@galaxy-tool-util/cli 1.10.1 → 1.13.1

package/dist/commands/tree.d.ts

@@ -12,6 +12,12 @@ export interface WorkflowInfo {
     path: string;
     relativePath: string;
     format: WorkflowFormat;
+    /**
+     * Set when a file with an unambiguous workflow extension (.ga, .gxwf.yml,
+     * .gxwf.yaml) failed to parse during discovery. Such files are still
+     * reported (as an error outcome) rather than silently dropped.
+     */
+    loadError?: string;
 }
 export interface WorkflowOutcome<T> {
     info: WorkflowInfo;
@@ -33,6 +39,12 @@ export interface TreeSummary {
 }
 /** Call from processOne to skip a workflow with a reason. */
 export declare function skipWorkflow(reason: string): never;
+/**
+ * Collapse a multi-line message to its first line. Tree outcome errors land in
+ * the per-workflow console listing and in `|`-delimited Markdown report table
+ * cells, both of which a raw multi-line YAML parse error would wreck.
+ */
+export declare function firstLine(msg: string): string;
 /** Discover workflow files recursively under root. */
 export declare function discoverWorkflows(root: string, includeFormat2?: boolean): Promise<WorkflowInfo[]>;
 /** Load and parse a discovered workflow file. Returns null on failure. */

