@galaxy-tool-util/cli 1.10.1 → 1.13.1
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/commands/add-local.d.ts +15 -0
- package/dist/commands/add-local.d.ts.map +1 -0
- package/dist/commands/add-local.js +44 -0
- package/dist/commands/add-local.js.map +1 -0
- package/dist/commands/convert-tree.d.ts +3 -0
- package/dist/commands/convert-tree.d.ts.map +1 -1
- package/dist/commands/convert-tree.js +7 -12
- package/dist/commands/convert-tree.js.map +1 -1
- package/dist/commands/convert.d.ts.map +1 -1
- package/dist/commands/convert.js +3 -8
- package/dist/commands/convert.js.map +1 -1
- package/dist/commands/embedded-tool.d.ts +33 -0
- package/dist/commands/embedded-tool.d.ts.map +1 -0
- package/dist/commands/embedded-tool.js +69 -0
- package/dist/commands/embedded-tool.js.map +1 -0
- package/dist/commands/lint-tree.d.ts.map +1 -1
- package/dist/commands/lint-tree.js +2 -1
- package/dist/commands/lint-tree.js.map +1 -1
- package/dist/commands/stateful-tool-inputs.d.ts +12 -0
- package/dist/commands/stateful-tool-inputs.d.ts.map +1 -1
- package/dist/commands/stateful-tool-inputs.js +24 -2
- package/dist/commands/stateful-tool-inputs.js.map +1 -1
- package/dist/commands/tool-search.d.ts.map +1 -1
- package/dist/commands/tool-search.js +20 -49
- package/dist/commands/tool-search.js.map +1 -1
- package/dist/commands/tree.d.ts +12 -0
- package/dist/commands/tree.d.ts.map +1 -1
- package/dist/commands/tree.js +48 -8
- package/dist/commands/tree.js.map +1 -1
- package/dist/commands/validate-tree.d.ts.map +1 -1
- package/dist/commands/validate-tree.js +24 -6
- package/dist/commands/validate-tree.js.map +1 -1
- package/dist/commands/validate-workflow-json-schema.d.ts.map +1 -1
- package/dist/commands/validate-workflow-json-schema.js +129 -46
- package/dist/commands/validate-workflow-json-schema.js.map +1 -1
- package/dist/commands/validate-workflow.d.ts +12 -2
- package/dist/commands/validate-workflow.d.ts.map +1 -1
- package/dist/commands/validate-workflow.js +150 -58
- package/dist/commands/validate-workflow.js.map +1 -1
- package/dist/programs/galaxy-tool-cache.d.ts.map +1 -1
- package/dist/programs/galaxy-tool-cache.js +2 -0
- package/dist/programs/galaxy-tool-cache.js.map +1 -1
- package/dist/spec/build-program.js +16 -3
- package/dist/spec/build-program.js.map +1 -1
- package/package.json +6 -5
- package/spec/galaxy-tool-cache.json +25 -0
- package/spec/gxwf.json +12 -4
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@@ -0,0 +1,15 @@
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export interface AddLocalOptions {
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toolId?: string;
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toolVersion?: string;
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cacheDir?: string;
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}
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/**
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* Cache a tool parsed from a local file — the local-ingest counterpart to `add`
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* (which fetches from the ToolShed). Dispatches on extension like Galaxy's
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* `get_tool_source` (`.yml` → YAML, else → XML; CWL unsupported). Mirrors
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* Galaxy's `run_add_local`: a bare `<tool id>` is not a valid cache key, so
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* `--tool-id` (the full toolshed tool_id) is required even when the file carries
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* an id; the parsed id is surfaced only as a hint.
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*/
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export declare function runAddLocal(toolPath: string, opts: AddLocalOptions): Promise<void>;
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//# sourceMappingURL=add-local.d.ts.map
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@@ -0,0 +1 @@
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{"version":3,"file":"add-local.d.ts","sourceRoot":"","sources":["../../src/commands/add-local.ts"],"names":[],"mappings":"AAGA,MAAM,WAAW,eAAe;IAC9B,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,QAAQ,CAAC,EAAE,MAAM,CAAC;CACnB;AAED;;;;;;;GAOG;AACH,wBAAsB,WAAW,CAAC,QAAQ,EAAE,MAAM,EAAE,IAAI,EAAE,eAAe,GAAG,OAAO,CAAC,IAAI,CAAC,CAkCxF"}
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@@ -0,0 +1,44 @@
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import { makeNodeToolInfoService } from "@galaxy-tool-util/core/node";
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import { loadToolFile } from "@galaxy-tool-util/tool-xml";
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/**
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* Cache a tool parsed from a local file — the local-ingest counterpart to `add`
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* (which fetches from the ToolShed). Dispatches on extension like Galaxy's
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* `get_tool_source` (`.yml` → YAML, else → XML; CWL unsupported). Mirrors
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* Galaxy's `run_add_local`: a bare `<tool id>` is not a valid cache key, so
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* `--tool-id` (the full toolshed tool_id) is required even when the file carries
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* an id; the parsed id is surfaced only as a hint.
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*/
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export async function runAddLocal(toolPath, opts) {
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let parsed;
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try {
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parsed = loadToolFile(toolPath);
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}
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catch (err) {
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const msg = err instanceof Error ? err.message : String(err);
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console.error(`Failed to parse ${toolPath}: ${msg}`);
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process.exitCode = 1;
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return;
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}
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const toolId = opts.toolId;
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if (toolId == null) {
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if (parsed.id && parsed.version) {
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console.log(`Parsed tool: ${parsed.id} v${parsed.version}`);
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console.log("Use --tool-id to specify the full toolshed tool_id for proper cache keying.");
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process.exitCode = 1;
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return;
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}
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console.error("Cannot determine tool_id from tool file. Use --tool-id.");
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process.exitCode = 1;
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return;
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}
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const version = opts.toolVersion || parsed.version;
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if (version == null) {
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console.error("Cannot determine version. Use --tool-version.");
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process.exitCode = 1;
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return;
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}
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const service = makeNodeToolInfoService({ cacheDir: opts.cacheDir });
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await service.addTool(toolId, version, parsed, "local", toolPath);
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console.log(`Cached ${toolId} ${version} from ${toolPath}`);
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}
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//# sourceMappingURL=add-local.js.map
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{"version":3,"file":"add-local.js","sourceRoot":"","sources":["../../src/commands/add-local.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,uBAAuB,EAAE,MAAM,6BAA6B,CAAC;AACtE,OAAO,EAAE,YAAY,EAAE,MAAM,4BAA4B,CAAC;AAQ1D;;;;;;;GAOG;AACH,MAAM,CAAC,KAAK,UAAU,WAAW,CAAC,QAAgB,EAAE,IAAqB;IACvE,IAAI,MAAM,CAAC;IACX,IAAI,CAAC;QACH,MAAM,GAAG,YAAY,CAAC,QAAQ,CAAC,CAAC;IAClC,CAAC;IAAC,OAAO,GAAG,EAAE,CAAC;QACb,MAAM,GAAG,GAAG,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;QAC7D,OAAO,CAAC,KAAK,CAAC,mBAAmB,QAAQ,KAAK,GAAG,EAAE,CAAC,CAAC;QACrD,OAAO,CAAC,QAAQ,GAAG,CAAC,CAAC;QACrB,OAAO;IACT,CAAC;IAED,MAAM,MAAM,GAAG,IAAI,CAAC,MAAM,CAAC;IAC3B,IAAI,MAAM,IAAI,IAAI,EAAE,CAAC;QACnB,IAAI,MAAM,CAAC,EAAE,IAAI,MAAM,CAAC,OAAO,EAAE,CAAC;YAChC,OAAO,CAAC,GAAG,CAAC,gBAAgB,MAAM,CAAC,EAAE,KAAK,MAAM,CAAC,OAAO,EAAE,CAAC,CAAC;YAC5D,OAAO,CAAC,GAAG,CAAC,6EAA6E,CAAC,CAAC;YAC3F,OAAO,CAAC,QAAQ,GAAG,CAAC,CAAC;YACrB,OAAO;QACT,CAAC;QACD,OAAO,CAAC,KAAK,CAAC,yDAAyD,CAAC,CAAC;QACzE,OAAO,CAAC,QAAQ,GAAG,CAAC,CAAC;QACrB,OAAO;IACT,CAAC;IAED,MAAM,OAAO,GAAG,IAAI,CAAC,WAAW,IAAI,MAAM,CAAC,OAAO,CAAC;IACnD,IAAI,OAAO,IAAI,IAAI,EAAE,CAAC;QACpB,OAAO,CAAC,KAAK,CAAC,+CAA+C,CAAC,CAAC;QAC/D,OAAO,CAAC,QAAQ,GAAG,CAAC,CAAC;QACrB,OAAO;IACT,CAAC;IAED,MAAM,OAAO,GAAG,uBAAuB,CAAC,EAAE,QAAQ,EAAE,IAAI,CAAC,QAAQ,EAAE,CAAC,CAAC;IACrE,MAAM,OAAO,CAAC,OAAO,CAAC,MAAM,EAAE,OAAO,EAAE,MAAM,EAAE,OAAO,EAAE,QAAQ,CAAC,CAAC;IAClE,OAAO,CAAC,GAAG,CAAC,UAAU,MAAM,IAAI,OAAO,SAAS,QAAQ,EAAE,CAAC,CAAC;AAC9D,CAAC"}
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/**
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* `gxwf convert-tree` — batch convert all workflows under a directory.
