Repository navigation

EHR queries - #103

Merged

jeremyestein merged 92 commits into

devfrom

ehr_queries_clean

Oct 2, 2026

Merged

EHR queries#103
jeremyestein merged 92 commits into
devfrom
ehr_queries_clean

Commits on Feb 2, 2026
- first query for flow sheets
  skeating
  committed
  820840d
Commits on Feb 4, 2026
- building up scripts
  skeating
  committed
  fb3d6da
Commits on Feb 19, 2026
- adding more files
  skeating
  committed
  8476351
Commits on Aug 5, 2026
- Merge branch 'dev' into sk/queries
  skeating
  committed
  47240ff
Commits on Sep 9, 2026
- Add and refine SQL scripts for EHR data extraction
  
  skeating
  authored and
  jeremyestein
  committed
  56ceb52
- Refactor lab results query for wide format output
  
  skeating
  authored and
  jeremyestein
  committed
  de65f8d
- Started on functions to wrap snakemake around sql calls
  
  thompson318
  authored and
  jeremyestein
  committed
  4426711
- Started to implement caboodle look up code
  
  thompson318
  authored and
  jeremyestein
  committed
  1b8545a
- Setting up config and docker bits
  
  thompson318
  authored and
  jeremyestein
  committed
  a854492
- Add a ehr location to snakefile
  
  thompson318
  authored and
  jeremyestein
  committed
  7784854
- Tidied up implementation and rewrote Snakefile logic, with help from Claude Sonnet 5.0
  
  thompson318
  authored and
  jeremyestein
  committed
  bdf0eb2
- We don't need a separate container for ehr lookup
  
  thompson318
  authored and
  jeremyestein
  committed
  f4382d2
- Added ehr variables to settings and added a testing flag.
  
  thompson318
  authored and
  jeremyestein
  committed
  de12629
- added some caboodle faking logic to enable local running
  
  thompson318
  authored and
  jeremyestein
  committed
  314a613
- Caboodle setup goes into exporter.env
  
  thompson318
  authored and
  jeremyestein
  committed
  f33621d
- Format fix
  
  thompson318
  authored and
  jeremyestein
  committed
  de875db
- Beginning of test for ehr integration
  
  thompson318
  authored and
  jeremyestein
  committed
  43e9f54
- SQL formatting
  
  thompson318
  authored and
  jeremyestein
  committed
  21e0e5b
- Test with ehr lookup
  
  thompson318
  authored and
  jeremyestein
  committed
  2b28e42
- use caboodle testing
  
  thompson318
  authored and
  jeremyestein
  committed
  d4f2121
- Trying to test ehr and hash lookup with ftps
  
  thompson318
  authored and
  jeremyestein
  committed
  a704072
- Moved sql
  
  thompson318
  authored and
  jeremyestein
  committed
  8bd10d2
- refactored db to make adding ehr lookup implementation clearer
  
  thompson318
  authored and
  jeremyestein
  committed
  76c8d9f
- Started on logic to get flowsheets, first need hospital visit number
  
  thompson318
  authored and
  jeremyestein
  committed
  b7e5ce3
- The exporter needs to access uds, do duplicated some of the config from controller
  
  thompson318
  authored and
  jeremyestein
  committed
  87a8ea1
- Use enviroment to manage sql locations as it varies between containers
  
  thompson318
  authored and
  jeremyestein
  committed
  8219da8
- path into test
  
  thompson318
  authored and
  jeremyestein
  committed
  76144af
- Use format rather than parameters for schema name
  
  thompson318
  authored and
  jeremyestein
  committed
  093563f
- Default for sql path to simplify testing
  
  thompson318
  authored and
  jeremyestein
  committed
  ece4174
- Updated mocked function name in test controller
  
  thompson318
  authored and
  jeremyestein
  committed
  6d3f470
- Enable a fake star db shortcut so that snakemake integration test can run
  
  thompson318
  authored and
  jeremyestein
  committed
  d6b51e8
- Don't connect for fake star
  
  thompson318
  authored and
  jeremyestein
  committed
  f4a629b
- Tidied up getting for hospital visit number
  
  thompson318
  authored and
  jeremyestein
  committed
  df0db43
- return integer hospital visit id
  
  thompson318
  authored and
  jeremyestein
  committed
  e84f031
- (with rewritten history) Merge branch 'sk/queries' into st/queries-to-snakemake
  jeremyestein
  committed
  1363c98
- Added flowsheet query to ehr
  
  thompson318
  authored and
  jeremyestein
  committed
  ca4789a
- moved sql and implemented lab results
  
  thompson318
  authored and
  jeremyestein
  committed
  cba9b54
- Fixed column names in pseudon
  
  thompson318
  authored and
  jeremyestein
  committed
  c0850e5
- Flowsheets and labresults are star, not caboodle
  
  thompson318
  authored and
  jeremyestein
  committed
  f497fc4
- Auto stash before merge of "sk/queries" and "st/queries-to-snakemake"
  
  skeating
  authored and
  jeremyestein
  committed
  8a08337
- star flow sheet query
  
  skeating
  authored and
  jeremyestein
  committed
  b93c17d
- finished star lab queries
  
  skeating
  authored and
  jeremyestein
  committed
  2fc2240
- removed un new scripts and moved read me to current script location
  
  skeating
  authored and
  jeremyestein
  committed
  f946149
- added note about getting scripts from the waveform-private-queries repository as part of deployment
  
