@cyanheads/pubmed-mcp-server 2.6.3 → 2.6.5

package/dist/services/ncbi/response-handler.js

@@ -4,8 +4,8 @@
  * NCBI's inconsistent XML structures where single-element lists are collapsed to scalars.
  * @module src/services/ncbi/response-handler
  */
-import { JsonRpcErrorCode, McpError } from '@cyanheads/mcp-ts-core/errors';
-import { logger } from '@cyanheads/mcp-ts-core/utils';
+import { serializationError, serviceUnavailable } from '@cyanheads/mcp-ts-core/errors';
+import { logger, requestContextService } from '@cyanheads/mcp-ts-core/utils';
 import { XMLParser as FastXmlParser, XMLValidator } from 'fast-xml-parser';
 /**
  * jpaths that NCBI may return as either a single value or an array.
@@ -232,16 +232,20 @@ export class NcbiResponseHandler {
         });
     }
     /**
-     * Extract a structured error from a parsed NCBI XML body and throw it as an
-     * `McpError`. Never returns.
+     * Extract a structured error from a parsed NCBI XML body and throw it via
+     * `serviceUnavailable()`. Never returns.
      */
     throwNcbiError(parsedXml, endpoint) {
         const errorMessages = this.extractNcbiErrorMessages(parsedXml);
-        logger.error('NCBI API returned an error in XML response.', {
+        logger.error('NCBI API returned an error in XML response.', requestContextService.createRequestContext({
+            operation: 'NcbiXmlError',
             endpoint,
             errors: errorMessages,
+        }));
+        throw serviceUnavailable(`NCBI API Error: ${errorMessages.join('; ')}`, {
+            endpoint,
+            ncbiErrors: errorMessages,
         });
-        throw new McpError(JsonRpcErrorCode.ServiceUnavailable, `NCBI API Error: ${errorMessages.join('; ')}`, { endpoint, ncbiErrors: errorMessages });
     }
     extractNcbiErrorMessages(parsedXml) {
         const messages = [];
@@ -264,26 +268,36 @@ export class NcbiResponseHandler {
     parseAndHandleResponse(responseText, endpoint, options) {
         const retmode = options?.retmode ?? 'xml';
         if (retmode === 'text') {
-            logger.debug('Received text response from NCBI.', { endpoint, retmode });
+            logger.debug('Received text response from NCBI.', requestContextService.createRequestContext({
+                operation: 'NcbiParseText',
+                endpoint,
+                retmode,
+            }));
             return responseText;
         }
         if (retmode === 'xml') {
-            logger.debug('Parsing XML response from NCBI.', { endpoint, retmode });
+            logger.debug('Parsing XML response from NCBI.', requestContextService.createRequestContext({
+                operation: 'NcbiParseXml',
+                endpoint,
+                retmode,
+            }));
             const xmlForValidation = responseText.replace(/<!DOCTYPE[^>]*>/gi, '');
             const validationResult = XMLValidator.validate(xmlForValidation);
             if (validationResult !== true) {
                 const isHtml = /^\s*<(!DOCTYPE\s+html|html[\s>])/i.test(responseText);
                 if (isHtml) {
-                    logger.warning('NCBI returned HTML instead of XML (likely rate-limited).', {
+                    logger.warning('NCBI returned HTML instead of XML (likely rate-limited).', requestContextService.createRequestContext({
+                        operation: 'NcbiHtmlResponse',
                         endpoint,
-                    });
-                    throw new McpError(JsonRpcErrorCode.ServiceUnavailable, 'NCBI API returned an HTML response instead of XML — likely rate-limited.', { endpoint });
+                    }));
+                    throw serviceUnavailable('NCBI API returned an HTML response instead of XML — likely rate-limited.', { endpoint });
                 }
-                logger.error('Invalid XML response from NCBI.', {
+                logger.error('Invalid XML response from NCBI.', requestContextService.createRequestContext({
+                    operation: 'NcbiInvalidXml',
                     endpoint,
                     responseSnippet: responseText.substring(0, 500),
-                });
-                throw new McpError(JsonRpcErrorCode.SerializationError, 'Received invalid XML from NCBI.', {
+                }));
+                throw serializationError('Received invalid XML from NCBI.', {
                     endpoint,
                     responseSnippet: responseText.substring(0, 200),
                 });
@@ -307,16 +321,17 @@ export class NcbiResponseHandler {
             }
             catch (error) {
                 const parserError = error instanceof Error ? error.message : String(error);
-                logger.error('Failed to parse validated XML response from NCBI.', {
+                logger.error('Failed to parse validated XML response from NCBI.', requestContextService.createRequestContext({
+                    operation: 'NcbiXmlParseError',
                     endpoint,
                     parserError,
                     responseSnippet: responseText.substring(0, 500),
-                });
-                throw new McpError(JsonRpcErrorCode.SerializationError, `Failed to parse XML response from NCBI: ${parserError}`, {
+                }));
+                throw serializationError(`Failed to parse XML response from NCBI: ${parserError}`, {
                     endpoint,
                     parserError,
                     responseSnippet: responseText.substring(0, 200),
-                });
+                }, { cause: error });
             }
             if (!useOrdered) {
                 const parsedObj = parsedXml;
@@ -326,39 +341,45 @@ export class NcbiResponseHandler {
                 }
             }
             if (options?.returnRawXml) {
-                logger.debug('Returning raw XML string after validation.', { endpoint });
+                logger.debug('Returning raw XML string after validation.', requestContextService.createRequestContext({ operation: 'NcbiRawXml', endpoint }));
                 return responseText;
             }
-            logger.debug('Successfully parsed XML response.', { endpoint });
+            logger.debug('Successfully parsed XML response.', requestContextService.createRequestContext({ operation: 'NcbiParseXmlOk', endpoint }));
             return parsedXml;
         }
         if (retmode === 'json') {
-            logger.debug('Parsing JSON response from NCBI.', { endpoint, retmode });
+            logger.debug('Parsing JSON response from NCBI.', requestContextService.createRequestContext({
+                operation: 'NcbiParseJson',
+                endpoint,
+                retmode,
+            }));
             let parsed;
             try {
                 parsed = JSON.parse(responseText);
             }
-            catch {
-                throw new McpError(JsonRpcErrorCode.SerializationError, 'Failed to parse NCBI JSON response.', { endpoint, responseSnippet: responseText.substring(0, 200) });
+            catch (error) {
+                throw serializationError('Failed to parse NCBI JSON response.', { endpoint, responseSnippet: responseText.substring(0, 200) }, { cause: error });
             }
             if (parsed && typeof parsed === 'object' && 'error' in parsed) {
                 const errorMessage = String(parsed.error);
-                logger.error('NCBI API returned an error in JSON response.', {
+                logger.error('NCBI API returned an error in JSON response.', requestContextService.createRequestContext({
+                    operation: 'NcbiJsonError',
                     endpoint,
                     error: errorMessage,
-                });
-                throw new McpError(JsonRpcErrorCode.ServiceUnavailable, `NCBI API Error: ${errorMessage}`, {
+                }));
+                throw serviceUnavailable(`NCBI API Error: ${errorMessage}`, {
                     endpoint,
                     ncbiError: errorMessage,
                 });
             }
-            logger.debug('Successfully parsed JSON response.', { endpoint });
+            logger.debug('Successfully parsed JSON response.', requestContextService.createRequestContext({ operation: 'NcbiParseJsonOk', endpoint }));
             return parsed;
         }
-        logger.warning(`Unhandled retmode "${retmode}". Returning raw response text.`, {
+        logger.warning(`Unhandled retmode "${retmode}". Returning raw response text.`, requestContextService.createRequestContext({
+            operation: 'NcbiUnknownRetmode',
             endpoint,
             retmode,
-        });
+        }));
         return responseText;
     }
 }

