@galaxy-tool-util/schema 1.8.2 → 1.10.0

package/dist/index.d.ts

@@ -116,7 +116,7 @@ type EdgeAnnotation, edgeAnnotationKey,
 /** Build Cytoscape.js elements from a Galaxy workflow. */
 cytoscapeElements, type CytoscapeOptions, 
 /** Flatten cytoscape elements into the list-of-dicts format cytoscape.js consumes. */
-elementsToList, type CytoscapeEdge, type CytoscapeEdgeData, type CytoscapeElements, type CytoscapeLayoutHint, type CytoscapeListItem, type CytoscapeNode, type CytoscapeNodeData, type CytoscapePosition, 
+elementsToList, type CytoscapeEdge, type CytoscapeEdgeData, type CytoscapeElements, type CytoscapeLayoutHint, type CytoscapeListItem, type CytoscapeNode, type CytoscapeNodeData, type CytoscapePlanReason, type CytoscapePosition, 
 /** Cross-language layout names + topological position computation. */
 COL_STRIDE, ROW_STRIDE, LAYOUT_NAMES, bakesCoordinates, isLayoutName, topologicalPositions, type LayoutName, 
 /** Detect whether a workflow dict is native (.ga) or format2 (.gxwf.yml). */
@@ -132,7 +132,13 @@ 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, 
+extractConcreteSubset, 
+/** Build a planned/concrete overlay from a raw draft for visualizers (mermaid/cytoscape). */
+resolveDraftOverlay, 
+/** Shared class-name token marking planned (draft) nodes/edges. */
+PLANNED_CLASS, type DraftOverlay, type DraftPlannedReason, 
+/** Render identity of a step (`label || id`), shared by detectDraft overlay + visualizers. */
+stepRenderIdentity, rawStepRenderIdentity, 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. */

