@galaxy-tool-util/cli 1.9.0 → 1.10.1
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/annotate-connections.js +2 -2
- package/dist/commands/annotate-connections.js.map +1 -1
- package/dist/commands/connection-validation.js +2 -2
- package/dist/commands/connection-validation.js.map +1 -1
- package/dist/commands/draft-validate.d.ts +2 -0
- package/dist/commands/draft-validate.d.ts.map +1 -1
- package/dist/commands/draft-validate.js +4 -4
- package/dist/commands/draft-validate.js.map +1 -1
- package/dist/commands/resolve-tool.d.ts +31 -2
- package/dist/commands/resolve-tool.d.ts.map +1 -1
- package/dist/commands/resolve-tool.js +42 -7
- package/dist/commands/resolve-tool.js.map +1 -1
- package/dist/commands/schema.js +2 -2
- package/dist/commands/schema.js.map +1 -1
- package/dist/commands/stateful-tool-inputs.js +2 -2
- package/dist/commands/stateful-tool-inputs.js.map +1 -1
- package/dist/commands/summarize.js +2 -2
- package/dist/commands/summarize.js.map +1 -1
- package/dist/commands/validate-workflow-json-schema.js +3 -3
- package/dist/commands/validate-workflow-json-schema.js.map +1 -1
- package/dist/commands/validate-workflow.d.ts +5 -3
- package/dist/commands/validate-workflow.d.ts.map +1 -1
- package/dist/commands/validate-workflow.js +21 -22
- package/dist/commands/validate-workflow.js.map +1 -1
- package/package.json +5 -5
- package/spec/gxwf.json +16 -0
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@@ -6,7 +6,7 @@
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import { buildEdgeAnnotations, buildGetToolInfo as _buildGetToolInfo, buildWorkflowGraph, validateConnectionGraph, } from "@galaxy-tool-util/connection-validation";
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import { makeNodeToolCache } from "@galaxy-tool-util/core/node";
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import { buildGetToolInfo } from "./connection-validation.js";
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import { isResolveError,
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import { isResolveError, resolveTool } from "./resolve-tool.js";
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export async function resolveEdgeAnnotations(data, opts = {}) {
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const cache = makeNodeToolCache({ cacheDir: opts.cacheDir });
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await cache.index.load();
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@@ -28,7 +28,7 @@ export async function resolveEdgeAnnotationsWithCache(data, cache) {
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export async function resolveEdgeAnnotationsAndSpecsWithCache(data, cache) {
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const specs = new Map();
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const getToolInfo = await _buildGetToolInfo(data, async (id, version) => {
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const r = await
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const r = await resolveTool(cache, id, version);
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if (isResolveError(r))
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return null;
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const ver = r.tool.version ?? version ?? "";
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@@ -1 +1 @@
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-
{"version":3,"file":"annotate-connections.js","sourceRoot":"","sources":["../../src/commands/annotate-connections.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EACL,oBAAoB,EACpB,gBAAgB,IAAI,iBAAiB,EACrC,kBAAkB,EAClB,uBAAuB,GAExB,MAAM,yCAAyC,CAAC;AAEjD,OAAO,EAAE,iBAAiB,EAAE,MAAM,6BAA6B,CAAC;AAGhE,OAAO,EAAE,gBAAgB,EAAE,MAAM,4BAA4B,CAAC;AAC9D,OAAO,EAAE,cAAc,EAAE,
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{"version":3,"file":"annotate-connections.js","sourceRoot":"","sources":["../../src/commands/annotate-connections.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EACL,oBAAoB,EACpB,gBAAgB,IAAI,iBAAiB,EACrC,kBAAkB,EAClB,uBAAuB,GAExB,MAAM,yCAAyC,CAAC;AAEjD,OAAO,EAAE,iBAAiB,EAAE,MAAM,6BAA6B,CAAC;AAGhE,OAAO,EAAE,gBAAgB,EAAE,MAAM,4BAA4B,CAAC;AAC9D,OAAO,EAAE,cAAc,EAAE,WAAW,EAAE,MAAM,mBAAmB,CAAC;AAMhE,MAAM,CAAC,KAAK,UAAU,sBAAsB,CAC1C,IAA6B,EAC7B,OAAsC,EAAE;IAExC,MAAM,KAAK,GAAG,iBAAiB,CAAC,EAAE,QAAQ,EAAE,IAAI,CAAC,QAAQ,EAAE,CAAC,CAAC;IAC7D,MAAM,KAAK,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC;IACzB,OAAO,+BAA+B,CAAC,IAAI,EAAE,KAAK,CAAC,CAAC;AACtD,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,+BAA+B,CACnD,IAA6B,EAC7B,KAAgB;IAEhB,MAAM,WAAW,GAAG,MAAM,gBAAgB,CAAC,IAAI,EAAE,KAAK,CAAC,CAAC;IACxD,MAAM,KAAK,GAAG,kBAAkB,CAAC,IAAI,EAAE,WAAW,CAAC,CAAC;IACpD,MAAM,CAAC,MAAM,CAAC,GAAG,uBAAuB,CAAC,KAAK,CAAC,CAAC;IAChD,OAAO,oBAAoB,CAAC,MAAM,CAAC,CAAC;AACtC,CAAC;AAQD;;;;;;GAMG;AACH,MAAM,CAAC,KAAK,UAAU,uCAAuC,CAC3D,IAA6B,EAC7B,KAAgB;IAKhB,MAAM,KAAK,GAAG,IAAI,GAAG,EAA4B,CAAC;IAClD,MAAM,WAAW,GAAG,MAAM,iBAAiB,CAAC,IAAI,EAAE,KAAK,EAAE,EAAE,EAAE,OAAO,EAAE,EAAE;QACtE,MAAM,CAAC,GAAG,MAAM,WAAW,CAAC,KAAK,EAAE,EAAE,EAAE,OAAO,CAAC,CAAC;QAChD,IAAI,cAAc,CAAC,CAAC,CAAC;YAAE,OAAO,IAAI,CAAC;QACnC,MAAM,GAAG,GAAG,CAAC,CAAC,IAAI,CAAC,OAAO,IAAI,OAAO,IAAI,EAAE,CAAC;QAC5C,KAAK,CAAC,GAAG,CAAC,GAAG,EAAE,IAAI,GAAG,EAAE,EAAE,EAAE,OAAO,EAAE,EAAE,EAAE,YAAY,EAAE,GAAG,EAAE,MAAM,EAAE,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC;QAC9E,OAAO,CAAC,CAAC,IAAI,CAAC;IAChB,CAAC,CAAC,CAAC;IACH,MAAM,KAAK,GAAG,kBAAkB,CAAC,IAAI,EAAE,WAAW,CAAC,CAAC;IACpD,MAAM,CAAC,MAAM,CAAC,GAAG,uBAAuB,CAAC,KAAK,CAAC,CAAC;IAChD,OAAO,EAAE,WAAW,EAAE,oBAAoB,CAAC,MAAM,CAAC,EAAE,KAAK,EAAE,CAAC;AAC9D,CAAC"}
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@@ -11,7 +11,7 @@
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* adapts the CLI's on-disk `ToolCache` to the lifted helper's `AsyncToolFetcher`.
