Vault Log

Append-only chronological record of vault operations. Append new entries at the bottom.

Entry types: ingest, query, lint, manual.

Excluded from frontmatter validator and Astro site; Obsidian-visible.

2026-04-22 ingest — Component - Tool Shed Search and Indexing

• source: vault/projects/workflow_state/COMPONENT_TOOL_SHED_SEARCHING.md (removed after import)
• created: Component - Tool Shed Search and Indexing
• updated:
  • PR 18524 - Add Tool-Centric APIs to Tool Shed 2.0 — cross-ref added

2026-04-28 ingest — PR 21828 - YAML Tool Hardening and Tool State

• source: https://github.com/galaxyproject/galaxy/pull/21828
• created: PR 21828 - YAML Tool Hardening and Tool State
• updated:
  • Component - YAML Tool Runtime — added cross-ref; PR lands runtimeify path
  • Component - Tool State Specification — added cross-ref; PR adds job_runtime/test_case_json reps
  • Component - Tool State Dynamic Models — added cross-ref; PR extends dynamic factory to recursive collection types
  • Component - Collection Models — added cross-ref; typed Pydantic runtime layer over DatasetCollection
  • Component - Collection Tool Execution Semantics — added cross-ref; runtime-state pipeline change
  • Component - Collections in Tool XML Tests — added cross-ref; new test_case_json validation
  • Component - Tool Testing Infrastructure — added cross-ref; YAML tool test framework hardening
  • Dependency - Pydantic Dynamic Models — added cross-ref; build_collection_model_for_type factory
  • Dependency - Pydantic Discriminated Unions — added cross-ref; CollectionRuntimeDiscriminated union
  • PR 18641 - Parameter Model Improvements Research — added cross-ref; same #17393 lineage
  • PR 18758 - Tool Execution Typing and Decomposition — added cross-ref; continues tool state typing
  • PR 19377 - Collection Types and Wizard UI — added cross-ref; runtime models for paired_or_unpaired/sample_sheet/record
  • PR 19434 - User Defined Tools — added cross-ref; collection input support for YAML tools
  • PR 20935 - Tool Request API — added cross-ref; runtime-side counterpart to request-side typing

2026-04-28 ingest — PR 21842 - Tool Execution Migrated to api jobs

• source: https://github.com/galaxyproject/galaxy/pull/21842
• created: PR 21842 - Tool Execution Migrated to api jobs
• updated:
  • PR 20935 - Tool Request API — added cross-ref; client cutover to its endpoint
  • PR 21828 - YAML Tool Hardening and Tool State — added cross-ref; client side of same typing pipeline
  • Component - Tool State Specification — added cross-ref; UI now sends RequestToolState
  • Component - Tool State Dynamic Models — added cross-ref; flat-to-nested client transform
  • Component - YAML Tool Runtime — added cross-ref; full request lifecycle now typed end-to-end
  • PR 18641 - Parameter Model Improvements Research — added cross-ref; same parameter model lineage
  • PR 18758 - Tool Execution Typing and Decomposition — added cross-ref; tool state typing
  • PR 19434 - User Defined Tools — added cross-ref; YAML tool submission now via /api/jobs

2026-04-29 ingest — PR 21942 - Shared Agent Operations and MCP Server

• source: https://github.com/galaxyproject/galaxy/pull/21942
• created: PR 21942 - Shared Agent Operations and MCP Server
• updated:
  • PR 21434 - AI Agent Framework and ChatGXY — added cross-ref; this PR refactors that framework
  • PR 21692 - Standardize Agent API Schemas — added cross-ref; ops manager bypasses these schemas
  • PR 21706 - Data Analysis Agent Integration — added cross-ref; sibling agent addition
  • PR 21463 - Jupyternaut Adapter for JupyterLite — added cross-ref; comparable external AI mounting pattern
  • Component - Agents Backend — added cross-ref; needs revision for ops manager + HistoryAgent
  • Component - Agents UX — added cross-ref; MCP is a new external surface
  • COMPONENT_AGENTS_CHATGXY_PERSISTENCE — added cross-ref; MCP is the non-persistent peer entry point

