@galaxy-tool-util/schema 1.2.0 → 1.5.0

package/dist/index.d.ts

@@ -109,6 +109,22 @@ elementsToList, type CytoscapeEdge, type CytoscapeEdgeData, type CytoscapeElemen
 COL_STRIDE, ROW_STRIDE, LAYOUT_NAMES, bakesCoordinates, isLayoutName, topologicalPositions, type LayoutName, 
 /** Detect whether a workflow dict is native (.ga) or format2 (.gxwf.yml). */
 detectFormat, type WorkflowFormat, 
+/** Draft workflow sentinel pattern (mirrors gxformat2/draft.py). */
+TODO_SENTINEL_PATTERN, PLAN_FIELDS, DRAFT_CLASS, isTodoSentinel, 
+/** True iff doc carries `class: GalaxyWorkflowDraft`. */
+isDraftWorkflow, 
+/** Walk a draft workflow once; collect every TODO sentinel + `_plan_*` field. */
+detectDraft, 
+/** Validate a draft workflow: structural decode + topology + sentinel-form + warnings. Does not throw. */
+validateDraft, 
+/** Topologically-ordered "what to work on next" for a draft workflow; prompt-shaped work[]. */
+nextDraftStep, type NextStepResult, 
+/** Trim a draft workflow to its concrete subset; cascade drops + multi-source rewrites. */
+extractConcreteSubset, type DropReason, type DroppedStep, type DroppedOutput, type RewrittenStepInput, type ExtractResult, 
+/** Strip `_plan_*` planning fields from every step + workflow root (recursive over draft subworkflows). */
+stripPlanFields, type StrippedPlanField, type StripPlanFieldsResult, 
+/** Flip `class: GalaxyWorkflowDraft` → `class: GalaxyWorkflow` on any (sub)workflow now fully concrete. */
+promoteFullyConcreteDrafts, type PromoteFullyConcreteDraftsResult, type PlanField, type StepPath, type TodoLocation, type TodoHit, type PlanHit, type DraftSurvey, type DraftValidationDiagnostic, type DraftValidationResult, 
 /** Format-aware workflow serializer (JSON/YAML, configurable indent and newline). */
 serializeWorkflow, type SerializeWorkflowOptions, 
 /** Resolve workflow format from an optional override, falling back to detectFormat. */
@@ -140,7 +156,7 @@ checkStrictStructure,
 /** Inject `class` discriminator into workflow dict when missing (recursive over step subworkflows). */
 withClass, 
 /** Effect-schema validator dispatch mirroring gxformat2/validators.py. */
-validateFormat2, validateFormat2Strict, validateNative, validateNativeStrict, validatorForFixture, type StepStatus, SKIP_STATUSES, type ValidationStepResult, type CleanStepResult, type ResolvedOutputType, type ConnectionResult, type ConnectionStepResult, type ConnectionValidationReport, type WorkflowEntry, type WorkflowIndex, type SingleValidationReport, type SingleLintReport, type SingleCleanReport, type DiffType, type DiffSeverity, type BenignArtifact, type StepDiff, type SkipWorkflowReason, type FailureClass, type StepResult, type RoundTripResult, type StepIdMappingResult, type RoundTripValidationResult, type SingleRoundTripReport, type SingleExportReport, type StepEncodeStatus, type ToNativeResult, type WorkflowSourceFormat, type ExportResult, type ConvertResult, type WorkflowValidationResult, type LintWorkflowResult, type WorkflowCleanResult, type CategoryGroup, type TreeValidationReport, type LintTreeReport, type TreeCleanReport, type WorkflowExportResult, type ExportTreeReport, type WorkflowToNativeResult, type ToNativeTreeReport, type ToolFailureMode, type RoundTripTreeReport, validationSummary, validationFailures, cleanDisplayLabel, categoryOf, groupByCategory, buildSingleValidationReport, buildSingleLintReport, buildSingleCleanReport, buildWorkflowValidationResult, buildLintWorkflowResult, buildWorkflowCleanResult, buildTreeValidationReport, buildLintTreeReport, buildTreeCleanReport, buildWorkflowExportResult, buildExportTreeReport, buildWorkflowToNativeResult, buildToNativeTreeReport, buildRoundTripTreeReport, type CleanWorkflowOptions, } from "./workflow/index.js";