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*/
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import { buildGetToolInfo as _buildGetToolInfo, collectToolRefs, validateConnectionsReport, } from "@galaxy-tool-util/connection-validation";
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import { isResolveError,
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import { isResolveError, resolveTool } from "./resolve-tool.js";
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export { collectToolRefs };
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export async function buildConnectionReport(data, cache) {
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const getToolInfo = await buildGetToolInfo(data, cache);
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}
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export async function buildGetToolInfo(data, cache) {
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return _buildGetToolInfo(data, async (id, version) => {
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const r = await
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const r = await resolveTool(cache, id, version);
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return isResolveError(r) ? null : r.tool;
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});
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}
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@@ -1 +1 @@
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-
{"version":3,"file":"connection-validation.js","sourceRoot":"","sources":["../../src/commands/connection-validation.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AAEH,OAAO,EACL,gBAAgB,IAAI,iBAAiB,EACrC,eAAe,EACf,yBAAyB,GAE1B,MAAM,yCAAyC,CAAC;AAIjD,OAAO,EAAE,cAAc,EAAE,
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{"version":3,"file":"connection-validation.js","sourceRoot":"","sources":["../../src/commands/connection-validation.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AAEH,OAAO,EACL,gBAAgB,IAAI,iBAAiB,EACrC,eAAe,EACf,yBAAyB,GAE1B,MAAM,yCAAyC,CAAC;AAIjD,OAAO,EAAE,cAAc,EAAE,WAAW,EAAE,MAAM,mBAAmB,CAAC;AAEhE,OAAO,EAAE,eAAe,EAAE,CAAC;AAG3B,MAAM,CAAC,KAAK,UAAU,qBAAqB,CACzC,IAA6B,EAC7B,KAAgB;IAEhB,MAAM,WAAW,GAAG,MAAM,gBAAgB,CAAC,IAAI,EAAE,KAAK,CAAC,CAAC;IACxD,OAAO,yBAAyB,CAAC,IAAI,EAAE,WAAW,CAAC,CAAC;AACtD,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,gBAAgB,CACpC,IAA6B,EAC7B,KAAgB;IAEhB,OAAO,iBAAiB,CAAC,IAAI,EAAE,KAAK,EAAE,EAAE,EAAE,OAAO,EAAE,EAAE;QACnD,MAAM,CAAC,GAAG,MAAM,WAAW,CAAC,KAAK,EAAE,EAAE,EAAE,OAAO,CAAC,CAAC;QAChD,OAAO,cAAc,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC;IAC3C,CAAC,CAAC,CAAC;AACL,CAAC"}
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{"version":3,"file":"draft-validate.d.ts","sourceRoot":"","sources":["../../src/commands/draft-validate.ts"],"names":[],"mappings":"AAuDA,OAAO,EAAwB,KAAK,aAAa,EAAE,MAAM,qBAAqB,CAAC;AAI/E,MAAM,WAAW,oBAAqB,SAAQ,aAAa;IACzD,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,UAAU,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC;IAC9B,cAAc,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC;IAClC,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,SAAS,CAAC,EAAE,OAAO,CAAC;IACpB,WAAW,CAAC,EAAE,OAAO,CAAC;CACvB;AAED,wBAAsB,gBAAgB,CACpC,QAAQ,EAAE,MAAM,EAChB,IAAI,EAAE,oBAAoB,GACzB,OAAO,CAAC,IAAI,CAAC,CA4Cf"}
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{"version":3,"file":"draft-validate.d.ts","sourceRoot":"","sources":["../../src/commands/draft-validate.ts"],"names":[],"mappings":"AAuDA,OAAO,EAAwB,KAAK,aAAa,EAAE,MAAM,qBAAqB,CAAC;AAI/E,MAAM,WAAW,oBAAqB,SAAQ,aAAa;IACzD,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,UAAU,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC;IAC9B,cAAc,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC;IAClC,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,SAAS,CAAC,EAAE,OAAO,CAAC;IACpB,WAAW,CAAC,EAAE,OAAO,CAAC;CACvB;AAED,wBAAsB,gBAAgB,CACpC,QAAQ,EAAE,MAAM,EAChB,IAAI,EAAE,oBAAoB,GACzB,OAAO,CAAC,IAAI,CAAC,CA4Cf"}
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* (class !== GalaxyWorkflowDraft, schema decode error)
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*/
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import { dirname } from "node:path";
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import { makeNodeToolCache } from "@galaxy-tool-util/core/node";
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import { buildSingleDraftValidationReport, checkStrictEncoding, checkStrictStructure, extractConcreteSubset, promoteFullyConcreteDrafts, resolveFormat, stripPlanFields, validateDraft, } from "@galaxy-tool-util/schema";
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import { decodeStructureErrors, validateFormat2Steps } from "./validate-workflow.js";
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import { makeValidationResolver } from "./resolve-tool.js";
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import { readWorkflowFile } from "./workflow-io.js";
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import { findStdoutSinkConflict, writeReportHtml, writeReportOutput } from "./report-output.js";
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import { resolveStrictOptions } from "./strict-options.js";
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// Tool-state defaults to ON (matches `gxwf validate`); --no-tool-state opts out.
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const toolStateEnabled = opts.toolState !== false;
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if (toolStateEnabled) {
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const cache =
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const { cache, service } = makeValidationResolver(opts);
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await cache.index.load();
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const expansionOpts = {
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resolver: createDefaultResolver({ workflowDirectory: dirname(filePath) }),
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};
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const stepResults = await validateFormat2Steps(trimmed, cache, "", expansionOpts);
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const stepResults = await validateFormat2Steps(trimmed, cache, "", expansionOpts, service);
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report.tool_state = {
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results: stepResults,
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summary: summarize(stepResults),
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}
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else if (opts.connections) {
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// --connections without tool-state still needs a cache to look up tools.
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const cache =
