Database Operations

Core Commands

Create DB:

biofilter db create-db --db-uri "sqlite:///biofilter_dev.db"

Check DB:

biofilter db ping --db-uri "sqlite:///biofilter_dev.db"

Migrate schema:

biofilter db migrate --target head
biofilter db migrate --status

Upgrade schema + master seeds:

biofilter db upgrade

Backup / restore:

biofilter db backup --out ./backups/dev.snapshot
biofilter db restore --in ./backups/dev.snapshot

Export / import logical bundle:

biofilter db export --out ./exports/biofilter_bundle --format parquet
biofilter db import --in ./exports/biofilter_bundle --format parquet