@galaxy-tool-util/cli 0.1.0 → 0.2.0

package/dist/commands/roundtrip-tree.js

@@ -0,0 +1,116 @@
+/**
+ * `gxwf roundtrip-tree` — batch roundtrip validation across a directory.
+ * Mirrors the patterns in convert-tree.ts.
+ */
+import { ToolCache } from "@galaxy-tool-util/core";
+import { roundtripValidate, } from "@galaxy-tool-util/schema";
+import { dirname, join } from "node:path";
+import { loadToolInputsForWorkflow } from "./stateful-tool-inputs.js";
+import { createDefaultResolver } from "./url-resolver.js";
+import { resolveFormat } from "./workflow-io.js";
+import { collectTree, skipWorkflow } from "./tree.js";
+import { countDiffs } from "./roundtrip.js";
+export async function runRoundtripTree(dir, opts) {
+    const cache = new ToolCache({ cacheDir: opts.cacheDir });
+    await cache.index.load();
+    if (cache.index.listAll().length === 0) {
+        console.warn("Tool cache is empty — all steps will fall back (no roundtrip possible)");
+    }
+    // Only native workflows are eligible; format2 files are skipped.
+    const treeResult = await collectTree(dir, async (info, data) => {
+        const sourceFormat = resolveFormat(data, opts.format);
+        if (sourceFormat !== "native") {
+            skipWorkflow(`not a native workflow (${sourceFormat})`);
+        }
+        const expansionOpts = {
+            resolver: createDefaultResolver({
+                workflowDirectory: dirname(join(dir, info.relativePath)),
+            }),
+        };
+        const { resolver, status: toolStatus } = await loadToolInputsForWorkflow(data, "native", cache, expansionOpts);
+        const failedLoads = toolStatus.filter((s) => !s.loaded);
+        const result = roundtripValidate(data, resolver);
+        return {
+            relativePath: info.relativePath,
+            result,
+            toolLoadErrors: failedLoads.length > 0 ? failedLoads : undefined,
+        };
+    }, false);
+    // Aggregate
+    let totalBenign = 0;
+    let totalErrors = 0;
+    let filesClean = 0;
+    let filesBenignOnly = 0;
+    let filesFailed = 0;
+    const fileResults = [];
+    for (const o of treeResult.outcomes) {
+        if (o.error || o.skipped || !o.result)
+            continue;
+        fileResults.push(o.result);
+        const counts = countDiffs(o.result.result);
+        totalBenign += counts.benign;
+        totalErrors += counts.error;
+        if (!o.result.result.success)
+            filesFailed++;
+        else if (o.result.result.clean)
+            filesClean++;
+        else
+            filesBenignOnly++;
+    }
+    if (opts.json) {
+        console.log(JSON.stringify({
+            root: treeResult.root,
+            files: fileResults,
+            summary: {
+                total: fileResults.length,
+                clean: filesClean,
+                benignOnly: filesBenignOnly,
+                failed: filesFailed,
+                benignDiffs: totalBenign,
+                errorDiffs: totalErrors,
+            },
+        }, null, 2));
+    }
+    else {
+        if (!opts.brief) {
+            for (const o of treeResult.outcomes) {
+                if (o.error) {
+                    // File-level errors always shown unless --benign-only.
+                    if (!opts.benignOnly) {
+                        console.error(`  ${o.info.relativePath}: ERROR (${o.error})`);
+                    }
+                    continue;
+                }
+                if (o.skipped)
+                    continue;
+                const r = o.result;
+                const c = countDiffs(r.result);
+                const isFail = !r.result.success;
+                const isClean = r.result.clean;
+                const isBenign = !isFail && !isClean;
+                if (opts.errorsOnly && !isFail)
+                    continue;
+                if (opts.benignOnly && !isBenign)
+                    continue;
+                const status = isFail ? "FAIL" : isClean ? "clean" : "benign";
+                console.log(`  ${r.relativePath}: ${status} (${c.benign} benign, ${c.error} real diff, ${c.failed} conversion failure)`);
+                if (r.toolLoadErrors) {
+                    for (const t of r.toolLoadErrors) {
+                        const ver = t.toolVersion ? `@${t.toolVersion}` : "";
+                        console.error(`    tool ${t.toolId}${ver}: ${t.error}`);
+                    }
+                }
+            }
+        }
+        console.log(`\nSummary: ${fileResults.length} file(s): ${filesClean} clean, ${filesBenignOnly} benign-only, ${filesFailed} failed`);
+        console.log(`Diffs: ${totalBenign} benign, ${totalErrors} real`);
+    }
+    // Exit code: 2 if any failure, 1 if benign-only, 0 if all clean
+    if (filesFailed > 0 || totalErrors > 0)
+        process.exitCode = 2;
+    else if (totalBenign > 0)
+        process.exitCode = 1;
+    else
+        process.exitCode = 0;
+}
+//# sourceMappingURL=roundtrip-tree.js.map

