@galaxy-tool-util/cli 0.1.0 → 0.2.0

package/dist/commands/convert.d.ts

@@ -0,0 +1,12 @@
+export interface ConvertOptions {
+    to?: string;
+    output?: string;
+    compact?: boolean;
+    json?: boolean;
+    yaml?: boolean;
+    format?: string;
+    stateful?: boolean;
+    cacheDir?: string;
+}
+export declare function runConvert(filePath: string, opts: ConvertOptions): Promise<void>;
+//# sourceMappingURL=convert.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"convert.d.ts","sourceRoot":"","sources":["../../src/commands/convert.ts"],"names":[],"mappings":"AAuBA,MAAM,WAAW,cAAc;IAC7B,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,CAoEtF"}

package/dist/commands/convert.js

@@ -0,0 +1,119 @@
+/**
+ * `gxwf convert` — convert between native (.ga) and format2 (.gxwf.yml) formats.
+ */
+import { ToolCache } from "@galaxy-tool-util/core";
+import { toFormat2, toFormat2Stateful, toNative, toNativeStateful, } from "@galaxy-tool-util/schema";
+import { dirname } from "node:path";
+import { loadToolInputsForWorkflow } from "./stateful-tool-inputs.js";
+import { createDefaultResolver } from "./url-resolver.js";
+import { readWorkflowFile, resolveFormat, serializeWorkflow, writeWorkflowOutput, } from "./workflow-io.js";
+export async function runConvert(filePath, opts) {
+    const data = await readWorkflowFile(filePath);
+    if (!data)
+        return;
+    const sourceFormat = resolveFormat(data, opts.format);
+    const targetFormat = resolveTargetFormat(sourceFormat, opts.to);
+    if (sourceFormat === targetFormat) {
+        console.error(`Source and target formats are both ${sourceFormat}. ` +
+            `Use --to to specify the target format.`);
+        process.exitCode = 1;
+        return;
+    }
+    let result;
+    let stepStatuses = null;
+    if (opts.stateful) {
+        const cache = new ToolCache({ cacheDir: opts.cacheDir });
+        await cache.index.load();
+        if (cache.index.listAll().length === 0) {
+            console.warn("Tool cache is empty — stateful conversion will fall back for every step");
+        }
+        const expansionOpts = {
+            resolver: createDefaultResolver({ workflowDirectory: dirname(filePath) }),
+        };
+        const { resolver, status: toolStatus } = await loadToolInputsForWorkflow(data, sourceFormat, cache, expansionOpts);
+        for (const s of toolStatus) {
+            if (!s.loaded) {
+                const ver = s.toolVersion ? `@${s.toolVersion}` : "";
+                console.error(`  tool ${s.toolId}${ver}: ${s.error}`);
+            }
+        }
+        if (targetFormat === "format2") {
+            const r = toFormat2Stateful(data, resolver);
+            result = r.workflow;
+            stepStatuses = r.steps;
+            if (opts.compact)
+                stripPositionInfo(result);
+        }
+        else {
+            const r = toNativeStateful(data, resolver);
+            result = r.workflow;
+            stepStatuses = r.steps;
+        }
+    }
+    else if (targetFormat === "format2") {
+        result = toFormat2(data);
+        if (opts.compact) {
+            stripPositionInfo(result);
+        }
+    }
+    else {
+        result = toNative(data);
+    }
+    const output = serializeWorkflow(result, targetFormat, { json: opts.json, yaml: opts.yaml });
+    await writeWorkflowOutput(output, opts.output, "Converted workflow");
+    if (stepStatuses !== null) {
+        reportStepStatuses(stepStatuses);
+    }
+}
+function reportStepStatuses(statuses) {
+    const converted = statuses.filter((s) => s.converted).length;
+    const failed = statuses.length - converted;
+    console.error(`\nStateful conversion: ${converted}/${statuses.length} steps converted` +
+        (failed > 0 ? `, ${failed} fell back` : ""));
+    // Aggregate fallbacks by failure class
+    if (failed > 0) {
+        const byClass = new Map();
+        for (const s of statuses) {
+            if (!s.converted) {
+                const cls = s.failureClass ?? "unknown";
+                byClass.set(cls, (byClass.get(cls) ?? 0) + 1);
+            }
+        }
+        const summary = Array.from(byClass.entries())
+            .map(([k, v]) => `${k}=${v}`)
+            .join(", ");
+        console.error(`  fallback breakdown: ${summary}`);
+    }
+    for (const s of statuses) {
+        if (!s.converted) {
+            const label = s.toolId ? `${s.stepId} (${s.toolId})` : s.stepId;
+            const cls = s.failureClass ?? "unknown";
+            console.error(`  step ${label} [${cls}]: ${s.error ?? "unknown error"}`);
+        }
+    }
+    if (failed > 0)
+        process.exitCode = 1;
+}
+function resolveTargetFormat(sourceFormat, toOpt) {
+    if (toOpt === "native" || toOpt === "format2")
+        return toOpt;
+    // Infer opposite
+    return sourceFormat === "native" ? "format2" : "native";
+}
+/** Recursively remove position-related keys from format2 output. */
+function stripPositionInfo(obj) {
+    delete obj.position;
+    for (const val of Object.values(obj)) {
+        if (Array.isArray(val)) {
+            for (const item of val) {
+                if (item && typeof item === "object") {
+                    stripPositionInfo(item);
+                }
+            }
+        }
+        else if (val && typeof val === "object") {
+            stripPositionInfo(val);
+        }
+    }
+}
+//# sourceMappingURL=convert.js.map

