@galaxy-tool-util/cli 0.1.0

package/README.md

@@ -0,0 +1,19 @@
+# @galaxy-tool-util/cli
+
+CLI tool for caching and inspecting Galaxy tool metadata.
+
+## Installation
+
+```bash
+npm install -g @galaxy-tool-util/cli
+```
+
+## Usage
+
+```bash
+galaxy-tool-cache --help
+```
+
+## License
+
+MIT

package/dist/bin/galaxy-tool-cache.d.ts

@@ -0,0 +1,3 @@
+#!/usr/bin/env node
+export {};
+//# sourceMappingURL=galaxy-tool-cache.d.ts.map

package/dist/bin/galaxy-tool-cache.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"galaxy-tool-cache.d.ts","sourceRoot":"","sources":["../../src/bin/galaxy-tool-cache.ts"],"names":[],"mappings":""}

package/dist/bin/galaxy-tool-cache.js

@@ -0,0 +1,50 @@
+#!/usr/bin/env node
+import { Command } from "commander";
+import { runAdd } from "../commands/add.js";
+import { runList } from "../commands/list.js";
+import { runInfo } from "../commands/info.js";
+import { runClear } from "../commands/clear.js";
+import { runSchema } from "../commands/schema.js";
+const program = new Command();
+program
+    .name("galaxy-tool-cache")
+    .description("Cache and inspect Galaxy tool metadata")
+    .version("1.0.0");
+program
+    .command("add")
+    .description("Fetch a tool from ToolShed/Galaxy and cache it")
+    .argument("<tool_id>", "Tool ID (full toolshed path or TRS ID)")
+    .option("--version <ver>", "Tool version")
+    .option("--cache-dir <dir>", "Cache directory")
+    .option("--galaxy-url <url>", "Galaxy instance URL for fallback")
+    .action(runAdd);
+program
+    .command("list")
+    .description("List cached tools")
+    .option("--json", "Output as JSON")
+    .option("--cache-dir <dir>", "Cache directory")
+    .action(runList);
+program
+    .command("info")
+    .description("Show metadata for a cached tool")
+    .argument("<tool_id>", "Tool ID")
+    .option("--version <ver>", "Tool version")
+    .option("--cache-dir <dir>", "Cache directory")
+    .action(runInfo);
+program
+    .command("clear")
+    .description("Clear cached tools")
+    .argument("[prefix]", "Only clear tools matching this prefix")
+    .option("--cache-dir <dir>", "Cache directory")
+    .action(runClear);
+program
+    .command("schema")
+    .description("Export JSON Schema for a cached tool's parameters")
+    .argument("<tool_id>", "Tool ID")
+    .option("--version <ver>", "Tool version")
+    .option("--representation <rep>", "State representation (e.g., workflow_step)", "workflow_step")
+    .option("--output <file>", "Output file (default: stdout)")
+    .option("--cache-dir <dir>", "Cache directory")
+    .action(runSchema);
+program.parse();
+//# sourceMappingURL=galaxy-tool-cache.js.map

package/dist/bin/galaxy-tool-cache.js.map

@@ -0,0 +1 @@
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package/dist/bin/galaxy-workflow-validate.d.ts

@@ -0,0 +1,3 @@
+#!/usr/bin/env node
+export {};
+//# sourceMappingURL=galaxy-workflow-validate.d.ts.map

package/dist/bin/galaxy-workflow-validate.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"galaxy-workflow-validate.d.ts","sourceRoot":"","sources":["../../src/bin/galaxy-workflow-validate.ts"],"names":[],"mappings":""}

package/dist/bin/galaxy-workflow-validate.js

@@ -0,0 +1,17 @@
+#!/usr/bin/env node
+import { Command } from "commander";
+import { runValidateWorkflow } from "../commands/validate-workflow.js";
+const program = new Command();
+program
+    .name("galaxy-workflow-validate")
+    .description("Validate Galaxy workflow files (structure + optional tool state)")
+    .version("1.0.0")
+    .argument("<file>", "Workflow file (.ga, .gxwf.yml)")
+    .option("--format <fmt>", "Force format: native or format2 (auto-detected by default)")
+    .option("--no-tool-state", "Skip tool state validation")
+    .option("--cache-dir <dir>", "Tool cache directory")
+    .option("--mode <mode>", "Validation backend: effect (default) or json-schema", "effect")
+    .option("--tool-schema-dir <dir>", "Directory of pre-exported per-tool JSON Schemas (for offline json-schema mode)")
+    .action(runValidateWorkflow);
+program.parse();
+//# sourceMappingURL=galaxy-workflow-validate.js.map