package/dist/index.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO;AACL,0FAA0F;AAC1F,gBAAgB,EAChB,KAAK,mBAAmB;AACxB,4CAA4C;AAC5C,qBAAqB;AACrB,wEAAwE;AACxE,yBAAyB;AACzB,6DAA6D;AAC7D,wBAAwB;AACxB,wEAAwE;AACxE,yBAAyB;AACzB,6DAA6D;AAC7D,wBAAwB;AACxB,gEAAgE;AAChE,qBAAqB;AACrB,gEAAgE;AAChE,qBAAqB,GACtB,MAAM,mBAAmB,CAAC;AAE3B,OAAO;AACL,2CAA2C;AAC3C,KAAK,wBAAwB;AAC7B,2EAA2E;AAC3E,KAAK,kBAAkB;AACvB,4DAA4D;AAC5D,KAAK,oBAAoB;AACzB,yEAAyE;AACzE,KAAK,uBAAuB;AAC5B,6DAA6D;AAC7D,KAAK,wBAAwB,EAC7B,KAAK,qBAAqB,EAC1B,KAAK,mBAAmB,EACxB,KAAK,kBAAkB,EACvB,KAAK,oBAAoB,EACzB,KAAK,yBAAyB,EAC9B,KAAK,uBAAuB,EAC5B,KAAK,qBAAqB,EAC1B,KAAK,qBAAqB,EAC1B,KAAK,oBAAoB,EACzB,KAAK,yBAAyB;AAC9B,sDAAsD;AACtD,KAAK,eAAe;AACpB,iEAAiE;AACjE,KAAK,UAAU,GAChB,MAAM,0BAA0B,CAAC;AAElC,OAAO;AACL,uFAAuF;AACvF,iBAAiB,EACjB,cAAc,EACd,cAAc,EACd,aAAa,EACb,kBAAkB,GACnB,MAAM,yBAAyB,CAAC;AAEjC,OAAO,EACL,UAAU,EACV,WAAW,EACX,QAAQ,EACR,QAAQ,EACR,WAAW,EACX,OAAO,EACP,QAAQ,EACR,4BAA4B,EAC5B,qCAAqC,EACrC,uCAAuC,EACvC,UAAU,EACV,iBAAiB,EACjB,6BAA6B,EAC7B,oBAAoB,EACpB,cAAc,EACd,iBAAiB,EACjB,eAAe,EACf,iBAAiB,EACjB,gBAAgB,GACjB,MAAM,yBAAyB,CAAC;AAEjC,OAAO,EACL,KAAK,cAAc;AACnB,6EAA6E;AAC7E,oBAAoB,EACpB,KAAK,mBAAmB;AACxB,2GAA2G;AAC3G,yBAAyB;AACzB,+HAA+H;AAC/H,6BAA6B,EAC7B,KAAK,iBAAiB;AACtB,mGAAmG;AACnG,uBAAuB,EACvB,KAAK,oBAAoB;AACzB,oDAAoD;AACpD,0BAA0B;AAC1B,mFAAmF;AACnF,iBAAiB;AACjB,+EAA+E;AAC/E,eAAe;AACf,wEAAwE;AACxE,gBAAgB,EAChB,+BAA+B,EAC/B,2BAA2B,EAC3B,4BAA4B,EAC5B,6BAA6B,EAC7B,gCAAgC,EAChC,iCAAiC,EACjC,KAAK,yBAAyB,EAC9B,KAAK,qBAAqB,EAC1B,KAAK,sBAAsB,EAC3B,KAAK,uBAAuB,EAC5B,KAAK,0BAA0B,EAC/B,KAAK,2BAA2B;AAChC,wFAAwF;AACxF,gBAAgB,EAChB,8BAA8B,EAC9B,0BAA0B,EAC1B,mBAAmB,EACnB,KAAK,wBAAwB,EAC7B,KAAK,oBAAoB,EACzB,KAAK,aAAa;AAClB,iEAAiE;AACjE,0BAA0B;AAC1B,oEAAoE;AACpE,oBAAoB;AACpB,4EAA4E;AAC5E,8BAA8B;AAC9B,oFAAoF;AACpF,uBAAuB;AACvB,kHAAkH;AAClH,qBAAqB;AACrB,+DAA+D;AAC/D,eAAe;AACf,sEAAsE;AACtE,gBAAgB;AAChB,wEAAwE;AACxE,SAAS,EACT,KAAK,kBAAkB;AACvB,iEAAiE;AACjE,aAAa,EACb,gBAAgB;AAChB,6CAA6C;AAC7C,mBAAmB;AACnB,qEAAqE;AACrE,eAAe;AACf,6DAA6D;AAC7D,mBAAmB;AACnB,gFAAgF;AAChF,eAAe;AACf,+EAA+E;AAC/E,cAAc;AACd,mEAAmE;AACnE,QAAQ,EACR,mBAAmB,EACnB,KAAK,uBAAuB,EAC5B,KAAK,mBAAmB,EACxB,KAAK,sBAAsB,EAC3B,KAAK,kBAAkB,EACvB,KAAK,WAAW,EAChB,KAAK,gBAAgB;AACrB,qDAAqD;AACrD,SAAS;AACT,qDAAqD;AACrD,QAAQ;AACR,0EAA0E;AAC1E,iBAAiB;AACjB,0EAA0E;AAC1E,gBAAgB,EAChB,KAAK,oBAAoB,EACzB,KAAK,0BAA0B,EAC/B,KAAK,oBAAoB,EACzB,KAAK,oBAAoB,EACzB,KAAK,kBAAkB;AACvB,+EAA+E;AAC/E,sBAAsB,EACtB,kBAAkB,EAClB,KAAK,cAAc,EACnB,KAAK,kBAAkB;AACvB,4EAA4E;AAC5E,2BAA2B,EAC3B,uBAAuB,EACvB