Galaxy Brain
Component Research (57)
| Name | Summary | Revised | Rev |
|---|---|---|---|
| Component Api Tests | API test plumbing: ApiTestCase base class, populators, fixtures, decorators, assertions, user context switching | 2026-09-10 | 6 |
| Component Cors Handling | Five CORS mechanisms — global origin-validated middleware, per-route reflected-origin landings, OPTIONS catch-all, legacy WSGI path, display-app proxy | 2026-09-10 | 3 |
| Component E2e Tests Writing | Layered test infrastructure: SeleniumTestCase, NavigatesGalaxy helpers, smart component system, Selenium/Playwright | 2026-09-10 | 5 |
| Component Tool Shed Data Model | Shed-side SQLAlchemy schema — 14 tables, hg-keyed RepositoryMetadata over a denormalized JSON blob, dead flags, two-revision alembic history | 2026-09-10 | 2 |
| Component Ui Error Handling | Backend MessageException serialization to JSON and frontend parsing via simple-error.ts | 2026-09-10 | 5 |
| Component User Password Management | PBKDF2 storage, 24-hour reset tokens, five password entry flows, and the legacy controllers behind them | 2026-09-10 | 1 |
| Component Galaxy Pulsar Runner Code Sharing | Four code-sharing channels between Galaxy and Pulsar, a manually synced util mirror with 20 of 23 files drifted, and stringly-typed job status mapping | 2026-09-09 | 2 |
| Component Tool Install Yaml | Declarative Tool Shed install-request YAML consumed by ephemeris shed-tools, ansible-galaxy-tools, and usegalaxy-tools; manifest-vs-lockfile curation | 2026-09-09 | 2 |
| Component Tool Shed Search And Indexing | Tool Shed's Whoosh repo/tool search and partial GA4GH TRS v2, indexed from hg-walked metadata with no auto-refresh on upload | 2026-09-09 | 5 |
| Component Backend Dependency Management | Python deps via uv: pyproject.toml, uv.lock, pinned-*.txt files, conditional dependency resolver, weekly updates | 2026-08-17 | 3 |
| Component Post Job Actions | Declarative post-processing operations on job outputs, transformations without explicit tools | 2026-08-17 | 3 |
| Component Private Object Stores | Storage-layer private flag vs permission-layer private roles, and why user-defined stores are private only by report | 2026-08-17 | 2 |
| Component Tool Testing Infrastructure | Framework for parsing, loading, executing tests in XML/YAML tool files via planemo | 2026-08-17 | 4 |
| Component Yaml Tool Runtime | YAML tool runtime converts tool state to CWL-style inputs with validated JobInternalToolState | 2026-08-17 | 7 |
| Component Worktree Bootstrapping | Backend Python and frontend Node.js dependency setup, configuration, and dev server bootstrap | 2026-08-17 | 3 |
| Component Drs Support | Client and server for GA4GH DRS URIs — file-source plugin, identifiers.org compact-identifier resolution, OIDC bearer token attachment | 2026-08-08 | 2 |
| Component Data Fetch | Import pipeline from URLs/paste/files/FTP via /api/tools/fetch wrapping __DATA_FETCH__ tool producing HDAs or HDCAs | 2026-08-08 | 5 |
| Component Workflow Api | REST API for workflow CRUD, execution, invocation monitoring via FastAPI controllers | 2026-08-08 | 7 |
| Component Workflow Format Ga | Galaxy JSON workflow format, steps/connections/comments/metadata, canonical serialization | 2026-06-12 | 3 |
| Component Format2 Workflows Gxformat2 | YAML format2 workflow parsing, detection via class=GalaxyWorkflow, conversion pipeline to native JSON | 2026-06-06 | 3 |
| Component Workflow Import | HTTP to database stack for workflow import spanning API controller, manager, and service layers | 2026-06-06 | 3 |
| Component Agents Backend | Multi-agent AI framework with pydantic-ai, five specialized agents, registry pattern, and async execution | 2026-06-03 | 6 |
| Component Agents Ux | Four agent UX surfaces: ChatGXY full-page chat, GalaxyWizard error widget, tool generator, Jupyternaut proxy | 2026-06-03 | 6 |
