#103
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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.
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.
…Claude Sonnet 5.0
test and would require mocking inside the container
way of testing this.
need a fixup Merge branch 'st/get_ehr' into ehr_queries_clean
I can test the rest of the pipeline
skeating
approved these changes
Sep 25, 2026
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failures when new versions are released. Fix mypy code issue that occurs in some versions.
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This is now deployed and apparently working on the GAE, along with the branch for PR 1 in the private queries repo.
(vs the original PR: I have linearised the previous branches somewhat and removed all merges from dev (or janitoring), then done a big merge at the end. This took us up to the equivalent of commit 061dca7 in the other branch. Then I made some further fixes.)