@galaxy-tool-util/cli 0.1.0 → 0.4.0

package/dist/commands/convert-tree.js

@@ -0,0 +1,229 @@
+import { makeNodeToolCache } from "@galaxy-tool-util/core/node";
+import { toFormat2, toFormat2Stateful, toNative, toNativeStateful, checkStrictEncoding, checkStrictStructure, } from "@galaxy-tool-util/schema";
+import { mkdir, writeFile } from "node:fs/promises";
+import { dirname, join, basename } from "node:path";
+import { loadToolInputsForWorkflow } from "./stateful-tool-inputs.js";
+import { createDefaultResolver } from "./url-resolver.js";
+import { resolveStrictOptions } from "./strict-options.js";
+import { resolveFormat, serializeWorkflow } from "./workflow-io.js";
+import { collectTree, summarizeOutcomes } from "./tree.js";
+export async function runConvertTree(dir, opts) {
+    const outputDir = opts.outputDir;
+    if (!outputDir) {
+        console.error("--output-dir is required for convert-tree");
+        process.exitCode = 1;
+        return;
+    }
+    // Shared tool cache for stateful mode (loaded once per run)
+    let cache = null;
+    if (opts.stateful) {
+        cache = makeNodeToolCache({ cacheDir: opts.cacheDir });
+        await cache.index.load();
+        if ((await cache.index.listAll()).length === 0) {
+            console.warn("Tool cache is empty — stateful conversion will fall back for every step");
+        }
+    }
+    const strict = resolveStrictOptions(opts);
+    const treeResult = await collectTree(dir, async (info, data) => {
+        const sourceFormat = resolveFormat(data, opts.format);
+        const targetFormat = resolveTargetFormat(sourceFormat, opts.to);
+        // Per-file strict checks on input
+        if (strict.strictEncoding) {
+            const encErrors = checkStrictEncoding(data, sourceFormat);
+            if (encErrors.length > 0) {
+                throw new Error(`Encoding: ${encErrors.join("; ")}`);
+            }
+        }
+        if (strict.strictStructure) {
+            const structErrors = checkStrictStructure(data, sourceFormat);
+            if (structErrors.length > 0) {
+                throw new Error(`Structure: ${structErrors.join("; ")}`);
+            }
+        }
+        if (sourceFormat === targetFormat) {
+            return {
+                relativePath: info.relativePath,
+                sourceFormat,
+                targetFormat,
+            };
+        }
+        let result;
+        let statefulSteps;
+        let toolLoadErrors;
+        if (opts.stateful && cache) {
+            const expansionOpts = {
+                resolver: createDefaultResolver({
+                    workflowDirectory: dirname(join(dir, info.relativePath)),
+                }),
+            };
+            const { resolver, status: toolStatus } = await loadToolInputsForWorkflow(data, sourceFormat, cache, expansionOpts);
+            const failedLoads = toolStatus.filter((s) => !s.loaded);
+            if (failedLoads.length > 0)
+                toolLoadErrors = failedLoads;
+            if (targetFormat === "format2") {
+                const r = toFormat2Stateful(data, resolver);
+                result = r.workflow;
+                statefulSteps = r.steps;
+                if (opts.compact)
+                    stripPositionInfo(result);
+            }
+            else {
+                const r = toNativeStateful(data, resolver);
+                result = r.workflow;
+                statefulSteps = r.steps;
+            }
+        }
+        else if (targetFormat === "format2") {
+            result = toFormat2(data);
+            if (opts.compact) {
+                stripPositionInfo(result);
+            }
+        }
+        else {
+            result = toNative(data);
+        }
+        const serialized = serializeWorkflow(result, targetFormat, {
+            json: opts.json,
+            yaml: opts.yaml,
+        });
+        // Write to output dir, adjusting extension for target format
+        const outName = renameForFormat(info.relativePath, targetFormat);
+        const outPath = join(outputDir, outName);
+        await mkdir(dirname(outPath), { recursive: true });
+        await writeFile(outPath, serialized, "utf-8");
+        // --strict-state: require all stateful steps to convert successfully
+        if (strict.strictState && statefulSteps?.some((s) => !s.converted)) {
+            throw new Error("Strict state: all steps must convert successfully");
