@galaxy-tool-util/schema 1.12.0 → 1.13.1

package/dist/index.d.ts

@@ -69,7 +69,9 @@ normalizedFormat2,
 /** Expand a step's raw `in` shorthand into normalized {id, source} entries. */
 normalizeStepIn, 
 /** Expand a step's raw `out` shorthand into normalized {id} entries. */
-normalizeStepOut, NormalizedFormat2WorkflowSchema, NormalizedFormat2StepSchema, NormalizedFormat2InputSchema, NormalizedFormat2OutputSchema, NormalizedFormat2StepInputSchema, NormalizedFormat2StepOutputSchema, type NormalizedFormat2Workflow, type NormalizedFormat2Step, type NormalizedFormat2Input, type NormalizedFormat2Output, type NormalizedFormat2StepInput, type NormalizedFormat2StepOutput, 
+normalizeStepOut, NormalizedFormat2WorkflowSchema, NormalizedFormat2StepSchema, NormalizedFormat2InputSchema, NormalizedFormat2OutputSchema, NormalizedFormat2StepInputSchema, NormalizedFormat2StepOutputSchema, GalaxyUserToolStubSchema, 
+/** True when a format2 step's `run:` embeds a user-defined tool (`class: GalaxyUserTool`). */
+isGalaxyUserToolRun, type GalaxyUserToolStub, type NormalizedFormat2Workflow, type NormalizedFormat2Step, type NormalizedFormat2Input, type NormalizedFormat2Output, type NormalizedFormat2StepInput, type NormalizedFormat2StepOutput, 
 /** Normalize a raw native (.ga) workflow — fills defaults, resolves implicit fields. */
 normalizedNative, NormalizedNativeWorkflowSchema, NormalizedNativeStepSchema, ToolReferenceSchema, type NormalizedNativeWorkflow, type NormalizedNativeStep, type ToolReference, 
 /** Merge step connection info into tool_state for validation. */

package/dist/index.d.ts.map

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

@@ -50,7 +50,9 @@ normalizedFormat2,
 /** Expand a step's raw `in` shorthand into normalized {id, source} entries. */
 normalizeStepIn, 
 /** Expand a step's raw `out` shorthand into normalized {id} entries. */
-normalizeStepOut, NormalizedFormat2WorkflowSchema, NormalizedFormat2StepSchema, NormalizedFormat2InputSchema, NormalizedFormat2OutputSchema, NormalizedFormat2StepInputSchema, NormalizedFormat2StepOutputSchema, 
+normalizeStepOut, NormalizedFormat2WorkflowSchema, NormalizedFormat2StepSchema, NormalizedFormat2InputSchema, NormalizedFormat2OutputSchema, NormalizedFormat2StepInputSchema, NormalizedFormat2StepOutputSchema, GalaxyUserToolStubSchema, 
+/** True when a format2 step's `run:` embeds a user-defined tool (`class: GalaxyUserTool`). */
+isGalaxyUserToolRun, 
 /** Normalize a raw native (.ga) workflow — fills defaults, resolves implicit fields. */
 normalizedNative, NormalizedNativeWorkflowSchema, NormalizedNativeStepSchema, ToolReferenceSchema, 
 /** Merge step connection info into tool_state for validation. */

package/dist/index.js.map

@@ -1 +1 @@
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package/dist/workflow/cytoscape.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"cytoscape.d.ts","sourceRoot":"","sources":["../../src/workflow/cytoscape.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,KAAK,EAEV,iBAAiB,EAIlB,MAAM,uBAAuB,CAAC;AAC/B,OAAO,KAAK,EAAE,UAAU,EAAE,MAAM,uBAAuB,CAAC;AAExD,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,mBAAmB,CAAC;AAOtD,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,sBAAsB,CAAC;AAG3D,OAAO,KAAK,EAGV,yBAAyB,EAC1B,MAAM,yBAAyB,CAAC;AAUjC,MAAM,WAAW,gBAAgB;IAC/B;;;;OAIG;IACH,eAAe,CAAC,EAAE,GAAG,CAAC,MAAM,EAAE,cAAc,CAAC,CAAC;IAC9C;;;;;;OAMG;IACH,MAAM,CAAC,EAAE,UAAU,CAAC;IACpB;;;;;;;OAOG;IACH,YAAY,CAAC,EAAE,YAAY,GAAG,IAAI,CAAC;CACpC;AAED,wBAAgB,iBAAiB,CAC/B,QAAQ,EAAE,OAAO,GAAG,yBAAyB,EAC7C,IAAI,GAAE,gBAAqB,GAC1B,iBAAiB,CAuEnB"}

