biomage-programmatic-interface

\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 = connection.create_experiment('experiment name')

# 3. Upload samples associated with the experiment
experiment.upload_samples('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

Development

If you cloned the repository and want to try using your local version, do the following:

• Install the local version of the pip package:

cd programmatic_interface
make install

• Now you can import the package and use your local version

import biomage_programmatic_interface as bpi

NOTE: There is NO need to run make install every time you make changes to the package. When the local changes have been saved the changes will be automatically reflected.

Running with local instance of Cellenics

When creating the connection object set the instance_url to local. Now the programmatic interface will use your local api (https://localhost:3000)

import biomage_programmatic_interface as bpi
conn = bpi.Connection(<YOUR EMAIL>, <YOUR PASSWORD>, 'local')
...

Running with staged environment

Set the full path of the instance url (e.g. https://api-{ENVIRONMENT NAME}.scp-staging.biomage.net/)

import biomage_programmatic_interface as bpi
conn = bpi.Connection(<YOUR EMAIL>, <YOUR PASSWORD>, 'https://api-{ENVIRONMENT NAME}.scp-staging.biomage.net/')
...

NOTE: the url is that of the api (i.e. api-) and not that of the ui