@cyanheads/pubmed-mcp-server/dist/mcp-server/tools/pubmedArticleConnections/logic/index.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 Main logic handler for the 'pubmed_article_connections' MCP tool.
 * Orchestrates calls to ELink or citation formatting handlers.
 * @module src/mcp-server/tools/pubmedArticleConnections/logic/index
 */
import { z } from "zod";
import { BaseErrorCode, McpError } from "../../../../types-global/errors.js";
import { logger, requestContextService, sanitizeInputForLogging, } from "../../../../utils/index.js";
import { handleCitationFormats } from "./citationFormatter.js";
import { handleELinkRelationships } from "./elinkHandler.js";
/**
 * Zod schema for the input parameters of the 'pubmed_article_connections' tool.
 */
export const PubMedArticleConnectionsInputSchema = z.object({
    sourcePmid: z
        .string()
        .regex(/^\d+$/)
        .describe("The PubMed Unique Identifier (PMID) of the source article for which to find connections or format citations. This PMID must be a valid number string."),
    relationshipType: z
        .enum([
        "pubmed_similar_articles",
        "pubmed_citedin",
        "pubmed_references",
        "citation_formats",
    ])
        .default("pubmed_similar_articles")
        .describe("Specifies the type of connection or action: 'pubmed_similar_articles' (finds similar articles), 'pubmed_citedin' (finds citing articles), 'pubmed_references' (finds referenced articles), or 'citation_formats' (retrieves formatted citations)."),
    maxRelatedResults: z
        .number()
        .int()
        .positive()
        .max(50, "Maximum 50 related results can be requested.")
        .optional()
        .default(5)
        .describe("Maximum number of related articles to retrieve for relationship-based searches. Default is 5, max is 50."),
    citationStyles: z
        .array(z.enum(["ris", "bibtex", "apa_string", "mla_string"]))
        .optional()
        .default(["ris"])
        .describe("An array of citation styles to format the source article into when 'relationshipType' is 'citation_formats'. Supported styles: 'ris', 'bibtex', 'apa_string', 'mla_string'. Default is ['ris']."),
});
/**
 * Main handler for the 'pubmed_article_connections' tool.
 * @param {PubMedArticleConnectionsInput} input - Validated input parameters.
 * @param {RequestContext} context - The request context for this tool invocation.
 * @returns {Promise<ToolOutputData>} The result of the tool call.
 */
export async function handlePubMedArticleConnections(input, context) {
    const toolLogicContext = requestContextService.createRequestContext({
        parentRequestId: context.requestId,
        operation: "handlePubMedArticleConnections",
        toolName: "pubmed_article_connections",
        input: sanitizeInputForLogging(input),
    });
    logger.info("Executing pubmed_article_connections tool", toolLogicContext);
    const outputData = {
        sourcePmid: input.sourcePmid,
        relationshipType: input.relationshipType,
        relatedArticles: [],
        citations: {},
        retrievedCount: 0,
        eUtilityUrl: undefined,
        message: undefined,
    };
    switch (input.relationshipType) {
        case "pubmed_similar_articles":
        case "pubmed_citedin":
        case "pubmed_references":
            await handleELinkRelationships(input, outputData, toolLogicContext);
            break;
        case "citation_formats":
            await handleCitationFormats(input, outputData, toolLogicContext);
            break;
        default:
            throw new McpError(BaseErrorCode.VALIDATION_ERROR, `Unsupported relationshipType: ${input.relationshipType}`, { ...toolLogicContext, receivedType: input.relationshipType });
    }
    if (outputData.retrievedCount === 0 &&
        !outputData.message &&
        (input.relationshipType !== "citation_formats" ||
            Object.keys(outputData.citations).length === 0)) {
        outputData.message = "No results found for the given parameters.";
    }
    logger.notice("Successfully executed pubmed_article_connections tool.", {
        ...toolLogicContext,
        relationshipType: input.relationshipType,
        retrievedCount: outputData.retrievedCount,
        citationsGenerated: Object.keys(outputData.citations).length,
    });
    return outputData;
}
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