@galaxy-tool-util/cli 0.2.0 → 0.4.0

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

@@ -1 +1 @@
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package/dist/commands/render-results.d.ts

@@ -1,11 +1,11 @@
 /**
- * Shared rendering for StepValidationResult arrays.
+ * Shared rendering for ValidationStepResult arrays.
  */
-import type { StepValidationResult } from "./validate-workflow.js";
+import { type ValidationStepResult } from "@galaxy-tool-util/schema";
 export interface RenderSummary {
     validated: number;
     skipped: number;
 }
 /** Render step validation results to console, returning counts. */
-export declare function renderStepResults(results: StepValidationResult[]): RenderSummary;
+export declare function renderStepResults(results: ValidationStepResult[]): RenderSummary;
 //# sourceMappingURL=render-results.d.ts.map

package/dist/commands/render-results.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"render-results.d.ts","sourceRoot":"","sources":["../../src/commands/render-results.ts"],"names":[],"mappings":"AAAA;;GAEG;AACH,OAAO,EAAiB,KAAK,oBAAoB,EAAE,MAAM,0BAA0B,CAAC;AAEpF,MAAM,WAAW,aAAa;IAC5B,SAAS,EAAE,MAAM,CAAC;IAClB,OAAO,EAAE,MAAM,CAAC;CACjB;AAED,mEAAmE;AACnE,wBAAgB,iBAAiB,CAAC,OAAO,EAAE,oBAAoB,EAAE,GAAG,aAAa,CAiBhF"}

package/dist/commands/render-results.js

@@ -1,21 +1,25 @@
+/**
+ * Shared rendering for ValidationStepResult arrays.
+ */
+import { SKIP_STATUSES } from "@galaxy-tool-util/schema";
 /** Render step validation results to console, returning counts. */
 export function renderStepResults(results) {
     let validated = 0;
     let skipped = 0;
     for (const r of results) {
-        if (r.status === "skip") {
+        if (SKIP_STATUSES.has(r.status)) {
             skipped++;
-            console.warn(`  [${r.stepLabel}] skipped — ${r.errors[0] ?? "unknown"}`);
+            console.warn(`  [${r.step}] skipped — ${r.errors[0] ?? "unknown"}`);
         }
         else if (r.status === "fail") {
             validated++;
-            console.error(`  [${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`);
         }
     }
     return { validated, skipped };

package/dist/commands/render-results.js.map

@@ -1 +1 @@
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+{"version":3,"file":"render-results.js","sourceRoot":"","sources":["../../src/commands/render-results.ts"],"names":[],"mappings":"AAAA;;GAEG;AACH,OAAO,EAAE,aAAa,EAA6B,MAAM,0BAA0B,CAAC;AAOpF,mEAAmE;AACnE,MAAM,UAAU,iBAAiB,CAAC,OAA+B;IAC/D,IAAI,SAAS,GAAG,CAAC,CAAC;IAClB,IAAI,OAAO,GAAG,CAAC,CAAC;IAChB,KAAK,MAAM,CAAC,IAAI,OAAO,EAAE,CAAC;QACxB,IAAI,aAAa,CAAC,GAAG,CAAC,CAAC,CAAC,MAAM,CAAC,EAAE,CAAC;YAChC,OAAO,EAAE,CAAC;YACV,OAAO,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,IAAI,eAAe,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,IAAI,SAAS,EAAE,CAAC,CAAC;QACtE,CAAC;aAAM,IAAI,CAAC,CAAC,MAAM,KAAK,MAAM,EAAE,CAAC;YAC/B,SAAS,EAAE,CAAC;YACZ,OAAO,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,IAAI,wBAAwB,CAAC,CAAC,OAAO,IAAI,CAAC,CAAC;YACjE,KAAK,MAAM,IAAI,IAAI,CAAC,CAAC,MAAM;gBAAE,OAAO,CAAC,KAAK,CAAC,OAAO,IAAI,EAAE,CAAC,CAAC;QAC5D,CAAC;aAAM,CAAC;YACN,SAAS,EAAE,CAAC;YACZ,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC,IAAI,kBAAkB,CAAC,CAAC;QAC9C,CAAC;IACH,CAAC;IACD,OAAO,EAAE,SAAS,EAAE,OAAO,EAAE,CAAC;AAChC,CAAC"}