package/dist/bin/galaxy-workflow-validate.js.map

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

@@ -0,0 +1,7 @@
+export interface AddOptions {
+    version?: string;
+    cacheDir?: string;
+    galaxyUrl?: string;
+}
+export declare function runAdd(toolId: string, opts: AddOptions): Promise<void>;
+//# sourceMappingURL=add.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"add.d.ts","sourceRoot":"","sources":["../../src/commands/add.ts"],"names":[],"mappings":"AAEA,MAAM,WAAW,UAAU;IACzB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,SAAS,CAAC,EAAE,MAAM,CAAC;CACpB;AAED,wBAAsB,MAAM,CAAC,MAAM,EAAE,MAAM,EAAE,IAAI,EAAE,UAAU,GAAG,OAAO,CAAC,IAAI,CAAC,CAa5E"}

package/dist/commands/add.js

@@ -0,0 +1,15 @@
+import { ToolInfoService } from "@galaxy-tool-util/core";
+export async function runAdd(toolId, opts) {
+    const service = new ToolInfoService({
+        cacheDir: opts.cacheDir,
+        galaxyUrl: opts.galaxyUrl,
+    });
+    const result = await service.getToolInfo(toolId, opts.version);
+    if (result === null) {
+        console.error(`Failed to fetch tool: ${toolId}`);
+        process.exitCode = 1;
+        return;
+    }
+    console.log(`Cached: ${result.name} (${result.id} v${result.version})`);
+}
+//# sourceMappingURL=add.js.map

package/dist/commands/add.js.map

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package/dist/commands/clear.d.ts

@@ -0,0 +1,5 @@
+export interface ClearOptions {
+    cacheDir?: string;
+}
+export declare function runClear(prefix: string | undefined, opts: ClearOptions): Promise<void>;
+//# sourceMappingURL=clear.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"clear.d.ts","sourceRoot":"","sources":["../../src/commands/clear.ts"],"names":[],"mappings":"AAEA,MAAM,WAAW,YAAY;IAC3B,QAAQ,CAAC,EAAE,MAAM,CAAC;CACnB;AAED,wBAAsB,QAAQ,CAAC,MAAM,EAAE,MAAM,GAAG,SAAS,EAAE,IAAI,EAAE,YAAY,GAAG,OAAO,CAAC,IAAI,CAAC,CAY5F"}

package/dist/commands/clear.js

@@ -0,0 +1,16 @@
+import { ToolCache } from "@galaxy-tool-util/core";
+export async function runClear(prefix, opts) {
+    const cache = new ToolCache({ cacheDir: opts.cacheDir });
+    await cache.index.load();
+    const before = cache.listCached().length;
+    await cache.clearCache(prefix);
+    const after = cache.listCached().length;
+    const removed = before - after;
+    if (prefix) {
+        console.log(`Removed ${removed} entries matching "${prefix}".`);
+    }
+    else {
+        console.log(`Cleared ${removed} entries from cache.`);
+    }
+}
+//# sourceMappingURL=clear.js.map

package/dist/commands/clear.js.map

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package/dist/commands/info.d.ts

@@ -0,0 +1,6 @@
+export interface InfoOptions {
+    version?: string;
+    cacheDir?: string;
+}
+export declare function runInfo(toolId: string, opts: InfoOptions): Promise<void>;
+//# sourceMappingURL=info.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"info.d.ts","sourceRoot":"","sources":["../../src/commands/info.ts"],"names":[],"mappings":"AAEA,MAAM,WAAW,WAAW;IAC1B,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,QAAQ,CAAC,EAAE,MAAM,CAAC;CACnB;AAED,wBAAsB,OAAO,CAAC,MAAM,EAAE,MAAM,EAAE,IAAI,EAAE,WAAW,GAAG,OAAO,CAAC,IAAI,CAAC,CA+B9E"}

