mmcdermott MEDS_transforms issues

mmcdermott / MEDS_transforms

A simple set of MEDS polars-based ETL and transformation functions

MIT License

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issues

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Update versions of polars and NRT

#228 mmcdermott closed 5 days ago
5
Fixed small typo in test leading to creation of weird directory

#227 mmcdermott closed 5 days ago
2
Should update log tests with pytest-loguru

#226 mmcdermott opened 5 days ago
0
Fix a few test typos

#225 mmcdermott closed 1 week ago
2
Minor fixes in MIMIC_example

#224 prenc closed 1 week ago
2
Adds examples for AUMCdb, eICU, and increases test coverage significantly.

#223 mmcdermott closed 2 weeks ago
2
Passing external splits during extraction fails due to type mismatch between string and Path

#222 mmcdermott closed 2 weeks ago
0
Filtering via the splits map file rather than shard names is broken.

#221 mmcdermott closed 2 weeks ago
0
Error case integration tests should check for the right error message.

#220 mmcdermott opened 2 weeks ago
0
Upgrade nested_ragged_tensors to >= 0.0.8

#219 Oufattole closed 2 weeks ago
1
Improve test coverage further.

#218 mmcdermott closed 2 weeks ago
2
File paths with spaces in them break the runner

#217 mmcdermott opened 2 weeks ago
0
Get test coverage to 100%

#216 mmcdermott opened 3 weeks ago
0
Shoud add a test with non-standard splits

#215 mmcdermott opened 3 weeks ago
0
Operating only on splits via a split file is not appropriately tested.

#214 mmcdermott closed 5 days ago
0
Single stage tester is likely not checking for the right kinds of errors when `should_error` is True

#213 mmcdermott opened 3 weeks ago
0
Update nested-ragged-tensors dependency to >=0.0.8

#212 Oufattole closed 5 days ago
0
Improve test coverage

#211 mmcdermott closed 3 weeks ago
3
Updated the mimic iv tutorial

#210 Oufattole closed 1 week ago
8
Attend to the new "MEDS_DEATH" code

#209 rvandewater closed 3 weeks ago
4
[DRAFT]: 204 we should be able to convert between different ontological code vocabularies

#208 ChaoPang closed 1 month ago
1
eICU example

#207 kingrc15 closed 4 weeks ago
3
#204 Add code translations

#206 prenc opened 1 month ago
7
Static DataFrame Missing Rows for Patients Without Static Data

#205 Oufattole closed 1 month ago
5
We should be able to convert between different ontological code vocabularies.

#204 mmcdermott opened 1 month ago
4
Adds AUMCdb Transformation Configuration

#203 rvandewater closed 3 weeks ago
5
add_time_derived_measurements breaks if you use _script in the meds_transform_runner

#202 Oufattole opened 2 months ago
1
All stages must have unique names or an error should be thrown.

#201 mmcdermott opened 2 months ago
0
Stages that depend on code metadata having been recently computed (e.g., `filter_measurements`) should be better documented

#200 mmcdermott opened 2 months ago
1
Hotfix 0.0.8

#199 mmcdermott closed 1 month ago
5
Tokenization Stage Misalignment Fix

#198 Oufattole closed 2 months ago
2
Misalignment Between Static and Event Sequence DataFrames

#197 Oufattole closed 2 months ago
2
Add wget blocks to run.sh for MIMIC and eICU pipelines

#196 coderabbitai[bot] opened 2 months ago
0
Should distribute / package typing information too

#195 mmcdermott opened 2 months ago
1
Lock files should be pipeline ID specific in some way -- this will enable pipelines to flag when old run locks are present.

#194 mmcdermott opened 2 months ago
1
Release Candidate 0.0.7

#193 mmcdermott closed 2 months ago
2
Add appropriate dots into MIMIC metadata files for omop matching.

#192 mmcdermott closed 2 months ago
2
Upgraded polars and set infer schema to false for metadata extraction.

#191 mmcdermott closed 2 months ago
2
`extract_code_metadata.py` should read in columns contributing to descriptions or parent codes as strings rather than inferring their types.

#190 mmcdermott closed 2 months ago
0
Various MIMIC-IV fixes and improvements

#189 mmcdermott closed 2 months ago
2
The unzipping solution causes errors if files have already been unzipped in the MIMIC-IV example

#188 mmcdermott closed 2 months ago
0
Adds a runner to run an entire pipeline in one command, with optional support for customized per-stage parallelization instructions.

#187 mmcdermott closed 2 months ago
2
Metadata extraction should log a warning if code-part column names are not uniformly either extracted or not extracted across metadata sources.

#186 mmcdermott opened 2 months ago
0
Adds a test case to document the behavior for #156.

#185 mmcdermott closed 2 months ago
2
Refactors and adds stage-specific extraction tests to enable more targeted testing of metadata extraction pipeline improvements.

#184 mmcdermott closed 2 months ago
2
MEDS-Extract Tests should be re-factored and split into multiple single-stage tests and one full-pipeline test

#183 mmcdermott closed 2 months ago
0
Duplication between `text_value` and `numeric_value` should be ignored when possible.

#182 mmcdermott closed 2 months ago
0
The MIMIC ETL does not fully normalize parent codes to omop vocabs.

#181 mmcdermott closed 2 months ago
2
Should pull the generic hydra resolvers (e.g., `get_script_docstring`) into a separate package

#180 mmcdermott opened 2 months ago
0
Improve tests and test coverage.

#179 mmcdermott closed 2 months ago
2