Version 17

Key Points

• Bento Public
  • Project/Dataset scope selection
    • Scoped and authorized requests to Katsu/Beacon
    • Reflected in the charts, provenance, search and Beacon results
  • Show individual search matches for authorized users
  • Bug fixes, improvements, libraries and image updates
• Bento Web (private portal)
  • Monitoring tab for users in the Grafana group
  • Advanced search tables for biosample experiments
  • Project/Dataset scoped discovery configuration
    • Set and edit the discovery configuration at the project and dataset levels
  • Improved error messages
  • Bug fixes, improvements, libraries and image updates
• Monitoring stack (NEW)
  • Initial work to improve observability on the Bento platform
  • Services logs can be queried from a Grafana interface that now ships with Bento
  • Authorized access by Keycloak group membership
  • Enabled by a feature flag
  • See documentation
• Katsu
  • Authorization support on public endpoints for uncensored data
  • Improved biosample experiment text search
  • Allow downloading DATS JSON as attachment
  • Continuous-Integration: publish JSON-schema files as a Katsu release artifact
  • Bug fixes, improvements, libraries and image updates
• Authorization
  • CLI: new command for public data access
  • Bug fixes, improvements, libraries and image updates
• Beacon
  • Beacon Network
    • Query multiple Beacon APIs
  • Handles authorized and scoped requests
  • Anonymous requests use the discovery config
  • Bug fixes, improvements, libraries and image updates
• Gateway
  • Allow endpoints that are now authorized server-side
  • Bug fixes, improvements, libraries and image updates
• WES
  • Library and image updates
• Reference
  • Fix refget response
  • Uses file streaming and DRS resolver
  • Bug fixes, improvements, libraries and image updates

New Services

• Grafana: 11.1.5
  • Secure web interface to query, analyse and aggregate logs produced by all Bento services
• Loki: 3.1.1
  • Logs storage
  • Data source for Grafana
• Promtail: 2.9.10
  • Forwards Docker logs to Loki

Service Updates

• Aggregation 0.19.5 -> 0.19.8
• Authorization 0.9.2 -> 0.10.1
• Beacon 0.15.2 -> 0.16.0
• Drop-box 1.1.8 -> 1.1.10
• DRS 0.17.1 -> 0.18.0
• Event-relay 3.1.3 -> 3.1.5
• Gateway 0.12.0 -> 0.13.0
• Gohan 5.0.1 -> 5.0.2
• Gohan-ES 5.0.1 -> 5.0.2
• Katsu 8.0.1 -> 9.0.0
• Keycloak (Bento distribution) 2024.06.03 -> 2024.09.26
• Notification 3.1.4 -> 3.1.6
• Public 0.19.1 -> 0.20.0
• Reference 0.2.2 -> 0.3.0
• Service-registry 1.4.1 -> 1.4.2
• Web 5.0.1 -> 6.0.0
• WES 0.14.2 -> 0.14.5

What's Changed

• feat: monitoring system by @v-rocheleau in #256
• fix: grafana oauth email by @v-rocheleau in #260
• refact(bentoctl): factor out common client/secret creation code by @davidlougheed in #262
• feat(grafana): authorization by group membership by @v-rocheleau in #261
• chore(deps): bump cryptography from 42.0.8 to 43.0.1 by @dependabot in #263
• docs: scoped discovery by @v-rocheleau in #247
• feat!: authorized Katsu endpoints + slightly auth-aware Beacon by @davidlougheed in #258
• Add beacon network by @gsfk in #259
• docs: monitoring tools documentation by @v-rocheleau in #265
• chore: update service patch versions by @davidlougheed in #266
• fix: remove adminer from local compose file by @v-rocheleau in #267
• update Bento Public to the Go-free version by @davidlougheed in #268
• Fixes/beacon network patch by @gsfk in #264
• fix: Bento healthchecks + patch Keycloak version by @davidlougheed in #269
• fix: reference service should wait for db to start by @davidlougheed in #270
• chore: bump gateway version to 0.13.0 by @v-rocheleau in #272
• chore: bump katsu to v9.0.0 by @v-rocheleau in #271
• chore: update translations by @v-rocheleau in #273
• [17] Fixes/beacon wait for auth by @gsfk in #274
• chore: bump bento_public to v0.20.0 by @v-rocheleau in #275
• Release v17 by @davidlougheed in #257

Full Changelog: v16...v17