package/dist/commands/report-output.d.ts

@@ -0,0 +1,34 @@
+export type ReportType = "validate" | "lint" | "clean" | "validate-tree" | "lint-tree" | "clean-tree" | "roundtrip-tree";
+export interface ReportOutputOptions {
+    /**
+     * Path to write Markdown report to. Commander sets this to `true` (boolean)
+     * when `--report-markdown` is passed without a filename — treat as stdout.
+     * Use `"-"` explicitly to write to stdout.
+     */
+    reportMarkdown?: string | boolean;
+    /** Same semantics as reportMarkdown but for HTML output. */
+    reportHtml?: string | boolean;
+}
+/**
+ * Render and write report output if --report-markdown / --report-html flags
+ * were passed. Both can be specified simultaneously.
+ *
+ * @param templateName - e.g. "validate_tree.md.j2"
+ * @param report - the tree report object
+ * @param opts - parsed CLI options
+ */
+export declare function writeReportOutput(templateName: string, report: unknown, opts: ReportOutputOptions): Promise<void>;
+/**
+ * Generate a standalone HTML page that loads the gxwf-report-shell IIFE
+ * bundle from CDN and renders the given report data.
+ *
+ * The resulting HTML is self-contained (aside from the CDN network request).
+ * Use this for --report-html on single-workflow and tree commands.
+ */
+export declare function buildReportHtml(type: ReportType, data: unknown, title?: string): string;
+/**
+ * Write an HTML report to the given destination if set.
+ * dest follows the same string | boolean convention as reportHtml/reportMarkdown.
+ */
+export declare function writeReportHtml(type: ReportType, data: unknown, dest: string | boolean | undefined, title?: string): Promise<void>;
+//# sourceMappingURL=report-output.d.ts.map

package/dist/commands/report-output.d.ts.map

@@ -0,0 +1 @@
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package/dist/commands/report-output.js

@@ -0,0 +1,70 @@
+/**
+ * Helpers for writing Markdown/HTML rendered reports from CLI commands.
+ */
+import { writeFile } from "node:fs/promises";
+import { renderReport } from "../workflow/report-templates.js";
+// Pin to a specific published gxwf-report-shell version.
+// Bump when a new shell version with user-visible changes is released to npm.
+const SHELL_CDN_VERSION = "0.1.0";
+const SHELL_CDN_BASE = `https://cdn.jsdelivr.net/npm/@galaxy-tool-util/gxwf-report-shell@${SHELL_CDN_VERSION}/dist`;
+/**
+ * Render and write report output if --report-markdown / --report-html flags
+ * were passed. Both can be specified simultaneously.
+ *
+ * @param templateName - e.g. "validate_tree.md.j2"
+ * @param report - the tree report object
+ * @param opts - parsed CLI options
+ */
+export async function writeReportOutput(templateName, report, opts) {
+    const dest = opts.reportMarkdown;
+    if (!dest)
+        return;
+    const content = await renderReport(templateName, report);
+    // Commander sets dest = true when flag is passed without a filename argument
+    if (dest === true || dest === "-") {
+        process.stdout.write(content);
+    }
+    else {
+        await writeFile(dest, content, "utf-8");
+    }
+}
+/**
+ * Generate a standalone HTML page that loads the gxwf-report-shell IIFE
+ * bundle from CDN and renders the given report data.
+ *
+ * The resulting HTML is self-contained (aside from the CDN network request).
+ * Use this for --report-html on single-workflow and tree commands.
+ */
+export function buildReportHtml(type, data, title = "gxwf Report") {
+    const payload = JSON.stringify({ type, data });
+    return `<!DOCTYPE html>
+<html lang="en">
+<head>
+  <meta charset="UTF-8">
+  <meta name="viewport" content="width=device-width, initial-scale=1.0">
+  <title>${title}</title>
+  <link rel="stylesheet" href="${SHELL_CDN_BASE}/shell.css">
+</head>
+<body>
+  <div id="gxwf-report"></div>
+  <script>window.__GXWF_REPORT__ = ${payload};</script>
+  <script src="${SHELL_CDN_BASE}/shell.iife.js"></script>
+</body>
+</html>`;
+}
+/**
+ * Write an HTML report to the given destination if set.
+ * dest follows the same string | boolean convention as reportHtml/reportMarkdown.
+ */
+export async function writeReportHtml(type, data, dest, title) {
+    if (!dest)
+        return;
+    const content = buildReportHtml(type, data, title);
+    if (dest === true || dest === "-") {
+        process.stdout.write(content);
+    }
+    else {
+        await writeFile(dest, content, "utf-8");
+    }
+}
+//# sourceMappingURL=report-output.js.map

package/dist/commands/report-output.js.map

@@ -0,0 +1 @@
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package/dist/commands/resolve-tool.js

@@ -7,7 +7,7 @@ export async function loadCachedTool(cache, toolId, version) {
     if (coords.version === null) {
         return { kind: "no_version", toolId };
     }
-    const key = cacheKey(coords.toolshedUrl, coords.trsToolId, coords.version);
+    const key = await cacheKey(coords.toolshedUrl, coords.trsToolId, coords.version);
     const tool = await cache.loadCached(key);
     if (tool === null) {
         return { kind: "not_cached", toolId, key };

