biosamples-scripts

Scripts for data manipulation in BioSamples

Script Details

• migrate_domain.py - Change domain of a sample
• curate_samples.py - Add curation to a set of samples
• hipsci_ega_link_import.py- Import EGA links to BioSamples using HipSci data

How to Run

• Copy relevant files into PROJECT_HOME/resources directory.
• Create .env file with configurations
• Install dependencies pip install requirements.txt (consider using virtualenv)
• Run desired script python biosamples/migrate_domain.py

Configurations

Configuration is read from .env file in your project directory. You can copy this from BioSamples internal repository. It should look like below.

BIOSAMPLES_URL=https:localhost:8081
AAP_URL=https://api.aai.ebi.ac.uk/auth
AAP_USERNAME=myUser
AAP_PASSWORD=myPassword
DOMAIN=self.myDomain

DB_URL=localhost
DB_USERNAME=dbUser
DB_PASSWORD=dbPass