@galaxy-tool-util/cli 0.1.0

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

@@ -0,0 +1,313 @@
+/**
+ * JSON Schema-based workflow validation.
+ *
+ * Two-level validation using AJV Draft 2020-12:
+ *   Level 1 (structural): validates workflow dict against generated JSON Schema
+ *   Level 2 (per-step tool state): validates each step's state against tool-specific JSON Schema
+ *
+ * Mirrors Galaxy's validation_json_schema.py.
+ */
+import { ToolCache } from "@galaxy-tool-util/core";
+import { createFieldModel, GalaxyWorkflowSchema, NativeGalaxyWorkflowSchema, expandedNative, expandedFormat2, injectConnectionsIntoState, scanForReplacements, } from "@galaxy-tool-util/schema";
+import * as JSONSchema from "effect/JSONSchema";
+import Ajv2020 from "ajv/dist/2020.js";
+import { readFileSync, existsSync } from "node:fs";
+import { join } from "node:path";
+import { isResolveError, loadCachedTool } from "./resolve-tool.js";
+const Ajv = Ajv2020.default ?? Ajv2020;
+const ajv = new Ajv({ allErrors: true, strict: false });
+// --- structural schema cache (generated once) ---
+let _nativeStructValidator;
+let _format2StructValidator;
+function nativeStructuralValidator() {
+    if (!_nativeStructValidator) {
+        const schema = JSONSchema.make(NativeGalaxyWorkflowSchema, { target: "jsonSchema2020-12" });
+        _nativeStructValidator = ajv.compile(schema);
+    }
+    return _nativeStructValidator;
+}
+function format2StructuralValidator() {
+    if (!_format2StructValidator) {
+        const schema = JSONSchema.make(GalaxyWorkflowSchema, { target: "jsonSchema2020-12" });
+        _format2StructValidator = ajv.compile(schema);
+    }
+    return _format2StructValidator;
+}
+// --- tool state validator cache ---
+const _toolStateCache = new Map();
+// Recursively strip additionalProperties from a JSON Schema to match
+// the Effect decode behavior of onExcessProperty: "ignore".
+// Until we implement stale key cleaning (jmchilton/galaxy-tool-util-ts#5),
+// real workflows have extra keys that would fail strict validation.
+function stripAdditionalProperties(schema) {
+    if (schema === null || typeof schema !== "object")
+        return schema;
+    if (Array.isArray(schema))
+        return schema.map(stripAdditionalProperties);
+    const obj = schema;
+    const result = {};
+    for (const [key, value] of Object.entries(obj)) {
+        if (key === "additionalProperties")
+            continue;
+        result[key] = stripAdditionalProperties(value);
+    }
+    return result;
+}
+function toolStateCacheKey(toolId, toolVersion, representation) {
+    return `${toolId}@${toolVersion ?? ""}@${representation}`;
+}
+function buildToolStateValidator(bundle, representation) {
+    const effectSchema = createFieldModel(bundle, representation);
+    if (!effectSchema)
+        return null;
+    try {
+        const jsonSchema = JSONSchema.make(effectSchema, { target: "jsonSchema2020-12" });
+        const relaxed = stripAdditionalProperties(jsonSchema);
+        return ajv.compile(relaxed);
+    }
+    catch {
+        return null;
+    }
+}
+function loadToolStateValidatorFromDir(toolId, toolVersion, schemaDir) {
+    const safeId = toolId.replace(/\//g, "~");
+    const version = toolVersion ?? "_default_";
+    const toolDir = join(schemaDir, safeId);
+    let schemaPath = join(toolDir, `${version}.json`);
+    if (!existsSync(schemaPath)) {
+        schemaPath = join(toolDir, "_default_.json");
+    }
+    if (!existsSync(schemaPath))
+        return null;
+    try {
+        const raw = JSON.parse(readFileSync(schemaPath, "utf-8"));
+        return ajv.compile(raw);
+    }
+    catch {
+        return null;
+    }
+}
+function getOrBuildValidator(toolId, toolVersion, bundle, representation, toolSchemaDir) {
+    const key = toolStateCacheKey(toolId, toolVersion, representation);
+    if (_toolStateCache.has(key))
+        return _toolStateCache.get(key);
+    let validator = null;
+    if (toolSchemaDir) {
+        validator = loadToolStateValidatorFromDir(toolId, toolVersion, toolSchemaDir);
