02 - Content Freshness Audit

Audited 2026-09-26 against galaxyproject/galaxy origin/dev @ 8cecbebdf98 (26.2.dev0). Local clone working tree is on merge_26.1_into_dev; path checks use git ls-tree origin/dev. Word counts exclude notes/ and plan/.

TL;DR

2026-researched topics are fresh: file-sources, markdown, tests, and the new async/aiocop section of frameworks. Almost no broken paths.
GTN-migrated topics are stale: startup is a 2016 Python 2.7 log dump. client/files/dependencies/principles still describe webpack, yarn, jest/qunit, symlinked packages/. frameworks and project-management keep 2021-era claims (“FastAPI required likely 21.09”, tox -e lint, tox -e mypy).
Major changes the docs miss:
- Client: Vite+vitest (webpack removed 2025-12-02), pnpm (2026-01-12), client/packages/api-client (openapi-typescript), prebuilt galaxy-web-client wheel (make install-client).
- Namespace packages (dbfcdb8bc93, Apr 2026): lib/galaxy/app.py → app/__init__.py, same for structured_app, di; packages/* pyproject/src layout, no setup.cfg/galaxy/__init__.py.
- FastAPI routers live in lib/galaxy/webapps/galaxy/api/ (74 files); controllers/api/ gone.
- Viz are npm packages (@galaxyproject/* via client/visualizations.yml), not Mako.
- New subsystems: AI agents/chat (lib/galaxy/agents, pydantic-ai), MCP server mounted in fast_app.py, TUS routers, slowapi rate limiting, ty (ty.toml), markdown directive codegen (make client-gen-markdown-directives).
Overlap with existing Galaxy docs: doc/source/dev/ has writing_tests.md (source of the tests topic), api_guidelines, database_session_management, build_a_job_runner, collection_semantics, data_types. Absorb/link, don’t duplicate. doc/source/dev/index.rst still links GTN architecture slides.
Biggest gap: no core execution-path topic. Jobs, tool execution, workflow scheduling, object stores, data model only appear in image-only slides.

Per-topic table

Staleness 1 = current, 5 = obsolete. Effort: S < 2h, M = half-day to 1 day, L = multi-day.