package/dist/commands/resolve-tool.js.map

@@ -1 +1 @@
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+{"version":3,"file":"resolve-tool.js","sourceRoot":"","sources":["../../src/commands/resolve-tool.ts"],"names":[],"mappings":"AAAA,OAAO,EAAkB,QAAQ,EAAmB,MAAM,wBAAwB,CAAC;AAWnF,MAAM,UAAU,cAAc,CAAC,CAA8B;IAC3D,OAAO,MAAM,IAAI,CAAC,CAAC;AACrB,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,cAAc,CAClC,KAAgB,EAChB,MAAc,EACd,OAAuB;IAEvB,MAAM,MAAM,GAAG,KAAK,CAAC,sBAAsB,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;IAC7D,IAAI,MAAM,CAAC,OAAO,KAAK,IAAI,EAAE,CAAC;QAC5B,OAAO,EAAE,IAAI,EAAE,YAAY,EAAE,MAAM,EAAE,CAAC;IACxC,CAAC;IACD,MAAM,GAAG,GAAG,MAAM,QAAQ,CAAC,MAAM,CAAC,WAAW,EAAE,MAAM,CAAC,SAAS,EAAE,MAAM,CAAC,OAAO,CAAC,CAAC;IACjF,MAAM,IAAI,GAAG,MAAM,KAAK,CAAC,UAAU,CAAC,GAAG,CAAC,CAAC;IACzC,IAAI,IAAI,KAAK,IAAI,EAAE,CAAC;QAClB,OAAO,EAAE,IAAI,EAAE,YAAY,EAAE,MAAM,EAAE,GAAG,EAAE,CAAC;IAC7C,CAAC;IACD,OAAO,EAAE,IAAI,EAAE,GAAG,EAAE,CAAC;AACvB,CAAC"}

package/dist/commands/roundtrip-tree.d.ts

@@ -1,4 +1,6 @@
-export interface RoundtripTreeOptions {
+import { type StrictOptions } from "./strict-options.js";
+import { type ReportOutputOptions } from "./report-output.js";
+export interface RoundtripTreeOptions extends StrictOptions, ReportOutputOptions {
     cacheDir?: string;
     format?: string;
     json?: boolean;

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

@@ -1 +1 @@
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+{"version":3,"file":"roundtrip-tree.d.ts","sourceRoot":"","sources":["../../src/commands/roundtrip-tree.ts"],"names":[],"mappings":"AAgBA,OAAO,EAAwB,KAAK,aAAa,EAAE,MAAM,qBAAqB,CAAC;AAI/E,OAAO,EAAsC,KAAK,mBAAmB,EAAE,MAAM,oBAAoB,CAAC;AAElG,MAAM,WAAW,oBAAqB,SAAQ,aAAa,EAAE,mBAAmB;IAC9E,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,6DAA6D;IAC7D,UAAU,CAAC,EAAE,OAAO,CAAC;IACrB,kEAAkE;IAClE,UAAU,CAAC,EAAE,OAAO,CAAC;IACrB,iEAAiE;IACjE,KAAK,CAAC,EAAE,OAAO,CAAC;CACjB;AAQD,wBAAsB,gBAAgB,CAAC,GAAG,EAAE,MAAM,EAAE,IAAI,EAAE,oBAAoB,GAAG,OAAO,CAAC,IAAI,CAAC,CA4I7F"}