package/dist/commands/convert.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"convert.js","sourceRoot":"","sources":["../../src/commands/convert.ts"],"names":[],"mappings":"AAAA;;GAEG;AACH,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AACnD,OAAO,EACL,SAAS,EACT,iBAAiB,EACjB,QAAQ,EACR,gBAAgB,GAIjB,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,EACL,gBAAgB,EAChB,aAAa,EACb,iBAAiB,EACjB,mBAAmB,GACpB,MAAM,kBAAkB,CAAC;AAa1B,MAAM,CAAC,KAAK,UAAU,UAAU,CAAC,QAAgB,EAAE,IAAoB;IACrE,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,YAAY,GAAG,mBAAmB,CAAC,YAAY,EAAE,IAAI,CAAC,EAAE,CAAC,CAAC;IAEhE,IAAI,YAAY,KAAK,YAAY,EAAE,CAAC;QAClC,OAAO,CAAC,KAAK,CACX,sCAAsC,YAAY,IAAI;YACpD,wCAAwC,CAC3C,CAAC;QACF,OAAO,CAAC,QAAQ,GAAG,CAAC,CAAC;QACrB,OAAO;IACT,CAAC;IAED,IAAI,MAA+B,CAAC;IACpC,IAAI,YAAY,GAAkC,IAAI,CAAC;IAEvD,IAAI,IAAI,CAAC,QAAQ,EAAE,CAAC;QAClB,MAAM,KAAK,GAAG,IAAI,SAAS,CAAC,EAAE,QAAQ,EAAE,IAAI,CAAC,QAAQ,EAAE,CAAC,CAAC;QACzD,MAAM,KAAK,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC;QAEzB,IAAI,KAAK,CAAC,KAAK,CAAC,OAAO,EAAE,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YACvC,OAAO,CAAC,IAAI,CAAC,yEAAyE,CAAC,CAAC;QAC1F,CAAC;QAED,MAAM,aAAa,GAAqB;YACtC,QAAQ,EAAE,qBAAqB,CAAC,EAAE,iBAAiB,EAAE,OAAO,CAAC,QAAQ,CAAC,EAAE,CAAC;SAC1E,CAAC;QACF,MAAM,EAAE,QAAQ,EAAE,MAAM,EAAE,UAAU,EAAE,GAAG,MAAM,yBAAyB,CACtE,IAAI,EACJ,YAAY,EACZ,KAAK,EACL,aAAa,CACd,CAAC;QACF,KAAK,MAAM,CAAC,IAAI,UAAU,EAAE,CAAC;YAC3B,IAAI,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC;gBACd,MAAM,GAAG,GAAG,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,WAAW,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;gBACrD,OAAO,CAAC,KAAK,CAAC,UAAU,CAAC,CAAC,MAAM,GAAG,GAAG,KAAK,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC;YACxD,CAAC;QACH,CAAC;QAED,IAAI,YAAY,KAAK,SAAS,EAAE,CAAC;YAC/B,MAAM,CAAC,GAAG,iBAAiB,CAAC,IAAI,EAAE,QAAQ,CAAC,CAAC;YAC5C,MAAM,GAAG,CAAC,CAAC,QAA8C,CAAC;YAC1D,YAAY,GAAG,CAAC,CAAC,KAAK,CAAC;YACvB,IAAI,IAAI,CAAC,OAAO;gBAAE,iBAAiB,CAAC,MAAM,CAAC,CAAC;QAC9C,CAAC;aAAM,CAAC;YACN,MAAM,CAAC,GAAG,gBAAgB,CAAC,IAAI,EAAE,QAAQ,CAAC,CAAC;YAC3C,MAAM,GAAG,CAAC,CAAC,QAA8C,CAAC;YAC1D,YAAY,GAAG,CAAC,CAAC,KAAK,CAAC;QACzB,CAAC;IACH,CAAC;SAAM,IAAI,YAAY,KAAK,SAAS,EAAE,CAAC;QACtC,MAAM,GAAG,SAAS,CAAC,IAAI,CAAuC,CAAC;QAC/D,IAAI,IAAI,CAAC,OAAO,EAAE,CAAC;YACjB,iBAAiB,CAAC,MAAM,CAAC,CAAC;QAC5B,CAAC;IACH,CAAC;SAAM,CAAC;QACN,MAAM,GAAG,QAAQ,CAAC,IAAI,CAAuC,CAAC;IAChE,CAAC;IAED,MAAM,MAAM,GAAG,iBAAiB,CAAC,MAAM,EAAE,YAAY,EAAE,EAAE,IAAI,EAAE,IAAI,CAAC,IAAI,EAAE,IAAI,EAAE,IAAI,CAAC,IAAI,EAAE,CAAC,CAAC;IAC7F,MAAM,mBAAmB,CAAC,MAAM,EAAE,IAAI,CAAC,MAAM,EAAE,oBAAoB,CAAC,CAAC;IAErE,IAAI,YAAY,KAAK,IAAI,EAAE,CAAC;QAC1B,kBAAkB,CAAC,YAAY,CAAC,CAAC;IACnC,CAAC;AACH,CAAC;AAED,SAAS,kBAAkB,CAAC,QAAgC;IAC1D,MAAM,SAAS,GAAG,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,MAAM,CAAC;IAC7D,MAAM,MAAM,GAAG,QAAQ,CAAC,MAAM,GAAG,SAAS,CAAC;IAC3C,OAAO,CAAC,KAAK,CACX,0BAA0B,SAAS,IAAI,QAAQ,CAAC,MAAM,kBAAkB;QACtE,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,KAAK,MAAM,YAAY,CAAC,CAAC,CAAC,EAAE,CAAC,CAC9C,CAAC;IACF,uCAAuC;IACvC,IAAI,MAAM,GAAG,CAAC,EAAE,CAAC;QACf,MAAM,OAAO,GAAG,IAAI,GAAG,EAAkB,CAAC;QAC1C,KAAK,MAAM,CAAC,IAAI,QAAQ,EAAE,CAAC;YACzB,IAAI,CAAC,CAAC,CAAC,SAAS,EAAE,CAAC;gBACjB,MAAM,GAAG,GAAG,CAAC,CAAC,YAAY,IAAI,SAAS,CAAC;gBACxC,OAAO,CAAC,GAAG,CAAC,GAAG,EAAE,CAAC,OAAO,CAAC,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC;YAChD,CAAC;QACH,CAAC;QACD,MAAM,OAAO,GAAG,KAAK,CAAC,IAAI,CAAC,OAAO,CAAC,OAAO,EAAE,CAAC;aAC1C,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,EAAE,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC;aAC5B,IAAI,CAAC,IAAI,CAAC,CAAC;QACd,OAAO,CAAC,KAAK,CAAC,yBAAyB,OAAO,EAAE,CAAC,CAAC;IACpD,CAAC;IACD,KAAK,MAAM,CAAC,IAAI,QAAQ,EAAE,CAAC;QACzB,IAAI,CAAC,CAAC,CAAC,SAAS,EAAE,CAAC;YACjB,MAAM,KAAK,GAAG,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,MAAM,KAAK,CAAC,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC;YAChE,MAAM,GAAG,GAAG,CAAC,CAAC,YAAY,IAAI,SAAS,CAAC;YACxC,OAAO,CAAC,KAAK,CAAC,UAAU,KAAK,KAAK,GAAG,MAAM,CAAC,CAAC,KAAK,IAAI,eAAe,EAAE,CAAC,CAAC;QAC3E,CAAC;IACH,CAAC;IACD,IAAI,MAAM,GAAG,CAAC;QAAE,OAAO,CAAC,QAAQ,GAAG,CAAC,CAAC;AACvC,CAAC;AAED,SAAS,mBAAmB,CAAC,YAA4B,EAAE,KAAc;IACvE,IAAI,KAAK,KAAK,QAAQ,IAAI,KAAK,KAAK,SAAS;QAAE,OAAO,KAAK,CAAC;IAC5D,iBAAiB;IACjB,OAAO,YAAY,KAAK,QAAQ,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,QAAQ,CAAC;AAC1D,CAAC;AAED,oEAAoE;AACpE,SAAS,iBAAiB,CAAC,GAA4B;IACrD,OAAO,GAAG,CAAC,QAAQ,CAAC;IACpB,KAAK,MAAM,GAAG,IAAI,MAAM,CAAC,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC;QACrC,IAAI,KAAK,CAAC,OAAO,CAAC,GAAG,CAAC,EAAE,CAAC;YACvB,KAAK,MAAM,IAAI,IAAI,GAAG,EAAE,CAAC;gBACvB,IAAI,IAAI,IAAI,OAAO,IAAI,KAAK,QAAQ,EAAE,CAAC;oBACrC,iBAAiB,CAAC,IAA+B,CAAC,CAAC;gBACrD,CAAC;YACH,CAAC;QACH,CAAC;aAAM,IAAI,GAAG,IAAI,OAAO,GAAG,KAAK,QAAQ,EAAE,CAAC;YAC1C,iBAAiB,CAAC,GAA8B,CAAC,CAAC;QACpD,CAAC;IACH,CAAC;AACH,CAAC"}