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package/dist/services/unpaywall/unpaywall-service.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"unpaywall-service.d.ts","sourceRoot":"","sources":["../../../src/services/unpaywall/unpaywall-service.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAMH,OAAO,EAEL,KAAK,gBAAgB,EACrB,KAAK,iBAAiB,EACtB,KAAK,mBAAmB,EAEzB,MAAM,YAAY,CAAC;AAIpB;;;GAGG;AACH,qBAAa,gBAAgB;IAEzB,OAAO,CAAC,QAAQ,CAAC,KAAK;IACtB,OAAO,CAAC,QAAQ,CAAC,SAAS;gBADT,KAAK,EAAE,MAAM,EACb,SAAS,EAAE,MAAM;IAGpC;;;;OAIG;IACG,OAAO,CAAC,GAAG,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,mBAAmB,CAAC;IAkD9E;;;;;OAKG;IACG,YAAY,CAAC,QAAQ,EAAE,iBAAiB,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,gBAAgB,CAAC;YAkBlF,OAAO;CAqDtB;AAiBD;;;;GAIG;AACH,wBAAgB,oBAAoB,IAAI,IAAI,CAU3C;AAED,qFAAqF;AACrF,wBAAgB,mBAAmB,IAAI,gBAAgB,GAAG,SAAS,CAElE"}
+{"version":3,"file":"unpaywall-service.d.ts","sourceRoot":"","sources":["../../../src/services/unpaywall/unpaywall-service.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAWH,OAAO,EAEL,KAAK,gBAAgB,EACrB,KAAK,iBAAiB,EACtB,KAAK,mBAAmB,EAEzB,MAAM,YAAY,CAAC;AAIpB;;;GAGG;AACH,qBAAa,gBAAgB;IAEzB,OAAO,CAAC,QAAQ,CAAC,KAAK;IACtB,OAAO,CAAC,QAAQ,CAAC,SAAS;gBADT,KAAK,EAAE,MAAM,EACb,SAAS,EAAE,MAAM;IAGpC;;;;OAIG;IACG,OAAO,CAAC,GAAG,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,mBAAmB,CAAC;IAsD9E;;;;;OAKG;IACG,YAAY,CAAC,QAAQ,EAAE,iBAAiB,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,gBAAgB,CAAC;YAsBlF,OAAO;CA8CtB;AAiBD;;;;GAIG;AACH,wBAAgB,oBAAoB,IAAI,IAAI,CAc3C;AAED,qFAAqF;AACrF,wBAAgB,mBAAmB,IAAI,gBAAgB,GAAG,SAAS,CAElE"}

