@galaxy-tool-util/cli 0.2.0 → 0.4.0

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

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

@@ -1,6 +1,6 @@
-import { type StepValidationResult } from "./validate-workflow.js";
-import { type TreeSummary } from "./tree.js";
-export interface ValidateTreeOptions {
+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;
@@ -8,22 +8,5 @@ export interface ValidateTreeOptions {
     toolSchemaDir?: string;
     json?: boolean;
 }
-export interface WorkflowValidateResult {
-    relativePath: string;
-    format: string;
-    steps: StepValidationResult[];
-}
-export interface ValidateTreeReport {
-    root: string;
-    results: (WorkflowValidateResult | {
-        relativePath: string;
-        error: string;
-    })[];
-    summary: TreeSummary & {
-        stepOk: number;
-        stepFail: number;
-        stepSkip: number;
-    };
-}
 export declare function runValidateTree(dir: string, opts: ValidateTreeOptions): Promise<void>;
 //# sourceMappingURL=validate-tree.d.ts.map

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

@@ -1 +1 @@
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+{"version":3,"file":"validate-tree.d.ts","sourceRoot":"","sources":["../../src/commands/validate-tree.ts"],"names":[],"mappings":"AAiBA,OAAO,EAAwB,KAAK,aAAa,EAAE,MAAM,qBAAqB,CAAC;AAQ/E,OAAO,EAAsC,KAAK,mBAAmB,EAAE,MAAM,oBAAoB,CAAC;AAElG,MAAM,WAAW,mBAAoB,SAAQ,aAAa,EAAE,mBAAmB;IAC7E,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,SAAS,CAAC,EAAE,OAAO,CAAC;IACpB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,IAAI,CAAC,EAAE,OAAO,CAAC;CAChB;AAED,wBAAsB,eAAe,CAAC,GAAG,EAAE,MAAM,EAAE,IAAI,EAAE,mBAAmB,GAAG,OAAO,CAAC,IAAI,CAAC,CAyG3F"}