  skeating
  authored and
  jeremyestein
  committed
  e249346
- Merge branch 'dev' into sk/queries
  jeremyestein
  committed
  65c74fd
- Post-merge linting fix
  jeremyestein
  committed
  1218cb5
- SCHEMA_NAME is accessed regardless of testing mode, so it has to exist
  jeremyestein
  committed
  6de2a63
Commits on Sep 10, 2026
- Create a space for scripts that can't be in this repo to be installed to
  jeremyestein
  committed
  8c4bf82
- Bring in private SQL scripts
  jeremyestein
  committed
  7968f17
Commits on Sep 11, 2026
- Linting fix
  jeremyestein
  committed
  85ea6ad
- Add private repo to setup instructions
  jeremyestein
  committed
  1e44668
Commits on Sep 14, 2026
- fixup docs for private sql scripts
  jeremyestein
  committed
  5b3222a
- Match changed signature in PIXL ftp method
  jeremyestein
  committed
  d990007
- Use importlib.resources to locate SQL files and thus remove need for
  jeremyestein
  committed
  1dac661
- Document how to do an ad hoc run
  jeremyestein
  committed
  44b1cf3
Commits on Sep 15, 2026
- First go at split of db.py into PG and SQL Server versions
  jeremyestein
  committed
  0163626
- Cursor's first go at PG->MSSQL conversion
  jeremyestein
  committed
  edc39a7
- Delete pointless test that doesn't test anything
  jeremyestein
  committed
  3d22cba
- Define all Caboodle timeouts in seconds to match API
  jeremyestein
  committed
  39d5be6
- timeout needs to be an int
  jeremyestein
  committed
  523407f
- Was getting runtime type error in pd.concat. Now always convert
  jeremyestein
  committed
  4312789
- Fix typo in SQL query
  jeremyestein
  committed
  d2a6775
- Also return DataFrame for MSSQL queries
  jeremyestein
  committed
  3a85bc9
- MSSQL column info is a bit different
  jeremyestein
  committed
  1d5f07d
- Update the list of safe EHR columns to match the queries
  jeremyestein
  committed
  76989a9
Commits on Sep 16, 2026
- First attempt at doing TZ conversion on the DB query input params. Still
  jeremyestein
  committed
  5669337
- Tidy up file structure and naming conventions
  thompson318
  committed
  b75f8ce
- Do pre- and post-query TZ adjustment for SQL Server
  jeremyestein
  committed
  f6944e1
- Merge branch 'ehr_queries_clean' into st/get_ehr
  thompson318
  committed
  ec62ca0
- Prefix EHR query result columns so we don't mix them up
  jeremyestein
  committed
  23d683b
- Fixed test_ehr
  thompson318
  committed
  56a1ac6
- Add sputum query
  jeremyestein
  committed
  fd7214e
- Attempt to switch to parquet but there are some numeric type conversion
  jeremyestein
  committed
  cc7c454
- Fix linting
  jeremyestein
  committed
  a22267c
- These come as floats from Emap so keep them as such here
  jeremyestein
  committed
  aba26b0
- Assert on some EHR parquet data and fix timezone issue in parquet (no
  jeremyestein
  committed
  f37a639
- More data assertions
  jeremyestein
  committed
  54cd710
Commits on Sep 17, 2026
- Check the entire returned dataframe
  jeremyestein
  committed
  8209ee7
- Exclude EHR lookups from the integration test as these have their own
  jeremyestein
  committed
  6151fa3
- Delete the test EHR code as it was out of date now and we have another
  jeremyestein
  committed
  6cbbf50
- Bring in file layout changes but this was assuming CSV EHR data so will
  jeremyestein
  committed
  ea3ea7d
- Merge fixup: make filenames reflect that they're parquets. Put them in
  jeremyestein
  committed
  3072b40
- Fixup to remove EHR from integration test
  jeremyestein
  committed
  51767f3
- Add exporter config flag to bypass EHR lookup with dummy output file so
  jeremyestein
  committed
  3c8a0c3
- Include EHR files in the DSH upload
  jeremyestein
  committed
  fc2d192
- Had forgotten TubeType column
  jeremyestein
  committed
  19cd385
- GROUP BY was using old names
  jeremyestein
  committed
  73db88a
- Add logging to show number of rows retrieved from EHR
  jeremyestein
  committed
  9c51055
Commits on Sep 28, 2026
- Clarify that we're not using wildcards here
  jeremyestein
  committed
  97cbeb4
- Clear up docs after review comments
  jeremyestein
  committed
  42ced62
Commits on Sep 30, 2026
- Pin versions of type stubs that mypy is using so we don't get sudden
  jeremyestein
  committed
  7091095
Commits on Oct 1, 2026
- Add repositioning query to the EHR queries
  jeremyestein
  committed
  d6efd26

Commits

Commits on Feb 2, 2026

Commits on Feb 4, 2026

Commits on Feb 19, 2026

Commits on Aug 5, 2026

Commits on Sep 9, 2026

Commits on Sep 10, 2026

Commits on Sep 11, 2026

Commits on Sep 14, 2026

Commits on Sep 15, 2026

Commits on Sep 16, 2026

Commits on Sep 17, 2026

Commits on Sep 28, 2026

Commits on Sep 30, 2026

Commits on Oct 1, 2026