feat: update according to production

[m0nhawk]

Link to Jira ticket if there is one:

Environments

• qa-midrc

Description of changes

• updating etlMapping and data-portal config according to production
• update everything relevant to 2022.11

[frankliuao]

Hi @m0nhawk , although I would love to approve it directly but unfortunately I couldn't tell whether the changes to etlMapping.yaml and qa-midrc.planx-pla.net/portal/gitops.json were all correct (I'm sure it is but I'm just not familiar with them enough yet). So I added @cgmeyer as a reviewer. Thanks.

[m0nhawk]

@frankliuao For reference, I copied from the production data.midrc.org, so it should be correct.

[PlanXCyborg]

qa-midrc.planx-pla.net/manifest.json

⚠️ Services on branch

• dicom-viewer
• dicom-server
• frontend-framework

Deployment changes

• 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)
• metadata
  • configuration files will need to be updated (PXP-8825 & BRH 206  metadata-service#65)
  • 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)
• metadata
  • The configuration file is not compatible with the previous release. This is due to the new support for defining a schema, new configuration options, and changes to the adapters. (PXP-8825 & BRH 206  metadata-service#65)
• 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)