+        }
+        return {
+            relativePath: info.relativePath,
+            sourceFormat,
+            targetFormat,
+            statefulSteps,
+            toolLoadErrors,
+        };
+    });
+    const report = buildConvertReport(treeResult);
+    // Aggregate stateful step counts across files
+    let statefulFallbacks = 0;
+    if (opts.stateful) {
+        for (const r of report.results) {
+            if ("statefulSteps" in r && r.statefulSteps) {
+                statefulFallbacks += r.statefulSteps.filter((s) => !s.converted).length;
+            }
+        }
+    }
+    if (opts.reportJson) {
+        console.log(JSON.stringify(report, null, 2));
+        process.exitCode = report.summary.error > 0 || statefulFallbacks > 0 ? 1 : 0;
+        return;
+    }
+    // Text output
+    for (const outcome of treeResult.outcomes) {
+        if (outcome.error) {
+            console.error(`  ${outcome.info.relativePath}: ERROR (${outcome.error})`);
+            continue;
+        }
+        const r = outcome.result;
+        if (r.sourceFormat === r.targetFormat) {
+            console.warn(`  ${r.relativePath}: already ${r.targetFormat}, skipped`);
+        }
+        else {
+            let line = `  ${r.relativePath}: ${r.sourceFormat} → ${r.targetFormat}`;
+            if (r.statefulSteps) {
+                const converted = r.statefulSteps.filter((s) => s.converted).length;
+                line += ` [stateful ${converted}/${r.statefulSteps.length}]`;
+            }
+            console.log(line);
+            if (r.toolLoadErrors) {
+                for (const t of r.toolLoadErrors) {
+                    const ver = t.toolVersion ? `@${t.toolVersion}` : "";
+                    console.error(`    tool ${t.toolId}${ver}: ${t.error}`);
+                }
+            }
+        }
+    }
+    const s = report.summary;
+    console.log(`\nSummary: ${s.total} workflows converted (written to ${outputDir})`);
+    if (opts.stateful) {
+        console.log(`Stateful: ${statefulFallbacks} step(s) fell back to schema-free`);
+        // Aggregate failure classes across all files
+        const byClass = new Map();
+        for (const r of report.results) {
+            if ("statefulSteps" in r && r.statefulSteps) {
+                for (const step of r.statefulSteps) {
+                    if (!step.converted) {
+                        const cls = step.failureClass ?? "unknown";
+                        byClass.set(cls, (byClass.get(cls) ?? 0) + 1);
+                    }
+                }
+            }
+        }
+        if (byClass.size > 0) {
+            const summary = Array.from(byClass.entries())
+                .map(([k, v]) => `${k}=${v}`)
+                .join(", ");
+            console.log(`  fallback breakdown: ${summary}`);
+        }
+    }
+    process.exitCode = s.error > 0 || statefulFallbacks > 0 ? 1 : 0;
+}
+function resolveTargetFormat(sourceFormat, toOpt) {
+    if (toOpt === "native" || toOpt === "format2")
+        return toOpt;
+    return sourceFormat === "native" ? "format2" : "native";
+}
+/** Rename a relative path's extension for the target format. */
+function renameForFormat(relPath, targetFormat) {
+    const dir = dirname(relPath);
+    let name = basename(relPath);
+    // Strip known workflow extensions
+    if (name.endsWith(".gxwf.yml"))
+        name = name.slice(0, -9);
+    else if (name.endsWith(".gxwf.yaml"))
+        name = name.slice(0, -10);
+    else if (name.endsWith(".ga"))
+        name = name.slice(0, -3);
+    else if (name.endsWith(".json"))
+        name = name.slice(0, -5);
+    else if (name.endsWith(".yml"))
+        name = name.slice(0, -4);
+    else if (name.endsWith(".yaml"))
+        name = name.slice(0, -5);
+    const ext = targetFormat === "format2" ? ".gxwf.yml" : ".ga";
+    const newName = name + ext;
+    return dir === "." ? newName : join(dir, newName);
+}
+/** 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);
+        }
+    }
+}
+function buildConvertReport(treeResult) {
+    const results = [];
+    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;
+        }
+        results.push(o.result);
+    }
+    const wfSummary = summarizeOutcomes(treeResult.outcomes);
+    return { root: treeResult.root, results, summary: wfSummary };
+}
+//# sourceMappingURL=convert-tree.js.map