package/dist/workflow/cytoscape.js

@@ -9,6 +9,7 @@ import { bakesCoordinates, topologicalPositions } from "./cytoscape-layout.js";
 import { isDraftWorkflow, isTodoSentinel, PLANNED_CLASS, resolveDraftOverlay, } from "./draft-checks.js";
 import { edgeAnnotationKey } from "./edge-annotation.js";
 import { ensureFormat2 } from "./normalized/ensure.js";
+import { isGalaxyUserToolRun } from "./normalized/format2.js";
 import { isUnlabeledStep, resolveSourceReference, stepRenderIdentity, } from "./normalized/labels.js";
 const MAIN_TS_PREFIX = "toolshed.g2.bx.psu.edu/repos/";
 export function cytoscapeElements(workflow, opts = {}) {
@@ -117,9 +118,10 @@ function _inputNode(inp, orderIndex) {
 }
 function _stepNode(step, orderIndex, overlay) {
     const stepId = stepRenderIdentity(step);
-    // The TS normalizer doesn't infer step.type the way gxformat2 does, so fall
-    // back to a `run`-derived hint for subworkflows (matches mermaid emitter).
-    const stepType = step.type || (step.run != null ? "subworkflow" : "tool");
+    // An embedded GalaxyUserTool run is a tool, while workflow runs are subworkflows.
+    const stepType = isGalaxyUserToolRun(step.run)
+        ? "tool"
+        : step.type || (step.run != null ? "subworkflow" : "tool");
     let strippedToolId = step.tool_id ?? null;
     if (strippedToolId && strippedToolId.startsWith(MAIN_TS_PREFIX)) {
         strippedToolId = strippedToolId.slice(MAIN_TS_PREFIX.length);

package/dist/workflow/cytoscape.js.map

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

@@ -120,7 +120,8 @@ export interface DraftValidationResult {
  *                    input labels, output labels, step labels, and step types
  *                    cannot be TODO sentinels. Step/port edge refs must
  *                    resolve to a declared step + declared port (TODO_*
- *                    ports count if declared in the step's `out:`).
+ *                    ports count if declared in the step's `out:`; an
+ *                    embedded `GalaxyUserTool` also declares its outputs).
  *   semanticErrors   TODO-shaped strings (start with `TODO`) that don't
  *                    match the canonical sentinel form (e.g. `TODO-foo`,
  *                    `TODOfoo`, `TODO_` trailing).

package/dist/workflow/draft-checks.d.ts.map

@@ -1 +1 @@
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package/dist/workflow/draft-checks.js

