Skip to content

September 2025

Published on October 1, 2025

September advanced platform coherence, developer reliability, and scientific user experience across the Sage monorepo with 96 pull requests merged. Highlights included centralized authentication and gateway evolution, resilient Synapse workflow hardening, Model-AD data+UX refinements, systematic OpenAPI normalization, and stronger local/compose infrastructure. Primary contributors included @tschaffter, @hallieswan, @rrchai, @sagely1, and automation support from @github-actions[bot].

Summary

  • Total Pull Requests: 96 merged PRs
  • Key Focus: Gateway & auth consolidation, Synapse workflow resilience, Model-AD data/model version alignment & UX, OpenAPI governance, infrastructure composability
  • Major Projects: OpenChallenges authorization redesign, Model-AD mv84→mv85 transition, Synapse automated update pipeline, cross-project OpenAPI/tag normalization, Caddy & Docker compose unification

Technical Architecture Overview

Platform evolution

Authentication moved toward centralized mediation via the OpenChallenges API gateway while BixArena added its own gateway foundation. Caddy image consolidation and consistent reverse-proxy patterns reduced divergence and simplified operational updates.

Developer experience

Deterministic environments improved through Gradle 9 adoption, ES target unification, dependency hygiene, and pruning unused config (implicit dependencies, deprecated libraries). A refreshed, security‑scanned dev container ships a fully pinned multi‑language toolchain so every contributor builds and tests with the same versions—eliminating "works on my machine" drift and shortening onboarding/setup time. Together these changes decrease friction and accelerate iterative feature delivery.

API modernization initiative

Kebab-case path/file conventions, tag singularization, vendor extension standardization (x-audience→x-internal), and removal of deprecated annotations drove a cleaner, more discoverable OpenAPI surface across Agora, Model-AD, AMP-ALS, Synapse, and Explorers—laying groundwork for consistent client generation.

User interface enhancements

Model-AD received iterative accessibility and interaction upgrades (keyboard navigation, highlight, scrolling behavior, adaptive layouts, improved placeholders, legend visibility) plus new data-driven conditional panels. Cross‑project search and visualization components were tuned for clarity and responsiveness.

Data & schema lifecycle

Successive data bumps (mv84, mv85), new comparative disease correlation endpoint, and alignment of omics card logic modernized scientific insights delivery while tightening frontend–backend semantic parity.

Workflow & automation resilience

The Synapse update workflow underwent multi-stage stabilization culminating in reliable automated artifact regeneration, while broader CI triggers and concurrency controls prevented redundant runs. It now executes a once‑per‑day scheduled check of the official upstream Synapse OpenAPI description; if a content diff is detected it regenerates the monorepo's OpenAPI‑derived client artifacts (including the Angular client) and raises a PR, otherwise it terminates as a no‑op. The generated Angular client, for example, is leveraged by Agora and Model-AD to interact with Synapse Wikis, keeping downstream integrations current without manual intervention.

Pull Requests Merged

Authentication & gateway centralization

  • #3438: feat(openchallenges): centralize authentication (JWT tokens & API keys) in the API gateway (SMR-444, SMR-445, SMR-446)
  • #3505: feat(bixarena): add BixArena API gateway (SMR-504)
  • #3485: fix(openchallenges): hotfix org login, replace org.acronym by org.shortName and adopt x-sage-internal (SMR-480, SMR-489)

