npm - @galaxy-tool-util/cli - Versions diffs - 1.12.0 → 1.14.0 - Mend

@galaxy-tool-util/cli 1.12.0 → 1.14.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (29) hide show

package/dist/commands/convert-tree.d.ts +3 -0
package/dist/commands/convert-tree.d.ts.map +1 -1
package/dist/commands/convert-tree.js +7 -12
package/dist/commands/convert-tree.js.map +1 -1
package/dist/commands/convert.d.ts.map +1 -1
package/dist/commands/convert.js +3 -8
package/dist/commands/convert.js.map +1 -1
package/dist/commands/embedded-tool.d.ts +33 -0
package/dist/commands/embedded-tool.d.ts.map +1 -0
package/dist/commands/embedded-tool.js +69 -0
package/dist/commands/embedded-tool.js.map +1 -0
package/dist/commands/stateful-tool-inputs.d.ts +12 -0
package/dist/commands/stateful-tool-inputs.d.ts.map +1 -1
package/dist/commands/stateful-tool-inputs.js +24 -2
package/dist/commands/stateful-tool-inputs.js.map +1 -1
package/dist/commands/url-resolver.d.ts +1 -1
package/dist/commands/url-resolver.d.ts.map +1 -1
package/dist/commands/url-resolver.js +18 -6
package/dist/commands/url-resolver.js.map +1 -1
package/dist/commands/validate-workflow-json-schema.d.ts.map +1 -1
package/dist/commands/validate-workflow-json-schema.js +86 -10
package/dist/commands/validate-workflow-json-schema.js.map +1 -1
package/dist/commands/validate-workflow.d.ts.map +1 -1
package/dist/commands/validate-workflow.js +83 -8
package/dist/commands/validate-workflow.js.map +1 -1
package/dist/spec/build-program.js +16 -3
package/dist/spec/build-program.js.map +1 -1
package/package.json +6 -6
package/spec/gxwf.json +12 -4

package/dist/commands/convert-tree.d.ts CHANGED Viewed

@@ -1,3 +1,6 @@
+/**
+ * `gxwf convert-tree` — batch convert all workflows under a directory.
+ */
 import { type StepConversionStatus } from "@galaxy-tool-util/schema";
 import { type ToolLoadStatus } from "./stateful-tool-inputs.js";
 import { type StrictOptions } from "./strict-options.js";

package/dist/commands/convert-tree.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"convert-tree.d.ts","sourceRoot":"","sources":["../../src/commands/convert-tree.ts"],"names":[],"mappings":"~~AAKA~~,OAAO,EAQL,KAAK,oBAAoB,EAE1B,MAAM,0BAA0B,CAAC;AAGlC,OAAO,~~EAA6B~~,KAAK,cAAc,~~EAAE~~,MAAM,2BAA2B,CAAC;~~AAE3F~~,OAAO,EAAwB,KAAK,aAAa,EAAE,MAAM,qBAAqB,CAAC;AAE/E,OAAO,EAAmD,KAAK,WAAW,EAAE,MAAM,WAAW,CAAC;AAE9F,MAAM,WAAW,kBAAmB,SAAQ,aAAa;IACvD,EAAE,CAAC,EAAE,MAAM,CAAC;IACZ,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,UAAU,CAAC,EAAE,OAAO,CAAC;IACrB,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB,QAAQ,CAAC,EAAE,MAAM,CAAC;CACnB;AAED,MAAM,WAAW,qBAAqB;IACpC,YAAY,EAAE,MAAM,CAAC;IACrB,YAAY,EAAE,MAAM,CAAC;IACrB,YAAY,EAAE,MAAM,CAAC;IACrB,aAAa,CAAC,EAAE,oBAAoB,EAAE,CAAC;IACvC,cAAc,CAAC,EAAE,cAAc,EAAE,CAAC;CACnC;AAED,MAAM,WAAW,iBAAiB;IAChC,IAAI,EAAE,MAAM,CAAC;IACb,OAAO,EAAE,CAAC,qBAAqB,GAAG;QAAE,YAAY,EAAE,MAAM,CAAC;QAAC,KAAK,EAAE,MAAM,CAAA;KAAE,CAAC,EAAE,CAAC;IAC7E,OAAO,EAAE,WAAW,CAAC;CACtB;AAED,wBAAsB,cAAc,CAAC,GAAG,EAAE,MAAM,EAAE,IAAI,EAAE,kBAAkB,GAAG,OAAO,CAAC,IAAI,CAAC,~~CA+KzF~~"}
1	+ {"version":3,"file":"convert-tree.d.ts","sourceRoot":"","sources":["../../src/commands/convert-tree.ts"],"names":[],"mappings":"AAAA;;GAEG;AACH,OAAO,EAQL,KAAK,oBAAoB,EAE1B,MAAM,0BAA0B,CAAC;AAGlC,OAAO,EAGL,KAAK,cAAc,EACpB,MAAM,2BAA2B,CAAC;AAEnC,OAAO,EAAwB,KAAK,aAAa,EAAE,MAAM,qBAAqB,CAAC;AAE/E,OAAO,EAAmD,KAAK,WAAW,EAAE,MAAM,WAAW,CAAC;AAE9F,MAAM,WAAW,kBAAmB,SAAQ,aAAa;IACvD,EAAE,CAAC,EAAE,MAAM,CAAC;IACZ,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,UAAU,CAAC,EAAE,OAAO,CAAC;IACrB,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB,QAAQ,CAAC,EAAE,MAAM,CAAC;CACnB;AAED,MAAM,WAAW,qBAAqB;IACpC,YAAY,EAAE,MAAM,CAAC;IACrB,YAAY,EAAE,MAAM,CAAC;IACrB,YAAY,EAAE,MAAM,CAAC;IACrB,aAAa,CAAC,EAAE,oBAAoB,EAAE,CAAC;IACvC,cAAc,CAAC,EAAE,cAAc,EAAE,CAAC;CACnC;AAED,MAAM,WAAW,iBAAiB;IAChC,IAAI,EAAE,MAAM,CAAC;IACb,OAAO,EAAE,CAAC,qBAAqB,GAAG;QAAE,YAAY,EAAE,MAAM,CAAC;QAAC,KAAK,EAAE,MAAM,CAAA;KAAE,CAAC,EAAE,CAAC;IAC7E,OAAO,EAAE,WAAW,CAAC;CACtB;AAED,wBAAsB,cAAc,CAAC,GAAG,EAAE,MAAM,EAAE,IAAI,EAAE,kBAAkB,GAAG,OAAO,CAAC,IAAI,CAAC,CAwKzF"}