+    }
+    if (!validator) {
+        validator = buildToolStateValidator(bundle, representation);
+    }
+    _toolStateCache.set(key, validator);
+    return validator;
+}
+// --- AJV error formatting ---
+function formatAjvErrors(validate) {
+    if (!validate.errors)
+        return [];
+    return validate.errors.map((e) => {
+        const path = e.instancePath ? e.instancePath.replace(/\//g, ".").slice(1) : "(root)";
+        return `${path}: ${e.message ?? "unknown error"}`;
+    });
+}
+// --- main entry point ---
+export async function runValidateWorkflowJsonSchema(data, format, opts, expansionOpts) {
+    // --- structural validation ---
+    const validationData = { ...data };
+    if (format === "native" && !("class" in validationData)) {
+        validationData.class = "NativeGalaxyWorkflow";
+    }
+    else if (format === "format2" && !("class" in validationData)) {
+        validationData.class = "GalaxyWorkflow";
+    }
+    const structValidator = format === "native"
+        ? nativeStructuralValidator()
+        : format2StructuralValidator();
+    const structOk = structValidator(validationData);
+    if (!structOk) {
+        console.error(`\nStructural validation errors (json-schema):`);
+        for (const line of formatAjvErrors(structValidator)) {
+            console.error(`  ${line}`);
+        }
+    }
+    else {
+        console.log(`Structural validation (json-schema): OK`);
+    }
+    // --- tool state validation ---
+    if (opts.toolState === false) {
+        process.exitCode = structOk ? 0 : 1;
+        return;
+    }
+    if (!structOk) {
+        process.exitCode = 1;
+        return;
+    }
+    const cache = new ToolCache({ cacheDir: opts.cacheDir });
+    await cache.index.load();
+    let results;
+    if (format === "native") {
+        results = await validateNativeStepsJsonSchema(data, cache, opts.toolSchemaDir, "", expansionOpts);
+    }
+    else {
+        results = await validateFormat2StepsJsonSchema(data, cache, opts.toolSchemaDir, "", expansionOpts);
+    }
+    if (results.length === 0) {
+        console.log("No tool steps to validate state for.");
+        process.exitCode = 0;
+        return;
+    }
+    let stateOk = true;
+    let validated = 0;
+    let skipped = 0;
+    for (const r of results) {
+        if (r.status === "skip") {
+            skipped++;
+            console.warn(`  [${r.stepLabel}] skipped — ${r.errors[0] ?? "unknown"}`);
+        }
+        else if (r.status === "fail") {
+            validated++;
+            stateOk = false;
+            console.error(`  [${r.stepLabel}] tool_state errors (${r.toolId}):`);
+            for (const line of r.errors) {
+                console.error(`    ${line}`);
+            }
+        }
+        else {
+            validated++;
+            console.log(`  [${r.stepLabel}] tool_state: OK`);
+        }
+    }
+    console.log(`\nTool state (json-schema): ${validated} validated, ${skipped} skipped`);
+    process.exitCode = stateOk ? 0 : 1;
+}
+// --- Native validation (json-schema) ---
+export async function validateNativeStepsJsonSchema(data, cache, toolSchemaDir, prefix = "", expansionOpts) {
+    const expanded = await expandedNative(data, expansionOpts);
+    return _validateNativeWorkflowJsonSchema(expanded, cache, toolSchemaDir, prefix);
+}
+async function _validateNativeWorkflowJsonSchema(wf, cache, toolSchemaDir, prefix) {
+    const results = [];
+    for (const [key, step] of Object.entries(wf.steps)) {
+        const stepLabel = prefix ? `${prefix}${key}` : key;
+        if (step.type === "subworkflow" && step.subworkflow) {
+            const subResults = await _validateNativeWorkflowJsonSchema(step.subworkflow, cache, toolSchemaDir, `${stepLabel}.`);
+            results.push(...subResults);
+            continue;
+        }
+        const toolId = step.tool_id;
+        if (!toolId)
+            continue;
+        const toolVersion = step.tool_version ?? null;