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

@@ -0,0 +1,27 @@
+import { type LintReport } from "./lint.js";
+import { type TreeSummary } from "./tree.js";
+export interface LintTreeOptions {
+    format?: string;
+    skipBestPractices?: boolean;
+    skipStateValidation?: boolean;
+    cacheDir?: string;
+    json?: boolean;
+}
+export interface WorkflowLintResult {
+    relativePath: string;
+    report: LintReport;
+}
+export interface LintTreeReport {
+    root: string;
+    results: (WorkflowLintResult | {
+        relativePath: string;
+        error: string;
+    })[];
+    summary: TreeSummary & {
+        lintErrors: number;
+        lintWarnings: number;
+        stateFail: number;
+    };
+}
+export declare function runLintTree(dir: string, opts: LintTreeOptions): Promise<void>;
+//# sourceMappingURL=lint-tree.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"lint-tree.d.ts","sourceRoot":"","sources":["../../src/commands/lint-tree.ts"],"names":[],"mappings":"AAKA,OAAO,EAAsB,KAAK,UAAU,EAAE,MAAM,WAAW,CAAC;AAChE,OAAO,EAAmD,KAAK,WAAW,EAAE,MAAM,WAAW,CAAC;AAE9F,MAAM,WAAW,eAAe;IAC9B,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,iBAAiB,CAAC,EAAE,OAAO,CAAC;IAC5B,mBAAmB,CAAC,EAAE,OAAO,CAAC;IAC9B,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,IAAI,CAAC,EAAE,OAAO,CAAC;CAChB;AAED,MAAM,WAAW,kBAAkB;IACjC,YAAY,EAAE,MAAM,CAAC;IACrB,MAAM,EAAE,UAAU,CAAC;CACpB;AAED,MAAM,WAAW,cAAc;IAC7B,IAAI,EAAE,MAAM,CAAC;IACb,OAAO,EAAE,CAAC,kBAAkB,GAAG;QAAE,YAAY,EAAE,MAAM,CAAC;QAAC,KAAK,EAAE,MAAM,CAAA;KAAE,CAAC,EAAE,CAAC;IAC1E,OAAO,EAAE,WAAW,GAAG;QAAE,UAAU,EAAE,MAAM,CAAC;QAAC,YAAY,EAAE,MAAM,CAAC;QAAC,SAAS,EAAE,MAAM,CAAA;KAAE,CAAC;CACxF;AAED,wBAAsB,WAAW,CAAC,GAAG,EAAE,MAAM,EAAE,IAAI,EAAE,eAAe,GAAG,OAAO,CAAC,IAAI,CAAC,CA6EnF"}

