@galaxy-tool-util/connection-validation 0.1.0 → 1.5.0

package/dist/build-get-tool-info.d.ts

@@ -0,0 +1,26 @@
+import type { ParsedTool } from "@galaxy-tool-util/schema";
+import type { GetToolInfo } from "./get-tool-info.js";
+import { type InlineToolEntry } from "./inline-resolver.js";
+export interface ToolRef {
+    toolId: string;
+    toolVersion: string | null;
+}
+export type InlineRef = InlineToolEntry;
+export type AsyncToolFetcher = (toolId: string, toolVersion: string | null) => Promise<ParsedTool | null>;
+export interface BuildGetToolInfoOptions {
+    /** Maximum in-flight fetches. Default 1 (serial) to match the CLI's prior behavior. */
+    concurrency?: number;
+    /** Called when a ref resolves to null or the fetcher rejects. */
+    onMiss?: (ref: ToolRef, reason: unknown) => void;
+    /** Called after each ref settles (resolved or missed). */
+    onProgress?: (resolved: number, total: number) => void;
+}
+/** Walk a workflow dict (steps + nested subworkflows + nested `run`) and dedupe tool refs. */
+export declare function collectToolRefs(data: Record<string, unknown>): ToolRef[];
+/**
+ * Preload every tool referenced by `data` via `fetcher` and return a sync
+ * `GetToolInfo` backed by the resulting Map. Misses are reported, not thrown —
+ * the validator runs against whatever resolved.
+ */
+export declare function buildGetToolInfo(data: Record<string, unknown>, fetcher: AsyncToolFetcher, opts?: BuildGetToolInfoOptions): Promise<GetToolInfo>;
+//# sourceMappingURL=build-get-tool-info.d.ts.map

package/dist/build-get-tool-info.d.ts.map

@@ -0,0 +1 @@
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package/dist/build-get-tool-info.js

@@ -0,0 +1,125 @@
+import { collectInlineTools, ensureInlineResolver, } from "./inline-resolver.js";
+/** Walk a workflow dict (steps + nested subworkflows + nested `run`) and dedupe tool refs. */
+export function collectToolRefs(data) {
+    const out = [];
+    const seen = new Set();
+    _walk(data, out, seen);
+    return out;
+}
+function _walk(node, out, seen) {
+    const steps = node.steps;
+    if (steps == null || typeof steps !== "object")
+        return;
+    const iter = Array.isArray(steps)
+        ? steps
+        : Object.values(steps);
+    for (const stepRaw of iter) {
+        if (stepRaw == null || typeof stepRaw !== "object")
+            continue;
+        const step = stepRaw;
+        const toolId = step.tool_id ?? null;
+        const toolVersion = step.tool_version ?? null;
+        if (toolId) {
+            const key = lookupKey(toolId, toolVersion);
+            if (!seen.has(key)) {
+                seen.add(key);
+                out.push({ toolId, toolVersion });
+            }
+        }
+        const subworkflow = step.subworkflow;
+        if (subworkflow && typeof subworkflow === "object") {
+            _walk(subworkflow, out, seen);
+        }
+        const run = step.run;
+        if (run && typeof run === "object" && !Array.isArray(run)) {
+            _walk(run, out, seen);
+        }
+    }
+}
+/**
+ * Preload every tool referenced by `data` via `fetcher` and return a sync
+ * `GetToolInfo` backed by the resulting Map. Misses are reported, not thrown —
+ * the validator runs against whatever resolved.
+ */
+export async function buildGetToolInfo(data, fetcher, opts = {}) {
+    const refs = collectToolRefs(data);
+    const lookup = new Map();
+    const concurrency = Math.max(1, opts.concurrency ?? 1);
+    let resolved = 0;
+    const handleOne = async (ref) => {
+        try {
+            const tool = await fetcher(ref.toolId, ref.toolVersion);
+            if (tool === null) {
+                opts.onMiss?.(ref, "not_found");
+            }
+            else {
+                lookup.set(lookupKey(ref.toolId, ref.toolVersion), tool);
+            }
+        }
+        catch (e) {
+            opts.onMiss?.(ref, e);
+        }
+        finally {
+            resolved += 1;
+            opts.onProgress?.(resolved, refs.length);
+        }
+    };
+    if (concurrency === 1) {
+        for (const ref of refs) {
+            await handleOne(ref);
+        }
+    }
+    else {
+        let cursor = 0;
+        const workers = [];
+        const next = async () => {
+            while (cursor < refs.length) {
+                const i = cursor++;
+                await handleOne(refs[i]);
+            }
+        };
+        for (let i = 0; i < Math.min(concurrency, refs.length); i++) {
+            workers.push(next());
+        }
+        await Promise.all(workers);
+    }
+    const remote = {
+        getToolInfo: (id, version) => {
+            const versioned = lookup.get(lookupKey(id, version ?? null));
+            if (versioned)
+                return versioned;
+            // Graph builder usually passes tool_version, but callers may omit it.
+            return lookup.get(lookupKey(id, null)) ?? firstByToolId(lookup, id);
+        },
+    };
+    // Parse inline tool representations up-front. Surfaces parse errors during
+    // preload (same `onMiss` channel ToolShed misses use) and warms the
+    // InlineResolver cache so the graph build avoids re-parsing.
+    const resolver = ensureInlineResolver(remote);
+    for (const entry of collectInlineTools(data)) {
+        if (entry.inlineClass !== "GalaxyUserTool") {
+            // GalaxyTool admin dynamic tools are out of scope; the graph builder
+            // emits `inline_source_unsupported` at validation time. No-op here.
+            continue;
+        }
+        try {
+            resolver.parseInlineOnce(entry.representation);
+        }
+        catch (e) {
+            opts.onMiss?.({ toolId: String(entry.representation.id ?? "(inline)"), toolVersion: null }, e);
+        }
+    }
+    return resolver;
+}
+function lookupKey(toolId, toolVersion) {
+    return `${toolId}@${toolVersion ?? ""}`;
+}
+function firstByToolId(lookup, toolId) {
+    const prefix = `${toolId}@`;
+    for (const [k, v] of lookup) {
+        if (k.startsWith(prefix))
+            return v;
+    }
+    return undefined;
+}
+//# sourceMappingURL=build-get-tool-info.js.map

