@galaxy-tool-util/cli 0.1.0 → 0.4.0

package/dist/commands/validate-workflow.js

@@ -1,38 +1,38 @@
-import { ToolCache } from "@galaxy-tool-util/core";
-import { createFieldModel, detectFormat, GalaxyWorkflowSchema, NativeGalaxyWorkflowSchema, expandedNative, expandedFormat2, injectConnectionsIntoState, stripConnectedValues, scanForReplacements, } from "@galaxy-tool-util/schema";
+import { makeNodeToolCache } from "@galaxy-tool-util/core/node";
+import { createFieldModel, GalaxyWorkflowSchema, NativeGalaxyWorkflowSchema, expandedNative, expandedFormat2, injectConnectionsIntoState, stripConnectedValues, scanForReplacements, checkStrictEncoding, checkStrictStructure, withClass, scanToolState, buildSingleValidationReport, } from "@galaxy-tool-util/schema";
 import * as ParseResult from "effect/ParseResult";
 import * as S from "effect/Schema";
-import { readFile } from "node:fs/promises";
 import { dirname } from "node:path";
-import * as YAML from "yaml";
 import { isResolveError, loadCachedTool } from "./resolve-tool.js";
 import { createDefaultResolver } from "./url-resolver.js";
+import { renderStepResults } from "./render-results.js";
+import { readWorkflowFile, resolveFormat } from "./workflow-io.js";
+import { resolveStrictOptions } from "./strict-options.js";
+import { writeReportHtml } from "./report-output.js";
 function formatIssues(error) {
     const issues = ParseResult.ArrayFormatter.formatErrorSync(error);
     return issues.map((i) => `${i.path.join(".")}: ${i.message}`);
 }
-export async function runValidateWorkflow(filePath, opts) {
-    const raw = await readFile(filePath, "utf-8");
-    let data;
-    try {
-        if (filePath.endsWith(".ga") || filePath.endsWith(".json")) {
-            data = JSON.parse(raw);
-        }
-        else {
-            data = YAML.parse(raw);
-        }
+/** Run Effect Schema decode on raw workflow data and return structural decode failures. */
+export function decodeStructureErrors(data, format) {
+    const cls = format === "native" ? "NativeGalaxyWorkflow" : "GalaxyWorkflow";
+    const validationData = withClass(data, cls);
+    const schema = format === "native" ? NativeGalaxyWorkflowSchema : GalaxyWorkflowSchema;
+    const decode = S.decodeUnknownEither(schema, { onExcessProperty: "ignore" });
+    const result = decode(validationData);
+    if (result._tag === "Left") {
+        return formatIssues(result.left);
     }
-    catch (e) {
-        const msg = e instanceof Error ? e.message : String(e);
-        console.error(`Failed to parse ${filePath}: ${msg}`);
-        process.exitCode = 1;
+    return [];
+}
+export async function runValidateWorkflow(filePath, opts) {
+    const data = await readWorkflowFile(filePath);
+    if (!data)
         return;
-    }
-    const format = opts.format === "native" || opts.format === "format2"
-        ? opts.format
-        : detectFormat(data);
+    const format = resolveFormat(data, opts.format);
     const mode = opts.mode === "json-schema" ? "json-schema" : "effect";
-    console.log(`Detected format: ${format}, mode: ${mode}`);
+    if (!opts.json)
+        console.log(`Detected format: ${format}, mode: ${mode}`);
     // Build expansion options for resolving external subworkflow references
     const workflowDirectory = dirname(filePath);
     const expansionOpts = {
@@ -40,71 +40,106 @@ export async function runValidateWorkflow(filePath, opts) {
     };
     if (mode === "json-schema") {
         const { runValidateWorkflowJsonSchema } = await import("./validate-workflow-json-schema.js");
-        return runValidateWorkflowJsonSchema(data, format, opts, expansionOpts);
-    }
-    // --- structural validation (effect mode) ---
-    const validationData = { ...data };
-    if (format === "native" && !("class" in validationData)) {
-        validationData.class = "NativeGalaxyWorkflow";
+        return runValidateWorkflowJsonSchema(filePath, data, format, opts, expansionOpts);
     }
-    else if (format === "format2" && !("class" in validationData)) {
-        validationData.class = "GalaxyWorkflow";
+    const strict = resolveStrictOptions(opts);
+    // --- strict encoding check (pre-normalization) ---
+    if (strict.strictEncoding) {
+        const encErrors = checkStrictEncoding(data, format);
+        if (encErrors.length > 0) {
+            console.error("Encoding errors:");
+            for (const e of encErrors)
+                console.error(`  ${e}`);
+            process.exitCode = 2;
+            return;
+        }
     }