package/dist/services/unpaywall/unpaywall-service.js

@@ -7,8 +7,8 @@
  * resolution; only genuine service failures (5xx, network, timeout) throw.
  * @module src/services/unpaywall/unpaywall-service
  */
-import { JsonRpcErrorCode, McpError } from '@cyanheads/mcp-ts-core/errors';
-import { fetchWithTimeout, logger, requestContextService } from '@cyanheads/mcp-ts-core/utils';
+import { serviceUnavailable } from '@cyanheads/mcp-ts-core/errors';
+import { fetchWithTimeout, httpErrorFromResponse, logger, requestContextService, } from '@cyanheads/mcp-ts-core/utils';
 import { getServerConfig } from '../../config/server-config.js';
 import { UNPAYWALL_API_BASE, } from './types.js';
 const USER_AGENT = 'pubmed-mcp-server (+https://github.com/cyanheads/pubmed-mcp-server)';
@@ -43,9 +43,7 @@ export class UnpaywallService {
         }
         catch (error) {
             const msg = error instanceof Error ? error.message : String(error);
-            throw new McpError(JsonRpcErrorCode.ServiceUnavailable, `Unpaywall request failed: ${msg}`, {
-                doi: normalized,
-            });
+            throw serviceUnavailable(`Unpaywall request failed: ${msg}`, { doi: normalized }, { cause: error });
         }
         if (response.status === 404)
             return { kind: 'no-oa', reason: 'DOI unknown to Unpaywall' };
@@ -53,9 +51,11 @@ export class UnpaywallService {
             return { kind: 'no-oa', reason: 'Invalid DOI format' };
         if (!response.ok) {
             const body = await response.text().catch(() => '');
-            throw new McpError(response.status >= 500
-                ? JsonRpcErrorCode.ServiceUnavailable
-                : JsonRpcErrorCode.InvalidRequest, `Unpaywall returned HTTP ${response.status}.`, { doi: normalized, status: response.status, body: body.substring(0, 300) });
+            throw await httpErrorFromResponse(response, {
+                service: 'Unpaywall',
+                captureBody: false,
+                data: { doi: normalized, body: body.substring(0, 300) },
+            });
         }
         const data = (await response.json());
         if (!data.is_oa)
@@ -63,12 +63,13 @@ export class UnpaywallService {
         const location = data.best_oa_location ?? data.oa_locations?.[0];
         if (!location?.url)
             return { kind: 'no-oa', reason: 'OA flagged but no usable location URL' };
-        logger.debug('Unpaywall resolved DOI', {
+        logger.debug('Unpaywall resolved DOI', requestContextService.createRequestContext({
+            operation: 'UnpaywallResolved',
             doi: normalized,
             hostType: location.host_type ?? null,
             license: location.license ?? null,
             version: location.version ?? null,
-        });
+        }));
         return { kind: 'found', location };
     }
     /**
@@ -85,10 +86,11 @@ export class UnpaywallService {
                 return await this.fetchAs(pdfUrl, 'pdf', signal);
             }
             catch (pdfErr) {
-                logger.debug('Unpaywall PDF fetch failed; falling back to HTML URL', {
+                logger.debug('Unpaywall PDF fetch failed; falling back to HTML URL', requestContextService.createRequestContext({
+                    operation: 'UnpaywallPdfFallback',
                     url: pdfUrl,
                     error: pdfErr instanceof Error ? pdfErr.message : String(pdfErr),
-                });
+                }));
             }
         }
         return this.fetchAs(htmlUrl, 'auto', signal);
@@ -112,12 +114,13 @@ export class UnpaywallService {
         }
         catch (error) {
             const msg = error instanceof Error ? error.message : String(error);
-            throw new McpError(JsonRpcErrorCode.ServiceUnavailable, `Unpaywall content fetch failed: ${msg}`, { url });
+            throw serviceUnavailable(`Unpaywall content fetch failed: ${msg}`, { url }, { cause: error });
         }
         if (!response.ok) {
-            throw new McpError(response.status >= 500
-                ? JsonRpcErrorCode.ServiceUnavailable
-                : JsonRpcErrorCode.InvalidRequest, `Unpaywall content fetch returned HTTP ${response.status}.`, { url, status: response.status });
+            throw await httpErrorFromResponse(response, {
+                service: 'Unpaywall content fetch',
+                data: { url },
+            });
         }
         const contentType = response.headers.get('content-type')?.toLowerCase() ?? '';
         const fetchedUrl = response.url || url;
@@ -154,9 +157,10 @@ export function initUnpaywallService() {
         return;
     }
     _service = new UnpaywallService(config.unpaywallEmail, config.unpaywallTimeoutMs);
-    logger.info('Unpaywall service initialized.', {
+    logger.info('Unpaywall service initialized.', requestContextService.createRequestContext({
+        operation: 'UnpaywallInit',
         timeoutMs: config.unpaywallTimeoutMs,
-    });
+    }));
 }
 /** Returns the initialized service, or `undefined` when the fallback is disabled. */
 export function getUnpaywallService() {