package/dist/commands/lint-tree.js

@@ -0,0 +1,116 @@
+/**
+ * `gxwf lint-tree` — batch lint all workflows under a directory.
+ */
+import { ToolCache } from "@galaxy-tool-util/core";
+import { resolveFormat } from "./workflow-io.js";
+import { lintWorkflowReport } from "./lint.js";
+import { collectTree, summarizeOutcomes } from "./tree.js";
+export async function runLintTree(dir, opts) {
+    // Load tool cache once for all files
+    let cache;
+    if (!opts.skipStateValidation) {
+        try {
+            cache = new ToolCache({ cacheDir: opts.cacheDir });
+            await cache.index.load();
+            if (cache.index.listAll().length === 0) {
+                console.warn("Tool cache is empty — skipping tool state validation for all files");
+                cache = undefined;
+            }
+        }
+        catch (e) {
+            const msg = e instanceof Error ? e.message : String(e);
+            console.warn(`Failed to load tool cache: ${msg}`);
+        }
+    }
+    const treeResult = await collectTree(dir, async (info, data) => {
+        const format = resolveFormat(data, opts.format);
+        const report = await lintWorkflowReport(info.path, data, format, {
+            skipBestPractices: opts.skipBestPractices,
+            skipStateValidation: opts.skipStateValidation,
+            cache,
+        });
+        return { relativePath: info.relativePath, report };
+    });
+    const report = buildLintTreeReport(treeResult);
+    if (opts.json) {
+        console.log(JSON.stringify(report, null, 2));
+        process.exitCode = computeLintExitCode(report);
+        return;
+    }
+    // Text output
+    for (const outcome of treeResult.outcomes) {
+        if (outcome.error) {
+            console.error(`  ${outcome.info.relativePath}: ERROR (${outcome.error})`);
+            continue;
+        }
+        if (outcome.skipped) {
+            console.warn(`  ${outcome.info.relativePath}: SKIPPED (${outcome.skipReason})`);
+            continue;
+        }
+        const r = outcome.result;
+        const lr = r.report;
+        const errors = lr.structural.error_count + (lr.bestPractices?.error_count ?? 0);
+        const warnings = lr.structural.warn_count + (lr.bestPractices?.warn_count ?? 0);
+        const stateFails = lr.stateValidation?.filter((s) => s.status === "fail").length ?? 0;
+        if (errors > 0 || stateFails > 0) {
+            console.error(`  ${r.relativePath}: ${errors} errors, ${warnings} warnings, ${stateFails} state failures`);
+            for (const e of lr.structural.errors)
+                console.error(`    [structural] ${e}`);
+            if (lr.bestPractices) {
+                for (const e of lr.bestPractices.errors)
+                    console.error(`    [best-practices] ${e}`);
+            }
+            if (lr.stateValidation) {
+                for (const s of lr.stateValidation.filter((s) => s.status === "fail")) {
+                    for (const err of s.errors)
+                        console.error(`    [state] Step ${s.stepLabel} (${s.toolId}): ${err}`);
+                }
+            }
+        }
+        else if (warnings > 0) {
+            console.warn(`  ${r.relativePath}: ${warnings} warnings`);
+        }
+        else {
+            console.log(`  ${r.relativePath}: OK`);
+        }
+    }
+    const s = report.summary;
+    console.log(`\nSummary: ${s.total} workflows | ${s.lintErrors} errors, ${s.lintWarnings} warnings, ${s.stateFail} state failures`);
+    process.exitCode = computeLintExitCode(report);
+}
+function buildLintTreeReport(treeResult) {
+    const results = [];
+    let lintErrors = 0;
+    let lintWarnings = 0;
+    let stateFail = 0;
+    for (const o of treeResult.outcomes) {
+        if (o.error) {
+            results.push({ relativePath: o.info.relativePath, error: o.error });
+            continue;
+        }
+        if (o.skipped) {
+            results.push({ relativePath: o.info.relativePath, error: `SKIPPED: ${o.skipReason}` });
+            continue;
+        }
+        const r = o.result;
+        results.push(r);
+        lintErrors += r.report.structural.error_count + (r.report.bestPractices?.error_count ?? 0);
+        lintWarnings += r.report.structural.warn_count + (r.report.bestPractices?.warn_count ?? 0);
+        stateFail += r.report.stateValidation?.filter((s) => s.status === "fail").length ?? 0;
+    }
+    const wfSummary = summarizeOutcomes(treeResult.outcomes, (r) => r.report.exitCode >= 2);
+    return {
+        root: treeResult.root,
+        results,
+        summary: { ...wfSummary, lintErrors, lintWarnings, stateFail },
+    };
+}
+function computeLintExitCode(report) {
+    const s = report.summary;
+    if (s.lintErrors > 0 || s.stateFail > 0 || s.error > 0)
+        return 2;
+    if (s.lintWarnings > 0)
+        return 1;
+    return 0;
+}
