python client for transmart rest api
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README.md

Python client for retrieving data from tranSMART

Build Status codecov Binder

This is meant to work with Python 3.x only.

Installation

pip3 install transmart for minimal dependencies, but only administrative calls are available.

pip3 install transmart[full] for the full thing.

Demo

Launch the live demo notebook using Binder

Usage

Main client

See the notebook in ./examples or go live via the binder link above.

Entry points

After installing via pip there should be a CLI tool available to add necessary roles to KeyCloak.

$ transmart-keycloak --help
Usage: transmart-keycloak [OPTIONS]

Options:
  -t, --transmart TEXT  tranSMART host url, e.g. https://transmart-
                        dev.thehyve.net.  [required]
  -k, --kc-url TEXT     KeyCloak host, e.g. https://keycloak-dwh-
                        test.thehyve.net.  [required]
  -r, --realm TEXT      KeyCloak realm.  [required]
  -u, --user TEXT       KeyCloak username.
  -p, --password TEXT   KeyCloak password, will be asked for if not provided.
  -s, --study TEXT      Add roles for this study IDs. If not provided, add all
                        studies.
  --version             Show the version and exit.
  --help                Show this message and exit.