package/dist/commands/tree.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"tree.d.ts","sourceRoot":"","sources":["../../src/commands/tree.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AACH,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,0BAA0B,CAAC;AAO/D,MAAM,WAAW,YAAY;IAC3B,IAAI,EAAE,MAAM,CAAC;IACb,YAAY,EAAE,MAAM,CAAC;IACrB,MAAM,EAAE,cAAc,CAAC;CACxB;AAED,MAAM,WAAW,eAAe,CAAC,CAAC;IAChC,IAAI,EAAE,YAAY,CAAC;IACnB,MAAM,CAAC,EAAE,CAAC,CAAC;IACX,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,UAAU,CAAC,EAAE,MAAM,CAAC;CACrB;AAED,MAAM,WAAW,UAAU,CAAC,CAAC;IAC3B,IAAI,EAAE,MAAM,CAAC;IACb,QAAQ,EAAE,eAAe,CAAC,CAAC,CAAC,EAAE,CAAC;CAChC;AAED,MAAM,WAAW,WAAW;IAC1B,KAAK,EAAE,MAAM,CAAC;IACd,EAAE,EAAE,MAAM,CAAC;IACX,IAAI,EAAE,MAAM,CAAC;IACb,KAAK,EAAE,MAAM,CAAC;IACd,OAAO,EAAE,MAAM,CAAC;CACjB;AAKD,6DAA6D;AAC7D,wBAAgB,YAAY,CAAC,MAAM,EAAE,MAAM,GAAG,KAAK,CAElD;AAyCD,sDAAsD;AACtD,wBAAsB,iBAAiB,CACrC,IAAI,EAAE,MAAM,EACZ,cAAc,UAAO,GACpB,OAAO,CAAC,YAAY,EAAE,CAAC,CAKzB;AAkDD,0EAA0E;AAC1E,wBAAsB,gBAAgB,CACpC,IAAI,EAAE,YAAY,GACjB,OAAO,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,IAAI,CAAC,CAOzC;AAID,MAAM,MAAM,UAAU,CAAC,CAAC,IAAI,CAAC,IAAI,EAAE,YAAY,EAAE,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,KAAK,OAAO,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC;AAElG,mEAAmE;AACnE,wBAAsB,WAAW,CAAC,CAAC,EACjC,IAAI,EAAE,MAAM,EACZ,UAAU,EAAE,UAAU,CAAC,CAAC,CAAC,EACzB,cAAc,UAAO,GACpB,OAAO,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,CAwBxB;AAED,kDAAkD;AAClD,wBAAgB,iBAAiB,CAAC,CAAC,EACjC,QAAQ,EAAE,eAAe,CAAC,CAAC,CAAC,EAAE,EAC9B,MAAM,CAAC,EAAE,CAAC,MAAM,EAAE,CAAC,KAAK,OAAO,GAC9B,WAAW,CAiBb"}
+{"version":3,"file":"tree.d.ts","sourceRoot":"","sources":["../../src/commands/tree.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AACH,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,0BAA0B,CAAC;AAO/D,MAAM,WAAW,YAAY;IAC3B,IAAI,EAAE,MAAM,CAAC;IACb,YAAY,EAAE,MAAM,CAAC;IACrB,MAAM,EAAE,cAAc,CAAC;IACvB;;;;OAIG;IACH,SAAS,CAAC,EAAE,MAAM,CAAC;CACpB;AAED,MAAM,WAAW,eAAe,CAAC,CAAC;IAChC,IAAI,EAAE,YAAY,CAAC;IACnB,MAAM,CAAC,EAAE,CAAC,CAAC;IACX,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,UAAU,CAAC,EAAE,MAAM,CAAC;CACrB;AAED,MAAM,WAAW,UAAU,CAAC,CAAC;IAC3B,IAAI,EAAE,MAAM,CAAC;IACb,QAAQ,EAAE,eAAe,CAAC,CAAC,CAAC,EAAE,CAAC;CAChC;AAED,MAAM,WAAW,WAAW;IAC1B,KAAK,EAAE,MAAM,CAAC;IACd,EAAE,EAAE,MAAM,CAAC;IACX,IAAI,EAAE,MAAM,CAAC;IACb,KAAK,EAAE,MAAM,CAAC;IACd,OAAO,EAAE,MAAM,CAAC;CACjB;AAKD,6DAA6D;AAC7D,wBAAgB,YAAY,CAAC,MAAM,EAAE,MAAM,GAAG,KAAK,CAElD;AAqBD;;;;GAIG;AACH,wBAAgB,SAAS,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,CAG7C;AAqCD,sDAAsD;AACtD,wBAAsB,iBAAiB,CACrC,IAAI,EAAE,MAAM,EACZ,cAAc,UAAO,GACpB,OAAO,CAAC,YAAY,EAAE,CAAC,CAKzB;AAiED,0EAA0E;AAC1E,wBAAsB,gBAAgB,CACpC,IAAI,EAAE,YAAY,GACjB,OAAO,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,IAAI,CAAC,CAOzC;AAID,MAAM,MAAM,UAAU,CAAC,CAAC,IAAI,CAAC,IAAI,EAAE,YAAY,EAAE,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,KAAK,OAAO,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC;AAElG,mEAAmE;AACnE,wBAAsB,WAAW,CAAC,CAAC,EACjC,IAAI,EAAE,MAAM,EACZ,UAAU,EAAE,UAAU,CAAC,CAAC,CAAC,EACzB,cAAc,UAAO,GACpB,OAAO,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,CA4BxB;AAED,kDAAkD;AAClD,wBAAgB,iBAAiB,CAAC,CAAC,EACjC,QAAQ,EAAE,eAAe,CAAC,CAAC,CAAC,EAAE,EAC9B,MAAM,CAAC,EAAE,CAAC,MAAM,EAAE,CAAC,KAAK,OAAO,GAC9B,WAAW,CAiBb"}

