@galaxy-tool-util/cli 0.1.0 → 0.2.0

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

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

@@ -0,0 +1,29 @@
+import { type StepValidationResult } from "./validate-workflow.js";
+import { type TreeSummary } from "./tree.js";
+export interface ValidateTreeOptions {
+    format?: string;
+    toolState?: boolean;
+    cacheDir?: string;
+    mode?: string;
+    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

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

@@ -0,0 +1,118 @@
+/**
+ * `gxwf validate-tree` — batch validate all workflows under a directory.
+ */
+import { ToolCache } from "@galaxy-tool-util/core";
+import { dirname } from "node:path";
+import { createDefaultResolver } from "./url-resolver.js";
+import { resolveFormat } from "./workflow-io.js";
+import { validateNativeSteps, validateFormat2Steps, } from "./validate-workflow.js";
+import { collectTree, summarizeOutcomes } from "./tree.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 });
+            await cache.index.load();
+        }
+        catch (e) {
+            const msg = e instanceof Error ? e.message : String(e);
+            console.warn(`Failed to load tool cache: ${msg}`);
+        }
+    }
+    // Lazy-load json-schema validators to avoid importing ajv when not needed
+    let validateNativeStepsJsonSchema;
+    let validateFormat2StepsJsonSchema;
+    if (mode === "json-schema") {
+        const mod = await import("./validate-workflow-json-schema.js");
+        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 treeResult = await collectTree(dir, async (info, data) => {
+        const format = resolveFormat(data, opts.format);
+        const expansionOpts = {
+            resolver: createDefaultResolver({ workflowDirectory: dirname(info.path) }),
+        };
+        let steps = [];
+        if (cache && opts.toolState !== false) {
+            const validateNative = validateNativeStepsJsonSchema ?? validateNativeSteps;
+            const validateF2 = validateFormat2StepsJsonSchema ?? validateFormat2Steps;
+            steps =
+                format === "native"
+                    ? await validateNative(data, cache, "", expansionOpts)
+                    : await validateF2(data, cache, "", expansionOpts);
+        }
+        return { relativePath: info.relativePath, format, steps };
+    });
+    const report = buildValidateReport(treeResult);
+    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})`);
+            continue;
+        }
+        if (outcome.skipped) {
+            console.warn(`  ${outcome.info.relativePath}: SKIPPED (${outcome.skipReason})`);
+            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}`);
+                }
+            }
+        }
+        else {
+            console.log(`  ${r.relativePath}: ${total} steps (${ok} OK, ${skip} SKIP)`);
+        }
+    }
+    const s = report.summary;
+    console.log(`\nSummary: ${s.total} workflows | ${s.stepOk} OK, ${s.stepFail} FAIL, ${s.stepSkip} SKIP`);
+    process.exitCode = computeValidateExitCode(report);
+}
+function buildValidateReport(treeResult) {
+    const results = [];
+    let stepOk = 0;
+    let stepFail = 0;
+    let stepSkip = 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);
+        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;
+    }
+    const wfSummary = summarizeOutcomes(treeResult.outcomes, (r) => r.steps.some((s) => s.status === "fail"));
+    return {
+        root: treeResult.root,
+        results,
+        summary: { ...wfSummary, stepOk, stepFail, stepSkip },
+    };
+}
+function computeValidateExitCode(report) {
+    const s = report.summary;
+    if (s.stepFail > 0 || s.error > 0)
+        return 1;
+    return 0;
+}
+//# sourceMappingURL=validate-tree.js.map

