@galaxy-tool-util/cli 0.1.0 → 0.4.0

package/dist/commands/tree.d.ts

@@ -0,0 +1,45 @@
+/**
+ * Shared tree-walking infrastructure for batch workflow operations.
+ *
+ * Provides a generic discover→load→process→aggregate loop so that
+ * each tree command only supplies a per-workflow processing function
+ * and an aggregation/formatting function.
+ *
+ * Mirrors Python's _tree_orchestrator.py pattern.
+ */
+import type { WorkflowFormat } from "@galaxy-tool-util/schema";
+export interface WorkflowInfo {
+    path: string;
+    relativePath: string;
+    format: WorkflowFormat;
+}
+export interface WorkflowOutcome<T> {
+    info: WorkflowInfo;
+    result?: T;
+    error?: string;
+    skipped?: boolean;
+    skipReason?: string;
+}
+export interface TreeResult<T> {
+    root: string;
+    outcomes: WorkflowOutcome<T>[];
+}
+export interface TreeSummary {
+    total: number;
+    ok: number;
+    fail: number;
+    error: number;
+    skipped: number;
+}
+/** Call from processOne to skip a workflow with a reason. */
+export declare function skipWorkflow(reason: string): never;
+/** Discover workflow files recursively under root. */
+export declare function discoverWorkflows(root: string, includeFormat2?: boolean): Promise<WorkflowInfo[]>;
+/** Load and parse a discovered workflow file. Returns null on failure. */
+export declare function loadWorkflowSafe(info: WorkflowInfo): Promise<Record<string, unknown> | null>;
+export type ProcessOne<T> = (info: WorkflowInfo, data: Record<string, unknown>) => Promise<T> | T;
+/** Discover, load, and process all workflows under a directory. */
+export declare function collectTree<T>(root: string, processOne: ProcessOne<T>, includeFormat2?: boolean): Promise<TreeResult<T>>;
+/** Compute a basic summary from tree outcomes. */
+export declare function summarizeOutcomes<T>(outcomes: WorkflowOutcome<T>[], isFail?: (result: T) => boolean): TreeSummary;
+//# sourceMappingURL=tree.d.ts.map

