Files Index: Workflow Tool State Project
Development Branches
| Repo | Branch/Worktree | Path |
|---|---|---|
| Galaxy | wf_tool_state | /Users/jxc755/projects/worktrees/galaxy/branch/wf_tool_state |
| gxformat2 | wf_state | /Users/jxc755/projects/worktrees/gxformat2/branch/wf_state |
Research & Planning (galaxy-brain vault)
| File | Contents |
|---|---|
/Users/jxc755/projects/repositories/galaxy-brain/vault/research/Component - Workflow Format Differences.md | Deep comparison of .ga vs Format2, including tool_state vs state analysis |
/Users/jxc755/projects/repositories/galaxy-brain/vault/research/Component - Tool State Specification.md | 12 state representations, Pydantic model architecture, test infrastructure |
/Users/jxc755/projects/repositories/galaxy-brain/vault/research/PR 18524 - Add Tool-Centric APIs to Tool Shed 2.0.md | Tool Shed API for serving tool schemas (ParsedTool, parameter models) |
/Users/jxc755/projects/repositories/galaxy-brain/vault/projects/workflow_state/PROBLEM_AND_GOAL.md | Problem description and deliverables (this project’s issue body) |
/Users/jxc755/projects/repositories/galaxy-brain/vault/projects/workflow_state/FIRST_STEPS.md | Next planning steps and unresolved questions |
/Users/jxc755/projects/repositories/galaxy-brain/vault/projects/workflow_state/COMPONENT_WORKFLOW_STATE_INITIAL_WORK.md | Summary of initial branch work |
Galaxy — Workflow State Validation & Conversion (new code on branch)
| File | Contents |
|---|---|
/Users/jxc755/projects/worktrees/galaxy/branch/wf_tool_state/lib/galaxy/tool_util/workflow_state/__init__.py | Package init |
/Users/jxc755/projects/worktrees/galaxy/branch/wf_tool_state/lib/galaxy/tool_util/workflow_state/_types.py | GetToolInfo protocol, type aliases for step/workflow dicts |
/Users/jxc755/projects/worktrees/galaxy/branch/wf_tool_state/lib/galaxy/tool_util/workflow_state/validation.py | Top-level validate_workflow() dispatcher (detects format, delegates) |
/Users/jxc755/projects/worktrees/galaxy/branch/wf_tool_state/lib/galaxy/tool_util/workflow_state/validation_format2.py | Format2 validator — state + in validation against tool models |
/Users/jxc755/projects/worktrees/galaxy/branch/wf_tool_state/lib/galaxy/tool_util/workflow_state/validation_native.py | Native validator — tool_state + input_connections validation |
/Users/jxc755/projects/worktrees/galaxy/branch/wf_tool_state/lib/galaxy/tool_util/workflow_state/convert.py | convert_state_to_format2() — native→format2 state conversion |
Galaxy — Format2 Abstraction Layer (new code on branch)
| File | Contents |
|---|---|
/Users/jxc755/projects/worktrees/galaxy/branch/wf_tool_state/lib/galaxy/workflow/format2.py | convert_to_format2(), convert_from_format2(), Format2ConverterGalaxyInterface |
/Users/jxc755/projects/worktrees/galaxy/branch/wf_tool_state/lib/galaxy/workflow/gx_validator.py | GalaxyGetToolInfo — concrete GetToolInfo using stock tools |
Galaxy — Tool State Specification Infrastructure (existing)
| File | Contents |
|---|---|
/Users/jxc755/projects/worktrees/galaxy/branch/wf_tool_state/lib/galaxy/tool_util_models/parameters.py | All parameter model classes, StateRepresentationT, DynamicModelInformation |
/Users/jxc755/projects/worktrees/galaxy/branch/wf_tool_state/lib/galaxy/tool_util_models/_types.py | Type helpers |
/Users/jxc755/projects/worktrees/galaxy/branch/wf_tool_state/lib/galaxy/tool_util_models/_base.py | Base model |
/Users/jxc755/projects/worktrees/galaxy/branch/wf_tool_state/lib/galaxy/tool_util/parameters/__init__.py | Public API re-exports |
/Users/jxc755/projects/worktrees/galaxy/branch/wf_tool_state/lib/galaxy/tool_util/parameters/state.py | ToolState base + 12 concrete subclasses |