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

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

@@ -0,0 +1,30 @@
+import { type RoundtripResult } from "@galaxy-tool-util/schema";
+export interface RoundtripOptions {
+    cacheDir?: string;
+    format?: string;
+    json?: boolean;
+    /** Only show steps with error-severity diffs. */
+    errorsOnly?: boolean;
+    /** Only show steps with benign diffs (suppress clean + real-error steps). */
+    benignOnly?: boolean;
+    /** Suppress the per-diff list; show only per-step counts and summary. */
+    brief?: boolean;
+}
+export declare function runRoundtrip(filePath: string, opts: RoundtripOptions): Promise<void>;
+export interface ReportFilter {
+    errorsOnly?: boolean;
+    benignOnly?: boolean;
+    brief?: boolean;
+}
+/**
+ * Exit code policy: 0 clean, 1 benign-only, 2 real diffs or errors.
+ * Exposed for reuse by the tree command.
+ */
+export declare function exitCodeFor(result: RoundtripResult): number;
+/** Count diffs across a result by severity — reused by tree aggregation. */
+export declare function countDiffs(result: RoundtripResult): {
+    benign: number;
+    error: number;
+    failed: number;
+};
+//# sourceMappingURL=roundtrip.d.ts.map

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

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

@@ -0,0 +1,122 @@
+/**
+ * `gxwf roundtrip` — roundtrip-validate a native workflow through format2
+ * and back, reporting per-step diffs and classifying them as benign or real.
+ *
+ * Exit codes:
+ *   0  clean roundtrip (no diffs)
+ *   1  benign diffs only (type coercions, stale keys, connection moves)
+ *   2  real diffs or conversion errors
+ */
+import { ToolCache } from "@galaxy-tool-util/core";
+import { roundtripValidate, } from "@galaxy-tool-util/schema";
+import { dirname } from "node:path";
+import { loadToolInputsForWorkflow } from "./stateful-tool-inputs.js";
+import { createDefaultResolver } from "./url-resolver.js";
+import { readWorkflowFile, resolveFormat } from "./workflow-io.js";
+export async function runRoundtrip(filePath, opts) {
+    const data = await readWorkflowFile(filePath);
+    if (!data)
+        return;
+    const sourceFormat = resolveFormat(data, opts.format);
+    if (sourceFormat !== "native") {
+        console.error(`Roundtrip source must be a native (.ga) workflow; got ${sourceFormat}.` +
+            ` Convert to native first or pass a .ga file.`);
+        process.exitCode = 2;
+        return;
+    }
+    const cache = new ToolCache({ cacheDir: opts.cacheDir });
+    await cache.index.load();
+    if (cache.index.listAll().length === 0) {
+        console.warn("Tool cache is empty — all steps will fall back (no roundtrip possible)");
+    }
+    const expansionOpts = {
+        resolver: createDefaultResolver({ workflowDirectory: dirname(filePath) }),
+    };
+    const { resolver, status: toolStatus } = await loadToolInputsForWorkflow(data, "native", cache, expansionOpts);
+    for (const s of toolStatus) {
+        if (!s.loaded) {
+            const ver = s.toolVersion ? `@${s.toolVersion}` : "";
+            console.error(`  tool ${s.toolId}${ver}: ${s.error}`);
+        }
+    }
+    const result = roundtripValidate(data, resolver);
+    if (opts.json) {
+        console.log(JSON.stringify(result, null, 2));
+    }
+    else {
+        reportResult(filePath, result, opts);
+    }
+    process.exitCode = exitCodeFor(result);
+}
+function reportResult(filePath, result, filter) {
+    const total = result.stepResults.length;
+    const failed = result.stepResults.filter((s) => !s.success).length;
+    const benignCount = result.stepResults.reduce((n, s) => n + s.diffs.filter((d) => d.severity === "benign").length, 0);
+    const errorCount = result.stepResults.reduce((n, s) => n + s.diffs.filter((d) => d.severity === "error").length, 0);
+    console.log(`Roundtrip: ${filePath}`);
+    console.log(`  ${total - failed}/${total} step(s) ok, ${benignCount} benign diff(s), ${errorCount} real diff(s)`);
+    // --brief short-circuits: skip the per-step detail entirely. Still prints
+    // the one-line summary above, which is the whole point of --brief.
+    if (filter.brief)
+        return;
+    for (const step of result.stepResults) {
+        const hasError = step.diffs.some((d) => d.severity === "error");
+        const hasBenign = step.diffs.some((d) => d.severity === "benign");
+        if (filter.errorsOnly && !hasError && step.success)
+            continue;
+        if (filter.benignOnly) {
+            // Show only steps with benign diffs and no errors and no failure.
+            if (!hasBenign || hasError || !step.success)
+                continue;
+        }
+        // Default: skip clean-passing tool steps but keep informational
+        // subworkflow notes (failureClass set, success true) visible.
+        if (!filter.errorsOnly &&
+            !filter.benignOnly &&
+            step.diffs.length === 0 &&
+            step.success &&
+            !step.failureClass) {
+            continue;
+        }
+        // Indent nested subworkflow steps (depth>0) so the hierarchy is visible.
+        const indent = "  ".repeat(step.depth);
+        const label = step.toolId ? `${step.stepId} (${step.toolId})` : step.stepId;
+        if (!step.success) {
+            console.error(`${indent}  step ${label}: ${step.failureClass ?? "failed"} — ${step.error ?? ""}`);
+        }
+        else if (step.failureClass) {
+            console.log(`${indent}  step ${label}: ${step.failureClass} (${step.error ?? ""})`);
+        }
+        const diffsToShow = filter.errorsOnly
+            ? step.diffs.filter((d) => d.severity === "error")
+            : filter.benignOnly
+                ? step.diffs.filter((d) => d.severity === "benign")
+                : step.diffs;
+        for (const d of diffsToShow) {
+            const tag = d.severity === "error" ? "ERROR" : `benign:${d.kind ?? "?"}`;
+            const loc = d.path || "<root>";
+            console.log(`${indent}    [${tag}] ${loc}: ${d.message}`);
+        }
+    }
+}
+/**
+ * Exit code policy: 0 clean, 1 benign-only, 2 real diffs or errors.
+ * Exposed for reuse by the tree command.
+ */
+export function exitCodeFor(result) {
+    if (!result.success)
+        return 2;
+    if (!result.clean)
+        return 1;
+    return 0;
+}
+/** Count diffs across a result by severity — reused by tree aggregation. */
+export function countDiffs(result) {
+    const flat = result.stepResults.flatMap((s) => s.diffs);
+    return {
+        benign: flat.filter((d) => d.severity === "benign").length,
+        error: flat.filter((d) => d.severity === "error").length,
+        failed: result.stepResults.filter((s) => !s.success).length,
+    };
+}
+//# sourceMappingURL=roundtrip.js.map