package/dist/commands/convert-tree.js CHANGED Viewed

@@ -1,8 +1,10 @@
-import { makeNodeToolCache } from "@galaxy-tool-util/core/node";
+/**
+ * `gxwf convert-tree` — batch convert all workflows under a directory.
+ */
 import { toFormat2, toFormat2Stateful, toNative, toNativeStateful, checkStrictEncoding, checkStrictStructure, } from "@galaxy-tool-util/schema";
 import { mkdir, writeFile } from "node:fs/promises";
 import { dirname, join, basename } from "node:path";
-import { loadToolInputsForWorkflow } from "./stateful-tool-inputs.js";
+import { loadToolInputsForWorkflow, resolveConversionCache, } from "./stateful-tool-inputs.js";
 import { createDefaultResolver } from "./url-resolver.js";
 import { resolveStrictOptions } from "./strict-options.js";
 import { resolveFormat, serializeWorkflow } from "./workflow-io.js";
@@ -15,14 +17,7 @@ export async function runConvertTree(dir, opts) {
         return;
     }
     // Shared tool cache for stateful mode (loaded once per run)
-    let cache = null;
-    if (opts.stateful) {
-        cache = makeNodeToolCache({ cacheDir: opts.cacheDir });
-        await cache.index.load();
-        if ((await cache.index.listAll()).length === 0) {
-            console.warn("Tool cache is empty — stateful conversion will fall back for every step");
-        }
-    }
+    const cache = await resolveConversionCache(opts);
     const strict = resolveStrictOptions(opts);
     const treeResult = await collectTree(dir, async (info, data) => {
         const sourceFormat = resolveFormat(data, opts.format);
@@ -50,7 +45,7 @@ export async function runConvertTree(dir, opts) {
         let result;
         let statefulSteps;
         let toolLoadErrors;
-        if (opts.stateful && cache) {
+        if (cache) {
             const expansionOpts = {
                 resolver: createDefaultResolver({
                     workflowDirectory: dirname(join(dir, info.relativePath)),
@@ -106,7 +101,7 @@ export async function runConvertTree(dir, opts) {
     const report = buildConvertReport(treeResult);
     // Aggregate stateful step counts across files
     let statefulFallbacks = 0;
-    if (opts.stateful) {
+    if (cache) {
         for (const r of report.results) {
             if ("statefulSteps" in r && r.statefulSteps) {
                 statefulFallbacks += r.statefulSteps.filter((s) => !s.converted).length;

package/dist/commands/convert-tree.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/commands/convert.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"convert.d.ts","sourceRoot":"","sources":["../../src/commands/convert.ts"],"names":[],"mappings":"~~AAkBA~~,OAAO,EAAwB,KAAK,aAAa,EAAE,MAAM,qBAAqB,CAAC;AAQ/E,MAAM,WAAW,cAAe,SAAQ,aAAa;IACnD,EAAE,CAAC,EAAE,MAAM,CAAC;IACZ,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB,QAAQ,CAAC,EAAE,MAAM,CAAC;CACnB;AAED,wBAAsB,UAAU,CAAC,QAAQ,EAAE,MAAM,EAAE,IAAI,EAAE,cAAc,GAAG,OAAO,CAAC,IAAI,CAAC,~~CAkGtF~~"}
1	+ {"version":3,"file":"convert.d.ts","sourceRoot":"","sources":["../../src/commands/convert.ts"],"names":[],"mappings":"AAiBA,OAAO,EAAwB,KAAK,aAAa,EAAE,MAAM,qBAAqB,CAAC;AAQ/E,MAAM,WAAW,cAAe,SAAQ,aAAa;IACnD,EAAE,CAAC,EAAE,MAAM,CAAC;IACZ,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB,QAAQ,CAAC,EAAE,MAAM,CAAC;CACnB;AAED,wBAAsB,UAAU,CAAC,QAAQ,EAAE,MAAM,EAAE,IAAI,EAAE,cAAc,GAAG,OAAO,CAAC,IAAI,CAAC,CA6FtF"}

package/dist/commands/convert.js CHANGED Viewed

@@ -1,10 +1,9 @@
 /**
  * `gxwf convert` — convert between native (.ga) and format2 (.gxwf.yml) formats.
  */
-import { makeNodeToolCache } from "@galaxy-tool-util/core/node";
 import { toFormat2, toFormat2Stateful, toNative, toNativeStateful, checkStrictEncoding, checkStrictStructure, } from "@galaxy-tool-util/schema";
 import { dirname } from "node:path";
-import { loadToolInputsForWorkflow } from "./stateful-tool-inputs.js";
+import { loadToolInputsForWorkflow, resolveConversionCache } from "./stateful-tool-inputs.js";
 import { createDefaultResolver } from "./url-resolver.js";
 import { resolveStrictOptions } from "./strict-options.js";
 import { readWorkflowFile, resolveFormat, serializeWorkflow, writeWorkflowOutput, } from "./workflow-io.js";
@@ -44,12 +43,8 @@ export async function runConvert(filePath, opts) {
     }
     let result;
     let stepStatuses = null;
-    if (opts.stateful) {
-        const cache = makeNodeToolCache({ cacheDir: opts.cacheDir });
-        await cache.index.load();
-        if ((await cache.index.listAll()).length === 0) {
-            console.warn("Tool cache is empty — stateful conversion will fall back for every step");
-        }
+    const cache = await resolveConversionCache(opts);
+    if (cache) {
         const expansionOpts = {
             resolver: createDefaultResolver({ workflowDirectory: dirname(filePath) }),
         };

package/dist/commands/convert.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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1	+ 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package/dist/commands/embedded-tool.d.ts ADDED Viewed

