@galaxy-tool-util/schema 1.5.0 → 1.6.0

package/dist/index.d.ts

@@ -42,7 +42,11 @@ isSelectLikeParam, isBooleanParam, isSectionParam, isRepeatParam, isConditionalP
 export { ParsedTool, HelpContent, XrefDict, Citation, DiscoverVia, SortKey, SortComp, DatasetCollectionDescription, ToolProvidedMetadataDatasetCollection, FilePatternDatasetCollectionDescription, ToolOutput, ToolOutputDataset, ToolOutputCollectionStructure, ToolOutputCollection, ToolOutputText, ToolOutputInteger, ToolOutputFloat, ToolOutputBoolean, parsedToolSchema, } from "./schema/parsed-tool.js";
 export { type GalaxyWorkflow, 
 /** Union schema accepting any Galaxy workflow format (format2 or native). */
-GalaxyWorkflowSchema, type NativeGalaxyWorkflow, 
+GalaxyWorkflowSchema, type GalaxyWorkflowDraft, 
+/** Relaxed format2 schema for in-progress drafts; permits TODO sentinels and `_plan_*` planning fields. */
+GalaxyWorkflowDraftSchema, type DraftWorkflowStep, 
+/** Schema for a single step inside a GalaxyWorkflowDraft; relaxed vs. the concrete step schema. */
+DraftWorkflowStepSchema, type NativeGalaxyWorkflow, 
 /** Schema for raw native (.ga) Galaxy workflows. */
 NativeGalaxyWorkflowSchema, 
 /** Normalize a raw format2 workflow — fills defaults, resolves implicit fields. */
@@ -156,7 +160,7 @@ 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 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";
+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 ConcreteValidationReport, 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. */

package/dist/index.d.ts.map

@@ -1 +1 @@
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package/dist/index.js

@@ -28,6 +28,10 @@ export { ParsedTool, HelpContent, XrefDict, Citation, DiscoverVia, SortKey, Sort
 export { 
 /** Union schema accepting any Galaxy workflow format (format2 or native). */
 GalaxyWorkflowSchema, 
+/** Relaxed format2 schema for in-progress drafts; permits TODO sentinels and `_plan_*` planning fields. */
+GalaxyWorkflowDraftSchema, 
+/** Schema for a single step inside a GalaxyWorkflowDraft; relaxed vs. the concrete step schema. */
+DraftWorkflowStepSchema, 
 /** Schema for raw native (.ga) Galaxy workflows. */
 NativeGalaxyWorkflowSchema, 
 /** Normalize a raw format2 workflow — fills defaults, resolves implicit fields. */

package/dist/index.js.map

@@ -1 +1 @@
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package/dist/workflow/draft-checks.d.ts

@@ -2,7 +2,7 @@
  * Pure logic for Galaxy draft workflows (`class: GalaxyWorkflowDraft`).
  *
  * Substrate for the `gxwf draft-validate`, `gxwf draft-next-step`, and
- * `gxwf _draft-extract` CLI commands. No I/O.
+ * `gxwf draft-extract` CLI commands. No I/O.
  *
  * The sentinel constants mirror `gxformat2/draft.py`. Drift is enforced by
  * `make check-sync-draft-sentinel` against the JSON snapshot in

package/dist/workflow/draft-checks.js

@@ -2,7 +2,7 @@
  * Pure logic for Galaxy draft workflows (`class: GalaxyWorkflowDraft`).
  *
  * Substrate for the `gxwf draft-validate`, `gxwf draft-next-step`, and
- * `gxwf _draft-extract` CLI commands. No I/O.
+ * `gxwf draft-extract` CLI commands. No I/O.
  *
  * The sentinel constants mirror `gxformat2/draft.py`. Drift is enforced by
  * `make check-sync-draft-sentinel` against the JSON snapshot in