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const { cache } = makeValidationResolver(opts);
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await cache.index.load();
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report.connection_report = await buildConnectionReport(trimmed, cache);
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}
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{"version":3,"file":"draft-validate.js","sourceRoot":"","sources":["../../src/commands/draft-validate.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAiCG;AACH,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AACpC,OAAO,
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{"version":3,"file":"draft-validate.js","sourceRoot":"","sources":["../../src/commands/draft-validate.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAiCG;AACH,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AACpC,OAAO,EACL,gCAAgC,EAChC,mBAAmB,EACnB,oBAAoB,EACpB,qBAAqB,EACrB,0BAA0B,EAC1B,aAAa,EACb,eAAe,EACf,aAAa,GAOd,MAAM,0BAA0B,CAAC;AAClC,OAAO,EAAE,qBAAqB,EAAE,oBAAoB,EAAE,MAAM,wBAAwB,CAAC;AACrF,OAAO,EAAE,sBAAsB,EAAE,MAAM,mBAAmB,CAAC;AAC3D,OAAO,EAAE,gBAAgB,EAAE,MAAM,kBAAkB,CAAC;AACpD,OAAO,EAAE,sBAAsB,EAAE,eAAe,EAAE,iBAAiB,EAAE,MAAM,oBAAoB,CAAC;AAChG,OAAO,EAAE,oBAAoB,EAAsB,MAAM,qBAAqB,CAAC;AAC/E,OAAO,EAAE,qBAAqB,EAAE,MAAM,4BAA4B,CAAC;AACnE,OAAO,EAAE,qBAAqB,EAAE,MAAM,mBAAmB,CAAC;AAe1D,MAAM,CAAC,KAAK,UAAU,gBAAgB,CACpC,QAAgB,EAChB,IAA0B;IAE1B,MAAM,QAAQ,GAAG,sBAAsB,CAAC,IAAI,CAAC,CAAC;IAC9C,IAAI,QAAQ,EAAE,CAAC;QACb,OAAO,CAAC,KAAK,CAAC,QAAQ,CAAC,CAAC;QACxB,OAAO,CAAC,QAAQ,GAAG,CAAC,CAAC;QACrB,OAAO;IACT,CAAC;IAED,MAAM,IAAI,GAAG,MAAM,gBAAgB,CAAC,QAAQ,CAAC,CAAC;IAC9C,IAAI,CAAC,IAAI,EAAE,CAAC;QACV,OAAO,CAAC,QAAQ,GAAG,CAAC,CAAC;QACrB,OAAO;IACT,CAAC;IAED,MAAM,MAAM,GAAG,aAAa,CAAC,IAAI,EAAE,IAAI,CAAC,MAAM,CAAC,CAAC;IAChD,IAAI,MAAM,KAAK,QAAQ,EAAE,CAAC;QACxB,OAAO,CAAC,KAAK,CAAC,qEAAqE,CAAC,CAAC;QACrF,OAAO,CAAC,QAAQ,GAAG,CAAC,CAAC;QACrB,OAAO;IACT,CAAC;IAED,uBAAuB,CAAC,IAAI,CAAC,CAAC;IAE9B,MAAM,MAAM,GAAG,aAAa,CAAC,IAAI,CAAC,CAAC;IACnC,gFAAgF;IAChF,6EAA6E;IAC7E,2EAA2E;IAC3E,4EAA4E;IAC5E,MAAM,QAAQ,GACZ,IAAI,CAAC,QAAQ,IAAI,MAAM,CAAC,eAAe,CAAC,MAAM,KAAK,CAAC;QAClD,CAAC,CAAC,MAAM,eAAe,CAAC,QAAQ,EAAE,IAAI,EAAE,IAAI,CAAC;QAC7C,CAAC,CAAC,SAAS,CAAC;IAChB,MAAM,MAAM,GAAG,gCAAgC,CAAC,QAAQ,EAAE,MAAM,EAAE,QAAQ,CAAC,CAAC;IAE5E,IAAI,IAAI,CAAC,IAAI,EAAE,CAAC;QACd,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,SAAS,CAAC,MAAM,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,CAAC;IAC/C,CAAC;SAAM,CAAC;QACN,eAAe,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IAClC,CAAC;IAED,MAAM,iBAAiB,CAAC,sBAAsB,EAAE,MAAM,EAAE,IAAI,CAAC,CAAC;IAC9D,MAAM,eAAe,CAAC,gBAAgB,EAAE,MAAM,EAAE,IAAI,CAAC,UAAU,CAAC,CAAC;IAEjE,OAAO,CAAC,QAAQ,GAAG,WAAW,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAC;AACnD,CAAC;AAED,SAAS,uBAAuB,CAAC,IAA0B;IACzD,IAAI,IAAI,CAAC,QAAQ,EAAE,CAAC;QAClB,IAAI,IAAI,CAAC,SAAS,KAAK,KAAK,IAAI,IAAI,CAAC,WAAW,EAAE,CAAC;YACjD,OAAO,CAAC,KAAK,CACX,gGAAgG,CACjG,CAAC;QACJ,CAAC;QACD,OAAO;IACT,CAAC;IACD,MAAM,OAAO,GAAa,EAAE,CAAC;IAC7B,IAAI,IAAI,CAAC,QAAQ;QAAE,OAAO,CAAC,IAAI,CAAC,aAAa,CAAC,CAAC;IAC/C,IAAI,IAAI,CAAC,SAAS,KAAK,KAAK;QAAE,OAAO,CAAC,IAAI,CAAC,iBAAiB,CAAC,CAAC;IAC9D,IAAI,IAAI,CAAC,WAAW;QAAE,OAAO,CAAC,IAAI,CAAC,eAAe,CAAC,CAAC;IACpD,IAAI,IAAI,CAAC,MAAM,IAAI,IAAI,CAAC,eAAe,IAAI,IAAI,CAAC,cAAc,IAAI,IAAI,CAAC,WAAW,EAAE,CAAC;QACnF,OAAO,CAAC,IAAI,CAAC,WAAW,CAAC,CAAC;IAC5B,CAAC;IACD,IAAI,OAAO,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QACvB,OAAO,CAAC,KAAK,CAAC,YAAY,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,uCAAuC,CAAC,CAAC;IACvF,CAAC;AACH,CAAC;AAED,KAAK,UAAU,eAAe,CAC5B,QAAgB,EAChB,IAA6B,EAC7B,IAA0B;IAE1B,MAAM,OAAO,GAAG,qBAAqB,CAAC,IAAI,CAAC,CAAC;IAC5C,eAAe,CAAC,OAAO,CAAC,QAAQ,CAAC,CAAC;IAClC,0BAA0B,CAAC,OAAO,CAAC,QAAQ,CAAC,CAAC;IAE7C,MAAM,OAAO,GACX,OAAO,CAAC,QAAQ,IAAI,IAAI,IAAI,OAAO,OAAO,CAAC,QAAQ,KAAK,QAAQ;QAC9D,CAAC,CAAE,OAAO,CAAC,QAAoC;QAC/C,CAAC,CAAC,EAAE,CAAC;IACT,MAAM,WAAW,GACf,OAAO,CAAC,KAAK,KAAK,gBAAgB,CAAC,CAAC,CAAC,gBAAgB,CAAC,CAAC,CAAC,qBAAqB,CAAC;IAEhF,uEAAuE;IACvE,2EAA2E;IAC3E,2EAA2E;IAC3E,0EAA0E;IAC1E,4EAA4E;IAC5E,IAAI,WAAW,KAAK,gBAAgB,EAAE,CAAC;QACrC,OAAO;YACL,WAAW;YACX,cAAc,EAAE,wDAAwD;YACxE,gBAAgB,EAAE,EAAE;YACpB,oEAAoE;YACpE,uEAAuE;YACvE,oCAAoC;YACpC,EAAE,EAAE,IAAI;SACT,CAAC;IACJ,CAAC;IAED,MAAM,MAAM,GAAG,oBAAoB,CAAC,IAAI,CAAC,CAAC;IAE1C,MAAM,MAAM,GAA6B;QACvC,WAAW;QACX,cAAc,EAAE,IAAI;QACpB,gBAAgB,EAAE,qBAAqB,CAAC,OAAO,EAAE,SAAS,CAAC;QAC3D,EAAE,EAAE,IAAI;KACT,CAAC;IAEF,IAAI,MAAM,CAAC,eAAe,EAAE,CAAC;QAC3B,MAAM,CAAC,uBAAuB,GAAG,oBAAoB,CAAC,OAAO,EAAE,SAAS,CAAC,CAAC;IAC5E,CAAC;IACD,IAAI,MAAM,CAAC,cAAc,EAAE,CAAC;QAC1B,MAAM,CAAC,sBAAsB,GAAG,mBAAmB,CAAC,OAAO,EAAE,SAAS,CAAC,CAAC;IAC1E,CAAC;IAED,iFAAiF;IACjF,MAAM,gBAAgB,GAAG,IAAI,CAAC,SAAS,KAAK,KAAK,CAAC;IAClD,IAAI,gBAAgB,EAAE,CAAC;QACrB,MAAM,EAAE,KAAK,EAAE,OAAO,EAAE,GAAG,sBAAsB,CAAC,IAAI,CAAC,CAAC;QACxD,MAAM,KAAK,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC;QACzB,MAAM,aAAa,GAAqB;YACtC,QAAQ,EAAE,qBAAqB,CAAC,EAAE,iBAAiB,EAAE,OAAO,CAAC,QAAQ,CAAC,EAAE,CAAC;SAC1E,CAAC;QACF,MAAM,WAAW,GAAG,MAAM,oBAAoB,CAAC,OAAO,EAAE,KAAK,EAAE,EAAE,EAAE,aAAa,EAAE,OAAO,CAAC,CAAC;QAC3F,MAAM,CAAC,UAAU,GAAG;YAClB,OAAO,EAAE,WAAW;YACpB,OAAO,EAAE,SAAS,CAAC,WAAW,CAAC;SAChC,CAAC;QACF,IAAI,MAAM,CAAC,WAAW,EAAE,CAAC;YACvB,MAAM,OAAO,GAAG,WAAW,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,MAAM,KAAK,IAAI,IAAI,CAAC,CAAC,MAAM,KAAK,MAAM,CAAC,CAAC;YACpF,MAAM,CAAC,mBAAmB,GAAG,OAAO,CAAC,GAAG,CACtC,CAAC,CAAC,EAAE,EAAE,CAAC,GAAG,CAAC,CAAC,IAAI,KAAK,CAAC,CAAC,OAAO,IAAI,GAAG,eAAe,CAAC,CAAC,MAAM,GAAG,CAChE,CAAC;QACJ,CAAC;QAED,IAAI,IAAI,CAAC,WAAW,EAAE,CAAC;YACrB,MAAM,CAAC,iBAAiB,GAAG,MAAM,qBAAqB,CAAC,OAAO,EAAE,KAAK,CAAC,CAAC;QACzE,CAAC;IACH,CAAC;SAAM,IAAI,IAAI,CAAC,WAAW,EAAE,CAAC;QAC5B,yEAAyE;QACzE,MAAM,EAAE,KAAK,EAAE,GAAG,sBAAsB,CAAC,IAAI,CAAC,CAAC;QAC/C,MAAM,KAAK,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC;QACzB,MAAM,CAAC,iBAAiB,GAAG,MAAM,qBAAqB,CAAC,OAAO,EAAE,KAAK,CA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|
|
@@ -1,4 +1,4 @@
|
|
|
1
|
-
import { type ToolCache } from "@galaxy-tool-util/core";
|
|
1
|
+
import { type ToolCache, type ToolInfoService } from "@galaxy-tool-util/core";
|
|
2
2
|
import type { ParsedTool } from "@galaxy-tool-util/schema";
|
|
3
3
|
export interface ResolvedTool {
|
|
4
4
|
tool: ParsedTool;
|
|
@@ -11,7 +11,36 @@ export type ResolveError = {
|
|
|
11
11
|
kind: "not_cached";
|
|
12
12
|
toolId: string;
|
|
13
13
|
key: string;
|
|
14
|
+
fetchAttempted?: boolean;
|
|
14
15
|
};
|
|
15
16
|
export declare function isResolveError(r: ResolvedTool | ResolveError): r is ResolveError;
|
|
16
|
-
|
|
17
|
+
/** Human-readable reason a tool failed to resolve, for skip messages. */
|
|
18
|
+
export declare function describeResolveError(err: ResolveError): string;
|
|
19
|
+
/**
|
|
20
|
+
* Resolve a tool to its parsed metadata and cache key. With a fetch `service`,
|
|
21
|
+
* the service reads the cache and fetches+caches on miss (it owns the key).
