@galaxy-tool-util/cli 0.1.0 → 0.2.0

package/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2025 John Chilton
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

package/dist/bin/galaxy-tool-cache.js

@@ -4,7 +4,9 @@ import { runAdd } from "../commands/add.js";
 import { runList } from "../commands/list.js";
 import { runInfo } from "../commands/info.js";
 import { runClear } from "../commands/clear.js";
+import { runPopulateWorkflow } from "../commands/populate-workflow.js";
 import { runSchema } from "../commands/schema.js";
+import { runStructuralSchema } from "../commands/structural-schema.js";
 const program = new Command();
 program
     .name("galaxy-tool-cache")
@@ -46,5 +48,18 @@ program
     .option("--output <file>", "Output file (default: stdout)")
     .option("--cache-dir <dir>", "Cache directory")
     .action(runSchema);
+program
+    .command("populate-workflow")
+    .description("Scan a workflow and cache all referenced tools")
+    .argument("<file>", "Workflow file (.ga, .gxwf.yml)")
+    .option("--cache-dir <dir>", "Cache directory")
+    .option("--galaxy-url <url>", "Galaxy instance URL for fallback")
+    .action(runPopulateWorkflow);
+program
+    .command("structural-schema")
+    .description("Export the structural JSON Schema for Galaxy workflows")
+    .option("--format <fmt>", "Workflow format: format2 (default) or native", "format2")
+    .option("--output <file>", "Output file (default: stdout)")
+    .action(runStructuralSchema);
 program.parse();
 //# sourceMappingURL=galaxy-tool-cache.js.map

package/dist/bin/galaxy-tool-cache.js.map

@@ -1 +1 @@
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+{"version":3,"file":"galaxy-tool-cache.js","sourceRoot":"","sources":["../../src/bin/galaxy-tool-cache.ts"],"names":[],"mappings":";AAEA,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AACpC,OAAO,EAAE,MAAM,EAAE,MAAM,oBAAoB,CAAC;AAC5C,OAAO,EAAE,OAAO,EAAE,MAAM,qBAAqB,CAAC;AAC9C,OAAO,EAAE,OAAO,EAAE,MAAM,qBAAqB,CAAC;AAC9C,OAAO,EAAE,QAAQ,EAAE,MAAM,sBAAsB,CAAC;AAChD,OAAO,EAAE,mBAAmB,EAAE,MAAM,kCAAkC,CAAC;AACvE,OAAO,EAAE,SAAS,EAAE,MAAM,uBAAuB,CAAC;AAClD,OAAO,EAAE,mBAAmB,EAAE,MAAM,kCAAkC,CAAC;AAEvE,MAAM,OAAO,GAAG,IAAI,OAAO,EAAE,CAAC;AAE9B,OAAO;KACJ,IAAI,CAAC,mBAAmB,CAAC;KACzB,WAAW,CAAC,wCAAwC,CAAC;KACrD,OAAO,CAAC,OAAO,CAAC,CAAC;AAEpB,OAAO;KACJ,OAAO,CAAC,KAAK,CAAC;KACd,WAAW,CAAC,gDAAgD,CAAC;KAC7D,QAAQ,CAAC,WAAW,EAAE,wCAAwC,CAAC;KAC/D,MAAM,CAAC,iBAAiB,EAAE,cAAc,CAAC;KACzC,MAAM,CAAC,mBAAmB,EAAE,iBAAiB,CAAC;KAC9C,MAAM,CAAC,oBAAoB,EAAE,kCAAkC,CAAC;KAChE,MAAM,CAAC,MAAM,CAAC,CAAC;AAElB,OAAO;KACJ,OAAO,CAAC,MAAM,CAAC;KACf,WAAW,CAAC,mBAAmB,CAAC;KAChC,MAAM,CAAC,QAAQ,EAAE,gBAAgB,CAAC;KAClC,MAAM,CAAC,mBAAmB,EAAE,iBAAiB,CAAC;KAC9C,MAAM,CAAC,OAAO,CAAC,CAAC;AAEnB,OAAO;KACJ,OAAO,CAAC,MAAM,CAAC;KACf,WAAW,CAAC,iCAAiC,CAAC;KAC9C,QAAQ,CAAC,WAAW,EAAE,SAAS,CAAC;KAChC,MAAM,CAAC,iBAAiB,EAAE,cAAc,CAAC;KACzC,MAAM,CAAC,mBAAmB,EAAE,iBAAiB,CAAC;KAC9C,MAAM,CAAC,OAAO,CAAC,CAAC;AAEnB,OAAO;KACJ,OAAO,CAAC,OAAO,CAAC;KAChB,WAAW,CAAC,oBAAoB,CAAC;KACjC,QAAQ,CAAC,UAAU,EAAE,uCAAuC,CAAC;KAC7D,MAAM,CAAC,mBAAmB,EAAE,iBAAiB,CAAC;KAC9C,MAAM,CAAC,QAAQ,CAAC,CAAC;AAEpB,OAAO;KACJ,OAAO,CAAC,QAAQ,CAAC;KACjB,WAAW,CAAC,mDAAmD,CAAC;KAChE,QAAQ,CAAC,WAAW,EAAE,SAAS,CAAC;KAChC,MAAM,CAAC,iBAAiB,EAAE,cAAc,CAAC;KACzC,MAAM,CAAC,wBAAwB,EAAE,4CAA4C,EAAE,eAAe,CAAC;KAC/F,MAAM,CAAC,iBAAiB,EAAE,+BAA+B,CAAC;KAC1D,MAAM,CAAC,mBAAmB,EAAE,iBAAiB,CAAC;KAC9C,MAAM,CAAC,SAAS,CAAC,CAAC;AAErB,OAAO;KACJ,OAAO,CAAC,mBAAmB,CAAC;KAC5B,WAAW,CAAC,gDAAgD,CAAC;KAC7D,QAAQ,CAAC,QAAQ,EAAE,gCAAgC,CAAC;KACpD,MAAM,CAAC,mBAAmB,EAAE,iBAAiB,CAAC;KAC9C,MAAM,CAAC,oBAAoB,EAAE,kCAAkC,CAAC;KAChE,MAAM,CAAC,mBAAmB,CAAC,CAAC;AAE/B,OAAO;KACJ,OAAO,CAAC,mBAAmB,CAAC;KAC5B,WAAW,CAAC,wDAAwD,CAAC;KACrE,MAAM,CAAC,gBAAgB,EAAE,8CAA8C,EAAE,SAAS,CAAC;KACnF,MAAM,CAAC,iBAAiB,EAAE,+BAA+B,CAAC;KAC1D,MAAM,CAAC,mBAAmB,CAAC,CAAC;AAE/B,OAAO,CAAC,KAAK,EAAE,CAAC"}