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

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

@@ -0,0 +1,155 @@
+import { readdir, readFile } from "node:fs/promises";
+import { join, relative, extname } from "node:path";
+import * as YAML from "yaml";
+/** Thrown by processOne to skip a workflow. */
+class SkipWorkflow extends Error {
+}
+/** Call from processOne to skip a workflow with a reason. */
+export function skipWorkflow(reason) {
+    throw new SkipWorkflow(reason);
+}
+// ── Discovery ──────────────────────────────────────────────────────────
+const EXCLUDE_DIRS = new Set([".git", ".hg", ".venv", "node_modules", "__pycache__", ".snakemake"]);
+const NATIVE_EXTENSIONS = new Set([".ga"]);
+const FORMAT2_SUFFIXES = [".gxwf.yml", ".gxwf.yaml"];
+function classifyFile(filename) {
+    // Check format2 compound extensions first
+    for (const suffix of FORMAT2_SUFFIXES) {
+        if (filename.endsWith(suffix))
+            return "format2";
+    }
+    const ext = extname(filename);
+    if (NATIVE_EXTENSIONS.has(ext))
+        return "native";
+    // Plain .json could be native, plain .yml/.yaml could be format2
+    if (ext === ".json")
+        return "native";
+    if (ext === ".yml" || ext === ".yaml")
+        return "format2";
+    return null;
+}
+function isWorkflowContent(data, format) {
+    if (format === "native") {
+        return data.a_galaxy_workflow === "true";
+    }
+    return data.class === "GalaxyWorkflow";
+}
+function parseFileContent(raw, format) {
+    try {
+        if (format === "native") {
+            const parsed = JSON.parse(raw);
+            return typeof parsed === "object" && parsed !== null ? parsed : null;
+        }
+        const parsed = YAML.parse(raw);
+        return typeof parsed === "object" && parsed !== null ? parsed : null;
+    }
+    catch {
+        return null;
+    }
+}
+/** Discover workflow files recursively under root. */
+export async function discoverWorkflows(root, includeFormat2 = true) {
+    const workflows = [];
+    await _walkDir(root, root, includeFormat2, workflows);
+    workflows.sort((a, b) => a.relativePath.localeCompare(b.relativePath));
+    return workflows;
+}
+async function _walkDir(dir, root, includeFormat2, out) {
+    let entries;
+    try {
+        entries = await readdir(dir, { withFileTypes: true });
+    }
+    catch {
+        return;
+    }
+    for (const entry of entries) {
+        if (entry.isDirectory()) {
+            if (!EXCLUDE_DIRS.has(entry.name)) {
+                await _walkDir(join(dir, entry.name), root, includeFormat2, out);
+            }
+            continue;
+        }
+        if (!entry.isFile())
+            continue;
+        const format = classifyFile(entry.name);
+        if (!format)
+            continue;
+        if (format === "format2" && !includeFormat2)
+            continue;
+        const filePath = join(dir, entry.name);
+        let raw;
+        try {
+            raw = await readFile(filePath, "utf-8");
+        }
+        catch {
+            continue;
+        }
+        const data = parseFileContent(raw, format);
+        if (!data || !isWorkflowContent(data, format))
+            continue;
+        out.push({
+            path: filePath,
+            relativePath: relative(root, filePath),
+            format,
+        });
+    }
+}
+// ── Load ───────────────────────────────────────────────────────────────
+/** Load and parse a discovered workflow file. Returns null on failure. */
+export async function loadWorkflowSafe(info) {
+    try {
+        const raw = await readFile(info.path, "utf-8");
+        return parseFileContent(raw, info.format);
+    }
+    catch {
+        return null;
+    }
+}
+/** Discover, load, and process all workflows under a directory. */
+export async function collectTree(root, processOne, includeFormat2 = true) {
+    const workflows = await discoverWorkflows(root, includeFormat2);
+    const outcomes = [];
+    for (const info of workflows) {
+        const data = await loadWorkflowSafe(info);
+        if (!data) {
+            outcomes.push({ info, error: "Failed to load workflow" });
+            continue;
+        }
+        try {
+            const result = await processOne(info, data);
+            outcomes.push({ info, result });
+        }
+        catch (e) {
+            if (e instanceof SkipWorkflow) {
+                outcomes.push({ info, skipped: true, skipReason: e.message });
+            }
+            else {
+                outcomes.push({ info, error: e instanceof Error ? e.message : String(e) });
+            }
+        }
+    }
+    return { root, outcomes };
+}
+/** Compute a basic summary from tree outcomes. */
+export function summarizeOutcomes(outcomes, isFail) {
+    let ok = 0;
+    let fail = 0;
+    let error = 0;
+    let skipped = 0;
+    for (const o of outcomes) {
+        if (o.error) {
+            error++;
+        }
+        else if (o.skipped) {
+            skipped++;
+        }
+        else if (isFail && o.result !== undefined && isFail(o.result)) {
+            fail++;
+        }
+        else {
+            ok++;
+        }
+    }
+    return { total: outcomes.length, ok, fail, error, skipped };
+}
+//# sourceMappingURL=tree.js.map

package/dist/commands/tree.js.map

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

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

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

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package/dist/commands/validate-tests-tree.js