package/dist/build-get-tool-info.js.map

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package/dist/connection-validator.d.ts.map

@@ -1 +1 @@
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package/dist/connection-validator.js

@@ -34,6 +34,7 @@ export function validateConnectionGraph(graph, seedOutputTypes) {
         const step = graph.steps[stepId];
         const stepResult = {
             stepId,
+            label: step.label ?? null,
             toolId: step.toolId,
             toolVersion: step.toolVersion,
             stepType: step.stepType,
@@ -121,15 +122,21 @@ function _validateSingleConnection(sourceStep, sourceOutput, targetStep, targetI
         };
     }
     const targetType = _inputToType(targetResolvedInput);
-    const ok = (mapping) => ({
-        sourceStep,
-        sourceOutput,
-        targetStep,
-        targetInput,
-        status: "ok",
-        mapping: mapping ?? null,
-        errors: [],
-    });
+    const ok = (mapping, extras) => {
+        const mappingValue = mapping ?? null;
+        const mapDepth = mappingValue ? mappingValue.split(":").length : 0;
+        return {
+            sourceStep,
+            sourceOutput,
+            targetStep,
+            targetInput,
+            status: "ok",
+            mapping: mappingValue,
+            mapDepth,
+            reduction: extras?.reduction ?? false,
+            errors: [],
+        };
+    };
     if (isNullDesc(sourceType)) {
         if (isNullDesc(targetType))
             return ok();
@@ -153,9 +160,9 @@ function _validateSingleConnection(sourceStep, sourceOutput, targetStep, targetI
                 const innerList = new CollectionTypeDescription("list");
                 if (sourceType.canMapOver(innerList)) {
                     const remaining = sourceType.effectiveMapOver(innerList);
-                    return ok(remaining.collectionType);
+                    return ok(remaining.collectionType, { reduction: true });
                 }
-                return ok();
+                return ok(null, { reduction: true });
             }
             // Non-list-like: fall through to can_match / map_over
         }

package/dist/connection-validator.js.map

@@ -1 +1 @@
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package/dist/edge-annotations.d.ts

@@ -0,0 +1,22 @@
+/**
+ * Edge-annotation lookup shared between workflow visualizers (mermaid,
+ * cytoscape) so they can encode map-over depth and reductions on edges.
+ *
+ * Keys are built using step *labels* (falling back to stepId for unlabeled
+ * native steps) — that's what the format2-driven emitters key off, so the
+ * lookup is direct on their side.
+ */
+import type { ConnectionValidationResult, WorkflowConnectionResult } from "./types.js";
+export interface EdgeAnnotation {
+    sourceStep: string;
+    sourceOutput: string;
+    targetStep: string;
+    targetInput: string;
+    mapDepth: number;
+    reduction: boolean;
+    mapping?: string | null;
+    status: ConnectionValidationResult["status"];
+}
+export declare function edgeAnnotationKey(sourceStep: string, sourceOutput: string, targetStep: string, targetInput: string): string;
+export declare function buildEdgeAnnotations(result: WorkflowConnectionResult): Map<string, EdgeAnnotation>;
+//# sourceMappingURL=edge-annotations.d.ts.map

package/dist/edge-annotations.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"edge-annotations.d.ts","sourceRoot":"","sources":["../src/edge-annotations.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,KAAK,EACV,0BAA0B,EAE1B,wBAAwB,EACzB,MAAM,YAAY,CAAC;AAEpB,MAAM,WAAW,cAAc;IAC7B,UAAU,EAAE,MAAM,CAAC;IACnB,YAAY,EAAE,MAAM,CAAC;IACrB,UAAU,EAAE,MAAM,CAAC;IACnB,WAAW,EAAE,MAAM,CAAC;IACpB,QAAQ,EAAE,MAAM,CAAC;IACjB,SAAS,EAAE,OAAO,CAAC;IACnB,OAAO,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;IACxB,MAAM,EAAE,0BAA0B,CAAC,QAAQ,CAAC,CAAC;CAC9C;AAED,wBAAgB,iBAAiB,CAC/B,UAAU,EAAE,MAAM,EAClB,YAAY,EAAE,MAAM,EACpB,UAAU,EAAE,MAAM,EAClB,WAAW,EAAE,MAAM,GAClB,MAAM,CAER;AAMD,wBAAgB,oBAAoB,CAClC,MAAM,EAAE,wBAAwB,GAC/B,GAAG,CAAC,MAAM,EAAE,cAAc,CAAC,CAyB7B"}

