feat(nlp): add a variety of --cohort-* args to filter notes #434
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
mikix
force-pushed
the
mikix/cohort-args
branch
from
9bfeb52 to
94c3e04
Compare
☂️ Python Coverage
Overall Coverage
New FilesNo new covered files... Modified Files
|
mikix
force-pushed
the
mikix/cohort-args
branch
from
94c3e04 to
cb3c027
Compare
mikix
changed the title
Three main new arguments: * --cohort-csv: a csv with a column like patient_id or note_ref * --cohort-anon-csv: same but with anonymized IDs * --cohort-athena-table: same but points at an Athena table To support the Athena option, we have some other new args: * --athena-workgroup: specify the workgroup to use * --athena-database: specify the database to use * --allow-large-cohort: if the table is gigantic, use it anyway (this is here because we have a typo-guard in there - if you accidentally point at the base observation table, we're gonna stop you from downloading a terabyte of data) You can specify the database in the table arg with a period. And the workgroup can be specified via env var or CLI. If we find a docref/dxreport ID/ref column, we'll use that. Otherwise, we'll use a patient ID column and grab all notes for those patients. This cohort filtering replaces instead of augments the previous default filtering of "final" status notes (i.e. skipping draft or superceded notes). But if the user is specifying the IDs manually for us, they must know what they want and we don't need to do the status check for them.
mikix
force-pushed
the
mikix/cohort-args
branch
from
cb3c027 to
5b27f89
Compare
dogversioning
approved these changes
Aug 19, 2025
Comment on lines
+36
to
+40
| - AWS_ATHENA_WORK_GROUP | ||
| - AWS_DEFAULT_PROFILE | ||
| - AWS_DEFAULT_REGION | ||
| - AWS_PROFILE | ||
| - AWS_REGION |
There was a problem hiding this comment.
just noting here that the library uses different names for these same fields - we might want to natter about harmonizing on one (probably this set)
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Three main new arguments:
To support the Athena option, we have some other new args:
You can specify the database in the table arg with a period. And the workgroup can be specified via env var or CLI.
If we find a docref/dxreport ID/ref column, we'll use that. Otherwise, we'll use a patient ID column and grab all notes for those patients.
This cohort filtering replaces instead of augments the previous default filtering of "final" status notes (i.e. skipping draft or superceded notes). But if the user is specifying the IDs manually for us, they must know what they want and we don't need to do the status check for them.
Checklist
docs/) needs to be updated