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

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

@@ -0,0 +1,13 @@
+import { type StrictOptions } from "./strict-options.js";
+export interface ConvertOptions extends StrictOptions {
+    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":"AAkBA,OAAO,EAAwB,KAAK,aAAa,EAAE,MAAM,qBAAqB,CAAC;AAQ/E,MAAM,WAAW,cAAe,SAAQ,aAAa;IACnD,EAAE,CAAC,EAAE,MAAM,CAAC;IACZ,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB,QAAQ,CAAC,EAAE,MAAM,CAAC;CACnB;AAED,wBAAsB,UAAU,CAAC,QAAQ,EAAE,MAAM,EAAE,IAAI,EAAE,cAAc,GAAG,OAAO,CAAC,IAAI,CAAC,CAkGtF"}

package/dist/commands/convert.js

@@ -0,0 +1,151 @@
+/**
+ * `gxwf convert` — convert between native (.ga) and format2 (.gxwf.yml) formats.
+ */
+import { makeNodeToolCache } from "@galaxy-tool-util/core/node";
+import { toFormat2, toFormat2Stateful, toNative, toNativeStateful, checkStrictEncoding, checkStrictStructure, } from "@galaxy-tool-util/schema";
+import { dirname } from "node:path";
+import { loadToolInputsForWorkflow } from "./stateful-tool-inputs.js";
+import { createDefaultResolver } from "./url-resolver.js";
+import { resolveStrictOptions } from "./strict-options.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);
+    const strict = resolveStrictOptions(opts);
+    // Pre-conversion strict checks on input
+    if (strict.strictEncoding) {
+        const encErrors = checkStrictEncoding(data, sourceFormat);
+        if (encErrors.length > 0) {
+            console.error("Encoding errors:");
+            for (const e of encErrors)
+                console.error(`  ${e}`);
+            process.exitCode = 2;
+            return;
+        }
+    }
+    if (strict.strictStructure) {
+        const structErrors = checkStrictStructure(data, sourceFormat);
+        if (structErrors.length > 0) {
+            console.error("Structure errors (strict):");
+            for (const e of structErrors)
+                console.error(`  ${e}`);
+            process.exitCode = 2;
+            return;
+        }
+    }
+    if (sourceFormat === targetFormat) {
+        console.error(`Source and target formats are both ${sourceFormat}. ` +
+            `Use --to to specify the target format.`);
+        process.exitCode = 1;
+        return;
+    }
+    let result;
+    let stepStatuses = null;
+    if (opts.stateful) {
+        const cache = makeNodeToolCache({ cacheDir: opts.cacheDir });
+        await cache.index.load();
+        if ((await cache.index.listAll()).length === 0) {
+            console.warn("Tool cache is empty — stateful conversion will fall back for every step");
+        }
+        const expansionOpts = {
+            resolver: createDefaultResolver({ workflowDirectory: dirname(filePath) }),
+        };
+        const { resolver, status: toolStatus } = await loadToolInputsForWorkflow(data, sourceFormat, cache, expansionOpts);
+        for (const s of toolStatus) {
+            if (!s.loaded) {
+                const ver = s.toolVersion ? `@${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);
+        // --strict-state: require all steps to convert successfully
+        if (strict.strictState) {
+            const hasFailures = stepStatuses.some((s) => !s.converted);
+            if (hasFailures) {
+                console.error("Strict state: all steps must convert successfully");
+                process.exitCode = 2;
+                return;
+            }
+        }
+    }
+}
+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 @@
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package/dist/commands/info.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"info.d.ts","sourceRoot":"","sources":["../../src/commands/info.ts"],"names":[],"mappings":"AAEA,MAAM,WAAW,WAAW;IAC1B,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,QAAQ,CAAC,EAAE,MAAM,CAAC;CACnB;AAED,wBAAsB,OAAO,CAAC,MAAM,EAAE,MAAM,EAAE,IAAI,EAAE,WAAW,GAAG,OAAO,CAAC,IAAI,CAAC,CA+B9E"}
+{"version":3,"file":"info.d.ts","sourceRoot":"","sources":["../../src/commands/info.ts"],"names":[],"mappings":"AAGA,MAAM,WAAW,WAAW;IAC1B,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,QAAQ,CAAC,EAAE,MAAM,CAAC;CACnB;AAED,wBAAsB,OAAO,CAAC,MAAM,EAAE,MAAM,EAAE,IAAI,EAAE,WAAW,GAAG,OAAO,CAAC,IAAI,CAAC,CA+B9E"}