package/dist/edge-annotations.js

@@ -0,0 +1,40 @@
+/**
+ * Edge-annotation lookup shared between workflow visualizers (mermaid,
+ * cytoscape) so they can encode map-over depth and reductions on edges.
+ *
+ * Keys are built using step *labels* (falling back to stepId for unlabeled
+ * native steps) — that's what the format2-driven emitters key off, so the
+ * lookup is direct on their side.
+ */
+export function edgeAnnotationKey(sourceStep, sourceOutput, targetStep, targetInput) {
+    return `${sourceStep}|${sourceOutput}->${targetStep}|${targetInput}`;
+}
+function _stepKey(sr) {
+    return sr.label ?? sr.stepId;
+}
+export function buildEdgeAnnotations(result) {
+    const stepIdToKey = new Map();
+    for (const sr of result.stepResults) {
+        stepIdToKey.set(sr.stepId, _stepKey(sr));
+    }
+    const out = new Map();
+    for (const sr of result.stepResults) {
+        const targetKey = _stepKey(sr);
+        for (const cr of sr.connections) {
+            const sourceKey = stepIdToKey.get(cr.sourceStep) ?? cr.sourceStep;
+            const annotation = {
+                sourceStep: sourceKey,
+                sourceOutput: cr.sourceOutput,
+                targetStep: targetKey,
+                targetInput: cr.targetInput,
+                mapDepth: cr.mapDepth ?? 0,
+                reduction: cr.reduction ?? false,
+                mapping: cr.mapping ?? null,
+                status: cr.status,
+            };
+            out.set(edgeAnnotationKey(sourceKey, cr.sourceOutput, targetKey, cr.targetInput), annotation);
+        }
+    }
+    return out;
+}
+//# sourceMappingURL=edge-annotations.js.map

package/dist/edge-annotations.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"edge-annotations.js","sourceRoot":"","sources":["../src/edge-annotations.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAmBH,MAAM,UAAU,iBAAiB,CAC/B,UAAkB,EAClB,YAAoB,EACpB,UAAkB,EAClB,WAAmB;IAEnB,OAAO,GAAG,UAAU,IAAI,YAAY,KAAK,UAAU,IAAI,WAAW,EAAE,CAAC;AACvE,CAAC;AAED,SAAS,QAAQ,CAAC,EAAwB;IACxC,OAAO,EAAE,CAAC,KAAK,IAAI,EAAE,CAAC,MAAM,CAAC;AAC/B,CAAC;AAED,MAAM,UAAU,oBAAoB,CAClC,MAAgC;IAEhC,MAAM,WAAW,GAAG,IAAI,GAAG,EAAkB,CAAC;IAC9C,KAAK,MAAM,EAAE,IAAI,MAAM,CAAC,WAAW,EAAE,CAAC;QACpC,WAAW,CAAC,GAAG,CAAC,EAAE,CAAC,MAAM,EAAE,QAAQ,CAAC,EAAE,CAAC,CAAC,CAAC;IAC3C,CAAC;IAED,MAAM,GAAG,GAAG,IAAI,GAAG,EAA0B,CAAC;IAC9C,KAAK,MAAM,EAAE,IAAI,MAAM,CAAC,WAAW,EAAE,CAAC;QACpC,MAAM,SAAS,GAAG,QAAQ,CAAC,EAAE,CAAC,CAAC;QAC/B,KAAK,MAAM,EAAE,IAAI,EAAE,CAAC,WAAW,EAAE,CAAC;YAChC,MAAM,SAAS,GAAG,WAAW,CAAC,GAAG,CAAC,EAAE,CAAC,UAAU,CAAC,IAAI,EAAE,CAAC,UAAU,CAAC;YAClE,MAAM,UAAU,GAAmB;gBACjC,UAAU,EAAE,SAAS;gBACrB,YAAY,EAAE,EAAE,CAAC,YAAY;gBAC7B,UAAU,EAAE,SAAS;gBACrB,WAAW,EAAE,EAAE,CAAC,WAAW;gBAC3B,QAAQ,EAAE,EAAE,CAAC,QAAQ,IAAI,CAAC;gBAC1B,SAAS,EAAE,EAAE,CAAC,SAAS,IAAI,KAAK;gBAChC,OAAO,EAAE,EAAE,CAAC,OAAO,IAAI,IAAI;gBAC3B,MAAM,EAAE,EAAE,CAAC,MAAM;aAClB,CAAC;YACF,GAAG,CAAC,GAAG,CAAC,iBAAiB,CAAC,SAAS,EAAE,EAAE,CAAC,YAAY,EAAE,SAAS,EAAE,EAAE,CAAC,WAAW,CAAC,EAAE,UAAU,CAAC,CAAC;QAChG,CAAC;IACH,CAAC;IACD,OAAO,GAAG,CAAC;AACb,CAAC"}

