MOLGENIS Commander

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.

Want to get started right away? Read Getting started on the wiki!

Teaser

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

How to install

You can install the Commander using pip. For more information and troubleshooting tips, see the Installation guide

Scripts

It's possible to collect multiple commands in a script. Please read the Scripts documentation for more information.

Development

Want to help out? Fork and clone this repository, go to the root of the project and create a virtual environment:

python -m venv 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.

Running tests

The project contains unit- and integration tests.

Running tests from the command line

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>" 

Running tests in PyCharm

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: