git clone --recurse-submodules https://github.com/MonashBioinformaticsPlatform/laxy.gitThe Laxy frontend is a Vue.js Single-Page Application that runs in the browser and communicates with a Laxy backend server.
cp -n .env.example .env
cd laxy_frontend
npm install
npm run build:dev
npm run server
open http://localhost:8002/Create .env (see .env.example), change frontend variables as required (eg LAXY_FRONTEND_*).
Environment variables (eg as seen via the env shell command) will override variables read from .env.
npm run build:prodThese variables are used by the Webpack (dotenv-webpack) build to substitute references to process.env.SOME_ENV_VAR.
Dependencies:
- Python 3.6+
# Create a Python virtual environment, install package dependencies
python3.6 -m venv venv
source venv/bin/activate
pip install -U -r requirements.txt
# For development
pip install -U -r requirements-dev.txtRun tests:
./manage.py test --noinputCreate a user and database on Postgres (run psql):
CREATE ROLE laxy WITH LOGIN PASSWORD 'blablafooword';
CREATE DATABASE laxy;
ALTER DATABASE laxy OWNER TO laxy;
GRANT ALL PRIVILEGES ON DATABASE laxy TO laxy;
Configuration is taken from a .env file.
Environment variables (eg LAXY_*) will override any variables defined in .env.
# Copy the example settings environment and edit as required,
# including the database name and password above.
cp -n .env.example .env
vi .env(To manually source the .env file into your login shell for some purpose, do export $(grep -v '^#' .env | xargs)).
Initialize the database, create an admin user:
# ./manage.py migrate contenttypes
./manage.py migrate
./manage.py makemigrations django_celery_results
./manage.py makemigrations sites
./manage.py makemigrations laxy_backend
./manage.py migrate --fake-initial
./manage.py createinitialrevisions
./manage.py makemigrations
./manage.py migrate
./manage.py createsuperuser
# You may want to prepopulate the database with some data
./manage.py loaddata laxy_backend/fixtures.jsonsource venv/bin/activate
DEBUG=yes python3.6 manage.py runserver 0.0.0.0:8000celery -A laxy worker -B -E -Ofair -l info \
--statedb=laxy_celery_worker.stateFLOWER_BASIC_AUTH=user:pass celery -A laxy flower --port=5555OpenAPI / Swagger API (via drf_openapi):
DRF CoreAPI docs: http://localhost:8000/coreapi/
Laxy (and associated services) can run under Docker Compose.
docker-compose -f docker-compose.yml -f docker-compose.dev.yml build --build-arg GIT_COMMIT=$(git log -1 --format=%H)
docker-compose -f docker-compose.yml -f docker-compose.dev.yml up -dOnce running, to watch the logs:
docker-compose logs -f -t
# or for just one service (eg django)
# docker-compose logs -f -t djangoTo manually create the admin user (docker-compose.dev.yml does this itself using
the LAXY_ADMIN_USERNAME and LAXY_ADMIN_PASSWORD environment variables):
docker container exec -it laxy_django_1 \
python manage.py shell -c "from django.contrib.auth import get_user_model; User = get_user_model(); \
User.objects.filter(username='admin').count() or \
User.objects.create_superuser('admin', 'admin@example.com', 'adminpass')"To pull down the stack, do:
docker-compose downMigrate database in Docker container:
export LAXY_ENV=dev
# or if the container isn't running:
docker-compose -f docker-compose.yml -f docker-compose.${LAXY_ENV}.yml run django python manage.py migrateDump fixtures (JSON formatted database records):
docker-compose -f docker-compose.yml -f docker-compose.${LAXY_ENV}.yml run django python manage.py dumpdata --indent 2
# Just the defined ComputeResource records:
docker-compose -f docker-compose.yml -f docker-compose.${LAXY_ENV}.yml run django python manage.py dumpdata \
laxy_backend.computeresource \
--indent 2
# Or a single model of interest, by primary key:
docker-compose -f docker-compose.yml -f docker-compose.${LAXY_ENV}.yml run django python manage.py dumpdata \
laxy_backend.sampleset \
--pks 3lSCcJPlvkMq1oCO6hM4XL \
--indent 2Load fixtures:
# Copy the fixtures to the container (if not already there)
docker cp fixtures.json laxy_django_1:/tmp/
# Apply fixture to the database via Django's loaddata command
docker container exec -it laxy_django_1 python manage.py loaddata /tmp/fixtures.json
# Remove copy of fixtures from container, may contain secrets
docker exec -it laxy_django_1 rm /tmp/fixtures.jsonDropping the test database when it's in use (eg, if tests we terminate prematurely before cleanup).
Run psql:
SELECT pg_terminate_backend(pid)
FROM pg_stat_activity
WHERE datname = 'test_laxy';
DROP DATABASE test_laxy;
In the Docker Compose setup the Postgres database lives in an attached volume container
named laxy_dbdata (dbdata, as defined by PGDATA in docker-compose.yml).
Assuming the Postgres service is called db and it's data volume is dbdata,
we can export a tar archive of the database files like:
DBTAR=postgres-dbdata-$(date +%s).tar
docker-compose run --no-deps --rm -v dbdata:/var/lib/postgresql/data/pgdata -v $(pwd):/backup db tar cvf /backup/${DBTAR} /var/lib/postgresql/data/pgdata
# We can also do this with plain Docker, if we use the correct container name (eg laxy_db_1_*)
# docker run --rm --volumes-from laxy_db_1 -v $(pwd):/backup busybox tar cvf /backup/${DBTAR} /var/lib/postgresql/data/pgdataWe can copy this archive back into a new volume container (database_copy) like:
# DBTAR=postgres-dbdata-*.tar
DBVOLNAME=database_copy
# DBVOLNAME=laxy_dbdata
docker-compose stop db
docker volume create ${DBVOLNAME}
docker run --rm -v ${DBVOLNAME}:/var/lib/postgresql/data/pgdata -v $(pwd):/backup busybox tar xvf /backup/${DBTAR}
docker-compose start dbTo clone the volume 'directly' into a new volume, use the
docker_clone_volume.sh script found here: https://github.com/gdiepen/docker-convenience-scripts like:
./docker_clone_volume.sh laxy_dbdata laxy_dbdata.bak
./docker_get_data_volume_info.shdocker-compose restart djangodocker-compose logs --timestamps --tail="10" -f django./manage.py graph_models --pygraphviz -g -o docs/models_uml.png laxy_backenddocker-compose -f docker-compose.yml -f docker-compose.prod.yml build
docker-compose -f docker-compose.yml -f docker-compose.prod.yml up -d