,wBAAwB;AACxB,6EAA6E;AAC7E,8BAA8B,EAC9B,KAAK,eAAe;AACpB,kFAAkF;AAClF,eAAe,EACf,KAAK,qBAAqB;AAC1B,yFAAyF;AACzF,iBAAiB,EACjB,KAAK,eAAe,EACpB,KAAK,sBAAsB,EAC3B,KAAK,mBAAmB,EACxB,KAAK,kBAAkB,EACvB,KAAK,qBAAqB;AAC1B,6EAA6E;AAC7E,aAAa,EACb,KAAK,4BAA4B,EACjC,KAAK,iBAAiB,EACtB,KAAK,wBAAwB;AAC7B,8EAA8E;AAC9E,aAAa,EACb,KAAK,mBAAmB,EACxB,iBAAiB,EACjB,KAAK,cAAc;AACnB,oGAAoG;AACpG,KAAK,cAAc,EACnB,iBAAiB;AACjB,0DAA0D;AAC1D,iBAAiB,EACjB,KAAK,gBAAgB;AACrB,sFAAsF;AACtF,cAAc,EACd,KAAK,aAAa,EAClB,KAAK,iBAAiB,EACtB,KAAK,iBAAiB,EACtB,KAAK,mBAAmB,EACxB,KAAK,iBAAiB,EACtB,KAAK,aAAa,EAClB,KAAK,iBAAiB,EACtB,KAAK,mBAAmB,EACxB,KAAK,iBAAiB;AACtB,sEAAsE;AACtE,UAAU,EACV,UAAU,EACV,YAAY,EACZ,gBAAgB,EAChB,YAAY,EACZ,oBAAoB,EACpB,KAAK,UAAU;AACf,6EAA6E;AAC7E,YAAY,EACZ,KAAK,cAAc;AACnB,oEAAoE;AACpE,qBAAqB,EACrB,WAAW,EACX,WAAW,EACX,cAAc;AACd,yDAAyD;AACzD,eAAe;AACf,iFAAiF;AACjF,WAAW;AACX,0GAA0G;AAC1G,aAAa;AACb,+FAA+F;AAC/F,aAAa,EACb,KAAK,cAAc;AACnB,2FAA2F;AAC3F,qBAAqB;AACrB,6FAA6F;AAC7F,mBAAmB;AACnB,mEAAmE;AACnE,aAAa,EACb,KAAK,YAAY,EACjB,KAAK,kBAAkB;AACvB,8FAA8F;AAC9F,kBAAkB,EAClB,qBAAqB,EACrB,KAAK,UAAU,EACf,KAAK,WAAW,EAChB,KAAK,aAAa,EAClB,KAAK,kBAAkB,EACvB,KAAK,aAAa;AAClB,2GAA2G;AAC3G,eAAe,EACf,KAAK,iBAAiB,EACtB,KAAK,qBAAqB;AAC1B,2GAA2G;AAC3G,0BAA0B,EAC1B,KAAK,gCAAgC,EACrC,KAAK,SAAS,EACd,KAAK,QAAQ,EACb,KAAK,YAAY,EACjB,KAAK,OAAO,EACZ,KAAK,OAAO,EACZ,KAAK,WAAW,EAChB,KAAK,yBAAyB,EAC9B,KAAK,qBAAqB;AAC1B,qFAAqF;AACrF,iBAAiB,EACjB,KAAK,wBAAwB;AAC7B,uFAAuF;AACvF,aAAa;AACb,6EAA6E;AAC7E,WAAW;AACX,0EAA0E;AAC1E,WAAW;AACX,+CAA+C;AAC/C,MAAM,EACN,WAAW,EACX,UAAU;AACV,kDAAkD;AAClD,UAAU;AACV,yDAAyD;AACzD,WAAW;AACX,8CAA8C;AAC9C,YAAY;AACZ,yDAAyD;AACzD,wBAAwB;AACxB,wDAAwD;AACxD,uBAAuB,EACvB,KAAK,SAAS,EACd,KAAK,UAAU,EACf,KAAK,SAAS,EACd,KAAK,WAAW;AAChB,2CAA2C;AAC3C,uBAAuB;AACvB,gEAAgE;AAChE,iBAAiB,EACjB,gBAAgB,EAChB,eAAe,EACf,UAAU,EACV,sBAAsB,EACtB,iBAAiB,EACjB,KAAK,WAAW;AAChB,2GAA2G;AAC3G,sBAAsB,EACtB,uBAAuB,EACvB,mBAAmB;AACnB,kFAAkF;AAClF,oBAAoB;AACpB,uGAAuG;AACvG,SAAS;AACT,0EAA0E;AAC1E,eAAe,EACf,qBAAqB,EACrB,cAAc,EACd,oBAAoB,EACpB,mBAAmB,EAEnB,KAAK,UAAU,EACf,aAAa,EACb,KAAK,oBAAoB,EACzB,KAAK,eAAe,EACpB,KAAK,kBAAkB,EACvB,KAAK,gBAAgB,EACrB,KAAK,oBAAoB,EACzB,KAAK,0BAA0B,EAC/B,KAAK,aAAa,EAClB,KAAK,aAAa,EAClB,KAAK,sBAAsB,EAC3B,KAAK,gBAAgB,EACrB,KAAK,iBAAiB,EACtB,KAAK,+BAA+B,EACpC,KAAK,iBAAiB,EACtB,KAAK,2BAA2B,EAChC,KAAK,wBAAwB,EAC7B,KAAK,sBAAsB,EAC3B,KAAK,yBAAyB,EAC9B,KAAK,wBAAwB,EAC7B,KAAK,QAAQ,EACb,KAAK,YAAY,EACjB,KAAK,cAAc,EACnB,KAAK,QAAQ,EACb,KAAK,kBAAk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package/dist/index.js

