mirna_precursor_converter
Convert between miRNA names and precursor names to support microRNA enrichment analysis and identifier management in bioinformatics workflows.
Instructions
Convert between miRNA names and precursor names.
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| input | Yes | ||
| direction | Yes |
Implementation Reference
- MiEAAMirnaPrecursorConverterHandler class with run() method implementing the tool logic: POST to miEAA API with form data, retry on 429, parse tab-separated text response into structured MCP output.export class MiEAAMirnaPrecursorConverterHandler { async run(args: { ids: string[]; direction: "mirna_to_precursor" | "precursor_to_mirna"; }) { const { ids, direction } = args; if (!ids || ids.length === 0) { throw new Error("ids must be a non-empty array"); } const url = "https://ccb-compute2.cs.uni-saarland.de/mieaa/api/v1/mirna_precursor_converter/"; /** * miEAA web-form compatible mapping * (IMPORTANT: these values are NOT documented in the API) */ const input_type = direction === "mirna_to_precursor" ? "to_precursor" : "to_mirna"; const params = new URLSearchParams(); // miEAA expects repeated "mirnas" fields ids.forEach(id => params.append("mirnas", id)); params.append("input_type", input_type); params.append("conversion_type", "all"); params.append("output_format", "tabsep"); let res: any = null; // retry logic for HTTP 429 for (let attempt = 1; attempt <= 5; attempt++) { res = await fetch(url, { method: "POST", headers: { "Content-Type": "application/x-www-form-urlencoded" }, body: params.toString() }); if (res.status !== 429) break; await sleep(1500 * attempt); } if (!res || !res.ok) { const errorText = await res?.text(); throw new Error( `Conversion failed (${res?.status}): ${errorText}` ); } /** * miEAA returns PLAIN TEXT, not JSON * Format: * input<TAB>output1;output2 */ const text: string = await res.text(); const input_label = direction === "mirna_to_precursor" ? "mirna" : "precursor"; const output_label = direction === "mirna_to_precursor" ? "precursor" : "mirna"; const results = text .trim() .split("\n") .filter(Boolean) .map((line: string) => { const [input, output] = line.split(/\t+/); return { input, output: output ? output.split(";") : [] }; }); const payload = { input_type: input_label, output_type: output_label, direction, results }; // MCP tool result (clean + spec-correct) return { content: [ { type: "text", text: JSON.stringify(payload) } ], structuredContent: payload }; } }
- src/server.ts:138-154 (schema)Input schema for mirna_precursor_converter tool defined in ListToolsRequestHandler response.// miRNA ↔ PRECURSOR CONVERTER // ------------------------------------------------- { name: "mirna_precursor_converter", description: "Convert between miRNA names and precursor names.", inputSchema: { type: "object", properties: { input: { type: "array", items: { type: "string" } }, direction: { type: "string", enum: ["mirna_to_precursor", "precursor_to_mirna"] } }, required: ["input", "direction"] } },
- src/server.ts:51-51 (registration)Instantiation of MiEAAMirnaPrecursorConverterHandler as mirnaPrecursorTool.const mirnaPrecursorTool = new MiEAAMirnaPrecursorConverterHandler();
- src/server.ts:207-215 (registration)Dispatch logic in CallToolRequestHandler: calls mirnaPrecursorTool.run() for mirna_precursor_converter, mapping input args.// -------------------------------------------------- // miRNA ↔ PRECURSOR CONVERTER // -------------------------------------------------- if (name === "mirna_precursor_converter") { return await mirnaPrecursorTool.run({ ids: (args as any).input, direction: (args as any).direction }); }
- src/server.ts:16-16 (registration)Import of the handler class.import { MiEAAMirnaPrecursorConverterHandler } from "./handlers/mieaa_mirna_precursor_converter_handler.js";