package/dist/commands/info.js

@@ -1,6 +1,7 @@
-import { ToolCache, cacheKey } from "@galaxy-tool-util/core";
+import { cacheKey } from "@galaxy-tool-util/core";
+import { makeNodeToolCache } from "@galaxy-tool-util/core/node";
 export async function runInfo(toolId, opts) {
-    const cache = new ToolCache({ cacheDir: opts.cacheDir });
+    const cache = makeNodeToolCache({ cacheDir: opts.cacheDir });
     await cache.index.load();
     const coords = cache.resolveToolCoordinates(toolId, opts.version);
     if (coords.version === null) {
@@ -8,14 +9,14 @@ export async function runInfo(toolId, opts) {
         process.exitCode = 1;
         return;
     }
-    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) {
         console.error(`Tool not found in cache: ${toolId}`);
         process.exitCode = 1;
         return;
     }
-    const indexEntry = cache.index.listAll().find((e) => e.cache_key === key);
+    const indexEntry = (await cache.index.listAll()).find((e) => e.cache_key === key);
     console.log(`Name:        ${tool.name}`);
     console.log(`ID:          ${tool.id}`);
     console.log(`Version:     ${tool.version ?? "unknown"}`);

package/dist/commands/info.js.map

@@ -1 +1 @@
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+{"version":3,"file":"info.js","sourceRoot":"","sources":["../../src/commands/info.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,QAAQ,EAAE,MAAM,wBAAwB,CAAC;AAClD,OAAO,EAAE,iBAAiB,EAAE,MAAM,6BAA6B,CAAC;AAOhE,MAAM,CAAC,KAAK,UAAU,OAAO,CAAC,MAAc,EAAE,IAAiB;IAC7D,MAAM,KAAK,GAAG,iBAAiB,CAAC,EAAE,QAAQ,EAAE,IAAI,CAAC,QAAQ,EAAE,CAAC,CAAC;IAC7D,MAAM,KAAK,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC;IACzB,MAAM,MAAM,GAAG,KAAK,CAAC,sBAAsB,CAAC,MAAM,EAAE,IAAI,CAAC,OAAO,CAAC,CAAC;IAClE,IAAI,MAAM,CAAC,OAAO,KAAK,IAAI,EAAE,CAAC;QAC5B,OAAO,CAAC,KAAK,CAAC,kCAAkC,MAAM,EAAE,CAAC,CAAC;QAC1D,OAAO,CAAC,QAAQ,GAAG,CAAC,CAAC;QACrB,OAAO;IACT,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,CAAC,KAAK,CAAC,4BAA4B,MAAM,EAAE,CAAC,CAAC;QACpD,OAAO,CAAC,QAAQ,GAAG,CAAC,CAAC;QACrB,OAAO;IACT,CAAC;IAED,MAAM,UAAU,GAAG,CAAC,MAAM,KAAK,CAAC,KAAK,CAAC,OAAO,EAAE,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,SAAS,KAAK,GAAG,CAAC,CAAC;IAElF,OAAO,CAAC,GAAG,CAAC,gBAAgB,IAAI,CAAC,IAAI,EAAE,CAAC,CAAC;IACzC,OAAO,CAAC,GAAG,CAAC,gBAAgB,IAAI,CAAC,EAAE,EAAE,CAAC,CAAC;IACvC,OAAO,CAAC,GAAG,CAAC,gBAAgB,IAAI,CAAC,OAAO,IAAI,SAAS,EAAE,CAAC,CAAC;IACzD,OAAO,CAAC,GAAG,CAAC,gBAAgB,IAAI,CAAC,WAAW,IAAI,EAAE,EAAE,CAAC,CAAC;IACtD,OAAO,CAAC,GAAG,CAAC,gBAAgB,IAAI,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,CAAC;IAClD,OAAO,CAAC,GAAG,CAAC,gBAAgB,IAAI,CAAC,OAAO,CAAC,MAAM,EAAE,CAAC,CAAC;IACnD,OAAO,CAAC,GAAG,CAAC,gBAAgB,IAAI,CAAC,OAAO,IAAI,MAAM,EAAE,CAAC,CAAC;IACtD,OAAO,CAAC,GAAG,CAAC,gBAAgB,IAAI,CAAC,OAAO,IAAI,MAAM,EAAE,CAAC,CAAC;IACtD,IAAI,UAAU,EAAE,CAAC;QACf,OAAO,CAAC,GAAG,CAAC,gBAAgB,UAAU,CAAC,MAAM,EAAE,CAAC,CAAC;QACjD,OAAO,CAAC,GAAG,CAAC,gBAAgB,UAAU,CAAC,SAAS,EAAE,CAAC,CAAC;IACtD,CAAC;AACH,CAAC"}

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

@@ -0,0 +1,11 @@
+import { type StrictOptions } from "./strict-options.js";
+import { type ReportOutputOptions } from "./report-output.js";
+export interface LintTreeOptions extends StrictOptions, ReportOutputOptions {
+    format?: string;
+    skipBestPractices?: boolean;
+    skipStateValidation?: boolean;
+    cacheDir?: string;
+    json?: boolean;
+}
+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 @@
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package/dist/commands/lint-tree.js