/Users/jxc755/projects/worktrees/galaxy/branch/wf_tool_state/lib/galaxy/tool_util/parameters/model_validation.py | validate_against_model() + per-representation validators |
/Users/jxc755/projects/worktrees/galaxy/branch/wf_tool_state/lib/galaxy/tool_util/parameters/factory.py | input_models_for_tool_source() — tool XML/YAML → parameter models |
/Users/jxc755/projects/worktrees/galaxy/branch/wf_tool_state/lib/galaxy/tool_util/parameters/convert.py | decode(), encode(), fill_static_defaults(), etc. |
/Users/jxc755/projects/worktrees/galaxy/branch/wf_tool_state/lib/galaxy/tool_util/parameters/visitor.py | visit_input_values() tree traversal |
/Users/jxc755/projects/worktrees/galaxy/branch/wf_tool_state/lib/galaxy/tool_util/model_factory.py | parse_tool(), parse_tool_custom() |
Galaxy — Tests (on branch)
| File | Contents |
|---|---|
/Users/jxc755/projects/worktrees/galaxy/branch/wf_tool_state/test/unit/workflows/test_workflow_validation.py | Native + Format2 workflow validation tests |
/Users/jxc755/projects/worktrees/galaxy/branch/wf_tool_state/test/unit/workflows/test_workflow_state_conversion.py | Native→Format2 state conversion tests |
/Users/jxc755/projects/worktrees/galaxy/branch/wf_tool_state/test/unit/workflows/test_workflow_validation_helpers.py | GalaxyGetToolInfo tests |
/Users/jxc755/projects/worktrees/galaxy/branch/wf_tool_state/test/unit/workflows/test_convert.py | Format2↔native roundtrip test |
/Users/jxc755/projects/worktrees/galaxy/branch/wf_tool_state/test/unit/workflows/valid/ | Valid Format2 workflow test fixtures |
/Users/jxc755/projects/worktrees/galaxy/branch/wf_tool_state/test/unit/workflows/invalid/ | Invalid Format2 workflow test fixtures |
Galaxy — Tool State Specification Tests (existing)
| File | Contents |
|---|---|
/Users/jxc755/projects/worktrees/galaxy/branch/wf_tool_state/test/unit/tool_util/test_parameter_specification.py | Spec-driven parameter validation test runner |
/Users/jxc755/projects/worktrees/galaxy/branch/wf_tool_state/test/unit/tool_util/parameter_specification.yml | ~2245 lines of valid/invalid payloads per representation |
/Users/jxc755/projects/worktrees/galaxy/branch/wf_tool_state/test/functional/tools/parameters/ | ~104 test tool XML/YAML/CWL files |
gxformat2 — Core Library
| File | Contents |
|---|---|
/Users/jxc755/projects/worktrees/gxformat2/branch/wf_state/gxformat2/converter.py | python_to_workflow() — Format2→native conversion, state/tool_state handling |
/Users/jxc755/projects/worktrees/gxformat2/branch/wf_state/gxformat2/export.py | from_galaxy_native() — native→Format2 export |
/Users/jxc755/projects/worktrees/gxformat2/branch/wf_state/gxformat2/interface.py | ImporterGalaxyInterface — extension point for Galaxy integration |
/Users/jxc755/projects/worktrees/gxformat2/branch/wf_state/gxformat2/lint.py | Format2 linting |
/Users/jxc755/projects/worktrees/gxformat2/branch/wf_state/gxformat2/normalize.py | Workflow normalization |
/Users/jxc755/projects/worktrees/gxformat2/branch/wf_state/gxformat2/model.py | Schema-salad workflow model |
Tool Shed API (existing, serves tool schemas)
| File | Contents |
|---|---|
/Users/jxc755/projects/worktrees/galaxy/branch/wf_tool_state/lib/tool_shed/webapp/api2/tools.py | show_tool, tool_state_request, parameter_landing_request_schema endpoints |
/Users/jxc755/projects/worktrees/galaxy/branch/wf_tool_state/lib/tool_shed/managers/tools.py | parsed_tool_model_cached_for(), tool_source_for() |
/Users/jxc755/projects/worktrees/galaxy/branch/wf_tool_state/lib/tool_shed/managers/model_cache.py | ModelCache — disk caching of parsed tool models |