For programmatic upload of files to Cellencis
Project description
biomage-programmatic-interface
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 biomage-programmatic-interface
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 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')
# 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.
Connection
class
The object accepts 3 parameters:
email
- Cellenics email
password
- Cellenics password
instance
- Cellenics instance
'biomage'
- (Default) Cellenics production build'staging'
- Cellenics staging environment
Troubleshooting
Max retries exceeded with url: / (Caused by SSLError(SSLEOFError(8, 'EOF occurred in violation of protocol (_ssl.c:2396)')))
- Navigate to your project in Cellenics and manually delete the failed sample
- 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
Project details
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Source Distribution
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