-    const schema = format === "native" ? NativeGalaxyWorkflowSchema : GalaxyWorkflowSchema;
-    const decode = S.decodeUnknownEither(schema, { onExcessProperty: "ignore" });
-    const structResult = decode(validationData);
-    let structOk = true;
-    if (structResult._tag === "Left") {
-        structOk = false;
-        console.error(`\nStructural validation errors:`);
-        for (const line of formatIssues(structResult.left)) {
-            console.error(`  ${line}`);
+    // --- strict structure check (pre-normalization) ---
+    if (strict.strictStructure) {
+        const structErrors = checkStrictStructure(data, format);
+        if (structErrors.length > 0) {
+            console.error("Structure errors (strict):");
+            for (const e of structErrors)
+                console.error(`  ${e}`);
+            process.exitCode = 2;
+            return;
         }
     }
-    else {
-        console.log(`Structural validation: OK`);
+    // --- structural validation (effect mode) ---
+    const structureErrors = decodeStructureErrors(data, format);
+    const structOk = structureErrors.length === 0;
+    if (!opts.json) {
+        if (!structOk) {
+            console.error(`\nStructural validation errors:`);
+            for (const line of structureErrors) {
+                console.error(`  ${line}`);
+            }
+        }
+        else {
+            console.log(`Structural validation: OK`);
+        }
     }
     // --- tool state validation (effect mode) ---
     if (opts.toolState === false) {
+        if (opts.json || opts.reportHtml) {
+            const report = buildSingleValidationReport(filePath, [], {
+                structure_errors: structureErrors,
+            });
+            if (opts.json) {
+                console.log(JSON.stringify(report, null, 2));
+            }
+            await writeReportHtml("validate", report, opts.reportHtml);
+        }
         process.exitCode = structOk ? 0 : 1;
         return;
     }
-    const cache = new ToolCache({ cacheDir: opts.cacheDir });
+    const cache = makeNodeToolCache({ cacheDir: opts.cacheDir });
     await cache.index.load();
-    let results;
-    if (format === "native") {
-        results = await validateNativeSteps(data, cache, "", expansionOpts);
+    let results = [];
+    const encodingErrors = [];
+    try {
+        if (format === "native") {
+            results = await validateNativeSteps(data, cache, "", expansionOpts);
+        }
+        else {
+            results = await validateFormat2Steps(data, cache, "", expansionOpts);
+        }
+    }
+    catch (error) {
+        // Catch legacy encoding errors thrown by walker and capture them
+        if (error instanceof Error && error.message.includes("legacy parameter encoding")) {
+            encodingErrors.push(error.message);
+        }
+        else {
+            throw error;
+        }
     }
-    else {
-        results = await validateFormat2Steps(data, cache, "", expansionOpts);
+    const stateOk = !results.some((r) => r.status === "fail");
+    if (opts.json || opts.reportHtml) {
+        const report = buildSingleValidationReport(filePath, results, {
+            structure_errors: structureErrors,
+            encoding_errors: encodingErrors,
+        });
+        if (opts.json) {
+            console.log(JSON.stringify(report, null, 2));
+        }
+        await writeReportHtml("validate", report, opts.reportHtml);
+        process.exitCode = structOk && stateOk ? 0 : 1;
+        return;
     }
     if (results.length === 0) {
         console.log("No tool steps to validate state for.");
         process.exitCode = structOk ? 0 : 1;
         return;
     }
-    let stateOk = true;
-    let validated = 0;
-    let skipped = 0;
-    for (const r of results) {
-        if (r.status === "skip") {
-            skipped++;
-            console.warn(`  [${r.stepLabel}] skipped — ${r.errors[0] ?? "unknown"}`);
-        }
-        else if (r.status === "fail") {
-            validated++;
-            stateOk = false;
-            console.error(`  [${r.stepLabel}] tool_state errors (${r.toolId}):`);
-            for (const line of r.errors) {
-                console.error(`    ${line}`);
-            }
-        }
-        else {
-            validated++;
-            console.log(`  [${r.stepLabel}] tool_state: OK`);
-        }
-    }
+    const { validated, skipped } = renderStepResults(results);
     console.log(`\nTool state: ${validated} validated, ${skipped} skipped`);
+    // --- strict state: promote skips to failures ---
