Gen3 Monthly Release 2025.01 staging.chordshealth.org 1736458135

[PlanXCyborg]

Applying version 2025.01 to staging.chordshealth.org

[github-actions]

staging.chordshealth.org/manifest.json

Deployment changes

• fence
  • activation of the feature depends on a new configuration setting: ALLOW_NEW_USER_ON_LOGIN (Feat: only allow login of onboarded users fence#1184)
  • any env that has S3 buckets in fence config that has wildcard characters should consider adopting this release (Fix/bucket name fence#1193)
  • New configuration has been added into Fence config for requester pay enabled AWS S3 buckets, please refer to /fence/config-default.yaml for details (aws requester pays fence#1173)
  • Requires database migration (Remove Foreign Key Constraints for Service Account fence#1172)
• guppy
  • To enable this feature in helm charts add "allowRefresh": {{ .Values.allowRefresh }} to gen3-helm/helm/guppy/templates/guppy_config.yaml and then in your values.yaml file, specify allowRefresh as the boolean true value. (Feature/refresh guppy#273)
  • Important: all envs that has tiered access enabled should deploy a Guppy that has this fix (fix apply hide number resolver to as text agg results guppy#274)
• indexd
  • sqlite databases are not supported anymore ((PPS-107): Feat/single table driver indexd#376)
  • To run single table migration check this doc: https://github.com/uc-cdis/indexd/blob/master/docs/migration_to_single_table_indexd.md ((PPS-107): Feat/single table driver indexd#376)
• portal
  • new config option dataDictionaryVersion that can be set to "new" or something else. If "new", then the new data dictionary component is loaded. This is a temporary solution until we have fully deprecated the old one. (Feat: enable old and new data dictionary for VA data-portal#1613)
  • The VLMD syntax in HEAL MDS has been updated (HP-1484 HP-1617 Feat/cde submission data-portal#1547)
  • kayakoConfig section in portal config has been replaced by zendeskConfig, please refer to /docs/portal_config.md (HP-1646 Feat/zendesk data-portal#1587)
  • for details (HP-1646 Feat/zendesk data-portal#1587)
  • Discovery: The Pending state has been renamed to Waiting and has became the default state for metadata that doesn't have an authz value. If an env is using this state, it needs to update its portal config accordingly (HP-1525 Feat/disco status icon data-portal#1558)
  • Need to update to CEDAR wrapper 0.5.0 https://github.com/uc-cdis/cedar-wrapper-service/releases/tag/0.5.0 for this feature (Chore/update get clinical trial metadata function data-portal#1540)
• sower.container.image.get-dbgap-metadata
  • Manifest.json files MUST be changed to use the new "batch-export-sa" service account and the "BUCKET" environment variable must be set to the batch-export-g3auto secret with the "bucket_name" key. You also no longer need to mount the batch-export-g3auto secret as this is now deprecated (it is replaced by the batch-export-g3auto configmap). (Export Job to IRSA sower-jobs#53)
• sower.container.image.metadata-manifest-ingestion
  • Manifest.json files MUST be changed to use the new "batch-export-sa" service account and the "BUCKET" environment variable must be set to the batch-export-g3auto secret with the "bucket_name" key. You also no longer need to mount the batch-export-g3auto secret as this is now deprecated (it is replaced by the batch-export-g3auto configmap). (Export Job to IRSA sower-jobs#53)
• sower.container.image.pelican-export
  • Our Helm charts utilize eternal secrets to create and manage our secrets. The new Peregrine-dbcreds secret is formatted differently and no longer uses json, so we need to edit the export job so the values can be read via environment variables. (updating job export to work with Helm pelican#89)
  • basing the pelican images off of a more secure AL base image. (making al base image updates to pelican export image pelican#88)

Breaking changes

• fence
  • remove role field from /admin/user POST endpoint (Feat: remove role from POST /admin/user endpoint fence#1202)
  • set User.is_admin to DEPRECATED (Feat: remove role from POST /admin/user endpoint fence#1202)
  • deprecation notices for future breaking changes where we'll remove a number of legacy endpoints (Feat: deprecate legacy unused /admin/ endpoints fence#1201)
  • some of the admin endpoints and methods now expect username instead of name. (Feat: add support for soft delete user fence#1189)
  • New Database Migration (using alembic) was added and is required. (Chore/pps-301 fence#1114)