package/dist/commands/validate-tree.js

@@ -1,19 +1,19 @@
-/**
- * `gxwf validate-tree` — batch validate all workflows under a directory.
- */
-import { ToolCache } from "@galaxy-tool-util/core";
+import { makeNodeToolCache } from "@galaxy-tool-util/core/node";
+import { checkStrictEncoding, checkStrictStructure, buildWorkflowValidationResult, buildTreeValidationReport, } from "@galaxy-tool-util/schema";
 import { dirname } from "node:path";
 import { createDefaultResolver } from "./url-resolver.js";
+import { resolveStrictOptions } from "./strict-options.js";
 import { resolveFormat } from "./workflow-io.js";
 import { validateNativeSteps, validateFormat2Steps, } from "./validate-workflow.js";
-import { collectTree, summarizeOutcomes } from "./tree.js";
+import { collectTree } from "./tree.js";
+import { writeReportOutput, writeReportHtml } from "./report-output.js";
 export async function runValidateTree(dir, opts) {
     const mode = opts.mode === "json-schema" ? "json-schema" : "effect";
     // Load tool cache once for all files
     let cache;
     if (opts.toolState !== false) {
         try {
-            cache = new ToolCache({ cacheDir: opts.cacheDir });
+            cache = makeNodeToolCache({ cacheDir: opts.cacheDir });
             await cache.index.load();
         }
         catch (e) {
@@ -29,89 +29,95 @@ export async function runValidateTree(dir, opts) {
         validateNativeStepsJsonSchema = (data, cache, prefix, expansionOpts) => mod.validateNativeStepsJsonSchema(data, cache, opts.toolSchemaDir, prefix, expansionOpts);
         validateFormat2StepsJsonSchema = (data, cache, prefix, expansionOpts) => mod.validateFormat2StepsJsonSchema(data, cache, opts.toolSchemaDir, prefix, expansionOpts);
     }
+    const strict = resolveStrictOptions(opts);
     const treeResult = await collectTree(dir, async (info, data) => {
         const format = resolveFormat(data, opts.format);
+        // Per-file strict checks
+        if (strict.strictEncoding) {
+            const encErrors = checkStrictEncoding(data, format);
+            if (encErrors.length > 0) {
+                throw new Error(`Encoding: ${encErrors.join("; ")}`);
+            }
+        }
+        if (strict.strictStructure) {
+            const structErrors = checkStrictStructure(data, format);
+            if (structErrors.length > 0) {
+                throw new Error(`Structure: ${structErrors.join("; ")}`);
+            }
+        }
         const expansionOpts = {
             resolver: createDefaultResolver({ workflowDirectory: dirname(info.path) }),
         };
-        let steps = [];
+        let stepResults = [];
         if (cache && opts.toolState !== false) {
             const validateNative = validateNativeStepsJsonSchema ?? validateNativeSteps;
             const validateF2 = validateFormat2StepsJsonSchema ?? validateFormat2Steps;
-            steps =
+            stepResults =
                 format === "native"
                     ? await validateNative(data, cache, "", expansionOpts)
                     : await validateF2(data, cache, "", expansionOpts);
         }
-        return { relativePath: info.relativePath, format, steps };
+        // --strict-state: promote skips to failures
+        if (strict.strictState && stepResults.some((s) => s.status !== "ok" && s.status !== "fail")) {
+            throw new Error("Strict state: skipped steps not allowed");
+        }
+        return buildWorkflowValidationResult(info.relativePath, stepResults);
     });
-    const report = buildValidateReport(treeResult);
+    const report = buildReport(treeResult);
+    await writeReportOutput("validate_tree.md.j2", report, { reportMarkdown: opts.reportMarkdown });
+    await writeReportHtml("validate-tree", report, opts.reportHtml);
     if (opts.json) {
         console.log(JSON.stringify(report, null, 2));
         process.exitCode = computeValidateExitCode(report);
         return;
     }
     // Text output
-    for (const outcome of treeResult.outcomes) {
-        if (outcome.error) {
-            console.error(`  ${outcome.info.relativePath}: ERROR (${outcome.error})`);
+    for (const wf of report.workflows) {
+        if (wf.error) {
+            console.error(`  ${wf.path}: ERROR (${wf.error})`);
             continue;
         }
-        if (outcome.skipped) {
-            console.warn(`  ${outcome.info.relativePath}: SKIPPED (${outcome.skipReason})`);
+        if (wf.skipped_reason) {
+            console.warn(`  ${wf.path}: SKIPPED (${wf.skipped_reason})`);
             continue;
         }
-        const r = outcome.result;
-        const ok = r.steps.filter((s) => s.status === "ok").length;
-        const fail = r.steps.filter((s) => s.status === "fail").length;
-        const skip = r.steps.filter((s) => s.status === "skip").length;
-        const total = r.steps.length;
-        if (fail > 0) {
-            console.error(`  ${r.relativePath}: ${total} steps (${ok} OK, ${fail} FAIL, ${skip} SKIP)`);
-            for (const s of r.steps.filter((s) => s.status === "fail")) {
-                for (const err of s.errors) {
-                    console.error(`    Step ${s.stepLabel} (${s.toolId}): ${err}`);
-                }
+        const s = wf.summary;
+        const total = s.ok + s.fail + s.skip;
+        if (s.fail > 0) {
+            console.error(`  ${wf.path}: ${total} steps (${s.ok} OK, ${s.fail} FAIL, ${s.skip} SKIP)`);
+            for (const f of wf.failures ?? []) {
+                console.error(`    Step ${f.step} (${f.tool_id}): ${f.message}`);
             }
         }
         else {
-            console.log(`  ${r.relativePath}: ${total} steps (${ok} OK, ${skip} SKIP)`);
+            console.log(`  ${wf.path}: ${total} steps (${s.ok} OK, ${s.skip} SKIP)`);
         }
     }
     const s = report.summary;
-    console.log(`\nSummary: ${s.total} workflows | ${s.stepOk} OK, ${s.stepFail} FAIL, ${s.stepSkip} SKIP`);
+    const total = report.workflows.length;
+    console.log(`\nSummary: ${total} workflows | ${s.ok} OK, ${s.fail} FAIL, ${s.skip} SKIP`);
     process.exitCode = computeValidateExitCode(report);
 }
-function buildValidateReport(treeResult) {
-    const results = [];
-    let stepOk = 0;
-    let stepFail = 0;
-    let stepSkip = 0;
+function buildReport(treeResult) {
+    const workflows = [];
     for (const o of treeResult.outcomes) {
         if (o.error) {
-            results.push({ relativePath: o.info.relativePath, error: o.error });
+            workflows.push(buildWorkflowValidationResult(o.info.relativePath, [], { error: o.error }));
             continue;
         }
         if (o.skipped) {
-            results.push({ relativePath: o.info.relativePath, error: `SKIPPED: ${o.skipReason}` });
+            workflows.push(buildWorkflowValidationResult(o.info.relativePath, [], {
+                skipped_reason: o.skipReason ?? null,
+            }));
             continue;
         }
-        const r = o.result;
-        results.push(r);
-        stepOk += r.steps.filter((s) => s.status === "ok").length;
-        stepFail += r.steps.filter((s) => s.status === "fail").length;
-        stepSkip += r.steps.filter((s) => s.status === "skip").length;
+        workflows.push(o.result);
     }
-    const wfSummary = summarizeOutcomes(treeResult.outcomes, (r) => r.steps.some((s) => s.status === "fail"));
-    return {
-        root: treeResult.root,
-        results,
-        summary: { ...wfSummary, stepOk, stepFail, stepSkip },
-    };
+    return buildTreeValidationReport(treeResult.root, workflows);
 }
 function computeValidateExitCode(report) {
     const s = report.summary;
-    if (s.stepFail > 0 || s.error > 0)
+    if (s.fail > 0 || s.error > 0)
         return 1;
     return 0;
 }

