Setup for local development

Prerequisites

Create hosts entries

Add the following to your hosts file:

127.0.0.1 genepanelbuilder.local api.genepanelbuilder.local

On linux/macs this is typically located at /etc/hosts. On Windows it is located at C:\Windows\System32\drivers\etc\hosts. You will need sudo or administrator privileges to edit this file.

Install git hooks

We use pre-commit to run some checks before committing code. To install pre-commit run the following command:

pip install pre-commit

which will install it globally on your python installation. On MacOS you might want to use brew

brew install pre-commit

Then run the following command to install the git hooks:

pre-commit install

The hooks will check your code for inconsistencies/errors before committing. If you want to run the checks manually, you can run:

pre-commit run

Running the entire stack

To run the entire stack, run the following command:

docker-compose up

You should now be able to access the application at http://genepanelbuilder.local:8080. The API is available at http://api.genepanelbuilder.local:8080.

Running individual services within VSCode

If you want to run individual services within VSCode, you can use the Remote - Containers extension. This will allow you to run the services within a Docker container, and will automatically mount the source code from your local machine.

Simply open VSCode in the directory of the service you want to work on. You will be prompted to reopen the folder in a container. Click "Reopen in Container" and the service will be started within a Docker container.

Testing locally

To run the tests locally, run the following command:

docker compose up -d

Backend unit tests:

docker exec -it gpbuilder pytest

BDD tests:

docker exec -it bdd behave tests

Make sure api types are up to date:

docker exec -it frontend yarn update-api-types
git diff frontend/frontend/api-types.d.ts

You should see no changes.

Development tips and tricks

Errors on running docker compose

A "catch-all" solution to errors when spinning up the app is:

docker compose down --remove-orphans
sudo rm -rf .gpbuilder-docker-data
docker compose build
docker compose up

Database

The following steps will give you a clean database:

docker compose stop postgres gpbuilder
sudo rm -rf .gpbuilder-docker-data/psql
docker compose up postgres gpbuilder (or start VSCode devcontainer)

By default, the folder .gpbuilder-docker-data/psql will be populated with data from the latest dump on dev. If you are making changes to the datamodel, the dump will be out of sync and the following needs to be done:

Repopulate database: gpb db populate
For bdd tests to run in CI, add "bdd-no-dump" to MR title

Set up TAB-TAB autocompletion in CLI

To se up autocompletion of CLI commands by pushing the TAB-key twice, enter an interactive shell in the gpbuilder container and run

gpb --install-completion
source /home/gpbuilder-user/.bashrc