biomage-programmatic-interface 0.0.23

For programmatic upload of files to Cellencis

\n# biomage-programmatic-interface

About

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

Installation

To install the package execute the following line: pip install biomage-programmatic-interface

Usage

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

Then the package is used in the following way:

import biomage_programmatic_interface as bpi

# 1. Authenticate user and create a connection tunnel with the api
# Default instance-url: https://api.scp.biomage.net/
connection = bpi.Connection('email', 'password', 'instance_url')

# 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 Biomage and process your project there.

Connection class

The object accepts 3 parameters:

1. email - Biomage email
2. password - Biomage password
3. instance_url - Biomage instance url
   • Copy the url of the Biomage instance excluding https://
   • If the url is https://scp.biomage.net/ enter just the domain name: scp.biomage.net

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 Biomage 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 in setup.cfg and requirements.txt then build it using the bash script:

./pip-build-upload.sh

How to build the docker images

After requirements.txt has been updated with the correct package version run:

./docker-build-upload.sh {version}

where version is the version of the docker image, e.g. 0.0.3