|
|
22
|
+
* Without a service, performs a network-free cache read. The passed `cache` is
|
|
23
|
+
* only consulted in the offline branch — online, the service's own cache is
|
|
24
|
+
* authoritative, so the two can never diverge.
|
|
25
|
+
*/
|
|
26
|
+
export declare function resolveTool(cache: ToolCache, toolId: string, version?: string | null, service?: ToolInfoService): Promise<ResolvedTool | ResolveError>;
|
|
27
|
+
/** Options shared by validation commands for resolving (and optionally fetching) tools. */
|
|
28
|
+
export interface ValidationFetchOptions {
|
|
29
|
+
cacheDir?: string;
|
|
30
|
+
/** Skip the network: read only the local cache (uncached tools are skipped). */
|
|
31
|
+
offline?: boolean;
|
|
32
|
+
/** Extra Galaxy instance tried as a tool source after the ToolShed. */
|
|
33
|
+
galaxyUrl?: string;
|
|
34
|
+
}
|
|
35
|
+
export interface ValidationResolver {
|
|
36
|
+
cache: ToolCache;
|
|
37
|
+
/** Present unless `offline` — fetches and caches tools missing locally. */
|
|
38
|
+
service?: ToolInfoService;
|
|
39
|
+
}
|
|
40
|
+
/**
|
|
41
|
+
* Build the cache (and, unless `offline`, the fetch service) for tool-state
|
|
42
|
+
* validation. When fetching is on, validation reads `service.cache` so freshly
|
|
43
|
+
* fetched tools are visible without a disk round-trip.
|
|
44
|
+
*/
|
|
45
|
+
export declare function makeValidationResolver(opts: ValidationFetchOptions): ValidationResolver;
|
|
17
46
|
//# sourceMappingURL=resolve-tool.d.ts.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"resolve-tool.d.ts","sourceRoot":"","sources":["../../src/commands/resolve-tool.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,SAAS,EAAY,MAAM,wBAAwB,CAAC;
|
|
1
|
+
{"version":3,"file":"resolve-tool.d.ts","sourceRoot":"","sources":["../../src/commands/resolve-tool.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,SAAS,EAAE,KAAK,eAAe,EAAY,MAAM,wBAAwB,CAAC;AAExF,OAAO,KAAK,EAAE,UAAU,EAAE,MAAM,0BAA0B,CAAC;AAE3D,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,CAAC;IAAC,cAAc,CAAC,EAAE,OAAO,CAAA;CAAE,CAAC;AAElF,wBAAgB,cAAc,CAAC,CAAC,EAAE,YAAY,GAAG,YAAY,GAAG,CAAC,IAAI,YAAY,CAEhF;AAED,yEAAyE;AACzE,wBAAgB,oBAAoB,CAAC,GAAG,EAAE,YAAY,GAAG,MAAM,CAK9D;AAED;;;;;;GAMG;AACH,wBAAsB,WAAW,CAC/B,KAAK,EAAE,SAAS,EAChB,MAAM,EAAE,MAAM,EACd,OAAO,CAAC,EAAE,MAAM,GAAG,IAAI,EACvB,OAAO,CAAC,EAAE,eAAe,GACxB,OAAO,CAAC,YAAY,GAAG,YAAY,CAAC,CAStC;AAcD,2FAA2F;AAC3F,MAAM,WAAW,sBAAsB;IACrC,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,gFAAgF;IAChF,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,uEAAuE;IACvE,SAAS,CAAC,EAAE,MAAM,CAAC;CACpB;AAED,MAAM,WAAW,kBAAkB;IACjC,KAAK,EAAE,SAAS,CAAC;IACjB,2EAA2E;IAC3E,OAAO,CAAC,EAAE,eAAe,CAAC;CAC3B;AAED;;;;GAIG;AACH,wBAAgB,sBAAsB,CAAC,IAAI,EAAE,sBAAsB,GAAG,kBAAkB,CAMvF"}
|
|
@@ -1,17 +1,52 @@
|
|
|
1
1
|
import { cacheKey } from "@galaxy-tool-util/core";
|
|
2
|
+
import { makeNodeToolCache, makeNodeToolInfoService } from "@galaxy-tool-util/core/node";
|
|
2
3
|
export function isResolveError(r) {
|
|
3
4
|
return "kind" in r;
|
|
4
5
|
}
|
|
5
|
-
|
|
6
|
+
/** Human-readable reason a tool failed to resolve, for skip messages. */
|
|
7
|
+
export function describeResolveError(err) {
|
|
8
|
+
if (err.kind === "no_version")
|
|
9
|
+
return `no version for ${err.toolId}`;
|
|
10
|
+
return err.fetchAttempted
|
|
11
|
+
? `${err.toolId} not in cache (fetch failed)`
|
|
12
|
+
: `${err.toolId} not in cache`;
|
|
13
|
+
}
|
|
14
|
+
/**
|
|
15
|
+
* Resolve a tool to its parsed metadata and cache key. With a fetch `service`,
|
|
16
|
+
* the service reads the cache and fetches+caches on miss (it owns the key).
|
|
17
|
+
* Without a service, performs a network-free cache read. The passed `cache` is
|
|
18
|
+
* only consulted in the offline branch — online, the service's own cache is
|
|
19
|
+
* authoritative, so the two can never diverge.
|
|
20
|
+
*/
|
|
21
|
+
export async function resolveTool(cache, toolId, version, service) {
|
|
22
|
+
if (service) {
|
|
23
|
+
const resolved = await service.resolveTool(toolId, version ?? null);
|
|
24
|
+
if (resolved !== null)
|
|
25
|
+
return resolved;
|
|
26
|
+
return notCached(cache, toolId, version, true);
|
|
27
|
+
}
|
|
28
|
+
const hit = await cache.loadByToolId(toolId, version ?? null);
|
|
29
|
+
if (hit !== null)
|
|
30
|
+
return hit;
|
|
31
|
+
return notCached(cache, toolId, version, false);
|
|
32
|
+
}
|
|
33
|
+
async function notCached(cache, toolId, version, fetchAttempted) {
|
|
6
34
|
const coords = cache.resolveToolCoordinates(toolId, version);
|
|
7
|
-
if (coords.version === null)
|
|
35
|
+
if (coords.version === null)
|
|
8
36
|
return { kind: "no_version", toolId };
|
|
9
|
-
}
|
|
10
37
|
const key = await cacheKey(coords.toolshedUrl, coords.trsToolId, coords.version);
|
|
11
|
-
|
|
12
|
-
|
|
13
|
-
|
|
38
|
+
return { kind: "not_cached", toolId, key, fetchAttempted };
|
|
39
|
+
}
|
|
40
|
+
/**
|
|
41
|
+
* Build the cache (and, unless `offline`, the fetch service) for tool-state
|
|
42
|
+
* validation. When fetching is on, validation reads `service.cache` so freshly
|
|
43
|
+
* fetched tools are visible without a disk round-trip.
