Gen3 Monthly Release 2022.12 nci-crdc.datacommons.io 1670653953

[PlanXCyborg]

Applying version 2022.12 to nci-crdc.datacommons.io

[PlanXCyborg]

nci-crdc.datacommons.io/manifest.json

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)
• portal
  • this change assumes WTS is already a core/central service. The dependency is hereby moved to the homepage (instead of the ./workspace page) (Centralize WTS refresh token initialization data-portal#1095)

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 (Revert "Revert "fix(migrate): improve acl->authz migration, remove de… indexd#338)
  • 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)

[frankliuao]

Monthly Gen3 release added to the manifest. Approved.

[PlanXCyborg]

nci-crdc.datacommons.io/manifest.json

Deployment changes

• metadata
  • configuration files will need to be updated (PXP-8825 & BRH 206  metadata-service#65)
• portal
  • this change assumes WTS is already a core/central service. The dependency is hereby moved to the homepage (instead of the ./workspace page) (Centralize WTS refresh token initialization data-portal#1095)

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)
• 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 (Revert "Revert "fix(migrate): improve acl->authz migration, remove de… indexd#338)
• 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)

[frankliuao]

Reviewed changes and approving it to run CI

[PlanXCyborg]

nci-crdc.datacommons.io/manifest.json

Deployment changes

• metadata
  • configuration files will need to be updated (PXP-8825 & BRH 206  metadata-service#65)
• portal
  • this change assumes WTS is already a core/central service. The dependency is hereby moved to the homepage (instead of the ./workspace page) (Centralize WTS refresh token initialization data-portal#1095)

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)
• 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 (Revert "Revert "fix(migrate): improve acl->authz migration, remove de… indexd#338)
• 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)

[PlanXCyborg]

nci-crdc.datacommons.io/manifest.json

Deployment changes

• metadata
  • configuration files will need to be updated (PXP-8825 & BRH 206  metadata-service#65)
• portal
  • this change assumes WTS is already a core/central service. The dependency is hereby moved to the homepage (instead of the ./workspace page) (Centralize WTS refresh token initialization data-portal#1095)
• sower
• ssjdispatcher

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)
• 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 (Revert "Revert "fix(migrate): improve acl->authz migration, remove de… indexd#338)
• 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)

[PlanXCyborg]

nci-crdc.datacommons.io/manifest.json

Deployment changes

• metadata
  • configuration files will need to be updated (PXP-8825 & BRH 206  metadata-service#65)
• portal
  • this change assumes WTS is already a core/central service. The dependency is hereby moved to the homepage (instead of the ./workspace page) (Centralize WTS refresh token initialization data-portal#1095)
• sower
• ssjdispatcher

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)
• 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 (Revert "Revert "fix(migrate): improve acl->authz migration, remove de… indexd#338)
• 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)

[PlanXCyborg]

nci-crdc.datacommons.io/manifest.json

Deployment changes

• metadata
  • configuration files will need to be updated (PXP-8825 & BRH 206  metadata-service#65)
• portal
  • this change assumes WTS is already a core/central service. The dependency is hereby moved to the homepage (instead of the ./workspace page) (Centralize WTS refresh token initialization data-portal#1095)
• sower
• ssjdispatcher

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)
• 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 (Revert "Revert "fix(migrate): improve acl->authz migration, remove de… indexd#338)
• 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)

[PlanXCyborg]

nci-crdc.datacommons.io/manifest.json

Deployment changes

• metadata
  • configuration files will need to be updated (PXP-8825 & BRH 206  metadata-service#65)
• portal
  • this change assumes WTS is already a core/central service. The dependency is hereby moved to the homepage (instead of the ./workspace page) (Centralize WTS refresh token initialization data-portal#1095)
• sower
• ssjdispatcher

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)
• 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 (Revert "Revert "fix(migrate): improve acl->authz migration, remove de… indexd#338)
• 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)

[PlanXCyborg]

nci-crdc.datacommons.io/manifest.json

Deployment changes

• metadata
  • configuration files will need to be updated (PXP-8825 & BRH 206  metadata-service#65)
• portal
  • this change assumes WTS is already a core/central service. The dependency is hereby moved to the homepage (instead of the ./workspace page) (Centralize WTS refresh token initialization data-portal#1095)
• sower
• ssjdispatcher

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)
• 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 (Revert "Revert "fix(migrate): improve acl->authz migration, remove de… indexd#338)
• 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)

[PlanXCyborg]

nci-crdc.datacommons.io/manifest.json

Deployment changes

• metadata
  • configuration files will need to be updated (PXP-8825 & BRH 206  metadata-service#65)
• portal
  • this change assumes WTS is already a core/central service. The dependency is hereby moved to the homepage (instead of the ./workspace page) (Centralize WTS refresh token initialization data-portal#1095)
• sower
• ssjdispatcher

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)
• 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 (Revert "Revert "fix(migrate): improve acl->authz migration, remove de… indexd#338)
• 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)

[PlanXCyborg]

nci-crdc.datacommons.io/manifest.json

Deployment changes

• metadata
  • configuration files will need to be updated (PXP-8825 & BRH 206  metadata-service#65)
• portal
  • this change assumes WTS is already a core/central service. The dependency is hereby moved to the homepage (instead of the ./workspace page) (Centralize WTS refresh token initialization data-portal#1095)
• sower
• ssjdispatcher

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)
• 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 (Revert "Revert "fix(migrate): improve acl->authz migration, remove de… indexd#338)
• 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)

[PlanXCyborg]

nci-crdc.datacommons.io/manifest.json

Deployment changes

• metadata
  • configuration files will need to be updated (PXP-8825 & BRH 206  metadata-service#65)
• portal
  • this change assumes WTS is already a core/central service. The dependency is hereby moved to the homepage (instead of the ./workspace page) (Centralize WTS refresh token initialization data-portal#1095)
• sower
• ssjdispatcher

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)
• 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 (Revert "Revert "fix(migrate): improve acl->authz migration, remove de… indexd#338)
• 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)

[PlanXCyborg]

nci-crdc.datacommons.io/manifest.json

Deployment changes

• metadata
  • configuration files will need to be updated (PXP-8825 & BRH 206  metadata-service#65)
• portal
  • this change assumes WTS is already a core/central service. The dependency is hereby moved to the homepage (instead of the ./workspace page) (Centralize WTS refresh token initialization data-portal#1095)
• sower
• ssjdispatcher

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)
• 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 (Revert "Revert "fix(migrate): improve acl->authz migration, remove de… indexd#338)
• 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)

[atharvar28]

The PR is consistently failing dbGaP tests, might be a configuration issue in GCP. Team is working on fixing it. Force merging due to delay by 2 weeks

[frankliuao]

Thank you @BinamB and @atharvar28. This is a special occasion where the deployment can't be held off any longer and we know the code is not breaking production because it has been in staging for almost a month now, plus the team has looked into the tests carefully. Nevertheless, I am responsible for recommending this special exception and for the consequences of it.