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Releases: bento-platform/bento

Version 17.1

28 Nov 17:01
@v-rocheleau v-rocheleau
v17.1
e19a547
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Version 17.1 Latest
Latest

Key Points

  • Beacon API
    • Search by gene ID
  • Gateway
    • Fix TLS termination
    • TLS termination reverse proxy guide
  • Gohan
    • Gohan can now work with non-human chromosomes
  • Katsu
    • Experiments results HTML support
    • Fix wrong search counts on nested properties
  • Public
    • Beacon network
    • Beacon chromosome selector + non-hard-coded chromosome options
    • Help text for Bento entities
    • Translation improvements
    • Dataset cards
    • Performance improvements and bug fixes
  • Reference
    • Fix Refget multi-accept headers
  • Web
    • HTML files display
    • Various bug fixes and improvements

Service Updates

  • Aggregation 0.19.8 -> 0.19.9
  • Authorization 0.10.1 -> 0.10.2
  • Beacon 0.16.0 -> 0.18.1
  • Drop Box 1.1.10 -> 1.1.11
  • DRS 0.18.0 -> 0.19.0
  • Event Relay 3.1.5 -> 3.1.6
  • Gateway 0.13.0 -> 0.13.2
  • Gohan 5.0.2 -> 6.0.0
  • Katsu 9.0.0 -> 9.1.0
  • Keycloak (Bento distribution) 2024.09.26 -> 2024.11.22
  • Notification 3.1.6 -> 3.1.7
  • Public 0.20.0 -> 0.22.0
  • Reference 0.3.0 -> 0.3.2
  • Service-registry 1.4.2 -> 1.4.3
  • Web 6.0.0 -> 6.1.1
  • WES 0.14.5 -> 0.14.6

What's Changed

Full Changelog: v17...v17.1

Contributors

davidlougheed, gsfk, and v-rocheleau
Assets 2
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Version 17

04 Oct 21:30
@v-rocheleau v-rocheleau
v17
c4a60d8
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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

Full Changelog: v16...v17

Contributors

davidlougheed, gsfk, and 2 other contributors
Assets 2
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Version 16

24 Jul 15:26
@v-rocheleau v-rocheleau
v16
0b4f527
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Version 16

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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Version 15.2

27 Mar 14:05
@davidlougheed davidlougheed
v15.2
f97c971
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Version 15.2

Key Points

  • Bento now properly supports plain-HTTP deployments that are behind an HTTPS-terminated proxy.
  • Gohan's Elasticsearch JVM now can be configured with an options file, which is recommended for production deployments.

Service Updates

  • Auth 2023.10.31 -> 2024.02.16 (Keycloak 22 to 23)
  • Authorization 0.7.0 -> 0.8.0
  • Beacon 0.13.0 -> 0.14.0
  • DRS 0.15.2 -> 0.15.3
  • Event Relay 3.1.0 -> 3.1.1
  • Gateway 0.10.0 -> 0.10.2
  • Notification 3.1.0 -> 3.1.1
  • Public 0.17.3 -> 0.18.0
  • Service Registry 1.3.5 -> 1.3.6

Additionally, Redis was updated from 7.0.14 -> 7.0.15.

Merged PRs

Full Changelog: v15.1...v15.2

Contributors

davidlougheed, dependabot, and v-rocheleau
Assets 2
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Version 15.1

14 Feb 21:30
@davidlougheed davidlougheed
v15.1
ed4b183
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Version 15.1

Key Points

  • The gateway can now handle plain-HTTP connections and/or a past-URL redirect to a new URL, if configured.
  • Experiment results in Katsu can now store URIs/index URI records
  • Sampled tissues on biosamples in Katsu are now correctly nullable
  • The private portal has received some miscellaneous improvements and bug fixes
  • The public portal has received some bug fixes and small styling tweaks
  • We have a new library, bento_auth_js, which we are now using for authx in bento_web which we will use for the public portal in the future too.

Service Updates

  • Aggregation 0.19.2 -> 0.19.3
  • Authorization 0.6.0 -> 0.7.0
  • Beacon 0.12.1 -> 0.13.0
  • Drop box 1.1.2 -> 1.1.5
  • DRS 0.15.1 -> 0.15.2
  • Gateway 0.8.1 -> 0.10.0
  • Katsu 6.0.0 -> 7.0.2
  • Public 0.17.0 -> 0.17.3
  • Reference 0.1.1 -> 0.1.2
  • Service registry 1.3.2 -> 1.3.5
  • Web 4.0.0 -> 4.1.4

Additionally, bentoctl has received some bug fixes and minor tweaks.