+//# sourceMappingURL=lint-tree.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"lint-tree.js","sourceRoot":"","sources":["../../src/commands/lint-tree.ts"],"names":[],"mappings":"AAAA;;GAEG;AACH,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AACnD,OAAO,EAAE,aAAa,EAAE,MAAM,kBAAkB,CAAC;AACjD,OAAO,EAAE,kBAAkB,EAAmB,MAAM,WAAW,CAAC;AAChE,OAAO,EAAE,WAAW,EAAE,iBAAiB,EAAqC,MAAM,WAAW,CAAC;AAqB9F,MAAM,CAAC,KAAK,UAAU,WAAW,CAAC,GAAW,EAAE,IAAqB;IAClE,qCAAqC;IACrC,IAAI,KAA4B,CAAC;IACjC,IAAI,CAAC,IAAI,CAAC,mBAAmB,EAAE,CAAC;QAC9B,IAAI,CAAC;YACH,KAAK,GAAG,IAAI,SAAS,CAAC,EAAE,QAAQ,EAAE,IAAI,CAAC,QAAQ,EAAE,CAAC,CAAC;YACnD,MAAM,KAAK,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC;YACzB,IAAI,KAAK,CAAC,KAAK,CAAC,OAAO,EAAE,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;gBACvC,OAAO,CAAC,IAAI,CAAC,oEAAoE,CAAC,CAAC;gBACnF,KAAK,GAAG,SAAS,CAAC;YACpB,CAAC;QACH,CAAC;QAAC,OAAO,CAAC,EAAE,CAAC;YACX,MAAM,GAAG,GAAG,CAAC,YAAY,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC;YACvD,OAAO,CAAC,IAAI,CAAC,8BAA8B,GAAG,EAAE,CAAC,CAAC;QACpD,CAAC;IACH,CAAC;IAED,MAAM,UAAU,GAAG,MAAM,WAAW,CAAC,GAAG,EAAE,KAAK,EAAE,IAAI,EAAE,IAAI,EAAE,EAAE;QAC7D,MAAM,MAAM,GAAG,aAAa,CAAC,IAAI,EAAE,IAAI,CAAC,MAAM,CAAC,CAAC;QAChD,MAAM,MAAM,GAAG,MAAM,kBAAkB,CAAC,IAAI,CAAC,IAAI,EAAE,IAAI,EAAE,MAAM,EAAE;YAC/D,iBAAiB,EAAE,IAAI,CAAC,iBAAiB;YACzC,mBAAmB,EAAE,IAAI,CAAC,mBAAmB;YAC7C,KAAK;SACN,CAAC,CAAC;QACH,OAAO,EAAE,YAAY,EAAE,IAAI,CAAC,YAAY,EAAE,MAAM,EAA+B,CAAC;IAClF,CAAC,CAAC,CAAC;IAEH,MAAM,MAAM,GAAG,mBAAmB,CAAC,UAAU,CAAC,CAAC;IAE/C,IAAI,IAAI,CAAC,IAAI,EAAE,CAAC;QACd,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,SAAS,CAAC,MAAM,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,CAAC;QAC7C,OAAO,CAAC,QAAQ,GAAG,mBAAmB,CAAC,MAAM,CAAC,CAAC;QAC/C,OAAO;IACT,CAAC;IAED,cAAc;IACd,KAAK,MAAM,OAAO,IAAI,UAAU,CAAC,QAAQ,EAAE,CAAC;QAC1C,IAAI,OAAO,CAAC,KAAK,EAAE,CAAC;YAClB,OAAO,CAAC,KAAK,CAAC,KAAK,OAAO,CAAC,IAAI,CAAC,YAAY,YAAY,OAAO,CAAC,KAAK,GAAG,CAAC,CAAC;YAC1E,SAAS;QACX,CAAC;QACD,IAAI,OAAO,CAAC,OAAO,EAAE,CAAC;YACpB,OAAO,CAAC,IAAI,CAAC,KAAK,OAAO,CAAC,IAAI,CAAC,YAAY,cAAc,OAAO,CAAC,UAAU,GAAG,CAAC,CAAC;YAChF,SAAS;QACX,CAAC;QACD,MAAM,CAAC,GAAG,OAAO,CAAC,MAAO,CAAC;QAC1B,MAAM,EAAE,GAAG,CAAC,CAAC,MAAM,CAAC;QACpB,MAAM,MAAM,GAAG,EAAE,CAAC,UAAU,CAAC,WAAW,GAAG,CAAC,EAAE,CAAC,aAAa,EAAE,WAAW,IAAI,CAAC,CAAC,CAAC;QAChF,MAAM,QAAQ,GAAG,EAAE,CAAC,UAAU,CAAC,UAAU,GAAG,CAAC,EAAE,CAAC,aAAa,EAAE,UAAU,IAAI,CAAC,CAAC,CAAC;QAChF,MAAM,UAAU,GAAG,EAAE,CAAC,eAAe,EAAE,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,MAAM,KAAK,MAAM,CAAC,CAAC,MAAM,IAAI,CAAC,CAAC;QAEtF,IAAI,MAAM,GAAG,CAAC,IAAI,UAAU,GAAG,CAAC,EAAE,CAAC;YACjC,OAAO,CAAC,KAAK,CACX,KAAK,CAAC,CAAC,YAAY,KAAK,MAAM,YAAY,QAAQ,cAAc,UAAU,iBAAiB,CAC5F,CAAC;YACF,KAAK,MAAM,CAAC,IAAI,EAAE,CAAC,UAAU,CAAC,MAAM;gBAAE,OAAO,CAAC,KAAK,CAAC,oBAAoB,CAAC,EAAE,CAAC,CAAC;YAC7E,IAAI,EAAE,CAAC,aAAa,EAAE,CAAC;gBACrB,KAAK,MAAM,CAAC,IAAI,EAAE,CAAC,aAAa,CAAC,MAAM;oBAAE,OAAO,CAAC,KAAK,CAAC,wBAAwB,CAAC,EAAE,CAAC,CAAC;YACtF,CAAC;YACD,IAAI,EAAE,CAAC,eAAe,EAAE,CAAC;gBACvB,KAAK,MAAM,CAAC,IAAI,EAAE,CAAC,eAAe,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,MAAM,KAAK,MAAM,CAAC,EAAE,CAAC;oBACtE,KAAK,MAAM,GAAG,IAAI,CAAC,CAAC,MAAM;wBACxB,OAAO,CAAC,KAAK,CAAC,oBAAoB,CAAC,CAAC,SAAS,KAAK,CAAC,CAAC,MAAM,MAAM,GAAG,EAAE,CAAC,CAAC;gBAC3E,CAAC;YACH,CAAC;QACH,CAAC;aAAM,IAAI,QAAQ,GAAG,CAAC,EAAE,CAAC;YACxB,OAAO,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,YAAY,KAAK,QAAQ,WAAW,CAAC,CAAC;QAC5D,CAAC;aAAM,CAAC;YACN,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,YAAY,MAAM,CAAC,CAAC;QACzC,CAAC;IACH,CAAC;IAED,MAAM,CAAC,GAAG,MAAM,CAAC,OAAO,CAAC;IACzB,OAAO,CAAC,GAAG,CACT,cAAc,CAAC,CAAC,KAAK,gBAAgB,CAAC,CAAC,UAAU,YAAY,CAAC,CAAC,YAAY,cAAc,CAAC,CAAC,SAAS,iBAAiB,CACtH,CAAC;IACF,OAAO,CAAC,QAAQ,GAAG,mBAAmB,CAAC,MAAM,CAAC,CAAC;AACjD,CAAC;AAED,SAAS,mBAAmB,CAAC,UAA0C;IACrE,MAAM,OAAO,GAA8B,EAAE,CAAC;IAC9C,IAAI,UAAU,GAAG,CAAC,CAAC;IACnB,IAAI,YAAY,GAAG,CAAC,CAAC;IACrB,IAAI,SAAS,GAAG,CAAC,CAAC;IAElB,KAAK,MAAM,CAAC,IAAI,UAAU,CAAC,QAAQ,EAAE,CAAC;QACpC,IAAI,CAAC,CAAC,KAAK,EAAE,CAAC;YACZ,OAAO,CAAC,IAAI,CAAC,EAAE,YAAY,EAAE,CAAC,CAAC,IAAI,CAAC,YAAY,EAAE,KAAK,EAAE,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC;YACpE,SAAS;QACX,CAAC;QACD,IAAI,CAAC,CAAC,OAAO,EAAE,CAAC;YACd,OAAO,CAAC,IAAI,CAAC,EAAE,YAAY,EAAE,CAAC,CAAC,IAAI,CAAC,YAAY,EAAE,KAAK,EAAE,YAAY,CAAC,CAAC,UAAU,EAAE,EAAE,CAAC,CAAC;YACvF,SAAS;QACX,CAAC;QACD,MAAM,CAAC,GAAG,CAAC,CAAC,MAAO,CAAC;QACpB,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;QAChB,UAAU,IAAI,CAAC,CAAC,MAAM,CAAC,UAAU,CAAC,WAAW,GAAG,CAAC,CAAC,CAAC,MAAM,CAAC,aAAa,EAAE,WAAW,IAAI,CAAC,CAAC,CAAC;QAC3F,YAAY,IAAI,CAAC,CAAC,MAAM,CAAC,UAAU,CAAC,UAAU,GAAG,CAAC,CAAC,CAAC,MAAM,CAAC,aAAa,EAAE,UAAU,IAAI,CAAC,CAAC,CAAC;QAC3F,SAAS,IAAI,CAAC,CAAC,MAAM,CAAC,eAAe,EAAE,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,MAAM,KAAK,MAAM,CAAC,CAAC,MAAM,IAAI,CAAC,CAAC;IACxF,CAAC;IAED,MAAM,SAAS,GAAG,iBAAiB,CAAC,UAAU,CAAC,QAAQ,EAAE,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,MAAM,CAAC,QAAQ,IAAI,CAAC,CAAC,CAAC;IAExF,OAAO;QACL,IAAI,EAAE,UAAU,CAAC,IAAI;QACrB,OAAO;QACP,OAAO,EAAE,EAAE,GAAG,SAAS,EAAE,UAAU,EAAE,YAAY,EAAE,SAAS,EAAE;KAC/D,CAAC;AACJ,CAAC;AAED,SAAS,mBAAmB,CAAC,MAAsB;IACjD,MAAM,CAAC,GAAG,MAAM,CAAC,OAAO,CAAC;IACzB,IAAI,CAAC,CAAC,UAAU,GAAG,CAAC,IAAI,CAAC,CAAC,SAAS,GAAG,CAAC,IAAI,CAAC,CAAC,KAAK,GAAG,CAAC;QAAE,OAAO,CAAC,CAAC;IACjE,IAAI,CAAC,CAAC,YAAY,GAAG,CAAC;QAAE,OAAO,CAAC,CAAC;IACjC,OAAO,CAAC,CAAC;AACX,CAAC"}