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

@@ -0,0 +1 @@
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package/dist/commands/validate-workflow-json-schema.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"validate-workflow-json-schema.d.ts","sourceRoot":"","sources":["../../src/commands/validate-workflow-json-schema.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AACnD,OAAO,EAcL,KAAK,gBAAgB,EACtB,MAAM,0BAA0B,CAAC;AAMlC,OAAO,KAAK,EAAE,uBAAuB,EAAE,cAAc,EAAE,oBAAoB,EAAE,MAAM,wBAAwB,CAAC;AAwH5G,wBAAsB,6BAA6B,CACjD,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC7B,MAAM,EAAE,cAAc,EACtB,IAAI,EAAE,uBAAuB,EAC7B,aAAa,CAAC,EAAE,gBAAgB,GAC/B,OAAO,CAAC,IAAI,CAAC,CA0Ef;AAID,wBAAsB,6BAA6B,CACjD,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC7B,KAAK,EAAE,SAAS,EAChB,aAAa,CAAC,EAAE,MAAM,EACtB,MAAM,SAAK,EACX,aAAa,CAAC,EAAE,gBAAgB,GAC/B,OAAO,CAAC,oBAAoB,EAAE,CAAC,CAGjC;AAgFD,wBAAsB,8BAA8B,CAClD,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC7B,KAAK,EAAE,SAAS,EAChB,aAAa,CAAC,EAAE,MAAM,EACtB,MAAM,SAAK,EACX,aAAa,CAAC,EAAE,gBAAgB,GAC/B,OAAO,CAAC,oBAAoB,EAAE,CAAC,CAGjC"}
+{"version":3,"file":"validate-workflow-json-schema.d.ts","sourceRoot":"","sources":["../../src/commands/validate-workflow-json-schema.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AACnD,OAAO,EAcL,KAAK,gBAAgB,EACtB,MAAM,0BAA0B,CAAC;AAMlC,OAAO,KAAK,EACV,uBAAuB,EACvB,cAAc,EACd,oBAAoB,EACrB,MAAM,wBAAwB,CAAC;AA4HhC,wBAAsB,6BAA6B,CACjD,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC7B,MAAM,EAAE,cAAc,EACtB,IAAI,EAAE,uBAAuB,EAC7B,aAAa,CAAC,EAAE,gBAAgB,GAC/B,OAAO,CAAC,IAAI,CAAC,CAqFf;AAID,wBAAsB,6BAA6B,CACjD,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC7B,KAAK,EAAE,SAAS,EAChB,aAAa,CAAC,EAAE,MAAM,EACtB,MAAM,SAAK,EACX,aAAa,CAAC,EAAE,gBAAgB,GAC/B,OAAO,CAAC,oBAAoB,EAAE,CAAC,CAGjC;AA4GD,wBAAsB,8BAA8B,CAClD,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC7B,KAAK,EAAE,SAAS,EAChB,aAAa,CAAC,EAAE,MAAM,EACtB,MAAM,SAAK,EACX,aAAa,CAAC,EAAE,gBAAgB,GAC/B,OAAO,CAAC,oBAAoB,EAAE,CAAC,CAGjC"}