+validateFormat2, validateFormat2Strict, validateNative, validateNativeStrict, validatorForFixture, type StepStatus, SKIP_STATUSES, type ValidationStepResult, type CleanStepResult, type ResolvedOutputType, type ConnectionResult, type ConnectionStepResult, type ConnectionValidationReport, type WorkflowEntry, type WorkflowIndex, type SingleValidationReport, type SingleLintReport, type SingleCleanReport, type DraftValidationDiagnosticReport, type DraftSurveyReport, type SingleDraftValidationReport, type DraftExtractDropReport, type DraftExtractRewriteReport, type SingleDraftExtractReport, type DiffType, type DiffSeverity, type BenignArtifact, type StepDiff, type SkipWorkflowReason, type FailureClass, type StepResult, type RoundTripResult, type StepIdMappingResult, type RoundTripValidationResult, type SingleRoundTripReport, type SingleExportReport, type StepEncodeStatus, type ToNativeResult, type WorkflowSourceFormat, type ExportResult, type ConvertResult, type WorkflowValidationResult, type LintWorkflowResult, type WorkflowCleanResult, type CategoryGroup, type TreeValidationReport, type LintTreeReport, type TreeCleanReport, type WorkflowExportResult, type ExportTreeReport, type WorkflowToNativeResult, type ToNativeTreeReport, type ToolFailureMode, type RoundTripTreeReport, validationSummary, validationFailures, cleanDisplayLabel, categoryOf, groupByCategory, buildSingleValidationReport, buildSingleLintReport, buildSingleCleanReport, buildSingleDraftValidationReport, buildSingleDraftExtractReport, buildWorkflowValidationResult, buildLintWorkflowResult, buildWorkflowCleanResult, buildTreeValidationReport, buildLintTreeReport, buildTreeCleanReport, buildWorkflowExportResult, buildExportTreeReport, buildWorkflowToNativeResult, buildToNativeTreeReport, buildRoundTripTreeReport, type CleanWorkflowOptions, } from "./workflow/index.js";
 export { ToolStateValidator, type ToolStateDiagnostic } from "./tool-state-validator.js";
 export { 
 /** Validate a parsed *.gxwf-tests.yml / Planemo *-tests.yml document. */
@@ -169,4 +185,14 @@ isCompatibleType,
 jsTypeOf, 
 /** Cross-check a tests doc against workflow shape; emits JSON-pointer diagnostics. */
 checkTestsAgainstWorkflow, } from "./test-format/index.js";
+export { 
+/** Validate a parsed user-defined Galaxy tool source document. */
+validateUserToolSource, 
+/** Raw JSON Schema synced from galaxy.tool_util_models.DynamicToolSources. */
+userToolSourceSchema, 
+/** Run only the semantic (model_validator) checks — internal helper, exposed for tests. */
+runSemanticChecks, type UserToolSourceDiagnostic, type ValidateUserToolSourceOptions, } from "./user-tool-source/index.js";
+export { 
+/** Parse an inline GalaxyUserTool `tool_representation` dict into a ParsedTool. */
+parseInlineTool, type InlineRepresentation, } from "./user-tool-parse/index.js";
 //# sourceMappingURL=index.d.ts.map