@@ -116,6 +116,12 @@ validateDraft,
 nextDraftStep, 
 /** Trim a draft workflow to its concrete subset; cascade drops + multi-source rewrites. */
 extractConcreteSubset, 
+/** Build a planned/concrete overlay from a raw draft for visualizers (mermaid/cytoscape). */
+resolveDraftOverlay, 
+/** Shared class-name token marking planned (draft) nodes/edges. */
+PLANNED_CLASS, 
+/** Render identity of a step (`label || id`), shared by detectDraft overlay + visualizers. */
+stepRenderIdentity, rawStepRenderIdentity, 
 /** 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. */

package/dist/index.js.map

@@ -1 +1 @@
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package/dist/tool-state-validator.d.ts.map

@@ -1 +1 @@
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package/dist/tool-state-validator.js

@@ -1,4 +1,5 @@
-import { ConversionValidationFailure, validateFormat2StepState, validateFormat2StepStateStrict, validateNativeStepState, } from "./workflow/stateful-validate.js";
+import { ConversionValidationFailure, stringContainerDiagnostic, validateFormat2StepState, validateFormat2StepStateStrict, validateNativeStepState, } from "./workflow/stateful-validate.js";
+import { StringContainerError } from "./workflow/walker.js";
 /**
  * High-level bridge: given a tool-info lookup, validate tool_state for a
  * single workflow step without exposing Effect internals to callers.
@@ -21,6 +22,9 @@ export class ToolStateValidator {
             if (e instanceof ConversionValidationFailure) {
                 return e.issues.map((msg) => ({ path: "", message: msg, severity: "error" }));
             }
+            if (e instanceof StringContainerError) {
+                return [stringContainerDiagnostic(e)];
+            }
             throw e;
         }
     }
@@ -37,6 +41,9 @@ export class ToolStateValidator {
             if (e instanceof ConversionValidationFailure) {
                 return e.issues.map((msg) => ({ path: "", message: msg, severity: "error" }));
             }
+            if (e instanceof StringContainerError) {
+                return [stringContainerDiagnostic(e)];
+            }
             throw e;
         }
     }

package/dist/tool-state-validator.js.map

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

@@ -4,10 +4,22 @@
  * Port of gxformat2/cytoscape/models.py. Field names stay snake_case so the
  * emitted JSON is byte-identical to the Python builder.
  */
+import type { PlanField } from "./draft-checks.js";
 export interface CytoscapePosition {
     x: number;
     y: number;
 }
+/**
+ * Per-node planning context surfaced for draft (planned) nodes — the structured
+ * twin of `DraftPlannedReason`, snake_cased for cytoscape JSON parity. Absent on
+ * concrete nodes so default emit stays byte-identical.
+ */
+export interface CytoscapePlanReason {
+    /** Formatted TODO sentinel locations on (or under) this step, in survey order. */
+    todos: string[];
+    /** Non-empty `_plan_*` fields on this step, kept structured. */
+    plan_fields: Partial<Record<PlanField, string>>;
+}
 export interface CytoscapeNodeData {
     id: string;
     label: string;
@@ -15,6 +27,14 @@ export interface CytoscapeNodeData {
     tool_id: string | null;
     step_type: string;
     repo_link: string | null;
+    /**
+     * True on planned (draft) step nodes. Optional so concrete emit stays
+     * byte-identical with the Python builder; the HTML viewer can key a
+     * dashed/muted treatment off it.
+     */
+    planned?: boolean;
+    /** Planning context for planned nodes; absent on concrete nodes. */
+    plan_reason?: CytoscapePlanReason;
 }
 export interface CytoscapeEdgeData {
     id: string;
@@ -31,6 +51,12 @@ export interface CytoscapeEdgeData {
     reduction?: boolean;
     /** Textual mapping (e.g. "list", "list:paired"); mirrors `ConnectionResult.mapping`. */
     mapping?: string | null;
+    /**
+     * True when this connection touches a planned step or a surviving `TODO_*`
+     * port. Optional so default emit stays byte-identical; coexists with
+     * `map_depth`/`reduction`/`mapping`.
+     */
+    planned?: boolean;
 }
 export interface CytoscapeNode {
     group: "nodes";

