molgenis-emx2-pyclient 10.47.0

Python client for the Molgenis EMX2 API

The Molgenis EMX2 Pyclient is Python package developed to be used for data management on Molgenis EMX2 servers. A detailed overview of the capabilities is presented in the MOLGENIS documentation.

Installation

The releases of the package are hosted at PyPI. The recommended way to install the latest version is through pip.

pip install molgenis-emx2-pyclient

How to use

Within your Python project import the class Client and instantiate it as a context manager. Operations and queries can then be executed from within the context.

from molgenis_emx2_pyclient import Client

username = 'username'
password = '...'

with Client('https://example.molgeniscloud.org') as client:
    client.signin(username, password)

    # Retrieve signin information
    print(client.status)
    """ Output:
    Host: https://example.molgeniscloud.org
    Status: Signed in
    Schemas:
        CatalogueOntologies
        catalogue
        ExampleSchema
        ...
    Version: v10.10.1
    """
    
    # Retrieve data from a table on a schema
    data = client.get(schema='ExampleSchema', table='Cohorts')
    
    # Create a new schema on the server
    client.create_schema(name='New Schema')
    
    # Delete a schema from the server
    client.delete_schema(name='New Schema')

Instead of signing in with a username and password the client can also be used while authorized by a (temporary) token that is generated on the server. See the MOLGENIS documentation for generating tokens

from molgenis_emx2_pyclient import Client

token = '...'

with Client('https://example.molgeniscloud.org', token=token) as client:

    # Retrieve signin information
    print(client.status)
    """ Output:
    Host: https://example.molgeniscloud.org
    User: token
    Status: session-less
    Schemas:
        CatalogueOntologies
        catalogue
        ExampleSchema
        ...
    Version: v10.32.1
    """
    
    ...
    ...

Development

Clone the molgenis-emx2 repository from GitHub

git clone [e-mail]:molgenis/molgenis-emx2.git

Change the working directory to .../tools/pyclient

Create a virtual Python environment

On macOS:

python -m venv venv

On Linux:

python3.11 -m venv venv

On Windows:

py -3.11 venv venv

Activate the virtual environment

On macOS and Linux:

source venv/bin/activate

On Windows:

.venv\Scripts\activate.bat

Install the script dependencies

pip install -r requirements.txt

Build

Before building the source, the package build needs to be installed.

(venv) $ pip install build

(venv) $ python -m build

(venv) $ pip install dist/molgenis_emx2_pyclient*.whl