package/dist/bin/gxwf.d.ts

@@ -0,0 +1,3 @@
+#!/usr/bin/env node
+export {};
+//# sourceMappingURL=gxwf.d.ts.map

package/dist/bin/gxwf.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"gxwf.d.ts","sourceRoot":"","sources":["../../src/bin/gxwf.ts"],"names":[],"mappings":""}

package/dist/bin/gxwf.js

@@ -0,0 +1,126 @@
+#!/usr/bin/env node
+import { Command } from "commander";
+import { runClean } from "../commands/clean.js";
+import { runCleanTree } from "../commands/clean-tree.js";
+import { runConvert } from "../commands/convert.js";
+import { runConvertTree } from "../commands/convert-tree.js";
+import { runRoundtrip } from "../commands/roundtrip.js";
+import { runRoundtripTree } from "../commands/roundtrip-tree.js";
+import { runLint } from "../commands/lint.js";
+import { runLintTree } from "../commands/lint-tree.js";
+import { runValidateWorkflow } from "../commands/validate-workflow.js";
+import { runValidateTree } from "../commands/validate-tree.js";
+const program = new Command();
+program
+    .name("gxwf")
+    .description("Galaxy workflow operations — validate, clean, lint, convert (single-file and tree)")
+    .version("1.0.0");
+program
+    .command("validate")
+    .description("Validate Galaxy workflow files (structure + optional tool state)")
+    .argument("<file>", "Workflow file (.ga, .gxwf.yml)")
+    .option("--format <fmt>", "Force format: native or format2 (auto-detected by default)")
+    .option("--no-tool-state", "Skip tool state validation")
+    .option("--cache-dir <dir>", "Tool cache directory")
+    .option("--mode <mode>", "Validation backend: effect (default) or json-schema", "effect")
+    .option("--tool-schema-dir <dir>", "Directory of pre-exported per-tool JSON Schemas (for offline json-schema mode)")
+    .action(runValidateWorkflow);
+program
+    .command("clean")
+    .description("Strip stale keys and decode legacy tool_state encoding")
+    .argument("<file>", "Workflow file (.ga, .gxwf.yml)")
+    .option("--output <file>", "Write cleaned workflow to file (default: stdout)")
+    .option("--diff", "Show diff of changes instead of writing output")
+    .option("--format <fmt>", "Force format: native or format2 (auto-detected by default)")
+    .action(runClean);
+program
+    .command("lint")
+    .description("Lint Galaxy workflow — structural checks, best practices, tool state validation")
+    .argument("<file>", "Workflow file (.ga, .gxwf.yml)")
+    .option("--skip-best-practices", "Skip annotation/creator/license/label checks")
+    .option("--skip-state-validation", "Skip tool state validation against cached tool definitions")
+    .option("--cache-dir <dir>", "Tool cache directory (for state validation)")
+    .option("--format <fmt>", "Force format: native or format2 (auto-detected by default)")
+    .option("--json", "Output structured JSON result")
+    .action(runLint);
+program
+    .command("convert")
+    .description("Convert between native (.ga) and format2 (.gxwf.yml) formats")
+    .argument("<file>", "Workflow file (.ga, .gxwf.yml)")
+    .option("--to <format>", "Target format: native or format2 (infers opposite by default)")
+    .option("--output <file>", "Write result to file (default: stdout)")
+    .option("--compact", "Omit position info in format2 output")
+    .option("--json", "Force JSON output")
+    .option("--yaml", "Force YAML output")
+    .option("--format <fmt>", "Force source format (auto-detected by default)")
+    .option("--stateful", "Use cached tool definitions for schema-aware state re-encoding")
+    .option("--cache-dir <dir>", "Tool cache directory (for --stateful)")
+    .action(runConvert);
+program
+    .command("roundtrip")
+    .description("Roundtrip-validate a native workflow: native → format2 → native, diff tool_state")
+    .argument("<file>", "Native workflow file (.ga)")