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

@@ -1 +1 @@
-{"version":3,"file":"cytoscape-models.d.ts","sourceRoot":"","sources":["../../src/workflow/cytoscape-models.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,MAAM,WAAW,iBAAiB;IAChC,CAAC,EAAE,MAAM,CAAC;IACV,CAAC,EAAE,MAAM,CAAC;CACX;AAED,MAAM,WAAW,iBAAiB;IAChC,EAAE,EAAE,MAAM,CAAC;IACX,KAAK,EAAE,MAAM,CAAC;IACd,GAAG,EAAE,MAAM,GAAG,IAAI,CAAC;IACnB,OAAO,EAAE,MAAM,GAAG,IAAI,CAAC;IACvB,SAAS,EAAE,MAAM,CAAC;IAClB,SAAS,EAAE,MAAM,GAAG,IAAI,CAAC;CAC1B;AAED,MAAM,WAAW,iBAAiB;IAChC,EAAE,EAAE,MAAM,CAAC;IACX,MAAM,EAAE,MAAM,CAAC;IACf,MAAM,EAAE,MAAM,CAAC;IACf,KAAK,EAAE,MAAM,CAAC;IACd,MAAM,EAAE,MAAM,GAAG,IAAI,CAAC;IACtB;;;OAGG;IACH,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,0FAA0F;IAC1F,SAAS,CAAC,EAAE,OAAO,CAAC;IACpB,wFAAwF;IACxF,OAAO,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;CACzB;AAED,MAAM,WAAW,aAAa;IAC5B,KAAK,EAAE,OAAO,CAAC;IACf,IAAI,EAAE,iBAAiB,CAAC;IACxB,OAAO,EAAE,MAAM,EAAE,CAAC;IAClB;;;;OAIG;IACH,QAAQ,CAAC,EAAE,iBAAiB,CAAC;CAC9B;AAED,MAAM,WAAW,aAAa;IAC5B,KAAK,EAAE,OAAO,CAAC;IACf,IAAI,EAAE,iBAAiB,CAAC;IACxB,iGAAiG;IACjG,OAAO,CAAC,EAAE,MAAM,EAAE,CAAC;CACpB;AAED,MAAM,WAAW,mBAAmB;IAClC,IAAI,EAAE,MAAM,CAAC;CACd;AAED,MAAM,WAAW,iBAAiB;IAChC,KAAK,EAAE,aAAa,EAAE,CAAC;IACvB,KAAK,EAAE,aAAa,EAAE,CAAC;IACvB;;;;OAIG;IACH,MAAM,CAAC,EAAE,mBAAmB,CAAC;CAC9B;AAED,MAAM,MAAM,iBAAiB,GAAG,aAAa,GAAG,aAAa,CAAC;AAE9D,wBAAgB,cAAc,CAAC,GAAG,EAAE,iBAAiB,GAAG,iBAAiB,EAAE,CAE1E"}
+{"version":3,"file":"cytoscape-models.d.ts","sourceRoot":"","sources":["../../src/workflow/cytoscape-models.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,mBAAmB,CAAC;AAEnD,MAAM,WAAW,iBAAiB;IAChC,CAAC,EAAE,MAAM,CAAC;IACV,CAAC,EAAE,MAAM,CAAC;CACX;AAED;;;;GAIG;AACH,MAAM,WAAW,mBAAmB;IAClC,kFAAkF;IAClF,KAAK,EAAE,MAAM,EAAE,CAAC;IAChB,gEAAgE;IAChE,WAAW,EAAE,OAAO,CAAC,MAAM,CAAC,SAAS,EAAE,MAAM,CAAC,CAAC,CAAC;CACjD;AAED,MAAM,WAAW,iBAAiB;IAChC,EAAE,EAAE,MAAM,CAAC;IACX,KAAK,EAAE,MAAM,CAAC;IACd,GAAG,EAAE,MAAM,GAAG,IAAI,CAAC;IACnB,OAAO,EAAE,MAAM,GAAG,IAAI,CAAC;IACvB,SAAS,EAAE,MAAM,CAAC;IAClB,SAAS,EAAE,MAAM,GAAG,IAAI,CAAC;IACzB;;;;OAIG;IACH,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,oEAAoE;IACpE,WAAW,CAAC,EAAE,mBAAmB,CAAC;CACnC;AAED,MAAM,WAAW,iBAAiB;IAChC,EAAE,EAAE,MAAM,CAAC;IACX,MAAM,EAAE,MAAM,CAAC;IACf,MAAM,EAAE,MAAM,CAAC;IACf,KAAK,EAAE,MAAM,CAAC;IACd,MAAM,EAAE,MAAM,GAAG,IAAI,CAAC;IACtB;;;OAGG;IACH,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,0FAA0F;IAC1F,SAAS,CAAC,EAAE,OAAO,CAAC;IACpB,wFAAwF;IACxF,OAAO,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;IACxB;;;;OAIG;IACH,OAAO,CAAC,EAAE,OAAO,CAAC;CACnB;AAED,MAAM,WAAW,aAAa;IAC5B,KAAK,EAAE,OAAO,CAAC;IACf,IAAI,EAAE,iBAAiB,CAAC;IACxB,OAAO,EAAE,MAAM,EAAE,CAAC;IAClB;;;;OAIG;IACH,QAAQ,CAAC,EAAE,iBAAiB,CAAC;CAC9B;AAED,MAAM,WAAW,aAAa;IAC5B,KAAK,EAAE,OAAO,CAAC;IACf,IAAI,EAAE,iBAAiB,CAAC;IACxB,iGAAiG;IACjG,OAAO,CAAC,EAAE,MAAM,EAAE,CAAC;CACpB;AAED,MAAM,WAAW,mBAAmB;IAClC,IAAI,EAAE,MAAM,CAAC;CACd;AAED,MAAM,WAAW,iBAAiB;IAChC,KAAK,EAAE,aAAa,EAAE,CAAC;IACvB,KAAK,EAAE,aAAa,EAAE,CAAC;IACvB;;;;OAIG;IACH,MAAM,CAAC,EAAE,mBAAmB,CAAC;CAC9B;AAED,MAAM,MAAM,iBAAiB,GAAG,aAAa,GAAG,aAAa,CAAC;AAE9D,wBAAgB,cAAc,CAAC,GAAG,EAAE,iBAAiB,GAAG,iBAAiB,EAAE,CAE1E"}