+        const result = await _validateNativeStepJsonSchema(step, stepLabel, toolId, toolVersion, cache, toolSchemaDir);
+        results.push(result);
+    }
+    return results;
+}
+async function _validateNativeStepJsonSchema(step, stepLabel, toolId, toolVersion, cache, toolSchemaDir) {
+    const resolved = await loadCachedTool(cache, toolId, toolVersion);
+    if (isResolveError(resolved)) {
+        const reason = resolved.kind === "no_version"
+            ? `no version for ${toolId}`
+            : `${toolId} not in cache`;
+        return { stepLabel, toolId, toolVersion, status: "skip", errors: [reason] };
+    }
+    const bundle = {
+        parameters: resolved.tool.inputs,
+    };
+    const replacementScan = scanForReplacements(bundle.parameters, step.tool_state);
+    if (replacementScan === "yes") {
+        return { stepLabel, toolId, toolVersion, status: "skip", errors: ["replacement parameters detected"] };
+    }
+    const state = structuredClone(step.tool_state);
+    const connections = {};
+    for (const [k, v] of Object.entries(step.input_connections)) {
+        connections[k] = v;
+    }
+    injectConnectionsIntoState(bundle.parameters, state, connections);
+    const validate = getOrBuildValidator(toolId, toolVersion, bundle, "workflow_step_native", toolSchemaDir);
+    if (!validate) {
+        return { stepLabel, toolId, toolVersion, status: "skip", errors: ["unsupported parameter types"] };
+    }
+    const valid = validate(state);
+    if (!valid) {
+        return { stepLabel, toolId, toolVersion, status: "fail", errors: formatAjvErrors(validate) };
+    }
+    return { stepLabel, toolId, toolVersion, status: "ok", errors: [] };
+}
+// --- Format2 validation (json-schema) ---
+export async function validateFormat2StepsJsonSchema(data, cache, toolSchemaDir, prefix = "", expansionOpts) {
+    const expanded = await expandedFormat2(data, expansionOpts);
+    return _validateFormat2WorkflowJsonSchema(expanded, cache, toolSchemaDir, prefix);
+}
+async function _validateFormat2WorkflowJsonSchema(wf, cache, toolSchemaDir, prefix) {
+    const results = [];
+    for (let i = 0; i < wf.steps.length; i++) {
+        const step = wf.steps[i];
+        const stepLabel = prefix ? `${prefix}${i}` : String(i);
+        if (step.run && typeof step.run === "object") {
+            const subResults = await _validateFormat2WorkflowJsonSchema(step.run, cache, toolSchemaDir, `${stepLabel}.`);
+            results.push(...subResults);
+            continue;
+        }
+        const toolId = step.tool_id;
+        if (!toolId)
+            continue;
+        const toolVersion = step.tool_version ?? null;
+        const result = await _validateFormat2StepJsonSchema(step, stepLabel, toolId, toolVersion, cache, toolSchemaDir);
+        results.push(result);
+    }
+    return results;
+}
+async function _validateFormat2StepJsonSchema(step, stepLabel, toolId, toolVersion, cache, toolSchemaDir) {
+    const resolved = await loadCachedTool(cache, toolId, toolVersion);
+    if (isResolveError(resolved)) {
+        const reason = resolved.kind === "no_version"
+            ? `no version for ${toolId}`
+            : `${toolId} not in cache`;
+        return { stepLabel, toolId, toolVersion, status: "skip", errors: [reason] };
+    }
+    const bundle = {
+        parameters: resolved.tool.inputs,
+    };
+    const rawState = step.state ?? step.tool_state ?? {};
+    const state = rawState;
+    // Level 1: base validation against workflow_step
+    const baseValidate = getOrBuildValidator(toolId, toolVersion, bundle, "workflow_step", toolSchemaDir);
+    if (!baseValidate) {
+        return { stepLabel, toolId, toolVersion, status: "skip", errors: ["unsupported parameter types"] };
+    }
+    const baseValid = baseValidate(state);
+    if (!baseValid) {
+        return { stepLabel, toolId, toolVersion, status: "fail", 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: linked validation with connections injected
+    if (Object.keys(connections).length > 0) {
+        const linkedState = structuredClone(state);
