Biota DB Zipper

A task that zips the local Biota MariaDB data folder so it can be uploaded to the cloud S3 bucket to declare a new version of the Biota database.

Overview

The Biota database is hosted in a MariaDB Docker container whose data directory (/var/lib/mysql) is mounted on the host through the LAB_VOLUME_HOST_NO_BACKUP volume defined in gws_biota/db/docker-compose.yml. This task locates the host directory backing that volume via DockerService.get_volume_local_path (with include_in_backup=False) and creates a zip archive of its content.

This replaces the manual prepare_db.sh script previously executed inside the database Docker container.

Input/Output

• Inputs: None
• Output: File resource pointing to the generated zip archive

Notes

• The Biota DB Docker compose must have been registered (e.g. via BiotaDbDownloader) so that the host volume exists.
• For consistency, it is recommended to stop the database container before running this task to avoid zipping data while MariaDB is writing to disk.