@cyanheads/pubmed-mcp-server
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Production-ready PubMed Model Context Protocol (MCP) server that empowers AI agents and research tools with comprehensive access to PubMed's article database. Enables advanced, automated LLM workflows for searching, retrieving, analyzing, and visualizing
119 lines • 5.92 kB
JavaScript
/**
* @fileoverview Core client for making HTTP requests to NCBI E-utilities.
* Handles request construction, API key injection, retries, and basic error handling.
* @module src/services/NCBI/core/ncbiCoreApiClient
*/
import axios from "axios";
import { config } from "../../../config/index.js";
import { BaseErrorCode, McpError } from "../../../types-global/errors.js";
import { logger, requestContextService, sanitizeInputForLogging, } from "../../../utils/index.js";
import { NCBI_EUTILS_BASE_URL, } from "./ncbiConstants.js";
export class NcbiCoreApiClient {
axiosInstance;
constructor() {
this.axiosInstance = axios.create({
timeout: 30000, // 30 seconds timeout for NCBI requests
});
}
/**
* Makes an HTTP request to the specified NCBI E-utility endpoint.
* Handles parameter assembly, API key injection, GET/POST selection, and retries.
* @param endpoint The E-utility endpoint (e.g., "esearch", "efetch").
* @param params The parameters for the E-utility.
* @param context The request context for logging.
* @param options Options for the request, like retmode and whether to use POST.
* @param retries The current retry attempt number.
* @returns A Promise resolving to the raw AxiosResponse.
* @throws {McpError} If the request fails after all retries or an unexpected error occurs.
*/
async makeRequest(endpoint, params, context, options = {}) {
const rawParams = {
tool: config.ncbiToolIdentifier,
email: config.ncbiAdminEmail,
api_key: config.ncbiApiKey,
...params,
};
const finalParams = {};
for (const key in rawParams) {
if (Object.prototype.hasOwnProperty.call(rawParams, key)) {
const value = rawParams[key];
if (value !== undefined && value !== null) {
finalParams[key] = String(value);
}
}
}
const requestConfig = {
method: options.usePost ? "POST" : "GET",
url: `${NCBI_EUTILS_BASE_URL}/${endpoint}.fcgi`,
};
if (options.usePost) {
requestConfig.data = new URLSearchParams(finalParams).toString();
requestConfig.headers = {
"Content-Type": "application/x-www-form-urlencoded",
};
}
else {
requestConfig.params = finalParams;
}
for (let attempt = 0; attempt <= config.ncbiMaxRetries; attempt++) {
try {
logger.debug(`Making NCBI HTTP request: ${requestConfig.method} ${requestConfig.url}`, requestContextService.createRequestContext({
...context,
operation: "NCBI_HttpRequest",
endpoint,
method: requestConfig.method,
requestParams: sanitizeInputForLogging(finalParams),
attempt: attempt + 1,
}));
const response = await this.axiosInstance(requestConfig);
return response;
}
catch (error) {
if (attempt < config.ncbiMaxRetries) {
const retryDelay = Math.pow(2, attempt) * 200;
logger.warning(`NCBI request to ${endpoint} failed. Retrying (${attempt + 1}/${config.ncbiMaxRetries}) in ${retryDelay}ms...`, requestContextService.createRequestContext({
...context,
operation: "NCBI_HttpRequestRetry",
endpoint,
error: error.message,
retryCount: attempt + 1,
maxRetries: config.ncbiMaxRetries,
delay: retryDelay,
}));
await new Promise((r) => setTimeout(r, retryDelay));
continue; // Continue to the next iteration of the loop
}
// If all retries are exhausted, handle the final error
if (axios.isAxiosError(error)) {
logger.error(`Axios error during NCBI request to ${endpoint} after ${attempt} retries`, error, requestContextService.createRequestContext({
...context,
operation: "NCBI_AxiosError",
endpoint,
status: error.response?.status,
responseData: sanitizeInputForLogging(error.response?.data),
}));
throw new McpError(BaseErrorCode.NCBI_SERVICE_UNAVAILABLE, `NCBI request failed: ${error.message}`, {
endpoint,
status: error.response?.status,
details: error.response?.data
? String(error.response.data).substring(0, 500)
: undefined,
});
}
if (error instanceof McpError)
throw error;
logger.error(`Unexpected error during NCBI request to ${endpoint} after ${attempt} retries`, error, requestContextService.createRequestContext({
...context,
operation: "NCBI_UnexpectedError",
endpoint,
errorMessage: error.message,
}));
throw new McpError(BaseErrorCode.INTERNAL_ERROR, `Unexpected error communicating with NCBI: ${error.message}`, { endpoint });
}
}
// This line should theoretically be unreachable, but it satisfies TypeScript's need
// for a return path if the loop completes without returning or throwing.
throw new McpError(BaseErrorCode.INTERNAL_ERROR, "Request failed after all retries.", { endpoint });
}
}
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