|
|
44
|
+
*/
|
|
45
|
+
export function makeValidationResolver(opts) {
|
|
46
|
+
if (opts.offline) {
|
|
47
|
+
return { cache: makeNodeToolCache({ cacheDir: opts.cacheDir }) };
|
|
14
48
|
}
|
|
15
|
-
|
|
49
|
+
const service = makeNodeToolInfoService({ cacheDir: opts.cacheDir, galaxyUrl: opts.galaxyUrl });
|
|
50
|
+
return { cache: service.cache, service };
|
|
16
51
|
}
|
|
17
52
|
//# sourceMappingURL=resolve-tool.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"resolve-tool.js","sourceRoot":"","sources":["../../src/commands/resolve-tool.ts"],"names":[],"mappings":"AAAA,OAAO,
|
|
1
|
+
{"version":3,"file":"resolve-tool.js","sourceRoot":"","sources":["../../src/commands/resolve-tool.ts"],"names":[],"mappings":"AAAA,OAAO,EAAwC,QAAQ,EAAE,MAAM,wBAAwB,CAAC;AACxF,OAAO,EAAE,iBAAiB,EAAE,uBAAuB,EAAE,MAAM,6BAA6B,CAAC;AAYzF,MAAM,UAAU,cAAc,CAAC,CAA8B;IAC3D,OAAO,MAAM,IAAI,CAAC,CAAC;AACrB,CAAC;AAED,yEAAyE;AACzE,MAAM,UAAU,oBAAoB,CAAC,GAAiB;IACpD,IAAI,GAAG,CAAC,IAAI,KAAK,YAAY;QAAE,OAAO,kBAAkB,GAAG,CAAC,MAAM,EAAE,CAAC;IACrE,OAAO,GAAG,CAAC,cAAc;QACvB,CAAC,CAAC,GAAG,GAAG,CAAC,MAAM,8BAA8B;QAC7C,CAAC,CAAC,GAAG,GAAG,CAAC,MAAM,eAAe,CAAC;AACnC,CAAC;AAED;;;;;;GAMG;AACH,MAAM,CAAC,KAAK,UAAU,WAAW,CAC/B,KAAgB,EAChB,MAAc,EACd,OAAuB,EACvB,OAAyB;IAEzB,IAAI,OAAO,EAAE,CAAC;QACZ,MAAM,QAAQ,GAAG,MAAM,OAAO,CAAC,WAAW,CAAC,MAAM,EAAE,OAAO,IAAI,IAAI,CAAC,CAAC;QACpE,IAAI,QAAQ,KAAK,IAAI;YAAE,OAAO,QAAQ,CAAC;QACvC,OAAO,SAAS,CAAC,KAAK,EAAE,MAAM,EAAE,OAAO,EAAE,IAAI,CAAC,CAAC;IACjD,CAAC;IACD,MAAM,GAAG,GAAG,MAAM,KAAK,CAAC,YAAY,CAAC,MAAM,EAAE,OAAO,IAAI,IAAI,CAAC,CAAC;IAC9D,IAAI,GAAG,KAAK,IAAI;QAAE,OAAO,GAAG,CAAC;IAC7B,OAAO,SAAS,CAAC,KAAK,EAAE,MAAM,EAAE,OAAO,EAAE,KAAK,CAAC,CAAC;AAClD,CAAC;AAED,KAAK,UAAU,SAAS,CACtB,KAAgB,EAChB,MAAc,EACd,OAAkC,EAClC,cAAuB;IAEvB,MAAM,MAAM,GAAG,KAAK,CAAC,sBAAsB,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;IAC7D,IAAI,MAAM,CAAC,OAAO,KAAK,IAAI;QAAE,OAAO,EAAE,IAAI,EAAE,YAAY,EAAE,MAAM,EAAE,CAAC;IACnE,MAAM,GAAG,GAAG,MAAM,QAAQ,CAAC,MAAM,CAAC,WAAW,EAAE,MAAM,CAAC,SAAS,EAAE,MAAM,CAAC,OAAO,CAAC,CAAC;IACjF,OAAO,EAAE,IAAI,EAAE,YAAY,EAAE,MAAM,EAAE,GAAG,EAAE,cAAc,EAAE,CAAC;AAC7D,CAAC;AAiBD;;;;GAIG;AACH,MAAM,UAAU,sBAAsB,CAAC,IAA4B;IACjE,IAAI,IAAI,CAAC,OAAO,EAAE,CAAC;QACjB,OAAO,EAAE,KAAK,EAAE,iBAAiB,CAAC,EAAE,QAAQ,EAAE,IAAI,CAAC,QAAQ,EAAE,CAAC,EAAE,CAAC;IACnE,CAAC;IACD,MAAM,OAAO,GAAG,uBAAuB,CAAC,EAAE,QAAQ,EAAE,IAAI,CAAC,QAAQ,EAAE,SAAS,EAAE,IAAI,CAAC,SAAS,EAAE,CAAC,CAAC;IAChG,OAAO,EAAE,KAAK,EAAE,OAAO,CAAC,KAAK,EAAE,OAAO,EAAE,CAAC;AAC3C,CAAC"}
|
package/dist/commands/schema.js
CHANGED
|
@@ -2,7 +2,7 @@ import { makeNodeToolCache } from "@galaxy-tool-util/core/node";
|
|
|
2
2
|
import { createFieldModel, STATE_REPRESENTATIONS, } from "@galaxy-tool-util/schema";
|
|
3
3
|
import * as JSONSchema from "effect/JSONSchema";
|
|
4
4
|
import { writeFile } from "node:fs/promises";
|
|
5
|
-
import { isResolveError,
|
|
5
|
+
import { isResolveError, resolveTool } from "./resolve-tool.js";
|
|
6
6
|
export async function runSchema(toolId, opts) {
|
|
7
7
|
const repName = opts.representation ?? "workflow_step";
|
|
8
8
|
if (!STATE_REPRESENTATIONS.includes(repName)) {
|
|
@@ -13,7 +13,7 @@ export async function runSchema(toolId, opts) {
|
|
|
13
13
|
const stateRep = repName;
|
|
14
14
|
const cache = makeNodeToolCache({ cacheDir: opts.cacheDir });
|
|
15
15
|
await cache.index.load();
|
|
16
|
-
const result = await
|
|
16
|
+
const result = await resolveTool(cache, toolId, opts.toolVersion);
|
|
17
17
|
if (isResolveError(result)) {
|
|
18
18
|
if (result.kind === "no_version") {
|
|
19
19
|
console.error(`No version specified for tool: ${toolId}`);
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"schema.js","sourceRoot":"","sources":["../../src/commands/schema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,iBAAiB,EAAE,MAAM,6BAA6B,CAAC;AAChE,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,
|
|
1
|
+
{"version":3,"file":"schema.js","sourceRoot":"","sources":["../../src/commands/schema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,iBAAiB,EAAE,MAAM,6BAA6B,CAAC;AAChE,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,WAAW,EAAE,MAAM,mBAAmB,CAAC;AAShE,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,iBAAiB,CAAC,EAAE,QAAQ,EAAE,IAAI,CAAC,QAAQ,EAAE,CAAC,CAAC;IAC7D,MAAM,KAAK,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC;IACzB,MAAM,MAAM,GAAG,MAAM,WAAW,CAAC,KAAK,EAAE,MAAM,EAAE,IAAI,CAAC,WAAW,CAAC,CAAC;IAClE,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"}
|
|
@@ -1,5 +1,5 @@
|
|
|
1
1
|
import { expandedFormat2, expandedNative, } from "@galaxy-tool-util/schema";
|
|
2
|
-
import { isResolveError,
|
|
2
|
+
import { isResolveError, resolveTool } from "./resolve-tool.js";
|
|
3
3
|
function toolKey(toolId, version) {
|
|
4
4
|
return `${toolId}\0${version ?? ""}`;
|
|
5
5
|
}
|
|
@@ -18,7 +18,7 @@ export async function loadToolInputsForWorkflow(data, format, cache, expansionOp
|
|
|
18
18
|
const key = toolKey(toolId, version);
|
|
19
19
|
if (loaded.has(key))
|
|
20
20
|
continue;
|
|
21
|
-
const resolved = await
|
|
21
|
+
const resolved = await resolveTool(cache, toolId, version);
|
|
22
22
|
if (isResolveError(resolved)) {
|
|
23
23
|
const reason = resolved.kind === "no_version" ? `no version for ${toolId}` : `${toolId} not in cache`;
|
|
24
24
|
status.push({ toolId, toolVersion: version, loaded: false, error: reason });
|
|
@@ -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,GASf,MAAM,0BAA0B,CAAC;AAClC,OAAO,EAAE,cAAc,EAAE,
|
|
1
|
+
{"version":3,"file":"stateful-tool-inputs.js","sourceRoot":"","sources":["../../src/commands/stateful-tool-inputs.ts"],"names":[],"mappings":"AAeA,OAAO,EACL,eAAe,EACf,cAAc,GASf,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,EAAE,CAAC;gBAC7C,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"}
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@@ -3,7 +3,7 @@ import { writeFile } from "node:fs/promises";
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3
3
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import { getCacheDir, makeNodeToolCache } from "@galaxy-tool-util/core/node";
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import { createFieldModel, } from "@galaxy-tool-util/schema";
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import * as JSONSchema from "effect/JSONSchema";
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-
import { isResolveError,
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+
import { isResolveError, resolveTool } from "./resolve-tool.js";
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function sourceKind(label) {
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if (label === "api")
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return "toolshed";
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@@ -32,7 +32,7 @@ export async function buildToolSummaryManifest(toolId, opts) {
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await cache.index.load();
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const result = await
|
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+
const result = await resolveTool(cache, toolId, opts.toolVersion);
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if (result.kind === "no_version") {
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console.error(`No version specified for tool: ${toolId}`);
