The HEAL Platform Software Development Kit (SDK) for Python provides classes and functions for handling HEAL specific tasks.
The qdr_downloads module include a retriever function for downloading files from Syracuse QDR.
This is intended to be called by gen3sdk external download functions. It is also possible to write a wrapper script for the qdr download functions.
In the notebooks directory there are jupyter notebooks that may be used to download files from a corresponding platform. For instance the qdr_data_download.ipynb notebook may be used to download files from Syracuse QDR.
These notebooks perform optimally within a HEAL Gen3 Workspace and the notebooks will be automatically installed to a user's workspace when the workspace is initiated. However, you may also use these notebooks on your local machine.
The VLMD validation docs describe how to use the SDK for validating VLMD dictionaries.
poetry run pytest -vv tests
Until the heal-platform-sdk is available on PyPI, any local pip installs should directly
reference the git repo.
As an example, pip install can be called from the command line for getting
the master branch of the heal-platform-sdk,
pip install -e git+https://github.com/uc-cdis/heal-platform-sdk.git#egg=heal
or a particular branch, eg,
pip install -e git+https://github.com/uc-cdis/heal-platform-sdk.git@my-branch#egg=heal
The specification can also be listed in requirements.txt file (with, say, a tag specification of 0.1.0)
pip install -e git+https://github.com/uc-cdis/[email protected]#egg=heal