CDSL MEDS ETL
Configuration-first MEDS-Extract ETL for
COVID Data for Shared Learning (CDSL) v1.0.0.
It maps the tabular EHR data and DICOM metadata, never the IMAGES/ tree.
Run
Three CDSL files are Latin-1 encoded, while MEDS-Extract's CSV reader requires UTF-8.
The MEDS_extract-CDSL command stages a UTF-8 view automatically, without changing
the downloaded files, and then runs meds-extract-run. It takes the same arguments:
uv run MEDS_extract-CDSL spec=CDSL output_dir=cdsl_meds \
do_download=false input_dir=raw_cdsl
Set input_dir to the directory that directly contains patient_01.csv if your
download layout differs. The internal staging step hard-links every other source file
and transcodes only atc7.csv, medication_05.csv, and vital_signs_04.csv.
Mapping
CDSL's dates are deidentified but preserve within-patient chronology and are emitted
directly. Diagnosis, procedure, and neoplasm tables supply no timestamps, so those events
use the explicit 1970-01-01 pseudotime anchor. See
docs/MEDS_ETL_MAPPING.md for the table-level mapping and
limitations.
1 maintainer
Metadata
1 maintainer
Release files for CDSL-MEDS 0.0.1
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| cdsl_meds-0.0.1-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 15.9 kB
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