package/dist/commands/info.js

@@ -0,0 +1,32 @@
+import { ToolCache, cacheKey } from "@galaxy-tool-util/core";
+export async function runInfo(toolId, opts) {
+    const cache = new ToolCache({ cacheDir: opts.cacheDir });
+    await cache.index.load();
+    const coords = cache.resolveToolCoordinates(toolId, opts.version);
+    if (coords.version === null) {
+        console.error(`No version specified for tool: ${toolId}`);
+        process.exitCode = 1;
+        return;
+    }
+    const key = cacheKey(coords.toolshedUrl, coords.trsToolId, coords.version);
+    const tool = await cache.loadCached(key);
+    if (tool === null) {
+        console.error(`Tool not found in cache: ${toolId}`);
+        process.exitCode = 1;
+        return;
+    }
+    const indexEntry = cache.index.listAll().find((e) => e.cache_key === key);
+    console.log(`Name:        ${tool.name}`);
+    console.log(`ID:          ${tool.id}`);
+    console.log(`Version:     ${tool.version ?? "unknown"}`);
+    console.log(`Description: ${tool.description ?? ""}`);
+    console.log(`Inputs:      ${tool.inputs.length}`);
+    console.log(`Outputs:     ${tool.outputs.length}`);
+    console.log(`Profile:     ${tool.profile ?? "none"}`);
+    console.log(`License:     ${tool.license ?? "none"}`);
+    if (indexEntry) {
+        console.log(`Source:      ${indexEntry.source}`);
+        console.log(`Cached at:   ${indexEntry.cached_at}`);
+    }
+}
+//# sourceMappingURL=info.js.map

package/dist/commands/info.js.map

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package/dist/commands/list.d.ts

@@ -0,0 +1,6 @@
+export interface ListOptions {
+    json?: boolean;
+    cacheDir?: string;
+}
+export declare function runList(opts: ListOptions): Promise<void>;
+//# sourceMappingURL=list.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"list.d.ts","sourceRoot":"","sources":["../../src/commands/list.ts"],"names":[],"mappings":"AAEA,MAAM,WAAW,WAAW;IAC1B,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,QAAQ,CAAC,EAAE,MAAM,CAAC;CACnB;AAED,wBAAsB,OAAO,CAAC,IAAI,EAAE,WAAW,GAAG,OAAO,CAAC,IAAI,CAAC,CA0B9D"}

package/dist/commands/list.js

@@ -0,0 +1,24 @@
+import { ToolCache } from "@galaxy-tool-util/core";
+export async function runList(opts) {
+    const cache = new ToolCache({ cacheDir: opts.cacheDir });
+    await cache.index.load();
+    const entries = cache.listCached();
+    if (entries.length === 0) {
+        console.log("Cache is empty.");
+        return;
+    }
+    if (opts.json) {
+        console.log(JSON.stringify(entries, null, 2));
+        return;
+    }
+    const header = ["Tool ID", "Version", "Source", "Cached At"];
+    const rows = entries.map((e) => [e.tool_id, e.tool_version, e.source, e.cached_at]);
+    const widths = header.map((h, i) => Math.max(h.length, ...rows.map((r) => r[i].length)));
+    const sep = widths.map((w) => "-".repeat(w)).join("  ");
+    console.log(header.map((h, i) => h.padEnd(widths[i])).join("  "));
+    console.log(sep);
+    for (const row of rows) {
+        console.log(row.map((c, i) => c.padEnd(widths[i])).join("  "));
+    }
+}
+//# sourceMappingURL=list.js.map

package/dist/commands/list.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"list.js","sourceRoot":"","sources":["../../src/commands/list.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AAOnD,MAAM,CAAC,KAAK,UAAU,OAAO,CAAC,IAAiB;IAC7C,MAAM,KAAK,GAAG,IAAI,SAAS,CAAC,EAAE,QAAQ,EAAE,IAAI,CAAC,QAAQ,EAAE,CAAC,CAAC;IACzD,MAAM,KAAK,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC;IACzB,MAAM,OAAO,GAAG,KAAK,CAAC,UAAU,EAAE,CAAC;IAEnC,IAAI,OAAO,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACzB,OAAO,CAAC,GAAG,CAAC,iBAAiB,CAAC,CAAC;QAC/B,OAAO;IACT,CAAC;IAED,IAAI,IAAI,CAAC,IAAI,EAAE,CAAC;QACd,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,SAAS,CAAC,OAAO,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,CAAC;QAC9C,OAAO;IACT,CAAC;IAED,MAAM,MAAM,GAAG,CAAC,SAAS,EAAE,SAAS,EAAE,QAAQ,EAAE,WAAW,CAAC,CAAC;IAC7D,MAAM,IAAI,GAAG,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,OAAO,EAAE,CAAC,CAAC,YAAY,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC;IAEpF,MAAM,MAAM,GAAG,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,MAAM,EAAE,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC;IACzF,MAAM,GAAG,GAAG,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;IAExD,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC;IAClE,OAAO,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC;IACjB,KAAK,MAAM,GAAG,IAAI,IAAI,EAAE,CAAC;QACvB,OAAO,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC;IACjE,CAAC;AACH,CAAC"}