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*/
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import { type StepConversionStatus } from "@galaxy-tool-util/schema";
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import { type ToolLoadStatus } from "./stateful-tool-inputs.js";
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import { type StrictOptions } from "./strict-options.js";
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{"version":3,"file":"convert-tree.d.ts","sourceRoot":"","sources":["../../src/commands/convert-tree.ts"],"names":[],"mappings":"
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{"version":3,"file":"convert-tree.d.ts","sourceRoot":"","sources":["../../src/commands/convert-tree.ts"],"names":[],"mappings":"AAAA;;GAEG;AACH,OAAO,EAQL,KAAK,oBAAoB,EAE1B,MAAM,0BAA0B,CAAC;AAGlC,OAAO,EAGL,KAAK,cAAc,EACpB,MAAM,2BAA2B,CAAC;AAEnC,OAAO,EAAwB,KAAK,aAAa,EAAE,MAAM,qBAAqB,CAAC;AAE/E,OAAO,EAAmD,KAAK,WAAW,EAAE,MAAM,WAAW,CAAC;AAE9F,MAAM,WAAW,kBAAmB,SAAQ,aAAa;IACvD,EAAE,CAAC,EAAE,MAAM,CAAC;IACZ,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,UAAU,CAAC,EAAE,OAAO,CAAC;IACrB,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB,QAAQ,CAAC,EAAE,MAAM,CAAC;CACnB;AAED,MAAM,WAAW,qBAAqB;IACpC,YAAY,EAAE,MAAM,CAAC;IACrB,YAAY,EAAE,MAAM,CAAC;IACrB,YAAY,EAAE,MAAM,CAAC;IACrB,aAAa,CAAC,EAAE,oBAAoB,EAAE,CAAC;IACvC,cAAc,CAAC,EAAE,cAAc,EAAE,CAAC;CACnC;AAED,MAAM,WAAW,iBAAiB;IAChC,IAAI,EAAE,MAAM,CAAC;IACb,OAAO,EAAE,CAAC,qBAAqB,GAAG;QAAE,YAAY,EAAE,MAAM,CAAC;QAAC,KAAK,EAAE,MAAM,CAAA;KAAE,CAAC,EAAE,CAAC;IAC7E,OAAO,EAAE,WAAW,CAAC;CACtB;AAED,wBAAsB,cAAc,CAAC,GAAG,EAAE,MAAM,EAAE,IAAI,EAAE,kBAAkB,GAAG,OAAO,CAAC,IAAI,CAAC,CAwKzF"}
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/**
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* `gxwf convert-tree` — batch convert all workflows under a directory.
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*/
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import { toFormat2, toFormat2Stateful, toNative, toNativeStateful, checkStrictEncoding, checkStrictStructure, } from "@galaxy-tool-util/schema";
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import { mkdir, writeFile } from "node:fs/promises";
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import { dirname, join, basename } from "node:path";
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import { loadToolInputsForWorkflow } from "./stateful-tool-inputs.js";
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import { loadToolInputsForWorkflow, resolveConversionCache, } from "./stateful-tool-inputs.js";
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import { createDefaultResolver } from "./url-resolver.js";
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import { resolveStrictOptions } from "./strict-options.js";
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import { resolveFormat, serializeWorkflow } from "./workflow-io.js";
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// Shared tool cache for stateful mode (loaded once per run)
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if (opts.stateful) {
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cache = makeNodeToolCache({ cacheDir: opts.cacheDir });
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await cache.index.load();
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if ((await cache.index.listAll()).length === 0) {
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console.warn("Tool cache is empty — stateful conversion will fall back for every step");
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}
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}
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const cache = await resolveConversionCache(opts);
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const strict = resolveStrictOptions(opts);
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const treeResult = await collectTree(dir, async (info, data) => {
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const sourceFormat = resolveFormat(data, opts.format);
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let result;
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let statefulSteps;
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let toolLoadErrors;
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if (
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if (cache) {
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const expansionOpts = {
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resolver: createDefaultResolver({
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workflowDirectory: dirname(join(dir, info.relativePath)),
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const report = buildConvertReport(treeResult);
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// Aggregate stateful step counts across files
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let statefulFallbacks = 0;
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if (
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if (cache) {
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for (const r of report.results) {
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if ("statefulSteps" in r && r.statefulSteps) {
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statefulFallbacks += r.statefulSteps.filter((s) => !s.converted).length;
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{"version":3,"file":"convert-tree.js","sourceRoot":"","sources":["../../src/commands/convert-tree.ts"],"names":[],"mappings":"
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+
{"version":3,"file":"convert-tree.js","sourceRoot":"","sources":["../../src/commands/convert-tree.ts"],"names":[],"mappings":"AAAA;;GAEG;AACH,OAAO,EACL,SAAS,EACT,iBAAiB,EACjB,QAAQ,EACR,gBAAgB,EAChB,mBAAmB,EACnB,oBAAoB,GAIrB,MAAM,0BAA0B,CAAC;AAClC,OAAO,EAAE,KAAK,EAAE,SAAS,EAAE,MAAM,kBAAkB,CAAC;AACpD,OAAO,EAAE,OAAO,EAAE,IAAI,EAAE,QAAQ,EAAE,MAAM,WAAW,CAAC;AACpD,OAAO,EACL,yBAAyB,EACzB,sBAAsB,GAEvB,MAAM,2BAA2B,CAAC;AACnC,OAAO,EAAE,qBAAqB,EAAE,MAAM,mBAAmB,CAAC;AAC1D,OAAO,EAAE,oBAAoB,EAAsB,MAAM,qBAAqB,CAAC;AAC/E,OAAO,EAAE,aAAa,EAAE,iBAAiB,EAAE,MAAM,kBAAkB,CAAC;AACpE,OAAO,EAAE,WAAW,EAAE,iBAAiB,EAAqC,MAAM,WAAW,CAAC;AA4B9F,MAAM,CAAC,KAAK,UAAU,cAAc,CAAC,GAAW,EAAE,IAAwB;IACxE,MAAM,SAAS,GAAG,IAAI,CAAC,SAAS,CAAC;IACjC,IAAI,CAAC,SAAS,EAAE,CAAC;QACf,OAAO,CAAC,KAAK,CAAC,2CAA2C,CAAC,CAAC;QAC3D,OAAO,CAAC,QAAQ,GAAG,CAAC,CAAC;QACrB,OAAO;IACT,CAAC;IAED,4DAA4D;IAC5D,MAAM,KAAK,GAAG,MAAM,sBAAsB,CAAC,IAAI,CAAC,CAAC;IAEjD,MAAM,MAAM,GAAG,oBAAoB,CAAC,IAAI,CAAC,CAAC;IAE1C,MAAM,UAAU,GAAG,MAAM,WAAW,CAAC,GAAG,EAAE,KAAK,EAAE,IAAI,EAAE,IAAI,EAAE,EAAE;QAC7D,MAAM,YAAY,GAAG,aAAa,CAAC,IAAI,EAAE,IAAI,CAAC,MAAM,CAAC,CAAC;QACtD,MAAM,YAAY,GAAG,mBAAmB,CAAC,YAAY,EAAE,IAAI,CAAC,EAAE,CAAC,CAAC;QAEhE,kCAAkC;QAClC,IAAI,MAAM,CAAC,cAAc,EAAE,CAAC;YAC1B,MAAM,SAAS,GAAG,mBAAmB,CAAC,IAAI,EAAE,YAAY,CAAC,CAAC;YAC1D,IAAI,SAAS,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;gBACzB,MAAM,IAAI,KAAK,CAAC,aAAa,SAAS,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;YACvD,CAAC;QACH,CAAC;QACD,IAAI,MAAM,CAAC,eAAe,EAAE,CAAC;YAC3B,MAAM,YAAY,GAAG,oBAAoB,CAAC,IAAI,EAAE,YAAY,CAAC,CAAC;YAC9D,IAAI,YAAY,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;gBAC5B,MAAM,IAAI,KAAK,CAAC,cAAc,YAAY,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;YAC3D,CAAC;QACH,CAAC;QAED,IAAI,YAAY,KAAK,YAAY,EAAE,CAAC;YAClC,OAAO;gBACL,YAAY,EAAE,IAAI,CAAC,YAAY;gBAC/B,YAAY;gBACZ,YAAY;aACmB,CAAC;QACpC,CAAC;QAED,IAAI,MAA+B,CAAC;QACpC,IAAI,aAAiD,CAAC;QACtD,IAAI,cAA4C,CAAC;QAEjD,IAAI,KAAK,EAAE,CAAC;YACV,MAAM,aAAa,GAAqB;gBACtC,QAAQ,EAAE,qBAAqB,CAAC;oBAC9B,iBAAiB,EAAE,OAAO,CAAC,IAAI,CAAC,GAAG,EAAE,IAAI,CAAC,YAAY,CAAC,CAAC;iBACzD,CAAC;aACH,CAAC;YACF,MAAM,EAAE,QAAQ,EAAE,MAAM,EAAE,UAAU,EAAE,GAAG,MAAM,yBAAyB,CACtE,IAAI,EACJ,YAAY,EACZ,KAAK,EACL,aAAa,CACd,CAAC;YACF,MAAM,WAAW,GAAG,UAAU,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC;YACxD,IAAI,WAAW,CAAC,MAAM,GAAG,CAAC;gBAAE,cAAc,GAAG,WAAW,CAAC;YACzD,IAAI,YAAY,KAAK,SAAS,EAAE,CAAC;gBAC/B,MAAM,CAAC,GAAG,iBAAiB,CAAC,IAAI,EAAE,QAAQ,CAAC,CAAC;gBAC5C,MAAM,GAAG,CAAC,CAAC,QAA8C,CAAC;gBAC1D,aAAa,GAAG,CAAC,CAAC,KAAK,CAAC;gBACxB,IAAI,IAAI,CAAC,OAAO;oBAAE,iBAAiB,CAAC,MAAM,CAAC,CAAC;YAC9C,CAAC;iBAAM,CAAC;gBACN,MAAM,CAAC,GAAG,gBAAgB,CAAC,IAAI,EAAE,QAAQ,CAAC,CAAC;gBAC3C,MAAM,GAAG,CAAC,CAAC,QAA8C,CAAC;gBAC1D,aAAa,GAAG,CAAC,CAAC,KAAK,CAAC;YAC1B,CAAC;QACH,CAAC;aAAM,IAAI,YAAY,KAAK,SAAS,EAAE,CAAC;YACtC,MAAM,GAAG,SAAS,CAAC,IAAI,CAAuC,CAAC;YAC/D,IAAI,IAAI,CAAC,OAAO,EAAE,CAAC;gBACjB,iBAAiB,CAAC,MAAM,CAAC,CAAC;YAC5B,CAAC;QACH,CAAC;aAAM,CAAC;YACN,MAAM,GAAG,QAAQ,CAAC,IAAI,CAAuC,CAAC;QAChE,CAAC;QAED,MAAM,UAAU,GAAG,iBAAiB,CAAC,MAAM,EAAE,YAAY,EAAE;YACzD,IAAI,EAAE,IAAI,CAAC,IAAI;YACf,IAAI,EAAE,IAAI,CAAC,IAAI;SAChB,CAAC,CAAC;QAEH,6DAA6D;QAC7D,MAAM,OAAO,GAAG,eAAe,CAAC,IAAI,CAAC,YAAY,EAAE,YAAY,CAAC,CAAC;QACjE,MAAM,OAAO,GAAG,IAAI,CAAC,SAAS,EAAE,OAAO,CAAC,CAAC;QACzC,MAAM,KAAK,CAAC,OAAO,CAAC,OAAO,CAAC,EAAE,EAAE,SAAS,EAAE,IAAI,EAAE,CAAC,CAAC;QACnD,MAAM,SAAS,CAAC,OAAO,EAAE,UAAU,EAAE,OAAO,CAAC,CAAC;QAE9C,qEAAqE;QACrE,IAAI,MAAM,CAAC,WAAW,IAAI,aAAa,EAAE,IAAI,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,EAAE,CAAC;YACnE,MAAM,IAAI,KAAK,CAAC,mDAAmD,CAAC,CAAC;QACvE,CAAC;QAED,OAAO;YACL,YAAY,EAAE,IAAI,CAAC,YAAY;YAC/B,YAAY;YACZ,YAAY;YACZ,aAAa;YACb,cAAc;SACiB,CAAC;IACpC,CAAC,CAAC,CAAC;IAEH,MAAM,MAAM,GAAG,kBAAkB,CAAC,UAAU,CAAC,CAAC;IAE9C,8CAA8C;IAC9C,IAAI,iBAAiB,GAAG,CAAC,CAAC;IAC1B,IAAI,KAAK,EAAE,CAAC;QACV,KAAK,MAAM,CAAC,IAAI,MAAM,CAAC,OAAO,EAAE,CAAC;YAC/B,IAAI,eAAe,IAAI,CAAC,IAAI,CAAC,CAAC,aAAa,EAAE,CAAC;gBAC5C,iBAAiB,IAAI,CAAC,CAAC,aAAa,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,MAAM,CAAC;YAC1E,CAAC;QACH,CAAC;IACH,CAAC;IAED,IAAI,IAAI,CAAC,UAAU,EAAE,CAAC;QACpB,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,SAAS,CAAC,MAAM,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,CAAC;QAC7C,OAAO,CAAC,QAAQ,GAAG,MAAM,CAAC,OAAO,CAAC,KAAK,GAAG,CAAC,IAAI,iBAAiB,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;QAC7E,OAAO;IACT,CAAC;IAED,cAAc;IACd,KAAK,MAAM,OAAO,IAAI,UAAU,CAAC,QAAQ,EAAE,CAAC;QAC1C,IAAI,OAAO,CAAC,KAAK,EAAE,CAAC;YAClB,OAAO,CAAC,KAAK,CAAC,KAAK,OAAO,CAAC,IAAI,CAAC,YAAY,YAAY,OAAO,CAAC,KAAK,GAAG,CAAC,CAAC;YAC1E,SAAS;QACX,CAAC;QACD,MAAM,CAAC,GAAG,OAAO,CAAC,MAAO,CAAC;QAC1B,IAAI,CAAC,CAAC,YAAY,KAAK,CAAC,CAAC,YAAY,EAAE,CAAC;YACtC,OAAO,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,YAAY,aAAa,CAAC,CAAC,YAAY,WAAW,CAAC,CAAC;QAC1E,CAAC;aAAM,CAAC;YACN,IAAI,IAAI,GAAG,KAAK,CAAC,CAAC,YAAY,KAAK,CAAC,CAAC,YAAY,MAAM,CAAC,CAAC,YAAY,EAAE,CAAC;YACxE,IAAI,CAAC,CAAC,aAAa,EAAE,CAAC;gBACpB,MAAM,SAAS,GAAG,CAAC,CAAC,aAAa,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,MAAM,CAAC;gBACpE,IAAI,IAAI,cAAc,SAAS,IAAI,CAAC,CAAC,aAAa,CAAC,MAAM,GAAG,CAAC;YAC/D,CAAC;YACD,OAAO,CAAC,GAAG,CAAC,IAA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|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"convert.d.ts","sourceRoot":"","sources":["../../src/commands/convert.ts"],"names":[],"mappings":"
|
|
1
|
+
{"version":3,"file":"convert.d.ts","sourceRoot":"","sources":["../../src/commands/convert.ts"],"names":[],"mappings":"AAiBA,OAAO,EAAwB,KAAK,aAAa,EAAE,MAAM,qBAAqB,CAAC;AAQ/E,MAAM,WAAW,cAAe,SAAQ,aAAa;IACnD,EAAE,CAAC,EAAE,MAAM,CAAC;IACZ,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB,QAAQ,CAAC,EAAE,MAAM,CAAC;CACnB;AAED,wBAAsB,UAAU,CAAC,QAAQ,EAAE,MAAM,EAAE,IAAI,EAAE,cAAc,GAAG,OAAO,CAAC,IAAI,CAAC,CA6FtF"}
|
package/dist/commands/convert.js
CHANGED
|
@@ -1,10 +1,9 @@
|
|
|
1
1
|
/**
|
|
2
2
|
* `gxwf convert` — convert between native (.ga) and format2 (.gxwf.yml) formats.
|
|
3
3
|
*/
|
|
4
|
-
import { makeNodeToolCache } from "@galaxy-tool-util/core/node";
|
|
5
4
|
import { toFormat2, toFormat2Stateful, toNative, toNativeStateful, checkStrictEncoding, checkStrictStructure, } from "@galaxy-tool-util/schema";
|
|
6
5
|
import { dirname } from "node:path";
|
|
7
|
-
import { loadToolInputsForWorkflow } from "./stateful-tool-inputs.js";
|
|
6
|
+
import { loadToolInputsForWorkflow, resolveConversionCache } from "./stateful-tool-inputs.js";
|
|
8
7
|
import { createDefaultResolver } from "./url-resolver.js";
|
|
9
8
|
import { resolveStrictOptions } from "./strict-options.js";
|
|
10
9
|
import { readWorkflowFile, resolveFormat, serializeWorkflow, writeWorkflowOutput, } from "./workflow-io.js";
|
|
@@ -44,12 +43,8 @@ export async function runConvert(filePath, opts) {
|
|
|
44
43
|
}
|
|
45
44
|
let result;
|
|
46
45
|
let stepStatuses = null;
|
|
47
|
-
|
|
48
|
-
|
|
49
|
-
await cache.index.load();
|
|
50
|
-
if ((await cache.index.listAll()).length === 0) {
|
|
51
|
-
console.warn("Tool cache is empty — stateful conversion will fall back for every step");
|
|
52
|
-
}
|
|
46
|
+
const cache = await resolveConversionCache(opts);
|
|
47
|
+
if (cache) {
|
|
53
48
|
const expansionOpts = {
|
|
54
49
|
resolver: createDefaultResolver({ workflowDirectory: dirname(filePath) }),
|
|
55
50
|
};
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"convert.js","sourceRoot":"","sources":["../../src/commands/convert.ts"],"names":[],"mappings":"AAAA;;GAEG;AACH,OAAO,
|
|
1
|
+
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ACjB,OAAO,YAAY,KAAK,QAAQ,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,QAAQ,CAAC;AAC1D,CAAC;AAED,oEAAoE;AACpE,SAAS,iBAAiB,CAAC,GAA4B;IACrD,OAAO,GAAG,CAAC,QAAQ,CAAC;IACpB,KAAK,MAAM,GAAG,IAAI,MAAM,CAAC,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC;QACrC,IAAI,KAAK,CAAC,OAAO,CAAC,GAAG,CAAC,EAAE,CAAC;YACvB,KAAK,MAAM,IAAI,IAAI,GAAG,EAAE,CAAC;gBACvB,IAAI,IAAI,IAAI,OAAO,IAAI,KAAK,QAAQ,EAAE,CAAC;oBACrC,iBAAiB,CAAC,IAA+B,CAAC,CAAC;gBACrD,CAAC;YACH,CAAC;QACH,CAAC;aAAM,IAAI,GAAG,IAAI,OAAO,GAAG,KAAK,QAAQ,EAAE,CAAC;YAC1C,iBAAiB,CAAC,GAA8B,CAAC,CAAC;QACpD,CAAC;IACH,CAAC;AACH,CAAC"}
|
|
@@ -0,0 +1,33 @@
|
|
|
1
|
+
/**
|
|
2
|
+
* Tool-state validation support for steps that embed their tool definition
|
|
3
|
+
* instead of referencing a cached tool: a format2 `run: {class: GalaxyUserTool}`
|
|
4
|
+
* or a native `tool_representation`. The parameter bundle is parsed from the
|
|
5
|
+
* embedded definition, so these steps validate without a tool cache lookup.
|
|
6
|
+
*/
|
|
7
|
+
import { type ToolParameterBundleModel, type ValidationStepResult } from "@galaxy-tool-util/schema";
|
|
8
|
+
export interface EmbeddedTool {
|
|
9
|
+
bundle: ToolParameterBundleModel;
|
|
10
|
+
toolId: string | null;
|
|
11
|
+
toolVersion: string | null;
|
|
12
|
+
}
|
|
13
|
+
/** The embedded tool definition a step carries, or null for a cache-referenced tool. */
|
|
14
|
+
export declare function embeddedToolDefinition(step: {
|
|
15
|
+
run?: unknown;
|
|
16
|
+
tool_representation?: unknown;
|
|
17
|
+
}): Record<string, unknown> | null;
|
|
18
|
+
/** The id/version an embedded tool definition declares, for step results. */
|
|
19
|
+
export declare function embeddedToolIdentity(repr: Record<string, unknown>): {
|
|
20
|
+
toolId: string | null;
|
|
21
|
+
toolVersion: string | null;
|
|
22
|
+
};
|
|
23
|
+
/**
|
|
24
|
+
* Build the parameter bundle for an embedded tool definition. Returns a
|
|
25
|
+
* finished step result instead when the definition can't be validated against:
|
|
26
|
+
* `skip_tool_not_found` for a class other than `GalaxyUserTool` (admin-installed
|
|
27
|
+
* `GalaxyTool` dynamic tools are out of scope), `fail` when the definition
|
|
28
|
+
* doesn't parse — it ships inside the workflow, so a broken one is the
|
|
29
|
+
* workflow's defect.