@@ -0,0 +1,191 @@
+/**
+ * ``gxwf validate-tests-tree`` — batch-validate every workflow-test file
+ * (``*-tests.yml``, ``*-tests.yaml``, ``*.gxwf-tests.yml``, ``*.gxwf-tests.yaml``)
+ * under a directory against the ``galaxy.tool_util_models.Tests`` JSON Schema.
+ *
+ * Unlike ``validate-tree`` this uses its own discovery pass because test
+ * documents don't carry a ``class: GalaxyWorkflow`` / ``a_galaxy_workflow``
+ * marker — classification is filename-based.
+ *
+ * With ``--auto-workflow``, each test file is paired with a sibling workflow
+ * by suffix convention and cross-checked. Silent no-op when no sibling is
+ * found.
+ */
+import { readdir, readFile, stat } from "node:fs/promises";
+import { dirname, join, relative } from "node:path";
+import { parse as parseYaml } from "yaml";
+import { checkTestsAgainstWorkflow, extractWorkflowInputs, extractWorkflowOutputs, resolveFormat, validateTestsFile, } from "@galaxy-tool-util/schema";
+const EXCLUDE_DIRS = new Set([".git", ".hg", ".venv", "node_modules", "__pycache__", ".snakemake"]);
+const TEST_SUFFIXES = [".gxwf-tests.yml", ".gxwf-tests.yaml", "-tests.yml", "-tests.yaml"];
+const WORKFLOW_EXTS = [".gxwf.yml", ".gxwf.yaml", ".yml", ".yaml", ".ga"];
+function isTestFile(name) {
+    return TEST_SUFFIXES.some((s) => name.endsWith(s));
+}
+/**
+ * Derive the workflow basename a given tests file pairs with.
+ * `foo.gxwf-tests.yml` → `foo`; `bar-tests.yml` → `bar`.
+ */
+function stripTestsSuffix(name) {
+    for (const suffix of TEST_SUFFIXES) {
+        if (name.endsWith(suffix))
+            return name.slice(0, -suffix.length);
+    }
+    return undefined;
+}
+async function fileExists(path) {
+    try {
+        const s = await stat(path);
+        return s.isFile();
+    }
+    catch {
+        return false;
+    }
+}
+/**
+ * Locate a sibling workflow for a tests file. Returns the first existing
+ * candidate in suffix-priority order, or undefined if none found.
+ */
+async function findSiblingWorkflow(testsPath) {
+    const base = stripTestsSuffix(testsPath.split("/").pop() ?? "");
+    if (!base)
+        return undefined;
+    const dir = dirname(testsPath);
+    for (const ext of WORKFLOW_EXTS) {
+        const candidate = join(dir, `${base}${ext}`);
+        if (await fileExists(candidate))
+            return candidate;
+    }
+    return undefined;
+}
+async function loadWorkflowShape(path) {
+    const raw = await readFile(path, "utf-8");
+    const parsed = path.endsWith(".ga") || path.endsWith(".json") ? JSON.parse(raw) : parseYaml(raw);
+    if (!parsed || typeof parsed !== "object" || Array.isArray(parsed)) {
+        throw new Error(`Workflow ${path} did not parse to an object.`);
+    }
+    const dict = parsed;
+    const format = resolveFormat(dict);
+    return {
+        inputs: extractWorkflowInputs(dict, format),
+        outputs: extractWorkflowOutputs(dict, format),
+    };
+}
+async function discoverTestFiles(root) {
+    const out = [];
+    await walk(root, out);
+    out.sort();
+    return out;
+}
+async function walk(dir, out) {
+    let entries;
+    try {
+        entries = await readdir(dir, { withFileTypes: true });
+    }
+    catch {
+        return;
+    }
+    for (const entry of entries) {
+        if (entry.isDirectory()) {
+            if (!EXCLUDE_DIRS.has(entry.name)) {
+                await walk(join(dir, entry.name), out);
+            }
+            continue;
+        }
+        if (entry.isFile() && isTestFile(entry.name)) {