package/dist/commands/resolve-tool.d.ts

@@ -0,0 +1,16 @@
+import { type ToolCache, type ParsedTool } from "@galaxy-tool-util/core";
+export interface ResolvedTool {
+    tool: ParsedTool;
+    key: string;
+}
+export type ResolveError = {
+    kind: "no_version";
+    toolId: string;
+} | {
+    kind: "not_cached";
+    toolId: string;
+    key: string;
+};
+export declare function isResolveError(r: ResolvedTool | ResolveError): r is ResolveError;
+export declare function loadCachedTool(cache: ToolCache, toolId: string, version?: string | null): Promise<ResolvedTool | ResolveError>;
+//# sourceMappingURL=resolve-tool.d.ts.map

package/dist/commands/resolve-tool.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"resolve-tool.d.ts","sourceRoot":"","sources":["../../src/commands/resolve-tool.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,SAAS,EAAY,KAAK,UAAU,EAAE,MAAM,wBAAwB,CAAC;AAEnF,MAAM,WAAW,YAAY;IAC3B,IAAI,EAAE,UAAU,CAAC;IACjB,GAAG,EAAE,MAAM,CAAC;CACb;AAED,MAAM,MAAM,YAAY,GACpB;IAAE,IAAI,EAAE,YAAY,CAAC;IAAC,MAAM,EAAE,MAAM,CAAA;CAAE,GACtC;IAAE,IAAI,EAAE,YAAY,CAAC;IAAC,MAAM,EAAE,MAAM,CAAC;IAAC,GAAG,EAAE,MAAM,CAAA;CAAE,CAAC;AAExD,wBAAgB,cAAc,CAAC,CAAC,EAAE,YAAY,GAAG,YAAY,GAAG,CAAC,IAAI,YAAY,CAEhF;AAED,wBAAsB,cAAc,CAClC,KAAK,EAAE,SAAS,EAChB,MAAM,EAAE,MAAM,EACd,OAAO,CAAC,EAAE,MAAM,GAAG,IAAI,GACtB,OAAO,CAAC,YAAY,GAAG,YAAY,CAAC,CAWtC"}

package/dist/commands/resolve-tool.js

@@ -0,0 +1,17 @@
+import { cacheKey } from "@galaxy-tool-util/core";
+export function isResolveError(r) {
+    return "kind" in r;
+}
+export async function loadCachedTool(cache, toolId, version) {
+    const coords = cache.resolveToolCoordinates(toolId, version);
+    if (coords.version === null) {
+        return { kind: "no_version", toolId };
+    }
+    const key = cacheKey(coords.toolshedUrl, coords.trsToolId, coords.version);
+    const tool = await cache.loadCached(key);
+    if (tool === null) {
+        return { kind: "not_cached", toolId, key };
+    }
+    return { tool, key };
+}
+//# sourceMappingURL=resolve-tool.js.map

package/dist/commands/resolve-tool.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"resolve-tool.js","sourceRoot":"","sources":["../../src/commands/resolve-tool.ts"],"names":[],"mappings":"AAAA,OAAO,EAAkB,QAAQ,EAAmB,MAAM,wBAAwB,CAAC;AAWnF,MAAM,UAAU,cAAc,CAAC,CAA8B;IAC3D,OAAO,MAAM,IAAI,CAAC,CAAC;AACrB,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,cAAc,CAClC,KAAgB,EAChB,MAAc,EACd,OAAuB;IAEvB,MAAM,MAAM,GAAG,KAAK,CAAC,sBAAsB,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;IAC7D,IAAI,MAAM,CAAC,OAAO,KAAK,IAAI,EAAE,CAAC;QAC5B,OAAO,EAAE,IAAI,EAAE,YAAY,EAAE,MAAM,EAAE,CAAC;IACxC,CAAC;IACD,MAAM,GAAG,GAAG,QAAQ,CAAC,MAAM,CAAC,WAAW,EAAE,MAAM,CAAC,SAAS,EAAE,MAAM,CAAC,OAAO,CAAC,CAAC;IAC3E,MAAM,IAAI,GAAG,MAAM,KAAK,CAAC,UAAU,CAAC,GAAG,CAAC,CAAC;IACzC,IAAI,IAAI,KAAK,IAAI,EAAE,CAAC;QAClB,OAAO,EAAE,IAAI,EAAE,YAAY,EAAE,MAAM,EAAE,GAAG,EAAE,CAAC;IAC7C,CAAC;IACD,OAAO,EAAE,IAAI,EAAE,GAAG,EAAE,CAAC;AACvB,CAAC"}