package/dist/commands/tree.js

@@ -28,20 +28,40 @@ function classifyFile(filename) {
         return "format2";
     return null;
 }
+/**
+ * Collapse a multi-line message to its first line. Tree outcome errors land in
+ * the per-workflow console listing and in `|`-delimited Markdown report table
+ * cells, both of which a raw multi-line YAML parse error would wreck.
+ */
+export function firstLine(msg) {
+    const idx = msg.indexOf("\n");
+    return idx === -1 ? msg : msg.slice(0, idx);
+}
+/**
+ * True for extensions that unambiguously denote a Galaxy workflow (.ga,
+ * .gxwf.yml, .gxwf.yaml). A parse failure on one of these is a real error to
+ * surface; a parse failure on a plain .yml/.json could be any unrelated file
+ * and is skipped silently.
+ */
+function isDefiniteWorkflowExtension(filename) {
+    if (FORMAT2_SUFFIXES.some((suffix) => filename.endsWith(suffix)))
+        return true;
+    return NATIVE_EXTENSIONS.has(extname(filename));
+}
 function isWorkflowContent(data, format) {
     if (format === "native") {
         return data.a_galaxy_workflow === "true";
     }
     return data.class === "GalaxyWorkflow";
 }
+/** Parse raw workflow content; throws on malformed JSON/YAML. */
+function parseFileContentOrThrow(raw, format) {
+    const parsed = format === "native" ? JSON.parse(raw) : YAML.parse(raw);
+    return typeof parsed === "object" && parsed !== null ? parsed : null;
+}
 function parseFileContent(raw, format) {
     try {
-        if (format === "native") {
-            const parsed = JSON.parse(raw);
-            return typeof parsed === "object" && parsed !== null ? parsed : null;
-        }
-        const parsed = YAML.parse(raw);
-        return typeof parsed === "object" && parsed !== null ? parsed : null;
+        return parseFileContentOrThrow(raw, format);
     }
     catch {
         return null;
@@ -84,7 +104,23 @@ async function _walkDir(dir, root, includeFormat2, out) {
         catch {
             continue;
         }
-        const data = parseFileContent(raw, format);
+        let data;
+        try {
+            data = parseFileContentOrThrow(raw, format);
+        }
+        catch (e) {
+            // A malformed file with an unambiguous workflow extension is a real
+            // error to report; a malformed plain .yml/.json is some other file.
+            if (isDefiniteWorkflowExtension(entry.name)) {
+                out.push({
+                    path: filePath,
+                    relativePath: relative(root, filePath),
+                    format,
+                    loadError: e instanceof Error ? e.message : String(e),
+                });
+            }
+            continue;
+        }
         if (!data || !isWorkflowContent(data, format))
             continue;
         out.push({
@@ -110,6 +146,10 @@ export async function collectTree(root, processOne, includeFormat2 = true) {
     const workflows = await discoverWorkflows(root, includeFormat2);
     const outcomes = [];
     for (const info of workflows) {
+        if (info.loadError) {
+            outcomes.push({ info, error: firstLine(info.loadError) });
+            continue;
+        }
         const data = await loadWorkflowSafe(info);
         if (!data) {
             outcomes.push({ info, error: "Failed to load workflow" });
@@ -124,7 +164,7 @@ export async function collectTree(root, processOne, includeFormat2 = true) {
                 outcomes.push({ info, skipped: true, skipReason: e.message });
             }
             else {
-                outcomes.push({ info, error: e instanceof Error ? e.message : String(e) });
+                outcomes.push({ info, error: firstLine(e instanceof Error ? e.message : String(e)) });
             }
         }
     }

package/dist/commands/tree.js.map

@@ -1 +1 @@
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package/dist/commands/validate-tree.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"validate-tree.d.ts","sourceRoot":"","sources":["../../src/commands/validate-tree.ts"],"names":[],"mappings":"AAiBA,OAAO,EAAwB,KAAK,aAAa,EAAE,MAAM,qBAAqB,CAAC;AAQ/E,OAAO,EAAsC,KAAK,mBAAmB,EAAE,MAAM,oBAAoB,CAAC;AAElG,MAAM,WAAW,mBAAoB,SAAQ,aAAa,EAAE,mBAAmB;IAC7E,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,SAAS,CAAC,EAAE,OAAO,CAAC;IACpB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,IAAI,CAAC,EAAE,OAAO,CAAC;CAChB;AAED,wBAAsB,eAAe,CAAC,GAAG,EAAE,MAAM,EAAE,IAAI,EAAE,mBAAmB,GAAG,OAAO,CAAC,IAAI,CAAC,CAgI3F"}

