The handover app provides a simple endpoint to submit a new database to be checked and copied to the staging server for further automated processing.
The handover app <./src/ensembl/handover/app/main.py>_ is a simple Flask app which defines endpoints for handover. After starting the app, full API documentation is available from /apidocs.
The submission of a handover job triggers the submission of a celery <https://github.com/Ensembl/ensembl-prodinf-handover/blob/master/docs/celery.rst>_ task (handover_database <https://github.com/Ensembl/ensembl-prodinf-handover/blob/master/src/ensembl/production/handover/celery_app/tasks.py>_) which coordinates the necessary processes for checking and importing a database.
First clone this repo
git clone https://github.com/Ensembl/ensembl-prodinf-handover
cd ensembl-prodinf-handover
To install Python requirements using pip:
pip install -r requirements.txt
pip install .
handover_api (for devlopment perpous)
Configuration is minimal and restricted to the contents of config.py <./src/ensembl/handover/config.py>_ which is restricted solely to basic Flask properties.
To start the main application as a standalone Flask application:
export FLASK_APP=ensembl.production.handover.app.main.py
flask run --port 5003 --host 0.0.0.0
or to start the main application as a standalone using gunicorn with 4 threads:
gunicorn -w 4 -b 0.0.0.0:5003 ensembl.production.handover.app.main:app
Note that for production, a different deployment option should be used as the standalone flask app can only serve one request at a time.
There are multiple options, described at:
* http://flask.pocoo.org/docs/0.12/deploying/wsgi-standalone/
* http://flask.pocoo.org/docs/0.12/deploying/uwsgi/
To use a standalone gunicorn server with 4 worker threads:
gunicorn -w 4 -b 0.0.0.0:5001 handover_app:app
The Celery task manager is currently used for coordinating handover jobs. The default backend in config.py is RabbitMQ. This can be installed as per https://www.rabbitmq.com/.
To start a celery worker to handle handover:
celery -A ensembl.production.handover.celery_app.tasks worker -l info -Q handover -n handover@%%h
sudo docker build -t handover .
sudo docker run -p 5000:5000 -it handover:latest