package/dist/commands/roundtrip-tree.js

@@ -2,20 +2,23 @@
  * `gxwf roundtrip-tree` — batch roundtrip validation across a directory.
  * Mirrors the patterns in convert-tree.ts.
  */
-import { ToolCache } from "@galaxy-tool-util/core";
-import { roundtripValidate, } from "@galaxy-tool-util/schema";
+import { makeNodeToolCache } from "@galaxy-tool-util/core/node";
+import { roundtripValidate, buildRoundTripTreeReport, categoryOf, } from "@galaxy-tool-util/schema";
 import { dirname, join } from "node:path";
 import { loadToolInputsForWorkflow } from "./stateful-tool-inputs.js";
 import { createDefaultResolver } from "./url-resolver.js";
+import { resolveStrictOptions } from "./strict-options.js";
 import { resolveFormat } from "./workflow-io.js";
 import { collectTree, skipWorkflow } from "./tree.js";
 import { countDiffs } from "./roundtrip.js";
+import { writeReportOutput, writeReportHtml } from "./report-output.js";
 export async function runRoundtripTree(dir, opts) {
-    const cache = new ToolCache({ cacheDir: opts.cacheDir });
+    const cache = makeNodeToolCache({ cacheDir: opts.cacheDir });
     await cache.index.load();
-    if (cache.index.listAll().length === 0) {
+    if ((await cache.index.listAll()).length === 0) {
         console.warn("Tool cache is empty — all steps will fall back (no roundtrip possible)");
     }
+    const strict = resolveStrictOptions(opts);
     // Only native workflows are eligible; format2 files are skipped.
     const treeResult = await collectTree(dir, async (info, data) => {
         const sourceFormat = resolveFormat(data, opts.format);
@@ -29,7 +32,15 @@ export async function runRoundtripTree(dir, opts) {
         };
         const { resolver, status: toolStatus } = await loadToolInputsForWorkflow(data, "native", cache, expansionOpts);
         const failedLoads = toolStatus.filter((s) => !s.loaded);
-        const result = roundtripValidate(data, resolver);
+        const result = roundtripValidate(data, resolver, {
+            strictEncoding: strict.strictEncoding,
+            strictStructure: strict.strictStructure,
+            strictState: strict.strictState,
+        });
+        if (result.encodingErrors.length > 0 || result.structureErrors.length > 0) {
+            const allErrors = [...result.encodingErrors, ...result.structureErrors];
+            throw new Error(`Strict: ${allErrors.join("; ")}`);
+        }
         return {
             relativePath: info.relativePath,
             result,
@@ -57,6 +68,20 @@ export async function runRoundtripTree(dir, opts) {
         else
             filesBenignOnly++;
     }
+    // Build RoundTripTreeReport for Markdown/HTML rendering
+    const roundtripWorkflows = treeResult.outcomes.map((o) => {
+        const relPath = o.info.relativePath;
+        if (o.error)
+            return makeRoundTripResult(relPath, null, o.error, null);
+        if (o.skipped)
+            return makeRoundTripResult(relPath, null, null, "legacy_encoding");
+        return makeRoundTripResult(relPath, o.result.result, null, null);
+    });
+    const roundtripReport = buildRoundTripTreeReport(treeResult.root, roundtripWorkflows);
+    await writeReportOutput("roundtrip_tree.md.j2", roundtripReport, {
+        reportMarkdown: opts.reportMarkdown,
+    });
+    await writeReportHtml("roundtrip-tree", roundtripReport, opts.reportHtml);
     if (opts.json) {
         console.log(JSON.stringify({
             root: treeResult.root,
@@ -113,4 +138,41 @@ export async function runRoundtripTree(dir, opts) {
     else
         process.exitCode = 0;
 }
+/** Map the TS-internal RoundtripResult to the report-model shape for template rendering. */
+function makeRoundTripResult(relPath, result, error, skippedReason) {
+    const allDiffs = result?.stepResults.flatMap((s) => s.diffs) ?? [];
+    const errorDiffs = allDiffs.filter((d) => d.severity === "error");
+    const benignDiffs = allDiffs.filter((d) => d.severity === "benign");
+    const ok = result ? result.success : false;
+    let status;
+    if (error)
+        status = "error";
+    else if (skippedReason)
+        status = "skipped";
+    else if (ok)
+        status = "ok";
+    else
+        status = "roundtrip_mismatch";
+    const conversionFailureLines = result?.stepResults
+        .filter((s) => !s.success)
+        .map((s) => s.error ?? `Step ${s.stepId} failed`) ?? [];
+    return {
+        workflow_path: relPath,
+        category: categoryOf(relPath),
+        conversion_result: null,
+        diffs: allDiffs,
+        step_id_mapping: null,
+        stale_clean_results: null,
+        error,
+        skipped_reason: skippedReason,
+        structure_errors: result?.structureErrors ?? [],
+        encoding_errors: result?.encodingErrors ?? [],
+        error_diffs: errorDiffs,
+        benign_diffs: benignDiffs,
+        ok,
+        status,
+        conversion_failure_lines: conversionFailureLines,
+        summary_line: status.toUpperCase(),
+    };
+}
 //# sourceMappingURL=roundtrip-tree.js.map

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

@@ -1 +1 @@
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package/dist/commands/roundtrip.d.ts

@@ -1,5 +1,6 @@
 import { type RoundtripResult } from "@galaxy-tool-util/schema";
-export interface RoundtripOptions {
+import { type StrictOptions } from "./strict-options.js";
+export interface RoundtripOptions extends StrictOptions {
     cacheDir?: string;
     format?: string;
     json?: boolean;

