neurostuff

Requirements: Docker and docker-compose.

Configuration

First, set up the main environment variables in .env (see: .env.example).

cp .env.example .env

Next, set up the Flask server's environment variables:

cp neurostuff/example_config.py neurostuff/config.py

Edit both of these template files to set the correct variables

Initalizing backend

Build the containers and start services using the development configuration:

docker-compose build
docker-compose -f docker-compose.yml -f docker-compose.dev.yml up -d

The server should now be running at http://localhost/

Next, migrate and upgrade the database migrations.

docker-compose exec neurostuff \
    bash -c \
        "python manage.py db merge heads && \
         python manage.py db stamp head && \
         python manage.py db migrate && \
         python manage.py db upgrade"

Note: python manage.py db merge heads is not strictly necessary unless you have multiple schema versions that are not from the same history (e.g., multiple files in the versions directory). However, python manage.py db merge heads makes the migration more robust when there are multiple versions from different histories.

Finally, add an admin user, and ingest data

docker-compose exec neurostuff \
    bash -c \
        "python manage.py add_user admin@neurostuff.org password && \
         python manage.py ingest_neurosynth"

Maintaining docker image and db

If you make a change to /neurostuff, you should be able to simply restart the server.

docker-compose restart neurostuff

If you need to upgrade the db after changing any models:

docker-compose exec neurostuff python manage.py db migrate
docker-compose exec neurostuff python manage.py db upgrade

Running tests

To run tests, after starting services, create a test database:

docker-compose exec postgres psql -h postgres -U postgres -c "create database test_db"

NOTE: This command will ask you for the postgres password which is defined in the .env file.

and execute:

docker-compose run -e "APP_SETTINGS=neurostuff.config.DockerTestConfig" --rm -w /neurostuff neurostuff python -m pytest neurostuff/tests