@@ -0,0 +1,33 @@
+/**
+ * Tool-state validation support for steps that embed their tool definition
+ * instead of referencing a cached tool: a format2 `run: {class: GalaxyUserTool}`
+ * or a native `tool_representation`. The parameter bundle is parsed from the
+ * embedded definition, so these steps validate without a tool cache lookup.
+ */
+import { type ToolParameterBundleModel, type ValidationStepResult } from "@galaxy-tool-util/schema";
+export interface EmbeddedTool {
+    bundle: ToolParameterBundleModel;
+    toolId: string | null;
+    toolVersion: string | null;
+}
+/** The embedded tool definition a step carries, or null for a cache-referenced tool. */
+export declare function embeddedToolDefinition(step: {
+    run?: unknown;
+    tool_representation?: unknown;
+}): Record<string, unknown> | null;
+/** The id/version an embedded tool definition declares, for step results. */
+export declare function embeddedToolIdentity(repr: Record<string, unknown>): {
+    toolId: string | null;
+    toolVersion: string | null;
+};
+/**
+ * Build the parameter bundle for an embedded tool definition. Returns a
+ * finished step result instead when the definition can't be validated against:
+ * `skip_tool_not_found` for a class other than `GalaxyUserTool` (admin-installed
+ * `GalaxyTool` dynamic tools are out of scope), `fail` when the definition
+ * doesn't parse — it ships inside the workflow, so a broken one is the
+ * workflow's defect.
+ */
+export declare function resolveEmbeddedTool(repr: Record<string, unknown>, stepLabel: string): EmbeddedTool | ValidationStepResult;
+export declare function isEmbeddedTool(value: EmbeddedTool | ValidationStepResult): value is EmbeddedTool;
+//# sourceMappingURL=embedded-tool.d.ts.map

package/dist/commands/embedded-tool.d.ts.map ADDED Viewed

@@ -0,0 +1 @@

+ {"version":3,"file":"embedded-tool.d.ts","sourceRoot":"","sources":["../../src/commands/embedded-tool.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AACH,OAAO,EAGL,KAAK,wBAAwB,EAC7B,KAAK,oBAAoB,EAC1B,MAAM,0BAA0B,CAAC;AAElC,MAAM,WAAW,YAAY;IAC3B,MAAM,EAAE,wBAAwB,CAAC;IACjC,MAAM,EAAE,MAAM,GAAG,IAAI,CAAC;IACtB,WAAW,EAAE,MAAM,GAAG,IAAI,CAAC;CAC5B;AAED,wFAAwF;AACxF,wBAAgB,sBAAsB,CAAC,IAAI,EAAE;IAC3C,GAAG,CAAC,EAAE,OAAO,CAAC;IACd,mBAAmB,CAAC,EAAE,OAAO,CAAC;CAC/B,GAAG,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,IAAI,CAOjC;AAED,6EAA6E;AAC7E,wBAAgB,oBAAoB,CAAC,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG;IACnE,MAAM,EAAE,MAAM,GAAG,IAAI,CAAC;IACtB,WAAW,EAAE,MAAM,GAAG,IAAI,CAAC;CAC5B,CAKA;AAED;;;;;;;GAOG;AACH,wBAAgB,mBAAmB,CACjC,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC7B,SAAS,EAAE,MAAM,GAChB,YAAY,GAAG,oBAAoB,CA+BrC;AAED,wBAAgB,cAAc,CAAC,KAAK,EAAE,YAAY,GAAG,oBAAoB,GAAG,KAAK,IAAI,YAAY,CAEhG"}

package/dist/commands/embedded-tool.js ADDED Viewed

@@ -0,0 +1,69 @@
+/**
+ * Tool-state validation support for steps that embed their tool definition
+ * instead of referencing a cached tool: a format2 `run: {class: GalaxyUserTool}`
+ * or a native `tool_representation`. The parameter bundle is parsed from the
+ * embedded definition, so these steps validate without a tool cache lookup.
+ */
+import { isGalaxyUserToolRun, parseInlineTool, } from "@galaxy-tool-util/schema";
+/** The embedded tool definition a step carries, or null for a cache-referenced tool. */
+export function embeddedToolDefinition(step) {
+    if (isGalaxyUserToolRun(step.run))
+        return step.run;
+    const repr = step.tool_representation;
+    if (repr && typeof repr === "object" && !Array.isArray(repr)) {
+        return repr;
+    }
+    return null;
+}
+/** The id/version an embedded tool definition declares, for step results. */
+export function embeddedToolIdentity(repr) {
+    return {
+        toolId: typeof repr.id === "string" ? repr.id : null,
+        toolVersion: repr.version == null ? null : String(repr.version),
+    };
+}
+/**
+ * Build the parameter bundle for an embedded tool definition. Returns a
+ * finished step result instead when the definition can't be validated against:
+ * `skip_tool_not_found` for a class other than `GalaxyUserTool` (admin-installed
+ * `GalaxyTool` dynamic tools are out of scope), `fail` when the definition
+ * doesn't parse — it ships inside the workflow, so a broken one is the
+ * workflow's defect.
+ */
+export function resolveEmbeddedTool(repr, stepLabel) {
+    const { toolId, toolVersion } = embeddedToolIdentity(repr);
+    if (repr.class !== "GalaxyUserTool") {
+        return {
+            step: stepLabel,
+            tool_id: toolId,
+            version: toolVersion,
+            status: "skip_tool_not_found",
+            errors: [
+                `embedded tool definition of class ${JSON.stringify(repr.class)} is not validated (only GalaxyUserTool is supported)`,
+            ],
+        };
+    }
+    try {
+        const parsed = parseInlineTool(repr);
+        return {
+            bundle: { parameters: parsed.inputs },
+            toolId,
+            toolVersion,
+        };
+    }
+    catch (e) {
+        return {
+            step: stepLabel,
+            tool_id: toolId,
+            version: toolVersion,
+            status: "fail",
+            errors: [
+                `embedded GalaxyUserTool definition could not be parsed: ${e instanceof Error ? e.message : String(e)}`,
+            ],
+        };
+    }
+}
+export function isEmbeddedTool(value) {
+    return "bundle" in value;
+}
+//# sourceMappingURL=embedded-tool.js.map