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@@ -1 +1 @@
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1
|
-
{"version":3,"file":"summarize.js","sourceRoot":"","sources":["../../src/commands/summarize.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,IAAI,EAAE,MAAM,WAAW,CAAC;AACjC,OAAO,EAAE,SAAS,EAAE,MAAM,kBAAkB,CAAC;AAC7C,OAAO,EAAE,WAAW,EAAE,iBAAiB,EAAE,MAAM,6BAA6B,CAAC;AAC7E,OAAO,EACL,gBAAgB,GAIjB,MAAM,0BAA0B,CAAC;AAClC,OAAO,KAAK,UAAU,MAAM,mBAAmB,CAAC;AAChD,OAAO,EAAE,cAAc,EAAE,
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1
|
+
{"version":3,"file":"summarize.js","sourceRoot":"","sources":["../../src/commands/summarize.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,IAAI,EAAE,MAAM,WAAW,CAAC;AACjC,OAAO,EAAE,SAAS,EAAE,MAAM,kBAAkB,CAAC;AAC7C,OAAO,EAAE,WAAW,EAAE,iBAAiB,EAAE,MAAM,6BAA6B,CAAC;AAC7E,OAAO,EACL,gBAAgB,GAIjB,MAAM,0BAA0B,CAAC;AAClC,OAAO,KAAK,UAAU,MAAM,mBAAmB,CAAC;AAChD,OAAO,EAAE,cAAc,EAAE,WAAW,EAAE,MAAM,mBAAmB,CAAC;AA+BhE,SAAS,UAAU,CAAC,KAAyB;IAC3C,IAAI,KAAK,KAAK,KAAK;QAAE,OAAO,UAAU,CAAC;IACvC,IAAI,KAAK,KAAK,QAAQ,IAAI,KAAK,KAAK,OAAO,IAAI,KAAK,KAAK,QAAQ;QAAE,OAAO,KAAK,CAAC;IAChF,OAAO,SAAS,CAAC;AACnB,CAAC;AAED,SAAS,cAAc,CACrB,IAAgB,EAChB,GAAwB,EACxB,QAAkB;IAElB,MAAM,MAAM,GAA6B;QACvC,UAAU,EAAE,IAAI,CAAC,MAAgD;KAClE,CAAC;IACF,MAAM,YAAY,GAAG,gBAAgB,CAAC,MAAM,EAAE,GAAG,CAAC,CAAC;IACnD,IAAI,YAAY,KAAK,SAAS,EAAE,CAAC;QAC/B,QAAQ,CAAC,IAAI,CAAC,GAAG,GAAG,oDAAoD,CAAC,CAAC;QAC1E,OAAO,IAAI,CAAC;IACd,CAAC;IACD,IAAI,CAAC;QACH,OAAO,UAAU,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC;IACvC,CAAC;IAAC,OAAO,GAAG,EAAE,CAAC;QACb,QAAQ,CAAC,IAAI,CACX,GAAG,GAAG,oCAAoC,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,EAAE,CAC7F,CAAC;QACF,OAAO,IAAI,CAAC;IACd,CAAC;AACH,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,wBAAwB,CAC5C,MAAc,EACd,IAAsB;IAEtB,MAAM,QAAQ,GAAG,WAAW,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC;IAC5C,MAAM,KAAK,GAAG,iBAAiB,CAAC,EAAE,QAAQ,EAAE,CAAC,CAAC;IAC9C,MAAM,KAAK,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC;IACzB,MAAM,MAAM,GAAG,MAAM,WAAW,CAAC,KAAK,EAAE,MAAM,EAAE,IAAI,CAAC,WAAW,CAAC,CAAC;IAClE,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,IAAI,CAAC;IACd,CAAC;IAED,MAAM,UAAU,GAAG,CAAC,MAAM,KAAK,CAAC,KAAK,CAAC,OAAO,EAAE,CAAC,CAAC,IAAI,CAAC,CAAC,KAAK,EAAE,EAAE,CAAC,KAAK,CAAC,SAAS,KAAK,MAAM,CAAC,GAAG,CAAC,CAAC;IACjG,MAAM,QAAQ,GAAa,EAAE,CAAC;IAC9B,MAAM,QAAQ,GAA8B;QAC1C,cAAc,EAAE,CAAC;QACjB,OAAO,EAAE,MAAM,CAAC,IAAI,CAAC,EAAE;QACvB,YAAY,EAAE,MAAM,CAAC,IAAI,CAAC,OAAO;QACjC,SAAS,EAAE,MAAM,CAAC,GAAG;QACrB,MAAM,EAAE;YACN,IAAI,EAAE,UAAU,CAAC,UAAU,EAAE,MAAM,CAAC;YACpC,KAAK,EAAE,UAAU,EAAE,MAAM,IAAI,SAAS;YACtC,GAAG,EAAE,UAAU,EAAE,UAAU,IAAI,EAAE;YACjC,SAAS,EAAE,UAAU,EAAE,SAAS,IAAI,IAAI;SACzC;QACD,SAAS,EAAE;YACT,gBAAgB,EAAE,IAAI,CAAC,QAAQ,EAAE,GAAG,MAAM,CAAC,GAAG,OAAO,CAAC;YACtD,oBAAoB,EAAE,IAAI;SAC3B;QACD,WAAW,EAAE,MAAM,CAAC,IAAI;QACxB,aAAa,EAAE;YACb,aAAa,EAAE,cAAc,CAAC,MAAM,CAAC,IAAI,EAAE,eAAe,EAAE,QAAQ,CAAC;YACrE,oBAAoB,EAAE,cAAc,CAAC,MAAM,CAAC,IAAI,EAAE,sBAAsB,EAAE,QAAQ,CAAC;SACpF;QACD,QAAQ;KACT,CAAC;IACF,OAAO,QAAQ,CAAC;AAClB,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,YAAY,CAAC,MAAc,EAAE,IAAsB;IACvE,MAAM,QAAQ,GAAG,MAAM,wBAAwB,CAAC,MAAM,EAAE,IAAI,CAAC,CAAC;IAC9D,IAAI,QAAQ,KAAK,IAAI;QAAE,OAAO;IAC9B,MAAM,MAAM,GAAG,GAAG,IAAI,CAAC,SAAS,CAAC,QAAQ,EAAE,IAAI,EAAE,CAAC,CAAC,IAAI,CAAC;IACxD,IAAI,IAAI,CAAC,MAAM,EAAE,CAAC;QAChB,MAAM,SAAS,CAAC,IAAI,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;QACrC,OAAO,CAAC,GAAG,CAAC,sBAAsB,IAAI,CAAC,MAAM,EAAE,CAAC,CAAC;IACnD,CAAC;SAAM,CAAC;QACN,OAAO,CAAC,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC;IAC/B,CAAC;AACH,CAAC"}
|
|
@@ -15,7 +15,7 @@ import { readFileSync, existsSync } from "node:fs";
|
|
|
15
15
|
import { join } from "node:path";
|
|
16
16
|
import { buildSingleValidationReport, SKIP_STATUSES, nativeConnectionsFromFormat2In, } from "@galaxy-tool-util/schema";
|
|
17
17
|
import { isEmptyState } from "./validate-workflow.js";
|
|
18
|
-
import { isResolveError,
|
|
18
|
+
import { isResolveError, resolveTool } from "./resolve-tool.js";
|
|
19
19
|
const Ajv = Ajv2020.default ?? Ajv2020;
|
|
20
20
|
// Recursively drop `$id` keys. Effect's JSONSchema.make inlines unknown/any
|
|
21
21
|
// params as `{$id: "/schemas/unknown", title: "unknown"}` (and `/schemas/any`)
|
|
@@ -261,7 +261,7 @@ async function _validateNativeWorkflowJsonSchema(wf, cache, toolSchemaDir, prefi
|
|
|
261
261
|
return results;
|
|
262
262
|
}
|
|
263
263
|
async function _validateNativeStepJsonSchema(step, stepLabel, toolId, toolVersion, cache, toolSchemaDir) {
|
|
264
|
-
const resolved = await
|
|
264
|
+
const resolved = await resolveTool(cache, toolId, toolVersion);
|
|
265
265
|
if (isResolveError(resolved)) {
|
|
266
266
|
const reason = resolved.kind === "no_version" ? `no version for ${toolId}` : `${toolId} not in cache`;
|
|
267
267
|
return {
|
|
@@ -348,7 +348,7 @@ async function _validateFormat2WorkflowJsonSchema(wf, cache, toolSchemaDir, pref
|
|
|
348
348
|
return results;
|
|
349
349
|
}
|
|
350
350
|
async function _validateFormat2StepJsonSchema(step, stepLabel, toolId, toolVersion, cache, toolSchemaDir) {
|
|
351
|
-
const resolved = await
|
|
351
|
+
const resolved = await resolveTool(cache, toolId, toolVersion);
|
|
352
352
|
if (isResolveError(resolved)) {
|
|
353
353
|
const reason = resolved.kind === "no_version" ? `no version for ${toolId}` : `${toolId} not in cache`;
|
|
354
354
|
return {
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
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BACd,MAAM,EAAE,eAAe,CAAC,cAAc,CAAC;aACxC,CAAC;QACJ,CAAC;IACH,CAAC;IAED,OAAO,EAAE,IAAI,EAAE,SAAS,EAAE,OAAO,EAAE,MAAM,EAAE,OAAO,EAAE,WAAW,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,EAAE,EAAE,EAAE,CAAC;AAC9F,CAAC"}
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@@ -1,4 +1,4 @@
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1
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-
import type { ToolCache } from "@galaxy-tool-util/core";
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1
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+
import type { ToolCache, ToolInfoService } from "@galaxy-tool-util/core";
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2
2
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import { type ExpansionOptions, type WorkflowFormat } from "@galaxy-tool-util/schema";
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3
3
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import { type StrictOptions } from "./strict-options.js";
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4
4
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export type { WorkflowFormat } from "@galaxy-tool-util/schema";
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@@ -7,6 +7,8 @@ export interface ValidateWorkflowOptions extends StrictOptions {
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7
7
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format?: string;
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8
8
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toolState?: boolean;
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9
9
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cacheDir?: string;
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10
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+
