@galaxy-tool-util/core 1.10.1 → 1.13.1

package/dist/tool-info.js

@@ -1,7 +1,10 @@
 import { DEFAULT_TOOL_VERSION, ToolCache } from "./cache/tool-cache.js";
 import { cacheKey } from "./cache/cache-key.js";
 import { fetchFromToolShed, fetchFromGalaxy } from "./client/toolshed.js";
+import { ToolFetchError } from "./client/toolshed.js";
+import { fetchToolSourceFromGalaxy, fetchToolSourceFromToolShed } from "./client/tool-source.js";
 import { getLatestTRSToolVersion } from "./client/trs.js";
+import { ignoreDiagnostic } from "./diagnostics.js";
 /**
  * High-level service for fetching Galaxy tool metadata with automatic caching.
  * Tries configured sources in order and caches on first successful fetch.
@@ -10,12 +13,15 @@ export class ToolInfoService {
     cache;
     sources;
     fetcher;
+    onDiagnostic;
     constructor(opts) {
         this.cache = new ToolCache({
             storage: opts.storage,
             defaultToolshedUrl: opts.defaultToolshedUrl,
+            onDiagnostic: opts.onDiagnostic,
         });
         this.fetcher = opts.fetcher ?? globalThis.fetch;
+        this.onDiagnostic = opts.onDiagnostic ?? ignoreDiagnostic;
         if (opts.sources) {
             this.sources = opts.sources;
         }
@@ -35,6 +41,55 @@ export class ToolInfoService {
         const resolved = await this.resolveTool(toolId, toolVersion);
         return resolved === null ? null : resolved.tool;
     }
+    /** Lazy wrapper-source fetch with write-through caching, independent of parsed metadata. */
+    async fetchToolSource(toolId, toolVersion) {
+        const coords = this.cache.resolveToolCoordinates(toolId, toolVersion);
+        const keyVersion = coords.version ?? (await this.resolveLatestVersion(coords.toolshedUrl, coords.trsToolId));
+        if (keyVersion === null)
+            return null;
+        const key = await cacheKey(coords.toolshedUrl, coords.trsToolId, keyVersion);
+        const cached = await this.cache.loadToolSource(key);
+        if (cached !== null)
+            return cached;
+        let fetchVersion = keyVersion;
+        if (keyVersion === DEFAULT_TOOL_VERSION) {
+            const parsed = await this.cache.loadCached(key);
+            fetchVersion =
+                parsed?.version ??
+                    (await this.resolveLatestVersion(coords.toolshedUrl, coords.trsToolId)) ??
+                    DEFAULT_TOOL_VERSION;
+        }
+        let failure;
+        for (const source of this.sources) {
+            let document;
+            try {
+                document =
+                    source.type === "toolshed"
+                        ? await fetchToolSourceFromToolShed(source.url, coords.trsToolId, fetchVersion, this.fetcher)
+                        : await fetchToolSourceFromGalaxy(source.url, coords.trsToolId.includes("~") ? coords.readableId : toolId, fetchVersion === DEFAULT_TOOL_VERSION ? null : fetchVersion, this.fetcher);
+            }
+            catch (err) {
+                this.onDiagnostic(`${source.type} source fetch failed (${source.url}) for ${coords.trsToolId}: ${err}`);
+                if (!(err instanceof ToolFetchError) || err.statusCode !== 404)
+                    failure = err;
+                continue;
+            }
+            try {
+                await this.cache.saveToolSource(key, document);
+                // Source-only entries must participate in cache deletion and prefix clearing.
+                if (!(await this.cache.index.has(key))) {
+                    await this.cache.index.add(key, coords.readableId, fetchVersion, source.type === "toolshed" ? "api" : "galaxy", source.url);
+                }
+            }
+            catch (err) {
+                this.onDiagnostic(`Failed to cache fetched tool source ${coords.trsToolId}: ${err}`);
+            }
+            return document;
+        }
+        if (failure !== undefined)
+            throw failure;
+        return null;
+    }
     /**
      * Like {@link getToolInfo}, but also returns the cache key the tool lives under
      * — the authoritative key this service caches with. Callers needing the key
@@ -51,7 +106,7 @@ export class ToolInfoService {
             // ToolShed tool without a pin — must resolve a concrete version before we can key it.
             const resolved = await this.resolveLatestVersion(coords.toolshedUrl, coords.trsToolId);
             if (resolved === null) {
-                console.debug(`No version available for tool: ${toolId}`);
+                this.onDiagnostic(`No version available for tool: ${toolId}`);
                 return null;
             }
             keyVersion = resolved;
@@ -73,10 +128,10 @@ export class ToolInfoService {
         }
