EHR queries - #103
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jeremyestein wants to merge 88 commits into
Open
EHR queries#103jeremyestein wants to merge 88 commits into
jeremyestein wants to merge 88 commits into
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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
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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
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Sep 25, 2026
| ON r.lab_order_id = o.lab_order_id | ||
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| WHERE | ||
| r.result_status LIKE 'FINAL' |
Collaborator
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Actually no you could just use =
| "LabCRP", | ||
| "LabWCC", | ||
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I had envisioned only recording one column of dateTime - but this is probably something we need feedback on
| ("TubeType", pa.string()), | ||
| ("TubeSize", pa.string()), | ||
| # ("Repositioned", ), | ||
| # ("Position frequency", ), |
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Should these be commented out
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| ## Unfinished scripts | ||
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| | script | arguments | record | location of script in repo | database | | ||
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| | script | arguments | record | location of script in repo | database | | ||
| |- | --- | --- |- | --- | | ||
| | airway.sql | csn/today/yesterday | part of the table above | waveform-private-queries/src/sql | caboodle | |
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This one is no longer unfinished
| ) -> pd.DataFrame: | ||
| """Retrieve airflow data from database.""" | ||
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| airway_query = get_sql_query_text("private/airway.sql") |
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Does that address the issue of differences between mssql and postgres time zones? If it does then it seems the most sensible thing to do, if not do you have plans to do that
| None, | ||
| "mL", | ||
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| # Temperature (why no units?) |
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epic doesn't record a unit for temperature !!
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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.)