@cyanheads/pubmed-mcp-server/dist/services/NCBI/core/ncbiService.js

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

/**
 * @fileoverview Service for interacting with NCBI E-utilities.
 * This module centralizes all communication with NCBI's E-utility APIs,
 * handling request construction, API key management, rate limiting,
 * retries, and parsing of XML/JSON responses. It aims to provide a robust
 * and compliant interface for other parts of the pubmed-mcp-server to
 * access PubMed data.
 * @module src/services/NCBI/core/ncbiService
 */
import { logger, requestContextService, } from "../../../utils/index.js";
import { NcbiCoreApiClient } from "./ncbiCoreApiClient.js";
import { NcbiRequestQueueManager } from "./ncbiRequestQueueManager.js";
import { NcbiResponseHandler } from "./ncbiResponseHandler.js";
export class NcbiService {
    queueManager;
    apiClient;
    responseHandler;
    constructor() {
        this.queueManager = new NcbiRequestQueueManager();
        this.apiClient = new NcbiCoreApiClient();
        this.responseHandler = new NcbiResponseHandler();
    }
    async performNcbiRequest(endpoint, params, context, options = {}) {
        const task = async () => {
            const rawResponse = await this.apiClient.makeRequest(endpoint, params, context, options);
            return this.responseHandler.parseAndHandleResponse(rawResponse, endpoint, context, options);
        };
        return this.queueManager.enqueueRequest(task, context, endpoint, params);
    }
    async eSearch(params, context) {
        const response = await this.performNcbiRequest("esearch", params, context, {
            retmode: "xml",
        });
        const esResult = response.eSearchResult;
        return {
            count: parseInt(esResult.Count, 10) || 0,
            retmax: parseInt(esResult.RetMax, 10) || 0,
            retstart: parseInt(esResult.RetStart, 10) || 0,
            queryKey: esResult.QueryKey,
            webEnv: esResult.WebEnv,
            idList: esResult.IdList?.Id || [],
            queryTranslation: esResult.QueryTranslation,
            errorList: esResult.ErrorList,
            warningList: esResult.WarningList,
        };
    }
    async eSummary(params, context) {
        // Determine retmode based on params, default to xml
        const retmode = params.version === "2.0" && params.retmode === "json" ? "json" : "xml";
        return this.performNcbiRequest("esummary", params, context, { retmode });
    }
    async eFetch(params, context, options = { retmode: "xml" }) {
        // Determine if POST should be used based on number of IDs
        const usePost = typeof params.id === "string" && params.id.split(",").length > 200;
        const fetchOptions = { ...options, usePost };
        return this.performNcbiRequest("efetch", params, context, fetchOptions);
    }
    async eLink(params, context) {
        return this.performNcbiRequest("elink", params, context, {
            retmode: "xml",
        });
    }
    async eInfo(params, context) {
        return this.performNcbiRequest("einfo", params, context, {
            retmode: "xml",
        });
    }
}
let ncbiServiceInstance;
export function getNcbiService() {
    if (!ncbiServiceInstance) {
        ncbiServiceInstance = new NcbiService();
        logger.debug("NcbiService lazily initialized.", requestContextService.createRequestContext({
            service: "NcbiService",
            operation: "getNcbiServiceInstance",
        }));
    }
    return ncbiServiceInstance;
}
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