package/dist/graph-builder.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"graph-builder.d.ts","sourceRoot":"","sources":["../src/graph-builder.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAOH,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,oBAAoB,CAAC;AACtD,OAAO,KAAK,EAOV,aAAa,EACd,MAAM,YAAY,CAAC;AAkBpB,wBAAgB,kBAAkB,CAAC,QAAQ,EAAE,OAAO,EAAE,WAAW,EAAE,WAAW,GAAG,aAAa,CAG7F"}
+{"version":3,"file":"graph-builder.d.ts","sourceRoot":"","sources":["../src/graph-builder.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAOH,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,oBAAoB,CAAC;AAEtD,OAAO,KAAK,EAOV,aAAa,EACd,MAAM,YAAY,CAAC;AAkBpB,wBAAgB,kBAAkB,CAAC,QAAQ,EAAE,OAAO,EAAE,WAAW,EAAE,WAAW,GAAG,aAAa,CAM7F"}

package/dist/graph-builder.js

@@ -6,6 +6,7 @@
  */
 import { normalizedNative } from "@galaxy-tool-util/schema";
 import { toNative } from "@galaxy-tool-util/schema";
+import { ensureInlineResolver, resolveForStep } from "./inline-resolver.js";
 import { topsort } from "./topsort.js";
 const PARAMETER_INPUT_TYPES = new Set([
     "gx_text",
@@ -17,7 +18,10 @@ const PARAMETER_INPUT_TYPES = new Set([
 ]);
 export function buildWorkflowGraph(workflow, getToolInfo) {
     const native = _coerceNormalizedNative(workflow);
-    return _buildFromNormalized(native, getToolInfo);
+    // Wrap once at the top so per-step parse results are memoized across the
+    // whole walk (including subworkflow recursion). Idempotent — if the caller
+    // already wrapped, we re-use their cache.
+    return _buildFromNormalized(native, ensureInlineResolver(getToolInfo));
 }
 function _coerceNormalizedNative(workflow) {
     if (workflow == null || typeof workflow !== "object") {
@@ -39,19 +43,25 @@ function _buildFromNormalized(workflow, getToolInfo) {
     return { steps, sortedStepIds: sorted };
 }
 function _resolveStep(stepId, step, getToolInfo) {
+    const label = step.label ?? null;
     const stepType = step.type ?? "tool";
+    let resolved;
     if (stepType === "data_input" ||
         stepType === "data_collection_input" ||
         stepType === "parameter_input") {
-        return _resolveInputStep(stepId, step, stepType);
+        resolved = _resolveInputStep(stepId, step, stepType);
     }
-    if (stepType === "tool") {
-        return _resolveToolStep(stepId, step, getToolInfo);
+    else if (stepType === "tool") {
+        resolved = _resolveToolStep(stepId, step, getToolInfo);
     }
-    if (stepType === "subworkflow") {
-        return _resolveSubworkflowStep(stepId, step, getToolInfo);
+    else if (stepType === "subworkflow") {
+        resolved = _resolveSubworkflowStep(stepId, step, getToolInfo);
     }
-    return _emptyStep(stepId, null, stepType);
+    else {
+        resolved = _emptyStep(stepId, null, stepType);
+    }
+    resolved.label = label;
+    return resolved;
 }
 function _emptyStep(stepId, toolId, stepType) {
     return {
@@ -98,26 +108,29 @@ function _resolveToolStep(stepId, step, getToolInfo) {
     const connections = _parseConnections(step);
     let inputs = {};
     let outputs = {};
-    if (step.tool_id) {
-        const parsed = getToolInfo.getToolInfo(step.tool_id, step.tool_version);
-        if (parsed) {
-            inputs = _collectInputs(parsed.inputs, step.tool_state ?? {});
-            outputs = _collectOutputs(parsed.outputs);
-            // Python additionally calls _resolve_rules_collection_types here to
-            // populate `collection_type` from a RuleSet mapping when the output
-            // declares `collection_type_from_rules`. RuleSet (galaxy.util.rules_dsl)
-            // is not yet ported — affected outputs stay unresolved (ANY) instead of
-            // gaining a concrete type. Outputs without rules-driven types behave
-            // identically to Python.
-        }
+    // resolveForStep handles inline UDT (`tool_representation`) too — when
+    // present, the inline parse wins over `tool_id`.
+    const parsed = resolveForStep(getToolInfo, step);
+    if (parsed) {
+        inputs = _collectInputs(parsed.inputs, step.tool_state ?? {});
+        outputs = _collectOutputs(parsed.outputs);
+        // Python additionally calls _resolve_rules_collection_types here to
+        // populate `collection_type` from a RuleSet mapping when the output
+        // declares `collection_type_from_rules`. RuleSet (galaxy.util.rules_dsl)
+        // is not yet ported — affected outputs stay unresolved (ANY) instead of
+        // gaining a concrete type. Outputs without rules-driven types behave
+        // identically to Python.
     }
     if (step.when && "when" in connections) {
         inputs.when = { name: "when", statePath: "when", type: "boolean" };
     }
     return {
         stepId,
-        toolId: step.tool_id ?? null,
-        toolVersion: step.tool_version ?? null,
+        // Inline UDT steps have null tool_id but carry the id inside the
+        // representation; surface that so reports/diagnostics have something to
+        // show.
+        toolId: step.tool_id ?? (parsed ? parsed.id : null) ?? null,
+        toolVersion: step.tool_version ?? (parsed ? parsed.version : null) ?? null,
         stepType: "tool",
         inputs,
         outputs,