package/dist/commands/validate-tree.js

@@ -26,8 +26,12 @@ export async function runValidateTree(dir, opts) {
     let validateFormat2StepsJsonSchema;
     if (mode === "json-schema") {
         const mod = await import("./validate-workflow-json-schema.js");
-        validateNativeStepsJsonSchema = (data, cache, prefix, expansionOpts) => mod.validateNativeStepsJsonSchema(data, cache, opts.toolSchemaDir, prefix, expansionOpts);
-        validateFormat2StepsJsonSchema = (data, cache, prefix, expansionOpts) => mod.validateFormat2StepsJsonSchema(data, cache, opts.toolSchemaDir, prefix, expansionOpts);
+        validateNativeStepsJsonSchema = (data, cache, prefix, expansionOpts) => cache
+            ? mod.validateNativeStepsJsonSchema(data, cache, opts.toolSchemaDir, prefix, expansionOpts)
+            : Promise.resolve([]);
+        validateFormat2StepsJsonSchema = (data, cache, prefix, expansionOpts) => cache
+            ? mod.validateFormat2StepsJsonSchema(data, cache, opts.toolSchemaDir, prefix, expansionOpts)
+            : Promise.resolve([]);
     }
     const strict = resolveStrictOptions(opts);
     const treeResult = await collectTree(dir, async (info, data) => {
@@ -48,7 +52,7 @@ export async function runValidateTree(dir, opts) {
         const expansionOpts = {
             resolver: createDefaultResolver({ workflowDirectory: dirname(info.path) }),
         };
-        let stepResults = [];
+        let stepResults;
         if (cache && opts.toolState !== false) {
             const validateNative = validateNativeStepsJsonSchema ?? validateNativeSteps;
             const validateF2 = validateFormat2StepsJsonSchema ?? validateFormat2Steps;
@@ -57,8 +61,21 @@ export async function runValidateTree(dir, opts) {
                     ? await validateNative(data, cache, "", expansionOpts)
                     : await validateF2(data, cache, "", expansionOpts);
         }
-        // --strict-state: promote skips to failures
-        if (strict.strictState && stepResults.some((s) => s.status !== "ok" && s.status !== "fail")) {
+        else {
+            // Tool-state validation disabled (or no cache): still enumerate tool
+            // steps so the step count is reported, marking each as skipped. No
+            // resolver is passed — enumeration must stay offline, so subworkflow
+            // expansion is inline-only rather than fetching external references.
+            stepResults =
+                format === "native"
+                    ? await validateNativeSteps(data, null)
+                    : await validateFormat2Steps(data, null);
+        }
+        // --strict-state: promote skips to failures. `skip_no_tool_state` is
+        // exempt — it means the user turned tool-state validation off, not that a
+        // step could not be checked, and `gxwf validate` treats it the same way.
+        if (strict.strictState &&
+            stepResults.some((s) => s.status !== "ok" && s.status !== "fail" && s.status !== "skip_no_tool_state")) {
             throw new Error("Strict state: skipped steps not allowed");
         }
         return buildWorkflowValidationResult(info.relativePath, stepResults);
@@ -95,7 +112,8 @@ export async function runValidateTree(dir, opts) {
     }
     const s = report.summary;
     const total = report.workflows.length;
-    console.log(`\nSummary: ${total} workflows | ${s.ok} OK, ${s.fail} FAIL, ${s.skip} SKIP`);
+    const errorSuffix = s.error > 0 ? `, ${s.error} ERROR` : "";
+    console.log(`\nSummary: ${total} workflows | ${s.ok} OK, ${s.fail} FAIL, ${s.skip} SKIP${errorSuffix}`);
     process.exitCode = computeValidateExitCode(report);
 }
 function buildReport(treeResult) {