2026-05-07 manual — Component - User-Defined Tools

• source: external agent draft (no upstream URL)
• created: Component - User-Defined Tools
• created: Component - User-Defined Tool Source Validation
• note: agent wrote both files directly as Whitepaper - *.md with subtype=whitepaper; renamed to Design - *.md, retyped as design-spec, dropped invalid tags (research/whitepaper, galaxy/agents, galaxy/agents/mcp, galaxy/tools/validation), added sources, trimmed editorial framing
• updated:
  • PR 19434 - User Defined Tools — backlink to both designs
  • PR 21828 - YAML Tool Hardening and Tool State — backlink to both designs
  • Component - YAML Tool Runtime — backlink to both designs
  • Component - Tool State Specification — backlink to both designs
  • Problem - YAML Tool Post-Hoc State Divergence — backlink to UDT design

2026-05-09 manual — Component - Collections - Records

• source: external agent draft (no upstream URL)
• created: Component - Collections - Records
• note: agent wrote file directly without /ingest; frontmatter already valid, no schema fixes needed
• updated:
  • Component - Collection Models — backlink
  • Component - Collection API — backlink
  • Component - Collections - Sample Sheets Backend — backlink
  • Component - Collections - Paired or Unpaired — backlink

2026-05-13 ingest — PR 21932 - History Graph API

• source: https://github.com/galaxyproject/galaxy/pull/21932
• created: PR 21932 - History Graph API
• updated:
  • PR 20935 - Tool Request API — backlink
  • PR 21842 - Tool Execution Migrated to api jobs — backlink
  • PR 21828 - YAML Tool Hardening and Tool State — backlink
  • PR 17413 - Invocation Graph View — backlink
  • PR 20390 - Workflow Graph Search — backlink
  • PR 18758 - Tool Execution Typing and Decomposition — backlink
  • Component - Workflow Extraction — backlink
  • Component - Workflow Extraction Models — backlink
  • Component - Collection Tool Execution Semantics — backlink
  • Component - Collection Models — backlink
  • Component - Invocation Graph View — backlink
  • Component - Workflow Editor Terminals — backlink
  • Issue 17506 - Convert Workflow Extraction Interface to Vue — backlink

2026-05-16 ingest — PR 22706 - Workflow Extraction by IDs

• source: https://github.com/galaxyproject/galaxy/pull/22706
• created: PR 22706 - Workflow Extraction by IDs
• updated:
  • Component - Workflow Extraction — backlink
  • Component - Workflow Extraction Models — backlink
  • Workflow Extraction Multiple Histories — backlink
  • Workflow Extraction Issues — backlink
  • Issue 17506 - Convert Workflow Extraction Interface to Vue — backlink
  • Component - Collection Models — backlink
  • Component - Collection Tool Execution Semantics — backlink
  • PR 20935 - Tool Request API — backlink
  • PR 21828 - YAML Tool Hardening and Tool State — backlink
  • PR 21842 - Tool Execution Migrated to api jobs — backlink
  • PR 18758 - Tool Execution Typing and Decomposition — backlink
  • Component - Workflow Editor Terminals — backlink
  • Component - Workflow API — backlink

2026-05-16 ingest — PR 21935 - Workflow Extraction Vue Conversion

• source: https://github.com/galaxyproject/galaxy/pull/21935
• created: PR 21935 - Workflow Extraction Vue Conversion
• updated:
  • Issue 17506 - Convert Workflow Extraction Interface to Vue — backlink (parent issue)
  • PR 22706 - Workflow Extraction by IDs — backlink (direct ID-native follow-up)
  • Component - Workflow Extraction — backlink
  • Component - Workflow Extraction Models — backlink
  • Workflow Extraction Multiple Histories — backlink
  • Workflow Extraction Issues — backlink
  • Component - Workflow API — backlink
  • Component - Workflow Editor Terminals — backlink
  • Component - Collection Models — backlink
  • Component - Collection Tool Execution Semantics — backlink