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

@@ -1 +1 @@
-{"version":3,"file":"cytoscape-models.js","sourceRoot":"","sources":["../../src/workflow/cytoscape-models.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAqEH,MAAM,UAAU,cAAc,CAAC,GAAsB;IACnD,OAAO,CAAC,GAAG,GAAG,CAAC,KAAK,EAAE,GAAG,GAAG,CAAC,KAAK,CAAC,CAAC;AACtC,CAAC"}
+{"version":3,"file":"cytoscape-models.js","sourceRoot":"","sources":["../../src/workflow/cytoscape-models.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAiGH,MAAM,UAAU,cAAc,CAAC,GAAsB;IACnD,OAAO,CAAC,GAAG,GAAG,CAAC,KAAK,EAAE,GAAG,GAAG,CAAC,KAAK,CAAC,CAAC;AACtC,CAAC"}

package/dist/workflow/cytoscape.d.ts

@@ -7,6 +7,7 @@
  */
 import type { CytoscapeElements } from "./cytoscape-models.js";
 import type { LayoutName } from "./cytoscape-layout.js";
+import type { DraftOverlay } from "./draft-checks.js";
 import type { EdgeAnnotation } from "./edge-annotation.js";
 import type { NormalizedFormat2Workflow } from "./normalized/format2.js";
 export interface CytoscapeOptions {
@@ -24,6 +25,15 @@ export interface CytoscapeOptions {
      * top-level `elements.layout = { name }` hint for the runtime renderer.
      */
     layout?: LayoutName;
+    /**
+     * Overlay marking planned (draft) nodes/edges with a `planned` class + plan
+     * context. Mirrors {@link MermaidOptions.draftOverlay}:
+     *   - omitted (`undefined`): auto-detect — a `GalaxyWorkflowDraft` input
+     *     resolves its own overlay, a concrete workflow emits unchanged.
+     *   - a `DraftOverlay`: use it verbatim.
+     *   - `null`: force plain (byte-identical) output even for a draft.
+     */
+    draftOverlay?: DraftOverlay | null;
 }
 export declare function cytoscapeElements(workflow: unknown | NormalizedFormat2Workflow, opts?: CytoscapeOptions): CytoscapeElements;
 //# sourceMappingURL=cytoscape.d.ts.map

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

@@ -1 +1 @@
-{"version":3,"file":"cytoscape.d.ts","sourceRoot":"","sources":["../../src/workflow/cytoscape.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,KAAK,EAEV,iBAAiB,EAGlB,MAAM,uBAAuB,CAAC;AAC/B,OAAO,KAAK,EAAE,UAAU,EAAE,MAAM,uBAAuB,CAAC;AAExD,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,sBAAsB,CAAC;AAG3D,OAAO,KAAK,EAGV,yBAAyB,EAC1B,MAAM,yBAAyB,CAAC;AAKjC,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;CACrB;AAED,wBAAgB,iBAAiB,CAC/B,QAAQ,EAAE,OAAO,GAAG,yBAAyB,EAC7C,IAAI,GAAE,gBAAqB,GAC1B,iBAAiB,CAiDnB"}
+{"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;AASjC,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

