Ensembl Metadata: Ensembl Production Service

The metadata service provides a set of endpoints to allow the ensembl_metadata database to be updated with new data. These endpoints are used by the Ensembl Production handover service and the client that performs bulk updates.

When the service is running, endpoint documentation is available at /api

Installation

Clone the necessary repositories:

git clone https://github.com/Ensembl/ensembl
git clone https://github.com/Ensembl/ensembl-hive
git clone https://github.com/Ensembl/ensembl-prodinf-core
git clone https://github.com/Ensembl/ensembl-prodinf-metadata

Create a virtual environment and install Python requirements:

mkvirtualenv prodinf -p /usr/bin/python3
workon prodinf
pip install -r ensembl-prodinf-core/requirements.txt
pip install -r ensembl-prodinf-metadata/requirements.txt

Hive configuration

The metadata service uses the MetadataUpdater_conf hive pipeline to perform the necessary updates.

SRV=h1-w # Or the MySQL command shortcut for another server
init_pipeline.pl Bio::EnsEMBL::MetaData::Pipeline::MetadataUpdater_conf $($SRV details hive)

Start the beekeeper with the --loop_until FOREVER parameter.

App configuration

The app requires the MySQL uri of the metadata database, and the uri of the pipeline database.

export HIVE_URI='mysql://user:password@host:port/hive_db'
export METADATA_URI='mysql://user:password@host:port/metadata_db'

Alternatively, a yaml file can be used to provide the uris:

export METADATA_CONFIG_PATH=<path>/metadata_config.yaml

Start a local Flask application

BASE_DIR=$(pwd) # Or wherever the repositories were installed
export PYTHONPATH=${BASE_DIR}/ensembl-prodinf-metadata/src:${BASE_DIR}/ensembl-prodinf-core/src
export FLASK_APP=ensembl.production.metadata.app.main
export FLASK_ENV=development
flask run