@cyanheads/pubmed-mcp-server 2.10.5 → 2.10.7

package/dist/services/ncbi/response-handler.d.ts

@@ -41,6 +41,17 @@ export declare class NcbiResponseHandler {
      * `htmlEntities`), so page-range en-dashes still resolve. (#69)
      */
     private readonly orderedXmlParser;
+    /**
+     * Flat, named-key parser with `parseTagValue: false`. Same shape as
+     * `xmlParser` — `response.eSpellResult.Query` still resolves — but tag text
+     * arrives verbatim. Used where a response echoes an arbitrary caller-supplied
+     * token: ESpell's `<Query>` is the only such field today, and coercion there
+     * destroys the text before application code runs (`007` → `7`, `1e5` →
+     * `100000`), which no read-site `String()` can undo. `orderedXmlParser` is
+     * not a substitute — it also sets `preserveOrder`, returning a node array
+     * rather than the property access the ESpell read depends on. (#108)
+     */
+    private readonly verbatimXmlParser;
     constructor();
     /**
      * Extract a structured error from a parsed NCBI XML body and throw it as

package/dist/services/ncbi/response-handler.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"response-handler.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/response-handler.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAiBH,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,YAAY,CAAC;AAkMrD;;;;;;;;;;;;;;;;GAgBG;AACH,wBAAgB,mBAAmB,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,CAMvD;AAED;;;GAGG;AACH,qBAAa,mBAAmB;IAC9B,OAAO,CAAC,QAAQ,CAAC,SAAS,CAAgB;IAC1C;;;;;;;;;;OAUG;IACH,OAAO,CAAC,QAAQ,CAAC,gBAAgB,CAAgB;IACjD;;;;;;;;;OASG;IACH,OAAO,CAAC,QAAQ,CAAC,iBAAiB,CAAgB;IAElD,cAqBC;IAED;;;;;;;;OAQG;IACH,OAAO,CAAC,cAAc;IA2BtB,wBAAwB,CAAC,SAAS,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,MAAM,EAAE,CAoBrE;IAED,sBAAsB,CAAC,CAAC,EACtB,YAAY,EAAE,MAAM,EACpB,QAAQ,EAAE,MAAM,EAChB,OAAO,CAAC,EAAE,kBAAkB,GAC3B,CAAC,CAsOH;CACF"}

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

@@ -17,7 +17,7 @@ import { logger, requestContextService } from '@cyanheads/mcp-ts-core/utils';
  */
 // biome-ignore lint/suspicious/noDeprecatedImports: staying on in-tree XMLValidator — see block comment above
 import { XMLParser as FastXmlParser, XMLValidator } from 'fast-xml-parser';
-import { recoveryFor } from '../../services/error-contracts.js';
+import { recoveryFor } from '../error-contracts.js';
 /**
  * jpaths that NCBI may return as either a single value or an array.
  * The `isArray` callback forces these to always parse as arrays for consistency.
@@ -239,15 +239,28 @@ export class NcbiResponseHandler {
      * `htmlEntities`), so page-range en-dashes still resolve. (#69)
      */
     orderedXmlParser;
+    /**
+     * Flat, named-key parser with `parseTagValue: false`. Same shape as
+     * `xmlParser` — `response.eSpellResult.Query` still resolves — but tag text
+     * arrives verbatim. Used where a response echoes an arbitrary caller-supplied
+     * token: ESpell's `<Query>` is the only such field today, and coercion there
+     * destroys the text before application code runs (`007` → `7`, `1e5` →
+     * `100000`), which no read-site `String()` can undo. `orderedXmlParser` is
+     * not a substitute — it also sets `preserveOrder`, returning a node array
+     * rather than the property access the ESpell read depends on. (#108)
+     */
+    verbatimXmlParser;
     constructor() {
-        this.xmlParser = new FastXmlParser({
+        // The two flat, named-key parsers differ only in `parseTagValue`.
+        const flatOptions = {
             ignoreAttributes: false,
             attributeNamePrefix: '@_',
-            parseTagValue: true,
             processEntities: NCBI_PROCESS_ENTITIES_OPTIONS,
             htmlEntities: true,
             isArray: (_name, jpath) => NCBI_ARRAY_JPATHS.has(jpath),
-        });
+        };
+        this.xmlParser = new FastXmlParser({ ...flatOptions, parseTagValue: true });
+        this.verbatimXmlParser = new FastXmlParser({ ...flatOptions, parseTagValue: false });
         this.orderedXmlParser = new FastXmlParser({
             preserveOrder: true,
             ignoreAttributes: false,
@@ -370,7 +383,13 @@ export class NcbiResponseHandler {
                 const errorParsed = this.xmlParser.parse(responseText);
                 this.throwNcbiError(errorParsed, endpoint);
             }
-            const parser = useOrdered ? this.orderedXmlParser : this.xmlParser;
+            // Ordered wins when both are set: it is the JATS mixed-content path, and
+            // it already parses tag values verbatim.
+            const parser = useOrdered
+                ? this.orderedXmlParser
+                : options?.useVerbatimParser
+                    ? this.verbatimXmlParser
+                    : this.xmlParser;
             // Pre-flatten <sup>/<sub>/<inf>/<i>/<b>/<u>/<sc> on the regular parser
             // path. The ordered parser walks mixed content correctly via
             // preserveOrder; the regular parser does not.