+            out.push(join(dir, entry.name));
+        }
+    }
+}
+async function validateOne(path, root, autoWorkflow) {
+    const rel = relative(root, path);
+    let parsed;
+    try {
+        const raw = await readFile(path, "utf-8");
+        parsed = parseYaml(raw);
+    }
+    catch (err) {
+        const msg = err instanceof Error ? err.message : String(err);
+        return {
+            path: rel,
+            valid: false,
+            loadError: true,
+            errors: [
+                { path: "(root)", message: `YAML parse error: ${msg}`, keyword: "yaml", params: {} },
+            ],
+        };
+    }
+    const { valid: schemaValid, errors } = validateTestsFile(parsed);
+    const allErrors = [...errors];
+    let pairedWorkflow;
+    if (autoWorkflow) {
+        const sibling = await findSiblingWorkflow(path);
+        if (sibling) {
+            pairedWorkflow = relative(root, sibling);
+            try {
+                const shape = await loadWorkflowShape(sibling);
+                allErrors.push(...checkTestsAgainstWorkflow(parsed, shape));
+            }
+            catch (err) {
+                const msg = err instanceof Error ? err.message : String(err);
+                allErrors.push({
+                    path: "(root)",
+                    message: `Failed to load workflow ${pairedWorkflow}: ${msg}`,
+                    keyword: "workflow_load_error",
+                    params: { workflow: pairedWorkflow },
+                });
+            }
+        }
+    }
+    const valid = schemaValid && allErrors.length === 0;
+    const report = { path: rel, valid, errors: allErrors };
+    if (pairedWorkflow)
+        report.workflow = pairedWorkflow;
+    return report;
+}
+export async function runValidateTestsTree(dir, opts = {}) {
+    const paths = await discoverTestFiles(dir);
+    const files = [];
+    for (const p of paths) {
+        files.push(await validateOne(p, dir, opts.autoWorkflow === true));
+    }
+    const summary = {
+        total: files.length,
+        ok: files.filter((f) => f.valid).length,
+        fail: files.filter((f) => !f.valid && !f.loadError).length,
+        error: files.filter((f) => f.loadError).length,
+    };
+    const report = {
+        root: dir,
+        files: files.map(({ path, valid, errors, workflow }) => {
+            const entry = { path, valid, errors };
+            if (workflow)
+                entry.workflow = workflow;
+            return entry;
+        }),
+        summary,
+    };
+    if (opts.json) {
+        console.log(JSON.stringify(report, null, 2));
+    }
+    else {
+        for (const f of files) {
+            const wfNote = f.workflow ? ` [workflow: ${f.workflow}]` : "";
+            if (f.loadError) {
+                console.error(`  ${f.path}: ERROR (${f.errors[0]?.message ?? "load failed"})`);
+            }
+            else if (f.valid) {
+                console.log(`  ${f.path}: OK${wfNote}`);
+            }
+            else {
+                console.error(`  ${f.path}: ${f.errors.length} validation error(s)${wfNote}`);
+                for (const e of f.errors) {
+                    console.error(`    ${e.path}: ${e.message} [${e.keyword}]`);
+                }
+            }
+        }
+        const s = summary;
+        console.log(`\nSummary: ${s.total} files | ${s.ok} OK, ${s.fail} FAIL, ${s.error} ERROR`);
+    }
+    process.exitCode = summary.fail > 0 || summary.error > 0 ? 1 : 0;
+}
+//# sourceMappingURL=validate-tests-tree.js.map

