@galaxy-tool-util/cli 0.2.0 → 0.4.0

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

@@ -7,12 +7,13 @@
  *
  * 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 { makeNodeToolCache } from "@galaxy-tool-util/core/node";
+import { createFieldModel, GalaxyWorkflowSchema, NativeGalaxyWorkflowSchema, expandedNative, expandedFormat2, injectConnectionsIntoState, scanForReplacements, withClass, } 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 { buildSingleValidationReport } from "@galaxy-tool-util/schema";
 import { isResolveError, loadCachedTool } from "./resolve-tool.js";
 const Ajv = Ajv2020.default ?? Ajv2020;
 const ajv = new Ajv({ allErrors: true, strict: false });
@@ -110,73 +111,100 @@ function formatAjvErrors(validate) {
         return `${path}: ${e.message ?? "unknown error"}`;
     });
 }
+/**
+ * Validate workflow structure using the AJV-compiled JSON Schema (Draft 2020-12).
+ * Returns an array of error strings; empty if valid.
+ * Mirrors `decodeStructureErrors` but uses the AJV path instead of Effect decode.
+ */
+export function decodeStructureErrorsJsonSchema(data, format) {
+    const cls = format === "native" ? "NativeGalaxyWorkflow" : "GalaxyWorkflow";
+    const validationData = withClass(data, cls);
+    const structValidator = format === "native" ? nativeStructuralValidator() : format2StructuralValidator();
+    const ok = structValidator(validationData);
+    return ok ? [] : formatAjvErrors(structValidator);
+}
 // --- main entry point ---
-export async function runValidateWorkflowJsonSchema(data, format, opts, expansionOpts) {
+export async function runValidateWorkflowJsonSchema(filePath, 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 cls = format === "native" ? "NativeGalaxyWorkflow" : "GalaxyWorkflow";
+    const validationData = withClass(data, cls);
     const structValidator = format === "native" ? nativeStructuralValidator() : format2StructuralValidator();
     const structOk = structValidator(validationData);
+    const structureErrors = [];
     if (!structOk) {
-        console.error(`\nStructural validation errors (json-schema):`);
-        for (const line of formatAjvErrors(structValidator)) {
-            console.error(`  ${line}`);
+        structureErrors.push(...formatAjvErrors(structValidator));
+        if (!opts.json) {
+            console.error(`\nStructural validation errors (json-schema):`);
+            for (const line of structureErrors) {
+                console.error(`  ${line}`);
+            }
         }
     }
     else {
-        console.log(`Structural validation (json-schema): OK`);
+        if (!opts.json)
+            console.log(`Structural validation (json-schema): OK`);
     }
     // --- tool state validation ---
     if (opts.toolState === false) {
+        if (opts.json) {
+            const report = buildSingleValidationReport(filePath, [], {
+                structure_errors: structureErrors,
+            });
+            console.log(JSON.stringify(report, null, 2));
+        }
         process.exitCode = structOk ? 0 : 1;
         return;
     }
-    if (!structOk) {
+    if (!structOk && !opts.json) {
         process.exitCode = 1;
         return;
     }
-    const cache = new ToolCache({ cacheDir: opts.cacheDir });
+    const cache = makeNodeToolCache({ cacheDir: opts.cacheDir });
     await cache.index.load();
-    let results;
-    if (format === "native") {
-        results = await validateNativeStepsJsonSchema(data, cache, opts.toolSchemaDir, "", expansionOpts);
+    let results = [];
+    if (structOk) {
+        if (format === "native") {
+            results = await validateNativeStepsJsonSchema(data, cache, opts.toolSchemaDir, "", expansionOpts);
+        }
+        else {
+            results = await validateFormat2StepsJsonSchema(data, cache, opts.toolSchemaDir, "", expansionOpts);
+        }
     }
-    else {
-        results = await validateFormat2StepsJsonSchema(data, cache, opts.toolSchemaDir, "", expansionOpts);
+    const stateOk = !results.some((r) => 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;
+        return;
     }
     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") {
+        if (r.status === "skip_tool_not_found" || r.status === "skip_replacement_params") {
             skipped++;
-            console.warn(`  [${r.stepLabel}] skipped — ${r.errors[0] ?? "unknown"}`);
+            console.warn(`  [${r.step}] skipped — ${r.errors[0] ?? "unknown"}`);
         }
         else if (r.status === "fail") {
             validated++;
-            stateOk = false;
-            console.error(`  [${r.stepLabel}] tool_state errors (${r.toolId}):`);
+            console.error(`  [${r.step}] tool_state errors (${r.tool_id}):`);
             for (const line of r.errors) {
                 console.error(`    ${line}`);
             }
         }
         else {
             validated++;
-            console.log(`  [${r.stepLabel}] tool_state: OK`);
+            console.log(`  [${r.step}] tool_state: OK`);
         }
     }
     console.log(`\nTool state (json-schema): ${validated} validated, ${skipped} skipped`);
-    process.exitCode = stateOk ? 0 : 1;
+    process.exitCode = structOk && stateOk ? 0 : 1;
 }
 // --- Native validation (json-schema) ---
 export async function validateNativeStepsJsonSchema(data, cache, toolSchemaDir, prefix = "", expansionOpts) {
