WormBase MCP Server

Instructions

Implementation Reference

• src/index.ts:132-153 (registration)

  MCP server.tool registration for the 'get_strain' tool, defining its name, description, input schema, and inline handler function.

  // Tool: Get Strain Information
  server.tool(
    "get_strain",
    "Get information about a C. elegans strain including genotype, available from, and associated phenotypes.",
    {
      id: z.string().describe("Strain identifier - strain name (e.g., 'N2', 'CB1370')"),
      widgets: z.array(z.string()).optional().describe("Specific widgets to fetch: overview, phenotypes, references"),
    },
    async ({ id, widgets }) => {
      try {
        const data = await client.getEntity("strain", id, widgets);
        return {
          content: [{ type: "text", text: JSON.stringify(data, null, 2) }],
        };
      } catch (error) {
        return {
          content: [{ type: "text", text: `Error fetching strain: ${error}` }],
          isError: true,
        };
      }
    }
  );

• src/index.ts:136-139 (schema)

  Zod input schema for the get_strain tool: required 'id' string and optional 'widgets' array.

  {
    id: z.string().describe("Strain identifier - strain name (e.g., 'N2', 'CB1370')"),
    widgets: z.array(z.string()).optional().describe("Specific widgets to fetch: overview, phenotypes, references"),
  },

• src/index.ts:140-152 (handler)

  Inline handler function for get_strain tool that calls WormBaseClient.getEntity("strain", id, widgets) and formats the response as text content or error.

  async ({ id, widgets }) => {
    try {
      const data = await client.getEntity("strain", id, widgets);
      return {
        content: [{ type: "text", text: JSON.stringify(data, null, 2) }],
      };
    } catch (error) {
      return {
        content: [{ type: "text", text: `Error fetching strain: ${error}` }],
        isError: true,
      };
    }
  }

• src/client.ts:111-132 (helper)

  WormBaseClient.getEntity generic helper method used by the handler to fetch widget data from WormBase REST API for the 'strain' entity type.

  async getEntity(
    type: EntityType,
    id: string,
    widgets?: string[]
  ): Promise<Record<string, unknown>> {
    const defaultWidgets = ["overview"];
    const requestedWidgets = widgets || defaultWidgets;
  
    const result: Record<string, unknown> = { id, type };
  
    for (const widget of requestedWidgets) {
      try {
        const url = `${this.baseUrl}/rest/widget/${type}/${encodeURIComponent(id)}/${widget}`;
        const data = await this.fetch<any>(url);
        result[widget] = this.cleanWidgetData(data);
      } catch (error) {
        result[widget] = { error: `Failed to fetch ${widget}` };
      }
    }
  
    return result;
  }