+    .option("--cache-dir <dir>", "Tool cache directory")
+    .option("--format <fmt>", "Force source format (must resolve to native)")
+    .option("--json", "Output structured JSON report")
+    .option("--errors-only", "Suppress benign diffs and clean steps from output")
+    .option("--benign-only", "Show only steps with benign diffs (no errors, no failures)")
+    .option("--brief", "Omit per-diff list; show only the one-line summary")
+    .action(runRoundtrip);
+// -- Tree (batch) variants --
+program
+    .command("validate-tree")
+    .description("Batch validate all workflows under a directory")
+    .argument("<dir>", "Directory to scan for workflows")
+    .option("--format <fmt>", "Force format: native or format2 (auto-detected by default)")
+    .option("--no-tool-state", "Skip tool state validation")
+    .option("--cache-dir <dir>", "Tool cache directory")
+    .option("--mode <mode>", "Validation backend: effect (default) or json-schema", "effect")
+    .option("--tool-schema-dir <dir>", "Directory of pre-exported per-tool JSON Schemas (for offline json-schema mode)")
+    .option("--json", "Output structured JSON report")
+    .action(runValidateTree);
+program
+    .command("lint-tree")
+    .description("Batch lint all workflows under a directory")
+    .argument("<dir>", "Directory to scan for workflows")
+    .option("--skip-best-practices", "Skip annotation/creator/license/label checks")
+    .option("--skip-state-validation", "Skip tool state validation against cached tool definitions")
+    .option("--cache-dir <dir>", "Tool cache directory (for state validation)")
+    .option("--format <fmt>", "Force format: native or format2 (auto-detected by default)")
+    .option("--json", "Output structured JSON report")
+    .action(runLintTree);
+program
+    .command("clean-tree")
+    .description("Batch clean all workflows under a directory")
+    .argument("<dir>", "Directory to scan for workflows")
+    .option("--output-dir <dir>", "Write cleaned workflows to directory (mirrors source tree)")
+    .option("--format <fmt>", "Force format: native or format2 (auto-detected by default)")
+    .option("--json", "Output structured JSON report")
+    .action(runCleanTree);
+program
+    .command("convert-tree")
+    .description("Batch convert all workflows under a directory")
+    .argument("<dir>", "Directory to scan for workflows")
+    .option("--to <format>", "Target format: native or format2 (infers opposite by default)")
+    .option("--output-dir <dir>", "Write converted workflows to directory (required)")
+    .option("--compact", "Omit position info in format2 output")
+    .option("--report-json", "Output structured JSON report")
+    .option("--json", "Force JSON output for converted files")
+    .option("--yaml", "Force YAML output")
+    .option("--format <fmt>", "Force source format (auto-detected by default)")
+    .option("--stateful", "Use cached tool definitions for schema-aware state re-encoding")
+    .option("--cache-dir <dir>", "Tool cache directory (for --stateful)")
+    .action(runConvertTree);
+program
+    .command("roundtrip-tree")
+    .description("Batch roundtrip-validate native workflows under a directory")
+    .argument("<dir>", "Directory to scan for native workflows")
+    .option("--cache-dir <dir>", "Tool cache directory")
+    .option("--format <fmt>", "Force source format (must resolve to native)")
+    .option("--json", "Output structured JSON report")
+    .option("--errors-only", "List only files with errors or failures")
+    .option("--benign-only", "List only files with benign diffs (no errors, no failures)")
+    .option("--brief", "Omit per-file lines; print only the aggregate summary")
+    .action(runRoundtripTree);
+program.parse();
+//# sourceMappingURL=gxwf.js.map