+        const remaining = injectConnectionsIntoState(bundle.parameters, linkedState, connections);
+        const unmatchedKeys = Object.keys(remaining);
+        if (unmatchedKeys.length > 0) {
+            return {
+                stepLabel, toolId, toolVersion, status: "fail",
+                errors: unmatchedKeys.map((k) => `No parameter definition matching connection key "${k}"`),
+            };
+        }
+        const linkedValidate = getOrBuildValidator(toolId, toolVersion, bundle, "workflow_step_linked", toolSchemaDir);
+        if (!linkedValidate) {
+            return { stepLabel, toolId, toolVersion, status: "skip", errors: ["unsupported parameter types"] };
+        }
+        const linkedValid = linkedValidate(linkedState);
+        if (!linkedValid) {
+            return { stepLabel, toolId, toolVersion, status: "fail", errors: formatAjvErrors(linkedValidate) };
+        }
+    }
+    return { stepLabel, toolId, toolVersion, status: "ok", errors: [] };
+}
+//# sourceMappingURL=validate-workflow-json-schema.js.map

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

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package/dist/commands/validate-workflow.d.ts

@@ -0,0 +1,21 @@
+import { ToolCache } from "@galaxy-tool-util/core";
+import { type ExpansionOptions } from "@galaxy-tool-util/schema";
+export type { WorkflowFormat } from "@galaxy-tool-util/schema";
+export type ValidationMode = "effect" | "json-schema";
+export interface ValidateWorkflowOptions {
+    format?: string;
+    toolState?: boolean;
+    cacheDir?: string;
+    mode?: ValidationMode;
+    toolSchemaDir?: string;
+}
+export interface StepValidationResult {
+    stepLabel: string;
+    toolId: string;
+    toolVersion: string | null;
+    status: "ok" | "fail" | "skip";
+    errors: string[];
+}
+export declare function runValidateWorkflow(filePath: string, opts: ValidateWorkflowOptions): Promise<void>;
+export declare function validateNativeSteps(data: Record<string, unknown>, cache: ToolCache, prefix?: string, expansionOpts?: ExpansionOptions): Promise<StepValidationResult[]>;
+//# sourceMappingURL=validate-workflow.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"validate-workflow.d.ts","sourceRoot":"","sources":["../../src/commands/validate-workflow.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AACnD,OAAO,EAeL,KAAK,gBAAgB,EAEtB,MAAM,0BAA0B,CAAC;AASlC,YAAY,EAAE,cAAc,EAAE,MAAM,0BAA0B,CAAC;AAE/D,MAAM,MAAM,cAAc,GAAG,QAAQ,GAAG,aAAa,CAAC;AAEtD,MAAM,WAAW,uBAAuB;IACtC,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,SAAS,CAAC,EAAE,OAAO,CAAC;IACpB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,IAAI,CAAC,EAAE,cAAc,CAAC;IACtB,aAAa,CAAC,EAAE,MAAM,CAAC;CACxB;AAOD,MAAM,WAAW,oBAAoB;IACnC,SAAS,EAAE,MAAM,CAAC;IAClB,MAAM,EAAE,MAAM,CAAC;IACf,WAAW,EAAE,MAAM,GAAG,IAAI,CAAC;IAC3B,MAAM,EAAE,IAAI,GAAG,MAAM,GAAG,MAAM,CAAC;IAC/B,MAAM,EAAE,MAAM,EAAE,CAAC;CAClB;AAED,wBAAsB,mBAAmB,CACvC,QAAQ,EAAE,MAAM,EAChB,IAAI,EAAE,uBAAuB,GAC5B,OAAO,CAAC,IAAI,CAAC,CAwGf;AAID,wBAAsB,mBAAmB,CACvC,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC7B,KAAK,EAAE,SAAS,EAChB,MAAM,SAAK,EACX,aAAa,CAAC,EAAE,gBAAgB,GAC/B,OAAO,CAAC,oBAAoB,EAAE,CAAC,CAGjC"}

package/dist/commands/validate-workflow.js

@@ -0,0 +1,257 @@
+import { ToolCache } from "@galaxy-tool-util/core";
+import { createFieldModel, detectFormat, GalaxyWorkflowSchema, NativeGalaxyWorkflowSchema, expandedNative, expandedFormat2, injectConnectionsIntoState, stripConnectedValues, scanForReplacements, } from "@galaxy-tool-util/schema";
+import * as ParseResult from "effect/ParseResult";
+import * as S from "effect/Schema";
+import { readFile } from "node:fs/promises";
+import { dirname } from "node:path";
+import * as YAML from "yaml";
+import { isResolveError, loadCachedTool } from "./resolve-tool.js";
+import { createDefaultResolver } from "./url-resolver.js";
+function formatIssues(error) {
+    const issues = ParseResult.ArrayFormatter.formatErrorSync(error);
+    return issues.map((i) => `${i.path.join(".")}: ${i.message}`);