package/dist/workflow/index.d.ts

@@ -1,5 +1,5 @@
 export { serializeWorkflow, resolveFormat, type SerializeWorkflowOptions } from "./serialize.js";
-export { type GalaxyWorkflow, GalaxyWorkflowSchema, type NativeGalaxyWorkflow, NativeGalaxyWorkflowSchema, } from "./raw/index.js";
+export { type GalaxyWorkflow, GalaxyWorkflowSchema, type GalaxyWorkflowDraft, GalaxyWorkflowDraftSchema, type DraftWorkflowStep, DraftWorkflowStepSchema, type NativeGalaxyWorkflow, NativeGalaxyWorkflowSchema, } from "./raw/index.js";
 export { normalizedFormat2, NormalizedFormat2WorkflowSchema, NormalizedFormat2StepSchema, NormalizedFormat2InputSchema, NormalizedFormat2OutputSchema, NormalizedFormat2StepInputSchema, NormalizedFormat2StepOutputSchema, type NormalizedFormat2Workflow, type NormalizedFormat2Step, type NormalizedFormat2Input, type NormalizedFormat2Output, type NormalizedFormat2StepInput, type NormalizedFormat2StepOutput, normalizedNative, NormalizedNativeWorkflowSchema, NormalizedNativeStepSchema, ToolReferenceSchema, type NormalizedNativeWorkflow, type NormalizedNativeStep, type ToolReference, toFormat2, type ToFormat2Options, type Format2StateOverride, toNative, type ToNativeOptions, toFormat2Stateful, toNativeStateful, type StepConversionStatus, type StepConversionFailureClass, type StatefulExportResult, type StatefulNativeResult, type ToolInputsResolver, ensureFormat2, ensureNative, expandedFormat2, expandedNative, isTrsUrl, MAX_EXPANSION_DEPTH, type ExpandedFormat2Workflow, type ExpandedFormat2Step, type ExpandedNativeWorkflow, type ExpandedNativeStep, type RefResolver, type ExpansionOptions, flattenCommentData, unflattenCommentData, resolveSourceReference, UNLABELED_INPUT_PREFIX, UNLABELED_STEP_PREFIX, } from "./normalized/index.js";
 export { flatStatePath, keysStartingWith, repeatInputsToArray, selectWhichWhen, } from "./walk-helpers.js";
 export { injectConnectionsIntoState, stripConnectedValues } from "./state-merge.js";
@@ -28,5 +28,5 @@ export { validateEncodingNative, validateEncodingFormat2, checkStrictEncoding, c
 export { LintContext, LintMessage, Linter, LEVEL_ERROR, LEVEL_WARN, lintNative, lintFormat2, lintWorkflow, lintBestPracticesFormat2, lintBestPracticesNative, type LintLevel, type LintResult, type LinterRef, type EmitOptions, } from "./lint.js";
 export { NativeStepKeyNotInteger } from "./lint-rules.js";
 export { parseLintProfiles, lintProfilesById, rulesForProfile, iwcRuleIds, LINT_PROFILES_FILENAME, IWC_PROFILE_NAMES, type LintProfile, } from "./lint-profiles.js";
-export { 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, } from "./report-models.js";
+export { 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 ConcreteValidationReport, 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, } from "./report-models.js";
 //# sourceMappingURL=index.d.ts.map

package/dist/workflow/index.d.ts.map

@@ -1 +1 @@
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package/dist/workflow/index.js

@@ -1,7 +1,7 @@
 // Format-aware serialization helpers
 export { serializeWorkflow, resolveFormat } from "./serialize.js";
 // Raw (generated) workflow schema types
-export { GalaxyWorkflowSchema, NativeGalaxyWorkflowSchema, } from "./raw/index.js";
+export { GalaxyWorkflowSchema, GalaxyWorkflowDraftSchema, DraftWorkflowStepSchema, NativeGalaxyWorkflowSchema, } from "./raw/index.js";
 // Normalized workflow types + normalizers
 export { normalizedFormat2, NormalizedFormat2WorkflowSchema, NormalizedFormat2StepSchema, NormalizedFormat2InputSchema, NormalizedFormat2OutputSchema, NormalizedFormat2StepInputSchema, NormalizedFormat2StepOutputSchema, normalizedNative, NormalizedNativeWorkflowSchema, NormalizedNativeStepSchema, ToolReferenceSchema, toFormat2, toNative, toFormat2Stateful, toNativeStateful, ensureFormat2, ensureNative, expandedFormat2, expandedNative, isTrsUrl, MAX_EXPANSION_DEPTH, flattenCommentData, unflattenCommentData, resolveSourceReference, UNLABELED_INPUT_PREFIX, UNLABELED_STEP_PREFIX, } from "./normalized/index.js";
 export { flatStatePath, keysStartingWith, repeatInputsToArray, selectWhichWhen, } from "./walk-helpers.js";

package/dist/workflow/index.js.map

@@ -1 +1 @@
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package/dist/workflow/report-models.d.ts