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

@@ -1 +1 @@
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package/dist/services/ncbi/types.d.ts

@@ -40,6 +40,17 @@ export interface NcbiRequestOptions {
     useOrderedParser?: boolean;
     /** Force HTTP POST (for large payloads). */
     usePost?: boolean;
+    /**
+     * Parse XML with `parseTagValue: false` while keeping the flat, named-key
+     * object shape (`response.eSpellResult.Query`). Required wherever a response
+     * echoes an arbitrary caller-supplied token that must survive verbatim: the
+     * coercing default turns `007` into `7` and `1e5` into `100000` before any
+     * application code runs, so a read-site `String()` cannot recover the text.
+     * Distinct from `useOrderedParser`, which also sets `preserveOrder` and hands
+     * back a document-ordered node array. Ignored when `useOrderedParser` is set.
+     * (#108)
+     */
+    useVerbatimParser?: boolean;
 }
 /**
  * Runtime options accepted by public NCBI service methods.
@@ -449,7 +460,12 @@ export interface ESpellResult {
     hasSuggestion: boolean;
     original: string;
 }
-/** Raw parsed XML container for eSpellResult. */
+/**
+ * Raw parsed XML container for eSpellResult. `Query` and `CorrectedQuery` are
+ * strings at runtime as well as in this declaration: the ESpell request opts
+ * into `useVerbatimParser`, so the coercing default parser never sees the
+ * echoed term. (#108)
+ */
 export interface ESpellResponseContainer {
     eSpellResult: {
         Query?: string;

package/dist/services/ncbi/types.d.ts.map

@@ -1 +1 @@
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package/dist/services/openalex/api-client.js

@@ -6,7 +6,7 @@
  */
 import { JsonRpcErrorCode, McpError, serviceUnavailable } from '@cyanheads/mcp-ts-core/errors';
 import { fetchWithTimeout, logger, requestContextService } from '@cyanheads/mcp-ts-core/utils';
-import { recoveryFor } from '../../services/error-contracts.js';
+import { recoveryFor } from '../error-contracts.js';
 import { OPENALEX_API_BASE } from './types.js';
 const USER_AGENT = 'pubmed-mcp-server (+https://github.com/cyanheads/pubmed-mcp-server)';
 /**

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

@@ -14,8 +14,8 @@
 import { internalError, JsonRpcErrorCode, McpError } from '@cyanheads/mcp-ts-core/errors';
 import { logger, requestContextService } from '@cyanheads/mcp-ts-core/utils';
 import { getServerConfig } from '../../config/server-config.js';
-import { recoveryFor } from '../../services/error-contracts.js';
-import { isTransient } from '../../services/retry-policy.js';
+import { recoveryFor } from '../error-contracts.js';
+import { isTransient } from '../retry-policy.js';
 import { OpenAlexApiClient } from './api-client.js';
 /** Transient codes eligible for retry. */
 const RETRYABLE_CODES = new Set([

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

@@ -27,8 +27,25 @@ export declare class UnpaywallService {
      * present (direct PDF bytes) and falls back to `url` (HTML landing page).
      * Throws `McpError(ServiceUnavailable)` on network/server failures or
      * unreadable responses — caller handles partial failures.
+     *
+     * Publishers routinely answer `url_for_pdf` with an HTML paywall or
+     * interstitial at `200 OK`. That is not a fetch failure, so it takes the same
+     * route as one: fall through to `location.url`, Unpaywall's designated
+     * landing page, which is likelier to hold real content. The HTML already
+     * received is kept and returned when a second fetch cannot improve on it —
+     * the two addresses are the same, or the fallback fetch itself fails. (#104)
      */
     fetchContent(location: UnpaywallLocation, signal?: AbortSignal): Promise<UnpaywallContent>;
+    /**
+     * Fetch one URL and classify what came back by its own bytes.
+     *
+     * `expected` steers the `Accept` header only. Classification reads the
+     * response body's magic header, because neither the caller's expectation nor
+     * the `content-type` describes it reliably: a genuine PDF is often served as
+     * `application/octet-stream`, and an HTML interstitial is sometimes served as
+     * `application/pdf`. Bytes opening with `%PDF-` are a PDF whatever the header
+     * says; everything else is treated as text. (#104)
+     */
     private fetchAs;
 }
 /**