+    if (strict.strictState && results.some((r) => r.status !== "ok" && r.status !== "fail")) {
+        console.error("Strict state: skipped steps not allowed");
+        process.exitCode = 2;
+        return;
+    }
     process.exitCode = structOk && stateOk ? 0 : 1;
 }
 // --- Native validation ---
@@ -134,10 +169,14 @@ async function _validateNativeWorkflow(wf, cache, prefix) {
 async function _validateNativeStep(step, stepLabel, toolId, toolVersion, cache) {
     const resolved = await loadCachedTool(cache, toolId, toolVersion);
     if (isResolveError(resolved)) {
-        const reason = resolved.kind === "no_version"
-            ? `no version for ${toolId}`
-            : `${toolId} not in cache`;
-        return { stepLabel, toolId, toolVersion, status: "skip", errors: [reason] };
+        const reason = resolved.kind === "no_version" ? `no version for ${toolId}` : `${toolId} not in cache`;
+        return {
+            step: stepLabel,
+            tool_id: toolId,
+            version: toolVersion,
+            status: "skip_tool_not_found",
+            errors: [reason],
+        };
     }
     const bundle = {
         parameters: resolved.tool.inputs,
@@ -145,7 +184,13 @@ async function _validateNativeStep(step, stepLabel, toolId, toolVersion, cache)
     // Skip validation if replacement parameters (${...}) are present in typed fields
     const replacementScan = scanForReplacements(bundle.parameters, step.tool_state);
     if (replacementScan === "yes") {
-        return { stepLabel, toolId, toolVersion, status: "skip", errors: ["replacement parameters detected"] };
+        return {
+            step: stepLabel,
+            tool_id: toolId,
+            version: toolVersion,
+            status: "skip_replacement_params",
+            errors: ["replacement parameters detected"],
+        };
     }
     // Deep copy state and inject connection markers
     const state = structuredClone(step.tool_state);
@@ -157,19 +202,31 @@ async function _validateNativeStep(step, stepLabel, toolId, toolVersion, cache)
     // Validate against workflow_step_native schema
     const fieldModel = createFieldModel(bundle, "workflow_step_native");
     if (!fieldModel) {
-        return { stepLabel, toolId, toolVersion, status: "skip", errors: ["unsupported parameter types"] };
+        return {
+            step: stepLabel,
+            tool_id: toolId,
+            version: toolVersion,
+            status: "skip_tool_not_found",
+            errors: ["unsupported parameter types"],
+        };
     }
     const validate = S.decodeUnknownEither(fieldModel, {
         onExcessProperty: "ignore",
     });
     const result = validate(state);
     if (result._tag === "Left") {
-        return { stepLabel, toolId, toolVersion, status: "fail", errors: formatIssues(result.left) };
+        return {
+            step: stepLabel,
+            tool_id: toolId,
+            version: toolVersion,
+            status: "fail",
+            errors: formatIssues(result.left),
+        };
     }
-    return { stepLabel, toolId, toolVersion, status: "ok", errors: [] };
+    return { step: stepLabel, tool_id: toolId, version: toolVersion, status: "ok", errors: [] };
 }
 // --- Format2 validation ---
-async function validateFormat2Steps(data, cache, prefix = "", expansionOpts) {
+export async function validateFormat2Steps(data, cache, prefix = "", expansionOpts) {
     const expanded = await expandedFormat2(data, expansionOpts);
     return _validateFormat2Workflow(expanded, cache, prefix);
 }
@@ -196,10 +253,14 @@ async function _validateFormat2Workflow(wf, cache, prefix) {
 async function _validateFormat2Step(step, stepLabel, toolId, toolVersion, cache) {
     const resolved = await loadCachedTool(cache, toolId, toolVersion);
     if (isResolveError(resolved)) {
-        const reason = resolved.kind === "no_version"
-            ? `no version for ${toolId}`
-            : `${toolId} not in cache`;
-        return { stepLabel, toolId, toolVersion, status: "skip", errors: [reason] };
+        const reason = resolved.kind === "no_version" ? `no version for ${toolId}` : `${toolId} not in cache`;
+        return {
+            step: stepLabel,
+            tool_id: toolId,
+            version: toolVersion,
+            status: "skip_tool_not_found",
+            errors: [reason],
+        };
     }
     const bundle = {
         parameters: resolved.tool.inputs,
@@ -212,14 +273,26 @@ async function _validateFormat2Step(step, stepLabel, toolId, toolVersion, cache)
     // Level 1: Validate base state against workflow_step