package/dist/commands/lint.d.ts

@@ -0,0 +1,30 @@
+/**
+ * `gxwf lint` — unified lint combining structural checks, best practices,
+ * and tool state validation.
+ */
+import { ToolCache } from "@galaxy-tool-util/core";
+import { type LintResult } from "@galaxy-tool-util/schema";
+import { type StepValidationResult } from "./validate-workflow.js";
+export interface LintOptions {
+    format?: string;
+    skipBestPractices?: boolean;
+    skipStateValidation?: boolean;
+    cacheDir?: string;
+    json?: boolean;
+}
+export interface LintReportOptions {
+    skipBestPractices?: boolean;
+    skipStateValidation?: boolean;
+    cache?: ToolCache;
+}
+export interface LintReport {
+    structural: LintResult;
+    bestPractices: LintResult | null;
+    stateValidation: StepValidationResult[] | null;
+    stateSkipped: boolean;
+    exitCode: number;
+}
+export declare function runLint(filePath: string, opts: LintOptions): Promise<void>;
+/** Lint a workflow, returning a structured report. Pure logic — no CLI I/O. */
+export declare function lintWorkflowReport(filePath: string, data: Record<string, unknown>, format: string, opts: LintReportOptions): Promise<LintReport>;
+//# sourceMappingURL=lint.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"lint.d.ts","sourceRoot":"","sources":["../../src/commands/lint.ts"],"names":[],"mappings":"AAAA;;;GAGG;AACH,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AACnD,OAAO,EAIL,KAAK,UAAU,EAEhB,MAAM,0BAA0B,CAAC;AAKlC,OAAO,EAGL,KAAK,oBAAoB,EAC1B,MAAM,wBAAwB,CAAC;AAEhC,MAAM,WAAW,WAAW;IAC1B,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,iBAAiB,CAAC,EAAE,OAAO,CAAC;IAC5B,mBAAmB,CAAC,EAAE,OAAO,CAAC;IAC9B,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,IAAI,CAAC,EAAE,OAAO,CAAC;CAChB;AAED,MAAM,WAAW,iBAAiB;IAChC,iBAAiB,CAAC,EAAE,OAAO,CAAC;IAC5B,mBAAmB,CAAC,EAAE,OAAO,CAAC;IAC9B,KAAK,CAAC,EAAE,SAAS,CAAC;CACnB;AAED,MAAM,WAAW,UAAU;IACzB,UAAU,EAAE,UAAU,CAAC;IACvB,aAAa,EAAE,UAAU,GAAG,IAAI,CAAC;IACjC,eAAe,EAAE,oBAAoB,EAAE,GAAG,IAAI,CAAC;IAC/C,YAAY,EAAE,OAAO,CAAC;IACtB,QAAQ,EAAE,MAAM,CAAC;CAClB;AAaD,wBAAsB,OAAO,CAAC,QAAQ,EAAE,MAAM,EAAE,IAAI,EAAE,WAAW,GAAG,OAAO,CAAC,IAAI,CAAC,CAuEhF;AAED,+EAA+E;AAC/E,wBAAsB,kBAAkB,CACtC,QAAQ,EAAE,MAAM,EAChB,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC7B,MAAM,EAAE,MAAM,EACd,IAAI,EAAE,iBAAiB,GACtB,OAAO,CAAC,UAAU,CAAC,CAoDrB"}

package/dist/commands/lint.js

@@ -0,0 +1,147 @@
+/**
+ * `gxwf lint` — unified lint combining structural checks, best practices,
+ * and tool state validation.
+ */
+import { ToolCache } from "@galaxy-tool-util/core";
+import { lintWorkflow, lintBestPracticesNative, lintBestPracticesFormat2, } from "@galaxy-tool-util/schema";
+import { dirname } from "node:path";
+import { renderStepResults } from "./render-results.js";
+import { readWorkflowFile, resolveFormat } from "./workflow-io.js";
+import { createDefaultResolver } from "./url-resolver.js";
+import { validateNativeSteps, validateFormat2Steps, } from "./validate-workflow.js";
+function mergeLintResults(...results) {
+    const errors = [];
+    const warnings = [];
+    for (const r of results) {
+        if (!r)
+            continue;
+        errors.push(...r.errors);
+        warnings.push(...r.warnings);
+    }
+    return { errors, warnings, error_count: errors.length, warn_count: warnings.length };
+}
+export async function runLint(filePath, opts) {
+    const data = await readWorkflowFile(filePath);
+    if (!data)
+        return;
+    const format = resolveFormat(data, opts.format);
+    // Build or load tool cache for state validation
+    let cache;
+    if (!opts.skipStateValidation) {
+        try {
+            cache = new ToolCache({ cacheDir: opts.cacheDir });
+            await cache.index.load();
+        }
+        catch (e) {
+            const msg = e instanceof Error ? e.message : String(e);
+            console.warn(`Failed to load tool cache: ${msg}`);
+        }
+    }
+    const report = await lintWorkflowReport(filePath, data, format, {
+        skipBestPractices: opts.skipBestPractices,
+        skipStateValidation: opts.skipStateValidation,
+        cache,
+    });
+    if (opts.json) {
+        console.log(JSON.stringify(report, null, 2));
+        process.exitCode = report.exitCode;
+        return;
+    }
+    // Structural lint
+    const { structural } = report;
+    if (structural.error_count > 0) {
+        console.error("Structural lint errors:");
+        for (const e of structural.errors)
+            console.error(`  ${e}`);
+    }
+    if (structural.warn_count > 0) {
+        console.warn("Structural lint warnings:");
+        for (const w of structural.warnings)
+            console.warn(`  ${w}`);
+    }
+    if (structural.error_count === 0 && structural.warn_count === 0) {
+        console.log("Structural lint: OK");
+    }
+    // Best practices
+    if (report.bestPractices) {
+        const bp = report.bestPractices;
+        if (bp.error_count > 0) {
+            console.error("Best practices errors:");
+            for (const e of bp.errors)
+                console.error(`  ${e}`);
+        }
+        if (bp.warn_count > 0) {
+            console.warn("Best practices warnings:");
+            for (const w of bp.warnings)
+                console.warn(`  ${w}`);
+        }
+        if (bp.error_count === 0 && bp.warn_count === 0) {
+            console.log("Best practices: OK");
+        }
+    }
+    // Tool state validation
+    if (report.stateValidation) {
+        const { validated, skipped } = renderStepResults(report.stateValidation);
+        if (report.stateValidation.length > 0) {
+            console.log(`\nTool state: ${validated} validated, ${skipped} skipped`);
+        }
+    }
+    else if (report.stateSkipped) {
+        console.log("Tool state validation: skipped");
+    }
+    process.exitCode = report.exitCode;
+}
+/** Lint a workflow, returning a structured report. Pure logic — no CLI I/O. */
+export async function lintWorkflowReport(filePath, data, format, opts) {
+    // Phase 1: Structural lint (always runs)
+    const structural = lintWorkflow(data);
+    // Phase 2: Best practices
+    let bestPractices = null;
+    if (!opts.skipBestPractices) {
+        bestPractices =
+            format === "native" ? lintBestPracticesNative(data) : lintBestPracticesFormat2(data);
+    }
+    // Phase 3: Tool state validation
+    let stateValidation = null;
+    let stateSkipped = !!opts.skipStateValidation;
+    if (!opts.skipStateValidation) {
+        const cache = opts.cache;
+        if (!cache) {
+            stateSkipped = true;
+        }
+        else {
+            try {
+                const isEmpty = cache.index.listAll().length === 0;
+                if (isEmpty) {
+                    console.warn("Tool cache is empty — skipping tool state validation");
+                    stateSkipped = true;
+                }
+                else {
+                    const workflowDirectory = dirname(filePath);
+                    const expansionOpts = {
+                        resolver: createDefaultResolver({ workflowDirectory }),
+                    };
+                    if (format === "native") {
+                        stateValidation = await validateNativeSteps(data, cache, "", expansionOpts);
+                    }
+                    else {
+                        stateValidation = await validateFormat2Steps(data, cache, "", expansionOpts);
+                    }
+                }
+            }
+            catch (e) {
+                const msg = e instanceof Error ? e.message : String(e);
+                console.warn(`Tool state validation failed: ${msg}`);
+                stateSkipped = true;
+            }
+        }
+    }
+    // Compute exit code: 0 = clean, 1 = warnings only, 2 = errors
+    const merged = mergeLintResults(structural, bestPractices);
+    const hasStateErrors = stateValidation?.some((r) => r.status === "fail") ?? false;
+    const hasErrors = merged.error_count > 0 || hasStateErrors;
+    const hasWarnings = merged.warn_count > 0;
+    const exitCode = hasErrors ? 2 : hasWarnings ? 1 : 0;
+    return { structural, bestPractices, stateValidation, stateSkipped, exitCode };
+}
+//# sourceMappingURL=lint.js.map

