DIG-1219: clinical_ETL_code as a package

CanDIG / clinical_ETL_code

A library to convert clinical data in csv format into json documents for CanDIG ingestion

GNU Lesser General Public License v3.0

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DIG-1219: clinical_ETL_code as a package #46

Closed daisieh closed 11 months ago

daisieh commented 11 months ago

If you download/pull the repo, you should be able to run:

# to install source code as a "package"
cd clinical_ETL_code
python -m pip install -e .
pytest

mshadbolt commented 11 months ago

It installs for me but I think we need some updates to the README file to show how to install and import as a package

daisieh commented 11 months ago

I added some info to the README, but then I added a bonus feature: you can now generally make a template for any openapi schema, if you make a schema class for it. I added one for the GenomicSample in ingest:

python src/clinical_etl/generate_schema.py --url https://raw.githubusercontent.com/CanDIG/candigv2-ingest/develop/ingest_openapi.yaml --schema GenomicSchema

will generate a template.csv based on that.