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FTYP Database Container

Docker container

The FTYP database is provided by a docker container running PostgreSQL 10 with the production Chado schema and select data from a production Chado instance. Upon starting DB container, the database will have an empty Chado instance with additional flybase specific functions added from the FlyBase Chado repo.

Requirements

  • A cloned fast-track-your-paper repo
  • Docker / Docker compose installed
  • A docker container running the db service
  • A connection (direct or ssh tunnel) to a production chado database

Data

The following describes how to get data in and out of the FTYP database.

Loading

FTYP requires a certain amount of data from a production Chado instance. Pulling all of the data is time consuming and overkill so only a slice of Chado is pulled into the FTYP database for its purposes. This mainly consists of reference and gene data. Pulling data from production Chado consists of the following steps

Pull data from db (outside of docker) ---> Store locally ---> Load (inside of docker)

To pull data, start the docker db service and execute the following script outside of docker. Replace all bracketed terms with their appropriate value.

Please ensure that your connection details are valid or this step will not work. In other words, check that the database or tunnel that you are pointing to is up and working.

cd fast-track-your-paper/db
PGHOST=<hostname> PGUSER=<username> PGPORT=<port> PGDATABASE=<dbname> ./scripts/pull_chado_data.sh

This will query the production chado database and place the data under the db/data directory. Once the data has been pulled, you initiate a load into the DB service container by this command.

cd fast-track-your-paper
docker-compose up -d --build
docker-compose exec -u postgres db /ftyp/scripts/load_chado_data.sh

Docker volumes

This docker container defines a local disk volume in which it stores all the database files. This ensures that your database sticks around in between start/stop operations.

To remove this volume and rebuild the container use the following commands:

docker-compose down -v
docker-compose up -d --build