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

@@ -1 +1 @@
-{"version":3,"file":"roundtrip.d.ts","sourceRoot":"","sources":["../../src/commands/roundtrip.ts"],"names":[],"mappings":"AAUA,OAAO,EAGL,KAAK,eAAe,EAErB,MAAM,0BAA0B,CAAC;AAMlC,MAAM,WAAW,gBAAgB;IAC/B,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,iDAAiD;IACjD,UAAU,CAAC,EAAE,OAAO,CAAC;IACrB,6EAA6E;IAC7E,UAAU,CAAC,EAAE,OAAO,CAAC;IACrB,yEAAyE;IACzE,KAAK,CAAC,EAAE,OAAO,CAAC;CACjB;AAED,wBAAsB,YAAY,CAAC,QAAQ,EAAE,MAAM,EAAE,IAAI,EAAE,gBAAgB,GAAG,OAAO,CAAC,IAAI,CAAC,CA6C1F;AAED,MAAM,WAAW,YAAY;IAC3B,UAAU,CAAC,EAAE,OAAO,CAAC;IACrB,UAAU,CAAC,EAAE,OAAO,CAAC;IACrB,KAAK,CAAC,EAAE,OAAO,CAAC;CACjB;AAmED;;;GAGG;AACH,wBAAgB,WAAW,CAAC,MAAM,EAAE,eAAe,GAAG,MAAM,CAI3D;AAED,4EAA4E;AAC5E,wBAAgB,UAAU,CAAC,MAAM,EAAE,eAAe,GAAG;IACnD,MAAM,EAAE,MAAM,CAAC;IACf,KAAK,EAAE,MAAM,CAAC;IACd,MAAM,EAAE,MAAM,CAAC;CAChB,CAOA"}
+{"version":3,"file":"roundtrip.d.ts","sourceRoot":"","sources":["../../src/commands/roundtrip.ts"],"names":[],"mappings":"AAUA,OAAO,EAGL,KAAK,eAAe,EAErB,MAAM,0BAA0B,CAAC;AAIlC,OAAO,EAAwB,KAAK,aAAa,EAAE,MAAM,qBAAqB,CAAC;AAG/E,MAAM,WAAW,gBAAiB,SAAQ,aAAa;IACrD,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,iDAAiD;IACjD,UAAU,CAAC,EAAE,OAAO,CAAC;IACrB,6EAA6E;IAC7E,UAAU,CAAC,EAAE,OAAO,CAAC;IACrB,yEAAyE;IACzE,KAAK,CAAC,EAAE,OAAO,CAAC;CACjB;AAED,wBAAsB,YAAY,CAAC,QAAQ,EAAE,MAAM,EAAE,IAAI,EAAE,gBAAgB,GAAG,OAAO,CAAC,IAAI,CAAC,CAmE1F;AAED,MAAM,WAAW,YAAY;IAC3B,UAAU,CAAC,EAAE,OAAO,CAAC;IACrB,UAAU,CAAC,EAAE,OAAO,CAAC;IACrB,KAAK,CAAC,EAAE,OAAO,CAAC;CACjB;AAmED;;;GAGG;AACH,wBAAgB,WAAW,CAAC,MAAM,EAAE,eAAe,GAAG,MAAM,CAI3D;AAED,4EAA4E;AAC5E,wBAAgB,UAAU,CAAC,MAAM,EAAE,eAAe,GAAG;IACnD,MAAM,EAAE,MAAM,CAAC;IACf,KAAK,EAAE,MAAM,CAAC;IACd,MAAM,EAAE,MAAM,CAAC;CAChB,CAOA"}

package/dist/commands/roundtrip.js

@@ -7,26 +7,28 @@
  *   1  benign diffs only (type coercions, stale keys, connection moves)
  *   2  real diffs or conversion errors
  */
-import { ToolCache } from "@galaxy-tool-util/core";
+import { makeNodeToolCache } from "@galaxy-tool-util/core/node";
 import { roundtripValidate, } from "@galaxy-tool-util/schema";
 import { dirname } from "node:path";
 import { loadToolInputsForWorkflow } from "./stateful-tool-inputs.js";
 import { createDefaultResolver } from "./url-resolver.js";
+import { resolveStrictOptions } from "./strict-options.js";
 import { readWorkflowFile, resolveFormat } from "./workflow-io.js";
 export async function runRoundtrip(filePath, opts) {
     const data = await readWorkflowFile(filePath);
     if (!data)
         return;
     const sourceFormat = resolveFormat(data, opts.format);
+    const strict = resolveStrictOptions(opts);
     if (sourceFormat !== "native") {
         console.error(`Roundtrip source must be a native (.ga) workflow; got ${sourceFormat}.` +
             ` Convert to native first or pass a .ga file.`);
         process.exitCode = 2;
         return;
     }
-    const cache = new ToolCache({ cacheDir: opts.cacheDir });
+    const cache = makeNodeToolCache({ cacheDir: opts.cacheDir });
     await cache.index.load();
-    if (cache.index.listAll().length === 0) {
+    if ((await cache.index.listAll()).length === 0) {
         console.warn("Tool cache is empty — all steps will fall back (no roundtrip possible)");
     }
     const expansionOpts = {
@@ -39,14 +41,34 @@ export async function runRoundtrip(filePath, opts) {
             console.error(`  tool ${s.toolId}${ver}: ${s.error}`);
         }
     }
-    const result = roundtripValidate(data, resolver);
+    const result = roundtripValidate(data, resolver, {
+        strictEncoding: strict.strictEncoding,
+        strictStructure: strict.strictStructure,
+        strictState: strict.strictState,
+    });
     if (opts.json) {
         console.log(JSON.stringify(result, null, 2));
     }
     else {
+        // Report strict errors before step-level results
+        if (result.encodingErrors.length > 0) {
+            console.error("Encoding errors:");
+            for (const e of result.encodingErrors)
+                console.error(`  ${e}`);
+        }
+        if (result.structureErrors.length > 0) {
+            console.error("Structure errors (strict):");
+            for (const e of result.structureErrors)
+                console.error(`  ${e}`);
+        }
         reportResult(filePath, result, opts);
     }
-    process.exitCode = exitCodeFor(result);
+    let exitCode = exitCodeFor(result);
+    // --strict-state: require all steps to roundtrip (no skips/failures)
+    if (strict.strictState && result.stepResults.some((s) => !s.success)) {
+        exitCode = 2;
+    }
+    process.exitCode = exitCode;
 }
 function reportResult(filePath, result, filter) {
     const total = result.stepResults.length;
@@ -93,9 +115,9 @@ function reportResult(filePath, result, filter) {
                 ? step.diffs.filter((d) => d.severity === "benign")
                 : step.diffs;
         for (const d of diffsToShow) {
-            const tag = d.severity === "error" ? "ERROR" : `benign:${d.kind ?? "?"}`;
-            const loc = d.path || "<root>";
-            console.log(`${indent}    [${tag}] ${loc}: ${d.message}`);
+            const tag = d.severity === "error" ? "ERROR" : `benign:${d.benign_artifact?.reason ?? "?"}`;
+            const loc = d.key_path || "<root>";
+            console.log(`${indent}    [${tag}] ${loc}: ${d.description}`);
         }
     }
 }