offline?: boolean;
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11
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+
galaxyUrl?: string;
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10
12
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mode?: ValidationMode;
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11
13
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toolSchemaDir?: string;
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12
14
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json?: boolean;
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@@ -20,8 +22,8 @@ export declare function decodeStructureErrors(data: Record<string, unknown>, for
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20
22
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export type { ValidationStepResult as StepValidationResult } from "@galaxy-tool-util/schema";
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21
23
|
import type { ValidationStepResult as StepValidationResult } from "@galaxy-tool-util/schema";
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22
24
|
export declare function runValidateWorkflow(filePath: string, opts: ValidateWorkflowOptions): Promise<void>;
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23
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-
export declare function validateNativeSteps(data: Record<string, unknown>, cache: ToolCache, prefix?: string, expansionOpts?: ExpansionOptions): Promise<StepValidationResult[]>;
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24
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-
export declare function validateFormat2Steps(data: Record<string, unknown>, cache: ToolCache, prefix?: string, expansionOpts?: ExpansionOptions): Promise<StepValidationResult[]>;
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25
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+
export declare function validateNativeSteps(data: Record<string, unknown>, cache: ToolCache, prefix?: string, expansionOpts?: ExpansionOptions, service?: ToolInfoService): Promise<StepValidationResult[]>;
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26
|
+
export declare function validateFormat2Steps(data: Record<string, unknown>, cache: ToolCache, prefix?: string, expansionOpts?: ExpansionOptions, service?: ToolInfoService): Promise<StepValidationResult[]>;
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25
27
|
/**
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26
28
|
* Detect legacy parameter encoding in workflow tool_state fields.
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27
29
|
*
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"validate-workflow.d.ts","sourceRoot":"","sources":["../../src/commands/validate-workflow.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;
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+
{"version":3,"file":"validate-workflow.d.ts","sourceRoot":"","sources":["../../src/commands/validate-workflow.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,SAAS,EAAE,eAAe,EAAE,MAAM,wBAAwB,CAAC;AACzE,OAAO,EAoBL,KAAK,gBAAgB,EACrB,KAAK,cAAc,EACpB,MAAM,0BAA0B,CAAC;AAalC,OAAO,EAAwB,KAAK,aAAa,EAAE,MAAM,qBAAqB,CAAC;AAK/E,YAAY,EAAE,cAAc,EAAE,MAAM,0BAA0B,CAAC;AAE/D,MAAM,MAAM,cAAc,GAAG,QAAQ,GAAG,aAAa,CAAC;AAEtD,MAAM,WAAW,uBAAwB,SAAQ,aAAa;IAC5D,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,SAAS,CAAC,EAAE,OAAO,CAAC;IACpB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,IAAI,CAAC,EAAE,cAAc,CAAC;IACtB,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,UAAU,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC;IAC9B,WAAW,CAAC,EAAE,OAAO,CAAC;CACvB;AAOD,gHAAgH;AAChH,wBAAgB,YAAY,CAAC,KAAK,EAAE,OAAO,GAAG,OAAO,CAEpD;AAED,2FAA2F;AAC3F,wBAAgB,qBAAqB,CACnC,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC7B,MAAM,EAAE,cAAc,GACrB,MAAM,EAAE,CAaV;AAED,YAAY,EAAE,oBAAoB,IAAI,oBAAoB,EAAE,MAAM,0BAA0B,CAAC;AAG7F,OAAO,KAAK,EAAE,oBAAoB,IAAI,oBAAoB,EAAE,MAAM,0BAA0B,CAAC;AAE7F,wBAAsB,mBAAmB,CACvC,QAAQ,EAAE,MAAM,EAChB,IAAI,EAAE,uBAAuB,GAC5B,OAAO,CAAC,IAAI,CAAC,CAmJf;AAwBD,wBAAsB,mBAAmB,CACvC,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC7B,KAAK,EAAE,SAAS,EAChB,MAAM,SAAK,EACX,aAAa,CAAC,EAAE,gBAAgB,EAChC,OAAO,CAAC,EAAE,eAAe,GACxB,OAAO,CAAC,oBAAoB,EAAE,CAAC,CAGjC;AAwID,wBAAsB,oBAAoB,CACxC,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC7B,KAAK,EAAE,SAAS,EAChB,MAAM,SAAK,EACX,aAAa,CAAC,EAAE,gBAAgB,EAChC,OAAO,CAAC,EAAE,eAAe,GACxB,OAAO,CAAC,oBAAoB,EAAE,CAAC,CAGjC;AAsKD;;;;;GAKG;AACH,wBAAsB,oBAAoB,CACxC,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC7B,KAAK,EAAE,SAAS,EAChB,MAAM,EAAE,cAAc,EACtB,aAAa,CAAC,EAAE,gBAAgB,GAC/B,OAAO,CAAC,MAAM,EAAE,CAAC,CAOnB"}
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1
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import { makeNodeToolCache } from "@galaxy-tool-util/core/node";
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import { createFieldModel, GalaxyWorkflowSchema, NativeGalaxyWorkflowSchema, expandedNative, expandedFormat2, injectConnectionsIntoState, stripConnectedValues, nativeConnectionsFromFormat2In, scanForReplacements, checkStrictEncoding, checkStrictStructure, withClass, scanToolState, buildSingleValidationReport, } from "@galaxy-tool-util/schema";
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import * as ParseResult from "effect/ParseResult";
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import * as S from "effect/Schema";
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import { isResolveError,
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import { isResolveError, resolveTool, describeResolveError, makeValidationResolver, } from "./resolve-tool.js";
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import { renderStepResults } from "./render-results.js";
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import { readWorkflowFile, resolveFormat } from "./workflow-io.js";
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@@ -104,16 +103,16 @@ export async function runValidateWorkflow(filePath, opts) {
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process.exitCode = structOk ? 0 : 1;
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return;
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const cache =
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results = await validateNativeSteps(data, cache, "", expansionOpts);
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results = await validateFormat2Steps(data, cache, "", expansionOpts);
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export async function validateNativeSteps(data, cache, prefix = "", expansionOpts) {
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export async function validateNativeSteps(data, cache, prefix = "", expansionOpts, service) {
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const expanded = await expandedNative(data, expansionOpts);
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return _validateNativeWorkflow(expanded, cache, prefix);
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return _validateNativeWorkflow(expanded, cache, prefix, service);
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async function _validateNativeWorkflow(wf, cache, prefix) {