| Component Agents Chatgxy Persistence | ChatGXY persistence model, API flow, and frontend state management for chat conversations | 2026-05-21 | 5 |
| Component Tool State Dynamic Models | Pydantic dynamic models for validating tool parameter state across 12 representations | 2026-05-21 | 5 |
| Component Tool State Specification | YAML-driven test suite validating 12 tool state representations, each form context-specific | 2026-05-21 | 6 |
| Component Collection Models | Core model classes: DatasetCollection, DatasetCollectionElement, HDCA/LDCA instances, implicit collections from mapping | 2026-05-16 | 8 |
| Component Collection Tool Execution Semantics | Collection types (list, paired, record), mapping semantics, linked vs cross-product multiple inputs, element identifier flow | 2026-05-16 | 6 |
| Component Workflow Editor Terminals | Terminal connection logic, compatibility checking, map-over propagation, plain class instances | 2026-05-16 | 6 |
| Component Workflow Extraction Models | ORM model relationships for reconstructing workflows from history via dataset ancestry | 2026-05-16 | 5 |
| Component Workflow Extraction | Extract history to workflow via Mako UI, traces jobs/datasets back to reconstruct graph | 2026-05-16 | 5 |
| Component Invocation Graph View | Visual DAG rendering of workflow invocation with real-time job state, readonly editor canvas | 2026-05-13 | 3 |
| Component Collection Api | Full collection API surface: POST/GET/PUT/DELETE endpoints, DatasetCollectionsService, fuzzy drill-down, export | 2026-05-09 | 4 |
| Component Collections Records | Heterogeneous fixed-shape collection: CWL-derived `fields` schema of named typed slots; no implicit mapping | 2026-05-09 | 1 |
| Component Collections Sample Sheets Backend | Tabular metadata per collection element: column_definitions, columns row on elements, typed validation, cross-refs | 2026-05-09 | 2 |
| Component Collections Paired Or Unpaired | Discriminated union type of 1 or 2 elements with asymmetric subtyping where paired IS-A paired_or_unpaired | 2026-05-09 | 4 |
| Component Api Tests Tools | Tool API testing split: ~3500 lines legacy unittest tests + ~775 lines modern fluent pytest with input parametrization | 2026-04-28 | 3 |
| Component Collections In Tool Xml Tests | Test syntax for collections: nested 'collection' tags with type, elements, fields for records and paired variants | 2026-04-28 | 3 |
| Component Auto Pairing | Automatic forward/reverse read pairing: parallel frontend/backend implementations validated against shared YAML spec | 2026-04-22 | 2 |
| Component Cwl Ephemeral Collections | Lightweight non-persisted collections created during CWL execution for MultipleInputFeatureRequirement merge strategies | 2026-04-22 | 2 |
| Component Cwl Workflow State | CWL workflow import to persistence to execution: parsed via WorkflowProxy, state encoded/decoded, tool_inputs dict | 2026-04-22 | 2 |
| Component Collection Creation Api | Two-path collection creation: direct POST with element identifiers or fetch API uploading new data atomically | 2026-04-22 | 2 |
| Component Collection Adapters | Ephemeral wrappers promoting datasets/pairs to collections at tool runtime (PromoteDatasetToCollection family) | 2026-04-22 | 3 |
| Component E2e Tests Smart Components | Component system: navigation.yml, Component tree, SmartComponent/SmartTarget wrappers, parameterized selectors | 2026-04-22 | 2 |
| Component Galaxy Workflow Expression Context | CWL-based workflow expressions evaluated as JavaScript with $job, $self, $runtime variables | 2026-04-22 | 2 |
| Component Invocation Report To Pages | Pipeline for converting invocation reports to Pages with encoded ID transformation and markdown | 2026-04-22 | 2 |
| Component Markdown Visualizations | Five fenced block types for galaxy directives, Vega charts, visualizations, Vitessce dashboards | 2026-04-22 | 2 |