package/dist/commands/roundtrip.js.map

@@ -1 +1 @@
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+{"version":3,"file":"roundtrip.js","sourceRoot":"","sources":["../../src/commands/roundtrip.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AACH,OAAO,EAAE,iBAAiB,EAAE,MAAM,6BAA6B,CAAC;AAChE,OAAO,EACL,iBAAiB,GAIlB,MAAM,0BAA0B,CAAC;AAClC,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AACpC,OAAO,EAAE,yBAAyB,EAAE,MAAM,2BAA2B,CAAC;AACtE,OAAO,EAAE,qBAAqB,EAAE,MAAM,mBAAmB,CAAC;AAC1D,OAAO,EAAE,oBAAoB,EAAsB,MAAM,qBAAqB,CAAC;AAC/E,OAAO,EAAE,gBAAgB,EAAE,aAAa,EAAE,MAAM,kBAAkB,CAAC;AAcnE,MAAM,CAAC,KAAK,UAAU,YAAY,CAAC,QAAgB,EAAE,IAAsB;IACzE,MAAM,IAAI,GAAG,MAAM,gBAAgB,CAAC,QAAQ,CAAC,CAAC;IAC9C,IAAI,CAAC,IAAI;QAAE,OAAO;IAElB,MAAM,YAAY,GAAG,aAAa,CAAC,IAAI,EAAE,IAAI,CAAC,MAAM,CAAC,CAAC;IACtD,MAAM,MAAM,GAAG,oBAAoB,CAAC,IAAI,CAAC,CAAC;IAE1C,IAAI,YAAY,KAAK,QAAQ,EAAE,CAAC;QAC9B,OAAO,CAAC,KAAK,CACX,yDAAyD,YAAY,GAAG;YACtE,8CAA8C,CACjD,CAAC;QACF,OAAO,CAAC,QAAQ,GAAG,CAAC,CAAC;QACrB,OAAO;IACT,CAAC;IAED,MAAM,KAAK,GAAG,iBAAiB,CAAC,EAAE,QAAQ,EAAE,IAAI,CAAC,QAAQ,EAAE,CAAC,CAAC;IAC7D,MAAM,KAAK,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC;IACzB,IAAI,CAAC,MAAM,KAAK,CAAC,KAAK,CAAC,OAAO,EAAE,CAAC,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QAC/C,OAAO,CAAC,IAAI,CAAC,wEAAwE,CAAC,CAAC;IACzF,CAAC;IAED,MAAM,aAAa,GAAqB;QACtC,QAAQ,EAAE,qBAAqB,CAAC,EAAE,iBAAiB,EAAE,OAAO,CAAC,QAAQ,CAAC,EAAE,CAAC;KAC1E,CAAC;IACF,MAAM,EAAE,QAAQ,EAAE,MAAM,EAAE,UAAU,EAAE,GAAG,MAAM,yBAAyB,CACtE,IAAI,EACJ,QAAQ,EACR,KAAK,EACL,aAAa,CACd,CAAC;IACF,KAAK,MAAM,CAAC,IAAI,UAAU,EAAE,CAAC;QAC3B,IAAI,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC;YACd,MAAM,GAAG,GAAG,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,WAAW,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;YACrD,OAAO,CAAC,KAAK,CAAC,UAAU,CAAC,CAAC,MAAM,GAAG,GAAG,KAAK,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC;QACxD,CAAC;IACH,CAAC;IAED,MAAM,MAAM,GAAG,iBAAiB,CAAC,IAAI,EAAE,QAAQ,EAAE;QAC/C,cAAc,EAAE,MAAM,CAAC,cAAc;QACrC,eAAe,EAAE,MAAM,CAAC,eAAe;QACvC,WAAW,EAAE,MAAM,CAAC,WAAW;KAChC,CAAC,CAAC;IAEH,IAAI,IAAI,CAAC,IAAI,EAAE,CAAC;QACd,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,SAAS,CAAC,MAAM,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,CAAC;IAC/C,CAAC;SAAM,CAAC;QACN,iDAAiD;QACjD,IAAI,MAAM,CAAC,cAAc,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;YACrC,OAAO,CAAC,KAAK,CAAC,kBAAkB,CAAC,CAAC;YAClC,KAAK,MAAM,CAAC,IAAI,MAAM,CAAC,cAAc;gBAAE,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;QACjE,CAAC;QACD,IAAI,MAAM,CAAC,eAAe,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;YACtC,OAAO,CAAC,KAAK,CAAC,4BAA4B,CAAC,CAAC;YAC5C,KAAK,MAAM,CAAC,IAAI,MAAM,CAAC,eAAe;gBAAE,