BioKey is the cancer bioinformatics user registration and profile application.

It's to enable current and future users of LabCAS to help manage their identities, including:

• Registering for a non-EDRN account
• Updating your details, such as your email address or name
• Changing your non-EDRN password

👉 Note: If you have an account with EDRN (Early Detection Research Network), you can use it to access LabCAS and other EDRN applications. If you're not sure if you have an account, visit the EDRN Data Management and Coordinating Center and try to log in. If you can't, you don't.

Make the DB

createdb biokey
./manage.sh makemigrations
./manage.sh migrate wagtailimages  # not sure why this needs to be done separately
./manage.sh migrate

Maybe this is needed?

./manage.sh makemigrations --empty jpledrnbiokeystreams
./manage.sh makemigrations --empty jpledrnbiokeypolicy
./manage.sh makemigrations jpledrnbiokeycontent
./manage.sh makemigrations

Launch it

./manage.sh runserver 6468  # or pick your favorite port

TBD.

TBD.

TBD.

TBD.

First, build the wheels by running:

support/build-wheels.sh

Then build the image:

docker image build --file docker/Dockerfile --tag edrndocker/biokey .

You can do a spot check to see if the image is viable by running

docker container run --rm --env SIGNING_KEY=key --env ALLOWED_HOSTS='*' --publish 8000:8000 \
    edrndocker/biokey:latest

and then visiting http://localhost:8000/. If you get "Server Error (500)", congratulations! It's working.

To launch the orchestrated services (BioKey application, PostgreSQL database, Redis cache/message queue, and Celery worker)—or in other words, to start the composition—run:

docker compose --project-name biokey --file docker/docker-compose.yaml up --detach

Note the many environment variables that are needed. You'll want to put these into a .env file; see the "Environemnt Variables" section, below. Also, after the first launch only, the database is empty and needs to be structured and populated; see the next section.

Create the biokey database in PostgreSQL:

docker compose --project-name biokey --file docker/docker-compose.yaml \
    exec db createdb --username=postgres --encoding=UTF8 --owner=postgres biokey

Make sure the POSTGRES_PASSWORD environment variable has the same value when running this command as you did when you started the composition, above.

Next, run the Django database migrations to turn the empty biokey database into a Django-, Wagtail-, and BioKey-capable database:

docker compose --project-name biokey --file docker/docker-compose.yaml \
    exec app /app/bin/django-admin migrate

Finally, populate the content with:

docker compose --project-name biokey --file docker/docker-compose.yaml \
    exec app /app/bin/django-admin biokey_bloom

TBD.

TBD.

TBD.

TBD.

TBD.

TBD.

You can start by looking at the open issues, forking the project, and submitting a pull request. You can also contact us by email with suggestions.

We use the SemVer philosophy for versioning this software. For versions available, see the releases made on this project.

The principal developer is:

• Sean Kelly

The QA team consists of:

• Heather Kincaid

To contact the team as a whole, email the Informatics Center.

Images used in this software from Pexels, namely:

• "Person Holding A Book" by "cottonbro studio"
• "Red and Green Tree Leaves on a Sunny Day" by "le vy"
• "Black and White Wooden Welcome Sign" by Tim Mossholder

See the Pexels license.

The software is licensed under the Apache version 2 license.