package/dist/commands/embedded-tool.js.map ADDED Viewed

@@ -0,0 +1 @@

+ {"version":3,"file":"embedded-tool.js","sourceRoot":"","sources":["../../src/commands/embedded-tool.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AACH,OAAO,EACL,mBAAmB,EACnB,eAAe,GAGhB,MAAM,0BAA0B,CAAC;AAQlC,wFAAwF;AACxF,MAAM,UAAU,sBAAsB,CAAC,IAGtC;IACC,IAAI,mBAAmB,CAAC,IAAI,CAAC,GAAG,CAAC;QAAE,OAAO,IAAI,CAAC,GAAG,CAAC;IACnD,MAAM,IAAI,GAAG,IAAI,CAAC,mBAAmB,CAAC;IACtC,IAAI,IAAI,IAAI,OAAO,IAAI,KAAK,QAAQ,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC;QAC7D,OAAO,IAA+B,CAAC;IACzC,CAAC;IACD,OAAO,IAAI,CAAC;AACd,CAAC;AAED,6EAA6E;AAC7E,MAAM,UAAU,oBAAoB,CAAC,IAA6B;IAIhE,OAAO;QACL,MAAM,EAAE,OAAO,IAAI,CAAC,EAAE,KAAK,QAAQ,CAAC,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI;QACpD,WAAW,EAAE,IAAI,CAAC,OAAO,IAAI,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,MAAM,CAAC,IAAI,CAAC,OAAO,CAAC;KAChE,CAAC;AACJ,CAAC;AAED;;;;;;;GAOG;AACH,MAAM,UAAU,mBAAmB,CACjC,IAA6B,EAC7B,SAAiB;IAEjB,MAAM,EAAE,MAAM,EAAE,WAAW,EAAE,GAAG,oBAAoB,CAAC,IAAI,CAAC,CAAC;IAC3D,IAAI,IAAI,CAAC,KAAK,KAAK,gBAAgB,EAAE,CAAC;QACpC,OAAO;YACL,IAAI,EAAE,SAAS;YACf,OAAO,EAAE,MAAM;YACf,OAAO,EAAE,WAAW;YACpB,MAAM,EAAE,qBAAqB;YAC7B,MAAM,EAAE;gBACN,qCAAqC,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,KAAK,CAAC,sDAAsD;aACtH;SACF,CAAC;IACJ,CAAC;IACD,IAAI,CAAC;QACH,MAAM,MAAM,GAAG,eAAe,CAAC,IAAI,CAAC,CAAC;QACrC,OAAO;YACL,MAAM,EAAE,EAAE,UAAU,EAAE,MAAM,CAAC,MAAgD,EAAE;YAC/E,MAAM;YACN,WAAW;SACZ,CAAC;IACJ,CAAC;IAAC,OAAO,CAAC,EAAE,CAAC;QACX,OAAO;YACL,IAAI,EAAE,SAAS;YACf,OAAO,EAAE,MAAM;YACf,OAAO,EAAE,WAAW;YACpB,MAAM,EAAE,MAAM;YACd,MAAM,EAAE;gBACN,2DAA2D,CAAC,YAAY,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE;aACxG;SACF,CAAC;IACJ,CAAC;AACH,CAAC;AAED,MAAM,UAAU,cAAc,CAAC,KAA0C;IACvE,OAAO,QAAQ,IAAI,KAAK,CAAC;AAC3B,CAAC"}

package/dist/commands/stateful-tool-inputs.d.ts CHANGED Viewed

@@ -30,4 +30,16 @@ export interface LoadedToolInputs {
  * plus a per-tool load status list.
  */
 export declare function loadToolInputsForWorkflow(data: Record<string, unknown>, format: WorkflowFormat, cache: ToolCache, expansionOpts?: ExpansionOptions): Promise<LoadedToolInputs>;
+/**
+ * Resolve whether a conversion runs state-aware, and load the cache it needs.
+ *
+ * `stateful` is tri-state: `true` forces it on, `false` forces it off, and
+ * `undefined` — no flag — turns it on whenever the tool cache holds anything
+ * to resolve against. Returns the cache to convert with, or `null` to take
+ * the schema-free path.
+ */
+export declare function resolveConversionCache(opts: {
+    stateful?: boolean;
+    cacheDir?: string;
+}): Promise<ToolCache | null>;
 //# sourceMappingURL=stateful-tool-inputs.d.ts.map