|
|
30
|
+
*/
|
|
31
|
+
export declare function resolveEmbeddedTool(repr: Record<string, unknown>, stepLabel: string): EmbeddedTool | ValidationStepResult;
|
|
32
|
+
export declare function isEmbeddedTool(value: EmbeddedTool | ValidationStepResult): value is EmbeddedTool;
|
|
33
|
+
//# sourceMappingURL=embedded-tool.d.ts.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"embedded-tool.d.ts","sourceRoot":"","sources":["../../src/commands/embedded-tool.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AACH,OAAO,EAGL,KAAK,wBAAwB,EAC7B,KAAK,oBAAoB,EAC1B,MAAM,0BAA0B,CAAC;AAElC,MAAM,WAAW,YAAY;IAC3B,MAAM,EAAE,wBAAwB,CAAC;IACjC,MAAM,EAAE,MAAM,GAAG,IAAI,CAAC;IACtB,WAAW,EAAE,MAAM,GAAG,IAAI,CAAC;CAC5B;AAED,wFAAwF;AACxF,wBAAgB,sBAAsB,CAAC,IAAI,EAAE;IAC3C,GAAG,CAAC,EAAE,OAAO,CAAC;IACd,mBAAmB,CAAC,EAAE,OAAO,CAAC;CAC/B,GAAG,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,IAAI,CAOjC;AAED,6EAA6E;AAC7E,wBAAgB,oBAAoB,CAAC,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG;IACnE,MAAM,EAAE,MAAM,GAAG,IAAI,CAAC;IACtB,WAAW,EAAE,MAAM,GAAG,IAAI,CAAC;CAC5B,CAKA;AAED;;;;;;;GAOG;AACH,wBAAgB,mBAAmB,CACjC,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC7B,SAAS,EAAE,MAAM,GAChB,YAAY,GAAG,oBAAoB,CA+BrC;AAED,wBAAgB,cAAc,CAAC,KAAK,EAAE,YAAY,GAAG,oBAAoB,GAAG,KAAK,IAAI,YAAY,CAEhG"}
|
|
@@ -0,0 +1,69 @@
|
|
|
1
|
+
/**
|
|
2
|
+
* Tool-state validation support for steps that embed their tool definition
|
|
3
|
+
* instead of referencing a cached tool: a format2 `run: {class: GalaxyUserTool}`
|
|
4
|
+
* or a native `tool_representation`. The parameter bundle is parsed from the
|
|
5
|
+
* embedded definition, so these steps validate without a tool cache lookup.
|
|
6
|
+
*/
|
|
7
|
+
import { isGalaxyUserToolRun, parseInlineTool, } from "@galaxy-tool-util/schema";
|
|
8
|
+
/** The embedded tool definition a step carries, or null for a cache-referenced tool. */
|
|
9
|
+
export function embeddedToolDefinition(step) {
|
|
10
|
+
if (isGalaxyUserToolRun(step.run))
|
|
11
|
+
return step.run;
|
|
12
|
+
const repr = step.tool_representation;
|
|
13
|
+
if (repr && typeof repr === "object" && !Array.isArray(repr)) {
|
|
14
|
+
return repr;
|
|
15
|
+
}
|
|
16
|
+
return null;
|
|
17
|
+
}
|
|
18
|
+
/** The id/version an embedded tool definition declares, for step results. */
|
|
19
|
+
export function embeddedToolIdentity(repr) {
|
|
20
|
+
return {
|
|
21
|
+
toolId: typeof repr.id === "string" ? repr.id : null,
|
|
22
|
+
toolVersion: repr.version == null ? null : String(repr.version),
|
|
23
|
+
};
|
|
24
|
+
}
|
|
25
|
+
/**
|
|
26
|
+
* Build the parameter bundle for an embedded tool definition. Returns a
|
|
27
|
+
* finished step result instead when the definition can't be validated against:
|
|
28
|
+
* `skip_tool_not_found` for a class other than `GalaxyUserTool` (admin-installed
|
|
29
|
+
* `GalaxyTool` dynamic tools are out of scope), `fail` when the definition
|
|
30
|
+
* doesn't parse — it ships inside the workflow, so a broken one is the
|
|
31
|
+
* workflow's defect.
|
|
32
|
+
*/
|
|
33
|
+
export function resolveEmbeddedTool(repr, stepLabel) {
|
|
34
|
+
const { toolId, toolVersion } = embeddedToolIdentity(repr);
|
|
35
|
+
if (repr.class !== "GalaxyUserTool") {
|
|
36
|
+
return {
|
|
37
|
+
step: stepLabel,
|
|
38
|
+
tool_id: toolId,
|
|
39
|
+
version: toolVersion,
|
|
40
|
+
status: "skip_tool_not_found",
|
|
41
|
+
errors: [
|
|
42
|
+
`embedded tool definition of class ${JSON.stringify(repr.class)} is not validated (only GalaxyUserTool is supported)`,
|
|
43
|
+
],
|
|
44
|
+
};
|
|
45
|
+
}
|
|
46
|
+
try {
|
|
47
|
+
const parsed = parseInlineTool(repr);
|
|
48
|
+
return {
|
|
49
|
+
bundle: { parameters: parsed.inputs },
|
|
50
|
+
toolId,
|
|
51
|
+
toolVersion,
|
|
52
|
+
};
|
|
53
|
+
}
|
|
54
|
+
catch (e) {
|
|
55
|
+
return {
|
|
56
|
+
step: stepLabel,
|
|
57
|
+
tool_id: toolId,
|
|
58
|
+
version: toolVersion,
|
|
59
|
+
status: "fail",
|
|
60
|
+
errors: [
|
|
61
|
+
`embedded GalaxyUserTool definition could not be parsed: ${e instanceof Error ? e.message : String(e)}`,
|
|
62
|
+
],
|
|
63
|
+
};
|
|
64
|
+
}
|
|
65
|
+
}
|
|
66
|
+
export function isEmbeddedTool(value) {
|
|
67
|
+
return "bundle" in value;
|
|
68
|
+
}
|
|
69
|
+
//# sourceMappingURL=embedded-tool.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"embedded-tool.js","sourceRoot":"","sources":["../../src/commands/embedded-tool.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AACH,OAAO,EACL,mBAAmB,EACnB,eAAe,GAGhB,MAAM,0BAA0B,CAAC;AAQlC,wFAAwF;AACxF,MAAM,UAAU,sBAAsB,CAAC,IAGtC;IACC,IAAI,mBAAmB,CAAC,IAAI,CAAC,GAAG,CAAC;QAAE,OAAO,IAAI,CAAC,GAAG,CAAC;IACnD,MAAM,IAAI,GAAG,IAAI,CAAC,mBAAmB,CAAC;IACtC,IAAI,IAAI,IAAI,OAAO,IAAI,KAAK,QAAQ,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC;QAC7D,OAAO,IAA+B,CAAC;IACzC,CAAC;IACD,OAAO,IAAI,CAAC;AACd,CAAC;AAED,6EAA6E;AAC7E,MAAM,UAAU,oBAAoB,CAAC,IAA6B;IAIhE,OAAO;QACL,MAAM,EAAE,OAAO,IAAI,CAAC,EAAE,KAAK,QAAQ,CAAC,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI;QACpD,WAAW,EAAE,IAAI,CAAC,OAAO,IAAI,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,MAAM,CAAC,IAAI,CAAC,OAAO,CAAC;KAChE,CAAC;AACJ,CAAC;AAED;;;;;;;GAOG;AACH,MAAM,UAAU,mBAAmB,CACjC,IAA6B,EAC7B,SAAiB;IAEjB,MAAM,EAAE,MAAM,EAAE,WAAW,EAAE,GAAG,oBAAoB,CAAC,IAAI,CAAC,CAAC;IAC3D,IAAI,IAAI,CAAC,KAAK,KAAK,gBAAgB,EAAE,CAAC;QACpC,OAAO;YACL,IAAI,EAAE,SAAS;YACf,OAAO,EAAE,MAAM;YACf,OAAO,EAAE,WAAW;YACpB,MAAM,EAAE,qBAAqB;YAC7B,MAAM,EAAE;gBACN,qCAAqC,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,KAAK,CAAC,sDAAsD;aACtH;SACF,CAAC;IACJ,CAAC;IACD,IAAI,CAAC;QACH,MAAM,MAAM,GAAG,eAAe,CAAC,IAAI,CAAC,CAAC;QACrC,OAAO;YACL,MAAM,EAAE,EAAE,UAAU,EAAE,MAAM,CAAC,MAAgD,EAAE;YAC/E,MAAM;YACN,WAAW;SACZ,CAAC;IACJ,CAAC;IAAC,OAAO,CAAC,EAAE,CAAC;QACX,OAAO;YACL,IAAI,EAAE,SAAS;YACf,OAAO,EAAE,MAAM;YACf,OAAO,EAAE,WAAW;YACpB,MAAM,EAAE,MAAM;YACd,MAAM,EAAE;gBACN,2DAA2D,CAAC,YAAY,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE;aACxG;SACF,CAAC;IACJ,CAAC;AACH,CAAC;AAED,MAAM,UAAU,cAAc,CAAC,KAA0C;IACvE,OAAO,QAAQ,IAAI,KAAK,CAAC;AAC3B,CAAC"}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"lint-tree.d.ts","sourceRoot":"","sources":["../../src/commands/lint-tree.ts"],"names":[],"mappings":"AAcA,OAAO,EAAwB,KAAK,aAAa,EAAE,MAAM,qBAAqB,CAAC;AAG/E,OAAO,EAAsC,KAAK,mBAAmB,EAAE,MAAM,oBAAoB,CAAC;AAElG,MAAM,WAAW,eAAgB,SAAQ,aAAa,EAAE,mBAAmB;IACzE,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,iBAAiB,CAAC,EAAE,OAAO,CAAC;IAC5B,mBAAmB,CAAC,EAAE,OAAO,CAAC;IAC9B,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,IAAI,CAAC,EAAE,OAAO,CAAC;CAChB;AAUD,wBAAsB,WAAW,CAAC,GAAG,EAAE,MAAM,EAAE,IAAI,EAAE,eAAe,GAAG,OAAO,CAAC,IAAI,CAAC,
|
|
1
|
+
{"version":3,"file":"lint-tree.d.ts","sourceRoot":"","sources":["../../src/commands/lint-tree.ts"],"names":[],"mappings":"AAcA,OAAO,EAAwB,KAAK,aAAa,EAAE,MAAM,qBAAqB,CAAC;AAG/E,OAAO,EAAsC,KAAK,mBAAmB,EAAE,MAAM,oBAAoB,CAAC;AAElG,MAAM,WAAW,eAAgB,SAAQ,aAAa,EAAE,mBAAmB;IACzE,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,iBAAiB,CAAC,EAAE,OAAO,CAAC;IAC5B,mBAAmB,CAAC,EAAE,OAAO,CAAC;IAC9B,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,IAAI,CAAC,EAAE,OAAO,CAAC;CAChB;AAUD,wBAAsB,WAAW,CAAC,GAAG,EAAE,MAAM,EAAE,IAAI,EAAE,eAAe,GAAG,OAAO,CAAC,IAAI,CAAC,CA0EnF"}
|
|
@@ -73,7 +73,8 @@ export async function runLintTree(dir, opts) {
|
|
|
73
73
|
}
|
|
74
74
|
const s = report.summary;
|
|
75
75
|
const total = report.workflows.length;
|
|
76
|
-
|
|
76
|
+
const loadErrorSuffix = s.errors > 0 ? `, ${s.errors} load errors` : "";
|
|
77
|
+
console.log(`\nSummary: ${total} workflows | ${s.lint_errors} errors, ${s.lint_warnings} warnings, ${s.state_fail} state failures${loadErrorSuffix}`);
|
|
77
78
|
process.exitCode = computeLintExitCode(report);
|
|
78
79
|
}
|
|
79
80
|
function buildReport(treeResult) {
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"lint-tree.js","sourceRoot":"","sources":["../../src/commands/lint-tree.ts"],"names":[],"mappings":"AAIA,OAAO,EAAE,iBAAiB,EAAE,MAAM,6BAA6B,CAAC;AAKhE,OAAO,EACL,uBAAuB,EACvB,mBAAmB,IAAI,yBAAyB,GACjD,MAAM,0BAA0B,CAAC;AAClC,OAAO,EAAE,aAAa,EAAE,MAAM,kBAAkB,CAAC;AACjD,OAAO,EAAE,oBAAoB,EAAsB,MAAM,qBAAqB,CAAC;AAC/E,OAAO,EAAE,kBAAkB,EAAmB,MAAM,WAAW,CAAC;AAChE,OAAO,EAAE,WAAW,EAAmB,MAAM,WAAW,CAAC;AACzD,OAAO,EAAE,iBAAiB,EAAE,eAAe,EAA4B,MAAM,oBAAoB,CAAC;AAUlG,0EAA0E;AAC1E,SAAS,oBAAoB,CAAC,YAAoB,EAAE,EAAc;IAChE,MAAM,WAAW,GAAG,EAAE,CAAC,UAAU,CAAC,WAAW,GAAG,CAAC,EAAE,CAAC,aAAa,EAAE,WAAW,IAAI,CAAC,CAAC,CAAC;IACrF,MAAM,aAAa,GAAG,EAAE,CAAC,UAAU,CAAC,UAAU,GAAG,CAAC,EAAE,CAAC,aAAa,EAAE,UAAU,IAAI,CAAC,CAAC,CAAC;IACrF,MAAM,WAAW,GAAG,EAAE,CAAC,eAAe,IAAI,EAAE,CAAC;IAC7C,OAAO,uBAAuB,CAAC,YAAY,EAAE,WAAW,EAAE,aAAa,EAAE,WAAW,CAAC,CAAC;AACxF,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,WAAW,CAAC,GAAW,EAAE,IAAqB;IAClE,qCAAqC;IACrC,IAAI,KAA4B,CAAC;IACjC,IAAI,CAAC,IAAI,CAAC,mBAAmB,EAAE,CAAC;QAC9B,IAAI,CAAC;YACH,KAAK,GAAG,iBAAiB,CAAC,EAAE,QAAQ,EAAE,IAAI,CAAC,QAAQ,EAAE,CAAC,CAAC;YACvD,MAAM,KAAK,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC;YACzB,IAAI,CAAC,MAAM,KAAK,CAAC,KAAK,CAAC,OAAO,EAAE,CAAC,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;gBAC/C,OAAO,CAAC,IAAI,CAAC,oEAAoE,CAAC,CAAC;gBACnF,KAAK,GAAG,SAAS,CAAC;YACpB,CAAC;QACH,CAAC;QAAC,OAAO,CAAC,EAAE,CAAC;YACX,MAAM,GAAG,GAAG,CAAC,YAAY,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC;YACvD,OAAO,CAAC,IAAI,CAAC,8BAA8B,GAAG,EAAE,CAAC,CAAC;QACpD,CAAC;IACH,CAAC;IAED,MAAM,MAAM,GAAG,oBAAoB,CAAC,IAAI,CAAC,CAAC;IAE1C,MAAM,UAAU,GAAG,MAAM,WAAW,CAAqB,GAAG,EAAE,KAAK,EAAE,IAAI,EAAE,IAAI,EAAE,EAAE;QACjF,MAAM,MAAM,GAAG,aAAa,CAAC,IAAI,EAAE,IAAI,CAAC,MAAM,CAAC,CAAC;QAChD,MAAM,EAAE,GAAG,MAAM,kBAAkB,CAAC,IAAI,CAAC,IAAI,EAAE,IAAI,EAAE,MAAM,EAAE;YAC3D,iBAAiB,EAAE,IAAI,CAAC,iBAAiB;YACzC,mBAAmB,EAAE,IAAI,CAAC,mBAAmB;YAC7C,KAAK;YACL,MAAM;SACP,CAAC,CAAC;QACH,OAAO,oBAAoB,CAAC,IAAI,CAAC,YAAY,EAAE,EAAE,CAAC,CAAC;IACrD,CAAC,CAAC,CAAC;IAEH,MAAM,MAAM,GAAG,WAAW,CAAC,UAAU,CAAC,CAAC;IAEvC,MAAM,iBAAiB,CAAC,iBAAiB,EAAE,MAAM,EAAE,EAAE,cAAc,EAAE,IAAI,CAAC,cAAc,EAAE,CAAC,CAAC;IAC5F,MAAM,eAAe,CAAC,WAAW,EAAE,MAAM,EAAE,IAAI,CAAC,UAAU,CAAC,CAAC;IAE5D,IAAI,IAAI,CAAC,IAAI,EAAE,CAAC;QACd,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,SAAS,CAAC,MAAM,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,CAAC;QAC7C,OAAO,CAAC,QAAQ,GAAG,mBAAmB,CAAC,MAAM,CAAC,CAAC;QAC/C,OAAO;IACT,CAAC;IAED,cAAc;IACd,KAAK,MAAM,EAAE,IAAI,MAAM,CAAC,SAAS,EAAE,CAAC;QAClC,IAAI,EAAE,CAAC,KAAK,EAAE,CAAC;YACb,OAAO,CAAC,KAAK,CAAC,KAAK,EAAE,CAAC,IAAI,YAAY,EAAE,CAAC,KAAK,GAAG,CAAC,CAAC;YACnD,SAAS;QACX,CAAC;QACD,IAAI,EAAE,CAAC,cAAc,EAAE,CAAC;YACtB,OAAO,CAAC,IAAI,CAAC,KAAK,EAAE,CAAC,IAAI,cAAc,EAAE,CAAC,cAAc,GAAG,CAAC,CAAC;YAC7D,SAAS;QACX,CAAC;QAED,MAAM,UAAU,GAAG,EAAE,CAAC,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,MAAM,KAAK,MAAM,CAAC,CAAC,MAAM,CAAC;QAExE,IAAI,EAAE,CAAC,WAAW,GAAG,CAAC,IAAI,UAAU,GAAG,CAAC,EAAE,CAAC;YACzC,OAAO,CAAC,KAAK,CACX,KAAK,EAAE,CAAC,IAAI,KAAK,EAAE,CAAC,WAAW,YAAY,EAAE,CAAC,aAAa,cAAc,UAAU,iBAAiB,CACrG,CAAC;YACF,+DAA+D;YAC/D,2DAA2D;QAC7D,CAAC;aAAM,IAAI,EAAE,CAAC,aAAa,GAAG,CAAC,EAAE,CAAC;YAChC,OAAO,CAAC,IAAI,CAAC,KAAK,EAAE,CAAC,IAAI,KAAK,EAAE,CAAC,aAAa,WAAW,CAAC,CAAC;QAC7D,CAAC;aAAM,CAAC;YACN,OAAO,CAAC,GAAG,CAAC,KAAK,EAAE,CAAC,IAAI,MAAM,CAAC,CAAC;QAClC,CAAC;IACH,CAAC;IAED,MAAM,CAAC,GAAG,MAAM,CAAC,OAAO,CAAC;IACzB,MAAM,KAAK,GAAG,MAAM,CAAC,SAAS,CAAC,MAAM,CAAC;IACtC,OAAO,CAAC,GAAG,CACT,cAAc,KAAK,gBAAgB,CAAC,CAAC,WAAW,YAAY,CAAC,CAAC,aAAa,cAAc,CAAC,CAAC,UAAU,