package/dist/graph-builder.js.map

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package/dist/index.d.ts

@@ -2,7 +2,12 @@ export type { ConnectionRef, ResolvedInput, ResolvedInputType, ResolvedOutput, R
 export { buildWorkflowGraph } from "./graph-builder.js";
 export { validateConnections, validateConnectionGraph } from "./connection-validator.js";
 export { validateConnectionsReport, toConnectionValidationReport } from "./report-builder.js";
+export { buildEdgeAnnotations, edgeAnnotationKey } from "./edge-annotations.js";
+export type { EdgeAnnotation } from "./edge-annotations.js";
 export type { ConnectionValidationReport, ConnectionStepResult, ConnectionResult, ResolvedOutputType, } from "@galaxy-tool-util/schema";
 export type { GetToolInfo } from "./get-tool-info.js";
+export { collectToolRefs, buildGetToolInfo } from "./build-get-tool-info.js";
+export type { ToolRef, AsyncToolFetcher, BuildGetToolInfoOptions } from "./build-get-tool-info.js";
+export { resolveForStep, InlineResolver, ensureInlineResolver, collectInlineTools, type InlineToolEntry, } from "./inline-resolver.js";
 export { canMatch, canMapOver, compatible, effectiveMapOver, isListLike, collectionTypeRank, isNullDesc, isAnyDesc, describe as describeCollectionType, } from "./collection-type-functions.js";
 //# sourceMappingURL=index.d.ts.map

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,YAAY,EACV,aAAa,EACb,aAAa,EACb,iBAAiB,EACjB,cAAc,EACd,sBAAsB,EACtB,YAAY,EACZ,aAAa,EACb,gBAAgB,EAChB,0BAA0B,EAC1B,oBAAoB,EACpB,wBAAwB,EACxB,iBAAiB,GAClB,MAAM,YAAY,CAAC;AAEpB,OAAO,EAAE,kBAAkB,EAAE,MAAM,oBAAoB,CAAC;AACxD,OAAO,EAAE,mBAAmB,EAAE,uBAAuB,EAAE,MAAM,2BAA2B,CAAC;AACzF,OAAO,EAAE,yBAAyB,EAAE,4BAA4B,EAAE,MAAM,qBAAqB,CAAC;AAC9F,OAAO,EAAE,oBAAoB,EAAE,iBAAiB,EAAE,MAAM,uBAAuB,CAAC;AAChF,YAAY,EAAE,cAAc,EAAE,MAAM,uBAAuB,CAAC;AAC5D,YAAY,EACV,0BAA0B,EAC1B,oBAAoB,EACpB,gBAAgB,EAChB,kBAAkB,GACnB,MAAM,0BAA0B,CAAC;AAClC,YAAY,EAAE,WAAW,EAAE,MAAM,oBAAoB,CAAC;AACtD,OAAO,EAAE,eAAe,EAAE,gBAAgB,EAAE,MAAM,0BAA0B,CAAC;AAC7E,YAAY,EAAE,OAAO,EAAE,gBAAgB,EAAE,uBAAuB,EAAE,MAAM,0BAA0B,CAAC;AACnG,OAAO,EACL,cAAc,EACd,cAAc,EACd,oBAAoB,EACpB,kBAAkB,EAClB,KAAK,eAAe,GACrB,MAAM,sBAAsB,CAAC;AAC9B,OAAO,EACL,QAAQ,EACR,UAAU,EACV,UAAU,EACV,gBAAgB,EAChB,UAAU,EACV,kBAAkB,EAClB,UAAU,EACV,SAAS,EACT,QAAQ,IAAI,sBAAsB,GACnC,MAAM,gCAAgC,CAAC"}

package/dist/index.js

@@ -1,5 +1,8 @@
 export { buildWorkflowGraph } from "./graph-builder.js";
 export { validateConnections, validateConnectionGraph } from "./connection-validator.js";
 export { validateConnectionsReport, toConnectionValidationReport } from "./report-builder.js";
+export { buildEdgeAnnotations, edgeAnnotationKey } from "./edge-annotations.js";
+export { collectToolRefs, buildGetToolInfo } from "./build-get-tool-info.js";
+export { resolveForStep, InlineResolver, ensureInlineResolver, collectInlineTools, } from "./inline-resolver.js";
 export { canMatch, canMapOver, compatible, effectiveMapOver, isListLike, collectionTypeRank, isNullDesc, isAnyDesc, describe as describeCollectionType, } from "./collection-type-functions.js";
 //# sourceMappingURL=index.js.map