+}
+export async function runValidateWorkflow(filePath, opts) {
+    const raw = await readFile(filePath, "utf-8");
+    let data;
+    try {
+        if (filePath.endsWith(".ga") || filePath.endsWith(".json")) {
+            data = JSON.parse(raw);
+        }
+        else {
+            data = YAML.parse(raw);
+        }
+    }
+    catch (e) {
+        const msg = e instanceof Error ? e.message : String(e);
+        console.error(`Failed to parse ${filePath}: ${msg}`);
+        process.exitCode = 1;
+        return;
+    }
+    const format = opts.format === "native" || opts.format === "format2"
+        ? opts.format
+        : detectFormat(data);
+    const mode = opts.mode === "json-schema" ? "json-schema" : "effect";
+    console.log(`Detected format: ${format}, mode: ${mode}`);
+    // Build expansion options for resolving external subworkflow references
+    const workflowDirectory = dirname(filePath);
+    const expansionOpts = {
+        resolver: createDefaultResolver({ workflowDirectory }),
+    };
+    if (mode === "json-schema") {
+        const { runValidateWorkflowJsonSchema } = await import("./validate-workflow-json-schema.js");
+        return runValidateWorkflowJsonSchema(data, format, opts, expansionOpts);
+    }
+    // --- structural validation (effect mode) ---
+    const validationData = { ...data };
+    if (format === "native" && !("class" in validationData)) {
+        validationData.class = "NativeGalaxyWorkflow";
+    }
+    else if (format === "format2" && !("class" in validationData)) {
+        validationData.class = "GalaxyWorkflow";
+    }
+    const schema = format === "native" ? NativeGalaxyWorkflowSchema : GalaxyWorkflowSchema;
+    const decode = S.decodeUnknownEither(schema, { onExcessProperty: "ignore" });
+    const structResult = decode(validationData);
+    let structOk = true;
+    if (structResult._tag === "Left") {
+        structOk = false;
+        console.error(`\nStructural validation errors:`);
+        for (const line of formatIssues(structResult.left)) {
+            console.error(`  ${line}`);
+        }
+    }
+    else {
+        console.log(`Structural validation: OK`);
+    }
+    // --- tool state validation (effect mode) ---
+    if (opts.toolState === false) {
+        process.exitCode = structOk ? 0 : 1;
+        return;
+    }
+    const cache = new ToolCache({ cacheDir: opts.cacheDir });
+    await cache.index.load();
+    let results;
+    if (format === "native") {
+        results = await validateNativeSteps(data, cache, "", expansionOpts);
+    }
+    else {
+        results = await validateFormat2Steps(data, cache, "", expansionOpts);
+    }
+    if (results.length === 0) {
+        console.log("No tool steps to validate state for.");
+        process.exitCode = structOk ? 0 : 1;
+        return;
+    }
+    let stateOk = true;
+    let validated = 0;
+    let skipped = 0;
+    for (const r of results) {
+        if (r.status === "skip") {
+            skipped++;
+            console.warn(`  [${r.stepLabel}] skipped — ${r.errors[0] ?? "unknown"}`);
+        }
+        else if (r.status === "fail") {
+            validated++;
+            stateOk = false;
+            console.error(`  [${r.stepLabel}] tool_state errors (${r.toolId}):`);
+            for (const line of r.errors) {
+                console.error(`    ${line}`);
+            }
+        }
+        else {
+            validated++;
+            console.log(`  [${r.stepLabel}] tool_state: OK`);
+        }
+    }
+    console.log(`\nTool state: ${validated} validated, ${skipped} skipped`);
+    process.exitCode = structOk && stateOk ? 0 : 1;
+}
+// --- Native validation ---
+export async function validateNativeSteps(data, cache, prefix = "", expansionOpts) {
+    const expanded = await expandedNative(data, expansionOpts);
+    return _validateNativeWorkflow(expanded, cache, prefix);
+}
+async function _validateNativeWorkflow(wf, cache, prefix) {
+    const results = [];
+    for (const [key, step] of Object.entries(wf.steps)) {
