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St/queries to snakemake - #85

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thompson318 wants to merge 31 commits into
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st/queries-to-snakemake
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St/queries to snakemake#85
thompson318 wants to merge 31 commits into
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st/queries-to-snakemake

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@thompson318

@thompson318 thompson318 commented Aug 19, 2026 •
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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.

  • There some incomplete logic to get EHR in src/electronic_health_records.py
  • Snakemake has been modified to include an ehr_lookup step.
  • Some testing has been done.
  • Runs locally, not tested on GAE yet.
  • snakemake integration tests fails on github as there is not fakeuds. Could add some mocker bits like in test controller.

skeating and others added 29 commits February 2, 2026 15:06
@skeating
first query for flow sheets
820840d
@skeating
building up scripts
fb3d6da
@skeating
adding more files
8476351
@skeating
Merge branch 'dev' into sk/queries
47240ff
@skeating
Add and refine SQL scripts for EHR data extraction
3961143 
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.
@thompson318
Started on functions to wrap snakemake around sql calls
cdec5ca
@thompson318
Started to implement caboodle look up code
9897259
@thompson318
Moved airway sql to sql directory
1f2cfbe
@thompson318
Setting up config and docker bits
bd72361
@thompson318
Add a ehr location to snakefile
5e303f0
@thompson318
Tidied up implementation and rewrote Snakefile logic, with help from …
89e9526 
…Claude Sonnet 5.0
@thompson318
We don't need a separate container for ehr lookup
e0498a2
@thompson318
Added ehr variables to settings and added a testing flag.
f7ac2db
@thompson318
added some caboodle faking logic to enable local running
291be43
@thompson318
Caboodle setup goes into exporter.env
33e2c08
@thompson318
Format fix
9b291cb
@thompson318
Beginning of test for ehr integration
d4fde59
@thompson318
SQL formatting
d910831
@thompson318
Merge branch 'dev' into st/queries-to-snakemake
654db91
@thompson318
Test with ehr lookup
e8f29a7
@thompson318
use caboodle testing
86d5dea
@thompson318
Trying to test ehr and hash lookup with ftps
7fbcfc0
@thompson318
Moved sql
af487e6
@thompson318
refactored db to make adding ehr lookup implementation clearer
b535191
@thompson318
Started on logic to get flowsheets, first need hospital visit number
4f0ba6f
@thompson318
The exporter needs to access uds, do duplicated some of the config fr…
88ba017 
…om controller
@thompson318
Use enviroment to manage sql locations as it varies between containers
72f4935
@thompson318
path into test
29865e0
@thompson318
Use format rather than parameters for schema name
de94422
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2 participants

@thompson318 @skeating