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async function _validateNativeWorkflow(wf, cache, prefix, service) {
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const subResults = await _validateNativeWorkflow(step.subworkflow, cache, `${stepLabel}
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const subResults = await _validateNativeWorkflow(step.subworkflow, cache, `${stepLabel}.`, service);
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|
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async function _validateNativeStep(step, stepLabel, toolId, toolVersion, cache) {
|
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|
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const resolved = await
|
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|
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async function _validateNativeStep(step, stepLabel, toolId, toolVersion, cache, service) {
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|
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const resolved = await resolveTool(cache, toolId, toolVersion, service);
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|
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|
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const reason = resolved
|
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|
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|
step: stepLabel,
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@@ -280,18 +279,18 @@ function _validateNativeState(bundle, toolState, connections, stepLabel, toolId,
|
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|
return { step: stepLabel, tool_id: toolId, version: toolVersion, status: "ok", errors: [] };
|
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|
}
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|
// --- Format2 validation ---
|
|
283
|
-
export async function validateFormat2Steps(data, cache, prefix = "", expansionOpts) {
|
|
282
|
+
export async function validateFormat2Steps(data, cache, prefix = "", expansionOpts, service) {
|
|
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283
|
const expanded = await expandedFormat2(data, expansionOpts);
|
|
285
|
-
return _validateFormat2Workflow(expanded, cache, prefix);
|
|
284
|
+
return _validateFormat2Workflow(expanded, cache, prefix, service);
|
|
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285
|
}
|
|
287
|
-
async function _validateFormat2Workflow(wf, cache, prefix) {
|
|
286
|
+
async function _validateFormat2Workflow(wf, cache, prefix, service) {
|
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|
const results = [];
|
|
289
288
|
for (let i = 0; i < wf.steps.length; i++) {
|
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|
const step = wf.steps[i];
|
|
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|
const stepLabel = prefix ? `${prefix}${i}` : String(i);
|
|
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|
// Recurse into inline subworkflows
|
|
293
292
|
if (step.run && typeof step.run === "object") {
|
|
294
|
-
const subResults = await _validateFormat2Workflow(step.run, cache, `${stepLabel}
|
|
293
|
+
const subResults = await _validateFormat2Workflow(step.run, cache, `${stepLabel}.`, service);
|
|
295
294
|
results.push(...subResults);
|
|
296
295
|
continue;
|
|
297
296
|
}
|
|
@@ -299,15 +298,15 @@ async function _validateFormat2Workflow(wf, cache, prefix) {
|
|
|
299
298
|
if (!toolId)
|
|
300
299
|
continue;
|
|
301
300
|
const toolVersion = step.tool_version ?? null;
|
|
302
|
-
const result = await _validateFormat2Step(step, stepLabel, toolId, toolVersion, cache);
|
|
301
|
+
const result = await _validateFormat2Step(step, stepLabel, toolId, toolVersion, cache, service);
|
|
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302
|
results.push(result);
|
|
304
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|
}
|
|
305
304
|
return results;
|
|
306
305
|
}
|
|
307
|
-
async function _validateFormat2Step(step, stepLabel, toolId, toolVersion, cache) {
|
|
308
|
-
const resolved = await
|
|
306
|
+
async function _validateFormat2Step(step, stepLabel, toolId, toolVersion, cache, service) {
|
|
307
|
+
const resolved = await resolveTool(cache, toolId, toolVersion, service);
|
|
309
308
|
if (isResolveError(resolved)) {
|
|
310
|
-
const reason = resolved
|
|
309
|
+
const reason = describeResolveError(resolved);
|
|
311
310
|
return {
|
|
312
311
|
step: stepLabel,
|
|
313
312
|
tool_id: toolId,
|
|
@@ -432,7 +431,7 @@ async function _detectNativeEncodingErrors(wf, cache, prefix) {
|
|
|
432
431
|
const toolId = step.tool_id;
|
|
433
432
|
if (!toolId)
|
|
434
433
|
continue;
|
|
435
|
-
const resolved = await
|
|
434
|
+
const resolved = await resolveTool(cache, toolId, step.tool_version ?? null);
|
|
436
435
|
if (isResolveError(resolved))
|
|
437
436
|
continue;
|
|
438
437
|
const inputs = resolved.tool.inputs;
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
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+
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|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@galaxy-tool-util/cli",
|
|
3
|
-
"version": "1.
|
|
3
|
+
"version": "1.10.1",
|
|
4
4
|
"description": "galaxy-tool-cache CLI — cache and inspect Galaxy tool metadata",
|
|
5
5
|
"type": "module",
|
|
6
6
|
"bin": {
|
|
@@ -39,10 +39,10 @@
|
|
|
39
39
|
"effect": "^3.21.0",
|
|
40
40
|
"nunjucks": "^3.2.4",
|
|
41
41
|
"yaml": "^2.8.3",
|
|
42
|
-
"@galaxy-tool-util/connection-validation": "1.
|
|
43
|
-
"@galaxy-tool-util/core": "1.
|
|
44
|
-
"@galaxy-tool-util/schema": "1.
|
|
45
|
-
"@galaxy-tool-util/search": "1.
|
|
42
|
+
"@galaxy-tool-util/connection-validation": "1.10.1",
|
|
43
|
+
"@galaxy-tool-util/core": "1.10.1",
|
|
44
|
+
"@galaxy-tool-util/schema": "1.10.1",
|
|
45
|
+
"@galaxy-tool-util/search": "1.10.1"
|
|
46
46
|
},
|
|
47
47
|
"devDependencies": {
|
|
48
48
|
"@types/node": "^25.5.0",
|
package/spec/gxwf.json
CHANGED
|
@@ -46,6 +46,14 @@
|
|
|
46
46
|
"flags": "--cache-dir <dir>",
|
|
47
47
|
"description": "Tool cache directory"
|
|
48
48
|
},
|
|
49
|
+
{
|
|
50
|
+
"flags": "--offline",
|
|
51
|
+
"description": "Do not fetch uncached tools; read only the local cache (uncached tools are skipped)"
|
|
52
|
+
},
|
|
53
|
+
{
|
|
54
|
+
"flags": "--galaxy-url <url>",
|
|
55
|
+
"description": "Galaxy instance to try as a tool source after the ToolShed when fetching uncached tools"
|
|
56
|
+
},
|
|
49
57
|
{
|
|
50
58
|
"flags": "--mode <mode>",
|
|
51
59
|
"description": "Validation backend: effect (default) or json-schema",
|
|
@@ -126,6 +134,14 @@
|
|
|
126
134
|
"flags": "--cache-dir <dir>",
|
|
127
135
|
"description": "Tool cache directory (for --concrete tool-state validation)"
|
|
128
136
|
},
|
|
137
|
+
{
|
|
138
|
+
"flags": "--offline",
|
|
139
|
+
"description": "Do not fetch uncached tools; read only the local cache (uncached tools are skipped)"
|
|
140
|
+
},
|
|
141
|
+
{
|
|
142
|
+
"flags": "--galaxy-url <url>",
|
|
143
|
+
"description": "Galaxy instance to try as a tool source after the ToolShed when fetching uncached tools"
|
|
144
|
+
},
|
|
129
145
|
{
|
|
130
146
|
"flags": "--no-tool-state",
|
|
131
147
|
"description": "Skip tool-state validation in the --concrete pass (default: enabled when --concrete is set)"
|