molgenis-emx2-pyclient 8.218.2

Python client for the Molgenis EMX2 API

Installation

pip install molgenis_emx2_pyclient

How to use

Within your Python project import the class Client and use it as a context manager

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: v8.214.1
    """
    
    # Retrieve data from a table on a schema
    data = client.get(schema='ExampleSchame', table='Cohorts')

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

(venv) $ python -m build

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