agr-mcp-server 4.0.0 → 4.0.1

package/dist/client.d.ts

@@ -50,12 +50,9 @@ export declare class AllianceClient {
      */
     searchAlleles(query: string, limit?: number): Promise<SearchResponse>;
     /**
-     * Get list of supported species
+     * Get list of supported species from API
      */
-    getSpeciesList(): Array<{
-        name: Species;
-        shortName: string;
-    }>;
+    getSpeciesList(): Promise<unknown>;
     /**
      * Helper to resolve species short name
      */

package/dist/client.js

@@ -51,9 +51,8 @@ export class AllianceClient {
                     id: r.id,
                     symbol: r.symbol,
                     name: r.name || r.name_key || r.id,
-                    species: r.species?.name,
+                    species: r.species,
                     category: r.category,
-                    description: r.highlights?.description?.[0],
                     highlights: r.highlights,
                 })),
                 total: response.total,
@@ -202,22 +201,29 @@ export class AllianceClient {
         return this.search(query, "allele", undefined, limit);
     }
     /**
-     * Get list of supported species
+     * Get list of supported species from API
      */
-    getSpeciesList() {
-        // Return hardcoded list of Alliance model organisms
-        const speciesList = [
-            { name: "Homo sapiens", shortName: "human" },
-            { name: "Mus musculus", shortName: "mouse" },
-            { name: "Rattus norvegicus", shortName: "rat" },
-            { name: "Danio rerio", shortName: "zebrafish" },
-            { name: "Drosophila melanogaster", shortName: "fly" },
-            { name: "Caenorhabditis elegans", shortName: "worm" },
-            { name: "Saccharomyces cerevisiae", shortName: "yeast" },
-            { name: "Xenopus laevis", shortName: "frog" },
-            { name: "Xenopus tropicalis", shortName: "xenopus" },
-        ];
-        return speciesList;
+    async getSpeciesList() {
+        const url = `${this.agrApiUrl}/api/species`;
+        try {
+            return await this.fetch(url);
+        }
+        catch {
+            // Fallback to hardcoded list
+            return {
+                results: [
+                    { name: "Homo sapiens", shortName: "Hsa", commonNames: ["human"] },
+                    { name: "Mus musculus", shortName: "Mmu", commonNames: ["mouse"] },
+                    { name: "Rattus norvegicus", shortName: "Rno", commonNames: ["rat"] },
+                    { name: "Danio rerio", shortName: "Dre", commonNames: ["zebrafish"] },
+                    { name: "Drosophila melanogaster", shortName: "Dme", commonNames: ["fly"] },
+                    { name: "Caenorhabditis elegans", shortName: "Cel", commonNames: ["worm"] },
+                    { name: "Saccharomyces cerevisiae", shortName: "Sce", commonNames: ["yeast"] },
+                    { name: "Xenopus tropicalis", shortName: "Xtr", commonNames: ["xenopus"] },
+                ],
+                total: 8,
+            };
+        }
     }
     /**
      * Helper to resolve species short name

package/dist/index.js

@@ -220,17 +220,9 @@ server.tool("search_alleles", "Search for alleles/variants in the Alliance datab
 // Tool: Get Species List
 server.tool("get_species_list", "Get list of model organisms supported by Alliance of Genome Resources.", {}, async () => {
     try {
-        const species = client.getSpeciesList();
+        const data = await client.getSpeciesList();
         return {
-            content: [
-                {
-                    type: "text",
-                    text: JSON.stringify({
-                        description: "Model organisms in the Alliance of Genome Resources",
-                        species,
-                    }, null, 2),
-                },
-            ],
+            content: [{ type: "text", text: JSON.stringify(data, null, 2) }],
         };
     }
     catch (error) {
@@ -259,18 +251,18 @@ server.resource("entity-types", "agr://entity-types", async () => ({
     ],
 }));
 // Resource: Species
-server.resource("species", "agr://species", async () => ({
-    contents: [
-        {
-            uri: "agr://species",
-            mimeType: "application/json",
-            text: JSON.stringify({
-                description: "Model organisms in Alliance of Genome Resources",
-                species: client.getSpeciesList(),
-            }, null, 2),
-        },
-    ],
-}));
+server.resource("species", "agr://species", async () => {
+    const data = await client.getSpeciesList();
+    return {
+        contents: [
+            {
+                uri: "agr://species",
+                mimeType: "application/json",
+                text: JSON.stringify(data, null, 2),
+            },
+        ],
+    };
+});
 function getEntityDescription(type) {
     const descriptions = {
         gene: "Genes across all model organisms",

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "agr-mcp-server",
-  "version": "4.0.0",
+  "version": "4.0.1",
   "description": "MCP server for Alliance of Genome Resources - access genomics data across model organisms",
   "main": "dist/index.js",
   "bin": {