package/dist/commands/schema.d.ts

@@ -0,0 +1,8 @@
+export interface SchemaOptions {
+    version?: string;
+    representation?: string;
+    output?: string;
+    cacheDir?: string;
+}
+export declare function runSchema(toolId: string, opts: SchemaOptions): Promise<void>;
+//# sourceMappingURL=schema.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"schema.d.ts","sourceRoot":"","sources":["../../src/commands/schema.ts"],"names":[],"mappings":"AAWA,MAAM,WAAW,aAAa;IAC5B,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,cAAc,CAAC,EAAE,MAAM,CAAC;IACxB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,QAAQ,CAAC,EAAE,MAAM,CAAC;CACnB;AAED,wBAAsB,SAAS,CAAC,MAAM,EAAE,MAAM,EAAE,IAAI,EAAE,aAAa,GAAG,OAAO,CAAC,IAAI,CAAC,CAoDlF"}

package/dist/commands/schema.js

@@ -0,0 +1,55 @@
+import { ToolCache } from "@galaxy-tool-util/core";
+import { createFieldModel, STATE_REPRESENTATIONS, } from "@galaxy-tool-util/schema";
+import * as JSONSchema from "effect/JSONSchema";
+import { writeFile } from "node:fs/promises";
+import { isResolveError, loadCachedTool } from "./resolve-tool.js";
+export async function runSchema(toolId, opts) {
+    const repName = opts.representation ?? "workflow_step";
+    if (!STATE_REPRESENTATIONS.includes(repName)) {
+        console.error(`Unknown representation: ${repName}. Available: ${STATE_REPRESENTATIONS.join(", ")}`);
+        process.exitCode = 1;
+        return;
+    }
+    const stateRep = repName;
+    const cache = new ToolCache({ cacheDir: opts.cacheDir });
+    await cache.index.load();
+    const result = await loadCachedTool(cache, toolId, opts.version);
+    if (isResolveError(result)) {
+        if (result.kind === "no_version") {
+            console.error(`No version specified for tool: ${toolId}`);
+        }
+        else {
+            console.error(`Tool not found in cache: ${toolId}. Run 'galaxy-tool-cache add' first.`);
+        }
+        process.exitCode = 1;
+        return;
+    }
+    const bundle = {
+        parameters: result.tool.inputs,
+    };
+    const effectSchema = createFieldModel(bundle, stateRep);
+    if (effectSchema === undefined) {
+        console.error(`Could not generate schema — tool may contain unsupported parameter types.`);
+        process.exitCode = 1;
+        return;
+    }
+    let jsonSchema;
+    try {
+        jsonSchema = JSONSchema.make(effectSchema);
+    }
+    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);
+    if (opts.output) {
+        await writeFile(opts.output, output);
+        console.log(`Schema written to ${opts.output}`);
+    }
+    else {
+        console.log(output);
+    }
+}
+//# sourceMappingURL=schema.js.map

