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mmcdermott
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MEDS_transforms
A simple set of MEDS polars-based ETL and transformation functions
MIT License
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[WIP] Adds AUMCdb example
#203
rvandewater
opened
14 hours ago
1
add_time_derived_measurements breaks if you use _script in the meds_transform_runner
#202
Oufattole
opened
2 weeks ago
1
All stages must have unique names or an error should be thrown.
#201
mmcdermott
opened
2 weeks ago
0
Stages that depend on code metadata having been recently computed (e.g., `filter_measurements`) should be better documented
#200
mmcdermott
opened
2 weeks ago
1
Hotfix 0.0.8
#199
mmcdermott
closed
2 weeks ago
2
Tokenization Stage Misalignment Fix
#198
Oufattole
closed
2 weeks ago
2
Misalignment Between Static and Event Sequence DataFrames
#197
Oufattole
closed
2 weeks ago
2
Add wget blocks to run.sh for MIMIC and eICU pipelines
#196
coderabbitai[bot]
opened
2 weeks ago
0
Should distribute / package typing information too
#195
mmcdermott
opened
2 weeks 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 weeks ago
1
Release Candidate 0.0.7
#193
mmcdermott
closed
2 weeks ago
2
Add appropriate dots into MIMIC metadata files for omop matching.
#192
mmcdermott
closed
2 weeks ago
2
Upgraded polars and set infer schema to false for metadata extraction.
#191
mmcdermott
closed
2 weeks 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 weeks ago
0
Various MIMIC-IV fixes and improvements
#189
mmcdermott
closed
2 weeks ago
2
The unzipping solution causes errors if files have already been unzipped in the MIMIC-IV example
#188
mmcdermott
closed
2 weeks 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 weeks 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
3 weeks ago
0
Adds a test case to document the behavior for #156.
#185
mmcdermott
closed
3 weeks ago
2
Refactors and adds stage-specific extraction tests to enable more targeted testing of metadata extraction pipeline improvements.
#184
mmcdermott
closed
3 weeks ago
2
MEDS-Extract Tests should be re-factored and split into multiple single-stage tests and one full-pipeline test
#183
mmcdermott
closed
3 weeks ago
0
Duplication between `text_value` and `numeric_value` should be ignored when possible.
#182
mmcdermott
closed
2 weeks ago
0
The MIMIC ETL does not fully normalize parent codes to omop vocabs.
#181
mmcdermott
closed
2 weeks ago
2
Should pull the generic hydra resolvers (e.g., `get_script_docstring`) into a separate package
#180
mmcdermott
opened
3 weeks ago
0
Improve tests and test coverage.
#179
mmcdermott
closed
3 weeks ago
2
MEDS-transforms should be usable under python 3.11 as well as 3.12
#178
mmcdermott
closed
3 weeks ago
2
We need a more robust interface for ways of (a) processing numerical and categorical values and (b) normalizing output data in light of those modes.
#177
mmcdermott
opened
3 weeks ago
5
See if we can support Python 3.11
#176
mmcdermott
closed
3 weeks ago
0
Release Candidate 0.0.6
#175
mmcdermott
closed
3 weeks ago
2
There should be an immediate way to identify when an entire stage has completed so entire pipelines can more directly short-circuit
#174
mmcdermott
closed
2 weeks ago
1
Updating to MEDS v0.3.2 by correcting the subject ID field name.
#173
mmcdermott
closed
3 weeks ago
2
Make compatible with MEDS v0.3.2
#172
mmcdermott
closed
3 weeks ago
0
Added badges to the README.
#171
mmcdermott
closed
1 month ago
2
Add badges to README
#170
mmcdermott
closed
1 month ago
0
DO NOT SUBMIT
#169
mmcdermott
closed
1 month ago
2
If a shard is empty, tensorization crashes.
#168
mmcdermott
closed
1 month ago
0
Adds a multi-stage integration test for pre-processing.
#167
mmcdermott
closed
1 month ago
2
Fixes and expands tests for `aggregate_code_metadata` across various aggregations
#166
mmcdermott
closed
1 month ago
2
Using `do_summarize_all_codes` with `values/quantile` object configuration breaks the mapper
#165
mmcdermott
closed
1 month ago
0
Error message when `aggregate_code_metadata.py` gets an aggregation that should be an object but is just a string should be clearer.
#164
mmcdermott
opened
1 month ago
0
Aggregation integration test should cover all integrations
#163
mmcdermott
closed
1 month ago
0
aggregate_code_metadata Quantile Binning CLI Bug
#162
Oufattole
closed
1 month ago
1
Metadata input dir may be being set improperly to the last metadata stage's output directory instead of the `reducer_output_dir`
#161
mmcdermott
closed
1 month ago
1
Multi-stage integration tests for pre-processing stages in sequence should be added.
#160
mmcdermott
closed
1 month ago
0
Fix tests to expect Float32 throughout and time derived to specifically compute age in float32
#159
mmcdermott
closed
1 month ago
2
Typing should use Float32 Throughout
#158
mmcdermott
closed
1 month ago
1
Remove aggregation of code metadata from default extraction ETL.
#157
mmcdermott
closed
1 month ago
2
Metadata extraction does not appear to be extracting some columns correctly
#156
mmcdermott
closed
3 weeks ago
4
Pipeline Configuration Improvements
#155
mmcdermott
opened
1 month ago
1
Exit metadata extraction if there is no _metadata in the event configs
#154
prenc
closed
1 month ago
5
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