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;QAClE,CAAC;QACD,YAAY,CAAC,QAAQ,EAAE,MAAM,EAAE,IAAI,CAAC,CAAC;IACvC,CAAC;IAED,IAAI,QAAQ,GAAG,WAAW,CAAC,MAAM,CAAC,CAAC;IAEnC,qEAAqE;IACrE,IAAI,MAAM,CAAC,WAAW,IAAI,MAAM,CAAC,WAAW,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,EAAE,CAAC;QACrE,QAAQ,GAAG,CAAC,CAAC;IACf,CAAC;IAED,OAAO,CAAC,QAAQ,GAAG,QAAQ,CAAC;AAC9B,CAAC;AAQD,SAAS,YAAY,CAAC,QAAgB,EAAE,MAAuB,EAAE,MAAoB;IACnF,MAAM,KAAK,GAAG,MAAM,CAAC,WAAW,CAAC,MAAM,CAAC;IACxC,MAAM,MAAM,GAAG,MAAM,CAAC,WAAW,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,MAAM,CAAC;IACnE,MAAM,WAAW,GAAG,MAAM,CAAC,WAAW,CAAC,MAAM,CAC3C,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,GAAG,CAAC,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,QAAQ,KAAK,QAAQ,CAAC,CAAC,MAAM,EACnE,CAAC,CACF,CAAC;IACF,MAAM,UAAU,GAAG,MAAM,CAAC,WAAW,CAAC,MAAM,CAC1C,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,GAAG,CAAC,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,QAAQ,KAAK,OAAO,CAAC,CAAC,MAAM,EAClE,CAAC,CACF,CAAC;IAEF,OAAO,CAAC,GAAG,CAAC,cAAc,QAAQ,EAAE,CAAC,CAAC;IACtC,OAAO,CAAC,GAAG,CACT,KAAK,KAAK,GAAG,MAAM,IAAI,KAAK,gBAAgB,WAAW,oBAAoB,UAAU,eAAe,CACrG,CAAC;IAEF,0EAA0E;IAC1E,mEAAmE;IACnE,IAAI,MAAM,CAAC,KAAK;QAAE,OAAO;IAEzB,KAAK,MAAM,IAAI,IAAI,MAAM,CAAC,WAAW,EAAE,CAAC;QACtC,MAAM,QAAQ,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,QAAQ,KAAK,OAAO,CAAC,CAAC;QAChE,MAAM,SAAS,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,QAAQ,KAAK,QAAQ,CAAC,CAAC;QAElE,IAAI,MAAM,CAAC,UAAU,IAAI,CAAC,QAAQ,IAAI,IAAI,CAAC,OAAO;YAAE,SAAS;QAC7D,IAAI,MAAM,CAAC,UAAU,EAAE,CAAC;YACtB,kEAAkE;YAClE,IAAI,CAAC,SAAS,IAAI,QAAQ,IAAI,CAAC,IAAI,CAAC,OAAO;gBAAE,SAAS;QACxD,CAAC;QACD,gEAAgE;QAChE,8DAA8D;QAC9D,IACE,CAAC,MAAM,CAAC,UAAU;YAClB,CAAC,MAAM,CAAC,UAAU;YAClB,IAAI,CAAC,KAAK,CAAC,MAAM,KAAK,CAAC;YACvB,IAAI,CAAC,OAAO;YACZ,CAAC,IAAI,CAAC,YAAY,EAClB,CAAC;YACD,SAAS;QACX,CAAC;QAED,yEAAyE;QACzE,MAAM,MAAM,GAAG,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;QACvC,MAAM,KAAK,GAAG,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,MAAM,KAAK,IAAI,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC;QAC5E,IAAI,CAAC,IAAI,CAAC,OAAO,EAAE,CAAC;YAClB,OAAO,CAAC,KAAK,CACX,GAAG,MAAM,UAAU,KAAK,KAAK,IAAI,CAAC,YAAY,IAAI,QAAQ,MAAM,IAAI,CAAC,KAAK,IAAI,EAAE,EAAE,CACnF,CAAC;QACJ,CAAC;aAAM,IAAI,IAAI,CAAC,YAAY,EAAE,CAAC;YAC7B,OAAO,CAAC,GAAG,CAAC,GAAG,MAAM,UAAU,KAAK,KAAK,IAAI,CAAC,YAAY,KAAK,IAAI,CAAC,KAAK,IAAI,EAAE,GAAG,CAAC,CAAC;QACtF,CAAC;QACD,MAAM,WAAW,GAAG,MAAM,CAAC,UAAU;YACnC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,QAAQ,KAAK,OAAO,CAAC;YAClD,CAAC,CAAC,MAAM,CAAC,UAAU;gBACjB,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,QAAQ,KAAK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package/dist/commands/schema.js