package/dist/commands/stateful-tool-inputs.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"stateful-tool-inputs.d.ts","sourceRoot":"","sources":["../../src/commands/stateful-tool-inputs.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;GAaG;AACH,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AAExD,OAAO,EAIL,KAAK,gBAAgB,EAKrB,KAAK,kBAAkB,EAEvB,KAAK,cAAc,EACpB,MAAM,0BAA0B,CAAC;AAKlC,MAAM,WAAW,cAAc;IAC7B,MAAM,EAAE,MAAM,CAAC;IACf,WAAW,EAAE,MAAM,GAAG,IAAI,CAAC;IAC3B,MAAM,EAAE,OAAO,CAAC;IAChB,KAAK,CAAC,EAAE,MAAM,CAAC;CAChB;AAED,MAAM,WAAW,gBAAgB;IAC/B,QAAQ,EAAE,kBAAkB,CAAC;IAC7B,MAAM,EAAE,cAAc,EAAE,CAAC;CAC1B;AAMD;;;;GAIG;AACH,wBAAsB,yBAAyB,CAC7C,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC7B,MAAM,EAAE,cAAc,EACtB,KAAK,EAAE,SAAS,EAChB,aAAa,CAAC,EAAE,gBAAgB,GAC/B,OAAO,CAAC,gBAAgB,CAAC,CAyB3B;AA4CD;;;;;;;GAOG;AACH,wBAAsB,sBAAsB,CAAC,IAAI,EAAE;IACjD,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB,QAAQ,CAAC,EAAE,MAAM,CAAC;CACnB,GAAG,OAAO,CAAC,SAAS,GAAG,IAAI,CAAC,CAY5B"}

package/dist/commands/stateful-tool-inputs.js CHANGED Viewed

@@ -1,4 +1,5 @@
-import { expandedFormat2, expandedNative, } from "@galaxy-tool-util/schema";
+import { makeNodeToolCache } from "@galaxy-tool-util/core/node";
+import { expandedFormat2, expandedNative, isGalaxyUserToolRun, } from "@galaxy-tool-util/schema";
 import { isResolveError, resolveTool } from "./resolve-tool.js";
 function toolKey(toolId, version) {
     return `${toolId}\0${version ?? ""}`;
@@ -62,7 +63,7 @@ function collectFormat2ToolRefs(wf) {
                     refs.push([step.tool_id, step.tool_version ?? null]);
                 }
             }
-            if (step.run && typeof step.run === "object") {
+            if (step.run && typeof step.run === "object" && !isGalaxyUserToolRun(step.run)) {
                 walk(step.run.steps);
             }
         }
@@ -70,4 +71,25 @@ function collectFormat2ToolRefs(wf) {
     walk(wf.steps);
     return refs;
 }
+/**
+ * Resolve whether a conversion runs state-aware, and load the cache it needs.
+ *
+ * `stateful` is tri-state: `true` forces it on, `false` forces it off, and
+ * `undefined` — no flag — turns it on whenever the tool cache holds anything
+ * to resolve against. Returns the cache to convert with, or `null` to take
+ * the schema-free path.
+ */
+export async function resolveConversionCache(opts) {
+    if (opts.stateful === false)
+        return null;
+    const cache = makeNodeToolCache({ cacheDir: opts.cacheDir });
+    await cache.index.load();
+    if ((await cache.index.listAll()).length > 0)
+        return cache;
+    if (opts.stateful === true) {
+        console.warn("Tool cache is empty — stateful conversion will fall back for every step");
+        return cache;
+    }
+    return null;
+}
 //# sourceMappingURL=stateful-tool-inputs.js.map

package/dist/commands/stateful-tool-inputs.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/commands/url-resolver.d.ts CHANGED Viewed

@@ -3,7 +3,7 @@
  *
  * Handles:
  * - base64:// URLs: base64-decode inline content, parse as YAML/JSON
- * - TRS URLs (GA4GH pattern): fetch descriptor endpoint, extract `content`
+ * - TRS URLs (GA4GH pattern): fetch the `GALAXY` descriptor endpoint, extract `content`
  * - Plain HTTP/HTTPS URLs: fetch and parse based on content-type
  * - File paths (no ://): read from workflowDirectory
  *

package/dist/commands/url-resolver.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"url-resolver.d.ts","sourceRoot":"","sources":["../../src/commands/url-resolver.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;GAUG;AAKH,OAAO,~~EAAY~~,KAAK,WAAW,EAAE,MAAM,0BAA0B,CAAC;~~AAEtE~~,MAAM,WAAW,sBAAsB;IACrC,iEAAiE;IACjE,OAAO,CAAC,EAAE,OAAO,KAAK,CAAC;IACvB,6DAA6D;IAC7D,iBAAiB,CAAC,EAAE,MAAM,CAAC;CAC5B;AAED;;GAEG;AACH,wBAAgB,qBAAqB,CAAC,IAAI,GAAE,sBAA2B,GAAG,WAAW,~~CA2CpF~~"}
1	+ {"version":3,"file":"url-resolver.d.ts","sourceRoot":"","sources":["../../src/commands/url-resolver.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;GAUG;AAKH,OAAO,EAAoB,KAAK,WAAW,EAAE,MAAM,0BAA0B,CAAC;AAE9E,MAAM,WAAW,sBAAsB;IACrC,iEAAiE;IACjE,OAAO,CAAC,EAAE,OAAO,KAAK,CAAC;IACvB,6DAA6D;IAC7D,iBAAiB,CAAC,EAAE,MAAM,CAAC;CAC5B;AAED;;GAEG;AACH,wBAAgB,qBAAqB,CAAC,IAAI,GAAE,sBAA2B,GAAG,WAAW,CAsDpF"}