@@ -205,7 +233,13 @@ async function _validateNativeStepJsonSchema(step, stepLabel, toolId, toolVersio
     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] };
+        return {
+            step: stepLabel,
+            tool_id: toolId,
+            version: toolVersion,
+            status: "skip_tool_not_found",
+            errors: [reason],
+        };
     }
     const bundle = {
         parameters: resolved.tool.inputs,
@@ -213,10 +247,10 @@ async function _validateNativeStepJsonSchema(step, stepLabel, toolId, toolVersio
     const replacementScan = scanForReplacements(bundle.parameters, step.tool_state);
     if (replacementScan === "yes") {
         return {
-            stepLabel,
-            toolId,
-            toolVersion,
-            status: "skip",
+            step: stepLabel,
+            tool_id: toolId,
+            version: toolVersion,
+            status: "skip_replacement_params",
             errors: ["replacement parameters detected"],
         };
     }
@@ -229,18 +263,24 @@ async function _validateNativeStepJsonSchema(step, stepLabel, toolId, toolVersio
     const validate = getOrBuildValidator(toolId, toolVersion, bundle, "workflow_step_native", toolSchemaDir);
     if (!validate) {
         return {
-            stepLabel,
-            toolId,
-            toolVersion,
-            status: "skip",
+            step: stepLabel,
+            tool_id: toolId,
+            version: toolVersion,
+            status: "skip_tool_not_found",
             errors: ["unsupported parameter types"],
         };
     }
     const valid = validate(state);
     if (!valid) {
-        return { stepLabel, toolId, toolVersion, status: "fail", errors: formatAjvErrors(validate) };
+        return {
+            step: stepLabel,
+            tool_id: toolId,
+            version: toolVersion,
+            status: "fail",
+            errors: formatAjvErrors(validate),
+        };
     }
-    return { stepLabel, toolId, toolVersion, status: "ok", errors: [] };
+    return { step: stepLabel, tool_id: toolId, version: toolVersion, status: "ok", errors: [] };
 }
 // --- Format2 validation (json-schema) ---
 export async function validateFormat2StepsJsonSchema(data, cache, toolSchemaDir, prefix = "", expansionOpts) {
@@ -270,7 +310,13 @@ async function _validateFormat2StepJsonSchema(step, stepLabel, toolId, toolVersi
     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] };
+        return {
+            step: stepLabel,
+            tool_id: toolId,
+            version: toolVersion,
+            status: "skip_tool_not_found",
+            errors: [reason],
+        };
     }
     const bundle = {
         parameters: resolved.tool.inputs,
@@ -281,19 +327,19 @@ async function _validateFormat2StepJsonSchema(step, stepLabel, toolId, toolVersi
     const baseValidate = getOrBuildValidator(toolId, toolVersion, bundle, "workflow_step", toolSchemaDir);
     if (!baseValidate) {
         return {
-            stepLabel,
-            toolId,
-            toolVersion,
-            status: "skip",
+            step: stepLabel,
+            tool_id: toolId,
+            version: toolVersion,
+            status: "skip_tool_not_found",
             errors: ["unsupported parameter types"],
         };
     }
     const baseValid = baseValidate(state);
     if (!baseValid) {
         return {
-            stepLabel,
-            toolId,
-            toolVersion,
+            step: stepLabel,
+            tool_id: toolId,
+            version: toolVersion,
             status: "fail",
             errors: formatAjvErrors(baseValidate),
         };
@@ -313,9 +359,9 @@ async function _validateFormat2StepJsonSchema(step, stepLabel, toolId, toolVersi
         const unmatchedKeys = Object.keys(remaining);
         if (unmatchedKeys.length > 0) {
             return {
-                stepLabel,
-                toolId,
-                toolVersion,
+                step: stepLabel,
+                tool_id: toolId,
+                version: toolVersion,
                 status: "fail",
                 errors: unmatchedKeys.map((k) => `No parameter definition matching connection key "${k}"`),
             };
@@ -323,24 +369,24 @@ async function _validateFormat2StepJsonSchema(step, stepLabel, toolId, toolVersi
         const linkedValidate = getOrBuildValidator(toolId, toolVersion, bundle, "workflow_step_linked", toolSchemaDir);
         if (!linkedValidate) {
             return {
-                stepLabel,
-                toolId,
-                toolVersion,
-                status: "skip",
+                step: stepLabel,
+                tool_id: toolId,
+                version: toolVersion,
+                status: "skip_tool_not_found",
                 errors: ["unsupported parameter types"],
             };
         }
         const linkedValid = linkedValidate(linkedState);
         if (!linkedValid) {
             return {
-                stepLabel,
-                toolId,
-                toolVersion,
+                step: stepLabel,
+                tool_id: toolId,
+                version: toolVersion,
                 status: "fail",
                 errors: formatAjvErrors(linkedValidate),
             };
         }
     }
-    return { stepLabel, toolId, toolVersion, status: "ok", errors: [] };
+    return { step: stepLabel, tool_id: toolId, version: 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