@@ -127,6 +127,48 @@ export interface DraftSurveyReport {
     /** Distinct step paths carrying at least one `_plan_*` field, in walk order. */
     plan_step_paths: string[][];
 }
+/**
+ * Result of `--concrete` validation pass: extract the concrete subset, then
+ * run the regular `gxwf validate` checks on it. The set of populated buckets
+ * depends on which flags were forwarded (cache-dir / no-tool-state /
+ * connections / strict-*). Empty arrays mean the check ran cleanly; absence
+ * of the buckets below means the check was skipped.
+ */
+export interface ConcreteValidationReport {
+    /** Class on the outermost workflow after extract + strip + promote. */
+    class_after: "GalaxyWorkflow" | "GalaxyWorkflowDraft";
+    /**
+     * Reason concrete decode was skipped (e.g., "subset is still a draft —
+     * not fully promoted"). null when decode actually ran.
+     */
+    skipped_reason: string | null;
+    /** Effect Schema decode errors against `GalaxyWorkflowSchema`. */
+    structure_errors: string[];
+    /** Strict-structure check errors. Present only when --strict-structure (or --strict) was set. */
+    strict_structure_errors?: string[];
+    /** Strict-encoding check errors. Present only when --strict-encoding (or --strict) was set. */
+    strict_encoding_errors?: string[];
+    /** Strict-state errors — skipped steps treated as failures. Present only when --strict-state (or --strict) was set. */
+    strict_state_errors?: string[];
+    /** Per-step tool-state validation. Present only when tool-state validation ran. */
+    tool_state?: {
+        results: ValidationStepResult[];
+        summary: {
+            ok: number;
+            fail: number;
+            skip: number;
+        };
+    };
+    /** Connection-type compatibility report. Present only when --connections was set. */
+    connection_report?: ConnectionValidationReport;
+    /**
+     * Tri-state: `true` if every check that ran came back clean, `false` if any
+     * failed, `null` if the concrete pass was skipped (`skipped_reason !== null`).
+     * Consumers must distinguish `null` from `true` — a skipped pass is **not**
+     * an endorsement that the subset would have validated.
+     */
+    ok: boolean | null;
+}
 export interface SingleDraftValidationReport {
     workflow: string;
     ok: boolean;
@@ -135,6 +177,8 @@ export interface SingleDraftValidationReport {
     semantic_errors: DraftValidationDiagnosticReport[];
     warnings: DraftValidationDiagnosticReport[];
     survey: DraftSurveyReport;
+    /** Present only when --concrete was requested. */
+    concrete?: ConcreteValidationReport;
     summary: string;
 }
 export interface DraftExtractDropReport {
@@ -386,7 +430,7 @@ export declare function buildSingleLintReport(workflow: string, lint_errors: num
     lint_warning_messages?: string[];
 }): SingleLintReport;
 export declare function buildSingleCleanReport(workflow: string, results: CleanStepResult[]): SingleCleanReport;
-export declare function buildSingleDraftValidationReport(workflow: string, result: DraftValidationResult): SingleDraftValidationReport;
+export declare function buildSingleDraftValidationReport(workflow: string, result: DraftValidationResult, concrete?: ConcreteValidationReport): SingleDraftValidationReport;
 export declare function buildSingleDraftExtractReport(workflow: string, output: string | null, extract: ExtractResult, promote: PromoteFullyConcreteDraftsResult, classAfter: "GalaxyWorkflowDraft" | "GalaxyWorkflow"): SingleDraftExtractReport;
 export declare function buildWorkflowValidationResult(relativePath: string, stepResults: ValidationStepResult[], opts?: {
     error?: string | null;

package/dist/workflow/report-models.d.ts.map

@@ -1 +1 @@
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package/dist/workflow/report-models.js

@@ -116,15 +116,21 @@ export function buildSingleCleanReport(workflow, results) {
         steps_with_removals: results.filter((r) => r.removed_keys.length > 0).length,
     };
 }
-export function buildSingleDraftValidationReport(workflow, result) {
-    const errorCount = result.structureErrors.length + result.topologyErrors.length + result.semanticErrors.length;
+export function buildSingleDraftValidationReport(workflow, result, concrete) {
+    const errorCount = result.structureErrors.length +
+        result.topologyErrors.length +
+        result.semanticErrors.length +
+        (concrete ? concreteErrorCount(concrete) : 0);
     const warnCount = result.warnings.length;
     const summary = errorCount === 0
         ? `draft valid${warnCount > 0 ? ` (${warnCount} warning${warnCount === 1 ? "" : "s"})` : ""}`
         : `${errorCount} error${errorCount === 1 ? "" : "s"}${warnCount > 0 ? `, ${warnCount} warning${warnCount === 1 ? "" : "s"}` : ""}`;
-    return {
+    // Skipped concrete (ok === null) does NOT drag the aggregate down — it's
+    // informational. Only explicit `false` counts as a failure.
+    const ok = result.ok && concrete?.ok !== false;
+    const report = {
         workflow,
-        ok: result.ok,
+        ok,
         structure_errors: result.structureErrors.map(diagnosticToReport),
         topology_errors: result.topologyErrors.map(diagnosticToReport),
         semantic_errors: result.semanticErrors.map(diagnosticToReport),
@@ -132,10 +138,21 @@ export function buildSingleDraftValidationReport(workflow, result) {
         survey: buildDraftSurveyReport(result.survey),
         summary,
     };
+    if (concrete)
+        report.concrete = concrete;
+    return report;
 }
 function diagnosticToReport(d) {
     return { path: [...d.path], message: d.message };
 }
+function concreteErrorCount(c) {
+    return (c.structure_errors.length +
+        (c.strict_structure_errors?.length ?? 0) +
+        (c.strict_encoding_errors?.length ?? 0) +
+        (c.strict_state_errors?.length ?? 0) +
+        (c.tool_state?.summary.fail ?? 0) +
+        (c.connection_report && !c.connection_report.valid ? 1 : 0));
+}
 export function buildSingleDraftExtractReport(workflow, output, extract, promote, classAfter) {
     const dropped_steps = extract.dropped_steps.map((d) => ({
         path: [...d.path],

package/dist/workflow/report-models.js.map

@@ -1 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@galaxy-tool-util/schema",
-  "version": "1.5.0",
+  "version": "1.6.0",
   "description": "Effect Schema parameter types and validators for Galaxy tools",
   "type": "module",
   "exports": {