package/dist/commands/schema.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"schema.js","sourceRoot":"","sources":["../../src/commands/schema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AACnD,OAAO,EACL,gBAAgB,EAChB,qBAAqB,GAGtB,MAAM,0BAA0B,CAAC;AAClC,OAAO,KAAK,UAAU,MAAM,mBAAmB,CAAC;AAChD,OAAO,EAAE,SAAS,EAAE,MAAM,kBAAkB,CAAC;AAC7C,OAAO,EAAE,cAAc,EAAE,cAAc,EAAE,MAAM,mBAAmB,CAAC;AASnE,MAAM,CAAC,KAAK,UAAU,SAAS,CAAC,MAAc,EAAE,IAAmB;IACjE,MAAM,OAAO,GAAG,IAAI,CAAC,cAAc,IAAI,eAAe,CAAC;IACvD,IAAI,CAAC,qBAAqB,CAAC,QAAQ,CAAC,OAA8B,CAAC,EAAE,CAAC;QACpE,OAAO,CAAC,KAAK,CACX,2BAA2B,OAAO,gBAAgB,qBAAqB,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CACrF,CAAC;QACF,OAAO,CAAC,QAAQ,GAAG,CAAC,CAAC;QACrB,OAAO;IACT,CAAC;IACD,MAAM,QAAQ,GAAG,OAA8B,CAAC;IAEhD,MAAM,KAAK,GAAG,IAAI,SAAS,CAAC,EAAE,QAAQ,EAAE,IAAI,CAAC,QAAQ,EAAE,CAAC,CAAC;IACzD,MAAM,KAAK,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC;IACzB,MAAM,MAAM,GAAG,MAAM,cAAc,CAAC,KAAK,EAAE,MAAM,EAAE,IAAI,CAAC,OAAO,CAAC,CAAC;IACjE,IAAI,cAAc,CAAC,MAAM,CAAC,EAAE,CAAC;QAC3B,IAAI,MAAM,CAAC,IAAI,KAAK,YAAY,EAAE,CAAC;YACjC,OAAO,CAAC,KAAK,CAAC,kCAAkC,MAAM,EAAE,CAAC,CAAC;QAC5D,CAAC;aAAM,CAAC;YACN,OAAO,CAAC,KAAK,CAAC,4BAA4B,MAAM,sCAAsC,CAAC,CAAC;QAC1F,CAAC;QACD,OAAO,CAAC,QAAQ,GAAG,CAAC,CAAC;QACrB,OAAO;IACT,CAAC;IAED,MAAM,MAAM,GAA6B;QACvC,UAAU,EAAE,MAAM,CAAC,IAAI,CAAC,MAAgD;KACzE,CAAC;IAEF,MAAM,YAAY,GAAG,gBAAgB,CAAC,MAAM,EAAE,QAA+B,CAAC,CAAC;IAC/E,IAAI,YAAY,KAAK,SAAS,EAAE,CAAC;QAC/B,OAAO,CAAC,KAAK,CAAC,2EAA2E,CAAC,CAAC;QAC3F,OAAO,CAAC,QAAQ,GAAG,CAAC,CAAC;QACrB,OAAO;IACT,CAAC;IAED,IAAI,UAAmB,CAAC;IACxB,IAAI,CAAC;QACH,UAAU,GAAG,UAAU,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC;IAC7C,CAAC;IAAC,OAAO,CAAC,EAAE,CAAC;QACX,MAAM,GAAG,GAAG,CAAC,YAAY,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC;QACvD,OAAO,CAAC,KAAK,CAAC,kCAAkC,GAAG,EAAE,CAAC,CAAC;QACvD,OAAO,CAAC,QAAQ,GAAG,CAAC,CAAC;QACrB,OAAO;IACT,CAAC;IACD,MAAM,MAAM,GAAG,IAAI,CAAC,SAAS,CAAC,UAAU,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC;IAEnD,IAAI,IAAI,CAAC,MAAM,EAAE,CAAC;QAChB,MAAM,SAAS,CAAC,IAAI,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;QACrC,OAAO,CAAC,GAAG,CAAC,qBAAqB,IAAI,CAAC,MAAM,EAAE,CAAC,CAAC;IAClD,CAAC;SAAM,CAAC;QACN,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC;IACtB,CAAC;AACH,CAAC"}

package/dist/commands/url-resolver.d.ts

@@ -0,0 +1,23 @@
+/**
+ * Default URL resolver for subworkflow expansion.
+ *
+ * Handles:
+ * - base64:// URLs: base64-decode inline content, parse as YAML/JSON
+ * - TRS URLs (GA4GH pattern): fetch descriptor endpoint, extract `content`
+ * - Plain HTTP/HTTPS URLs: fetch and parse based on content-type
+ * - File paths (no ://): read from workflowDirectory
+ *
+ * Port of gxformat2/options.py default_url_resolver + resolve_import.
+ */
+import { type RefResolver } from "@galaxy-tool-util/schema";
+export interface DefaultResolverOptions {
+    /** Custom fetch implementation. Defaults to globalThis.fetch. */
+    fetcher?: typeof fetch;
+    /** Directory for resolving relative file path references. */
+    workflowDirectory?: string;
+}
+/**
+ * Create a default RefResolver that handles base64, TRS, HTTP, and file paths.
+ */
+export declare function createDefaultResolver(opts?: DefaultResolverOptions): RefResolver;
+//# sourceMappingURL=url-resolver.d.ts.map

