biomage-programmatic-interface 0.0.4

For programmatic upload of files to Cellencis

cellenics-api

About

This python package provides an easy way to create projects and upload samples into Cellenics.

Installation

To install the package execute the following line: pip install cellenics_api

Usage

In order to use the package you first need to create an account in Cellenics (https://scp.biomage.net/) if you don't have one yet.

Then the package is used in the following way:

import cellenics_api

# 1. Authenticate user and create a connection tunnel with the api
connection = cellenics_api.Connection('email', 'password')

# 2. Create an experiment
experiment_id = connection.create_experiment()

# 3. Upload samples associated with the experiment
connection.upload_samples(experiment_id, 'local/path/to/samples')

Once the upload is complete you can navigate to Cellenics and process your project there.

Troubleshooting

Max retries exceeded with url: / (Caused by SSLError(SSLEOFError(8, 'EOF occurred in violation of protocol (_ssl.c:2396)')))

1. Navigate to your project in Cellenics and manually delete the failed sample
2. Run step #3 again

This will be fixed when error handling is introduced

How to build the pip package

Update the version of the package and then build it:

python3 -m build

twine upload dist/*

How to build the docker images