package/dist/commands/validate-workflow-json-schema.js

@@ -120,9 +120,7 @@ export async function runValidateWorkflowJsonSchema(data, format, opts, expansio
     else if (format === "format2" && !("class" in validationData)) {
         validationData.class = "GalaxyWorkflow";
     }
-    const structValidator = format === "native"
-        ? nativeStructuralValidator()
-        : format2StructuralValidator();
+    const structValidator = format === "native" ? nativeStructuralValidator() : format2StructuralValidator();
     const structOk = structValidator(validationData);
     if (!structOk) {
         console.error(`\nStructural validation errors (json-schema):`);
@@ -206,9 +204,7 @@ async function _validateNativeWorkflowJsonSchema(wf, cache, toolSchemaDir, prefi
 async function _validateNativeStepJsonSchema(step, stepLabel, toolId, toolVersion, cache, toolSchemaDir) {
     const resolved = await loadCachedTool(cache, toolId, toolVersion);
     if (isResolveError(resolved)) {
-        const reason = resolved.kind === "no_version"
-            ? `no version for ${toolId}`
-            : `${toolId} not in cache`;
+        const reason = resolved.kind === "no_version" ? `no version for ${toolId}` : `${toolId} not in cache`;
         return { stepLabel, toolId, toolVersion, status: "skip", errors: [reason] };
     }
     const bundle = {
@@ -216,7 +212,13 @@ async function _validateNativeStepJsonSchema(step, stepLabel, toolId, toolVersio
     };
     const replacementScan = scanForReplacements(bundle.parameters, step.tool_state);
     if (replacementScan === "yes") {
-        return { stepLabel, toolId, toolVersion, status: "skip", errors: ["replacement parameters detected"] };
+        return {
+            stepLabel,
+            toolId,
+            toolVersion,
+            status: "skip",
+            errors: ["replacement parameters detected"],
+        };
     }
     const state = structuredClone(step.tool_state);
     const connections = {};
@@ -226,7 +228,13 @@ async function _validateNativeStepJsonSchema(step, stepLabel, toolId, toolVersio
     injectConnectionsIntoState(bundle.parameters, state, connections);
     const validate = getOrBuildValidator(toolId, toolVersion, bundle, "workflow_step_native", toolSchemaDir);
     if (!validate) {
-        return { stepLabel, toolId, toolVersion, status: "skip", errors: ["unsupported parameter types"] };
+        return {
+            stepLabel,
+            toolId,
+            toolVersion,
+            status: "skip",
+            errors: ["unsupported parameter types"],
+        };
     }
     const valid = validate(state);
     if (!valid) {
@@ -261,9 +269,7 @@ async function _validateFormat2WorkflowJsonSchema(wf, cache, toolSchemaDir, pref
 async function _validateFormat2StepJsonSchema(step, stepLabel, toolId, toolVersion, cache, toolSchemaDir) {
     const resolved = await loadCachedTool(cache, toolId, toolVersion);
     if (isResolveError(resolved)) {
-        const reason = resolved.kind === "no_version"
-            ? `no version for ${toolId}`
-            : `${toolId} not in cache`;
+        const reason = resolved.kind === "no_version" ? `no version for ${toolId}` : `${toolId} not in cache`;
         return { stepLabel, toolId, toolVersion, status: "skip", errors: [reason] };
     }
     const bundle = {
@@ -274,11 +280,23 @@ async function _validateFormat2StepJsonSchema(step, stepLabel, toolId, toolVersi
     // Level 1: base validation against workflow_step
     const baseValidate = getOrBuildValidator(toolId, toolVersion, bundle, "workflow_step", toolSchemaDir);
     if (!baseValidate) {
-        return { stepLabel, toolId, toolVersion, status: "skip", errors: ["unsupported parameter types"] };
+        return {
+            stepLabel,
+            toolId,
+            toolVersion,
+            status: "skip",
+            errors: ["unsupported parameter types"],
+        };
     }
     const baseValid = baseValidate(state);
     if (!baseValid) {
-        return { stepLabel, toolId, toolVersion, status: "fail", errors: formatAjvErrors(baseValidate) };
+        return {
+            stepLabel,
+            toolId,
+            toolVersion,
+            status: "fail",
+            errors: formatAjvErrors(baseValidate),
+        };
     }
     // Build connections dict from step.in
     const connections = {};
@@ -295,17 +313,32 @@ async function _validateFormat2StepJsonSchema(step, stepLabel, toolId, toolVersi
         const unmatchedKeys = Object.keys(remaining);
         if (unmatchedKeys.length > 0) {
             return {
-                stepLabel, toolId, toolVersion, status: "fail",
+                stepLabel,
+                toolId,
+                toolVersion,
+                status: "fail",
                 errors: unmatchedKeys.map((k) => `No parameter definition matching connection key "${k}"`),
             };
         }
         const linkedValidate = getOrBuildValidator(toolId, toolVersion, bundle, "workflow_step_linked", toolSchemaDir);
         if (!linkedValidate) {
-            return { stepLabel, toolId, toolVersion, status: "skip", errors: ["unsupported parameter types"] };
+            return {
+                stepLabel,
+                toolId,
+                toolVersion,
+                status: "skip",
+                errors: ["unsupported parameter types"],
+            };
         }
         const linkedValid = linkedValidate(linkedState);
         if (!linkedValid) {
-            return { stepLabel, toolId, toolVersion, status: "fail", errors: formatAjvErrors(linkedValidate) };
+            return {
+                stepLabel,
+                toolId,
+                toolVersion,
+                status: "fail",
+                errors: formatAjvErrors(linkedValidate),
+            };
         }
     }
     return { stepLabel, toolId, toolVersion, status: "ok", errors: [] };

package/dist/commands/validate-workflow-json-schema.js.map

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

@@ -18,4 +18,5 @@ export interface StepValidationResult {
 }
 export declare function runValidateWorkflow(filePath: string, opts: ValidateWorkflowOptions): Promise<void>;
 export declare function validateNativeSteps(data: Record<string, unknown>, cache: ToolCache, prefix?: string, expansionOpts?: ExpansionOptions): Promise<StepValidationResult[]>;
+export declare function validateFormat2Steps(data: Record<string, unknown>, cache: ToolCache, prefix?: string, expansionOpts?: ExpansionOptions): Promise<StepValidationResult[]>;
 //# sourceMappingURL=validate-workflow.d.ts.map

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

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