NCBI Entrez MCP Server

# Using Entrez MCP Tools from Cloudflare Code Mode Cloudflare's Code Mode runtime mounts MCP tools on a `codemode` proxy object whose keys mirror the tool names. This server now advertises underscore names (for example `tool_Z1YjsltQ_entrez_capabilities`) so `codemode.tool_Z1YjsltQ_entrez_capabilities` works with normal dot access. Legacy hyphenated aliases (such as `tool_Z1YjsltQ_entrez-capabilities`) are still available for backwards compatibility, but JavaScript parses `codemode.tool_Z1YjsltQ_entrez-capabilities` as `(codemode.tool_Z1YjsltQ_entrez) - capabilities`, which throws `ReferenceError: capabilities is not defined`. If you ever need to call the legacy alias, access it with bracket notation (e.g., `codemode["tool_Z1YjsltQ_entrez-capabilities"](args)`). The proxy object is also non-enumerable, so `Object.keys(codemode)` will not expose the available tool IDs—store the IDs you expect to use. ## Minimal Helper ```ts const TOOL_IDS = { apiKey: "tool_Z1YjsltQ_system_api_key_status", query: "tool_Z1YjsltQ_entrez_query", data: "tool_Z1YjsltQ_entrez_data", external: "tool_Z1YjsltQ_entrez_external", capabilities: "tool_Z1YjsltQ_entrez_capabilities", }; async function callTool(toolId, input) { const fn = codemode[toolId]; if (typeof fn !== "function") { throw new Error(`Tool ${toolId} is not available in this Code Mode sandbox.`); } return fn(input); } ``` Use `callTool(TOOL_IDS.query, { ... })` instead of dotted access. If you ever see the legacy hyphenated names, swap `-` for `_` in the string or switch to bracket notation. ## End-to-End Demo Snippet The following Code Mode function reproduces the “use all tools” workflow from the README by leveraging the helper above. It handles partial failures, avoids assuming array shapes, and returns a compact JSON payload. ```ts async function runNcbiWorkflow() { const TOOL_IDS = { apiKey: "tool_Z1YjsltQ_system_api_key_status", query: "tool_Z1YjsltQ_entrez_query", data: "tool_Z1YjsltQ_entrez_data", external: "tool_Z1YjsltQ_entrez_external", capabilities: "tool_Z1YjsltQ_entrez_capabilities", }; const callTool = async (toolId, input) => { const fn = codemode[toolId]; if (typeof fn !== "function") { throw new Error(`Tool ${toolId} unavailable`); } return fn(input); }; const result = { systemApiKey: {}, tools: {}, pubmed: {}, staging: {}, pubchem: {}, pmc: {}, }; // 1) API key + rate limits try { const apiStatus = await callTool(TOOL_IDS.apiKey, {}); result.systemApiKey = { present: !!apiStatus.keyPresent ?? apiStatus.present, rateLimits: apiStatus.rateLimits ?? apiStatus.rate_limit ?? apiStatus, }; } catch (error) { result.systemApiKey = { error: error.message ?? String(error) }; } // 2) Tool manifest / guidance try { const tools = await callTool(TOOL_IDS.capabilities, { format: "summary", include_metadata: false, }); result.tools = tools; } catch (error) { result.tools = { error: error.message ?? String(error) }; } // 3) PubMed search + summaries (last 7 days) let idList = []; try { const search = await callTool(TOOL_IDS.query, { operation: "search", database: "pubmed", term: "cancer immunotherapy", datetype: "pdat", reldate: 7, retmax: 3, retmode: "json", }); idList = search?.esearchresult?.idlist ?? []; let firstTitle; if (idList.length) { const summaries = await callTool(TOOL_IDS.query, { operation: "summary", database: "pubmed", ids: idList.join(","), retmode: "json", }); const uids = Array.isArray(summaries?.result?.uids) ? summaries.result.uids : Object.keys(summaries?.result ?? {}).filter((key) => key !== "uids"); if (uids.length && summaries.result[uids[0]]?.title) { firstTitle = summaries.result[uids[0]].title; } result.pubmed.summaries = { count: uids.length, firstTitle }; } result.pubmed.search = { ids: idList, count: idList.length, }; } catch (error) { result.pubmed = { error: error.message ?? String(error) }; idList = []; } // 4) Stage + SQL + smart summary try { if (idList.length) { const staged = await callTool(TOOL_IDS.data, { operation: "fetch_and_stage", database: "pubmed", ids: idList.join(","), rettype: "summary", }); const accessId = staged?.data_access_id; result.staging.status = staged?.status ?? staged?.staging_status ?? staged; if (accessId) { const sql = await callTool(TOOL_IDS.data, { operation: "query", data_access_id: accessId, sql: "SELECT COUNT(*) AS total FROM data", }); result.staging.count = Array.isArray(sql?.output) && sql.output[0]?.total !== undefined ? sql.output[0].total : sql; const summary = await callTool(TOOL_IDS.data, { operation: "query", data_access_id: accessId, smart_summary: true, max_tokens: 120, }); result.staging.smartSummary = summary?.summary ?? summary?.output ?? summary; } } else { result.staging = { error: "No IDs to stage" }; } } catch (error) { result.staging = { error: error.message ?? String(error) }; } // 5) PubChem compounds try { const fetchCompound = async (cid) => { const data = await callTool(TOOL_IDS.external, { service: "pubchem", operation: "compound", identifier: `${cid}`, identifier_type: "cid", output_format: "json", }); return { cid, raw: data }; }; const [caffeine, aspirin] = await Promise.all([ fetchCompound(2519), fetchCompound(2244), ]); result.pubchem = { caffeine, aspirin }; } catch (error) { result.pubchem = { error: error.message ?? String(error) }; } // 6) PMC metadata try { const pmc = await callTool(TOOL_IDS.external, { service: "pmc", operation: "oa_service", id: "PMC7394273", output_format: "json", }); result.pmc = { id: "PMC7394273", title: pmc?.record?.title ?? pmc?.title ?? pmc?.article_title, }; } catch (error) { result.pmc = { error: error.message ?? String(error) }; } return result; } ``` Paste the helper or the entire workflow into the Code Mode editor, press “Run,” and the script will execute against the Entrez MCP server without hitting `capabilities is not defined`, `api is not defined`, etc.