molgenis-emx2-pyclient

The Molgenis EMX2 Pyclient is a 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

Changelog

Releases of the Molgenis EMX2 Pyclient follow the release number of the accompanying release of the Molgenis EMX2 software. Therefore, releases of the Pyclient are less frequent than those of EMX2 and the latest version of the Pyclient may differ from the latest version of Molgenis EMX2.

11.23.0

Added: an optional job argument to the Client initialization, allowing the Pyclient to run asynchronous methods within a job in EMX2."

11.11.1

Added: option to specify filename in method export and to return the exported data in a function

11.8.0

Breaking: introduced asynchronous methods. Users need to explicitly address the asynchronous methods

10.109.3

Added: the ability to use the Pyclient on an EMX2 instance running on a local machine.

10.98.0

Added: the option to filter the results obtained from the get method based on columns

10.92.1

Added: the method upload_file which allows the direct upload of files of multiple types to the API

10.72.1

Fixed: issue where NA values were not properly read in or returned by the API

10.48.9

Fixed: issue in managing data of a table where the table id differs from the table name

10.48.0

Added: option to save data from the get method as a pandas DataFrame

10.47.2

Fixed: exceptions for metadata classes Column and Schema

10.47.0

Added: metadata classes for Column, Table, Schema

10.13.1

Added: methods create_schema, delete_schema, update_schema, recreate_schema, get_schema_metadata

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