package/dist/index.d.ts.map

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package/dist/index.js

@@ -92,6 +92,22 @@ elementsToList,
 COL_STRIDE, ROW_STRIDE, LAYOUT_NAMES, bakesCoordinates, isLayoutName, topologicalPositions, 
 /** Detect whether a workflow dict is native (.ga) or format2 (.gxwf.yml). */
 detectFormat, 
+/** Draft workflow sentinel pattern (mirrors gxformat2/draft.py). */
+TODO_SENTINEL_PATTERN, PLAN_FIELDS, DRAFT_CLASS, isTodoSentinel, 
+/** True iff doc carries `class: GalaxyWorkflowDraft`. */
+isDraftWorkflow, 
+/** Walk a draft workflow once; collect every TODO sentinel + `_plan_*` field. */
+detectDraft, 
+/** Validate a draft workflow: structural decode + topology + sentinel-form + warnings. Does not throw. */
+validateDraft, 
+/** Topologically-ordered "what to work on next" for a draft workflow; prompt-shaped work[]. */
+nextDraftStep, 
+/** Trim a draft workflow to its concrete subset; cascade drops + multi-source rewrites. */
+extractConcreteSubset, 
+/** Strip `_plan_*` planning fields from every step + workflow root (recursive over draft subworkflows). */
+stripPlanFields, 
+/** Flip `class: GalaxyWorkflowDraft` → `class: GalaxyWorkflow` on any (sub)workflow now fully concrete. */
+promoteFullyConcreteDrafts, 
 /** Format-aware workflow serializer (JSON/YAML, configurable indent and newline). */
 serializeWorkflow, 
 /** Resolve workflow format from an optional override, falling back to detectFormat. */
@@ -123,7 +139,7 @@ checkStrictStructure,
 /** Inject `class` discriminator into workflow dict when missing (recursive over step subworkflows). */
 withClass, 
 /** Effect-schema validator dispatch mirroring gxformat2/validators.py. */
-validateFormat2, validateFormat2Strict, validateNative, validateNativeStrict, validatorForFixture, SKIP_STATUSES, validationSummary, validationFailures, cleanDisplayLabel, categoryOf, groupByCategory, buildSingleValidationReport, buildSingleLintReport, buildSingleCleanReport, buildWorkflowValidationResult, buildLintWorkflowResult, buildWorkflowCleanResult, buildTreeValidationReport, buildLintTreeReport, buildTreeCleanReport, buildWorkflowExportResult, buildExportTreeReport, buildWorkflowToNativeResult, buildToNativeTreeReport, buildRoundTripTreeReport, } from "./workflow/index.js";
+validateFormat2, validateFormat2Strict, validateNative, validateNativeStrict, validatorForFixture, SKIP_STATUSES, validationSummary, validationFailures, cleanDisplayLabel, categoryOf, groupByCategory, buildSingleValidationReport, buildSingleLintReport, buildSingleCleanReport, buildSingleDraftValidationReport, buildSingleDraftExtractReport, buildWorkflowValidationResult, buildLintWorkflowResult, buildWorkflowCleanResult, buildTreeValidationReport, buildLintTreeReport, buildTreeCleanReport, buildWorkflowExportResult, buildExportTreeReport, buildWorkflowToNativeResult, buildToNativeTreeReport, buildRoundTripTreeReport, } from "./workflow/index.js";
 export { ToolStateValidator } from "./tool-state-validator.js";
 export { 
 /** Validate a parsed *.gxwf-tests.yml / Planemo *-tests.yml document. */
@@ -144,4 +160,14 @@ isCompatibleType,
 jsTypeOf, 
 /** Cross-check a tests doc against workflow shape; emits JSON-pointer diagnostics. */
 checkTestsAgainstWorkflow, } from "./test-format/index.js";
+export { 
+/** Validate a parsed user-defined Galaxy tool source document. */
+validateUserToolSource, 
+/** Raw JSON Schema synced from galaxy.tool_util_models.DynamicToolSources. */
+userToolSourceSchema, 
+/** Run only the semantic (model_validator) checks — internal helper, exposed for tests. */
+runSemanticChecks, } from "./user-tool-source/index.js";
+export { 
+/** Parse an inline GalaxyUserTool `tool_representation` dict into a ParsedTool. */
+parseInlineTool, } from "./user-tool-parse/index.js";
 //# sourceMappingURL=index.js.map

package/dist/index.js.map

@@ -1 +1 @@
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package/dist/schema/parsed-tool.d.ts

