girder / miqa

MIQA v2

MIQA

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

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 3.8
3. Install psycopg2 build prerequisites
4. Create and activate a new Python virtualenv
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

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 miqa.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.

miqa's Issues

Track provenance of annotation changes

Keep a record of who made an annotation change at what time.

I believe auto-generated notes would be acceptable, though something tied more explicitly to annotation values (a separate list of time/user/value instead of converting the value to note text) could be done instead.

Rename domain objects in UI

I think I have this right:

• Rename Session to Scan on main page
• Rename Sessions to Experiments on top nav and sidebar

Bulk insert, possibly use UUID pkeys

Disable editing of historical notes

A possible exception is to be able to edit the last note (or the last note made by you?), but I'd recommend just disabling note editing for now. Provenance of notes was stated as an important feature, so just making them read-only after creation seems safest.

Fix Site/Experiment name display in UI

Display user-friendly name instead of database ID.

Perform performance benchmarking test against prior version

I believe the critical time to measure is the time elapsed from selecting an experiment to load on the left panel to being able to scrub through all scan images in the experiment and have them render on screen for rapid inspection.