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@v-rocheleau v-rocheleau released this 24 Jul 15:26
· 207 commits to main since this release
v16
0b4f527
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Learn about vigilant mode.

Key Points

  • Bento Public:
    • Various bug fixes
    • Users can now authenticate on Bento Public to have unlimited Beacon filters
    • Updated user interface with new colour scheme for charts and side menu
    • Histogram charts
    • Removed "missing" notion in charts
  • Bento Web (private portal)
    • Various bug fixes
    • Uses Ant Design 5
    • Increased permissions awareness
      • Data Manager now includes an access control tab to manage grants and groups permissions
      • Hide/show UI elements based on the user's permissions
      • Dataset level permissions awareness coming in v17
    • Workflow
      • Workflow run output tab
      • Run wizard steps for export workflows
    • Explorer
      • Show biosample ID with link in experiment data
      • Experiment type filtering for experiments
    • Data Manager
      • DRS object search with details and delete button
      • DRS resource validity column
    • Reference Service
      • Support for GFF3 ingestion
      • Public read access
    • Drop-box
      • Search bar
  • Katsu
    • Various bug fixes
    • Support for charts/search using nested JSONField data
    • Biosample time_of_collection included in CSV exports
    • Experiment results with files ingestion
    • JSON Schemas endpoints with subschema resolving
    • Public rules endpoint, rules de-coupled from overview responses
    • Project/Dataset scoped discovery (to be integrated in Bento Public and Web in v17)
      • Discovery config can be specified at three different levels: node, project, dataset
        • For now, only node level is supported through the Katsu config for backwards compatibility
        • Will allow project/dataset selection with granular search and charts config in Bento Public
      • Project/Dataset scoping of endpoints with Discovery
        • Will allow Bento Public to retrieve censored data belonging to a specific project/dataset
  • Authorization
    • Grant list endpoint
    • Data type narrowing
  • Beacon
    • Public info endpoints don't require permissions
    • Uses Katsu's public rules endpoint
  • DRS
    • Extension properties in ingest response
    • Object deletion
  • Gateway
    • Pass-troughs for non-authz service endpoints
  • WES
    • Ensembl-VEP and VCF2MAF for cBio workflows
    • Require persistent data dir, persist file artifacts from workflows
  • Reference
    • Genome feature support
    • IGV.js search endpoint
    • REFGET v2 implementation

Service Updates

  • Aggregation 0.19.3 -> 0.19.5
  • Authorization 0.8.0 -> 0.9.2
  • Beacon 0.14.0 -> 0.15.2
  • cBioPortal 4.1.13 -> 5.4.10
  • cBioPortal-session 0.5.0 -> 0.6.2
  • cBioPortal-database 6.0.4 -> 6.0.15
  • Drop-box 1.1.5 -> 1.1.8
  • DRS 0.15.3 -> 0.17.1
  • Event-relay 3.1.1 -> 3.1.3
  • Gateway 0.10.2 -> 0.12.0
  • Gohan 5.0.0 -> 5.0.1
  • Gohan-ES 5.0.0 -> 5.0.1
  • Katsu 7.0.2 -> 8.0.1
  • Keycloak (Bento distribution) 2024.02.16 -> 2024.06.03
  • Notification 3.1.1 -> 3.1.4
  • Public 0.18.0 -> 0.19.1
  • Reference 0.1.2 -> 0.2.2
  • Service-registry 1.3.6 -> 1.4.1
  • Web 4.1.4 -> 5.0.1
  • WES 0.12.8 -> 0.14.2

What's Changed

Full Changelog: v15.2...v16

Contributors

davidlougheed, gsfk, and 3 other contributors
Assets 2
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