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Migrating to Bento v15

Bento v15 migrates to Phenopackets v2, and as such requires that Phenopackets are updated and re-ingested.

This version also adds the reference service, so permissions must be updated in order to give reference service permissions to administrators and the WES client.

1. Pre-update data removal

Before updating, perform the following steps:

  • Shut down Bento with ./bentoctl.bash stop
  • Remove the Katsu data volume
  • Remove the WES data volume

2. Update images

./bentoctl.bash pull

3. Create new Docker volume directories and networks

./bentoctl.bash init-docker  # new networks for reference and reference-db
./bentoctl.bash init-dirs  # new volume directory for DRS temporary files

4. Set new environment variables

In local.env, set a secure value for BENTO_REFERENCE_DB_PASSWORD.

5. Restart Bento

./bentoctl.bash start

6. Add permissions

Add permissions as needed for reference service content management:

./bentoctl.bash shell authz  # start a shell session in the authz service container to access the authz CLI
bento_authz list grants
# In this list, find the grant IDs for the existing superuser/permissions managers and WES 
bento_authz add-grant-permissions <superuser-grant-id> ingest:reference_material delete:reference_material
bento_authz add-grant-permissions <wes-grant-id> ingest:reference_material delete:reference_material