     const baseModel = createFieldModel(bundle, "workflow_step");
     if (!baseModel) {
-        return { stepLabel, toolId, toolVersion, status: "skip", errors: ["unsupported parameter types"] };
+        return {
+            step: stepLabel,
+            tool_id: toolId,
+            version: toolVersion,
+            status: "skip_tool_not_found",
+            errors: ["unsupported parameter types"],
+        };
     }
     const baseValidate = S.decodeUnknownEither(baseModel, {
         onExcessProperty: "ignore",
     });
     const baseResult = baseValidate(state);
     if (baseResult._tag === "Left") {
-        return { stepLabel, toolId, toolVersion, status: "fail", errors: formatIssues(baseResult.left) };
+        return {
+            step: stepLabel,
+            tool_id: toolId,
+            version: toolVersion,
+            status: "fail",
+            errors: formatIssues(baseResult.left),
+        };
     }
     // Build connections dict from step.in entries
     const connections = {};
@@ -236,22 +309,76 @@ async function _validateFormat2Step(step, stepLabel, toolId, toolVersion, cache)
         const unmatchedKeys = Object.keys(remaining);
         if (unmatchedKeys.length > 0) {
             return {
-                stepLabel, toolId, toolVersion, status: "fail",
+                step: stepLabel,
+                tool_id: toolId,
+                version: toolVersion,
+                status: "fail",
                 errors: unmatchedKeys.map((k) => `No parameter definition matching connection key "${k}"`),
             };
         }
         const linkedModel = createFieldModel(bundle, "workflow_step_linked");
         if (!linkedModel) {
-            return { stepLabel, toolId, toolVersion, status: "skip", errors: ["unsupported parameter types"] };
+            return {
+                step: stepLabel,
+                tool_id: toolId,
+                version: toolVersion,
+                status: "skip_tool_not_found",
+                errors: ["unsupported parameter types"],
+            };
         }
         const linkedValidate = S.decodeUnknownEither(linkedModel, {
             onExcessProperty: "ignore",
         });
         const linkedResult = linkedValidate(linkedState);
         if (linkedResult._tag === "Left") {
-            return { stepLabel, toolId, toolVersion, status: "fail", errors: formatIssues(linkedResult.left) };
+            return {
+                step: stepLabel,
+                tool_id: toolId,
+                version: toolVersion,
+                status: "fail",
+                errors: formatIssues(linkedResult.left),
+            };
+        }
+    }
+    return { step: stepLabel, tool_id: toolId, version: toolVersion, status: "ok", errors: [] };
+}
+// --- Encoding error detection ---
+/**
+ * Detect legacy parameter encoding in workflow tool_state fields.
+ *
+ * Scans each tool step's tool_state for legacy encoding signals
+ * (string-encoded containers, quoted select values) using scanToolState().
+ */
+export async function detectEncodingErrors(data, cache, format, expansionOpts) {
+    if (format === "native") {
+        const expanded = await expandedNative(data, expansionOpts);
+        return _detectNativeEncodingErrors(expanded, cache, "");
+    }
+    // Format2 workflows don't have legacy encoding issues
+    return [];
+}
+async function _detectNativeEncodingErrors(wf, cache, prefix) {
+    const errors = [];
+    for (const [key, step] of Object.entries(wf.steps)) {
+        const stepLabel = prefix ? `${prefix}${key}` : key;
+        if (step.type === "subworkflow" && step.subworkflow) {
+            const subErrors = await _detectNativeEncodingErrors(step.subworkflow, cache, `${stepLabel}.`);
+            errors.push(...subErrors);
+            continue;
+        }
+        const toolId = step.tool_id;
+        if (!toolId)
+            continue;
+        const resolved = await loadCachedTool(cache, toolId, step.tool_version ?? null);
+        if (isResolveError(resolved))
+            continue;
+        const inputs = resolved.tool.inputs;
+        const result = scanToolState(inputs, step.tool_state);
+        if (result.classification === "yes") {
+            const details = result.hits.map((h) => `${h.parameterName}: ${h.detail}`).join("; ");
+            errors.push(`Step ${stepLabel} (${toolId}): legacy parameter encoding (${details})`);
         }
     }
-    return { stepLabel, toolId, toolVersion, status: "ok", errors: [] };
+    return errors;
 }
 //# sourceMappingURL=validate-workflow.js.map