+        const stepLabel = prefix ? `${prefix}${key}` : key;
+        // Recurse into subworkflows
+        if (step.type === "subworkflow" && step.subworkflow) {
+            const subResults = await _validateNativeWorkflow(step.subworkflow, cache, `${stepLabel}.`);
+            results.push(...subResults);
+            continue;
+        }
+        const toolId = step.tool_id;
+        if (!toolId)
+            continue;
+        const toolVersion = step.tool_version ?? null;
+        const result = await _validateNativeStep(step, stepLabel, toolId, toolVersion, cache);
+        results.push(result);
+    }
+    return results;
+}
+async function _validateNativeStep(step, stepLabel, toolId, toolVersion, cache) {
+    const resolved = await loadCachedTool(cache, toolId, toolVersion);
+    if (isResolveError(resolved)) {
+        const reason = resolved.kind === "no_version"
+            ? `no version for ${toolId}`
+            : `${toolId} not in cache`;
+        return { stepLabel, toolId, toolVersion, status: "skip", errors: [reason] };
+    }
+    const bundle = {
+        parameters: resolved.tool.inputs,
+    };
+    // Skip validation if replacement parameters (${...}) are present in typed fields
+    const replacementScan = scanForReplacements(bundle.parameters, step.tool_state);
+    if (replacementScan === "yes") {
+        return { stepLabel, toolId, toolVersion, status: "skip", errors: ["replacement parameters detected"] };
+    }
+    // Deep copy state and inject connection markers
+    const state = structuredClone(step.tool_state);
+    const connections = {};
+    for (const [key, val] of Object.entries(step.input_connections)) {
+        connections[key] = val;
+    }
+    injectConnectionsIntoState(bundle.parameters, state, connections);
+    // Validate against workflow_step_native schema
+    const fieldModel = createFieldModel(bundle, "workflow_step_native");
+    if (!fieldModel) {
+        return { stepLabel, toolId, toolVersion, status: "skip", errors: ["unsupported parameter types"] };
+    }
+    const validate = S.decodeUnknownEither(fieldModel, {
+        onExcessProperty: "ignore",
+    });
+    const result = validate(state);
+    if (result._tag === "Left") {
+        return { stepLabel, toolId, toolVersion, status: "fail", errors: formatIssues(result.left) };
+    }
+    return { stepLabel, toolId, toolVersion, status: "ok", errors: [] };
+}
+// --- Format2 validation ---
+async function validateFormat2Steps(data, cache, prefix = "", expansionOpts) {
+    const expanded = await expandedFormat2(data, expansionOpts);
+    return _validateFormat2Workflow(expanded, cache, prefix);
+}
+async function _validateFormat2Workflow(wf, cache, prefix) {
+    const results = [];
+    for (let i = 0; i < wf.steps.length; i++) {
+        const step = wf.steps[i];
+        const stepLabel = prefix ? `${prefix}${i}` : String(i);
+        // Recurse into inline subworkflows
+        if (step.run && typeof step.run === "object") {
+            const subResults = await _validateFormat2Workflow(step.run, cache, `${stepLabel}.`);
+            results.push(...subResults);
+            continue;
+        }
+        const toolId = step.tool_id;
+        if (!toolId)
+            continue;
+        const toolVersion = step.tool_version ?? null;
+        const result = await _validateFormat2Step(step, stepLabel, toolId, toolVersion, cache);
+        results.push(result);
+    }
+    return results;
+}
+async function _validateFormat2Step(step, stepLabel, toolId, toolVersion, cache) {
+    const resolved = await loadCachedTool(cache, toolId, toolVersion);
+    if (isResolveError(resolved)) {
+        const reason = resolved.kind === "no_version"
+            ? `no version for ${toolId}`
+            : `${toolId} not in cache`;
+        return { stepLabel, toolId, toolVersion, status: "skip", errors: [reason] };
+    }
+    const bundle = {
+        parameters: resolved.tool.inputs,
+    };
+    // Get state from step.state or step.tool_state.