Topic	Words	Last	Stale	Top issues (evidence)	Effort
startup	2196	2026-02 (content ~2016)	5	2016 log: `checkout master`, cp27 wheels, `lib/galaxy/model/migrate` (sqlalchemy-migrate, gone since 22.05), `lib/tool_shed/galaxy_install/migrate`, Paste :8080, `migrated_tools_conf.xml`, Trackster/Circster, `requests_common` controllers. 26 broken-path hits.	L rewrite (gravity/gunicorn/uvicorn, alembic, `app/__init__.py` init order, toolbox/search index, celery)
client	2184	2026-02	4	webpack slides/`config/webpack.config.js` (removed 2025-12); yarn targets (now pnpm; `client-watch` gone; `client-dev-server` = Vite HMR); jest/qunit paths missing (now `vitest.config.mts`, `client/tests/vitest/`); vuejs.org/v2 link; “Future components” GAlert/GCollapse/GTabs already exist; nothing on api-client/openapi-typescript or Vue 2.7 (`vue ^2.7.16`, `@vitejs/plugin-vue2`). Component-library half fine.	M
files	1075	2025-11	4	`client/src/bundleEntries.js`, `client/webpack.config.js`, `client/tests/jest` missing; `packages/tool_util/{setup.cfg,galaxy/__init__.py,galaxy/tool_util}` missing; “directory symlinks” outdated; `CITATION` → `CITATION.cff`; tox.ini described as lint entry point. Mindmap SVGs generated from these fragments, so also stale.	M
dependencies	313	2026-02	4	`script/common_startup.sh` (typo → `scripts/`); describes virtualenv+pip; script now prefers `uv venv`, conda fallback, `pinned-*.txt`, `GALAXY_WHEELS_INDEX_URL`. No pnpm. Too thin to stand alone.	S (merge)
principles	667	2025-11	3	”Built with webpack”; MySQL “sort of”. Ideas timeless.	S
production	587	2026-02	3	Admin content; “gunicorn production-grade ASGI”; old usegalaxy.org diagrams; no TPV/Pulsar/celery.	S-M
frameworks	3842	2026-05	3 (split)	Async/aiocop current. Old half: `webapps/galaxy/controllers/api/` (dead → `api/`); roles example uses pydantic v1 `__root__`/`RoleManager`/`List[]` (current uses `RolesService`, `RoleListResponse`); “WSGI API controllers until 21.09”; “favor uWSGI”; fast_factory/initialize_fast_app snippets pre-MCP/TUS/limiter/a2wsgi; fastapi-utils link.	M
dependency-injection	2715	2026-02	2	Concepts accurate (`DatasetCollectionManager` injected, `depends()` in `api/__init__.py`). Metadata `app.py`/`structured_app.py` broken. Celery slide shows `magic_bind_to_container` in tasks.py, replaced by magic partial in 2022 (`98019394223`). “Python 2” diagram framing.	S
tasks	1333	2025-11	3	`galaxy_task` + pydantic serialization valid. “Future Work” cites 2021 #11721 (tool requests/celery submission since landed). 2022 gravity output, external cloudfront image. PR stories read like release notes. No beat, queues (`galaxy.internal`/`external`), pebble pool.	M
application-components	1492	2026-01	2	Alembic text correct. Mostly image-only slides (models/HDA/workflow/libraries), diagrams unaudited. Services slide thin (`webapps/galaxy/services/` exists).	M (diagrams)
plugins	1044	2026-02	4	Viz = XML+Mako, `config/plugins/visualizations` examples (now npm); “DrammaJobRunner” typo; no TPV/job-conf YAML; `bit.ly/gcc21files`; Py2-style container-resolver code; jobs/objectstore coverage image-only.	M
markdown	3298	2026-02	2	Well researched. “Adding a Directive” likely stale (dev has `make client-gen-markdown-directives` generating reference/requirements/validator registry from directives.yml). Recheck “History Markdown (planned)”. `NewDirective.vue` placeholder.	S
file-sources	1890	2026-02	1	16/16 code paths valid; `mycloud.py` placeholder.	S
tests	11365	2026-02	1-2	Current (Playwright, vitest, populators). Metadata `client/tests/vitest/helpers.ts` → `.js`. Duplicates `doc/source/dev/writing_tests.md`. Far larger than any other topic.	S (dedupe decision)
project-management	1046	2025-11	4	`tox -e lint`/`tox -e mypy` gone (tox.ini only mako_count, check_indexes…; Makefile `mypy:`; `ty.toml`); `SECURITY_POLICY.md` → `SECURITY.md`; Gitpod; 21.01 types history; 25.1 release issue example.	S / drop
ecosystem	1782	2025-11	3	Link directory of external repos (starforge, cargo-port, tiaas2… some likely archived). Not Galaxy-repo architecture.	Drop / keep in GTN

Broken paths (origin/dev)

(P) = placeholder.

dependency-injection (metadata): lib/galaxy/app.py → app/__init__.py; lib/galaxy/structured_app.py → structured_app/__init__.py.
frameworks: lib/galaxy/webapps/galaxy/controllers/api/, .../controllers/api/roles.py → webapps/galaxy/api/roles.py (also in agent-context); test/specs/main.html (GTN leftover).
client: client/src/jest/jest.config.js, client/test/qunit/tests, client/test/jest/standalone/, config/webpack.config.js, client/docs/src/component-design/unit-testing.
files: client/src/bundleEntries.js, client/webpack.config.js, client/tests/jest, packages/tool_util/setup.cfg, packages/tool_util/galaxy/__init__.py, packages/tool_util/galaxy/tool_util, CITATION.
dependencies: script/common_startup.sh.
project-management: SECURITY_POLICY.md.
startup: config/{migrated_tools_conf,shed_tool_conf,shed_tool_data_table_conf,shed_data_manager_conf}.xml, lib/galaxy/model/migrate/**, lib/tool_shed/galaxy_install/migrate/**, 5 cp27 wheels.
tests: client/tests/vitest/helpers.ts (→ .js), test/helpers (P), test/functional/tools/some_tool.xml (P).
markdown: Elements/NewDirective.vue (P).
file-sources: lib/galaxy/files/sources/mycloud.py (P).
ecosystem/plugins: test/main, test/dev/data_types.html (GTN Jekyll links).
Not checked: paths inside images/*.plantuml/mermaid sources and PNG screenshots. Needs separate diagram audit; many slides are image-only.

