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The storage for the experimental data used for modeling: omics, strains, media etc

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warehouse

master Branch master Build Status master Codecov

devel Branch devel Build Status devel Codecov

Development

Run make setup first when initializing the project for the first time. Type make to see all commands.

Testing

To run the tests locally, run the following commands

To start the containers:

make start

To run the database migrations for the clean database:

make upgrade

To test locally (will only work correctly if all the commands above are executed):

make test

To stop and delete containers (will not delete the database)

make clean

Environment

Specify environment variables in a .env file. See docker-compose.yml for the possible variables and their default values.

  • Set ENVIRONMENT to either
    • development,
    • testing, or
    • production.
  • SECRET_KEY Flask secret key. Will be randomly generated in development and testing environments.
  • SENTRY_DSN DSN for reporting exceptions to Sentry.
  • ALLOWED_ORIGINS: Comma-seperated list of CORS allowed origins.
  • FLASK_APP: src/warehouse/wsgi.py

Updating Python dependencies

To compile a new requirements file and then re-build the service with the new requirements, run:

make pip-compile build

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