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

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

@@ -0,0 +1,7 @@
+export { resolveFormat, serializeWorkflow } from "@galaxy-tool-util/schema";
+export type { SerializeWorkflowOptions } from "@galaxy-tool-util/schema";
+/** Read and parse a workflow file, auto-detecting JSON vs YAML by extension. */
+export declare function readWorkflowFile(filePath: string): Promise<Record<string, unknown> | null>;
+/** Write serialized workflow content to a file or stdout. */
+export declare function writeWorkflowOutput(content: string, output?: string, label?: string): Promise<void>;
+//# sourceMappingURL=workflow-io.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"workflow-io.d.ts","sourceRoot":"","sources":["../../src/commands/workflow-io.ts"],"names":[],"mappings":"AAWA,OAAO,EAAE,aAAa,EAAE,iBAAiB,EAAE,MAAM,0BAA0B,CAAC;AAC5E,YAAY,EAAE,wBAAwB,EAAE,MAAM,0BAA0B,CAAC;AAEzE,gFAAgF;AAChF,wBAAsB,gBAAgB,CAAC,QAAQ,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,IAAI,CAAC,CAahG;AAED,6DAA6D;AAC7D,wBAAsB,mBAAmB,CACvC,OAAO,EAAE,MAAM,EACf,MAAM,CAAC,EAAE,MAAM,EACf,KAAK,SAAa,GACjB,OAAO,CAAC,IAAI,CAAC,CAOf"}

package/dist/commands/workflow-io.js

@@ -0,0 +1,38 @@
+/**
+ * Workflow file I/O helpers for CLI commands.
+ *
+ * `resolveFormat` and `serializeWorkflow` are now provided by
+ * `@galaxy-tool-util/schema` so the web server can share them; this file
+ * re-exports them for callers that used the older cli-local paths and keeps
+ * the fs-based read/write helpers here (Node-only).
+ */
+import { readFile, writeFile } from "node:fs/promises";
+import * as YAML from "yaml";
+export { resolveFormat, serializeWorkflow } from "@galaxy-tool-util/schema";
+/** Read and parse a workflow file, auto-detecting JSON vs YAML by extension. */
+export async function readWorkflowFile(filePath) {
+    const raw = await readFile(filePath, "utf-8");
+    try {
+        if (filePath.endsWith(".ga") || filePath.endsWith(".json")) {
+            return JSON.parse(raw);
+        }
+        return YAML.parse(raw);
+    }
+    catch (e) {
+        const msg = e instanceof Error ? e.message : String(e);
+        console.error(`Failed to parse ${filePath}: ${msg}`);
+        process.exitCode = 1;
+        return null;
+    }
+}
+/** Write serialized workflow content to a file or stdout. */
+export async function writeWorkflowOutput(content, output, label = "Workflow") {
+    if (output) {
+        await writeFile(output, content, "utf-8");
+        console.log(`${label} written to ${output}`);
+    }
+    else {
+        process.stdout.write(content);
+    }
+}
+//# sourceMappingURL=workflow-io.js.map