@@ -374,6 +374,9 @@ export declare const ParsedTool: S.Struct<{
     }>, typeof S.Null]>>;
 }>;
 export declare const parsedToolSchema: JSONSchema.JsonSchema7Root;
+export type HelpContent = S.Schema.Type<typeof HelpContent>;
+export type XrefDict = S.Schema.Type<typeof XrefDict>;
+export type Citation = S.Schema.Type<typeof Citation>;
 export type DiscoverVia = S.Schema.Type<typeof DiscoverVia>;
 export type SortKey = S.Schema.Type<typeof SortKey>;
 export type SortComp = S.Schema.Type<typeof SortComp>;

package/dist/schema/parsed-tool.d.ts.map

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package/dist/user-tool-parse/index.d.ts

@@ -0,0 +1,12 @@
+/**
+ * Parse a Galaxy inline `tool_representation` (class: `GalaxyUserTool`) into a
+ * `ParsedTool` — the same shape Galaxy's `/api/tools/:id/parsed` endpoint and
+ * ToolShed serve up. This is the TS port of Galaxy's
+ * `parse_tool(YamlToolSource(repr))` path; it covers the fields included in
+ * the TS `ParsedTool` schema (id/version/name/description, inputs, outputs,
+ * citations, license, profile, edam, xrefs, help). Stdio, requirements and
+ * containers are intentionally out of scope — they're not on the TS
+ * `ParsedTool` shape consumers depend on.
+ */
+export { parseInlineTool, type InlineRepresentation } from "./parse.js";
+//# sourceMappingURL=index.d.ts.map

package/dist/user-tool-parse/index.d.ts.map

@@ -0,0 +1 @@
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package/dist/user-tool-parse/index.js

@@ -0,0 +1,12 @@
+/**
+ * Parse a Galaxy inline `tool_representation` (class: `GalaxyUserTool`) into a
+ * `ParsedTool` — the same shape Galaxy's `/api/tools/:id/parsed` endpoint and
+ * ToolShed serve up. This is the TS port of Galaxy's
+ * `parse_tool(YamlToolSource(repr))` path; it covers the fields included in
+ * the TS `ParsedTool` schema (id/version/name/description, inputs, outputs,
+ * citations, license, profile, edam, xrefs, help). Stdio, requirements and
+ * containers are intentionally out of scope — they're not on the TS
+ * `ParsedTool` shape consumers depend on.
+ */
+export { parseInlineTool } from "./parse.js";
+//# sourceMappingURL=index.js.map

package/dist/user-tool-parse/index.js.map

@@ -0,0 +1 @@
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package/dist/user-tool-parse/inputs.d.ts

@@ -0,0 +1,13 @@
+/**
+ * Inline tool input parser. Mirrors
+ * `galaxy.tool_util.parameters.factory._from_input_source_galaxy`, normalized
+ * to the YAML pathway only (no XML). Produces the Galaxy `ToolParameterModel`
+ * union from `bundle-types.ts`. Validator handling is best-effort: we read
+ * `validators: [{type, ...}]` entries verbatim, mirroring
+ * `static_validators(parse_dict_validators(...))` once you've stripped the XML
+ * shorthand handling and the `in_range` synthesis from `min`/`max` (which is
+ * what Python does too).
+ */
+import type { ToolParameterModel } from "../schema/bundle-types.js";
+export declare function parseInputs(raw: unknown): ToolParameterModel[];
+//# sourceMappingURL=inputs.d.ts.map

package/dist/user-tool-parse/inputs.d.ts.map

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