+    // Deep-copy and strip ConnectedValue markers left by $link normalization —
+    // these are captured in step.in and will be injected during linked validation.
+    const state = structuredClone((step.state ?? step.tool_state ?? {}));
+    stripConnectedValues(bundle.parameters, state);
+    // Level 1: Validate base state against workflow_step
+    const baseModel = createFieldModel(bundle, "workflow_step");
+    if (!baseModel) {
+        return { stepLabel, toolId, toolVersion, status: "skip", errors: ["unsupported parameter types"] };
+    }
+    const baseValidate = S.decodeUnknownEither(baseModel, {
+        onExcessProperty: "ignore",
+    });
+    const baseResult = baseValidate(state);
+    if (baseResult._tag === "Left") {
+        return { stepLabel, toolId, toolVersion, status: "fail", errors: formatIssues(baseResult.left) };
+    }
+    // Build connections dict from step.in entries
+    const connections = {};
+    for (const stepInput of step.in) {
+        if (stepInput.id && stepInput.source) {
+            const src = stepInput.source;
+            connections[stepInput.id] = Array.isArray(src) ? src : [src];
+        }
+    }
+    // Level 2: Validate with connections injected against workflow_step_linked
+    if (Object.keys(connections).length > 0) {
+        const linkedState = structuredClone(state);
+        const remaining = injectConnectionsIntoState(bundle.parameters, linkedState, connections);
+        const unmatchedKeys = Object.keys(remaining);
+        if (unmatchedKeys.length > 0) {
+            return {
+                stepLabel, toolId, toolVersion, status: "fail",
+                errors: unmatchedKeys.map((k) => `No parameter definition matching connection key "${k}"`),
+            };
+        }
+        const linkedModel = createFieldModel(bundle, "workflow_step_linked");
+        if (!linkedModel) {
+            return { stepLabel, toolId, toolVersion, status: "skip", errors: ["unsupported parameter types"] };
+        }
+        const linkedValidate = S.decodeUnknownEither(linkedModel, {
+            onExcessProperty: "ignore",
+        });
+        const linkedResult = linkedValidate(linkedState);
+        if (linkedResult._tag === "Left") {
+            return { stepLabel, toolId, toolVersion, status: "fail", errors: formatIssues(linkedResult.left) };
+        }
+    }
+    return { stepLabel, toolId, toolVersion, status: "ok", errors: [] };
+}
+//# sourceMappingURL=validate-workflow.js.map

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

@@ -0,0 +1 @@
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package/dist/index.d.ts

@@ -0,0 +1,19 @@
+/**
+ * @module @galaxy-tool-util/cli
+ *
+ * CLI command implementations for `galaxy-tool-cache`.
+ * Each function corresponds to a CLI subcommand and can also be called programmatically.
+ */
+/** Fetch a tool from ToolShed/Galaxy and save to the local cache. */
+export { runAdd } from "./commands/add.js";
+/** List all tools in the local cache. */
+export { runList } from "./commands/list.js";
+/** Display metadata for a cached tool. */
+export { runInfo } from "./commands/info.js";
+/** Clear cached tools, optionally filtered by ID prefix. */
+export { runClear } from "./commands/clear.js";
+/** Export a JSON Schema for a cached tool's parameters at a given state representation. */
+export { runSchema } from "./commands/schema.js";
+/** Validate a Galaxy workflow file (structure + optional tool state). */
+export { runValidateWorkflow } from "./commands/validate-workflow.js";
+//# sourceMappingURL=index.d.ts.map