package/dist/commands/workflow-io.js.map

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

@@ -16,4 +16,45 @@ export { runClear } from "./commands/clear.js";
 export { runSchema } from "./commands/schema.js";
 /** Validate a Galaxy workflow file (structure + optional tool state). */
 export { runValidateWorkflow } from "./commands/validate-workflow.js";
+/** Validate a workflow-test file (*-tests.yml / *.gxwf-tests.yml). */
+export { runValidateTests } from "./commands/validate-tests.js";
+export type { ValidateTestsOptions, ValidateTestsReport } from "./commands/validate-tests.js";
+/** Batch-validate workflow-test files under a directory. */
+export { runValidateTestsTree } from "./commands/validate-tests-tree.js";
+export type { ValidateTestsTreeOptions, ValidateTestsTreeReport, } from "./commands/validate-tests-tree.js";
+/** Clean a Galaxy workflow — strip stale keys and decode legacy encoding. */
+export { runClean } from "./commands/clean.js";
+/** Lint a Galaxy workflow — structural checks, best practices, tool state validation. */
+export { runLint, lintWorkflowReport } from "./commands/lint.js";
+export type { LintReport, LintReportOptions } from "./commands/lint.js";
+/** Convert a Galaxy workflow between native and format2 formats. */
+export { runConvert } from "./commands/convert.js";
+/** Scan a workflow and cache all referenced tools. */
+export { runPopulateWorkflow } from "./commands/populate-workflow.js";
+/** Export the structural JSON Schema for Galaxy workflows. */
+export { runStructuralSchema } from "./commands/structural-schema.js";
+/** Batch validate all workflows under a directory. */
+export { runValidateTree } from "./commands/validate-tree.js";
+/** Batch lint all workflows under a directory. */
+export { runLintTree } from "./commands/lint-tree.js";
+/** Batch clean all workflows under a directory. */
+export { runCleanTree } from "./commands/clean-tree.js";
+/** Batch convert all workflows under a directory. */
+export { runConvertTree } from "./commands/convert-tree.js";
+/** Tree orchestrator infrastructure. */
+export { discoverWorkflows, collectTree, summarizeOutcomes, skipWorkflow, loadWorkflowSafe, } from "./commands/tree.js";
+export type { WorkflowInfo, WorkflowOutcome, TreeResult, TreeSummary } from "./commands/tree.js";
+/** Render step validation results to console. */
+export { renderStepResults } from "./commands/render-results.js";
+/** Write workflow content to file or stdout. */
+export { writeWorkflowOutput } from "./commands/workflow-io.js";
+/** Validate native/format2 workflow steps programmatically (no CLI I/O). */
+export { validateNativeSteps, validateFormat2Steps, decodeStructureErrors, detectEncodingErrors, } from "./commands/validate-workflow.js";
+/** Preload tool inputs from a ToolCache into a synchronous ToolInputsResolver. */
+export { loadToolInputsForWorkflow } from "./commands/stateful-tool-inputs.js";
+export type { ToolLoadStatus, LoadedToolInputs } from "./commands/stateful-tool-inputs.js";
+/** Default subworkflow ref resolver (base64, TRS, HTTP, file paths). */
+export { createDefaultResolver } from "./commands/url-resolver.js";
+/** JSON-Schema-based (AJV) step validation and structural error decoding. */
+export { validateNativeStepsJsonSchema, validateFormat2StepsJsonSchema, decodeStructureErrorsJsonSchema, } from "./commands/validate-workflow-json-schema.js";
 //# sourceMappingURL=index.d.ts.map