@@ -0,0 +1,104 @@
+import { makeNodeToolCache } from "@galaxy-tool-util/core/node";
+import { buildLintWorkflowResult, buildLintTreeReport as schemaBuildLintTreeReport, } from "@galaxy-tool-util/schema";
+import { resolveFormat } from "./workflow-io.js";
+import { resolveStrictOptions } from "./strict-options.js";
+import { lintWorkflowReport } from "./lint.js";
+import { collectTree } from "./tree.js";
+import { writeReportOutput, writeReportHtml } from "./report-output.js";
+/** Map internal LintReport to schema's flat LintWorkflowResult fields. */
+function toLintWorkflowResult(relativePath, lr) {
+    const lint_errors = lr.structural.error_count + (lr.bestPractices?.error_count ?? 0);
+    const lint_warnings = lr.structural.warn_count + (lr.bestPractices?.warn_count ?? 0);
+    const stepResults = lr.stateValidation ?? [];
+    return buildLintWorkflowResult(relativePath, lint_errors, lint_warnings, stepResults);
+}
+export async function runLintTree(dir, opts) {
+    // Load tool cache once for all files
+    let cache;
+    if (!opts.skipStateValidation) {
+        try {
+            cache = makeNodeToolCache({ cacheDir: opts.cacheDir });
+            await cache.index.load();
+            if ((await 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 strict = resolveStrictOptions(opts);
+    const treeResult = await collectTree(dir, async (info, data) => {
+        const format = resolveFormat(data, opts.format);
+        const lr = await lintWorkflowReport(info.path, data, format, {
+            skipBestPractices: opts.skipBestPractices,
+            skipStateValidation: opts.skipStateValidation,
+            cache,
+            strict,
+        });
+        return toLintWorkflowResult(info.relativePath, lr);
+    });
+    const report = buildReport(treeResult);
+    await writeReportOutput("lint_tree.md.j2", report, { reportMarkdown: opts.reportMarkdown });
+    await writeReportHtml("lint-tree", report, opts.reportHtml);
+    if (opts.json) {
+        console.log(JSON.stringify(report, null, 2));
+        process.exitCode = computeLintExitCode(report);
+        return;
+    }
+    // Text output
+    for (const wf of report.workflows) {
+        if (wf.error) {
+            console.error(`  ${wf.path}: ERROR (${wf.error})`);
+            continue;
+        }
+        if (wf.skipped_reason) {
+            console.warn(`  ${wf.path}: SKIPPED (${wf.skipped_reason})`);
+            continue;
+        }
+        const stateFails = wf.results.filter((s) => s.status === "fail").length;
+        if (wf.lint_errors > 0 || stateFails > 0) {
+            console.error(`  ${wf.path}: ${wf.lint_errors} errors, ${wf.lint_warnings} warnings, ${stateFails} state failures`);
