flybase/ftyp-db repository overview

⁠Fast Track Your Paper (FTYP)

A tool for expediting curation of published research in genetic databases.

⁠Requirements

• Docker
• Docker compose
• Git
• PostgreSQL client (pg_dump and psql commands)

⁠Getting started

1. Clone repo

git clone https://github.com/FlyBase/fast-track-your-paper.git
cd fast-track-your-paper

1. Create credentials file

touch .env

Edit the .env to add your SVN and PostgreSQL credentials. Be sure to replace all values within the angle brackets <> with values for your environment.

SVN_USER=<SVN USERNAME>
SVN_PASSWORD=<SVN PASSWORD>

SRC_PGHOST=<HOSTNAME>
SRC_PGDATABASE=<DATABASE NAME>
SRC_PGPORT=<POSTGRES PORT>
SRC_PGUSER=<POSTGRES USER>

FTYP_PGPASSWORD=<FTYP DATABASE PASSWORD>

1. Pull / load data and start docker containers

make

For full details see the db README⁠.

⁠Makefile targets

• all - Default target that pulls data, starts the containers, and loads the data.
• up - Brings up the docker containers
• down - Brings down and removes the disk volumes
• start - Starts the docker containers
• stop - Stops the docker containers
• clean - Stops the containers, removes the disk volumes, and removes all pulled DB data.
• pull-data - Pulls data from the production Chado database.
• load-data - Loads data from the pulled sources and stores it in the docker DB container.
• build-client - Updates the header/footer and builds the compiled javascript client app.
• export-submissions - Exports the unprocessed submissions into a JSON file suitable for curation processing.
• backup-submissions - Produces a SQL data file containing all rows of the submissions table.
• restore-submissions - Restores all rows from the file produced by backup-submissions.

⁠export-submissions

This target creates a file under db/data/ called ftyp_json.yymmdd.json by default where yymmdd represents the two digit year, month, and day. To override the file you need to pass a variable called SUBMISSION_JSON to this target.

make export-submissions SUBMISSION_JSON=db/data/my-submissions.json
make export-submissions SUBMISSION_JSON=ftyp.json

After the submissions have been exported, they will be marked as processed so that subsequent exports will ignore them.

⁠backup-submissions

Calls the backup_submissions.sh⁠ script to dump all rows of the submissions table. The output is in the db/data/submissions/ directory.

⁠restore-submissions

Calls the restore_submissions.sh⁠ script to restore all rows of the submissions table from the file produced by backup-submissions. This target loads any .sql or .sql.gz file in the db/data/submissions/ directory into the database.

⁠Docker containers

The FTYP tool is broken up into individual docker containers. These containers include:

1. api - A GraphQL interface (Postgraphile) for the Postgres database.
2. client - The React UI code.
3. db - The Postgres database.
4. proxy - An nginx proxy server to put the API and client UI behind a single host/port interface.