package/dist/commands/validate-tests-tree.js.map

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

@@ -0,0 +1,21 @@
+/**
+ * ``gxwf validate-tests`` — validate a workflow-test file (``*-tests.yml`` /
+ * ``*.gxwf-tests.yml``) against the JSON Schema synced from Galaxy's
+ * ``galaxy.tool_util_models.Tests`` Pydantic model.
+ *
+ * With ``--workflow <path>`` also cross-checks inputs/outputs against the
+ * referenced workflow: unknown job keys, missing required inputs, type
+ * mismatches, unknown output assertions.
+ */
+import { type TestFormatDiagnostic } from "@galaxy-tool-util/schema";
+export interface ValidateTestsOptions {
+    json?: boolean;
+    workflow?: string;
+}
+export interface ValidateTestsReport {
+    file: string;
+    valid: boolean;
+    errors: TestFormatDiagnostic[];
+}
+export declare function runValidateTests(filePath: string, opts?: ValidateTestsOptions): Promise<void>;
+//# sourceMappingURL=validate-tests.d.ts.map

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

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package/dist/commands/validate-tests.js

@@ -0,0 +1,83 @@
+/**
+ * ``gxwf validate-tests`` — validate a workflow-test file (``*-tests.yml`` /
+ * ``*.gxwf-tests.yml``) against the JSON Schema synced from Galaxy's
+ * ``galaxy.tool_util_models.Tests`` Pydantic model.
+ *
+ * With ``--workflow <path>`` also cross-checks inputs/outputs against the
+ * referenced workflow: unknown job keys, missing required inputs, type
+ * mismatches, unknown output assertions.
+ */
+import { readFile } from "node:fs/promises";
+import { parse as parseYaml } from "yaml";
+import { checkTestsAgainstWorkflow, extractWorkflowInputs, extractWorkflowOutputs, resolveFormat, validateTestsFile, } from "@galaxy-tool-util/schema";
+async function loadWorkflowShape(path) {
+    const raw = await readFile(path, "utf-8");
+    const parsed = path.endsWith(".ga") || path.endsWith(".json") ? JSON.parse(raw) : parseYaml(raw);
+    if (!parsed || typeof parsed !== "object" || Array.isArray(parsed)) {
+        throw new Error(`Workflow ${path} did not parse to an object.`);
+    }
+    const dict = parsed;
+    const format = resolveFormat(dict);
+    return {
+        inputs: extractWorkflowInputs(dict, format),
+        outputs: extractWorkflowOutputs(dict, format),
+    };
+}
+export async function runValidateTests(filePath, opts = {}) {
+    const raw = await readFile(filePath, "utf-8");
+    let parsed;
+    try {
+        parsed = parseYaml(raw);
+    }
+    catch (err) {
+        const msg = err instanceof Error ? err.message : String(err);
+        if (opts.json) {
+            const report = {
+                file: filePath,
+                valid: false,
+                errors: [
+                    { path: "(root)", message: `YAML parse error: ${msg}`, keyword: "yaml", params: {} },
+                ],
+            };
+            console.log(JSON.stringify(report, null, 2));
+        }
+        else {
+            console.error(`${filePath}: YAML parse error: ${msg}`);
+        }
+        process.exitCode = 2;
+        return;
+    }
+    const { valid: schemaValid, errors } = validateTestsFile(parsed);
+    const allErrors = [...errors];
+    if (opts.workflow) {
+        try {
+            const shape = await loadWorkflowShape(opts.workflow);
+            allErrors.push(...checkTestsAgainstWorkflow(parsed, shape));
+        }
+        catch (err) {
+            const msg = err instanceof Error ? err.message : String(err);
+            allErrors.push({
+                path: "(root)",
+                message: `Failed to load workflow ${opts.workflow}: ${msg}`,
+                keyword: "workflow_load_error",
+                params: { workflow: opts.workflow },
+            });
+        }
+    }
+    const valid = schemaValid && allErrors.length === 0;
+    if (opts.json) {
+        const report = { file: filePath, valid, errors: allErrors };
+        console.log(JSON.stringify(report, null, 2));
+    }
+    else if (valid) {
+        console.log(`${filePath}: OK`);
+    }
+    else {
+        console.error(`${filePath}: ${allErrors.length} validation error(s)`);
+        for (const e of allErrors) {
+            console.error(`  ${e.path}: ${e.message} [${e.keyword}]`);
+        }
+    }
+    process.exitCode = valid ? 0 : 1;
+}
+//# sourceMappingURL=validate-tests.js.map

package/dist/commands/validate-tests.js.map

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

@@ -0,0 +1,12 @@
+import { type StrictOptions } from "./strict-options.js";
+import { type ReportOutputOptions } from "./report-output.js";
+export interface ValidateTreeOptions extends StrictOptions, ReportOutputOptions {
+    format?: string;
+    toolState?: boolean;
+    cacheDir?: string;
+    mode?: string;
+    toolSchemaDir?: string;
+    json?: boolean;
+}
+export declare function runValidateTree(dir: string, opts: ValidateTreeOptions): Promise<void>;
+//# sourceMappingURL=validate-tree.d.ts.map

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

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