Optimal Transport Morphometry

Develop with Docker (recommended quickstart)

This is the simplest configuration for developers to start with.

Initial Setup

1. Run docker-compose run --rm django ./manage.py migrate
2. Run docker-compose run --rm django ./manage.py createsuperuser and follow the prompts to create your own user
3. Run docker-compose run --rm django ./manage.py populate_db --include-images sample_data/oasis_small.csv to seed the database and generate a sample dataset.

Run Application

1. Run docker-compose up
2. Access the site, starting at http://localhost:8000/admin/
3. When finished, use Ctrl+C

Application Maintenance

Occasionally, new package dependencies or schema changes will necessitate maintenance. To non-destructively update your development stack at any time:

1. Run docker-compose pull
2. Run docker-compose build --pull --no-cache
3. Run docker-compose run --rm django ./manage.py migrate

Develop Natively (advanced)

This configuration still uses Docker to run attached services in the background, but allows developers to run Python code on their native system.

Initial Setup

1. Run docker-compose -f ./docker-compose.yml up -d
2. Install Python 3.9
3. Install psycopg2 build prerequisites
4. Create and activate a new Python virtual environment
5. Run pip install -e .[dev]
6. Run source ./dev/export-env.sh
7. Run ./manage.py migrate
8. Run ./manage.py createsuperuser and follow the prompts to create your own user
9. Run ./manage.py populate_db sample_data/oasis_small.csv

Run Application

1. Ensure docker-compose -f ./docker-compose.yml up -d is still active
2. Run:
   1. source ./dev/export-env.sh
   2. ./manage.py runserver
3. Run in a separate terminal:
   1. source ./dev/export-env.sh
   2. celery --app optimal_transport_morphometry.celery worker --loglevel INFO --without-heartbeat
4. When finished, run docker-compose stop

Remap Service Ports (optional)

Attached services may be exposed to the host system via alternative ports. Developers who work on multiple software projects concurrently may find this helpful to avoid port conflicts.

To do so, before running any docker-compose commands, set any of the environment variables:

• DOCKER_POSTGRES_PORT
• DOCKER_RABBITMQ_PORT
• DOCKER_MINIO_PORT

The Django server must be informed about the changes:

• When running the "Develop with Docker" configuration, override the environment variables:
  • DJANGO_MINIO_STORAGE_MEDIA_URL, using the port from DOCKER_MINIO_PORT.
• When running the "Develop Natively" configuration, override the environment variables:
  • DJANGO_DATABASE_URL, using the port from DOCKER_POSTGRES_PORT
  • DJANGO_CELERY_BROKER_URL, using the port from DOCKER_RABBITMQ_PORT
  • DJANGO_MINIO_STORAGE_ENDPOINT, using the port from DOCKER_MINIO_PORT

Since most of Django's environment variables contain additional content, use the values from the appropriate dev/.env.docker-compose* file as a baseline for overrides.

Testing

Initial Setup

tox is used to execute all tests. tox is installed automatically with the dev package extra.

When running the "Develop with Docker" configuration, all tox commands must be run as docker-compose run --rm django tox; extra arguments may also be appended to this form.

Running Tests

Run tox to launch the full test suite.

Individual test environments may be selectively run. This also allows additional options to be be added. Useful sub-commands include:

• tox -e lint: Run only the style checks
• tox -e type: Run only the type checks
• tox -e test: Run only the pytest-driven tests

To automatically reformat all code to comply with some (but not all) of the style checks, run tox -e format.

Database seeding

Developers should run the following command to generate a dataset and relevant image data in their dev instance:

docker-compose run --rm django ./manage.py populate_db sample_data/oasis_small.csv

For now, this ensures the existence of a test dataset, and generates a pending upload batch into it.

Authentication Setup

In order to set up authentication for your local development environment, you need to create an application which will issue a client_id to set in your client app. Visit http://localhost:8000/admin/oauth2_provider/application/ and create a new one.

The settings for your new application should be as follows:

• Redirect URLs: http://localhost:8080/datasets (no trailing slash)
• Client type: Public
• Authorization grant type: Authorization code
• Client Secret: empty
• Name: A descriptive name of your choosing

In the client app directory (otm-client, currently a private repository), create a new file .env.development.local and set VUE_APP_OAUTH_CLIENT_ID to the value found in your application's "Client ID" field. This value represents a new OAuth2 public client ID.

Acknowledgement

This work was supported by the National Institute Of Mental Health of the National Institutes of Health under Award Number R42MH118845. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.