Python client for the Molgenis EMX2 API
Project description
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
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 git@github.com: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
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