Gen3 Monthly Release 2022.07 vpodc.data-commons.org 1658767196

[PlanXCyborg]

Applying version 2022.07 to vpodc.data-commons.org

[PlanXCyborg]

vpodc.data-commons.org

❌ etlMapping.yaml - gitops.json mismatch

• Field error: Field [patients] in explorerConfig.guppyConfig.dataType not found in etlMapping
• Field error: Field [project_id] in explorerConfig.filters.tabs.fields not found in etlMapping
• Field error: Field [Days_To_Birth] in explorerConfig.filters.tabs.fields not found in etlMapping
• Field error: Field [Days_To_Death] in explorerConfig.filters.tabs.fields not found in etlMapping
• Field error: Field [DeceasedFlag] in explorerConfig.filters.tabs.fields not found in etlMapping
• Field error: Field [Ethnicity] in explorerConfig.filters.tabs.fields not found in etlMapping
• Field error: Field [Gender] in explorerConfig.filters.tabs.fields not found in etlMapping
• Field error: Field [Race] in explorerConfig.filters.tabs.fields not found in etlMapping
• Field error: Field [project_id] in explorerConfig.filters.tabs.fields not found in etlMapping
• Field error: Field [ActionableMutations.Lab] in explorerConfig.filters.tabs.fields not found in etlMapping
• Field error: Field [ActionableMutations.Gene] in explorerConfig.filters.tabs.fields not found in etlMapping
• Field error: Field [ActionableMutations.DaysFromAnchorDateToBxDate] in explorerConfig.filters.tabs.fields not found in etlMapping
• Field error: Field [project_id] in explorerConfig.filters.tabs.fields not found in etlMapping
• Field error: Field [Oncology_Primary.Multiplicitycounter] in explorerConfig.filters.tabs.fields not found in etlMapping
• Field error: Field [Oncology_Primary.ICDOSite] in explorerConfig.filters.tabs.fields not found in etlMapping
• Field error: Field [Oncology_Primary.Radiation] in explorerConfig.filters.tabs.fields not found in etlMapping
• Field error: Field [Oncology_Primary.Chemotherapy] in explorerConfig.filters.tabs.fields not found in etlMapping
• Field error: Field [Oncology_Primary.DaysFromAnchorDateToDiagnosisDate] in explorerConfig.filters.tabs.fields not found in etlMapping
• Field error: Field [Oncology_Primary.Gradedifferentiation] in explorerConfig.filters.tabs.fields not found in etlMapping
• Field error: Field [Oncology_Primary.Laterality] in explorerConfig.filters.tabs.fields not found in etlMapping
• Field error: Field [Oncology_Primary.Stagegroupbest] in explorerConfig.filters.tabs.fields not found in etlMapping
• Field error: Field [Oncology_Primary.RadiationsurgerySequence] in explorerConfig.filters.tabs.fields not found in etlMapping
• Field error: Field [Oncology_Primary.Histologyicdo3X] in explorerConfig.filters.tabs.fields not found in etlMapping
• Field error: Field [Oncology_Primary.Lymphvascularinvasionl] in explorerConfig.filters.tabs.fields not found in etlMapping
• Field error: Field [Oncology_Primary.SeerSummaryStage2000] in explorerConfig.filters.tabs.fields not found in etlMapping
• Field error: Field [Oncology_Primary.PhysiciansStage] in explorerConfig.filters.tabs.fields not found in etlMapping
• Field error: Field [Oncology_Primary.DaysFromAnchorDateToMostdefinitivesurgDate] in explorerConfig.filters.tabs.fields not found in etlMapping
• Field error: Field [Oncology_Primary.ChemotherapyFac] in explorerConfig.filters.tabs.fields not found in etlMapping
• Field error: Field [Oncology_Primary.TumorSize] in explorerConfig.filters.tabs.fields not found in etlMapping
• Field error: Field [Oncology_Primary.SequenceNumber] in explorerConfig.filters.tabs.fields not found in etlMapping
• Field error: Field [project_id] in explorerConfig.table.fields not found in etlMapping
• Field error: Field [Race] in explorerConfig.table.fields not found in etlMapping
• Field error: Field [Ethnicity] in explorerConfig.table.fields not found in etlMapping
• Field error: Field [Gender] in explorerConfig.table.fields not found in etlMapping
• Field error: Field [ActionableMutations.Lab] in explorerConfig.table.fields not found in etlMapping
• Field error: Field [Oncology_Primary.Multiplicitycounter] in explorerConfig.table.fields not found in etlMapping
• Field error: Field [Oncology_Primary.ICDOSite] in explorerConfig.table.fields not found in etlMapping

[PlanXCyborg]

vpodc.data-commons.org/manifest.json

Deployment changes

• arborist
  • Replace Travis with a GitHub workflow for CI (Fix lint CI + replace travis with GH workflow arborist#150)
• fence
  • Requires database migration for a new table to Fence, google Access expiration to add new expires column, and to create iss_sub_pair_to_user table Update manifest.json #968 updated BRAIN production data model to 1.0.0 #963 feat(stage-tiered-access): Updated portal versions to fix tiered acce… #973 (Feat/passport fence#964)
  • Requires Arborist >= 2022.04 OR >=3.4.0 (PXP-9480): Support merge param for PUT /resource endpoint arborist#143 (Feat/passport fence#964)
  • To enable Passports -> DRS in an environment you must update Fence Configuration to at a minimum specify GA4GH_PASSPORTS_TO_DRS_ENABLED: true (only do this after coordinating with the environment owner as this has several requirements before it can be enabled, including the need to use Indexd's authz field in ALL records rather than acl) (Feat/passport fence#964)
• portal
  • Added new optional field stridesPortalURL in portal config which can display a link to the STRIDES admin portal on workspace page (HP-708 Feat/multiple paymodels data-portal#978)
  • For decoupled workspace, must work with Hatchery 1.0.0+ (HP-708 Feat/multiple paymodels data-portal#978)

Breaking changes

• fence
  • URL Signing when no_force_sign query param is provided: Previously Fence would make a decision based off if the data was public and no_force_sign provided. Fence will now NEVER sign if no_force_sign is provided (since the concept of "public" data has been abstracted out of Fence. Data access - public or not - is the sole responsibility of the policy engine). In other words, if no_force_sign is provided at the API level, Fence will respect that regardless of whether the resulting URL will actually work. The default Fence behavior should remain the same. chore(jupyter-nde1.1.0) #988 (Feat/passport fence#964)
• hatchery
  • In pay model configs, name has been changed to workspace_type (HP-682 Feat/multiple paymodels  hatchery#44)
  • In pay model configs, aws_account_id has been changed to account_id (HP-682 Feat/multiple paymodels  hatchery#44)
  • In pay model configs, ecs has its type changed from string to bool (HP-682 Feat/multiple paymodels  hatchery#44)
  • In pay model configs, vpcid has been removed (HP-682 Feat/multiple paymodels  hatchery#44)