package/dist/commands/url-resolver.js CHANGED Viewed

@@ -3,7 +3,7 @@
  *
  * Handles:
  * - base64:// URLs: base64-decode inline content, parse as YAML/JSON
- * - TRS URLs (GA4GH pattern): fetch descriptor endpoint, extract `content`
+ * - TRS URLs (GA4GH pattern): fetch the `GALAXY` descriptor endpoint, extract `content`
  * - Plain HTTP/HTTPS URLs: fetch and parse based on content-type
  * - File paths (no ://): read from workflowDirectory
  *
@@ -12,7 +12,7 @@
 import { readFile } from "node:fs/promises";
 import { join } from "node:path";
 import * as yaml from "yaml";
-import { isTrsUrl } from "@galaxy-tool-util/schema";
+import { trsDescriptorUrl } from "@galaxy-tool-util/schema";
 /**
  * Create a default RefResolver that handles base64, TRS, HTTP, and file paths.
  */
@@ -28,15 +28,27 @@ export function createDefaultResolver(opts = {}) {
         }
         // URL — fetch via HTTP
         if (ref.includes("://")) {
-            const response = await fetcher(ref, {
+            const descriptorUrl = trsDescriptorUrl(ref);
+            const url = descriptorUrl ?? ref;
+            const source = descriptorUrl ? `${ref} (${descriptorUrl})` : ref;
+            const response = await fetcher(url, {
                 headers: { Accept: "application/json, application/x-yaml, text/yaml, */*" },
                 signal: AbortSignal.timeout(30_000),
             });
             if (!response.ok) {
-                throw new Error(`Failed to fetch ${ref}: ${response.status}`);
+                throw new Error(`Failed to fetch ${source}: ${response.status}`);
             }
-            if (isTrsUrl(ref)) {
-                const descriptor = (await response.json());
+            if (descriptorUrl) {
+                let descriptor;
+                try {
+                    descriptor = (await response.json());
+                }
+                catch {
+                    throw new Error(`TRS descriptor at ${source} is not JSON`);
+                }
+                if (typeof descriptor?.content !== "string") {
+                    throw new Error(`TRS descriptor at ${source} has no string 'content' field`);
+                }
                 return yaml.parse(descriptor.content);
             }
             const contentType = response.headers.get("content-type") ?? "";

package/dist/commands/url-resolver.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/commands/validate-workflow-json-schema.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"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 CHANGED Viewed

@@ -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, stripConnectedValues, 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);
@@ -362,11 +429,20 @@ 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);
@@ -379,7 +455,7 @@ async function _validateFormat2StepJsonSchema(step, stepLabel, toolId, toolVersi
         }
     }
     // Level 1: validate the stored, unlinked editor state.
-    const baseValidate = getOrBuildValidator(toolId, toolVersion, bundle, "workflow_step", toolSchemaDir);
+    const baseValidate = validators("workflow_step");
     if (!baseValidate) {
         return {
             step: stepLabel,
@@ -405,7 +481,7 @@ async function _validateFormat2StepJsonSchema(step, stepLabel, toolId, toolVersi
     const remaining = injectConnectionsIntoState(bundle.parameters, linkedState, connections, {
         linked: true,
     });
-    const unmatchedKeys = Object.keys(remaining);
+    const unmatchedKeys = unmatchedConnectionKeys(remaining, step.when);
     if (unmatchedKeys.length > 0) {
         return {
             step: stepLabel,
@@ -415,7 +491,7 @@ async function _validateFormat2StepJsonSchema(step, stepLabel, toolId, toolVersi
             errors: unmatchedKeys.map((k) => `No parameter definition matching connection key "${k}"`),
         };
     }
-    const linkedValidate = getOrBuildValidator(toolId, toolVersion, bundle, "workflow_step_linked", toolSchemaDir);
+    const linkedValidate = validators("workflow_step_linked");
     if (!linkedValidate) {
         return {
             step: stepLabel,

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

	@@ -1 +1 @@
1	- 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package/dist/commands/validate-workflow.d.ts.map CHANGED Viewed

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package/dist/commands/validate-workflow.js CHANGED Viewed

