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Core Gen3 Release 2024.02 (Amazonite)

uc-cdis/cloud-automation

Improvements

  • Add CSRF protection for Guppy paths (#2430)
  • Protect Guppy paths from CSRF (#2425)
  • Skip Gender tags for HEAL Cedar ingestion script (#2376)
  • Adds creation of cedar-client and secret if not already present (#2407)

Deployment Changes

  • After merging this, envs must use a data-portal version that contains uc-cdis/data-portal#1464. Otherwise the communication between portal and guppy will be interrupted (#2430)

uc-cdis/data-portal

New Features

  • add ability to hide login link in navigation (#1469)
  • Updates Cohort Middleware API endpoints to use team project, updates storybooks associated with Cohort Middleware API calls with team project (#1472)
  • Adds buttons for Download Study-Level Metadata, Download File Manifest and Download All Files (#1450)
  • adds Login dropdown for single-entry InCommon login (#1466)
  • Adds placeholder application for VADC data dictionary (#1463)
  • Updates the three VADC analysis apps, Gen3 GWAS, GWAS Results and OHDSI Atlas to use API request including query parameter for team projects. (#1451)
  • Adds selected team project in each of the apps: Atlas, GWAS App and Results App and reroutes user back to Analysis Apps view if they do not have a team project selected (#1451)

Improvements

  • Shows error message now for error status from Cohort Definitions endpoint request (#1472)
  • Replace nested empty values with 'null' in explorer display (#1468)
  • Use new Guppy version which supports handling with CSRF tokens (#1464)
  • Ensure CSRF token is passed to Guppy (#1464)
  • remove webform from NCT homepage (#1452)
  • Lints TeamProjectModal.test.jsx to abide by code formatting style guide (#1451)

Bug Fixes

  • Adds an additional check to DiscoverySummary renderAggregation to only sum strings or number values. If the value is something other than a string or number, an array, for example, the sum value explodes. (#1467)
  • Fixed a bug about misconfigured webpack publicPath (#1464)
  • Fix problem where previously submitted outcome phenotype interfered with generating histogram for newly selected variable. (#1463)
  • fix error handling in /workflows endpoint response processing (in fetchGwasWorkflows()) (#1457)
  • Discovery: the display of system-level popup (DUA) will take precedence over the Discovery Details drawer (#1454)
  • revert back the GWAS app names so navigation can work again as before (follow-up fix after uc-cdis/data-portal#1446) (#1451)
  • Fixes the an issue introduced in uc-cdis/data-portal#1444, where the url of some applications would not work anymore. (#1451)

Dependency Updates

Deployment Changes

Features

  • Implements redirect functionality for users with expired team project names stored locally (#1457)

uc-cdis/fence

Bug Fixes

  • Another CI fix (#1129)
  • Fixed a bug causing the metadata ingestion CI test to fail (#1128)
  • Fixes issue with usersync and MFA policy management in cases where a user has not been persisted by Fence. (#1125)
  • Fixes issue where users not present in arborist would have blank resources and authz fields when they should have values for open access data within the commons. (#1122)

Improvements

  • Add a new log that includes data information per signed URL generation which includes the size, bucket used, authz, acl, and requesting user (#1124)

uc-cdis/guppy

Improvements

  • Guppy will send CSRF token in request headers if available (#251)

Dependency Updates

  • Remove unused dep csurf (#251)
  • Bumps @babel/traverse to 7.23.2 and updates ancestor dependency storybook. These dependencies need to be updated together. (#245)

Bug Fixes

  • Fixed a bug cause inaccurate total count being returned from query after updating to ES7 (#250)

uc-cdis/hatchery

New Features

  • New endpoints GET /mount-files and GET /mount-files?id=foobar return files to be mounted to the workspace container (#86)
  • New endpoint GET /options?id=foobar returns information about the specified workspace option only (#86)

Improvements

  • Add ability to authenticate AWS batch with ECR repositories via user data (#87)
  • Nextflow in Batch: Ignore "invalid" state before updating a compute environment, instead of waiting for it to be valid (#88)
  • Set environment variable WORKSPACE_FLAVOR in the workspace and sidecar containers for downstream use (#86)

uc-cdis/indexd

Dependency Updates

  • Upgrade Flask (#371)

uc-cdis/manifestservice

Improvements

  • Remediate path traversal vulnerability (#36)

uc-cdis/metadata-service

Bug Fixes

  • A limit to the amount of nested objects was created in ES7. elastic/elasticsearch#26962 (#100)
  • In order to resolve this error from occurring when running the aggMDS job- we must increase this limit. (#100)

uc-cdis/peregrine

Dependency Updates

  • PyYAML to >=5.4.1 (#208)
  • gen3dictionary to >= 2.0.3 (#208)
  • dictionaryutils to >=3.4.10 (#208)
  • Re-add sheepdog, v5.1.2, with upgraded flask (#207)
  • gen3dictionary to 2.0.3 (#207)

uc-cdis/sheepdog

Dependency Updates

  • PyYAML to >=5.4.1 (#404)
  • gen3dictionary to >= 2.0.3 (#404)
  • dictionaryutils to >=3.4.10 (#404)
  • Upgrade flask (#403)

uc-cdis/sower-jobs

Improvements

  • Use poetry for installing dependencies for batch-export (#45)

uc-cdis/workspace-token-service

Dependency Updates