package/dist/commands/roundtrip.js.map

@@ -0,0 +1 @@
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package/dist/commands/stateful-tool-inputs.d.ts

@@ -0,0 +1,33 @@
+/**
+ * Helper for stateful workflow conversion: expand a workflow, walk every
+ * step (including subworkflows), and preload tool parameter definitions
+ * from a `ToolCache` into a synchronous `ToolInputsResolver` suitable for
+ * `toFormat2Stateful` / `toNativeStateful`.
+ *
+ * Using `expandedNative` / `expandedFormat2` ensures externally-referenced
+ * subworkflows (@import, URL, TRS) contribute their tools — not just
+ * inline subworkflows (which is all `unique_tools` would cover).
+ *
+ * Keys inputs by `${tool_id}\0${tool_version ?? ""}` so multi-version
+ * workflows don't collide. Matches gxformat2's `ConversionOptions`
+ * callback-shaped design: callers pass the resolver, not the map.
+ */
+import type { ToolCache } from "@galaxy-tool-util/core";
+import { type ExpansionOptions, type ToolInputsResolver, type WorkflowFormat } from "@galaxy-tool-util/schema";
+export interface ToolLoadStatus {
+    toolId: string;
+    toolVersion: string | null;
+    loaded: boolean;
+    error?: string;
+}
+export interface LoadedToolInputs {
+    resolver: ToolInputsResolver;
+    status: ToolLoadStatus[];
+}
+/**
+ * Expand the workflow, walk every step, and preload tool inputs from the
+ * cache. Returns a sync resolver for `toFormat2Stateful` / `toNativeStateful`
+ * plus a per-tool load status list.
+ */
+export declare function loadToolInputsForWorkflow(data: Record<string, unknown>, format: WorkflowFormat, cache: ToolCache, expansionOpts?: ExpansionOptions): Promise<LoadedToolInputs>;
+//# sourceMappingURL=stateful-tool-inputs.d.ts.map

package/dist/commands/stateful-tool-inputs.d.ts.map

@@ -0,0 +1 @@
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package/dist/commands/stateful-tool-inputs.js