package/dist/services/unpaywall/unpaywall-service.js.map

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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@cyanheads/pubmed-mcp-server",
-  "version": "2.6.3",
+  "version": "2.6.5",
   "mcpName": "io.github.cyanheads/pubmed-mcp-server",
   "description": "MCP server for PubMed/NCBI E-utilities integration. Search articles, fetch metadata and open-access full text (PMC + Unpaywall), generate citations, explore MeSH terms, and discover related research.",
   "type": "module",
@@ -19,6 +19,8 @@
     "format": "biome check --write --unsafe",
     "test": "bunx vitest run",
     "lint:mcp": "bun run scripts/lint-mcp.ts",
+    "changelog:build": "bun run scripts/build-changelog.ts",
+    "changelog:check": "bun run scripts/build-changelog.ts --check",
     "publish-mcp": "mcp-publisher login github -token \"$(security find-generic-password -a \"$USER\" -s mcp-publisher-github-pat -w)\" && mcp-publisher publish",
     "dev:stdio": "MCP_TRANSPORT_TYPE=stdio bun --watch src/index.ts",
     "dev:http": "MCP_TRANSPORT_TYPE=http bun --watch src/index.ts",
@@ -71,13 +73,13 @@
     "access": "public"
   },
   "dependencies": {
-    "@cyanheads/mcp-ts-core": "^0.7.5",
+    "@cyanheads/mcp-ts-core": "^0.8.2",
     "defuddle": "^0.18.1",
     "fast-xml-parser": "^5.7.2",
     "linkedom": "^0.18.12",
     "pino-pretty": "^13.1.3",
     "sanitize-html": "^2.17.3",
-    "unpdf": "^1.6.0"
+    "unpdf": "^1.6.1"
   },
   "devDependencies": {
     "@biomejs/biome": "^2.4.13",
@@ -85,6 +87,7 @@
     "@types/sanitize-html": "^2.16.1",
     "@vitest/coverage-istanbul": "^4.1.5",
     "depcheck": "^1.4.7",
+    "fast-check": "^4.7.0",
     "ignore": "^7.0.5",
     "tsc-alias": "^1.8.16",
     "typescript": "^6.0.3",

package/server.json

@@ -6,7 +6,7 @@
     "url": "https://github.com/cyanheads/pubmed-mcp-server",
     "source": "github"
   },
-  "version": "2.6.3",
+  "version": "2.6.5",
   "remotes": [
     {
       "type": "streamable-http",
@@ -19,7 +19,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubmed-mcp-server",
       "runtimeHint": "bun",
-      "version": "2.6.3",
+      "version": "2.6.5",
       "packageArguments": [
         {
           "type": "positional",
@@ -66,7 +66,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubmed-mcp-server",
       "runtimeHint": "bun",
-      "version": "2.6.3",
+      "version": "2.6.5",
       "packageArguments": [
         {
           "type": "positional",