MOLGENIS Commander makes managing your MOLGENIS application a breeze! It offers a rich set of commands for oft-repeated actions like importing datasets and managing groups and users. Besides catering to the data oriented user it also aims to provide an extensive toolkit for developers working on MOLGENIS.
Easily add groups and users and configure their roles:
Import datasets with a single command:
Tie it all together by creating a script:
For a full list of features, go:
mcmd --help
In a terminal, run:
pip install molgenis-commander
Want to help out? Fork and clone this repository, go to the root of the project and create a virtual environment:
python -m virtualenv env
Now activate the environment. How to do this depends on your operating system, read the virtualenv docs for more info. The following example assumes MacOS:
source env/bin/activate
Then install the project in development mode:
pip install -e .
The mcmd command will now be available in this virtual environment! If you want to
leave the environment, use deactivate.
The project contains unit- and integration tests.
To run all the unit tests from the command line, go:
python setup.py test --addopts "-m unit --ignore=tests/integration/"
The integration tests require a running MOLGENIS application to test against. They can be run like this:
python setup.py test --addopts "-m integration --ignore=tests/unit/"
By default the localhost is chosen (username: admin, password: admin), but it's possible to configure a different server:
python setup.py test --addopts "-m integration --ignore=tests/unit/ --url=<your_url> --username=<admins username> --password=<admins password>"
To run the tests in PyCharm, first set the default test runner to 'pytest'.
Then create pytest run configurations, by going to Edit Configurations -> + -> Python tests -> pytest and using
the same arguments as above:
