BDCat staging release 1666107045

[PlanXCyborg]

copying files from preprod.gen3.biodatacatalyst.nhlbi.nih.gov to staging.gen3.biodatacatalyst.nhlbi.nih.gov

[PlanXCyborg]

staging.gen3.biodatacatalyst.nhlbi.nih.gov/manifest.json

Deployment changes

• awshelper
  • Completely new setup for OHDSI tools (Atlas + WebAPI) — now automated, and similar to any other services and require only kube-setup-ohdsi to configure and roll everything (kube-setup-ohdsi script cloud-automation#2015)
• fence
  • Configure the ALLOWED_DATA_UPLOAD_BUCKETS setting to allow users to upload to buckets other than DATA_UPLOAD_BUCKET (PXP-10361 Allow specifying the upload bucket fence#1051)
  • B/c the default session expiration changed from 30 minutes to 15 minutes to comply with FedRAMP, you MUST ensure that an instance that should comply with FedRAMP does NOT override this fence configuration (e.g. it should be 15 minutes) SESSION_TIMEOUT: 900 (feat(session): change default to 15 minutes [PPS-122] fence#1040)
  • Requires a Fence DB migration (Client.redirect_uri is now optional) (PXP-10113 Client credentials grant fence#1033)
• metadata
  • Database migration for MDS (PXP-10258 feat/alias metadata-service#63)

Breaking changes

• arborist
  • The GET /auth/mapping endpoint does not accept username as a query parameter anymore. It only supports parsing the username from the provided JWT. To specify a username, use the POST /auth/mapping endpoint. (PXP-10229 Client auth mapping arborist#153)
• fence
  • Default session expiration changed from 30 minutes to 15 minutes to comply with FedRAMP (feat(session): change default to 15 minutes [PPS-122] fence#1040)
• indexd
  • Ensure you are using Fence>=2021.10. Remove deprecated GA4GH access endpoints. these have existed (and been used) from the Fence microservice since last year. See cloud automation change here (fix(migrate): improve acl->authz migration, remove deprecated endpoints indexd#336)
• portal
  • Replaced loading the data in iframes in Workspace page with Redirect component. (Add Workspace Registration to Data-Portal data-portal#1067)
  • Deprecating the use of default-workspaces i. e an individual commons will no longer be able to deploy standalone jupyterhub images, they may use hatchery service instead. (Add Workspace Registration to Data-Portal data-portal#1067)
  • studyRegistrationConfig in gitops.json must now be placed within the regsitrationConfigs.features block [Refer this PR] (Add Workspace Registration to Data-Portal data-portal#1067)