| Component Tool Xml Collection Commands | DatasetCollectionWrapper objects in Cheetah command templates, paired/list iteration access | 2026-04-22 | 2 |
| Component Window Manager | Floating window system using WinBox.js, intercepting router.push to render iframe overlays | 2026-04-22 | 2 |
| Component Workflow Comments | Visual annotation system for workflows, text/markdown/frames/freehand without execution impact | 2026-04-22 | 2 |
| Component Workflow Format Differences | Native .ga vs Format2 .gxwf.yml serialization, machine vs human-authored designs and structural trade-offs | 2026-04-22 | 3 |
| Component Workflow Refactoring Api | PUT endpoint for refactoring workflows, routes through service layer with validation | 2026-04-22 | 2 |
| Component Workflow Testing | YAML declarative and Python procedural testing frameworks for workflow execution validation | 2026-04-22 | 2 |
| Component Gxformat2 Parsing And Syntax | Format2 YAML detection, conversion pipeline to Galaxy JSON before import processing | 2026-04-22 | 2 |
| Component Backend Logging Architecture | Python logging with custom TRACE level, dictConfig defaults, app stack filters, Sentry/Fluentd, Gravity support | 2026-03-03 | 1 |
| Component Workflow Editor Terminal Tests | Unit tests for editor terminal connection rules, datatype/collection compatibility validation | 2026-02-09 | 1 |
| Component Implicit Dataset Conversion | Transparent datatype conversion mechanism via ImplicitlyConvertedDatasetAssociation, invisible HDAs | 2026-02-05 | 1 |
Merged Pull Request Research (27)
| Name | Summary | Revised | Rev |
|---|---|---|---|
| Pr 18524 Add Tool Centric Apis To Tool Shed 20 | Tool Shed 2.0 APIs expose parsed tool metadata and parameter schemas for external tooling without Galaxy internals | 2026-09-09 | 3 |
| Pr 20936 Resource Requirements Via Tpv | Tool resource requirements forwarded to TPV for job destination routing and scheduling decisions | 2026-08-17 | 4 |
| Pr 21335 Ga4gh Wes Api | GA4GH WES API exposing Galaxy workflow runs with gxworkflow URI loading state mapping and keyset pagination | 2026-07-13 | 2 |
| Pr 21942 Shared Agent Operations And Mcp Server | Shared AgentOperationsManager wraps Galaxy services for HistoryAgent and an in-process FastMCP server mounted at /api/mcp | 2026-06-18 | 5 |
| Pr 20935 Tool Request Api | Asynchronous job submission via POST /api/jobs with Pydantic-validated state transformations | 2026-06-06 | 8 |
| Pr 21434 Ai Agent Framework And Chatgxy | Pydantic-ai multi-agent framework with router, error analysis, custom tool, orchestrator agents | 2026-06-03 | 7 |
| Pr 21692 Standardize Agent Api Schemas | Standardizes agent response metadata, typing, validates suggestions, removes deprecated endpoints | 2026-06-03 | 5 |
| Pr 22070 Static Yaml Agent Backend For Deterministic Testing | Static YAML agent backend replaces mocked tests with deterministic API and Selenium coverage; drive-by detect_errors.xml fix | 2026-06-03 | 3 |
| Pr 22692 Llm Eval Harness For Agents | Real-LLM eval harness scores Galaxy agents across models with baseline diffing plus router file-source awareness via fast-path and MCP tools | 2026-06-03 | 1 |
| Pr 22706 Workflow Extraction By Ids | ID-based workflow extraction endpoint selecting implicit collection jobs by encoded id instead of HID inference for map-over steps | 2026-05-23 | 3 |
| Pr 19434 User Defined Tools | Users create YAML tools via UI with sandboxed JavaScript expressions and required containerization | 2026-05-22 | 6 |
| Pr 22615 Usertoolsource Pydantic Semantic Validation | Pushes id pattern, blank-field, citation DOI/BibTeX, input-ref, and output-claim checks onto UserToolSource pydantic validators benefiting agent and API | 2026-05-22 | 1 |
| Pr 21463 Jupyternaut Adapter For Jupyterlite | OpenAI Chat Completions endpoint supports Jupyternaut AI assistant in JupyterLite visualizations | 2026-05-21 | 5 |
