Follow-up: Additional Workflow Operations (galaxy-tool-util)

Deferred from the initial normalized models plan. Implement after normalizedFormat2 and normalizedNative land and their declarative tests pass.

Expanded Models ✅

• expandedFormat2(raw) — extends NormalizedFormat2, resolves inline subworkflows recursively. External URL/@import resolution not yet wired (no test expectations require it).
• expandedNative(raw) — extends NormalizedNativeWorkflow, resolves inline subworkflow references recursively.
• $graph multi-document resolution already handled by normalizedFormat2; expanded models go further by fetching/inlining external references (future).

New: packages/schema/src/workflow/normalized/expanded.ts

Expectation files

• normalized_format2.yml contains test_steps_without_run_unchanged (operation: expanded_format2) and test_inline_subworkflow_expanded (operation: expanded_native) — both passing.

Conversion Operations ✅

• toFormat2(native) — native → format2 conversion
• toNative(format2) — format2 → native conversion
• ensureFormat2(any) — polymorphic: accepts either format, returns NormalizedFormat2
• ensureNative(any) — polymorphic: accepts either format, returns NormalizedNativeWorkflow

New files:

• packages/schema/src/workflow/normalized/toFormat2.ts — full native→format2 conversion with label map, step conversion (tool/subworkflow/pause), PJA→out conversion (all 7 action types), input_connections→in conversion, comments conversion (native→format2), anonymous output reference rewriting
• packages/schema/src/workflow/normalized/toNative.ts — full format2→native conversion with ConversionContext (label registry + source resolution), input step building (type mapping), step dispatch (tool/subworkflow/pause), connection building with subworkflow input wiring, PJA building from out properties, workflow output wiring, comments conversion (format2→native)
• packages/schema/src/workflow/normalized/ensure.ts — format detection via a_galaxy_workflow / class: GalaxyWorkflow and dispatch
• packages/schema/src/workflow/normalized/comments.ts — flattenCommentData (native→format2) and unflattenCommentData (format2→native), port of gxformat2/_comment_helpers.py
• packages/schema/src/workflow/normalized/labels.ts — resolveSourceReference, Labels class, UNLABELED_* prefixes, isUnlabeled/isAnonymousOutputLabel predicates, port of gxformat2/_labels.py

Expectation files

• to_format2.yml — 8 tests, all passing
• to_native.yml — 10 tests (+ 1 comments), all passing
• ensure_format2.yml — 2 tests, all passing
• ensure_native.yml — 2 tests, all passing

Changes to existing files

• normalizedFormat2 now passes comments through on the result object (not in schema, but accessible via cast)
• normalizedNative now passes comments through similarly
• Test runner: added format_version → format-version to FIELD_ALIASES
• UNSUPPORTED_OPERATIONS emptied; all 6 operations now in OPERATIONS dispatch map

Implementation order (as executed)

1. ✅ Shared utilities: comments.ts, labels.ts
2. ✅ toFormat2 (native → format2)
3. ✅ toNative (format2 → native)
4. ✅ ensureFormat2 / ensureNative (polymorphic entry points)
5. ✅ expandedFormat2 / expandedNative (inline-only expansion)
6. ✅ Wired into test runner + exports

Test results

• 61/61 declarative tests passing (0 skipped)
• Full suite: 4012 passed, 61 skipped (unrelated), 11 test files
• TypeScript: clean build (noEmit)

Resolved questions

• _toSource strips /output suffix when output_name === “output” (matches Python)
• Full PJA set implemented: Rename, Hide, DeleteIntermediates, ChangeDatatype, ColumnSet, TagDataset, RemoveTagDataset
• Comments conversion implemented in both directions using shared helpers ported from gxformat2/_comment_helpers.py
• Default positions generated as (10idx, 10idx) matching Python
• UUIDs not generated for to_native (tests don’t check them, Python generates random UUIDs)

Unresolved questions

• Expanded models: URL resolution / @import resolution not implemented (no test expectations, would need async resolver or callback pattern)
• pick_value step type: partially handled in toFormat2 (falls through to tool handler) — no test expectations exist
• GalaxyUserTool step type: not handled (no test expectations)
• $graph deduplication in toNative: Python supports deduplicate_subworkflows option — not implemented (no test expectations)

Integration with validate-workflow CLI

Once normalized + expanded models exist, validate-workflow could:

• Normalize before tool-state validation (catches malformed shorthands earlier)
• Report normalization warnings (e.g. deprecated input type aliases)
• Accept either format and convert via ensure* for uniform validation