package/dist/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAeA,OAAO,EAAE,kBAAkB,EAAE,MAAM,oBAAoB,CAAC;AACxD,OAAO,EAAE,mBAAmB,EAAE,uBAAuB,EAAE,MAAM,2BAA2B,CAAC;AACzF,OAAO,EAAE,yBAAyB,EAAE,4BAA4B,EAAE,MAAM,qBAAqB,CAAC;AAQ9F,OAAO,EACL,QAAQ,EACR,UAAU,EACV,UAAU,EACV,gBAAgB,EAChB,UAAU,EACV,kBAAkB,EAClB,UAAU,EACV,SAAS,EACT,QAAQ,IAAI,sBAAsB,GACnC,MAAM,gCAAgC,CAAC"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAeA,OAAO,EAAE,kBAAkB,EAAE,MAAM,oBAAoB,CAAC;AACxD,OAAO,EAAE,mBAAmB,EAAE,uBAAuB,EAAE,MAAM,2BAA2B,CAAC;AACzF,OAAO,EAAE,yBAAyB,EAAE,4BAA4B,EAAE,MAAM,qBAAqB,CAAC;AAC9F,OAAO,EAAE,oBAAoB,EAAE,iBAAiB,EAAE,MAAM,uBAAuB,CAAC;AAShF,OAAO,EAAE,eAAe,EAAE,gBAAgB,EAAE,MAAM,0BAA0B,CAAC;AAE7E,OAAO,EACL,cAAc,EACd,cAAc,EACd,oBAAoB,EACpB,kBAAkB,GAEnB,MAAM,sBAAsB,CAAC;AAC9B,OAAO,EACL,QAAQ,EACR,UAAU,EACV,UAAU,EACV,gBAAgB,EAChB,UAAU,EACV,kBAAkB,EAClB,UAAU,EACV,SAAS,EACT,QAAQ,IAAI,sBAAsB,GACnC,MAAM,gCAAgC,CAAC"}

package/dist/inline-resolver.d.ts

@@ -0,0 +1,63 @@
+/**
+ * Inline UDT resolver layered over `GetToolInfo`. TS port of Python's
+ * `galaxy.tool_util.workflow_state._inline_tool.{resolve_for_step,
+ * InlineResolver, ensure_inline_resolver}` — the connection-validation surface
+ * for inline `tool_representation` steps. Without this, inline-UDT steps
+ * resolve to empty inputs/outputs (their `tool_id` is `null`).
+ *
+ * Scope discrimination:
+ *  - `class: GalaxyUserTool` → parse locally and return.
+ *  - `class: GalaxyTool` (admin dynamic tool) → return `null` so the caller can
+ *    emit `inline_source_unsupported`.
+ *  - Both `tool_id` and `tool_representation` set → `tool_representation` wins
+ *    (Galaxy's exporter clears `tool_id` on UDT export but third-party exporters
+ *    might not).
+ */
+import type { ParsedTool } from "@galaxy-tool-util/schema";
+import type { GetToolInfo } from "./get-tool-info.js";
+type Dict = Record<string, unknown>;
+export declare function resolveForStep(getToolInfo: GetToolInfo, step: unknown): ParsedTool | undefined;
+/**
+ * Per-walk memoization layered over {@link resolveForStep}. Wraps a
+ * {@link GetToolInfo} and caches per-step parse results so repeated
+ * `resolveForStep` calls on the same step object — common when multiple
+ * validation phases walk the same workflow — re-use one parse invocation.
+ *
+ * Structurally satisfies `GetToolInfo` by delegating `getToolInfo(toolId,
+ * version)` to the wrapped instance, so callers can pass an `InlineResolver`
+ * anywhere a `GetToolInfo` is expected.
+ *
+ * Keyed by step identity (`WeakMap`) — content-hash dedupe deferred until
+ * profiling says it matters. Lifetime is bound to a single workflow walk.
+ */
+export declare class InlineResolver implements GetToolInfo {
+    private readonly inner;
+    private readonly representationCache;
+    constructor(getToolInfo: GetToolInfo);
+    getToolInfo(toolId: string, toolVersion?: string | null): ParsedTool | undefined;
+    resolve(step: unknown): ParsedTool | undefined;
+    /**
+     * Parse a single inline representation and cache it by representation
+     * identity. Public so callers (e.g. `buildGetToolInfo`) can warm the cache
+     * up-front during preload to surface parse errors before graph build.
+     */
+    parseInlineOnce(representation: Dict): ParsedTool;
+}
+/**
+ * Walk a workflow dict (steps + nested subworkflows + nested `run`) and
+ * collect every inline tool representation. Used by `buildGetToolInfo` to
+ * pre-parse inline tools alongside the async tool_id preload.
+ */
+export interface InlineToolEntry {
+    representation: Dict;
+    inlineClass: "GalaxyUserTool" | "GalaxyTool";
+}
+export declare function collectInlineTools(data: Dict): InlineToolEntry[];
+/**
+ * Wrap *getToolInfo* in an {@link InlineResolver}, idempotently. Returns the
+ * input unchanged if it is already an `InlineResolver` (so existing caches are
+ * preserved).
+ */
+export declare function ensureInlineResolver(getToolInfo: GetToolInfo): InlineResolver;
+export {};
+//# sourceMappingURL=inline-resolver.d.ts.map

package/dist/inline-resolver.d.ts.map

@@ -0,0 +1 @@
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package/dist/inline-resolver.js