2026-05-21 ingest — Problem - basic.py Parameter Hierarchy

• source: lib/galaxy/tools/parameters/basic.py (synthesized dossier from 4 parallel subagent reports on branch refactor-data-options-builder)
• created: Problem - basic.py Parameter Hierarchy
• updated:
  • Component - Tool State Specification — backlink
  • Component - Tool State Dynamic Models — backlink
  • Component - YAML Tool Runtime — backlink
  • Component - User-Defined Tools — backlink
  • Problem - YAML Tool Post-Hoc State Divergence — backlink
  • Workflow Extraction Issues — backlink
  • PR 21828 - YAML Tool Hardening and Tool State — backlink
  • PR 20935 - Tool Request API — backlink
  • PR 21842 - Tool Execution Migrated to api jobs — backlink

2026-05-21 rename — COMPONENT_* → Component - * convention

• source: filename hygiene
• updated:
  • Component - Agents ChatGXY Persistence — renamed from COMPONENT_AGENTS_CHATGXY_PERSISTENCE.md
  • Component - UI Error Handling — renamed from COMPONENT_UI_ERROR_HANDLING.md; added missing research/component tag
  • Component - Agents UX — wiki-link updates
  • Component - Agents Backend — wiki-link updates
  • PR 21434 - AI Agent Framework and ChatGXY — wiki-link updates
  • PR 21692 - Standardize Agent API Schemas — wiki-link updates
  • PR 21942 - Shared Agent Operations and MCP Server — wiki-link updates

2026-05-21 ingest — PR 22070 - Static YAML Agent Backend for Deterministic Testing

• source: https://github.com/galaxyproject/galaxy/pull/22070
• created: PR 22070 - Static YAML Agent Backend for Deterministic Testing
• updated:
  • PR 21434 - AI Agent Framework and ChatGXY — backlink to PR 22070 (alternate registry impl)
  • PR 21692 - Standardize Agent API Schemas — backlink to PR 22070 (static backend emits these shapes)
  • PR 21942 - Shared Agent Operations and MCP Server — backlink to PR 22070 (sibling agent-stack PR)
  • PR 21706 - Data Analysis Agent Integration — backlink to PR 22070 (deterministic test regression guard)
  • PR 21463 - Jupyternaut Adapter for JupyterLite — backlink to PR 22070 (shares inference_services surface)
  • Component - Agents Backend — backlink to PR 22070 (alternate AgentRegistry impl)
  • Component - Agents UX — backlink to PR 22070 (Selenium coverage for ChatGXY/Wizard)
  • Component - Agents ChatGXY Persistence — backlink to PR 22070 (surface now rebranded GalaxyAI post-merge)
  • Component - E2E Tests - Writing — backlink to PR 22070 (new data-description selector tests)

2026-05-21 ingest — Plan - ChatGXY Notebook Convergence

• source: vault/plans/CHATGXY_NOTEBOOK_CONVERGE_PLAN.md (renamed)
• created: Plan - ChatGXY Notebook Convergence
• updated:
  • meta_tags.yml — added galaxy/agents tag (covers chat/agent surfaces)
  • Component - Agents Backend — added galaxy/agents tag
  • Component - Agents UX — added galaxy/agents tag; revision bump
  • Component - Agents ChatGXY Persistence — added galaxy/agents tag; revision bump
  • PR 21434 - AI Agent Framework and ChatGXY — added galaxy/agents tag; revision bump
  • PR 21463 - Jupyternaut Adapter for JupyterLite — added galaxy/agents tag; revision bump
  • PR 21692 - Standardize Agent API Schemas — added galaxy/agents tag
  • PR 21706 - Data Analysis Agent Integration — added galaxy/agents tag
  • PR 21942 - Shared Agent Operations and MCP Server — added galaxy/agents tag; revision bump
  • PR 22070 - Static YAML Agent Backend for Deterministic Testing — added galaxy/agents tag; revision bump
  • vault/plans/TOOL_FORM_POPULATE_REFACTOR.md — added missing title; dropped non-registered galaxy/refactor tag; revision bump