@@ -1,4 +1,4 @@
-import { createFieldModel, GalaxyWorkflowSchema, NativeGalaxyWorkflowSchema, expandedNative, expandedFormat2, injectConnectionsIntoState, stripConnectedValues, nativeConnectionsFromFormat2In, scanForReplacements, checkStrictEncoding, checkStrictStructure, withClass, scanToolState, buildSingleValidationReport, } from "@galaxy-tool-util/schema";
+import { createFieldModel, GalaxyWorkflowSchema, NativeGalaxyWorkflowSchema, expandedNative, expandedFormat2, injectConnectionsIntoState, stripConnectedValues, nativeConnectionsFromFormat2In, scanForReplacements, checkStrictEncoding, checkStrictStructure, withClass, scanToolState, isGalaxyUserToolRun, buildSingleValidationReport, } from "@galaxy-tool-util/schema";
 import * as ParseResult from "effect/ParseResult";
 import * as S from "effect/Schema";
 import { dirname } from "node:path";
@@ -9,6 +9,7 @@ import { readWorkflowFile, resolveFormat } from "./workflow-io.js";
 import { resolveStrictOptions } from "./strict-options.js";
 import { findStdoutSinkConflict, writeReportHtml } from "./report-output.js";
 import { buildConnectionReport } from "./connection-validation.js";
+import { embeddedToolDefinition, embeddedToolIdentity, isEmbeddedTool, resolveEmbeddedTool, } from "./embedded-tool.js";
 function formatIssues(error) {
     const issues = ParseResult.ArrayFormatter.formatErrorSync(error);
     return issues.map((i) => `${i.path.join(".")}: ${i.message}`);
@@ -125,6 +126,7 @@ export async function runValidateWorkflow(filePath, opts) {
         }
     }
     const stateOk = !results.some((r) => r.status === "fail");
+    const strictStateSkipped = strict.strictState && results.some((r) => r.status !== "ok" && r.status !== "fail");
     let connectionReport = null;
     if (opts.connections) {
         connectionReport = await buildConnectionReport(data, cache);
@@ -142,7 +144,7 @@ export async function runValidateWorkflow(filePath, opts) {
             console.log(JSON.stringify(report, null, 2));
         }
         await writeReportHtml("validate", report, opts.reportHtml);
-        process.exitCode = structOk && stateOk && connectionsOk ? 0 : 1;
+        process.exitCode = strictStateSkipped ? 2 : structOk && stateOk && connectionsOk ? 0 : 1;
         return;
     }
     if (results.length === 0) {
@@ -157,7 +159,7 @@ export async function runValidateWorkflow(filePath, opts) {
     if (connectionReport !== null)
         printConnectionReport(connectionReport);
     // --- strict state: promote skips to failures ---
-    if (strict.strictState && results.some((r) => r.status !== "ok" && r.status !== "fail")) {
+    if (strictStateSkipped) {
         console.error("Strict state: skipped steps not allowed");
         process.exitCode = 2;
         return;
@@ -207,6 +209,12 @@ async function _validateNativeWorkflow(wf, cache, prefix, service) {
             results.push(...subResults);
             continue;
         }
+        // An embedded definition wins over tool_id, matching connection validation.
+        const embedded = embeddedToolDefinition(step);
+        if (embedded) {
+            results.push(_validateEmbeddedNativeStep(step, stepLabel, embedded, cache));
+            continue;
+        }
         const toolId = step.tool_id;
         if (!toolId)
             continue;
@@ -240,7 +248,25 @@ async function _validateNativeStep(step, stepLabel, toolId, toolVersion, cache,
     const bundle = {
         parameters: resolved.tool.inputs,
     };
-    return _validateNativeState(bundle, step.tool_state, step.input_connections, stepLabel, toolId, toolVersion);
+    return _validateNativeState(bundle, step.tool_state, step.input_connections, stepLabel, toolId, toolVersion, step.when);
+}
+function _validateEmbeddedNativeStep(step, stepLabel, repr, cache) {
+    if (!cache)
+        return _stateValidationDisabled(stepLabel, repr);
+    const tool = resolveEmbeddedTool(repr, stepLabel);
+    if (!isEmbeddedTool(tool))
+        return tool;
+    return _validateNativeState(tool.bundle, step.tool_state, step.input_connections, stepLabel, tool.toolId, tool.toolVersion, step.when);
+}
+function _stateValidationDisabled(stepLabel, repr) {
+    const { toolId, toolVersion } = embeddedToolIdentity(repr);
+    return {
+        step: stepLabel,
+        tool_id: toolId,
+        version: toolVersion,
+        status: "skip_no_tool_state",
+        errors: ["tool state validation disabled"],
+    };
 }
 /**
  * Validate a native-encoded tool_state block against the `workflow_step_native`
@@ -249,7 +275,29 @@ async function _validateNativeStep(step, stepLabel, toolId, toolVersion, cache,
  * encoding (double-encoded scalars, inline ConnectedValue/RuntimeValue markers)
  * is identical regardless of workflow format, so the same model validates both.
  */
-function _validateNativeState(bundle, toolState, connections, stepLabel, toolId, toolVersion) {
+/**
+ * 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 _validateNativeState(bundle, toolState, connections, stepLabel, toolId, toolVersion, whenExpression) {
     // Skip validation if replacement parameters (${...}) are present in typed fields
     const replacementScan = scanForReplacements(bundle.parameters, toolState);
     if (replacementScan === "yes") {
@@ -263,7 +311,19 @@ function _validateNativeState(bundle, toolState, connections, stepLabel, toolId,
     }
     // Deep copy state and inject connection markers
     const state = structuredClone(toolState);
-    injectConnectionsIntoState(bundle.parameters, state, connections);
+    const remaining = injectConnectionsIntoState(bundle.parameters, state, connections);
+    // A connection key that matches no parameter is a defect whichever state block
+    // the step carries; the `state` path reports it below and this one must agree.
+    const unmatchedKeys = unmatchedConnectionKeys(remaining, whenExpression);
+    if (unmatchedKeys.length > 0) {
+        return {
+            step: stepLabel,
+            tool_id: toolId,
+            version: toolVersion,
+            status: "fail",
+            errors: unmatchedKeys.map((k) => `No parameter definition matching connection key "${k}"`),
+        };
+    }
     const fieldModel = createFieldModel(bundle, "workflow_step_native");
     if (!fieldModel) {
         return {
@@ -303,6 +363,10 @@ async function _validateFormat2Workflow(wf, cache, prefix, service) {
     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(_validateEmbeddedFormat2Step(step, stepLabel, step.run, cache));
+            continue;
+        }
         // Recurse into inline subworkflows
         if (step.run && typeof step.run === "object") {
             const subResults = await _validateFormat2Workflow(step.run, cache, `${stepLabel}.`, service);
@@ -342,12 +406,23 @@ async function _validateFormat2Step(step, stepLabel, toolId, toolVersion, cache,
     const bundle = {
         parameters: resolved.tool.inputs,
     };
+    return _validateFormat2State(bundle, step, stepLabel, toolId, toolVersion);
+}
+function _validateEmbeddedFormat2Step(step, stepLabel, repr, cache) {
+    if (!cache)
+        return _stateValidationDisabled(stepLabel, repr);
+    const tool = resolveEmbeddedTool(repr, stepLabel);
+    if (!isEmbeddedTool(tool))
+        return tool;
+    return _validateFormat2State(tool.bundle, step, stepLabel, tool.toolId, tool.toolVersion);
+}
+function _validateFormat2State(bundle, step, stepLabel, toolId, toolVersion) {
     // A step carries either a schema-aware `state` block or a verbatim native
     // `tool_state` block (gxformat2's state-unaware conversion copies the latter).
     // State shape — not workflow format — picks the validator: tool_state validates
     // through the native path, the same one native-body steps use.
     if (isEmptyState(step.state) && !isEmptyState(step.tool_state)) {
-        return _validateNativeState(bundle, step.tool_state, nativeConnectionsFromFormat2In(step.in), stepLabel, toolId, toolVersion);
+        return _validateNativeState(bundle, step.tool_state, nativeConnectionsFromFormat2In(step.in), stepLabel, toolId, toolVersion, step.when);
     }
     // Only the schema-aware `state` block is validatable. Deep-copy and strip
     // ConnectedValue markers left by $link normalization — these are captured in
@@ -386,7 +461,7 @@ async function _validateFormat2Step(step, stepLabel, toolId, toolVersion, cache,
     const remaining = injectConnectionsIntoState(bundle.parameters, linkedState, connections, {
         linked: true,
     });
-    const unmatchedKeys = Object.keys(remaining);
+    const unmatchedKeys = unmatchedConnectionKeys(remaining, step.when);
     if (unmatchedKeys.length > 0) {
         return {
             step: stepLabel,