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

@@ -1 +1 @@
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package/dist/commands/validate-workflow-json-schema.d.ts

@@ -7,10 +7,16 @@
  *
  * Mirrors Galaxy's validation_json_schema.py.
  */
-import { ToolCache } from "@galaxy-tool-util/core";
+import type { ToolCache } from "@galaxy-tool-util/core";
 import { type ExpansionOptions } from "@galaxy-tool-util/schema";
 import type { ValidateWorkflowOptions, WorkflowFormat, StepValidationResult } from "./validate-workflow.js";
-export declare function runValidateWorkflowJsonSchema(data: Record<string, unknown>, format: WorkflowFormat, opts: ValidateWorkflowOptions, expansionOpts?: ExpansionOptions): Promise<void>;
+/**
+ * Validate workflow structure using the AJV-compiled JSON Schema (Draft 2020-12).
+ * Returns an array of error strings; empty if valid.
+ * Mirrors `decodeStructureErrors` but uses the AJV path instead of Effect decode.
+ */
+export declare function decodeStructureErrorsJsonSchema(data: Record<string, unknown>, format: WorkflowFormat): string[];
+export declare function runValidateWorkflowJsonSchema(filePath: string, data: Record<string, unknown>, format: WorkflowFormat, opts: ValidateWorkflowOptions, expansionOpts?: ExpansionOptions): Promise<void>;
 export declare function validateNativeStepsJsonSchema(data: Record<string, unknown>, cache: ToolCache, toolSchemaDir?: string, prefix?: string, expansionOpts?: ExpansionOptions): Promise<StepValidationResult[]>;
 export declare function validateFormat2StepsJsonSchema(data: Record<string, unknown>, cache: ToolCache, toolSchemaDir?: string, prefix?: string, expansionOpts?: ExpansionOptions): Promise<StepValidationResult[]>;
 //# sourceMappingURL=validate-workflow-json-schema.d.ts.map

package/dist/commands/validate-workflow-json-schema.d.ts.map

@@ -1 +1 @@
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