package/dist/index.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,qEAAqE;AACrE,OAAO,EAAE,MAAM,EAAE,MAAM,mBAAmB,CAAC;AAC3C,yCAAyC;AACzC,OAAO,EAAE,OAAO,EAAE,MAAM,oBAAoB,CAAC;AAC7C,0CAA0C;AAC1C,OAAO,EAAE,OAAO,EAAE,MAAM,oBAAoB,CAAC;AAC7C,4DAA4D;AAC5D,OAAO,EAAE,QAAQ,EAAE,MAAM,qBAAqB,CAAC;AAC/C,2FAA2F;AAC3F,OAAO,EAAE,SAAS,EAAE,MAAM,sBAAsB,CAAC;AACjD,yEAAyE;AACzE,OAAO,EAAE,mBAAmB,EAAE,MAAM,iCAAiC,CAAC;AACtE,sEAAsE;AACtE,OAAO,EAAE,gBAAgB,EAAE,MAAM,8BAA8B,CAAC;AAChE,YAAY,EAAE,oBAAoB,EAAE,mBAAmB,EAAE,MAAM,8BAA8B,CAAC;AAC9F,4DAA4D;AAC5D,OAAO,EAAE,oBAAoB,EAAE,MAAM,mCAAmC,CAAC;AACzE,YAAY,EACV,wBAAwB,EACxB,uBAAuB,GACxB,MAAM,mCAAmC,CAAC;AAC3C,6EAA6E;AAC7E,OAAO,EAAE,QAAQ,EAAE,MAAM,qBAAqB,CAAC;AAC/C,yFAAyF;AACzF,OAAO,EAAE,OAAO,EAAE,kBAAkB,EAAE,MAAM,oBAAoB,CAAC;AACjE,YAAY,EAAE,UAAU,EAAE,iBAAiB,EAAE,MAAM,oBAAoB,CAAC;AACxE,oEAAoE;AACpE,OAAO,EAAE,UAAU,EAAE,MAAM,uBAAuB,CAAC;AACnD,sDAAsD;AACtD,OAAO,EAAE,mBAAmB,EAAE,MAAM,iCAAiC,CAAC;AACtE,8DAA8D;AAC9D,OAAO,EAAE,mBAAmB,EAAE,MAAM,iCAAiC,CAAC;AACtE,sDAAsD;AACtD,OAAO,EAAE,eAAe,EAAE,MAAM,6BAA6B,CAAC;AAC9D,kDAAkD;AAClD,OAAO,EAAE,WAAW,EAAE,MAAM,yBAAyB,CAAC;AACtD,mDAAmD;AACnD,OAAO,EAAE,YAAY,EAAE,MAAM,0BAA0B,CAAC;AACxD,qDAAqD;AACrD,OAAO,EAAE,cAAc,EAAE,MAAM,4BAA4B,CAAC;AAC5D,wCAAwC;AACxC,OAAO,EACL,iBAAiB,EACjB,WAAW,EACX,iBAAiB,EACjB,YAAY,EACZ,gBAAgB,GACjB,MAAM,oBAAoB,CAAC;AAC5B,YAAY,EAAE,YAAY,EAAE,eAAe,EAAE,UAAU,EAAE,WAAW,EAAE,MAAM,oBAAoB,CAAC;AACjG,iDAAiD;AACjD,OAAO,EAAE,iBAAiB,EAAE,MAAM,8BAA8B,CAAC;AACjE,gDAAgD;AAChD,OAAO,EAAE,mBAAmB,EAAE,MAAM,2BAA2B,CAAC;AAChE,4EAA4E;AAC5E,OAAO,EACL,mBAAmB,EACnB,oBAAoB,EACpB,qBAAqB,EACrB,oBAAoB,GACrB,MAAM,iCAAiC,CAAC;AACzC,kFAAkF;AAClF,OAAO,EAAE,yBAAyB,EAAE,MAAM,oCAAoC,CAAC;AAC/E,YAAY,EAAE,cAAc,EAAE,gBAAgB,EAAE,MAAM,oCAAoC,CAAC;AAC3F,wEAAwE;AACxE,OAAO,EAAE,qBAAqB,EAAE,MAAM,4BAA4B,CAAC;AACnE,6EAA6E;AAC7E,OAAO,EACL,6BAA6B,EAC7B,8BAA8B,EAC9B,+BAA+B,GAChC,MAAM,6CAA6C,CAAC"}