@@ -1,22 +1,29 @@
-import { ToolCache } from "@galaxy-tool-util/core";
-import { type ExpansionOptions } from "@galaxy-tool-util/schema";
+import type { ToolCache } from "@galaxy-tool-util/core";
+import { type ExpansionOptions, type WorkflowFormat } from "@galaxy-tool-util/schema";
+import { type StrictOptions } from "./strict-options.js";
 export type { WorkflowFormat } from "@galaxy-tool-util/schema";
 export type ValidationMode = "effect" | "json-schema";
-export interface ValidateWorkflowOptions {
+export interface ValidateWorkflowOptions extends StrictOptions {
     format?: string;
     toolState?: boolean;
     cacheDir?: string;
     mode?: ValidationMode;
     toolSchemaDir?: string;
+    json?: boolean;
+    reportHtml?: string | boolean;
 }
-export interface StepValidationResult {
-    stepLabel: string;
-    toolId: string;
-    toolVersion: string | null;
-    status: "ok" | "fail" | "skip";
-    errors: string[];
-}
+/** Run Effect Schema decode on raw workflow data and return structural decode failures. */
+export declare function decodeStructureErrors(data: Record<string, unknown>, format: WorkflowFormat): string[];
+export type { ValidationStepResult as StepValidationResult } from "@galaxy-tool-util/schema";
+import type { ValidationStepResult as StepValidationResult } from "@galaxy-tool-util/schema";
 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[]>;
 export declare function validateFormat2Steps(data: Record<string, unknown>, cache: ToolCache, prefix?: string, expansionOpts?: ExpansionOptions): Promise<StepValidationResult[]>;
+/**
+ * Detect legacy parameter encoding in workflow tool_state fields.
+ *
+ * Scans each tool step's tool_state for legacy encoding signals
+ * (string-encoded containers, quoted select values) using scanToolState().
+ */
+export declare function detectEncodingErrors(data: Record<string, unknown>, cache: ToolCache, format: WorkflowFormat, expansionOpts?: ExpansionOptions): Promise<string[]>;
 //# sourceMappingURL=validate-workflow.d.ts.map

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

@@ -1 +1 @@
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