@@ -6,9 +6,10 @@
  * the standalone HTML template.
  */
 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 { isUnlabeledStep, resolveSourceReference } from "./normalized/labels.js";
+import { isUnlabeledStep, resolveSourceReference, stepRenderIdentity, } from "./normalized/labels.js";
 const MAIN_TS_PREFIX = "toolshed.g2.bx.psu.edu/repos/";
 export function cytoscapeElements(workflow, opts = {}) {
     const wf = typeof workflow === "object" &&
@@ -18,6 +19,14 @@ export function cytoscapeElements(workflow, opts = {}) {
         "unique_tools" in workflow
         ? workflow
         : ensureFormat2(workflow);
+    // Resolve the draft overlay from the RAW input (normalization strips
+    // `_plan_*` and rewrites the class). `undefined` → auto-detect; `null` →
+    // caller forced plain rendering. Mirrors workflowToMermaid.
+    const overlay = opts.draftOverlay === undefined
+        ? isDraftWorkflow(workflow)
+            ? resolveDraftOverlay(workflow)
+            : undefined
+        : (opts.draftOverlay ?? undefined);
     const layout = opts.layout ?? "preset";
     const nodes = [];
     const edges = [];
@@ -28,11 +37,22 @@ export function cytoscapeElements(workflow, opts = {}) {
     const knownLabels = new Set();
     for (const inp of wf.inputs)
         knownLabels.add(inp.id);
-    for (const step of wf.steps)
-        knownLabels.add(step.label || step.id);
+    // Maps a source-reference key (a step's dict `id` OR its render identity) to
+    // the render identity the node id is keyed by. `in:` sources address steps by
+    // `id` (e.g. `meme/out`) even when the step has a distinct `label:`.
+    const identityByKey = new Map();
+    for (const step of wf.steps) {
+        const identity = stepRenderIdentity(step);
+        knownLabels.add(identity);
+        identityByKey.set(identity, identity);
+        if (step.id) {
+            knownLabels.add(step.id);
+            identityByKey.set(step.id, identity);
+        }
+    }
     wf.steps.forEach((step, i) => {
-        nodes.push(_stepNode(step, i + inputsOffset));
-        edges.push(..._stepEdges(step, knownLabels, opts.edgeAnnotations));
+        nodes.push(_stepNode(step, i + inputsOffset, overlay));
+        edges.push(..._stepEdges(step, knownLabels, identityByKey, opts.edgeAnnotations, overlay));
     });
     const elements = { nodes, edges };
     if (layout === "preset") {
@@ -95,8 +115,8 @@ function _inputNode(inp, orderIndex) {
         position: _toPosition(inp.position, orderIndex),
     };
 }
-function _stepNode(step, orderIndex) {
-    const stepId = step.label || step.id;
+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");
@@ -115,7 +135,7 @@ function _stepNode(step, orderIndex) {
         const changesetRevision = repo.changeset_revision;
         repoLink = `https://${toolShed}/view/${owner}/${name}/${changesetRevision}`;
     }
-    return {
+    const node = {
         group: "nodes",
         data: {
             id: stepId,
@@ -128,9 +148,26 @@ function _stepNode(step, orderIndex) {
         classes: [`type_${stepType}`, "runnable"],
         position: _toPosition(step.position, orderIndex),
     };
+    // Planned (draft) node: keep `type_*`/`runnable` (they still encode node kind)
+    // and append `planned` LAST so concrete-node `value_set` goldens are
+    // unaffected. Carry plan context in `data` for the viewer's tooltip. Gated on
+    // overlay presence so concrete emit stays byte-identical.
+    if (overlay?.plannedSteps.has(stepId)) {
+        node.classes = [...node.classes, PLANNED_CLASS];
+        node.data.planned = true;
+        const reason = overlay.plannedReason.get(stepId);
+        if (reason != null) {
+            const planReason = {
+                todos: reason.todos,
+                plan_fields: reason.planFields,
+            };
+            node.data.plan_reason = planReason;
+        }
+    }
+    return node;
 }
-function _stepEdges(step, knownLabels, edgeAnnotations) {
-    const stepId = step.label || step.id;
+function _stepEdges(step, knownLabels, identityByKey, edgeAnnotations, overlay) {
+    const stepId = stepRenderIdentity(step);
     const edges = [];
     for (const stepInput of step.in) {
         if (stepInput.source == null)
@@ -138,7 +175,10 @@ function _stepEdges(step, knownLabels, edgeAnnotations) {
         const inputId = stepInput.id || "unknown";
         const sources = Array.isArray(stepInput.source) ? stepInput.source : [stepInput.source];
         for (const source of sources) {
-            const [sourceLabel, outputName] = resolveSourceReference(source, knownLabels);
+            const [sourceRef, outputName] = resolveSourceReference(source, knownLabels);
+            // Fold a step `id` reference back to the render identity the node id is
+            // keyed by; input refs (not in the map) pass through unchanged.
+            const sourceLabel = identityByKey.get(sourceRef) ?? sourceRef;
             const output = outputName === "output" ? null : outputName;
             const edgeId = `${stepId}__${inputId}__from__${sourceLabel}`;
             const edge = {
@@ -151,19 +191,32 @@ function _stepEdges(step, knownLabels, edgeAnnotations) {
                     output,
                 },
             };
+            const classes = [];
             const annotation = edgeAnnotations?.get(edgeAnnotationKey(sourceLabel, outputName, stepId, inputId));
             if (annotation) {
                 edge.data.map_depth = annotation.mapDepth;
                 edge.data.reduction = annotation.reduction;
                 edge.data.mapping = annotation.mapping ?? null;
-                const classes = [];
                 if (annotation.mapDepth > 0)
                     classes.push(`mapover_${annotation.mapDepth}`);
                 if (annotation.reduction)
                     classes.push("reduction");
-                if (classes.length > 0)
-                    edge.classes = classes;
             }
+            // An edge is planned when either endpoint step is planned, or a port it
+            // touches is still a TODO sentinel. Computed inline (no overlay port set)
+            // and gated on overlay presence so concrete emit stays byte-identical.
+            // `planned` coexists with any `mapover_*`/`reduction` class.
+            const planned = overlay != null &&
+                (overlay.plannedSteps.has(sourceLabel) ||
+                    overlay.plannedSteps.has(stepId) ||
+                    isTodoSentinel(outputName) ||
+                    isTodoSentinel(inputId));
+            if (planned) {
+                classes.push(PLANNED_CLASS);
+                edge.data.planned = true;
+            }
+            if (classes.length > 0)
+                edge.classes = classes;
             edges.push(edge);
         }
     }

