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

• [13] chore: rm unused env var for public by @davidlougheed in #144
• [13] chore: bump redis to 7.0.12 by @davidlougheed in #149
• [13] feat!: new notification service with authz by @davidlougheed in #151
• [13] pass BENTO_BEACON_UI_ENABLED param to beacon by @gsfk in #145
• [13] chore: bump gateway to 0.5.5 by @davidlougheed in #154
• [13] chore: don't run keycloak with legacy logout redirect uri flag by @davidlougheed in #153
• chore(deps): bump cryptography from 39.0.1 to 41.0.2 by @dependabot in #155
• [13] feat!: new DRS (0.10.2 --> 0.12.3) with authz + CORS by @davidlougheed in #148
• chore(deps): bump certifi from 2022.12.7 to 2023.7.22 by @dependabot in #157
• chore(deps): bump requests from 2.28.1 to 2.31.0 by @dependabot in #156
• [13] chore: disable Keycloak plain HTTP and use Bento Keycloak image by @davidlougheed in #158
• [13] chore: bump authz to 0.4.0 by @davidlougheed in #162
• [13] chore: bump public to 0.14.0 by @davidlougheed in #163
• [13] feat!: connect bento_public to WES for showing last ingest times by @noctillion in #146
• [13] Beacon updates by @davidlougheed in #152
• [13] remove stale values from beacon config by @gsfk in #169
• [13] feat!: new WES with authz by @davidlougheed in #150
• [13] docs: add v13 migration guide by @davidlougheed in #168
• [13] chore: set up new aggregation service by @davidlougheed in #165
• [13] chore: clean up pointless props in bento_services.json by @davidlougheed in #171
• chore: update service registry to 1.1.0 by @davidlougheed in #172
• [13] table removal integration by @v-rocheleau in #160
• chore: upgrade service-registry to 1.1.1 by @davidlougheed in #173
• chore: pin aggregation to 0.19.0 by @davidlougheed in #174
• chore: pin WES to 0.10.0 by @davidlougheed in #175
• add org urls to beacon config by @gsfk in #177
• chore: gateway no longer depends on redis by @davidlougheed in #180
• chore(bentoctl): remove orphan containers on docker compose down by @davidlougheed in #181
• bump beacon to v0.9.1 by @gsfk in #182
• Release v13 by @davidlougheed in #147

New Contributors

• @dependabot made their first contribution in #155

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

Version 12.2

What's Changed

• fix: bump web to 2.1.2 to fix a crash happening in the Workflow Runs tab

Full Changelog: v12.1...v12.2

Version 12.1

What's changed

Updated services

• authz: 0.2.0 -> 0.2.1
• beacon: 0.6.0 -> 0.7.1
• drop box: 0.12.0 -> 1.0.0
• gohan: 3.9.0 -> 3.9.1
• katsu: 3.0.0 -> 3.0.1
• public: 0.12.1 -> 0.13.2
• service registry: 0.11.2 -> 1.0.0
• web: 2.0.0 -> 2.1.1

Features

• feat: public portal enhancements + fixes (Public)
• feat: beacon wildcard support + auto-generation of IDs + fixes
• feat: drop box authorization implementation + enhancements (Web)
• feat: service registry authorization implementation

Other

• chore: update Redis patch version

Version 12.0

What's changed

Updated services

• gateway: 0.3.5 -> 0.5.3
• web: 1.8.3 -> 2.0.0
• drop box: 0.11.1 -> 0.12.0
• event relay: 2.5.0 -> 3.0.2
• DRS: 0.10.1 -> 0.10.2
• Katsu: 2.18.2 -> 3.0.0
• Gohan: 3.7.4 -> 3.9.0
• public: 0.10.2 -> 0.12.1
• beacon: 0.4.0 -> 0.6.0

Features

• feat!: new authorization service
  • requires Keycloak settings changes & various other migrations, see the migration guide
• feat: Beacon feature flag
• feat: Gohan feature flag
• feat: typed extra properties (Katsu/Web)
• feat: haploid zygosity handling (Gohan)
• feat: initial version of Beacon UI, with toggle flag

Bug fixes

• fix: log out errors from Keycloak
• fix: debug settings for drop box
• fix: Adminer start/stop not working as expected
• fix: service registry external port binding in dev mode

Documentation

• docs: add port binding list

Version 2.11.2

• fix: adminer in dev mode
• fix: update gateway to fix beacon rate limiter

Version 2.11.1

• bento-public assets mount patch
• update WES to 0.9.0 to raise timeout
• fix Elasticsearch memory issue

Version 2.11.0

Features

• Bentoctl: Makefile deployments deprecated in favor of new CLI tool bentoctl
• Include mechanism to set git config information in dev containers
• Improved local dev containers experience and reliability
• keycloak: upgrade to new docker images (quay.io/keycloak/keycloak)
• Containerized gateway
• Beacon: Improved dev container for local development experience
• Bento-Charts: ReCharts, React and TS library for web app charts
• DRS: search and object/bundle view interface
• Web: Show local/pre-built status in service list
• Web: Show analysis and export workflows in UI
• bento_public: Initial typescript support, now uses Bento-Charts
• Drop box: separate notion of local file path vs. URI
• Improved search in bento_lib/katsu
• New bento services format, show local/pre-built status in services list
• cBioPortal deployment with embeded UI in bento_web (dev mode only for v2.11.0)

Security

• Containers no longer run as root
• Segmented Docker networks to isolate services
• Beacon: rate limiting

Fixes

• DRS: file deduplication and malformed URLs
• Web: various display bug fixes
• Web: Phenopackets ingestion in Data Manager
• Aggregation: fail gracefully
• Bento: service containers use host machine's user PUID/PGID to fix read/write access issues on volumes
• WES: state updates via event-relay

Version 2.10.2

• federation: 0.15.0 --> 0.15.1 (fix: error with bad table responses)

Version 2.10.1

• remove old base image artifacts
• add environment for beacon to eventually support auth
• drop box: 0.6.0 --> 0.7.0
• DRS: 0.8.0 --> 0.9.0
• Gohan: 3.7.2 --> 3.7.3
• Katsu: 2.17.0 --> 2.17.3
• public: 0.9.2 --> 0.9.4
• web: 1.7.1 --> 1.7.2

Version 2.10.0

Merge pull request #96 from bento-platform/releases/v2.10

Release v2.10