CEDAR / NVIDIA collaboration
Project description
nvidia-collaboration
OHSU CEDAR Cyclic IF and H&E images
Getting started
Setup python environment
source venv/bin/activate
python3 -m pip install -r requirements.txt
python3 -m pip install -r requirements-dev.txt
python3 -m pip install -e .
Run the import with --plugin_path
gen3_util meta import dir INPUT_PATH OUTPUT_PATH --project_id aced-nvidia --plugin_path {plugin_path}
expected results
data
├── fhir
│ ├── DocumentReference.ndjson
│ ├── Patient.ndjson
│ ├── ResearchStudy.ndjson
│ ├── ResearchSubject.ndjson
│ ├── Specimen.ndjson
│ └── Task.ndjson
Run the tests
pytest tests/
Distribution
- PyPi
# update pypi
# pypi credentials - see https://twine.readthedocs.io/en/stable/#environment-variables
export TWINE_USERNAME= # the username to use for authentication to the repository.
export TWINE_PASSWORD= # the password to use for authentication to the repository.
# this could be maintained as so: export $(cat .env | xargs)
rm -r dist/
python3 setup.py sdist bdist_wheel
twine upload dist/*
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