@@ -1,4 +1,4 @@
-import { ToolCache } from "@galaxy-tool-util/core";
+import { makeNodeToolCache } from "@galaxy-tool-util/core/node";
 import { createFieldModel, STATE_REPRESENTATIONS, } from "@galaxy-tool-util/schema";
 import * as JSONSchema from "effect/JSONSchema";
 import { writeFile } from "node:fs/promises";
@@ -11,7 +11,7 @@ export async function runSchema(toolId, opts) {
         return;
     }
     const stateRep = repName;
-    const cache = new ToolCache({ cacheDir: opts.cacheDir });
+    const cache = makeNodeToolCache({ cacheDir: opts.cacheDir });
     await cache.index.load();
     const result = await loadCachedTool(cache, toolId, opts.version);
     if (isResolveError(result)) {

package/dist/commands/schema.js.map

@@ -1 +1 @@
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package/dist/commands/strict-options.d.ts

@@ -0,0 +1,22 @@
+/**
+ * Strict validation options — decomposed into three orthogonal dimensions.
+ *
+ * --strict is shorthand for --strict-structure --strict-encoding --strict-state.
+ */
+import type { Command } from "commander";
+export interface StrictOptions {
+    strict?: boolean;
+    strictStructure?: boolean;
+    strictEncoding?: boolean;
+    strictState?: boolean;
+}
+export interface ResolvedStrictOptions {
+    strictStructure: boolean;
+    strictEncoding: boolean;
+    strictState: boolean;
+}
+/** Expand --strict shorthand into the three individual flags. */
+export declare function resolveStrictOptions(opts: StrictOptions): ResolvedStrictOptions;
+/** Register --strict, --strict-structure, --strict-encoding, --strict-state on a Commander command. */
+export declare function addStrictOptions(cmd: Command): Command;
+//# sourceMappingURL=strict-options.d.ts.map

package/dist/commands/strict-options.d.ts.map

@@ -0,0 +1 @@
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package/dist/commands/strict-options.js

@@ -0,0 +1,18 @@
+/** Expand --strict shorthand into the three individual flags. */
+export function resolveStrictOptions(opts) {
+    const all = !!opts.strict;
+    return {
+        strictStructure: all || !!opts.strictStructure,
+        strictEncoding: all || !!opts.strictEncoding,
+        strictState: all || !!opts.strictState,
+    };
+}
+/** Register --strict, --strict-structure, --strict-encoding, --strict-state on a Commander command. */
+export function addStrictOptions(cmd) {
+    return cmd
+        .option("--strict", "Shorthand for --strict-structure --strict-encoding --strict-state")
+        .option("--strict-structure", "Reject unknown keys at envelope/step level")
+        .option("--strict-encoding", "Reject JSON-string tool_state and format2 field misuse")
+        .option("--strict-state", "Require every tool step to validate; no skips allowed");
+}
+//# sourceMappingURL=strict-options.js.map

package/dist/commands/strict-options.js.map

@@ -0,0 +1 @@
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package/dist/commands/validate-tests-tree.d.ts

@@ -0,0 +1,36 @@
+/**
+ * ``gxwf validate-tests-tree`` — batch-validate every workflow-test file
+ * (``*-tests.yml``, ``*-tests.yaml``, ``*.gxwf-tests.yml``, ``*.gxwf-tests.yaml``)
+ * under a directory against the ``galaxy.tool_util_models.Tests`` JSON Schema.
+ *
+ * Unlike ``validate-tree`` this uses its own discovery pass because test
+ * documents don't carry a ``class: GalaxyWorkflow`` / ``a_galaxy_workflow``
+ * marker — classification is filename-based.
+ *
+ * With ``--auto-workflow``, each test file is paired with a sibling workflow
+ * by suffix convention and cross-checked. Silent no-op when no sibling is
+ * found.
+ */
+import { type TestFormatDiagnostic } from "@galaxy-tool-util/schema";
+export interface ValidateTestsTreeOptions {
+    json?: boolean;
+    autoWorkflow?: boolean;
+}
+export interface TestsTreeFileReport {
+    path: string;
+    valid: boolean;
+    errors: TestFormatDiagnostic[];
+    workflow?: string;
+}
+export interface ValidateTestsTreeReport {
+    root: string;
+    files: TestsTreeFileReport[];
+    summary: {
+        total: number;
+        ok: number;
+        fail: number;
+        error: number;
+    };
+}
+export declare function runValidateTestsTree(dir: string, opts?: ValidateTestsTreeOptions): Promise<void>;
+//# sourceMappingURL=validate-tests-tree.d.ts.map

package/dist/commands/validate-tests-tree.d.ts.map

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