package/dist/commands/lint.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"lint.js","sourceRoot":"","sources":["../../src/commands/lint.ts"],"names":[],"mappings":"AAAA;;;GAGG;AACH,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AACnD,OAAO,EACL,YAAY,EACZ,uBAAuB,EACvB,wBAAwB,GAGzB,MAAM,0BAA0B,CAAC;AAClC,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AACpC,OAAO,EAAE,iBAAiB,EAAE,MAAM,qBAAqB,CAAC;AACxD,OAAO,EAAE,gBAAgB,EAAE,aAAa,EAAE,MAAM,kBAAkB,CAAC;AACnE,OAAO,EAAE,qBAAqB,EAAE,MAAM,mBAAmB,CAAC;AAC1D,OAAO,EACL,mBAAmB,EACnB,oBAAoB,GAErB,MAAM,wBAAwB,CAAC;AAwBhC,SAAS,gBAAgB,CAAC,GAAG,OAA8B;IACzD,MAAM,MAAM,GAAa,EAAE,CAAC;IAC5B,MAAM,QAAQ,GAAa,EAAE,CAAC;IAC9B,KAAK,MAAM,CAAC,IAAI,OAAO,EAAE,CAAC;QACxB,IAAI,CAAC,CAAC;YAAE,SAAS;QACjB,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,MAAM,CAAC,CAAC;QACzB,QAAQ,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,QAAQ,CAAC,CAAC;IAC/B,CAAC;IACD,OAAO,EAAE,MAAM,EAAE,QAAQ,EAAE,WAAW,EAAE,MAAM,CAAC,MAAM,EAAE,UAAU,EAAE,QAAQ,CAAC,MAAM,EAAE,CAAC;AACvF,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,OAAO,CAAC,QAAgB,EAAE,IAAiB;IAC/D,MAAM,IAAI,GAAG,MAAM,gBAAgB,CAAC,QAAQ,CAAC,CAAC;IAC9C,IAAI,CAAC,IAAI;QAAE,OAAO;IAElB,MAAM,MAAM,GAAG,aAAa,CAAC,IAAI,EAAE,IAAI,CAAC,MAAM,CAAC,CAAC;IAEhD,gDAAgD;IAChD,IAAI,KAA4B,CAAC;IACjC,IAAI,CAAC,IAAI,CAAC,mBAAmB,EAAE,CAAC;QAC9B,IAAI,CAAC;YACH,KAAK,GAAG,IAAI,SAAS,CAAC,EAAE,QAAQ,EAAE,IAAI,CAAC,QAAQ,EAAE,CAAC,CAAC;YACnD,MAAM,KAAK,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC;QAC3B,CAAC;QAAC,OAAO,CAAC,EAAE,CAAC;YACX,MAAM,GAAG,GAAG,CAAC,YAAY,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC;YACvD,OAAO,CAAC,IAAI,CAAC,8BAA8B,GAAG,EAAE,CAAC,CAAC;QACpD,CAAC;IACH,CAAC;IAED,MAAM,MAAM,GAAG,MAAM,kBAAkB,CAAC,QAAQ,EAAE,IAAI,EAAE,MAAM,EAAE;QAC9D,iBAAiB,EAAE,IAAI,CAAC,iBAAiB;QACzC,mBAAmB,EAAE,IAAI,CAAC,mBAAmB;QAC7C,KAAK;KACN,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;QAC7C,OAAO,CAAC,QAAQ,GAAG,MAAM,CAAC,QAAQ,CAAC;QACnC,OAAO;IACT,CAAC;IAED,kBAAkB;IAClB,MAAM,EAAE,UAAU,EAAE,GAAG,MAAM,CAAC;IAC9B,IAAI,UAAU,CAAC,WAAW,GAAG,CAAC,EAAE,CAAC;QAC/B,OAAO,CAAC,KAAK,CAAC,yBAAyB,CAAC,CAAC;QACzC,KAAK,MAAM,CAAC,IAAI,UAAU,CAAC,MAAM;YAAE,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IAC7D,CAAC;IACD,IAAI,UAAU,CAAC,UAAU,GAAG,CAAC,EAAE,CAAC;QAC9B,OAAO,CAAC,IAAI,CAAC,2BAA2B,CAAC,CAAC;QAC1C,KAAK,MAAM,CAAC,IAAI,UAAU,CAAC,QAAQ;YAAE,OAAO,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IAC9D,CAAC;IACD,IAAI,UAAU,CAAC,WAAW,KAAK,CAAC,IAAI,UAAU,CAAC,UAAU,KAAK,CAAC,EAAE,CAAC;QAChE,OAAO,CAAC,GAAG,CAAC,qBAAqB,CAAC,CAAC;IACrC,CAAC;IAED,iBAAiB;IACjB,IAAI,MAAM,CAAC,aAAa,EAAE,CAAC;QACzB,MAAM,EAAE,GAAG,MAAM,CAAC,aAAa,CAAC;QAChC,IAAI,EAAE,CAAC,WAAW,GAAG,CAAC,EAAE,CAAC;YACvB,OAAO,CAAC,KAAK,CAAC,wBAAwB,CAAC,CAAC;YACxC,KAAK,MAAM,CAAC,IAAI,EAAE,CAAC,MAAM;gBAAE,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;QACrD,CAAC;QACD,IAAI,EAAE,CAAC,UAAU,GAAG,CAAC,EAAE,CAAC;YACtB,OAAO,CAAC,IAAI,CAAC,0BAA0B,CAAC,CAAC;YACzC,KAAK,MAAM,CAAC,IAAI,EAAE,CAAC,QAAQ;gBAAE,OAAO,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;QACtD,CAAC;QACD,IAAI,EAAE,CAAC,WAAW,KAAK,CAAC,IAAI,EAAE,CAAC,UAAU,KAAK,CAAC,EAAE,CAAC;YAChD,OAAO,CAAC,GAAG,CAAC,oBAAoB,CAAC,CAAC;QACpC,CAAC;IACH,CAAC;IAED,wBAAwB;IACxB,IAAI,MAAM,CAAC,eAAe,EAAE,CAAC;QAC3B,MAAM,EAAE,SAAS,EAAE,OAAO,EAAE,GAAG,iBAAiB,CAAC,MAAM,CAAC,eAAe,CAAC,CAAC;QACzE,IAAI,MAAM,CAAC,eAAe,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;YACtC,OAAO,CAAC,GAAG,CAAC,iBAAiB,SAAS,eAAe,OAAO,UAAU,CAAC,CAAC;QAC1E,CAAC;IACH,CAAC;SAAM,IAAI,MAAM,CAAC,YAAY,EAAE,CAAC;QAC/B,OAAO,CAAC,GAAG,CAAC,gCAAgC,CAAC,CAAC;IAChD,CAAC;IAED,OAAO,CAAC,QAAQ,GAAG,MAAM,CAAC,QAAQ,CAAC;AACrC,CAAC;AAED,+EAA+E;AAC/E,MAAM,CAAC,KAAK,UAAU,kBAAkB,CACtC,QAAgB,EAChB,IAA6B,EAC7B,MAAc,EACd,IAAuB;IAEvB,yCAAyC;IACzC,MAAM,UAAU,GAAG,YAAY,CAAC,IAAI,CAAC,CAAC;IAEtC,0BAA0B;IAC1B,IAAI,aAAa,GAAsB,IAAI,CAAC;IAC5C,IAAI,CAAC,IAAI,CAAC,iBAAiB,EAAE,CAAC;QAC5B,aAAa;YACX,MAAM,KAAK,QAAQ,CAAC,CAAC,CAAC,uBAAuB,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,wBAAwB,CAAC,IAAI,CAAC,CAAC;IACzF,CAAC;IAED,iCAAiC;IACjC,IAAI,eAAe,GAAkC,IAAI,CAAC;IAC1D,IAAI,YAAY,GAAG,CAAC,CAAC,IAAI,CAAC,mBAAmB,CAAC;IAC9C,IAAI,CAAC,IAAI,CAAC,mBAAmB,EAAE,CAAC;QAC9B,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC;QACzB,IAAI,CAAC,KAAK,EAAE,CAAC;YACX,YAAY,GAAG,IAAI,CAAC;QACtB,CAAC;aAAM,CAAC;YACN,IAAI,CAAC;gBACH,MAAM,OAAO,GAAG,KAAK,CAAC,KAAK,CAAC,OAAO,EAAE,CAAC,MAAM,KAAK,CAAC,CAAC;gBACnD,IAAI,OAAO,EAAE,CAAC;oBACZ,OAAO,CAAC,IAAI,CAAC,sDAAsD,CAAC,CAAC;oBACrE,YAAY,GAAG,IAAI,CAAC;gBACtB,CAAC;qBAAM,CAAC;oBACN,MAAM,iBAAiB,GAAG,OAAO,CAAC,QAAQ,CAAC,CAAC;oBAC5C,MAAM,aAAa,GAAqB;wBACtC,QAAQ,EAAE,qBAAqB,CAAC,EAAE,iBAAiB,EAAE,CAAC;qBACvD,CAAC;oBACF,IAAI,MAAM,KAAK,QAAQ,EAAE,CAAC;wBACxB,eAAe,GAAG,MAAM,mBAAmB,CAAC,IAAI,EAAE,KAAK,EAAE,EAAE,EAAE,aAAa,CAAC,CAAC;oBAC9E,CAAC;yBAAM,CAAC;wBACN,eAAe,GAAG,MAAM,oBAAoB,CAAC,IAAI,EAAE,KAAK,EAAE,EAAE,EAAE,aAAa,CAAC,CAAC;oBAC/E,CAAC;gBACH,CAAC;YACH,CAAC;YAAC,OAAO,CAAC,EAAE,CAAC;gBACX,MAAM,GAAG,GAAG,CAAC,YAAY,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC;gBACvD,OAAO,CAAC,IAAI,CAAC,iCAAiC,GAAG,EAAE,CAAC,CAAC;gBACrD,YAAY,GAAG,IAAI,CAAC;YACtB,CAAC;QACH,CAAC;IACH,CAAC;IAED,8DAA8D;IAC9D,MAAM,MAAM,GAAG,gBAAgB,CAAC,UAAU,EAAE,aAAa,CAAC,CAAC;IAC3D,MAAM,cAAc,GAAG,eAAe,EAAE,IAAI,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,MAAM,KAAK,MAAM,CAAC,IAAI,KAAK,CAAC;IAClF,MAAM,SAAS,GAAG,MAAM,CAAC,WAAW,GAAG,CAAC,IAAI,cAAc,CAAC;IAC3D,MAAM,WAAW,GAAG,MAAM,CAAC,UAAU,GAAG,CAAC,CAAC;IAE1C,MAAM,QAAQ,GAAG,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;IAErD,OAAO,EAAE,UAAU,EAAE,aAAa,EAAE,eAAe,EAAE,YAAY,EAAE,QAAQ,EAAE,CAAC;AAChF,CAAC"}