Missing topics (prioritized for new devs)

Jobs & tool execution: ToolAction → Job → handler/JobWrapper → runners → job_execution → metadata → finish; job conf YAML, TPV, Pulsar, job cache, tool requests. Link build_a_job_runner.
Data model & DB access: SQLAlchemy 2.0 models, galaxy_scoped_session, HDA/HDCA/Dataset/LDDA, alembic. Link database_session_management.
API layer & schema: webapps/galaxy/api + services + galaxy.schema → OpenAPI → client/packages/api-client (make update-client-api-schema). Link api_guidelines. Could absorb old half of frameworks.
Workflows: modules, scheduling manager/invocations, refactor, gxformat2, subworkflows.
Object stores & storage: hierarchical/distributed/S3/irods, user-selectable storage, quotas, short_term_storage, cleanup.
Tools & tool-state models: tool_util, tool_util_models, parameter models, toolbox/search, user-defined tools.
Datatypes & collections: registry, sniffing, converters, metadata, collection semantics (doc exists).
Auth/users/security: sessions/API keys, OIDC/PSA, roles/permissions, id encoding, vault.
AI agents / MCP (beta): lib/galaxy/agents, /api/ai, /api/chat, MCP mount.
Tool Shed & installs.
Client app architecture: router, Pinia, api-client usage, composables, Vue 2.7 → 3 plan.
Lower: notifications, interactive tools, viz framework (npm), model stores/RO-Crate export, config schema pipeline, carbon emissions, webhooks/tours.

Merge / drop

Drop from Galaxy dev docs: ecosystem (keep in GTN/hub), production (admin docs cover it), project-management (CONTRIBUTING/doc/source/project cover it).
Merge: dependencies + files + client-build half + lint → “Repository layout & dev environment” (uv/pnpm/Vite/namespace packages).
Split: frameworks → request path + async rules; API/pydantic part → new API topic.
Dedupe: tests vs doc/source/dev/writing_tests.md.
Rewrite: startup as narrative “what happens at boot”.

Suggested refresh order

Quick path fixes (≤1h): DI metadata, frameworks controller path, tests helpers.js, SECURITY.md, CITATION.cff, scripts/ typo, DRMAA, remove client “Future components”.
client + files + dependencies → dev-environment topic.
frameworks old half + new API-layer topic.
plugins (viz npm, TPV), then new jobs/tool-execution topic.
startup rewrite.
tasks refresh, then DI celery slide.
New topics: data model → workflows → object stores → tools → datatypes/collections.
Diagram audit (images/).
Decide ecosystem/production/project-management + tests dedupe before migration.

Method / limits

Paths checked with git ls-tree origin/dev. Claims spot-checked in Makefile, client/package.json, vitest.config.mts, fast_app.py, api/roles.py, celery/tasks.py, common_startup.sh, pinned-requirements.txt, tox.ini.
Tmp volume filled (ENOSPC) partway through; later checks were working-tree only (merge_26.1_into_dev). Recheck against dev: History Markdown status; which WSGI API routes remain in buildapp.py; which old viz dirs remain in config/plugins/visualizations; whether ecosystem repos are archived.

02_content_freshness