| Pr 21706 Data Analysis Agent Integration | Integrates data analysis agent with DSPy generating Python code executed in browser via Pyodide | 2026-05-21 | 4 |
| Pr 21828 Yaml Tool Hardening And Tool State | Typed Pydantic collection runtime models, Job.tool_state column, YAML test case JSON validation, collection inputs for YAML tools | 2026-05-21 | 7 |
| Pr 21842 Tool Execution Migrated To Api Jobs | Tool form submits via POST /api/jobs with client-side flat-to-nested state, polls tool_requests until terminal | 2026-05-21 | 5 |
| Pr 18758 Tool Execution Typing And Decomposition | Adds type aliases documenting tool state lifecycle through execution from request to job completion | 2026-05-16 | 6 |
| Pr 21935 Workflow Extraction Vue Conversion | Mako to Vue conversion of workflow extraction UI with new HID-keyed FastAPI extraction summary and extract workflow endpoints replacing legacy controller | 2026-05-16 | 1 |
| Pr 17413 Invocation Graph View | Invocation graph view reuses workflow editor DAG in read-only mode overlaying job states | 2026-05-13 | 3 |
| Pr 20390 Workflow Graph Search | Workflow editor search panel finds steps, inputs, outputs, comments with fuzzy matching and canvas highlight | 2026-05-13 | 3 |
| Pr 21932 History Graph Api | GET /api/histories/{id}/graph returns bounded provenance DAG over HDAs HDCAs tool_requests | 2026-05-13 | 1 |
| Pr 18641 Parameter Model Improvements Research | Extended parameter models with drill_down, data_column, conditional_select types and improved validation | 2026-04-28 | 4 |
| Pr 19377 Collection Types And Wizard Ui | Paired_or_unpaired and record collection types plus collection adapters enable flexible tool input matching | 2026-04-28 | 5 |
| Pr 16612 Workflow Comments | Workflow Comments feature supports text, markdown, frames, and freehand drawing annotations | 2026-04-22 | 2 |
| Pr 19305 Implement Sample Sheets | Sample sheets attach typed columnar metadata to dataset collection elements for bioinformatics workflows | 2026-04-22 | 3 |
| Pr 4830 Workflow Resource Parameters | Administrators define workflow-level resource parameters users set when invoking workflows for scheduling | 2026-04-22 | 2 |
| Pr 5378 Tool Resource Requirements | Tools declare resource requirements like cores and memory modeled after CWL ResourceRequirement | 2026-04-22 | 2 |
Dependency Research (7)
| Name | Summary | Revised | Rev |
|---|---|---|---|
| Dependency Pydantic Discriminated Unions | Pydantic 2.x discriminated unions route validation by field tags instead of sequential checks | 2026-08-08 | 4 |
| Dependency Pydantic Dynamic Models | Pydantic create_model API dynamically builds BaseModel subclasses with field definitions | 2026-05-22 | 4 |
| Dependency Cwl Conformance Tests | CWL conformance test suite infrastructure for spec compliance validation across v1.0, v1.1, v1.2 | 2026-04-22 | 2 |
| Dependency Collection Graphviz | Graphviz diagram generator for Galaxy dataset collection hierarchies with nested box layout | 2026-04-22 | 2 |
| Dependency Planemo Workflow Tests Collection Inputs | Workflow test collection inputs using CWL list, explicit class, and nested collection syntaxes | 2026-04-22 | 2 |
| Dependency Cwl Utils | CWL document parser and transformer with autogenerated dataclasses for v1.0, v1.1, v1.2 | 2026-04-22 | 2 |
| Dependency Gxformat2 | Bidirectional conversion between native .ga and Format2 YAML with linting and visualization | 2026-04-22 | 2 |
Issues (1)
| Name | Summary | Revised | Rev |
|---|---|---|---|
| Issue 17506 Convert Workflow Extraction Interface To Vue | Convert build_from_current_history mako to FastAPI and Vue, extract directly to editor | 2026-05-16 | 5 |
Plans (4)
| Name | Summary | Revised | Rev |
|---|---|---|---|