Workflow & CI resilience

  • #3534: chore: update trigger for Lint PR workflow and CI workflow (SMR-507)
  • #3532: chore(synapse): disable Nx Cloud in the Synapse API workflow
  • #3528: fix(synapse): set COREPACK_ENABLE_DOWNLOAD_PROMPT in Synapse API workflow (SMR-507)
  • #3527: fix(synapse): update the Synapse API workflow to create PR that triggers downstream workflows (SMR-507)
  • #3523: fix(synapse): use alternative method to run the dev container to update Synapse API (SMR-435)
  • #3521: feat(synapse): simplify the workflow that update the Synapse API
  • #3520: fix(synapse): specify base branch in workflow that updates the API
  • #3519: refactor(synapse): create commit inside the dev container in the update workflow
  • #3518: refactor(synapse): rewrite the Synapse update workflow
  • #3517: fix(synapse): pass env var GITHUB_TOKEN to the dev container in the workflow that updates Synapse API
  • #3515: fix(synapse): simplify PR description in the workflow that updates the API description and clients
  • #3514: fix(synapse): fix issue because of missing GitHub env var inside the dev container
  • #3513: fix(synapse): fix nested single quotes in GitHub workflow that updates Synapse API (SMR-435)
  • #3512: fix(synapse): fix GitHub workflow that updates Synapse API - Take 4 (SMR-435)
  • #3511: fix(synapse): fix GitHub workflow that updates Synapse API - Take 3 (SMR-435)
  • #3510: fix(synapse): fix GitHub workflow that updates Synapse API - Take 2 (SMR-435)
  • #3509: fix(synapse): fix GitHub workflow that updates Synapse API (SMR-435)
  • #3467: fix(explorers): skip nx cloud for e2e tests (SMR-463)

OpenAPI governance & consistency

  • #3469: chore: replace OpenAPI extension x-audience by x-internal (SMR-465)
  • #3457: chore(amp-als): remove x-java annotations from AMP-ALS OpenAPI description (SMR-385)
  • #3455: chore(model-ad): update API paths and files to use kebab case (MG-405)
  • #3454: chore(amp-als): generate Angular API client files in kebab case for AMP-ALS (SMR-416)
  • #3443: chore(agora): remove @ from Agora openapi file and directory names (AG-1844, SMR-336)
  • #3441: chore(synapse): generate Angular API client files in kebab case (SMR-415)
  • #3440: chore(agora): update Agora OpenAPI tags to use spaces and singular form (SMR-338)
  • #3439: chore(model-ad): update Model-AD OpenAPI tags to use spaces and singular form (SMR-337)
  • #3436: chore(explorers): generate Angular API client files in kebab case (MG-383, AG-1851)

UI/UX & accessibility refinement

  • #3484: fix(model-ad): ensure scroll to section after same-document navigation (MG-413)
  • #3483: fix(model-ad): copying section links shouldn't change the current URL (MG-412)
  • #3481: fix(model-ad): clean up section link fragments (MG-414)
  • #3479: fix(model-ad): conditionally display omics tab, fallback to default tab when invalid or disabled tab in URL (MG-282, MG-415)
  • #3471: fix(model-ad): update 'no results' message in search input (MG-409)
  • #3465: fix(model-ad): wrap boxplots grid to enable complete image downloads (MG-407)
  • #3463: feat(model-ad): align boxplot style with design (MG-298)
  • #3462: feat(model-ad): allow search results to be selected with mouse or keyboard (MG-361)
  • #3460: chore(explorers): update boxplot chart to use axis tooltips built into echarts 5.6.0+ (MG-270)
  • #3456: fix(model-ad): unstick the toc (MG-403)
  • #3453: feat(model-ad): matched control(s) value(s) in hero link to JAX (MG-397)
  • #3450: feat(model-ad): update search tile wording (MG-366)
  • #3449: fix(model-ad): update hero image (MG-303)
  • #3451: fix(model-ad): style terms of service content (MG-296)
  • #3448: feat(model-ad): scroll to panel content when tab specified in url, delay scroll when changing between tabs to give content time to load (MG-390)
  • #3447: fix(model-ad): move allen institute card to resources (MG-396)
  • #3446: feat(model-ad): highlight search query in search results, modernize search input to use signals, fix display of long search results (MG-360)
  • #3445: fix(model-ad): reset model details variables when route is updated to ensure default tab is loaded for each model (MG-394)
  • #3444: feat(model-ad): share link tooltip and copy behavior improvements (MG-399)
  • #3442: fix(model-ad): allow model details boxplots container to stretch wider than the section (MG-330)
  • #3435: feat(model-ad): align style of "no data" boxplot placeholder with design, fix bug where legend is not displayed when last boxplot doesn't have data (MG-317)
  • #3433: fix(model-ad): fix bug preventing display of all boxplots (MG-387, MG-392)