@@ -0,0 +1,73 @@
+import { expandedFormat2, expandedNative, } from "@galaxy-tool-util/schema";
+import { isResolveError, loadCachedTool } from "./resolve-tool.js";
+function toolKey(toolId, version) {
+    return `${toolId}\0${version ?? ""}`;
+}
+/**
+ * Expand the workflow, walk every step, and preload tool inputs from the
+ * cache. Returns a sync resolver for `toFormat2Stateful` / `toNativeStateful`
+ * plus a per-tool load status list.
+ */
+export async function loadToolInputsForWorkflow(data, format, cache, expansionOpts) {
+    const refs = format === "native"
+        ? collectNativeToolRefs(await expandedNative(data, expansionOpts))
+        : collectFormat2ToolRefs(await expandedFormat2(data, expansionOpts));
+    const loaded = new Map();
+    const status = [];
+    for (const [toolId, version] of refs) {
+        const key = toolKey(toolId, version);
+        if (loaded.has(key))
+            continue;
+        const resolved = await loadCachedTool(cache, toolId, version);
+        if (isResolveError(resolved)) {
+            const reason = resolved.kind === "no_version" ? `no version for ${toolId}` : `${toolId} not in cache`;
+            status.push({ toolId, toolVersion: version, loaded: false, error: reason });
+            continue;
+        }
+        loaded.set(key, resolved.tool.inputs);
+        status.push({ toolId, toolVersion: version, loaded: true });
+    }
+    const resolver = (toolId, version) => loaded.get(toolKey(toolId, version));
+    return { resolver, status };
+}
+// --- Step walkers over expanded workflows ---
+function collectNativeToolRefs(wf) {
+    const seen = new Set();
+    const refs = [];
+    const walk = (steps) => {
+        for (const step of Object.values(steps)) {
+            if (step.tool_id != null) {
+                const key = toolKey(step.tool_id, step.tool_version ?? null);
+                if (!seen.has(key)) {
+                    seen.add(key);
+                    refs.push([step.tool_id, step.tool_version ?? null]);
+                }
+            }
+            if (step.subworkflow)
+                walk(step.subworkflow.steps);
+        }
+    };
+    walk(wf.steps);
+    return refs;
+}
+function collectFormat2ToolRefs(wf) {
+    const seen = new Set();
+    const refs = [];
+    const walk = (steps) => {
+        for (const step of steps) {
+            if (step.tool_id != null) {
+                const key = toolKey(step.tool_id, step.tool_version ?? null);
+                if (!seen.has(key)) {
+                    seen.add(key);
+                    refs.push([step.tool_id, step.tool_version ?? null]);
+                }
+            }
+            if (step.run && typeof step.run === "object") {
+                walk(step.run.steps);
+            }
+        }
+    };
+    walk(wf.steps);
+    return refs;
+}
+//# sourceMappingURL=stateful-tool-inputs.js.map

package/dist/commands/stateful-tool-inputs.js.map

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package/dist/commands/structural-schema.d.ts

@@ -0,0 +1,6 @@
+export interface StructuralSchemaOptions {
+    format?: string;
+    output?: string;
+}
+export declare function runStructuralSchema(opts: StructuralSchemaOptions): Promise<void>;
+//# sourceMappingURL=structural-schema.d.ts.map

package/dist/commands/structural-schema.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"structural-schema.d.ts","sourceRoot":"","sources":["../../src/commands/structural-schema.ts"],"names":[],"mappings":"AAQA,MAAM,WAAW,uBAAuB;IACtC,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,MAAM,CAAC,EAAE,MAAM,CAAC;CACjB;AAED,wBAAsB,mBAAmB,CAAC,IAAI,EAAE,uBAAuB,GAAG,OAAO,CAAC,IAAI,CAAC,CAuBtF"}

package/dist/commands/structural-schema.js

@@ -0,0 +1,31 @@
+/**
+ * `galaxy-tool-cache structural-schema` — export the structural JSON Schema
+ * for Galaxy workflow validation (gxformat2 or native).
+ */
+import { GalaxyWorkflowSchema, NativeGalaxyWorkflowSchema } from "@galaxy-tool-util/schema";
+import * as JSONSchema from "effect/JSONSchema";
+import { writeWorkflowOutput } from "./workflow-io.js";
+export async function runStructuralSchema(opts) {
+    const format = opts.format ?? "format2";
+    if (format !== "format2" && format !== "native") {
+        console.error(`Unknown format: ${format}. Use 'format2' (default) or 'native'.`);
+        process.exitCode = 1;
+        return;
+    }
+    let jsonSchema;
+    try {
+        jsonSchema =
+            format === "native"
+                ? JSONSchema.make(NativeGalaxyWorkflowSchema)
+                : JSONSchema.make(GalaxyWorkflowSchema);
+    }
+    catch (e) {
+        const msg = e instanceof Error ? e.message : String(e);
+        console.error(`JSON Schema generation failed: ${msg}`);
+        process.exitCode = 1;
+        return;
+    }
+    const output = JSON.stringify(jsonSchema, null, 2) + "\n";
+    await writeWorkflowOutput(output, opts.output, "Structural schema");
+}
+//# sourceMappingURL=structural-schema.js.map

package/dist/commands/structural-schema.js.map

@@ -0,0 +1 @@
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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

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