+            // Detailed error output would require the internal LintReport;
+            // for tree output we show the summary counts per workflow.
+        }
+        else if (wf.lint_warnings > 0) {
+            console.warn(`  ${wf.path}: ${wf.lint_warnings} warnings`);
+        }
+        else {
+            console.log(`  ${wf.path}: OK`);
+        }
+    }
+    const s = report.summary;
+    const total = report.workflows.length;
+    console.log(`\nSummary: ${total} workflows | ${s.lint_errors} errors, ${s.lint_warnings} warnings, ${s.state_fail} state failures`);
+    process.exitCode = computeLintExitCode(report);
+}
+function buildReport(treeResult) {
+    const workflows = [];
+    for (const o of treeResult.outcomes) {
+        if (o.error) {
+            workflows.push(buildLintWorkflowResult(o.info.relativePath, 0, 0, [], { error: o.error }));
+            continue;
+        }
+        if (o.skipped) {
+            workflows.push(buildLintWorkflowResult(o.info.relativePath, 0, 0, [], {
+                skipped_reason: o.skipReason ?? null,
+            }));
+            continue;
+        }
+        workflows.push(o.result);
+    }
+    return schemaBuildLintTreeReport(treeResult.root, workflows);
+}
+function computeLintExitCode(report) {
+    const s = report.summary;
+    if (s.lint_errors > 0 || s.state_fail > 0 || s.errors > 0)
+        return 2;
+    if (s.lint_warnings > 0)
+        return 1;
+    return 0;
+}
+//# sourceMappingURL=lint-tree.js.map

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

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package/dist/commands/lint.d.ts

@@ -0,0 +1,34 @@
+/**
+ * `gxwf lint` — unified lint combining structural checks, best practices,
+ * and tool state validation.
+ */
+import type { ToolCache } from "@galaxy-tool-util/core";
+import { type LintResult, type ValidationStepResult as StepValidationResult } from "@galaxy-tool-util/schema";
+import { type StrictOptions, type ResolvedStrictOptions } from "./strict-options.js";
+export interface LintOptions extends StrictOptions {
+    format?: string;
+    skipBestPractices?: boolean;
+    skipStateValidation?: boolean;
+    cacheDir?: string;
+    json?: boolean;
+    reportHtml?: string | boolean;
+}
+export interface LintReportOptions {
+    skipBestPractices?: boolean;
+    skipStateValidation?: boolean;
+    cache?: ToolCache;
+    strict?: ResolvedStrictOptions;
+}
+export interface LintReport {
+    structural: LintResult;
+    bestPractices: LintResult | null;
+    stateValidation: StepValidationResult[] | null;
+    stateSkipped: boolean;
+    encodingErrors: string[];
+    structureErrors: string[];
+    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 @@
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