Metadata-Version: 2.2
Name: OMOP-MEDS
Version: 0.0.3
Summary: An ETL to convert OMOP data to the MEDS format.
Author-email: Robin van de Water <robin.vandewater@hpi.de>, Matthew McDermott <mattmcdermott8@gmail.com>
Project-URL: Homepage, https://github.com/rvandewater/OMOP_MEDS
Project-URL: Issues, https://github.com/rvandewater/OMOP_MEDS/issues
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.11
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: meds-transforms>=0.1
Requires-Dist: requests
Requires-Dist: beautifulsoup4
Requires-Dist: hydra-core
Requires-Dist: loguru
Requires-Dist: polars
Provides-Extra: dev
Requires-Dist: pre-commit<4; extra == "dev"
Provides-Extra: tests
Requires-Dist: pytest; extra == "tests"
Requires-Dist: pytest-cov; extra == "tests"
Provides-Extra: local-parallelism
Requires-Dist: hydra-joblib-launcher; extra == "local-parallelism"
Provides-Extra: slurm-parallelism
Requires-Dist: hydra-submitit-launcher; extra == "slurm-parallelism"

# MEDS OMOP ETL with MEDS-Transforms

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An ETL pipeline for transforming OMOP datasets into the MEDS format using the MEDS-Transforms library.
Thanks to the developers of the first OMOP MEDS ETL, from which we took inspiration,
which can be found here: https://github.com/Medical-Event-Data-Standard/meds_etl.
We currently support OMOP 5.3 and 5.4 datasets.

```bash
pip install OMOP_MEDS # you can do this locally or via PyPI
# Download your data or set download credentials
OMOP_MEDS root_output_dir=$ROOT_OUTPUT_DIR

```

Example config:

```yaml
dataset_name: MIMIC_IV_OMOP
raw_dataset_version: 1.0
omop_version: 5.3

urls:
  dataset:
    - https://physionet.org/content/mimic-iv-demo-omop/0.9/
    - url: EXAMPLE_CONTROLLED_URL
      username: ${oc.env:DATASET_DOWNLOAD_USERNAME}
      password: ${oc.env:DATASET_DOWNLOAD_PASSWORD}
  demo:
    - https://physionet.org/content/mimic-iv-demo-omop/0.9/
  common:
    - EXAMPLE_SHARED_URL # Often used for shared metadata files
```

## Citation