package/dist/commands/validate-tree.js.map

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package/dist/commands/validate-workflow-json-schema.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"validate-workflow-json-schema.d.ts","sourceRoot":"","sources":["../../src/commands/validate-workflow-json-schema.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AAExD,OAAO,EAiBL,KAAK,gBAAgB,EACtB,MAAM,0BAA0B,CAAC;AAWlC,OAAO,KAAK,EACV,uBAAuB,EACvB,cAAc,EACd,oBAAoB,EACrB,MAAM,wBAAwB,CAAC;AA8KhC;;;;GAIG;AACH,wBAAgB,+BAA+B,CAC7C,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC7B,MAAM,EAAE,cAAc,GACrB,MAAM,EAAE,CAOV;AAID,wBAAsB,6BAA6B,CACjD,QAAQ,EAAE,MAAM,EAChB,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC7B,MAAM,EAAE,cAAc,EACtB,IAAI,EAAE,uBAAuB,EAC7B,aAAa,CAAC,EAAE,gBAAgB,GAC/B,OAAO,CAAC,IAAI,CAAC,CA8Gf;AAID,wBAAsB,6BAA6B,CACjD,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC7B,KAAK,EAAE,SAAS,EAChB,aAAa,CAAC,EAAE,MAAM,EACtB,MAAM,SAAK,EACX,aAAa,CAAC,EAAE,gBAAgB,GAC/B,OAAO,CAAC,oBAAoB,EAAE,CAAC,CAGjC;AA4MD,wBAAsB,8BAA8B,CAClD,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC7B,KAAK,EAAE,SAAS,EAChB,aAAa,CAAC,EAAE,MAAM,EACtB,MAAM,SAAK,EACX,aAAa,CAAC,EAAE,gBAAgB,GAC/B,OAAO,CAAC,oBAAoB,EAAE,CAAC,CAGjC"}

