heal-platform-sdk

The HEAL Platform Software Development Kit (SDK) for Python provides classes and functions for handling HEAL specific tasks.

qdr_downloads

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.

Notebooks

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.

VLMD extraction and validation

The VLMD documentation describes how to use the SDK for extracting and validating VLMD dictionaries.

Run tests

poetry run pytest -vv tests

Pip install for using heal-platform-sdk

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

CLI

The SDK exposes a Command Line Interface (CLI) for some functions.

The CLI can be invoked as follows

heal [OPTIONS] COMMAND [ARGS]

For a list of commands and options run

heal --help

For example, the following can validate a VLMD file in csv format:

heal vlmd validate --input_file "vlmd_for_validation.csv"

The VLMD documentation provides information on using the VLMD functions, such as extract and validate.