package/dist/bin/gxwf.js.map

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

@@ -0,0 +1,23 @@
+import { type TreeSummary } from "./tree.js";
+export interface CleanTreeOptions {
+    outputDir?: string;
+    format?: string;
+    json?: boolean;
+}
+export interface WorkflowCleanResult {
+    relativePath: string;
+    changed: boolean;
+}
+export interface CleanTreeReport {
+    root: string;
+    results: (WorkflowCleanResult | {
+        relativePath: string;
+        error: string;
+    })[];
+    summary: TreeSummary & {
+        changed: number;
+        unchanged: number;
+    };
+}
+export declare function runCleanTree(dir: string, opts: CleanTreeOptions): Promise<void>;
+//# sourceMappingURL=clean-tree.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"clean-tree.d.ts","sourceRoot":"","sources":["../../src/commands/clean-tree.ts"],"names":[],"mappings":"AAOA,OAAO,EAAmD,KAAK,WAAW,EAAE,MAAM,WAAW,CAAC;AAE9F,MAAM,WAAW,gBAAgB;IAC/B,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,IAAI,CAAC,EAAE,OAAO,CAAC;CAChB;AAED,MAAM,WAAW,mBAAmB;IAClC,YAAY,EAAE,MAAM,CAAC;IACrB,OAAO,EAAE,OAAO,CAAC;CAClB;AAED,MAAM,WAAW,eAAe;IAC9B,IAAI,EAAE,MAAM,CAAC;IACb,OAAO,EAAE,CAAC,mBAAmB,GAAG;QAAE,YAAY,EAAE,MAAM,CAAC;QAAC,KAAK,EAAE,MAAM,CAAA;KAAE,CAAC,EAAE,CAAC;IAC3E,OAAO,EAAE,WAAW,GAAG;QAAE,OAAO,EAAE,MAAM,CAAC;QAAC,SAAS,EAAE,MAAM,CAAA;KAAE,CAAC;CAC/D;AAED,wBAAsB,YAAY,CAAC,GAAG,EAAE,MAAM,EAAE,IAAI,EAAE,gBAAgB,GAAG,OAAO,CAAC,IAAI,CAAC,CA4CrF"}

package/dist/commands/clean-tree.js

@@ -0,0 +1,68 @@
+/**
+ * `gxwf clean-tree` — batch clean all workflows under a directory.
+ */
+import { cleanWorkflow } from "@galaxy-tool-util/schema";
+import { mkdir, writeFile } from "node:fs/promises";
+import { dirname, join } from "node:path";
+import { resolveFormat, serializeWorkflow } from "./workflow-io.js";
+import { collectTree, summarizeOutcomes } from "./tree.js";
+export async function runCleanTree(dir, opts) {
+    const outputDir = opts.outputDir;
+    const treeResult = await collectTree(dir, async (info, data) => {
+        const format = resolveFormat(data, opts.format);
+        const before = JSON.stringify(data);
+        cleanWorkflow(data);
+        const changed = JSON.stringify(data) !== before;
+        if (outputDir) {
+            const outPath = join(outputDir, info.relativePath);
+            await mkdir(dirname(outPath), { recursive: true });
+            const serialized = serializeWorkflow(data, format);
+            await writeFile(outPath, serialized, "utf-8");
+        }
+        return { relativePath: info.relativePath, changed };
+    });
+    const report = buildCleanReport(treeResult);
+    if (opts.json) {
+        console.log(JSON.stringify(report, null, 2));
+        process.exitCode = report.summary.changed > 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;
+        console.log(`  ${r.relativePath}: ${r.changed ? "CHANGED" : "clean"}`);
+    }
+    const s = report.summary;
+    const suffix = outputDir ? ` (written to ${outputDir})` : "";
+    console.log(`\nSummary: ${s.total} workflows | ${s.changed} changed, ${s.unchanged} unchanged${suffix}`);
+    // Exit 1 if any workflows had stale keys (like Python's clean-tree)
+    process.exitCode = s.changed > 0 ? 1 : 0;
+}
+function buildCleanReport(treeResult) {
+    const results = [];
+    let changed = 0;
+    let unchanged = 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);
+        if (r.changed)
+            changed++;
+        else
+            unchanged++;
+    }
+    const wfSummary = summarizeOutcomes(treeResult.outcomes, (r) => r.changed);
+    return { root: treeResult.root, results, summary: { ...wfSummary, changed, unchanged } };
+}
+//# sourceMappingURL=clean-tree.js.map