package/dist/commands/validate-workflow-json-schema.js

@@ -8,7 +8,7 @@
  * Mirrors Galaxy's validation_json_schema.py.
  */
 import { makeNodeToolCache } from "@galaxy-tool-util/core/node";
-import { createFieldModel, GalaxyWorkflowSchema, NativeGalaxyWorkflowSchema, expandedNative, expandedFormat2, injectConnectionsIntoState, scanForReplacements, withClass, } from "@galaxy-tool-util/schema";
+import { createFieldModel, GalaxyWorkflowSchema, NativeGalaxyWorkflowSchema, expandedNative, expandedFormat2, injectConnectionsIntoState, stripConnectedValues, scanForReplacements, withClass, isGalaxyUserToolRun, } from "@galaxy-tool-util/schema";
 import * as JSONSchema from "effect/JSONSchema";
 import Ajv2020 from "ajv/dist/2020.js";
 import { readFileSync, existsSync } from "node:fs";
@@ -16,6 +16,8 @@ import { join } from "node:path";
 import { buildSingleValidationReport, SKIP_STATUSES, nativeConnectionsFromFormat2In, } from "@galaxy-tool-util/schema";
 import { isEmptyState } from "./validate-workflow.js";
 import { isResolveError, resolveTool } from "./resolve-tool.js";
+import { embeddedToolDefinition, isEmbeddedTool, resolveEmbeddedTool } from "./embedded-tool.js";
+import { resolveStrictOptions } from "./strict-options.js";
 const Ajv = Ajv2020.default ?? Ajv2020;
 // Recursively drop `$id` keys. Effect's JSONSchema.make inlines unknown/any
 // params as `{$id: "/schemas/unknown", title: "unknown"}` (and `/schemas/any`)
@@ -133,6 +135,15 @@ function getOrBuildValidator(toolId, toolVersion, bundle, representation, toolSc
     _toolStateCache.set(key, validator);
     return validator;
 }
+function cachedValidators(toolId, toolVersion, bundle, toolSchemaDir) {
+    return (representation) => getOrBuildValidator(toolId, toolVersion, bundle, representation, toolSchemaDir);
+}
+// Embedded definitions are built per step: their id is not a cache identity
+// (two workflows may embed different tools under one id) and --tool-schema-dir
+// holds schemas for cached tools only.
+function embeddedValidators(bundle) {
+    return (representation) => buildToolStateValidator(bundle, representation);
+}
 // --- AJV error formatting ---
 function formatAjvErrors(validate) {
     if (!validate.errors)
@@ -202,12 +213,14 @@ export async function runValidateWorkflowJsonSchema(filePath, data, format, opts
         }
     }
     const stateOk = !results.some((r) => r.status === "fail");
+    const strictStateSkipped = resolveStrictOptions(opts).strictState &&
+        results.some((r) => r.status !== "ok" && r.status !== "fail");
     if (opts.json) {
         const report = buildSingleValidationReport(filePath, results, {
             structure_errors: structureErrors,
         });
         console.log(JSON.stringify(report, null, 2));
-        process.exitCode = structOk && stateOk ? 0 : 1;
+        process.exitCode = strictStateSkipped ? 2 : structOk && stateOk ? 0 : 1;
         return;
     }
     if (results.length === 0) {
@@ -235,6 +248,11 @@ export async function runValidateWorkflowJsonSchema(filePath, data, format, opts
         }
     }
     console.log(`\nTool state (json-schema): ${validated} validated, ${skipped} skipped`);
+    if (strictStateSkipped) {
+        console.error("Strict state: skipped steps not allowed");
+        process.exitCode = 2;
+        return;
+    }
     process.exitCode = structOk && stateOk ? 0 : 1;
 }
 // --- Native validation (json-schema) ---
@@ -251,6 +269,11 @@ async function _validateNativeWorkflowJsonSchema(wf, cache, toolSchemaDir, prefi
             results.push(...subResults);
             continue;
         }
+        const embedded = embeddedToolDefinition(step);
+        if (embedded) {
+            results.push(_validateEmbeddedNativeStepJsonSchema(step, stepLabel, embedded));
+            continue;
+        }
         const toolId = step.tool_id;
         if (!toolId)
             continue;
@@ -279,7 +302,13 @@ async function _validateNativeStepJsonSchema(step, stepLabel, toolId, toolVersio
     for (const [k, v] of Object.entries(step.input_connections)) {
         connections[k] = v;
     }
-    return _validateNativeStateJsonSchema(bundle, step.tool_state, connections, stepLabel, toolId, toolVersion, toolSchemaDir);
+    return _validateNativeStateJsonSchema(bundle, step.tool_state, connections, stepLabel, toolId, toolVersion, cachedValidators(toolId, toolVersion, bundle, toolSchemaDir), step.when);
+}
+function _validateEmbeddedNativeStepJsonSchema(step, stepLabel, repr) {
+    const tool = resolveEmbeddedTool(repr, stepLabel);
+    if (!isEmbeddedTool(tool))
+        return tool;