package/dist/commands/url-resolver.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"url-resolver.d.ts","sourceRoot":"","sources":["../../src/commands/url-resolver.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;GAUG;AAKH,OAAO,EAAY,KAAK,WAAW,EAAE,MAAM,0BAA0B,CAAC;AAEtE,MAAM,WAAW,sBAAsB;IACrC,iEAAiE;IACjE,OAAO,CAAC,EAAE,OAAO,KAAK,CAAC;IACvB,6DAA6D;IAC7D,iBAAiB,CAAC,EAAE,MAAM,CAAC;CAC5B;AAED;;GAEG;AACH,wBAAgB,qBAAqB,CAAC,IAAI,GAAE,sBAA2B,GAAG,WAAW,CA2CpF"}

package/dist/commands/url-resolver.js

@@ -0,0 +1,58 @@
+/**
+ * Default URL resolver for subworkflow expansion.
+ *
+ * Handles:
+ * - base64:// URLs: base64-decode inline content, parse as YAML/JSON
+ * - TRS URLs (GA4GH pattern): fetch descriptor endpoint, extract `content`
+ * - Plain HTTP/HTTPS URLs: fetch and parse based on content-type
+ * - File paths (no ://): read from workflowDirectory
+ *
+ * Port of gxformat2/options.py default_url_resolver + resolve_import.
+ */
+import { readFile } from "node:fs/promises";
+import { join } from "node:path";
+import * as yaml from "yaml";
+import { isTrsUrl } from "@galaxy-tool-util/schema";
+/**
+ * Create a default RefResolver that handles base64, TRS, HTTP, and file paths.
+ */
+export function createDefaultResolver(opts = {}) {
+    const fetcher = opts.fetcher ?? globalThis.fetch;
+    const workflowDirectory = opts.workflowDirectory;
+    return async (ref) => {
+        // base64:// — inline encoded workflow
+        if (ref.startsWith("base64://")) {
+            const encoded = ref.slice("base64://".length);
+            const content = Buffer.from(encoded, "base64").toString("utf-8");
+            return yaml.parse(content);
+        }
+        // URL — fetch via HTTP
+        if (ref.includes("://")) {
+            const response = await fetcher(ref, {
+                headers: { Accept: "application/json, application/x-yaml, text/yaml, */*" },
+                signal: AbortSignal.timeout(30_000),
+            });
+            if (!response.ok) {
+                throw new Error(`Failed to fetch ${ref}: ${response.status}`);
+            }
+            if (isTrsUrl(ref)) {
+                const descriptor = (await response.json());
+                return yaml.parse(descriptor.content);
+            }
+            const contentType = response.headers.get("content-type") ?? "";
+            if (contentType.includes("json")) {
+                return (await response.json());
+            }
+            const text = await response.text();
+            return yaml.parse(text);
+        }
+        // File path — read from workflowDirectory
+        if (!workflowDirectory) {
+            throw new Error(`Cannot resolve file path '${ref}' without workflowDirectory`);
+        }
+        const fullPath = join(workflowDirectory, ref);
+        const content = await readFile(fullPath, "utf-8");
+        return yaml.parse(content);
+    };
+}
+//# sourceMappingURL=url-resolver.js.map