| Chat Context and Docked Panel Tests | API + Selenium coverage for GalaxyAI docked panel, interface context attachment, and @mention entity context, on the PR 22070 static backend | 2026-05-21 | 1 |
| ChatGXY Notebook Convergence | Converge PR 22096's docked ChatGXY and history_pages PageChatPanel into one Analysis-level chat surface; notebooks become a router context | 2026-05-21 | 2 |
| Tool Form Build Pipeline Refactor | Extract tool-form-building from Tool.to_json into ToolFormBuilder with Pydantic envelope models; regression gate is a declarative YAML expectation suite. | 2026-05-21 | 4 |
| Workflow Extraction Vue Conversion | Convert the last non-data-display Mako template (workflow extraction) to Vue + FastAPI; tracks issue #17506. | 2026-02-05 | 1 |
Projects (14)
| Name | Summary | Revised | Rev |
|---|---|---|---|
| Skill Maintenance | Tracks canonical homes, documentation, packaging, provenance, and maintenance status for reusable agent skills. | 2026-09-25 | 2 |
| Playwright Migration | Migrate the full Galaxy Selenium suite to Playwright and recover the core of PR #21199, via small atomic PRs. | 2026-09-21 | 17 |
| NF-Core Modules to Galaxy Tools | Project for translating nf-core modules into maintainable Galaxy tool wrappers. | 2026-09-15 | 1 |
| Workflow Backlog | Running log of Galaxy workflow backlog issues, each line pairing an issue with its PR and the next action needed | 2026-09-12 | 1 |
| Tool Shed Maintenance | Ongoing Tool Shed maintenance, API modernization, dead-code cleanup, and feature work. | 2026-09-10 | 1 |
| Tool Shed Reviews | Conveying IUC-like review authority to non-IUC Tool Shed repositories, and publishing the gates an agentic tool-maturation pipeline passes | 2026-09-10 | 2 |
| Workflow Semantics | Formalizing Galaxy workflow evaluation semantics into a CI-validated documentation artifact, per issue #22200. | 2026-08-26 | 2 |
| History Markdown Use Cases | Galaxy Notebooks paper use cases: UC1–UC3 worked with extracted workflows; UC4–UC7 newly seeded as interview inputs from an IWC review. | 2026-06-19 | 2 |
| Galaxy Architecture | Mirrored view of the galaxy-architecture repo — training topics rendered as vault-readable markdown. | 2026-05-22 | 1 |
| History Markdown | Project implementing history-attached markdown pages in Galaxy's client and API. | 2026-03-02 | 1 |
| Workflow State | Workflow validation infrastructure: pre-execution parameter typing, format2 usability, VS Code tooling, tool search overhaul. | 2026-03-01 | 1 |
| Collection Semantics | Project formalizing Galaxy collection semantics and their documentation. | 2026-02-21 | 1 |
| CWL | Project tracking CWL implementation in Galaxy: conformance tests, conditionals, packing, tool loading. | 2026-02-21 | 1 |
| WF Refactor Persistence | Persisted undo/redo and workflow CHANGELOG by bridging frontend actions to the backend refactor API (#9166, #21113). | 2026-02-21 | 1 |
Papers (3)
| Name | Summary | Revised | Rev |
|---|---|---|---|
| Galaxy Workflow Foundry: Compiling Curated Workflow Knowledge into Provenanced Agent Skills | Paper workspace for Foundry as a provenance-bearing knowledge-to-skill compiler for Galaxy workflow authoring agents. | 2026-06-20 | 5 |
| Galaxy Notebooks: Reproducible Communication and Narrative-Driven Workflow Extraction | Paper workspace for Galaxy Notebooks as reproducible analysis communication and notebook-driven workflow extraction. | 2026-06-20 | 6 |
| Format 2 and gxwf: Schema-Aware Authoring and Validation of Galaxy Workflows | Paper workspace for Format 2 (Galaxy's writable workflow format), gxformat2 library, and gxwf schema-aware validation/CLI/browser/VS Code authoring stack. | 2026-06-20 | 8 |
Architecture (1)
| Name | Summary | Revised | Rev |
|---|---|---|---|
| Galaxy Architecture | Mirrored view of the galaxy-architecture repo — training topics rendered as vault-readable markdown. | 2026-05-22 | 1 |