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CONTRIBUTING.md

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Contributing

Setting up a development environment

  • Confirm you're using the tool versions specified in .tool_versions file, for convenience consider using a tool such as asdf or mise to manage this

  • Create a virtual python environment

  • Install development tools.

    pip install -r dev-requirements.txt
pip install -r website/website-requirements.txt
pip install -r worker/worker-requirements.txt

  • Install and configure git-secrets.

    git secrets --add --literal 'private_key'
git secrets --add --literal 'private_key_id'
git secrets --add --literal 'client_id'
git secrets --add --literal 'client_email'

  • Install pre-commit hooks.

    python -m pre_commit install

Preparing data

Run data pipelines to prepare a local copy of gnomAD and ClinVar data.

Some data pipeline scripts take an intervals argument to select a subset of data. All take a partitions argument to control the number of partitions in the resulting Hail Table.

The Docker Compose configuration for the development environment expects Hail Tables to be located in the data directory.

For example, to prepare data for variants in PCSK9:

python data-pipelines/prepare_gnomad_variants.py --gnomad-version 2 --intervals 1:55505221-55530525 --partitions 2 ./data/gnomAD_v2.1.1_variants.ht
python data-pipelines/prepare_gnomad_variants.py --gnomad-version 4 --intervals chr1:55039447-55064852 --partitions 2 ./data/gnomAD_v4.1.0_variants.ht

python data-pipelines/import_lof_curation_results.py --gnomad-version 2 -intervals 1:55505221-55530525 --partitions=2 ./data/gnomAD_v2.1.1_lof_curation_results.ht

python data-pipelines/import_clinvar.py --reference-genome GRCh37 --intervals 1:55505221-55530525 --partitions 2 ./data/ClinVar_GRCh37_variants.ht
python data-pipelines/import_clinvar.py --reference-genome GRCh38 --intervals chr1:55039447-55064852 --partitions 2 ./data/ClinVar_GRCh38_variants.ht

As a shortcut, to prepare data for variants in PCSK9, run ./scripts/prepare_test_data.sh.

Running in Docker

This assumes that BuildKit is enabled.

  • Configure app. Create a .env file and fill in values for environment variables.

    cat <<EOF > .env
SECRET_KEY=
DB_DATABASE=
DB_USER=
DB_PASSWORD=
GCP_PROJECT=
EOF

    To generate a random secret key, use:

    python -c 'from django.core.management.utils import get_random_secret_key; print(get_random_secret_key());'

  • On first run, start database and apply migrations.

    docker compose up database
docker compose run --rm website django-admin migrate

  • Start all services.

    docker compose up

  • On first run, create a user.

    Users created by the application are inactive by default. The first user cannot be activated through the application UI.

    • Start a REPL.

      docker compose exec website django-admin shell

    • Create a user or activate an existing user.

      from django.contrib.auth import get_user_model
User = get_user_model()

User.objects.create(username="new_user")

User.objects.filter(username="existing_user").update(is_active=True)

Running development tasks

Use nox to run tasks in a virtualenv with necessary dependencies.

Use nox -l to list available tasks. Use nox -s <name> to run a specific task.