package/dist/commands/url-resolver.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"url-resolver.js","sourceRoot":"","sources":["../../src/commands/url-resolver.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;GAUG;AAEH,OAAO,EAAE,QAAQ,EAAE,MAAM,kBAAkB,CAAC;AAC5C,OAAO,EAAE,IAAI,EAAE,MAAM,WAAW,CAAC;AACjC,OAAO,KAAK,IAAI,MAAM,MAAM,CAAC;AAC7B,OAAO,EAAE,QAAQ,EAAoB,MAAM,0BAA0B,CAAC;AAStE;;GAEG;AACH,MAAM,UAAU,qBAAqB,CAAC,OAA+B,EAAE;IACrE,MAAM,OAAO,GAAG,IAAI,CAAC,OAAO,IAAI,UAAU,CAAC,KAAK,CAAC;IACjD,MAAM,iBAAiB,GAAG,IAAI,CAAC,iBAAiB,CAAC;IAEjD,OAAO,KAAK,EAAE,GAAW,EAAoC,EAAE;QAC7D,sCAAsC;QACtC,IAAI,GAAG,CAAC,UAAU,CAAC,WAAW,CAAC,EAAE,CAAC;YAChC,MAAM,OAAO,GAAG,GAAG,CAAC,KAAK,CAAC,WAAW,CAAC,MAAM,CAAC,CAAC;YAC9C,MAAM,OAAO,GAAG,MAAM,CAAC,IAAI,CAAC,OAAO,EAAE,QAAQ,CAAC,CAAC,QAAQ,CAAC,OAAO,CAAC,CAAC;YACjE,OAAO,IAAI,CAAC,KAAK,CAAC,OAAO,CAA4B,CAAC;QACxD,CAAC;QAED,uBAAuB;QACvB,IAAI,GAAG,CAAC,QAAQ,CAAC,KAAK,CAAC,EAAE,CAAC;YACxB,MAAM,QAAQ,GAAG,MAAM,OAAO,CAAC,GAAG,EAAE;gBAClC,OAAO,EAAE,EAAE,MAAM,EAAE,sDAAsD,EAAE;gBAC3E,MAAM,EAAE,WAAW,CAAC,OAAO,CAAC,MAAM,CAAC;aACpC,CAAC,CAAC;YACH,IAAI,CAAC,QAAQ,CAAC,EAAE,EAAE,CAAC;gBACjB,MAAM,IAAI,KAAK,CAAC,mBAAmB,GAAG,KAAK,QAAQ,CAAC,MAAM,EAAE,CAAC,CAAC;YAChE,CAAC;YAED,IAAI,QAAQ,CAAC,GAAG,CAAC,EAAE,CAAC;gBAClB,MAAM,UAAU,GAAG,CAAC,MAAM,QAAQ,CAAC,IAAI,EAAE,CAA4B,CAAC;gBACtE,OAAO,IAAI,CAAC,KAAK,CAAC,UAAU,CAAC,OAAiB,CAA4B,CAAC;YAC7E,CAAC;YAED,MAAM,WAAW,GAAG,QAAQ,CAAC,OAAO,CAAC,GAAG,CAAC,cAAc,CAAC,IAAI,EAAE,CAAC;YAC/D,IAAI,WAAW,CAAC,QAAQ,CAAC,MAAM,CAAC,EAAE,CAAC;gBACjC,OAAO,CAAC,MAAM,QAAQ,CAAC,IAAI,EAAE,CAA4B,CAAC;YAC5D,CAAC;YACD,MAAM,IAAI,GAAG,MAAM,QAAQ,CAAC,IAAI,EAAE,CAAC;YACnC,OAAO,IAAI,CAAC,KAAK,CAAC,IAAI,CAA4B,CAAC;QACrD,CAAC;QAED,0CAA0C;QAC1C,IAAI,CAAC,iBAAiB,EAAE,CAAC;YACvB,MAAM,IAAI,KAAK,CAAC,6BAA6B,GAAG,6BAA6B,CAAC,CAAC;QACjF,CAAC;QACD,MAAM,QAAQ,GAAG,IAAI,CAAC,iBAAiB,EAAE,GAAG,CAAC,CAAC;QAC9C,MAAM,OAAO,GAAG,MAAM,QAAQ,CAAC,QAAQ,EAAE,OAAO,CAAC,CAAC;QAClD,OAAO,IAAI,CAAC,KAAK,CAAC,OAAO,CAA4B,CAAC;IACxD,CAAC,CAAC;AACJ,CAAC"}

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

@@ -0,0 +1,16 @@
+/**
+ * JSON Schema-based workflow validation.
+ *
+ * Two-level validation using AJV Draft 2020-12:
+ *   Level 1 (structural): validates workflow dict against generated JSON Schema
+ *   Level 2 (per-step tool state): validates each step's state against tool-specific JSON Schema
+ *
+ * Mirrors Galaxy's validation_json_schema.py.
+ */
+import { 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>;
+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

@@ -0,0 +1 @@
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