package/dist/index.js

@@ -16,4 +16,40 @@ export { runClear } from "./commands/clear.js";
 export { runSchema } from "./commands/schema.js";
 /** Validate a Galaxy workflow file (structure + optional tool state). */
 export { runValidateWorkflow } from "./commands/validate-workflow.js";
+/** Validate a workflow-test file (*-tests.yml / *.gxwf-tests.yml). */
+export { runValidateTests } from "./commands/validate-tests.js";
+/** Batch-validate workflow-test files under a directory. */
+export { runValidateTestsTree } from "./commands/validate-tests-tree.js";
+/** Clean a Galaxy workflow — strip stale keys and decode legacy encoding. */
+export { runClean } from "./commands/clean.js";
+/** Lint a Galaxy workflow — structural checks, best practices, tool state validation. */
+export { runLint, lintWorkflowReport } from "./commands/lint.js";
+/** Convert a Galaxy workflow between native and format2 formats. */
+export { runConvert } from "./commands/convert.js";
+/** Scan a workflow and cache all referenced tools. */
+export { runPopulateWorkflow } from "./commands/populate-workflow.js";
+/** Export the structural JSON Schema for Galaxy workflows. */
+export { runStructuralSchema } from "./commands/structural-schema.js";
+/** Batch validate all workflows under a directory. */
+export { runValidateTree } from "./commands/validate-tree.js";
+/** Batch lint all workflows under a directory. */
+export { runLintTree } from "./commands/lint-tree.js";
+/** Batch clean all workflows under a directory. */
+export { runCleanTree } from "./commands/clean-tree.js";
+/** Batch convert all workflows under a directory. */
+export { runConvertTree } from "./commands/convert-tree.js";
+/** Tree orchestrator infrastructure. */
+export { discoverWorkflows, collectTree, summarizeOutcomes, skipWorkflow, loadWorkflowSafe, } from "./commands/tree.js";
+/** Render step validation results to console. */
+export { renderStepResults } from "./commands/render-results.js";
+/** Write workflow content to file or stdout. */
+export { writeWorkflowOutput } from "./commands/workflow-io.js";
+/** Validate native/format2 workflow steps programmatically (no CLI I/O). */
+export { validateNativeSteps, validateFormat2Steps, decodeStructureErrors, detectEncodingErrors, } from "./commands/validate-workflow.js";
+/** Preload tool inputs from a ToolCache into a synchronous ToolInputsResolver. */
+export { loadToolInputsForWorkflow } from "./commands/stateful-tool-inputs.js";
+/** Default subworkflow ref resolver (base64, TRS, HTTP, file paths). */
+export { createDefaultResolver } from "./commands/url-resolver.js";
+/** JSON-Schema-based (AJV) step validation and structural error decoding. */
+export { validateNativeStepsJsonSchema, validateFormat2StepsJsonSchema, decodeStructureErrorsJsonSchema, } from "./commands/validate-workflow-json-schema.js";
 //# sourceMappingURL=index.js.map

package/dist/index.js.map

@@ -1 +1 @@
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package/dist/workflow/_templates-bundled.d.ts

@@ -0,0 +1,2 @@
+export declare const BUNDLED_TEMPLATES: Record<string, string>;
+//# sourceMappingURL=_templates-bundled.d.ts.map

package/dist/workflow/_templates-bundled.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"_templates-bundled.d.ts","sourceRoot":"","sources":["../../src/workflow/_templates-bundled.ts"],"names":[],"mappings":"AACA,eAAO,MAAM,iBAAiB,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAiUpD,CAAC"}