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;AAYH,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;IAF5B,YACmB,KAAK,EAAE,MAAM,EACb,SAAS,EAAE,MAAM,EAChC;IAEJ;;;;OAIG;IACG,OAAO,CAAC,GAAG,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,mBAAmB,CAAC,CA+D7E;IAED;;;;;OAKG;IACG,YAAY,CAAC,QAAQ,EAAE,iBAAiB,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,gBAAgB,CAAC,CAsB/F;YAEa,OAAO;CAiDtB;AAiBD;;;;GAIG;AACH,wBAAgB,oBAAoB,IAAI,IAAI,CAc3C;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;AAYH,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;IAF5B,YACmB,KAAK,EAAE,MAAM,EACb,SAAS,EAAE,MAAM,EAChC;IAEJ;;;;OAIG;IACG,OAAO,CAAC,GAAG,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,mBAAmB,CAAC,CA+D7E;IAED;;;;;;;;;;;;OAYG;IACG,YAAY,CAAC,QAAQ,EAAE,iBAAiB,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,gBAAgB,CAAC,CA6C/F;IAED;;;;;;;;;OASG;YACW,OAAO;CA+CtB;AA2BD;;;;GAIG;AACH,wBAAgB,oBAAoB,IAAI,IAAI,CAc3C;AAED,qFAAqF;AACrF,wBAAgB,mBAAmB,IAAI,gBAAgB,GAAG,SAAS,CAElE"}

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

@@ -10,7 +10,7 @@
 import { JsonRpcErrorCode, McpError, 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 { recoveryFor } from '../../services/error-contracts.js';
+import { recoveryFor } from '../error-contracts.js';
 import { UNPAYWALL_API_BASE, } from './types.js';
 const USER_AGENT = 'pubmed-mcp-server (+https://github.com/cyanheads/pubmed-mcp-server)';
 /**
@@ -89,13 +89,29 @@ export class UnpaywallService {
      * present (direct PDF bytes) and falls back to `url` (HTML landing page).
      * Throws `McpError(ServiceUnavailable)` on network/server failures or
      * unreadable responses — caller handles partial failures.
+     *
+     * Publishers routinely answer `url_for_pdf` with an HTML paywall or
+     * interstitial at `200 OK`. That is not a fetch failure, so it takes the same
+     * route as one: fall through to `location.url`, Unpaywall's designated
+     * landing page, which is likelier to hold real content. The HTML already
+     * received is kept and returned when a second fetch cannot improve on it —
+     * the two addresses are the same, or the fallback fetch itself fails. (#104)
      */
     async fetchContent(location, signal) {
         const pdfUrl = location.url_for_pdf ?? undefined;
         const htmlUrl = location.url;
         if (pdfUrl) {
+            /** HTML served where a PDF was advertised — a fallback candidate, not a result. */
+            let servedHtml;
             try {
-                return await this.fetchAs(pdfUrl, 'pdf', signal);
+                const content = await this.fetchAs(pdfUrl, 'pdf', signal);
+                if (content.kind === 'pdf')
+                    return content;
+                servedHtml = content;
+                logger.debug('Unpaywall PDF URL served non-PDF bytes; falling back to HTML URL', requestContextService.createRequestContext({
+                    operation: 'UnpaywallPdfNotPdf',
+                    additionalContext: { url: pdfUrl, fetchedUrl: content.fetchedUrl },
+                }));
             }
             catch (pdfErr) {
                 logger.debug('Unpaywall PDF fetch failed; falling back to HTML URL', requestContextService.createRequestContext({
@@ -106,9 +122,31 @@ export class UnpaywallService {
                     },
                 }));
             }
+            // Refetching an address we already read returns the same bytes.
+            if (servedHtml && (pdfUrl === htmlUrl || servedHtml.fetchedUrl === htmlUrl)) {
+                return servedHtml;
+            }
+            try {
+                return await this.fetchAs(htmlUrl, 'auto', signal);
+            }
+            catch (htmlErr) {
+                if (servedHtml)
+                    return servedHtml;
+                throw htmlErr;
+            }
         }
         return this.fetchAs(htmlUrl, 'auto', signal);
     }
+    /**
+     * Fetch one URL and classify what came back by its own bytes.
+     *
+     * `expected` steers the `Accept` header only. Classification reads the
+     * response body's magic header, because neither the caller's expectation nor
+     * the `content-type` describes it reliably: a genuine PDF is often served as
+     * `application/octet-stream`, and an HTML interstitial is sometimes served as
+     * `application/pdf`. Bytes opening with `%PDF-` are a PDF whatever the header
+     * says; everything else is treated as text. (#104)
+     */
     async fetchAs(url, expected, signal) {
         const ctx = requestContextService.createRequestContext({
             operation: 'UnpaywallFetch',
@@ -135,16 +173,21 @@ export class UnpaywallService {
                 data: { url },
             });
         }
-        const contentType = response.headers.get('content-type')?.toLowerCase() ?? '';
         const fetchedUrl = response.url || url;
-        if (contentType.includes('pdf') || expected === 'pdf') {
-            const bytes = new Uint8Array(await response.arrayBuffer());
+        // Read the body once — a Response body can only be consumed once, and the
+        // bytes are what the classification reads.
+        const bytes = new Uint8Array(await response.arrayBuffer());
+        if (hasPdfMagic(bytes))
             return { kind: 'pdf', fetchedUrl, body: bytes };
-        }
-        const text = await response.text();
-        return { kind: 'html', fetchedUrl, body: text };
+        return { kind: 'html', fetchedUrl, body: new TextDecoder().decode(bytes) };
     }
 }
+/** `%PDF-`, the five bytes every PDF file opens with. */
+const PDF_MAGIC = Uint8Array.of(0x25, 0x50, 0x44, 0x46, 0x2d);
+/** Whether the received bytes are a PDF, independent of any declared type. */
+function hasPdfMagic(bytes) {
+    return (bytes.length >= PDF_MAGIC.length && PDF_MAGIC.every((byte, index) => bytes[index] === byte));
+}
 /**
  * Strip a leading `doi:` prefix or URL wrapping and return a clean DOI, or
  * undefined when the input can't be coerced into one.