2026-05-21 ingest — Plan - Chat Context and Docked Panel Tests

• source: vault/plans/TEST_CHAT_CONTEXT.md (renamed)
• created: Plan - Chat Context and Docked Panel Tests
• updated: none

2026-05-22 ingest — PR 22615 - UserToolSource Pydantic Semantic Validation

• source: https://github.com/galaxyproject/galaxy/pull/22615
• created: PR 22615 - UserToolSource Pydantic Semantic Validation
• updated:
  • Component - User-Defined Tool Source Validation — added PR 22615 to related_prs/notes; direct extension of this surface
  • Component - User-Defined Tools — added PR 22615 to related_prs/notes; hardening step in the initiative
  • PR 19434 - User Defined Tools — backlink to PR 22615
  • PR 21434 - AI Agent Framework and ChatGXY — backlink to PR 22615; CustomToolAgent error path changed
  • Component - Agents Backend — backlink to PR 22615; validation flow into producer reflection loop
  • Dependency - Pydantic Dynamic Models — backlink to PR 22615; field_validator/model_validator usage

2026-06-03 ingest — PR 22692 - LLM Eval Harness for Agents

• source: https://github.com/galaxyproject/galaxy/pull/22692
• created: PR 22692 - LLM Eval Harness for Agents
• updated:
  • PR 21942 - Shared Agent Operations and MCP Server — backlink; this PR adds file-source methods + MCP tools on top
  • PR 22070 - Static YAML Agent Backend for Deterministic Testing — backlink; static-backend deterministic counterpart to this real-LLM harness
  • PR 21434 - AI Agent Framework and ChatGXY — backlink; defines the agent fleet under evaluation
  • PR 21692 - Standardize Agent API Schemas — backlink; AgentResponse shape the eval tasks read
  • Component - Agents Backend — backlink; system under eval
  • Component - Agents UX — backlink; routing decisions scored here drive these surfaces

2026-06-06 ingest — PR 21335 - GA4GH WES API

• source: https://github.com/galaxyproject/galaxy/pull/21335
• created: PR 21335 - GA4GH WES API
• updated:
  • Component - Workflow API — backlink; WES is a GA4GH front-end onto the same invocation machinery
  • Component - Workflow Import — backlink; WES submit_run reuses the import/normalize path
  • Component - Tool Shed Search and Indexing — backlink; sibling GA4GH surface (partial TRS)
  • PR 20935 - Tool Request API — backlink; parallel async submit-then-poll pattern
  • Component - Format2 Workflows (gxformat2) — backlink; WES accepts gx_workflow_format2
  • Component - API Tests — backlink; test_wes.py + new populator helpers build on this plumbing

2026-06-12 ingest — Component - Tool Install YAML

• source: /Users/jxc755/projects/worktrees/galaxy/branch/history_pages/COMPONENT_GALAXY_TOOL_INSTALL_YAML.md
• created: Component - Tool Install YAML
• updated:
  • Component - Tool Shed Search and Indexing — backlink; repos/revisions/GUID this format resolves against
  • Component - Workflow Format (.ga) — backlink; .ga tool_shed_repository records feed workflow-to-tools

2026-06-18 ingest — CORS Handling

• source: /Users/jxc755/projects/repositories/galaxy-brain/.ingest-dossiers/Component-CORS-Handling.md
• created: Component - CORS Handling
• updated:
  • Component - Data Fetch — reciprocal backlink; landing endpoints use allow_cors reflected-origin path
  • Component - Workflow API — reciprocal backlink; reconciles its "Public (CORS enabled)" landing claim
  • PR 21942 - Shared Agent Operations and MCP Server — reciprocal backlink; corrects MCP "inherits CORS via app.mount" claim