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

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

@@ -0,0 +1,7 @@
+export interface CleanOptions {
+    output?: string;
+    diff?: boolean;
+    format?: string;
+}
+export declare function runClean(filePath: string, opts: CleanOptions): Promise<void>;
+//# sourceMappingURL=clean.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"clean.d.ts","sourceRoot":"","sources":["../../src/commands/clean.ts"],"names":[],"mappings":"AAWA,MAAM,WAAW,YAAY;IAC3B,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,MAAM,CAAC,EAAE,MAAM,CAAC;CACjB;AAED,wBAAsB,QAAQ,CAAC,QAAQ,EAAE,MAAM,EAAE,IAAI,EAAE,YAAY,GAAG,OAAO,CAAC,IAAI,CAAC,CAgClF"}

package/dist/commands/clean.js

@@ -0,0 +1,38 @@
+/**
+ * `gxwf clean` — strip stale keys and decode legacy tool_state encoding.
+ */
+import { cleanWorkflow } from "@galaxy-tool-util/schema";
+import { readWorkflowFile, resolveFormat, serializeWorkflow, writeWorkflowOutput, } from "./workflow-io.js";
+export async function runClean(filePath, opts) {
+    const data = await readWorkflowFile(filePath);
+    if (!data)
+        return;
+    const format = resolveFormat(data, opts.format);
+    const before = opts.diff ? JSON.stringify(data, null, 2) : null;
+    cleanWorkflow(data);
+    if (opts.diff) {
+        const after = JSON.stringify(data, null, 2);
+        if (before === after) {
+            console.log("No changes.");
+            return;
+        }
+        // Simple line-by-line diff
+        const beforeLines = before.split("\n");
+        const afterLines = after.split("\n");
+        const maxLen = Math.max(beforeLines.length, afterLines.length);
+        for (let i = 0; i < maxLen; i++) {
+            const bLine = beforeLines[i];
+            const aLine = afterLines[i];
+            if (bLine !== aLine) {
+                if (bLine !== undefined)
+                    console.log(`- ${bLine}`);
+                if (aLine !== undefined)
+                    console.log(`+ ${aLine}`);
+            }
+        }
+        return;
+    }
+    const output = serializeWorkflow(data, format);
+    await writeWorkflowOutput(output, opts.output, "Cleaned workflow");
+}
+//# sourceMappingURL=clean.js.map

package/dist/commands/clean.js.map

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

@@ -0,0 +1,31 @@
+import { type StepConversionStatus } from "@galaxy-tool-util/schema";
+import { type ToolLoadStatus } from "./stateful-tool-inputs.js";
+import { type TreeSummary } from "./tree.js";
+export interface ConvertTreeOptions {
+    to?: string;
+    outputDir?: string;
+    compact?: boolean;
+    yaml?: boolean;
+    format?: string;
+    json?: boolean;
+    reportJson?: boolean;
+    stateful?: boolean;
+    cacheDir?: string;
+}
+export interface WorkflowConvertResult {
+    relativePath: string;
+    sourceFormat: string;
+    targetFormat: string;
+    statefulSteps?: StepConversionStatus[];
+    toolLoadErrors?: ToolLoadStatus[];
+}
+export interface ConvertTreeReport {
+    root: string;
+    results: (WorkflowConvertResult | {
+        relativePath: string;
+        error: string;
+    })[];
+    summary: TreeSummary;
+}
+export declare function runConvertTree(dir: string, opts: ConvertTreeOptions): Promise<void>;
+//# sourceMappingURL=convert-tree.d.ts.map

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

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package/dist/commands/convert-tree.js

@@ -0,0 +1,213 @@
+/**
+ * `gxwf convert-tree` — batch convert all workflows under a directory.
+ */
+import { ToolCache } from "@galaxy-tool-util/core";
+import { toFormat2, toFormat2Stateful, toNative, toNativeStateful, } 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 { 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 = 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 treeResult = await collectTree(dir, async (info, data) => {
+        const sourceFormat = resolveFormat(data, opts.format);
+        const targetFormat = resolveTargetFormat(sourceFormat, opts.to);
+        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");
+        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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