@@ -0,0 +1,170 @@
+/**
+ * Inline UDT resolver layered over `GetToolInfo`. TS port of Python's
+ * `galaxy.tool_util.workflow_state._inline_tool.{resolve_for_step,
+ * InlineResolver, ensure_inline_resolver}` — the connection-validation surface
+ * for inline `tool_representation` steps. Without this, inline-UDT steps
+ * resolve to empty inputs/outputs (their `tool_id` is `null`).
+ *
+ * Scope discrimination:
+ *  - `class: GalaxyUserTool` → parse locally and return.
+ *  - `class: GalaxyTool` (admin dynamic tool) → return `null` so the caller can
+ *    emit `inline_source_unsupported`.
+ *  - Both `tool_id` and `tool_representation` set → `tool_representation` wins
+ *    (Galaxy's exporter clears `tool_id` on UDT export but third-party exporters
+ *    might not).
+ */
+import { parseInlineTool } from "@galaxy-tool-util/schema";
+const INLINE_CLASSES = new Set(["GalaxyUserTool", "GalaxyTool"]);
+function viewStep(step) {
+    if (!step || typeof step !== "object") {
+        return { toolId: null, toolVersion: null, representation: null, inlineClass: null };
+    }
+    const s = step;
+    const representation = pickRepresentation(s);
+    const inlineClass = representation &&
+        typeof representation.class === "string" &&
+        INLINE_CLASSES.has(representation.class)
+        ? representation.class
+        : null;
+    return {
+        toolId: typeof s.tool_id === "string" ? s.tool_id : null,
+        toolVersion: typeof s.tool_version === "string" ? s.tool_version : null,
+        representation,
+        inlineClass,
+    };
+}
+function pickRepresentation(step) {
+    const native = step.tool_representation;
+    if (native && typeof native === "object" && !Array.isArray(native)) {
+        return native;
+    }
+    const run = step.run;
+    if (run && typeof run === "object" && !Array.isArray(run)) {
+        const cls = run.class;
+        if (typeof cls === "string" && INLINE_CLASSES.has(cls)) {
+            return run;
+        }
+    }
+    return null;
+}
+export function resolveForStep(getToolInfo, step) {
+    if (getToolInfo instanceof InlineResolver) {
+        return getToolInfo.resolve(step);
+    }
+    return _resolveForStepUncached(getToolInfo, step);
+}
+function _resolveForStepUncached(getToolInfo, step) {
+    const view = viewStep(step);
+    if (view.inlineClass !== null) {
+        if (view.inlineClass !== "GalaxyUserTool") {
+            // GalaxyTool admin dynamic tool — out of scope for connection validation.
+            return undefined;
+        }
+        if (view.representation === null)
+            return undefined;
+        return parseInlineTool(view.representation);
+    }
+    if (!view.toolId)
+        return undefined;
+    return getToolInfo.getToolInfo(view.toolId, view.toolVersion);
+}
+/**
+ * Per-walk memoization layered over {@link resolveForStep}. Wraps a
+ * {@link GetToolInfo} and caches per-step parse results so repeated
+ * `resolveForStep` calls on the same step object — common when multiple
+ * validation phases walk the same workflow — re-use one parse invocation.
+ *
+ * Structurally satisfies `GetToolInfo` by delegating `getToolInfo(toolId,
+ * version)` to the wrapped instance, so callers can pass an `InlineResolver`
+ * anywhere a `GetToolInfo` is expected.
+ *
+ * Keyed by step identity (`WeakMap`) — content-hash dedupe deferred until
+ * profiling says it matters. Lifetime is bound to a single workflow walk.
+ */
+export class InlineResolver {
+    inner;
+    // Keyed by representation-dict identity rather than step identity so the
+    // cache survives normalization (toNative/normalizedNative rebuild steps but
+    // keep the inline `tool_representation` leaf by reference).
+    representationCache = new WeakMap();
+    constructor(getToolInfo) {
+        this.inner = getToolInfo;
+    }
+    getToolInfo(toolId, toolVersion) {
+        return this.inner.getToolInfo(toolId, toolVersion);
+    }
+    resolve(step) {
+        const view = viewStep(step);
+        if (view.inlineClass !== null) {
+            if (view.inlineClass !== "GalaxyUserTool")
+                return undefined;
+            if (view.representation === null)
+                return undefined;
+            return this.parseInlineOnce(view.representation);
+        }
+        if (!view.toolId)
+            return undefined;
+        return this.inner.getToolInfo(view.toolId, view.toolVersion);
+    }
+    /**
+     * Parse a single inline representation and cache it by representation
+     * identity. Public so callers (e.g. `buildGetToolInfo`) can warm the cache
+     * up-front during preload to surface parse errors before graph build.
+     */
+    parseInlineOnce(representation) {
+        const key = representation;
+        const cached = this.representationCache.get(key);
+        if (cached)
+            return cached;
+        const parsed = parseInlineTool(representation);
+        this.representationCache.set(key, parsed);
+        return parsed;
+    }
+}
+export function collectInlineTools(data) {
+    const out = [];
+    _walkInline(data, out);
+    return out;
+}
+function _walkInline(node, out) {
+    const steps = node.steps;
+    if (steps == null || typeof steps !== "object")
+        return;
+    const iter = Array.isArray(steps)
+        ? steps
+        : Object.values(steps);
+    for (const stepRaw of iter) {
+        if (stepRaw == null || typeof stepRaw !== "object")
+            continue;
+        const step = stepRaw;
+        const view = viewStep(step);
+        if (view.representation && view.inlineClass) {
+            out.push({ representation: view.representation, inlineClass: view.inlineClass });
+        }
+        const sub = step.subworkflow;
+        if (sub && typeof sub === "object" && !Array.isArray(sub)) {
+            _walkInline(sub, out);
+        }
+        // For format2, `run:` may be a nested subworkflow (class: GalaxyWorkflow)
+        // — recurse so inner UDTs surface too. If `run:` is itself an inline UDT,
+        // viewStep already picked it up above; don't recurse in that case.
+        const run = step.run;
+        if (run &&
+            typeof run === "object" &&
+            !Array.isArray(run) &&
+            run.class === "GalaxyWorkflow") {
+            _walkInline(run, out);
+        }
+    }
+}
+/**
+ * Wrap *getToolInfo* in an {@link InlineResolver}, idempotently. Returns the
+ * input unchanged if it is already an `InlineResolver` (so existing caches are
+ * preserved).
+ */
+export function ensureInlineResolver(getToolInfo) {
+    if (getToolInfo instanceof InlineResolver)
+        return getToolInfo;
+    return new InlineResolver(getToolInfo);
+}
+//# sourceMappingURL=inline-resolver.js.map