Data & schema lifecycle evolution

  • #3464: chore(model-ad): bump model-ad-data to mv85 and align e2e tests with available data (MG-398)
  • #3434: chore(model-ad): bump model-ad-data to mv84 and align models with updated data structure (MG-362)
  • #3470: feat(model-ad): conditionally display omics cards (MG-278)
  • #3452: feat(model-ad): create api description and route for disease_correlation (MG-237)
  • #3472: fix(model-ad): remove frontend search query sanitization in favor of backend query escaping (MG-408)
  • #3488: feat(explorers): update site version in model-ad footer, create shared service to manage data version and site version (MG-373)

Developer environment determinism

  • #3531: chore(deps): remove packageManager from package.json (SMR-507)
  • #3530: chore: activate the dev container sha-db91d6849b048b6ef69472cdeb80caad262b3e68 (SMR-497)
  • #3526: chore(bixarena): switch bixarena-app task names to serve different versions
  • #3504: refactor: remove "-angular" suffix from TypeScript aliases
  • #3502: chore(deps): upgrade to Gradle 9 (SMR-494)
  • #3495: chore(deps): update dependencies with nx migrate latest and add SOP for updating packages (SMR-469)
  • #3494: chore(deps): adopt pnpm minimumReleaseAge (SMR-492)
  • #3501: chore(deps): update testing and storybook dependencies (SMR-469)
  • #3507: chore(deps): update dependencies with security vulnerabilities (SMR-469)
  • #3476: chore(deps): update all es targets to es2024 (SMR-284)
  • #3458: chore: remove empty implicitDependencies in project.json files (SMR-362)
  • #3437: chore(sage-monorepo): use chat.tools.terminal.autoApprove instead (SMR-388)

Infrastructure & local composability

  • #3474: feat: centralize all Caddy images and update to Caddy 2.10.2 - Take 2 (SMR-433)
  • #3459: feat: add Docker Compose extra_hosts to OC, Agora and Model-AD apexes (SMR-384)
  • #3466: chore(openchallenges): migrate from sse to streamable http transport
  • #3468: chore(sage-monorepo): remove the deprecated shiny-base Docker project
  • #3486: feat(openchallenges): make the image service zero-config (SMR-478)
  • #3487: feat(openchallenges): set allowlist used by Thumbor's HTTP loader (SMR-478)
  • #3480: feat(openchallenges): switch default Thumbor loader to thumbor.loaders.http_loader (SMR-477)
  • #3492: refactor(openchallenges): update app properties of the MCP server (SMR-479)
  • #3489: chore(openchallenges): remove unused Terraform infra project
  • #3508: refactor(openchallenges): remove the openchallenges-app-config-data Java library (SMR-462)

Security scope taxonomy & authorization redesign

No direct scope taxonomy–only PRs merged this month (authorization semantics were bundled with gateway consolidation above).

Automation & generated artifacts

  • #3535: chore(synapse): update Synapse API description and generated artifacts

Documentation framework foundation

  • #3473: chore: batch patch/minor Java dependencies update (SMR-468)
  • #3493: docs(sage-monorepo): redesign the main README (SMR-496)
  • #3431: docs(sage-monorepo): update nav structure of the docs site and add first monthly updates - Take 2 (SMR-418, SMR-419)

Community Impact

Consistent OpenAPI governance and automated regeneration reduce integration friction for downstream tools and clients. Centralized authentication plus emerging gateway patterns strengthen security posture while simplifying service composition. Model-AD’s refined interaction patterns and data alignment accelerate hypothesis exploration. Resilient Synapse workflows and deterministic dev environments shrink feedback cycles, and unified Caddy + Docker compose strategies make local multi-application orchestration more intuitive for contributors.

Thank You

Last but certainly not least, a big Thank You to the contributors of the Sage monorepo.

We continue to build an open, interoperable research platform that empowers communities to accelerate discovery. Join us and help shape the next wave of scientific tooling.