Merged PRs

New Contributors

Full Changelog: v15...v15.1

Contributors

davidlougheed, dbujold, and 2 other contributors
Assets 2
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Version 15

10 Jan 18:43
@davidlougheed davidlougheed
v15
a6acc5d
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Version 15

Key Points

  • Breaking: Katsu has switched to Phenopackets v2. All clinical/phenotypic metadata must be remapped to the new schema. We've also included a converter in bentoctl.
  • New service: reference service (for reference genomes and other reference material in the future)
    • Now, non-human variants can be ingested via first ingesting a non-human reference genome
    • A database password must be set in local.env: BENTO_REFERENCE_DB_PASSWORD=...
    • Permissions must be configured for the reference service
  • Several small improvements to the public portal, including translations and chart presentation

Service Updates

  • Authorization 0.4.0 -> 0.6.0
  • Beacon 0.11.0 -> 0.12.1
  • DRS 0.13.0 -> 0.15.1
  • Event relay 3.0.2 -> 3.1.0
  • Gateway 0.7.1 -> 0.8.1
  • Gohan 4.0.1 -> 5.0.0
  • Katsu 5.0.0 -> 6.0.0
  • Notification 3.0.1 -> 3.1.0
  • Public 0.16.2 -> 0.17.0
  • Service registry 1.2.2 -> 1.3.2
  • Web 3.2.2 -> 4.0.0
  • WES 0.11.0 -> 0.12.6
  • New service: Reference service 0.1.1

What's Changed

Full Changelog: v14...v15

Contributors

davidlougheed, gsfk, and 3 other contributors
Assets 2
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Version 14

02 Nov 20:11
@davidlougheed davidlougheed
v14
98982eb
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Version 14

Key Points

  • Breaking: MCODE was removed from Katsu
  • Beacon now can provide full response granularity when given an authorized bearer token
  • Documents such as PDFs and spreadsheets can now be ingested as experiment results into Katsu
  • The provenance display of bento_public has been improved
  • Several services' base images and dependencies have been updated (patch releases)

Service Updates

  • Aggregation 0.19.1 -> 0.19.2
  • Beacon 0.9.1 -> 0.11.0
  • DRS 0.12.6 -> 0.13.0
  • Gohan 4.0.0 -> 4.0.1
  • Katsu 4.4.0 -> 5.0.0
  • Keycloak 22.0.3 -> 22.0.5 (Bento distribution)
  • Notification 3.0.0 -> 3.0.1
  • Public 0.15.0 -> 0.16.2
  • Redis 7.0.12 -> 7.0.14
  • Service registry 1.2.1 -> 1.2.2
  • Web 3.1.2 -> 3.2.2
  • WES 0.10.1 -> 0.11.0

Merged PRs

Full Changelog: v13.2...v14

Contributors

davidlougheed, gsfk, and 2 other contributors
Assets 2
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Version 13.2

05 Oct 16:24
@davidlougheed davidlougheed
v13.2
92fed60
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Version 13.2

Key Points

  • A small web bugfix and a security patch for aggregation

Service Updates

  • Aggregation 0.19.0 -> 0.19.1
  • Web 3.1.1 -> 3.1.2

Full Changelog: v13.1...v13.2

Assets 2
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Version 13.1

04 Oct 17:36
@davidlougheed davidlougheed
v13.1
3ccbf31
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Version 13.1

Key Points

  • Improvements to the bento_web individual explorer interface
  • Katsu can now ingest more types of experiments/additional library strategies and sources

Service Updates

  • Drop box 1.0.0 -> 1.0.1
  • DRS 0.12.5 -> 0.12.6
  • Gateway 0.6.0 -> 0.7.1
  • Katsu 4.0.0 -> 4.4.0
  • Keycloak 22.0.0 -> 22.0.3 (Bento distribution)
  • Public 0.14.1 -> 0.15.0
  • Service registry 1.2.0 -> 1.2.1
  • Web 3.0.1 -> 3.1.1

Additionally, bentoctl was updated and is now v0.4.0

Merged PRs

Full Changelog: v13.0...v13.1

Contributors

davidlougheed, gsfk, and dependabot
Assets 2
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Version 13.0

07 Sep 17:06
@davidlougheed davidlougheed
v13.0
56db8a5
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Version 13.0

Key Points

  • Authorization checks were added to several more services
  • The Bento concept of "tables" was removed
  • Make sure to read the migration guide!

Service Updates

  • Aggregation 0.18.1 -> 0.19.0
  • Authorization 0.2.1 -> 0.4.0
  • Beacon 0.7.1 -> 0.9.1
  • DRS 0.10.2 -> 0.12.5
  • Gateway 0.5.3 -> 0.6.0
  • Gohan 3.9.1 -> 4.0.0
  • Katsu 3.0.1 -> 4.0.0
  • Keycloak 20.0 -> 22.0 (Bento distribution)
  • Notification 2.4.1 -> 3.0.0
  • Public 0.13.2 -> 0.14.1
  • Service registry 1.0.0 -> 1.2.0
  • Web 2.1.2 -> 3.0.1
  • WES 0.9.0 -> 0.10.1

Additionally, bentoctl was updated and is now v0.3.0

Merged PRs

New Contributors

Full Changelog: v12.2...v13.0

Contributors

davidlougheed, gsfk, and 3 other contributors
Assets 2
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