package/dist/inline-resolver.js.map

@@ -0,0 +1 @@
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package/dist/report-builder.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"report-builder.d.ts","sourceRoot":"","sources":["../src/report-builder.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAQH,OAAO,KAAK,EAGV,0BAA0B,EAE3B,MAAM,0BAA0B,CAAC;AAGlC,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,oBAAoB,CAAC;AAEtD,OAAO,KAAK,EAAE,iBAAiB,EAAE,wBAAwB,EAAE,MAAM,YAAY,CAAC;AAE9E,wBAAgB,yBAAyB,CACvC,QAAQ,EAAE,OAAO,EACjB,WAAW,EAAE,WAAW,GACvB,0BAA0B,CAI5B;AAED,wBAAgB,4BAA4B,CAC1C,MAAM,EAAE,wBAAwB,EAChC,mBAAmB,EAAE,iBAAiB,GACrC,0BAA0B,CA2C5B"}

package/dist/report-builder.js

@@ -17,21 +17,28 @@ export function validateConnectionsReport(workflow, getToolInfo) {
 }
 export function toConnectionValidationReport(result, resolvedOutputTypes) {
     const stepResults = result.stepResults.map((sr) => {
-        const connections = sr.connections.map((cr) => ({
-            source_step: cr.sourceStep,
-            source_output: cr.sourceOutput,
-            target_step: cr.targetStep,
-            target_input: cr.targetInput,
-            status: cr.status,
-            mapping: cr.mapping ?? null,
-            errors: cr.errors,
-        }));
+        const connections = sr.connections.map((cr) => {
+            const out = {
+                source_step: cr.sourceStep,
+                source_output: cr.sourceOutput,
+                target_step: cr.targetStep,
+                target_input: cr.targetInput,
+                status: cr.status,
+                mapping: cr.mapping ?? null,
+                errors: cr.errors,
+            };
+            if (cr.mapDepth !== undefined)
+                out.map_depth = cr.mapDepth;
+            if (cr.reduction !== undefined)
+                out.reduction = cr.reduction;
+            return out;
+        });
         const stepOutputs = resolvedOutputTypes[sr.stepId] ?? {};
         const resolved_outputs = Object.entries(stepOutputs).map(([name, t]) => ({
             name,
             collection_type: _sentinelToCollectionType(t),
         }));
-        return {
+        const stepResult = {
             step: sr.stepId,
             tool_id: sr.toolId ?? null,
             version: sr.toolVersion ?? null,
@@ -41,6 +48,9 @@ export function toConnectionValidationReport(result, resolvedOutputTypes) {
             resolved_outputs,
             errors: sr.errors,
         };
+        if (sr.label !== undefined && sr.label !== null)
+            stepResult.label = sr.label;
+        return stepResult;
     });
     const has_details = stepResults.some((sr) => sr.connections.length > 0 || sr.errors.length > 0);
     return {

package/dist/report-builder.js.map

@@ -1 +1 @@
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package/dist/types.d.ts

@@ -27,6 +27,7 @@ export interface ResolvedOutput {
 }
 export interface ResolvedStep {
     stepId: string;
+    label?: string | null;
     toolId?: string | null;
     toolVersion?: string | null;
     stepType: string;
@@ -49,10 +50,15 @@ export interface ConnectionValidationResult {
     targetInput: string;
     status: ConnectionStatus;
     mapping?: string | null;
+    /** Depth of map-over applied at this connection (0 = scalar passthrough, 1 = list, 2 = list:paired, …). */
+    mapDepth?: number;
+    /** True if this connection reduces a list-like source into a multi-data scalar input. */
+    reduction?: boolean;
     errors: string[];
 }
 export interface StepConnectionResult {
     stepId: string;
+    label?: string | null;
     toolId?: string | null;
     toolVersion?: string | null;
     stepType: string;

package/dist/types.d.ts.map

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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@galaxy-tool-util/connection-validation",
-  "version": "0.1.0",
+  "version": "1.5.0",
   "description": "Connection validator for Galaxy workflows — port of galaxy.tool_util.workflow_state.connection_validation",
   "type": "module",
   "sideEffects": false,
@@ -36,8 +36,8 @@
     "yaml": "^2.8.3"
   },
   "dependencies": {
-    "@galaxy-tool-util/schema": "1.1.0",
-    "@galaxy-tool-util/workflow-graph": "1.0.0"
+    "@galaxy-tool-util/schema": "1.5.0",
+    "@galaxy-tool-util/workflow-graph": "1.2.0"
   },
   "scripts": {
     "build": "tsc",