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.

Harvard downloads

The harvard_downloads module include a retriever function for downloading files from Harvard Dataverse.

This is intended to be called by Gen3SDK external download functions. It is also possible to write a wrapper script for the Dataverse download functions.

Notebooks

In the notebooks directory there are jupyter notebooks that may be used to download files from a corresponding platform that requires an external file retriever. For instance the external_data_download.ipynb notebook may be used to download files from data repositories like Syracuse QDR and/or Harvard Dataverse.

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.

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.

Installing the SDK

The heal-platform-sdk is available on PyPI. Local installs can be handled with pip:

pip install heal-sdk

or by poetry, say in a pyproject.toml file:

heal-sdk = ">=1.0.0"

Pip install for specific branches

If a particular branch is desired any pip installs should directly reference the git repo and branch. For example, the following installs the branch my-branch of the SDK:

pip install -e git+https://github.com/uc-cdis/heal-platform-sdk.git@my-branch#egg=heal

Run tests

For local development of the SDK the unit tests are run with:

poetry run pytest -vv tests