|
|
1
|
+
{"version":3,"file":"lint-tree.js","sourceRoot":"","sources":["../../src/commands/lint-tree.ts"],"names":[],"mappings":"AAIA,OAAO,EAAE,iBAAiB,EAAE,MAAM,6BAA6B,CAAC;AAKhE,OAAO,EACL,uBAAuB,EACvB,mBAAmB,IAAI,yBAAyB,GACjD,MAAM,0BAA0B,CAAC;AAClC,OAAO,EAAE,aAAa,EAAE,MAAM,kBAAkB,CAAC;AACjD,OAAO,EAAE,oBAAoB,EAAsB,MAAM,qBAAqB,CAAC;AAC/E,OAAO,EAAE,kBAAkB,EAAmB,MAAM,WAAW,CAAC;AAChE,OAAO,EAAE,WAAW,EAAmB,MAAM,WAAW,CAAC;AACzD,OAAO,EAAE,iBAAiB,EAAE,eAAe,EAA4B,MAAM,oBAAoB,CAAC;AAUlG,0EAA0E;AAC1E,SAAS,oBAAoB,CAAC,YAAoB,EAAE,EAAc;IAChE,MAAM,WAAW,GAAG,EAAE,CAAC,UAAU,CAAC,WAAW,GAAG,CAAC,EAAE,CAAC,aAAa,EAAE,WAAW,IAAI,CAAC,CAAC,CAAC;IACrF,MAAM,aAAa,GAAG,EAAE,CAAC,UAAU,CAAC,UAAU,GAAG,CAAC,EAAE,CAAC,aAAa,EAAE,UAAU,IAAI,CAAC,CAAC,CAAC;IACrF,MAAM,WAAW,GAAG,EAAE,CAAC,eAAe,IAAI,EAAE,CAAC;IAC7C,OAAO,uBAAuB,CAAC,YAAY,EAAE,WAAW,EAAE,aAAa,EAAE,WAAW,CAAC,CAAC;AACxF,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,WAAW,CAAC,GAAW,EAAE,IAAqB;IAClE,qCAAqC;IACrC,IAAI,KAA4B,CAAC;IACjC,IAAI,CAAC,IAAI,CAAC,mBAAmB,EAAE,CAAC;QAC9B,IAAI,CAAC;YACH,KAAK,GAAG,iBAAiB,CAAC,EAAE,QAAQ,EAAE,IAAI,CAAC,QAAQ,EAAE,CAAC,CAAC;YACvD,MAAM,KAAK,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC;YACzB,IAAI,CAAC,MAAM,KAAK,CAAC,KAAK,CAAC,OAAO,EAAE,CAAC,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;gBAC/C,OAAO,CAAC,IAAI,CAAC,oEAAoE,CAAC,CAAC;gBACnF,KAAK,GAAG,SAAS,CAAC;YACpB,CAAC;QACH,CAAC;QAAC,OAAO,CAAC,EAAE,CAAC;YACX,MAAM,GAAG,GAAG,CAAC,YAAY,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC;YACvD,OAAO,CAAC,IAAI,CAAC,8BAA8B,GAAG,EAAE,CAAC,CAAC;QACpD,CAAC;IACH,CAAC;IAED,MAAM,MAAM,GAAG,oBAAoB,CAAC,IAAI,CAAC,CAAC;IAE1C,MAAM,UAAU,GAAG,MAAM,WAAW,CAAqB,GAAG,EAAE,KAAK,EAAE,IAAI,EAAE,IAAI,EAAE,EAAE;QACjF,MAAM,MAAM,GAAG,aAAa,CAAC,IAAI,EAAE,IAAI,CAAC,MAAM,CAAC,CAAC;QAChD,MAAM,EAAE,GAAG,MAAM,kBAAkB,CAAC,IAAI,CAAC,IAAI,EAAE,IAAI,EAAE,MAAM,EAAE;YAC3D,iBAAiB,EAAE,IAAI,CAAC,iBAAiB;YACzC,mBAAmB,EAAE,IAAI,CAAC,mBAAmB;YAC7C,KAAK;YACL,MAAM;SACP,CAAC,CAAC;QACH,OAAO,oBAAoB,CAAC,IAAI,CAAC,YAAY,EAAE,EAAE,CAAC,CAAC;IACrD,CAAC,CAAC,CAAC;IAEH,MAAM,MAAM,GAAG,WAAW,CAAC,UAAU,CAAC,CAAC;IAEvC,MAAM,iBAAiB,CAAC,iBAAiB,EAAE,MAAM,EAAE,EAAE,cAAc,EAAE,IAAI,CAAC,cAAc,EAAE,CAAC,CAAC;IAC5F,MAAM,eAAe,CAAC,WAAW,EAAE,MAAM,EAAE,IAAI,CAAC,UAAU,CAAC,CAAC;IAE5D,IAAI,IAAI,CAAC,IAAI,EAAE,CAAC;QACd,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,SAAS,CAAC,MAAM,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,CAAC;QAC7C,OAAO,CAAC,QAAQ,GAAG,mBAAmB,CAAC,MAAM,CAAC,CAAC;QAC/C,OAAO;IACT,CAAC;IAED,cAAc;IACd,KAAK,MAAM,EAAE,IAAI,MAAM,CAAC,SAAS,EAAE,CAAC;QAClC,IAAI,EAAE,CAAC,KAAK,EAAE,CAAC;YACb,OAAO,CAAC,KAAK,CAAC,KAAK,EAAE,CAAC,IAAI,YAAY,EAAE,CAAC,KAAK,GAAG,CAAC,CAAC;YACnD,SAAS;QACX,CAAC;QACD,IAAI,EAAE,CAAC,cAAc,EAAE,CAAC;YACtB,OAAO,CAAC,IAAI,CAAC,KAAK,EAAE,CAAC,IAAI,cAAc,EAAE,CAAC,cAAc,GAAG,CAAC,CAAC;YAC7D,SAAS;QACX,CAAC;QAED,MAAM,UAAU,GAAG,EAAE,CAAC,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,MAAM,KAAK,MAAM,CAAC,CAAC,MAAM,CAAC;QAExE,IAAI,EAAE,CAAC,WAAW,GAAG,CAAC,IAAI,UAAU,GAAG,CAAC,EAAE,CAAC;YACzC,OAAO,CAAC,KAAK,CACX,KAAK,EAAE,CAAC,IAAI,KAAK,EAAE,CAAC,WAAW,YAAY,EAAE,CAAC,aAAa,cAAc,UAAU,iBAAiB,CACrG,CAAC;YACF,+DAA+D;YAC/D,2DAA2D;QAC7D,CAAC;aAAM,IAAI,EAAE,CAAC,aAAa,GAAG,CAAC,EAAE,CAAC;YAChC,OAAO,CAAC,IAAI,CAAC,KAAK,EAAE,CAAC,IAAI,KAAK,EAAE,CAAC,aAAa,WAAW,CAAC,CAAC;QAC7D,CAAC;aAAM,CAAC;YACN,OAAO,CAAC,GAAG,CAAC,KAAK,EAAE,CAAC,IAAI,MAAM,CAAC,CAAC;QAClC,CAAC;IACH,CAAC;IAED,MAAM,CAAC,GAAG,MAAM,CAAC,OAAO,CAAC;IACzB,MAAM,KAAK,GAAG,MAAM,CAAC,SAAS,CAAC,MAAM,CAAC;IACtC,MAAM,eAAe,GAAG,CAAC,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,MAAM,cAAc,CAAC,CAAC,CAAC,EAAE,CAAC;IACxE,OAAO,CAAC,GAAG,CACT,cAAc,KAAK,gBAAgB,CAAC,CAAC,WAAW,YAAY,CAAC,CAAC,aAAa,cAAc,CAAC,CAAC,UAAU,kBAAkB,eAAe,EAAE,CACzI,CAAC;IACF,OAAO,CAAC,QAAQ,GAAG,mBAAmB,CAAC,MAAM,CAAC,CAAC;AACjD,CAAC;AAED,SAAS,WAAW,CAAC,UAA0C;IAC7D,MAAM,SAAS,GAAyB,EAAE,CAAC;IAE3C,KAAK,MAAM,CAAC,IAAI,UAAU,CAAC,QAAQ,EAAE,CAAC;QACpC,IAAI,CAAC,CAAC,KAAK,EAAE,CAAC;YACZ,SAAS,CAAC,IAAI,CAAC,uBAAuB,CAAC,CAAC,CAAC,IAAI,CAAC,YAAY,EAAE,CAAC,EAAE,CAAC,EAAE,EAAE,EAAE,EAAE,KAAK,EAAE,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC,CAAC;YAC3F,SAAS;QACX,CAAC;QACD,IAAI,CAAC,CAAC,OAAO,EAAE,CAAC;YACd,SAAS,CAAC,IAAI,CACZ,uBAAuB,CAAC,CAAC,CAAC,IAAI,CAAC,YAAY,EAAE,CAAC,EAAE,CAAC,EAAE,EAAE,EAAE;gBACrD,cAAc,EAAG,CAAC,CAAC,UAAgC,IAAI,IAAI;aAC5D,CAAC,CACH,CAAC;YACF,SAAS;QACX,CAAC;QACD,SAAS,CAAC,IAAI,CAAC,CAAC,CAAC,MAAO,CAAC,CAAC;IAC5B,CAAC;IAED,OAAO,yBAAyB,CAAC,UAAU,CAAC,IAAI,EAAE,SAAS,CAAC,CAAC;AAC/D,CAAC;AAED,SAAS,mBAAmB,CAAC,MAA4B;IACvD,MAAM,CAAC,GAAG,MAAM,CAAC,OAAO,CAAC;IACzB,IAAI,CAAC,CAAC,WAAW,GAAG,CAAC,IAAI,CAAC,CAAC,UAAU,GAAG,CAAC,IAAI,CAAC,CAAC,MAAM,GAAG,CAAC;QAAE,OAAO,CAAC,CAAC;IACpE,IAAI,CAAC,CAAC,aAAa,GAAG,CAAC;QAAE,OAAO,CAAC,CAAC;IAClC,OAAO,CAAC,CAAC;AACX,CAAC"}
|
|
@@ -30,4 +30,16 @@ export interface LoadedToolInputs {
|
|
|
30
30
|
* plus a per-tool load status list.
|
|
31
31
|
*/
|
|
32
32
|
export declare function loadToolInputsForWorkflow(data: Record<string, unknown>, format: WorkflowFormat, cache: ToolCache, expansionOpts?: ExpansionOptions): Promise<LoadedToolInputs>;
|
|
33
|
+
/**
|
|
34
|
+
* Resolve whether a conversion runs state-aware, and load the cache it needs.
|
|
35
|
+
*
|
|
36
|
+
* `stateful` is tri-state: `true` forces it on, `false` forces it off, and
|
|
37
|
+
* `undefined` — no flag — turns it on whenever the tool cache holds anything
|
|
38
|
+
* to resolve against. Returns the cache to convert with, or `null` to take
|
|
39
|
+
* the schema-free path.