+    return _validateNativeStateJsonSchema(tool.bundle, step.tool_state, { ...step.input_connections }, stepLabel, tool.toolId, tool.toolVersion, embeddedValidators(tool.bundle), step.when);
 }
 /**
  * Validate a native-encoded tool_state block against the `workflow_step_native`
@@ -288,7 +317,29 @@ async function _validateNativeStepJsonSchema(step, stepLabel, toolId, toolVersio
  * workflow format. (JSON Schema can't enforce double-encoded scalar types, e.g.
  * "5" for an int, but still checks structure and unknown keys.)
  */
-function _validateNativeStateJsonSchema(bundle, toolState, connections, stepLabel, toolId, toolVersion, toolSchemaDir) {
+/**
+ * Connection keys that feed the step itself rather than the tool: Galaxy wires
+ * a conditional step's skip-if expression through `input_connections`, under
+ * the literal key `when` in native form and under whatever names the format2
+ * `when:` expression references. Neither names a tool parameter, so neither is
+ * matched by the parameter walk.
+ */
+function stepLevelConnectionKeys(whenExpression) {
+    const keys = new Set(["when"]);
+    if (typeof whenExpression === "string") {
+        for (const m of whenExpression.matchAll(/inputs\.([A-Za-z_]\w*)/g))
+            keys.add(m[1]);
+        for (const m of whenExpression.matchAll(/inputs\[['"]([^'"]+)['"]\]/g))
+            keys.add(m[1]);
+    }
+    return keys;
+}
+/** Connection keys that matched no tool parameter and are not step-level inputs. */
+function unmatchedConnectionKeys(remaining, whenExpression) {
+    const stepLevel = stepLevelConnectionKeys(whenExpression);
+    return Object.keys(remaining).filter((k) => !stepLevel.has(k));
+}
+function _validateNativeStateJsonSchema(bundle, toolState, connections, stepLabel, toolId, toolVersion, validators, whenExpression) {
     const replacementScan = scanForReplacements(bundle.parameters, toolState);
     if (replacementScan === "yes") {
         return {
@@ -300,8 +351,20 @@ function _validateNativeStateJsonSchema(bundle, toolState, connections, stepLabe
         };
     }
     const state = structuredClone(toolState);
-    injectConnectionsIntoState(bundle.parameters, state, connections);
-    const validate = getOrBuildValidator(toolId, toolVersion, bundle, "workflow_step_native", toolSchemaDir);
+    const remaining = injectConnectionsIntoState(bundle.parameters, state, connections);
+    // Mirrors the linked path below: an unmatched connection key is a defect
+    // regardless of which state block the step carries.
+    const unmatchedKeys = unmatchedConnectionKeys(remaining, whenExpression);
+    if (unmatchedKeys.length > 0) {
+        return {
+            step: stepLabel,
+            tool_id: toolId,
+            version: toolVersion,
+            status: "fail",
+            errors: unmatchedKeys.map((k) => `No parameter definition matching connection key "${k}"`),
+        };
+    }
+    const validate = validators("workflow_step_native");
     if (!validate) {
         return {
             step: stepLabel,
@@ -333,6 +396,10 @@ async function _validateFormat2WorkflowJsonSchema(wf, cache, toolSchemaDir, pref
     for (let i = 0; i < wf.steps.length; i++) {
         const step = wf.steps[i];
         const stepLabel = prefix ? `${prefix}${i}` : String(i);
+        if (isGalaxyUserToolRun(step.run)) {
+            results.push(_validateEmbeddedFormat2StepJsonSchema(step, stepLabel, step.run));
+            continue;
+        }
         if (step.run && typeof step.run === "object") {
             const subResults = await _validateFormat2WorkflowJsonSchema(step.run, cache, toolSchemaDir, `${stepLabel}.`);
             results.push(...subResults);
@@ -362,15 +429,33 @@ async function _validateFormat2StepJsonSchema(step, stepLabel, toolId, toolVersi
     const bundle = {
         parameters: resolved.tool.inputs,
     };
+    return _validateFormat2StateJsonSchema(bundle, step, stepLabel, toolId, toolVersion, cachedValidators(toolId, toolVersion, bundle, toolSchemaDir));
+}
+function _validateEmbeddedFormat2StepJsonSchema(step, stepLabel, repr) {
+    const tool = resolveEmbeddedTool(repr, stepLabel);
+    if (!isEmbeddedTool(tool))
+        return tool;
+    return _validateFormat2StateJsonSchema(tool.bundle, step, stepLabel, tool.toolId, tool.toolVersion, embeddedValidators(tool.bundle));
+}
+function _validateFormat2StateJsonSchema(bundle, step, stepLabel, toolId, toolVersion, validators) {
     // A verbatim native `tool_state` block validates through the native path
     // (same encoding regardless of workflow format); a schema-aware `state` block
     // validates below. State shape — not workflow format — picks the validator.
