LIFEDATA

Usage

Create a project specific conda environment (e.g. conda create -n myproject python=3.10) or use your conda base environment

Install lifedata in your environment via pip install lifedata

After lifedata installation use lifedata --help to get help for lifedata commands

Generate your LIFEDATA project by using the project template lifedata init <project instance name>

Further steps can be found in the project's README.

Custom Development

Setup

To create your local development environment (e.g. for integration with your IDE) run:

conda env create

This will create you a local environment called lifedata with all necessary dependencies installed.

Run development server

To start the project related services run:

docker-compose up

You can then access the frontend at http://localhost:3000/ in your browser. The API is available at http://localhost:8000/ and is also proxied via the frontend (to avoid CORS issues).

Storybook can be accessed at http://localhost:3001

Tests

There are tests for the python code as well as tests for the TypeScript based frontend code.

Python Tests

To always keep the tests running and see if everything is still working as expected, run::

ptw

To run the tests once, just do: py.test

TypeScript Tests

Run yarn test in the webui directory.

Database Migrations

If you want to adjust the database tables, you also need to prepare a migration script using alembic in order to provide executable instructions on how to alter the database.

For most cases it's sufficient to change the table definitions in the code and then run::

docker-compose run --rm webapi alembic revision --autogenerate -m "your change message here"

Now inspect the auto generated file if everything is as it is supposed to be.

Then run alembic upgrade head in the api container to apply these changes to your local database.

Citation

coming soon