         // Try each source in order
         for (const source of this.sources) {
+            let parsedTool;
+            let sourceLabel;
+            let sourceUrl;
             try {
-                let parsedTool;
-                let sourceLabel;
-                let sourceUrl;
                 if (source.type === "toolshed") {
                     parsedTool = await fetchFromToolShed(source.url, coords.trsToolId, fetchVersion, this.fetcher);
                     sourceLabel = "api";
@@ -87,17 +142,23 @@ export class ToolInfoService {
                     sourceLabel = "galaxy";
                     sourceUrl = `${source.url}/api/tools/${encodeURIComponent(toolId)}/parsed`;
                 }
-                // Key under `keyVersion` (may be `_default_`); record the concrete version the
-                // body reports (falling back to `fetchVersion`) as the index/display version so
-                // `list` surfaces it.
-                const indexVersion = parsedTool.version ?? fetchVersion;
+            }
+            catch (err) {
+                const msg = err instanceof Error ? err.message : String(err);
+                this.onDiagnostic(`${source.type} fetch failed (${source.url}) for ${coords.trsToolId}: ${msg}`);
+                continue;
+            }
+            // A cache failure must not discard an otherwise valid remote response.
+            // Report it separately and still return the fetched tool to the caller.
+            const indexVersion = parsedTool.version ?? fetchVersion;
+            try {
                 await this.cache.saveTool(key, parsedTool, coords.readableId, indexVersion, sourceLabel, sourceUrl);
-                return { tool: parsedTool, key };
             }
             catch (err) {
                 const msg = err instanceof Error ? err.message : String(err);
-                console.debug(`${source.type} fetch failed (${source.url}) for ${coords.trsToolId}: ${msg}`);
+                this.onDiagnostic(`Failed to cache fetched tool ${coords.trsToolId} version ${indexVersion}: ${msg}`);
             }
+            return { tool: parsedTool, key };
         }
         return null;
     }
@@ -111,7 +172,7 @@ export class ToolInfoService {
         }
         catch (err) {
             const msg = err instanceof Error ? err.message : String(err);
-            console.debug(`TRS latest-version lookup failed for ${trsToolId} on ${toolshedUrl}: ${msg}`);
+            this.onDiagnostic(`TRS latest-version lookup failed for ${trsToolId} on ${toolshedUrl}: ${msg}`);
             return null;
         }
     }
@@ -125,7 +186,10 @@ export class ToolInfoService {
      */
     async refetch(toolId, toolVersion, opts) {
         const coords = this.cache.resolveToolCoordinates(toolId, toolVersion ?? null);
-        const resolvedVersion = coords.version;
+        let resolvedVersion = coords.version;
+        if (opts?.force && resolvedVersion === null) {
+            resolvedVersion = await this.resolveLatestVersion(coords.toolshedUrl, coords.trsToolId);
+        }
         let alreadyCached = false;
         if (resolvedVersion !== null) {
             alreadyCached = await this.cache.hasCached(toolId, resolvedVersion);
@@ -134,7 +198,7 @@ export class ToolInfoService {
             const key = await cacheKey(coords.toolshedUrl, coords.trsToolId, resolvedVersion);
             return { cacheKey: key, fetched: false, alreadyCached: true };
         }
-        if (alreadyCached && opts?.force && resolvedVersion !== null) {
+        if (opts?.force && resolvedVersion !== null) {
             const key = await cacheKey(coords.toolshedUrl, coords.trsToolId, resolvedVersion);
             await this.cache.removeCached(key);
         }
@@ -148,12 +212,6 @@ export class ToolInfoService {
         // (coords.version); an unpinned ToolShed tool (coords.version === null) keys by
         // the resolved version. Must not key a stock tool by tool.version — its entry
         // lives under the `_default_` key, not `~<version>`.
-        //
-        // Known edge (tracked): a stock entry is keyed under `_default_` but its index/display
-        // version is the concrete one (e.g. `1.1.1`). A caller that refetches by the *display*
-        // version (gxwf-web inspector does) passes `1.1.1`, misses the `_default_` key, and
-        // writes a duplicate sibling instead of refreshing. Unreachable until the shed's TRS
-        // version-list endpoint is healthy; fix needs the request version persisted in the index.
         const keyVersion = coords.version ?? tool.version ?? "unknown";
         const key = await cacheKey(coords.toolshedUrl, coords.trsToolId, keyVersion);
         return { cacheKey: key, fetched: true, alreadyCached };