@@ -11,6 +11,7 @@
 import { Either, ParseResult, Schema } from "effect";
 import { GalaxyWorkflowDraftSchema } from "./raw/gxformat2-draft.effect.js";
 import { rawStepRenderIdentity, resolveSourceReference } from "./normalized/labels.js";
+import { isGalaxyUserToolRun } from "./normalized/format2.js";
 export const TODO_SENTINEL_PATTERN = /^TODO(_[a-zA-Z0-9_]+)?$/;
 // Heuristic for TODO-shaped strings — flags malformed sentinels (TODO-foo,
 // TODOfoo, TODO_) that the canonical pattern misses. Mixed-case suffixes
@@ -250,6 +251,28 @@ function* iterateStepOutIds(out) {
         }
     }
 }
+/**
+ * Output ports a step exposes: its declared `out:` ids, plus every output an
+ * embedded `GalaxyUserTool` run defines — Galaxy creates those whether or not
+ * `out:` lists them.
+ */
+function stepOutPorts(step) {
+    const ports = new Set(iterateStepOutIds(step.out));
+    if (isGalaxyUserToolRun(step.run)) {
+        const outputs = step.run.outputs;
+        if (Array.isArray(outputs)) {
+            for (const output of outputs) {
+                if (isRecord(output) && typeof output.name === "string")
+                    ports.add(output.name);
+            }
+        }
+        else if (isRecord(outputs)) {
+            for (const name of Object.keys(outputs))
+                ports.add(name);
+        }
+    }
+    return ports;
+}
 function isRecord(value) {
     return typeof value === "object" && value !== null && !Array.isArray(value);
 }
@@ -261,7 +284,8 @@ function isRecord(value) {
  *                    input labels, output labels, step labels, and step types
  *                    cannot be TODO sentinels. Step/port edge refs must
  *                    resolve to a declared step + declared port (TODO_*
- *                    ports count if declared in the step's `out:`).
+ *                    ports count if declared in the step's `out:`; an
+ *                    embedded `GalaxyUserTool` also declares its outputs).
  *   semanticErrors   TODO-shaped strings (start with `TODO`) that don't
  *                    match the canonical sentinel form (e.g. `TODO-foo`,
  *                    `TODOfoo`, `TODO_` trailing).
@@ -458,8 +482,7 @@ function buildStepIndex(steps) {
     for (const [label, step] of iterateSteps(steps)) {
         if (!isRecord(step))
             continue;
-        const outPorts = new Set(iterateStepOutIds(step.out));
-        index.set(label, { outPorts });
+        index.set(label, { outPorts: stepOutPorts(step) });
     }
     return index;
 }
@@ -864,7 +887,8 @@ function directDropReason(step) {
 }
 /**
  * For each surviving step, compute its currently-live output ports:
- *   - Non-subworkflow steps: all declared `out:` ids.
+ *   - Non-subworkflow steps: all declared `out:` ids, plus the outputs of an
+ *     embedded `GalaxyUserTool` run.
  *   - Inline-draft subworkflow steps: keys of the recursed inner workflow's
  *     surviving outputs (so outer refs that referenced now-dropped inner
  *     outputs evaluate as dead).
@@ -887,7 +911,7 @@ function computeLivePorts(stepEntries, drops, innerResults) {
             livePorts.set(label, surviving);
         }
         else {
-            livePorts.set(label, new Set(iterateStepOutIds(step.out)));
+            livePorts.set(label, stepOutPorts(step));
         }
     }
     return livePorts;

package/dist/workflow/draft-checks.js.map

@@ -1 +1 @@
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package/dist/workflow/index.d.ts

@@ -1,7 +1,7 @@
 export { serializeWorkflow, resolveFormat, type SerializeWorkflowOptions } from "./serialize.js";
 export { type GalaxyWorkflow, GalaxyWorkflowSchema, type GalaxyWorkflowDraft, GalaxyWorkflowDraftSchema, type DraftWorkflowStep, DraftWorkflowStepSchema, type NativeGalaxyWorkflow, NativeGalaxyWorkflowSchema, } from "./raw/index.js";
 export { galaxyWorkflowDraftJsonSchema } from "./json-schemas.js";
-export { normalizedFormat2, normalizeStepIn, normalizeStepOut, 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, stepRenderIdentity, rawStepRenderIdentity, UNLABELED_INPUT_PREFIX, UNLABELED_STEP_PREFIX, } from "./normalized/index.js";
+export { normalizedFormat2, normalizeStepIn, normalizeStepOut, NormalizedFormat2WorkflowSchema, NormalizedFormat2StepSchema, NormalizedFormat2InputSchema, NormalizedFormat2OutputSchema, NormalizedFormat2StepInputSchema, NormalizedFormat2StepOutputSchema, GalaxyUserToolStubSchema, isGalaxyUserToolRun, type GalaxyUserToolStub, 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, stepRenderIdentity, rawStepRenderIdentity, UNLABELED_INPUT_PREFIX, UNLABELED_STEP_PREFIX, } from "./normalized/index.js";
 export { flatStatePath, keysStartingWith, repeatInputsToArray, selectWhichWhen, } from "./walk-helpers.js";
 export { injectConnectionsIntoState, stripConnectedValues, nativeConnectionsFromFormat2In, } from "./state-merge.js";
 export { expandToolStateDefaults } from "./fill-defaults.js";