package/dist/workflow/cytoscape.js.map

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

@@ -63,6 +63,42 @@ export interface DraftSurvey {
  * per-step state.
  */
 export declare function detectDraft(workflow: unknown): DraftSurvey;
+/** CSS/class-name token marking a planned (draft) node or edge. Shared by every
+ * builder so `planned`/`draft`/`plan` can't drift apart across mermaid + cytoscape. */
+export declare const PLANNED_CLASS = "planned";
+export interface DraftPlannedReason {
+    /** Formatted TODO sentinel locations on (or under) this step, in survey order. */
+    todos: string[];
+    /** Non-empty `_plan_*` fields on this step, kept structured (not flattened). */
+    planFields: Partial<Record<PlanField, string>>;
+}
+/**
+ * Overlay describing which rendered nodes are *planned* (draft) and why.
+ * Keyed by step render identity (see {@link rawStepRenderIdentity}) so the keys
+ * line up with the node lookups mermaid/cytoscape perform on normalized steps.
+ *
+ * Edge planned-ness is intentionally NOT carried here — a builder computes it
+ * inline from `plannedSteps` plus the TODO-sentinel ports it already resolves,
+ * so there is one predicate, no port set to keep in sync.
+ */
+export interface DraftOverlay {
+    /** Render identities of planned steps. */
+    plannedSteps: Set<string>;
+    /** Per-identity planning context for label/tooltip enrichment. */
+    plannedReason: Map<string, DraftPlannedReason>;
+}
+/**
+ * Build a {@link DraftOverlay} from a RAW draft workflow (before normalization
+ * strips `_plan_*`). Returns `undefined` for non-draft input so callers treat
+ * "no overlay" uniformly.
+ *
+ * A step is planned iff it carries any TODO sentinel or any non-empty `_plan_*`
+ * field. A top-level subworkflow node is planned if it OR any descendant has a
+ * hit — each survey hit's `path[0]` maps back to the top-level node's render
+ * identity. Workflow-level hits (e.g. a TODO `outputSource` on the outermost
+ * document) have an empty path and mark no node.
+ */
+export declare function resolveDraftOverlay(workflow: unknown): DraftOverlay | undefined;
 export interface DraftValidationDiagnostic {
     /** Step path; empty array for workflow-level diagnostics. */
     path: StepPath;

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

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

@@ -10,6 +10,7 @@
  */
 import { Either, ParseResult, Schema } from "effect";
 import { GalaxyWorkflowDraftSchema } from "./raw/gxformat2-draft.effect.js";
+import { rawStepRenderIdentity } from "./normalized/labels.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
@@ -49,6 +50,67 @@ export function detectDraft(workflow) {
     walkDraftSteps(workflow, [], todos, planFields);
     return { isDraft: true, todos, planFields };
 }
+// -----------------------------------------------------------------------------
+// resolveDraftOverlay — classification surface consumed by visualizers
+// -----------------------------------------------------------------------------
+/** CSS/class-name token marking a planned (draft) node or edge. Shared by every
+ * builder so `planned`/`draft`/`plan` can't drift apart across mermaid + cytoscape. */
+export const PLANNED_CLASS = "planned";
+/**
+ * Build a {@link DraftOverlay} from a RAW draft workflow (before normalization
+ * strips `_plan_*`). Returns `undefined` for non-draft input so callers treat
+ * "no overlay" uniformly.
+ *
+ * A step is planned iff it carries any TODO sentinel or any non-empty `_plan_*`
+ * field. A top-level subworkflow node is planned if it OR any descendant has a
+ * hit — each survey hit's `path[0]` maps back to the top-level node's render
+ * identity. Workflow-level hits (e.g. a TODO `outputSource` on the outermost
+ * document) have an empty path and mark no node.
+ */
+export function resolveDraftOverlay(workflow) {
+    const survey = detectDraft(workflow);
+    if (!survey.isDraft)
+        return undefined;
+    // Map each top-level step's iterator key (the space detectDraft paths live
+    // in) to the render identity the visualizers key off.
+    const identityByIterKey = new Map();
+    if (isRecord(workflow)) {
+        for (const [key, step] of iterateSteps(workflow.steps)) {
+            identityByIterKey.set(key, rawStepRenderIdentity(step, key));
+        }
+    }
+    const plannedSteps = new Set();
+    const plannedReason = new Map();
+    const reasonFor = (identity) => {
+        let reason = plannedReason.get(identity);
+        if (reason == null) {
+            reason = { todos: [], planFields: {} };
+            plannedReason.set(identity, reason);
+        }
+        return reason;
+    };
+    const identityForPath = (path) => {
+        const top = path[0];
+        if (top == null)
+            return null; // workflow-level hit — not a step node
+        return identityByIterKey.get(top) ?? top;
+    };
+    for (const todo of survey.todos) {
+        const identity = identityForPath(todo.path);
+        if (identity == null)
+            continue;
+        plannedSteps.add(identity);
+        reasonFor(identity).todos.push(formatTodoLocation(todo.location));
+    }
+    for (const plan of survey.planFields) {
+        const identity = identityForPath(plan.path);
+        if (identity == null)
+            continue;
+        plannedSteps.add(identity);
+        reasonFor(identity).planFields[plan.field] = plan.value;
+    }
+    return { plannedSteps, plannedReason };
+}
 function walkDraftSteps(workflow, prefix, todos, planFields) {
     for (const [label, step] of iterateSteps(workflow.steps)) {
         if (!isRecord(step))