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

@@ -1 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@cyanheads/pubmed-mcp-server",
-  "version": "2.10.5",
+  "version": "2.10.7",
   "mcpName": "io.github.cyanheads/pubmed-mcp-server",
   "description": "Search PubMed/Europe PMC, fetch articles and full text (PMC/EPMC/Unpaywall), citations, MeSH terms via MCP. STDIO or Streamable HTTP.",
   "type": "module",
@@ -81,7 +81,7 @@
     "access": "public"
   },
   "dependencies": {
-    "@cyanheads/mcp-ts-core": "^0.12.5",
+    "@cyanheads/mcp-ts-core": "^0.12.7",
     "defuddle": "^0.19.3",
     "fast-xml-parser": "^5.11.1",
     "linkedom": "^0.18.13",
@@ -91,17 +91,17 @@
     "zod": "^4.5.4"
   },
   "devDependencies": {
-    "@biomejs/biome": "^2.5.11",
+    "@biomejs/biome": "^2.5.12",
     "@socketsecurity/bun-security-scanner": "^1.1.2",
-    "@types/node": "^26.4.0",
+    "@types/node": "^26.4.1",
     "@types/sanitize-html": "^2.16.1",
-    "@vitest/coverage-istanbul": "^4.1.11",
+    "@vitest/coverage-istanbul": "^5.0.0",
     "depcheck": "^1.4.7",
     "fast-check": "^4.9.0",
-    "ignore": "^7.0.7",
-    "tsc-alias": "^1.9.2",
+    "ignore": "^7.0.8",
+    "tsc-alias": "^1.9.4",
     "typescript": "^7.0.2",
-    "vitest": "^4.1.11"
+    "vitest": "^5.0.0"
   },
   "overrides": {
     "@hono/node-server": "^2.0.11",

package/server.json

@@ -6,7 +6,7 @@
     "url": "https://github.com/cyanheads/pubmed-mcp-server",
     "source": "github"
   },
-  "version": "2.10.5",
+  "version": "2.10.7",
   "remotes": [
     {
       "type": "streamable-http",
@@ -19,7 +19,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubmed-mcp-server",
       "runtimeHint": "bun",
-      "version": "2.10.5",
+      "version": "2.10.7",
       "packageArguments": [
         {
           "type": "positional",
@@ -66,7 +66,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubmed-mcp-server",
       "runtimeHint": "bun",
-      "version": "2.10.5",
+      "version": "2.10.7",
       "packageArguments": [
         {
           "type": "positional",