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

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

@@ -5,7 +5,7 @@ export { GalaxyWorkflowSchema, GalaxyWorkflowDraftSchema, DraftWorkflowStepSchem
 // Plain JSON Schema siblings for downstream packagers (issue #108)
 export { galaxyWorkflowDraftJsonSchema } from "./json-schemas.js";
 // Normalized workflow types + normalizers
-export { normalizedFormat2, normalizeStepIn, normalizeStepOut, 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, stepRenderIdentity, rawStepRenderIdentity, UNLABELED_INPUT_PREFIX, UNLABELED_STEP_PREFIX, } from "./normalized/index.js";
+export { normalizedFormat2, normalizeStepIn, normalizeStepOut, NormalizedFormat2WorkflowSchema, NormalizedFormat2StepSchema, NormalizedFormat2InputSchema, NormalizedFormat2OutputSchema, NormalizedFormat2StepInputSchema, NormalizedFormat2StepOutputSchema, GalaxyUserToolStubSchema, isGalaxyUserToolRun, normalizedNative, NormalizedNativeWorkflowSchema, NormalizedNativeStepSchema, ToolReferenceSchema, toFormat2, toNative, toFormat2Stateful, toNativeStateful, ensureFormat2, ensureNative, expandedFormat2, expandedNative, isTrsUrl, MAX_EXPANSION_DEPTH, flattenCommentData, unflattenCommentData, resolveSourceReference, stepRenderIdentity, rawStepRenderIdentity, UNLABELED_INPUT_PREFIX, UNLABELED_STEP_PREFIX, } from "./normalized/index.js";
 export { flatStatePath, keysStartingWith, repeatInputsToArray, selectWhichWhen, } from "./walk-helpers.js";
 export { injectConnectionsIntoState, stripConnectedValues, nativeConnectionsFromFormat2In, } from "./state-merge.js";
 export { expandToolStateDefaults } from "./fill-defaults.js";

package/dist/workflow/index.js.map

@@ -1 +1 @@
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package/dist/workflow/mermaid.d.ts

@@ -5,7 +5,7 @@
  */
 import type { DraftOverlay } from "./draft-checks.js";
 import type { EdgeAnnotation } from "./edge-annotation.js";
-import type { NormalizedFormat2Workflow } from "./normalized/format2.js";
+import { type NormalizedFormat2Workflow } from "./normalized/format2.js";
 export interface MermaidOptions {
     comments?: boolean;
     /**

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

@@ -1 +1 @@
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+{"version":3,"file":"mermaid.d.ts","sourceRoot":"","sources":["../../src/workflow/mermaid.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,mBAAmB,CAAC;AAOtD,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,sBAAsB,CAAC;AAG3D,OAAO,EAAuB,KAAK,yBAAyB,EAAE,MAAM,yBAAyB,CAAC;AA6B9F,MAAM,WAAW,cAAc;IAC7B,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB;;;OAGG;IACH,eAAe,CAAC,EAAE,GAAG,CAAC,MAAM,EAAE,cAAc,CAAC,CAAC;IAC9C;;;;;;OAMG;IACH,YAAY,CAAC,EAAE,YAAY,GAAG,IAAI,CAAC;CACpC;AA+CD,wBAAgB,iBAAiB,CAC/B,QAAQ,EAAE,OAAO,GAAG,yBAAyB,EAC7C,IAAI,GAAE,cAAmB,GACxB,MAAM,CAwJR"}

package/dist/workflow/mermaid.js

@@ -6,6 +6,7 @@
 import { isDraftWorkflow, isTodoSentinel, PLANNED_CLASS, resolveDraftOverlay, } from "./draft-checks.js";
 import { edgeAnnotationKey } from "./edge-annotation.js";
 import { ensureFormat2 } from "./normalized/ensure.js";
+import { isGalaxyUserToolRun } from "./normalized/format2.js";
 import { isUnlabeledStep, resolveSourceReference, stepRenderIdentity, } from "./normalized/labels.js";
 const SHAPE_INPUT = [">", "]"];
 const SHAPE_PARAM = ["{{", "}}"];
@@ -118,9 +119,10 @@ export function workflowToMermaid(workflow, opts = {}) {
         const displayId = step.id && !isUnlabeledStep(step.id) ? step.id : null;
         const rawLabel = step.label || displayId || (toolId ? `tool:${toolId}` : String(i));
         const label = sanitizeLabel(rawLabel);
-        // The TS normalizer does not infer step.type the way gxformat2 does, so
-        // fall back to `run` shape: anything non-null implies a subworkflow.
-        const stepType = step.type || (step.run != null ? "subworkflow" : "tool");
+        // An embedded GalaxyUserTool run is a tool, while workflow runs are subworkflows.
+        const stepType = isGalaxyUserToolRun(step.run)
+            ? "tool"
+            : step.type || (step.run != null ? "subworkflow" : "tool");
         const shape = STEP_TYPE_SHAPES[stepType] ?? SHAPE_TOOL;
         stepLines.set(stepLabel, nodeLine(nodeId, label, shape));
     });