package/dist/commands/validate-workflow.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/spec/build-program.js CHANGED Viewed

@@ -39,7 +39,9 @@ function validateSpec(spec, handlers) {
         if (!handlers[cmd.handler]) {
             throw new Error(`Missing handler "${cmd.handler}" for command "${cmd.name}"`);
         }
-        const seenOptions = new Set();
+        // A boolean may declare both `--foo` and `--no-foo`; they share one
+        // attribute name but are distinct flags, so track the two senses apart.
+        const seenOptions = new Map();
         const checkOptName = (flags) => {
             const optName = attributeNameFromFlags(flags);
             if (RESERVED_OPTION_NAMES.has(optName)) {
@@ -47,10 +49,16 @@ function validateSpec(spec, handlers) {
                     `--${optName} flag (it would silently trigger ${optName === "version" ? "the version" : "the help"} ` +
                     `action instead of binding). Rename it (e.g. --tool-version).`);
             }
-            if (seenOptions.has(optName)) {
+            const negated = isNegatedFlag(flags);
+            const senses = seenOptions.get(optName);
+            if (!senses) {
+                seenOptions.set(optName, new Set([negated]));
+                return;
+            }
+            if (senses.has(negated)) {
                 throw new Error(`Duplicate option "${optName}" on command "${cmd.name}"`);
             }
-            seenOptions.add(optName);
+            senses.add(negated);
         };
         for (const opt of cmd.options ?? [])
             checkOptName(opt.flags);
@@ -70,6 +78,11 @@ function validateSpec(spec, handlers) {
  * for duplicate detection here; commander itself owns the canonical
  * derivation at runtime.
  */
+/** True when the option's long flag is commander's `--no-` negation form. */
+function isNegatedFlag(flags) {
+    const long = flags.split(/[ ,|]+/).find((part) => part.startsWith("--"));
+    return long?.startsWith("--no-") ?? false;
+}
 function attributeNameFromFlags(flags) {
     const long = flags.split(/[ ,|]+/).find((part) => part.startsWith("--"));
     if (!long)

package/dist/spec/build-program.js.map CHANGED Viewed

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

@@ -1,6 +1,6 @@
 {
   "name": "@galaxy-tool-util/cli",
-  "version": "1.12.0",
+  "version": "1.14.0",
   "description": "galaxy-tool-cache CLI — cache and inspect Galaxy tool metadata",
   "type": "module",
   "bin": {
@@ -39,11 +39,11 @@
     "effect": "^3.21.0",
     "nunjucks": "^3.2.4",
     "yaml": "^2.8.3",
-    "@galaxy-tool-util/schema": "1.12.0",
-    "@galaxy-tool-util/connection-validation": "1.12.0",
-    "@galaxy-tool-util/core": "1.12.0",
-    "@galaxy-tool-util/search": "1.12.0",
-    "@galaxy-tool-util/tool-xml": "1.12.0"
+    "@galaxy-tool-util/core": "1.14.0",
+    "@galaxy-tool-util/schema": "1.14.0",
+    "@galaxy-tool-util/connection-validation": "1.14.0",
+    "@galaxy-tool-util/search": "1.14.0",
+    "@galaxy-tool-util/tool-xml": "1.14.0"
   },
   "devDependencies": {
     "@types/node": "^25.5.0",

package/spec/gxwf.json CHANGED Viewed

@@ -312,11 +312,15 @@
         },
         {
           "flags": "--stateful",
-          "description": "Use cached tool definitions for schema-aware state re-encoding"
+          "description": "Force schema-aware state re-encoding even if the tool cache is empty"
+        },
+        {
+          "flags": "--no-stateful",
+          "description": "Skip schema-aware state re-encoding; copy tool_state through verbatim"
         },
         {
           "flags": "--cache-dir <dir>",
-          "description": "Tool cache directory (for --stateful)"
+          "description": "Tool cache directory (default: schema-aware re-encoding when it is populated)"
         }
       ],
       "optionGroups": ["strict"]
@@ -596,11 +600,15 @@
         },
         {
           "flags": "--stateful",
-          "description": "Use cached tool definitions for schema-aware state re-encoding"
+          "description": "Force schema-aware state re-encoding even if the tool cache is empty"
+        },
+        {
+          "flags": "--no-stateful",
+          "description": "Skip schema-aware state re-encoding; copy tool_state through verbatim"
         },
         {
           "flags": "--cache-dir <dir>",
-          "description": "Tool cache directory (for --stateful)"
+          "description": "Tool cache directory (default: schema-aware re-encoding when it is populated)"
         }
       ],
       "optionGroups": ["strict"]