package/dist/tool-info.js.map

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package/dist/tool-source.d.ts

@@ -0,0 +1,9 @@
+/** A serialized wrapper document, as returned by Galaxy or the Tool Shed. */
+export interface ToolSourceDocument {
+    contents: string;
+    language: "xml" | "yaml" | "json" | "cwl" | "text";
+    /** XML serializers return the macro-expanded tree; other formats have no XML macros. */
+    macrosExpanded: boolean;
+}
+export declare function isToolSourceDocument(value: unknown): value is ToolSourceDocument;
+//# sourceMappingURL=tool-source.d.ts.map

package/dist/tool-source.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"tool-source.d.ts","sourceRoot":"","sources":["../src/tool-source.ts"],"names":[],"mappings":"AAAA,6EAA6E;AAC7E,MAAM,WAAW,kBAAkB;IACjC,QAAQ,EAAE,MAAM,CAAC;IACjB,QAAQ,EAAE,KAAK,GAAG,MAAM,GAAG,MAAM,GAAG,KAAK,GAAG,MAAM,CAAC;IACnD,wFAAwF;IACxF,cAAc,EAAE,OAAO,CAAC;CACzB;AAED,wBAAgB,oBAAoB,CAAC,KAAK,EAAE,OAAO,GAAG,KAAK,IAAI,kBAAkB,CAQhF"}

package/dist/tool-source.js

@@ -0,0 +1,9 @@
+export function isToolSourceDocument(value) {
+    if (value === null || typeof value !== "object")
+        return false;
+    const source = value;
+    return (typeof source.contents === "string" &&
+        ["xml", "yaml", "json", "cwl", "text"].includes(source.language) &&
+        typeof source.macrosExpanded === "boolean");
+}
+//# sourceMappingURL=tool-source.js.map

package/dist/tool-source.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"tool-source.js","sourceRoot":"","sources":["../src/tool-source.ts"],"names":[],"mappings":"AAQA,MAAM,UAAU,oBAAoB,CAAC,KAAc;IACjD,IAAI,KAAK,KAAK,IAAI,IAAI,OAAO,KAAK,KAAK,QAAQ;QAAE,OAAO,KAAK,CAAC;IAC9D,MAAM,MAAM,GAAG,KAA2B,CAAC;IAC3C,OAAO,CACL,OAAO,MAAM,CAAC,QAAQ,KAAK,QAAQ;QACnC,CAAC,KAAK,EAAE,MAAM,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,CAAC,CAAC,QAAQ,CAAC,MAAM,CAAC,QAAQ,CAAC;QAChE,OAAO,MAAM,CAAC,cAAc,KAAK,SAAS,CAC3C,CAAC;AACJ,CAAC"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@galaxy-tool-util/core",
-  "version": "1.10.1",
+  "version": "1.13.1",
   "description": "Galaxy tool cache, ToolShed client, and ParsedTool models",
   "type": "module",
   "sideEffects": false,
@@ -37,7 +37,7 @@
   "dependencies": {
     "effect": "^3.21.0",
     "yaml": "^2.8.3",
-    "@galaxy-tool-util/schema": "1.10.1"
+    "@galaxy-tool-util/schema": "1.13.1"
   },
   "scripts": {
     "build": "tsc",