     if (isEmptyState(step.state) && !isEmptyState(step.tool_state)) {
-        return _validateNativeStateJsonSchema(bundle, step.tool_state, nativeConnectionsFromFormat2In(step.in), stepLabel, toolId, toolVersion, toolSchemaDir);
+        return _validateNativeStateJsonSchema(bundle, step.tool_state, nativeConnectionsFromFormat2In(step.in), stepLabel, toolId, toolVersion, validators, step.when);
+    }
+    const state = structuredClone((step.state ?? {}));
+    stripConnectedValues(bundle.parameters, state);
+    // Build connections dict from step.in
+    const connections = {};
+    for (const stepInput of step.in) {
+        if (stepInput.id && stepInput.source) {
+            const src = stepInput.source;
+            connections[stepInput.id] = Array.isArray(src) ? src : [src];
+        }
     }
-    const state = (step.state ?? {});
-    // Level 1: base validation against workflow_step
-    const baseValidate = getOrBuildValidator(toolId, toolVersion, bundle, "workflow_step", toolSchemaDir);
+    // Level 1: validate the stored, unlinked editor state.
+    const baseValidate = validators("workflow_step");
     if (!baseValidate) {
         return {
             step: stepLabel,
@@ -390,43 +475,41 @@ async function _validateFormat2StepJsonSchema(step, stepLabel, toolId, toolVersi
             errors: formatAjvErrors(baseValidate),
         };
     }
-    // Build connections dict from step.in
-    const connections = {};
-    for (const stepInput of step.in) {
-        if (stepInput.id && stepInput.source) {
-            const src = stepInput.source;
-            connections[stepInput.id] = Array.isArray(src) ? src : [src];
-        }
+    // Level 2: validate effective state after connection injection. Always run
+    // this pass so missing, unconnected required values are rejected.
+    const linkedState = structuredClone(state);
+    const remaining = injectConnectionsIntoState(bundle.parameters, linkedState, connections, {
+        linked: true,
+    });
+    const unmatchedKeys = unmatchedConnectionKeys(remaining, step.when);
+    if (unmatchedKeys.length > 0) {
+        return {
+            step: stepLabel,
+            tool_id: toolId,
+            version: toolVersion,
+            status: "fail",
+            errors: unmatchedKeys.map((k) => `No parameter definition matching connection key "${k}"`),
+        };
     }
-    // Level 2: linked validation with connections injected
-    if (Object.keys(connections).length > 0) {
-        const linkedState = structuredClone(state);
-        // Unmatched connection keys (e.g. the synthetic `when` gate on conditional
-        // steps) are discarded, not failed — mirrors Python's
-        // validate_workflow_json_schema, which injects connections and ignores the
-        // returned unmatched paths. (The Pydantic path raises on unmatched; the
-        // JSON Schema path is intentionally lenient.)
-        injectConnectionsIntoState(bundle.parameters, linkedState, connections, { linked: true });
-        const linkedValidate = getOrBuildValidator(toolId, toolVersion, bundle, "workflow_step_linked", toolSchemaDir);
-        if (!linkedValidate) {
-            return {
-                step: stepLabel,
-                tool_id: toolId,
-                version: toolVersion,
-                status: "skip_tool_not_found",
-                errors: ["unsupported parameter types"],
-            };
-        }
-        const linkedValid = linkedValidate(linkedState);
-        if (!linkedValid) {
-            return {
-                step: stepLabel,
-                tool_id: toolId,
-                version: toolVersion,
-                status: "fail",
-                errors: formatAjvErrors(linkedValidate),
-            };
-        }
+    const linkedValidate = validators("workflow_step_linked");
+    if (!linkedValidate) {
+        return {
+            step: stepLabel,
+            tool_id: toolId,
+            version: toolVersion,
+            status: "skip_tool_not_found",
+            errors: ["unsupported parameter types"],
+        };
+    }
+    const linkedValid = linkedValidate(linkedState);
+    if (!linkedValid) {
+        return {
+            step: stepLabel,
+            tool_id: toolId,
+            version: toolVersion,
+            status: "fail",
+            errors: formatAjvErrors(linkedValidate),
+        };
     }
     return { step: stepLabel, tool_id: toolId, version: toolVersion, status: "ok", errors: [] };
 }

package/dist/commands/validate-workflow-json-schema.js.map

@@ -1 +1 @@
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