|
|
40
|
+
*/
|
|
41
|
+
export declare function resolveConversionCache(opts: {
|
|
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|
+
stateful?: boolean;
|
|
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|
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cacheDir?: string;
|
|
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|
+
}): Promise<ToolCache | null>;
|
|
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|
//# sourceMappingURL=stateful-tool-inputs.d.ts.map
|
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@@ -1 +1 @@
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1
|
-
{"version":3,"file":"stateful-tool-inputs.d.ts","sourceRoot":"","sources":["../../src/commands/stateful-tool-inputs.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;GAaG;AACH,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;
|
|
1
|
+
{"version":3,"file":"stateful-tool-inputs.d.ts","sourceRoot":"","sources":["../../src/commands/stateful-tool-inputs.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;GAaG;AACH,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AAExD,OAAO,EAIL,KAAK,gBAAgB,EAKrB,KAAK,kBAAkB,EAEvB,KAAK,cAAc,EACpB,MAAM,0BAA0B,CAAC;AAKlC,MAAM,WAAW,cAAc;IAC7B,MAAM,EAAE,MAAM,CAAC;IACf,WAAW,EAAE,MAAM,GAAG,IAAI,CAAC;IAC3B,MAAM,EAAE,OAAO,CAAC;IAChB,KAAK,CAAC,EAAE,MAAM,CAAC;CAChB;AAED,MAAM,WAAW,gBAAgB;IAC/B,QAAQ,EAAE,kBAAkB,CAAC;IAC7B,MAAM,EAAE,cAAc,EAAE,CAAC;CAC1B;AAMD;;;;GAIG;AACH,wBAAsB,yBAAyB,CAC7C,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC7B,MAAM,EAAE,cAAc,EACtB,KAAK,EAAE,SAAS,EAChB,aAAa,CAAC,EAAE,gBAAgB,GAC/B,OAAO,CAAC,gBAAgB,CAAC,CAyB3B;AA4CD;;;;;;;GAOG;AACH,wBAAsB,sBAAsB,CAAC,IAAI,EAAE;IACjD,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB,QAAQ,CAAC,EAAE,MAAM,CAAC;CACnB,GAAG,OAAO,CAAC,SAAS,GAAG,IAAI,CAAC,CAY5B"}
|
|
@@ -1,4 +1,5 @@
|
|
|
1
|
-
import {
|
|
1
|
+
import { makeNodeToolCache } from "@galaxy-tool-util/core/node";
|
|
2
|
+
import { expandedFormat2, expandedNative, isGalaxyUserToolRun, } from "@galaxy-tool-util/schema";
|
|
2
3
|
import { isResolveError, resolveTool } from "./resolve-tool.js";
|
|
3
4
|
function toolKey(toolId, version) {
|
|
4
5
|
return `${toolId}\0${version ?? ""}`;
|
|
@@ -62,7 +63,7 @@ function collectFormat2ToolRefs(wf) {
|
|
|
62
63
|
refs.push([step.tool_id, step.tool_version ?? null]);
|
|
63
64
|
}
|
|
64
65
|
}
|
|
65
|
-
if (step.run && typeof step.run === "object") {
|
|
66
|
+
if (step.run && typeof step.run === "object" && !isGalaxyUserToolRun(step.run)) {
|
|
66
67
|
walk(step.run.steps);
|
|
67
68
|
}
|
|
68
69
|
}
|
|
@@ -70,4 +71,25 @@ function collectFormat2ToolRefs(wf) {
|
|
|
70
71
|
walk(wf.steps);
|
|
71
72
|
return refs;
|
|
72
73
|
}
|
|
74
|
+
/**
|
|
75
|
+
* Resolve whether a conversion runs state-aware, and load the cache it needs.
|
|
76
|
+
*
|
|
77
|
+
* `stateful` is tri-state: `true` forces it on, `false` forces it off, and
|
|
78
|
+
* `undefined` — no flag — turns it on whenever the tool cache holds anything
|
|
79
|
+
* to resolve against. Returns the cache to convert with, or `null` to take
|
|
80
|
+
* the schema-free path.
|
|
81
|
+
*/
|
|
82
|
+
export async function resolveConversionCache(opts) {
|
|
83
|
+
if (opts.stateful === false)
|
|
84
|
+
return null;
|
|
85
|
+
const cache = makeNodeToolCache({ cacheDir: opts.cacheDir });
|
|
86
|
+
await cache.index.load();
|
|
87
|
+
if ((await cache.index.listAll()).length > 0)
|
|
88
|
+
return cache;
|
|
89
|
+
if (opts.stateful === true) {
|
|
90
|
+
console.warn("Tool cache is empty — stateful conversion will fall back for every step");
|
|
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|
+
return cache;
|
|
92
|
+
}
|
|
93
|
+
return null;
|
|
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|
+
}
|
|
73
95
|
//# sourceMappingURL=stateful-tool-inputs.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"stateful-tool-inputs.js","sourceRoot":"","sources":["../../src/commands/stateful-tool-inputs.ts"],"names":[],"mappings":"AAeA,OAAO,EACL,eAAe,EACf,cAAc,
|
|
1
|
+
{"version":3,"file":"stateful-tool-inputs.js","sourceRoot":"","sources":["../../src/commands/stateful-tool-inputs.ts"],"names":[],"mappings":"AAeA,OAAO,EAAE,iBAAiB,EAAE,MAAM,6BAA6B,CAAC;AAChE,OAAO,EACL,eAAe,EACf,cAAc,EACd,mBAAmB,GASpB,MAAM,0BAA0B,CAAC;AAClC,OAAO,EAAE,cAAc,EAAE,WAAW,EAAE,MAAM,mBAAmB,CAAC;AAgBhE,SAAS,OAAO,CAAC,MAAc,EAAE,OAAsB;IACrD,OAAO,GAAG,MAAM,KAAK,OAAO,IAAI,EAAE,EAAE,CAAC;AACvC,CAAC;AAED;;;;GAIG;AACH,MAAM,CAAC,KAAK,UAAU,yBAAyB,CAC7C,IAA6B,EAC7B,MAAsB,EACtB,KAAgB,EAChB,aAAgC;IAEhC,MAAM,IAAI,GACR,MAAM,KAAK,QAAQ;QACjB,CAAC,CAAC,qBAAqB,CAAC,MAAM,cAAc,CAAC,IAAI,EAAE,aAAa,CAAC,CAAC;QAClE,CAAC,CAAC,sBAAsB,CAAC,MAAM,eAAe,CAAC,IAAI,EAAE,aAAa,CAAC,CAAC,CAAC;IAEzE,MAAM,MAAM,GAA4B,IAAI,GAAG,EAAE,CAAC;IAClD,MAAM,MAAM,GAAqB,EAAE,CAAC;IAEpC,KAAK,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,IAAI,IAAI,EAAE,CAAC;QACrC,MAAM,GAAG,GAAG,OAAO,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;QACrC,IAAI,MAAM,CAAC,GAAG,CAAC,GAAG,CAAC;YAAE,SAAS;QAC9B,MAAM,QAAQ,GAAG,MAAM,WAAW,CAAC,KAAK,EAAE,MAAM,EAAE,OAAO,CAAC,CAAC;QAC3D,IAAI,cAAc,CAAC,QAAQ,CAAC,EAAE,CAAC;YAC7B,MAAM,MAAM,GACV,QAAQ,CAAC,IAAI,KAAK,YAAY,CAAC,CAAC,CAAC,kBAAkB,MAAM,EAAE,CAAC,CAAC,CAAC,GAAG,MAAM,eAAe,CAAC;YACzF,MAAM,CAAC,IAAI,CAAC,EAAE,MAAM,EAAE,WAAW,EAAE,OAAO,EAAE,MAAM,EAAE,KAAK,EAAE,KAAK,EAAE,MAAM,EAAE,CAAC,CAAC;YAC5E,SAAS;QACX,CAAC;QACD,MAAM,CAAC,GAAG,CAAC,GAAG,EAAE,QAAQ,CAAC,IAAI,CAAC,MAAoB,CAAC,CAAC;QACpD,MAAM,CAAC,IAAI,CAAC,EAAE,MAAM,EAAE,WAAW,EAAE,OAAO,EAAE,MAAM,EAAE,IAAI,EAAE,CAAC,CAAC;IAC9D,CAAC;IAED,MAAM,QAAQ,GAAuB,CAAC,MAAM,EAAE,OAAO,EAAE,EAAE,CAAC,MAAM,CAAC,GAAG,CAAC,OAAO,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC,CAAC;IAC/F,OAAO,EAAE,QAAQ,EAAE,MAAM,EAAE,CAAC;AAC9B,CAAC;AAED,+CAA+C;AAE/C,SAAS,qBAAqB,CAAC,EAA4B;IACzD,MAAM,IAAI,GAAG,IAAI,GAAG,EAAU,CAAC;IAC/B,MAAM,IAAI,GAAmC,EAAE,CAAC;IAChD,MAAM,IAAI,GAAG,CAAC,KAAwC,EAAQ,EAAE;QAC9D,KAAK,MAAM,IAAI,IAAI,MAAM,CAAC,MAAM,CAAC,KAAK,CAA2B,EAAE,CAAC;YAClE,IAAI,IAAI,CAAC,OAAO,IAAI,IAAI,EAAE,CAAC;gBACzB,MAAM,GAAG,GAAG,OAAO,CAAC,IAAI,CAAC,OAAO,EAAE,IAAI,CAAC,YAAY,IAAI,IAAI,CAAC,CAAC;gBAC7D,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC;oBACnB,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC;oBACd,IAAI,CAAC,IAAI,CAAC,CAAC,IAAI,CAAC,OAAO,EAAE,IAAI,CAAC,YAAY,IAAI,IAAI,CAAC,CAAC,CAAC;gBACvD,CAAC;YACH,CAAC;YACD,IAAI,IAAI,CAAC,WAAW;gBAAE,IAAI,CAAC,IAAI,CAAC,WAAW,CAAC,KAAK,CAAC,CAAC;QACrD,CAAC;IACH,CAAC,CAAC;IACF,IAAI,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC;IACf,OAAO,IAAI,CAAC;AACd,CAAC;AAED,SAAS,sBAAsB,CAAC,EAA6B;IAC3D,MAAM,IAAI,GAAG,IAAI,GAAG,EAAU,CAAC;IAC/B,MAAM,IAAI,GAAmC,EAAE,CAAC;IAChD,MAAM,IAAI,GAAG,CAAC,KAAuC,EAAQ,EAAE;QAC7D,KAAK,MAAM,IAAI,IAAI,KAAK,EAAE,CAAC;YACzB,IAAI,IAAI,CAAC,OAAO,IAAI,IAAI,EAAE,CAAC;gBACzB,MAAM,GAAG,GAAG,OAAO,CAAC,IAAI,CAAC,OAAO,EAAE,IAAI,CAAC,YAAY,IAAI,IAAI,CAAC,CAAC;gBAC7D,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC;oBACnB,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC;oBACd,IAAI,CAAC,IAAI,CAAC,CAAC,IAAI,CAAC,OAAO,EAAE,IAAI,CAAC,YAAY,IAAI,IAAI,CAAC,CAAC,CAAC;gBACvD,CAAC;YACH,CAAC;YACD,IAAI,IAAI,CAAC,GAAG,IAAI,OAAO,IAAI,CAAC,GAAG,KAAK,QAAQ,IAAI,CAAC,mBAAmB,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;gBAC/E,IAAI,CAAE,IAAI,CAAC,GAAiC,CAAC,KAAK,CAAC,CAAC;YACtD,CAAC;QACH,CAAC;IACH,CAAC,CAAC;IACF,IAAI,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC;IACf,OAAO,IAAI,CAAC;AACd,CAAC;AAED;;;;;;;GAOG;AACH,MAAM,CAAC,KAAK,UAAU,sBAAsB,CAAC,IAG5C;IACC,IAAI,IAAI,CAAC,QAAQ,KAAK,KAAK;QAAE,OAAO,IAAI,CAAC;IAEzC,MAAM,KAAK,GAAG,iBAAiB,CAAC,EAAE,QAAQ,EAAE,IAAI,CAAC,QAAQ,EAAE,CAAC,CAAC;IAC7D,MAAM,KAAK,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC;IACzB,IAAI,CAAC,MAAM,KAAK,CAAC,KAAK,CAAC,OAAO,EAAE,CAAC,CAAC,MAAM,GAAG,CAAC;QAAE,OAAO,KAAK,CAAC;IAE3D,IAAI,IAAI,CAAC,QAAQ,KAAK,IAAI,EAAE,CAAC;QAC3B,OAAO,CAAC,IAAI,CAAC,yEAAyE,CAAC,CAAC;QACxF,OAAO,KAAK,CAAC;IACf,CAAC;IACD,OAAO,IAAI,CAAC;AACd,CAAC"}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"tool-search.d.ts","sourceRoot":"","sources":["../../src/commands/tool-search.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAAE,iBAAiB,EAAE,MAAM,0BAA0B,CAAC;AAGlE,MAAM,WAAW,iBAAiB;IAChC,QAAQ,CAAC,EAAE,MAAM,GAAG,MAAM,CAAC;IAC3B,UAAU,CAAC,EAAE,MAAM,GAAG,MAAM,CAAC;IAC7B,IAAI,CAAC,EAAE,MAAM,GAAG,MAAM,CAAC;IACvB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,SAAS,CAAC,EAAE,OAAO,CAAC;IACpB,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,MAAM,CAAC,EAAE,OAAO,CAAC;IACjB,QAAQ,CAAC,EAAE,MAAM,CAAC;CACnB;AAED,MAAM,WAAW,oBAAoB;IACnC,KAAK,EAAE,MAAM,CAAC;IACd,IAAI,EAAE,iBAAiB,EAAE,CAAC;CAC3B;AAQD,wBAAsB,aAAa,CAAC,KAAK,EAAE,MAAM,EAAE,IAAI,EAAE,iBAAiB,GAAG,OAAO,CAAC,IAAI,CAAC,
|
|
1
|
+
{"version":3,"file":"tool-search.d.ts","sourceRoot":"","sources":["../../src/commands/tool-search.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAAE,iBAAiB,EAAE,MAAM,0BAA0B,CAAC;AAGlE,MAAM,WAAW,iBAAiB;IAChC,QAAQ,CAAC,EAAE,MAAM,GAAG,MAAM,CAAC;IAC3B,UAAU,CAAC,EAAE,MAAM,GAAG,MAAM,CAAC;IAC7B,IAAI,CAAC,EAAE,MAAM,GAAG,MAAM,CAAC;IACvB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,SAAS,CAAC,EAAE,OAAO,CAAC;IACpB,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,MAAM,CAAC,EAAE,OAAO,CAAC;IACjB,QAAQ,CAAC,EAAE,MAAM,CAAC;CACnB;AAED,MAAM,WAAW,oBAAoB;IACnC,KAAK,EAAE,MAAM,CAAC;IACd,IAAI,EAAE,iBAAiB,EAAE,CAAC;CAC3B;AAQD,wBAAsB,aAAa,CAAC,KAAK,EAAE,MAAM,EAAE,IAAI,EAAE,iBAAiB,GAAG,OAAO,CAAC,IAAI,CAAC,CA+CzF"}
|
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
import { DEFAULT_TOOLSHED_URL } from "@galaxy-tool-util/core";
|
|
2
2
|
import { makeNodeToolInfoService } from "@galaxy-tool-util/core/node";
|
|
3
|
-
import { ToolFetchError,
|
|
3
|
+
import { ToolFetchError, ToolSearchService } from "@galaxy-tool-util/search";
|
|
4
4
|
function toInt(value, fallback) {
|
|
5
5
|
if (value === undefined)
|
|
6
6
|
return fallback;
|
|
@@ -11,26 +11,27 @@ export async function runToolSearch(query, opts) {
|
|
|
11
11
|
const pageSize = toInt(opts.pageSize, 20);
|
|
12
12
|
const maxResults = toInt(opts.maxResults, 50);
|
|
13
13
|
const page = toInt(opts.page, 1);
|
|
14
|
-
const owner = opts.owner?.toLowerCase();
|
|
15
|
-
const matchName = opts.matchName === true;
|
|
16
|
-
const queryTokens = queryNameTokens(query);
|
|
17
14
|
const source = { type: "toolshed", url: DEFAULT_TOOLSHED_URL };
|
|
18
|
-
const
|
|
15
|
+
const onDiagnostic = (message) => console.error(message);
|
|
16
|
+
const info = makeNodeToolInfoService({
|
|
17
|
+
cacheDir: opts.cacheDir,
|
|
18
|
+
onDiagnostic,
|
|
19
|
+
});
|
|
20
|
+
const search = new ToolSearchService({
|
|
21
|
+
sources: [source],
|
|
22
|
+
info,
|
|
23
|
+
onDiagnostic,
|
|
24
|
+
});
|
|
25
|
+
let hits;
|
|
19
26
|
try {
|
|
20
|
-
|
|
21
|
-
|
|
22
|
-
|
|
23
|
-
|
|
24
|
-
|
|
25
|
-
|
|
26
|
-
|
|
27
|
-
|
|
28
|
-
if (hits.length >= maxResults)
|
|
29
|
-
break;
|
|
30
|
-
}
|
|
31
|
-
if (hits.length >= maxResults)
|
|
32
|
-
break;
|
|
33
|
-
}
|
|
27
|
+
hits = await search.searchTools(query, {
|
|
28
|
+
page,
|
|
29
|
+
pageSize,
|
|
30
|
+
maxResults,
|
|
31
|
+
owner: opts.owner,
|
|
32
|
+
matchName: opts.matchName,
|
|
33
|
+
enrich: opts.enrich,
|
|
34
|
+
});
|
|
34
35
|
}
|
|
35
36
|
catch (err) {
|
|
36
37
|
if (err instanceof ToolFetchError) {
|
|
@@ -40,21 +41,6 @@ export async function runToolSearch(query, opts) {
|
|
|
40
41
|
}
|
|
41
42
|
throw err;
|
|
42
43
|
}
|
|
43
|
-
hits.sort((a, b) => b.score - a.score);
|
|
44
|
-
if (opts.enrich && hits.length > 0) {
|
|
45
|
-
const info = makeNodeToolInfoService({ cacheDir: opts.cacheDir });
|
|
46
|
-
await Promise.all(hits.map(async (hit) => {
|
|
47
|
-
try {
|
|
48
|
-
const parsed = await info.getToolInfo(hit.trsToolId, hit.version ?? null);
|
|
49
|
-
if (parsed !== null)
|
|
50
|
-
hit.parsedTool = parsed;
|
|
51
|
-
}
|
|
52
|
-
catch (err) {
|
|
53
|
-
const msg = err instanceof Error ? err.message : String(err);
|
|
54
|
-
console.error(`Enrichment failed for ${hit.trsToolId}: ${msg}`);
|
|
55
|
-
}
|
|
56
|
-
}));
|
|
57
|
-
}
|
|
58
44
|
if (opts.json) {
|
|
59
45
|
const envelope = { query, hits };
|
|
60
46
|
console.log(JSON.stringify(envelope, null, 2));
|
|
@@ -89,19 +75,4 @@ function truncate(s, max) {
|
|
|
89
75
|
const flat = s.replace(/\s+/g, " ").trim();
|
|
90
76
|
return flat.length > max ? `${flat.slice(0, max - 1)}…` : flat;
|
|
91
77
|
}
|
|
92
|
-
function tokenize(s) {
|
|
93
|
-
return s
|
|
94
|
-
.toLowerCase()
|
|
95
|
-
.split(/[^a-z0-9+]+/)
|
|
96
|
-
.filter((t) => t.length > 0);
|
|
97
|
-
}
|
|
98
|
-
function queryNameTokens(query) {
|
|
99
|
-
return tokenize(query);
|
|
100
|
-
}
|
|
101
|
-
function nameMatchesQuery(name, queryTokens) {
|
|
102
|
-
if (queryTokens.length === 0)
|
|
103
|
-
return true;
|
|
104
|
-
const nameTokens = new Set(tokenize(name));
|
|
105
|
-
return queryTokens.some((t) => nameTokens.has(t));
|
|
106
|
-
}
|
|
107
78
|
//# sourceMappingURL=tool-search.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"tool-search.js","sourceRoot":"","sources":["../../src/commands/tool-search.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,oBAAoB,EAAE,MAAM,wBAAwB,CAAC;AAC9D,OAAO,EAAE,uBAAuB,EAAE,MAAM,6BAA6B,CAAC;AAEtE,OAAO,EAAE,cAAc,EAAE,
|
|
1
|
+
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