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

@@ -0,0 +1,6 @@
+export interface PopulateWorkflowOptions {
+    cacheDir?: string;
+    galaxyUrl?: string;
+}
+export declare function runPopulateWorkflow(filePath: string, opts: PopulateWorkflowOptions): Promise<void>;
+//# sourceMappingURL=populate-workflow.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"populate-workflow.d.ts","sourceRoot":"","sources":["../../src/commands/populate-workflow.ts"],"names":[],"mappings":"AAeA,MAAM,WAAW,uBAAuB;IACtC,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,SAAS,CAAC,EAAE,MAAM,CAAC;CACpB;AAED,wBAAsB,mBAAmB,CACvC,QAAQ,EAAE,MAAM,EAChB,IAAI,EAAE,uBAAuB,GAC5B,OAAO,CAAC,IAAI,CAAC,CAgDf"}

package/dist/commands/populate-workflow.js

@@ -0,0 +1,55 @@
+/**
+ * `galaxy-tool-cache populate-workflow` — scan workflow(s) for tool references
+ * and populate the cache with each unique tool.
+ */
+import { ToolInfoService } from "@galaxy-tool-util/core";
+import { expandedNative, expandedFormat2, } from "@galaxy-tool-util/schema";
+import { dirname } from "node:path";
+import { readWorkflowFile, resolveFormat } from "./workflow-io.js";
+import { createDefaultResolver } from "./url-resolver.js";
+export async function runPopulateWorkflow(filePath, opts) {
+    const data = await readWorkflowFile(filePath);
+    if (!data)
+        return;
+    const format = resolveFormat(data);
+    const workflowDirectory = dirname(filePath);
+    const expansionOpts = {
+        resolver: createDefaultResolver({ workflowDirectory }),
+    };
+    let tools;
+    if (format === "native") {
+        const expanded = await expandedNative(data, expansionOpts);
+        tools = expanded.unique_tools;
+    }
+    else {
+        const expanded = await expandedFormat2(data, expansionOpts);
+        tools = expanded.unique_tools;
+    }
+    if (tools.size === 0) {
+        console.log("No tool steps found in workflow.");
+        return;
+    }
+    const service = new ToolInfoService({
+        cacheDir: opts.cacheDir,
+        galaxyUrl: opts.galaxyUrl,
+    });
+    let cached = 0;
+    let failed = 0;
+    const total = tools.size;
+    for (const ref of tools) {
+        const result = await service.getToolInfo(ref.tool_id, ref.tool_version);
+        if (result) {
+            cached++;
+            console.log(`  Cached: ${ref.tool_id} v${ref.tool_version ?? "latest"}`);
+        }
+        else {
+            failed++;
+            console.warn(`  Failed: ${ref.tool_id} v${ref.tool_version ?? "latest"}`);
+        }
+    }
+    console.log(`\nPopulated ${cached}/${total} tools${failed > 0 ? `, ${failed} failed` : ""}`);
+    if (failed > 0) {
+        process.exitCode = 1;
+    }
+}
+//# sourceMappingURL=populate-workflow.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"populate-workflow.js","sourceRoot":"","sources":["../../src/commands/populate-workflow.ts"],"names":[],"mappings":"AAAA;;;GAGG;AACH,OAAO,EAAE,eAAe,EAAE,MAAM,wBAAwB,CAAC;AACzD,OAAO,EACL,cAAc,EACd,eAAe,GAGhB,MAAM,0BAA0B,CAAC;AAClC,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AACpC,OAAO,EAAE,gBAAgB,EAAE,aAAa,EAAE,MAAM,kBAAkB,CAAC;AACnE,OAAO,EAAE,qBAAqB,EAAE,MAAM,mBAAmB,CAAC;AAO1D,MAAM,CAAC,KAAK,UAAU,mBAAmB,CACvC,QAAgB,EAChB,IAA6B;IAE7B,MAAM,IAAI,GAAG,MAAM,gBAAgB,CAAC,QAAQ,CAAC,CAAC;IAC9C,IAAI,CAAC,IAAI;QAAE,OAAO;IAElB,MAAM,MAAM,GAAG,aAAa,CAAC,IAAI,CAAC,CAAC;IACnC,MAAM,iBAAiB,GAAG,OAAO,CAAC,QAAQ,CAAC,CAAC;IAC5C,MAAM,aAAa,GAAqB;QACtC,QAAQ,EAAE,qBAAqB,CAAC,EAAE,iBAAiB,EAAE,CAAC;KACvD,CAAC;IAEF,IAAI,KAAyB,CAAC;IAC9B,IAAI,MAAM,KAAK,QAAQ,EAAE,CAAC;QACxB,MAAM,QAAQ,GAAG,MAAM,cAAc,CAAC,IAAI,EAAE,aAAa,CAAC,CAAC;QAC3D,KAAK,GAAG,QAAQ,CAAC,YAAY,CAAC;IAChC,CAAC;SAAM,CAAC;QACN,MAAM,QAAQ,GAAG,MAAM,eAAe,CAAC,IAAI,EAAE,aAAa,CAAC,CAAC;QAC5D,KAAK,GAAG,QAAQ,CAAC,YAAY,CAAC;IAChC,CAAC;IAED,IAAI,KAAK,CAAC,IAAI,KAAK,CAAC,EAAE,CAAC;QACrB,OAAO,CAAC,GAAG,CAAC,kCAAkC,CAAC,CAAC;QAChD,OAAO;IACT,CAAC;IAED,MAAM,OAAO,GAAG,IAAI,eAAe,CAAC;QAClC,QAAQ,EAAE,IAAI,CAAC,QAAQ;QACvB,SAAS,EAAE,IAAI,CAAC,SAAS;KAC1B,CAAC,CAAC;IAEH,IAAI,MAAM,GAAG,CAAC,CAAC;IACf,IAAI,MAAM,GAAG,CAAC,CAAC;IACf,MAAM,KAAK,GAAG,KAAK,CAAC,IAAI,CAAC;IAEzB,KAAK,MAAM,GAAG,IAAI,KAAK,EAAE,CAAC;QACxB,MAAM,MAAM,GAAG,MAAM,OAAO,CAAC,WAAW,CAAC,GAAG,CAAC,OAAO,EAAE,GAAG,CAAC,YAAY,CAAC,CAAC;QACxE,IAAI,MAAM,EAAE,CAAC;YACX,MAAM,EAAE,CAAC;YACT,OAAO,CAAC,GAAG,CAAC,aAAa,GAAG,CAAC,OAAO,KAAK,GAAG,CAAC,YAAY,IAAI,QAAQ,EAAE,CAAC,CAAC;QAC3E,CAAC;aAAM,CAAC;YACN,MAAM,EAAE,CAAC;YACT,OAAO,CAAC,IAAI,CAAC,aAAa,GAAG,CAAC,OAAO,KAAK,GAAG,CAAC,YAAY,IAAI,QAAQ,EAAE,CAAC,CAAC;QAC5E,CAAC;IACH,CAAC;IAED,OAAO,CAAC,GAAG,CAAC,eAAe,MAAM,IAAI,KAAK,SAAS,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,KAAK,MAAM,SAAS,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;IAC7F,IAAI,MAAM,GAAG,CAAC,EAAE,CAAC;QACf,OAAO,CAAC,QAAQ,GAAG,CAAC,CAAC;IACvB,CAAC;AACH,CAAC"}

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

@@ -0,0 +1,11 @@
+/**
+ * Shared rendering for StepValidationResult arrays.
+ */
+import type { StepValidationResult } from "./validate-workflow.js";
+export interface RenderSummary {
+    validated: number;
+    skipped: number;
+}
+/** Render step validation results to console, returning counts. */
+export declare function renderStepResults(results: StepValidationResult[]): RenderSummary;
+//# sourceMappingURL=render-results.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"render-results.d.ts","sourceRoot":"","sources":["../../src/commands/render-results.ts"],"names":[],"mappings":"AAAA;;GAEG;AACH,OAAO,KAAK,EAAE,oBAAoB,EAAE,MAAM,wBAAwB,CAAC;AAEnE,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

@@ -0,0 +1,23 @@
+/** 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") {
+            skipped++;
+            console.warn(`  [${r.stepLabel}] skipped — ${r.errors[0] ?? "unknown"}`);
+        }
+        else if (r.status === "fail") {
+            validated++;
+            console.error(`  [${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`);
+        }
+    }
+    return { validated, skipped };
+}
+//# sourceMappingURL=render-results.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"render-results.js","sourceRoot":"","sources":["../../src/commands/render-results.ts"],"names":[],"mappings":"AAUA,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,CAAC,CAAC,MAAM,KAAK,MAAM,EAAE,CAAC;YACxB,OAAO,EAAE,CAAC;YACV,OAAO,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,SAAS,eAAe,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,IAAI,SAAS,EAAE,CAAC,CAAC;QAC3E,CAAC;aAAM,IAAI,CAAC,CAAC,MAAM,KAAK,MAAM,EAAE,CAAC;YAC/B,SAAS,EAAE,CAAC;YACZ,OAAO,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,SAAS,wBAAwB,CAAC,CAAC,MAAM,IAAI,CAAC,CAAC;YACrE,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,SAAS,kBAAkB,CAAC,CAAC;QACnD,CAAC;IACH,CAAC;IACD,OAAO,EAAE,SAAS,EAAE,OAAO,EAAE,CAAC;AAChC,CAAC"}

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

@@ -0,0 +1,13 @@
+export interface RoundtripTreeOptions {
+    cacheDir?: string;
+    format?: string;
+    json?: boolean;
+    /** Only list files with error-severity diffs or failures. */
+    errorsOnly?: boolean;
+    /** Only list files with benign diffs (no errors, no failures). */
+    benignOnly?: boolean;
+    /** Suppress per-file lines; print only the aggregate summary. */
+    brief?: boolean;
+}
+export declare function runRoundtripTree(dir: string, opts: RoundtripTreeOptions): Promise<void>;
+//# sourceMappingURL=roundtrip-tree.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"roundtrip-tree.d.ts","sourceRoot":"","sources":["../../src/commands/roundtrip-tree.ts"],"names":[],"mappings":"AAiBA,MAAM,WAAW,oBAAoB;IACnC,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,CAoH7F"}