npm - @cyanheads/pubmed-mcp-server - Versions diffs - 2.10.8 → 2.10.10 - Mend

@cyanheads/pubmed-mcp-server 2.10.8 → 2.10.10

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (67) hide show

package/dist/mcp-server/tools/definitions/spell-check.tool.js CHANGED Viewed

@@ -4,7 +4,7 @@
  * @module src/mcp-server/tools/definitions/spell-check.tool
  */
 import { tool, z } from '@cyanheads/mcp-ts-core';
-import { NCBI_SERVICE_ERRORS } from '../../../services/error-contracts.js';
+import { NCBI_QUERY_INPUT_ERRORS, NCBI_SERVICE_ERRORS } from '../../../services/error-contracts.js';
 import { getNcbiService } from '../../../services/ncbi/ncbi-service.js';
 import { conceptMeta, SCHEMA_SEARCH_ACTION } from './_concepts.js';
 export const spellCheckTool = tool('pubmed_spell_check', {
@@ -12,9 +12,12 @@ export const spellCheckTool = tool('pubmed_spell_check', {
     annotations: { readOnlyHint: true, openWorldHint: true },
     _meta: conceptMeta([SCHEMA_SEARCH_ACTION]),
     sourceUrl: 'https://github.com/cyanheads/pubmed-mcp-server/blob/main/src/mcp-server/tools/definitions/spell-check.tool.ts',
-    errors: [...NCBI_SERVICE_ERRORS],
+    errors: [...NCBI_SERVICE_ERRORS, ...NCBI_QUERY_INPUT_ERRORS],
     input: z.object({
-        query: z.string().min(2).describe('PubMed search query to spell-check'),
+        query: z
+            .string()
+            .min(2)
+            .describe('PubMed search query to spell-check. Must carry a term: a blank or whitespace-only value is rejected rather than sent to ESpell.'),
     }),
     output: z.object({
         original: z.string().describe('Original query'),
@@ -23,6 +26,15 @@ export const spellCheckTool = tool('pubmed_spell_check', {
     }),
     async handler(input, ctx) {
         ctx.log.info('Executing pubmed_spell_check tool', { query: input.query });
+        // `min(2)` counts the spaces, so a whitespace-only query passes the schema.
+        // ESpell answers a blank term with an empty `<ERROR/>` element the response
+        // handler does not detect, and the tool would report the blank input as
+        // spell-checked. Reject before the call. (#133)
+        if (input.query.trim().length === 0) {
+            throw ctx.fail('blank_query', 'The `query` is blank — there is nothing to spell-check.', {
+                ...ctx.recoveryFor('blank_query'),
+            });
+        }
         const result = await getNcbiService().eSpell({ db: 'pubmed', term: input.query }, { signal: ctx.signal });
         return {
             original: result.original,

package/dist/mcp-server/tools/definitions/spell-check.tool.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"spell-check.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/spell-check.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,uBAAuB,EAAE,mBAAmB,EAAE,MAAM,+BAA+B,CAAC;AAC7F,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AACjE,OAAO,EAAE,WAAW,EAAE,oBAAoB,EAAE,MAAM,gBAAgB,CAAC;AAEnE,MAAM,CAAC,MAAM,cAAc,GAAG,IAAI,CAAC,oBAAoB,EAAE;IACvD,WAAW,EACT,8FAA8F;IAChG,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IACxD,KAAK,EAAE,WAAW,CAAC,CAAC,oBAAoB,CAAC,CAAC;IAC1C,SAAS,EACP,+GAA+G;IAEjH,MAAM,EAAE,CAAC,GAAG,mBAAmB,EAAE,GAAG,uBAAuB,CAAU;IAErE,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,KAAK,EAAE,CAAC;aACL,MAAM,EAAE;aACR,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,CACP,iIAAiI,CAClI;KACJ,CAAC;IAEF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,gBAAgB,CAAC;QAC/C,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,qDAAqD,CAAC;QACrF,aAAa,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC,QAAQ,CAAC,qCAAqC,CAAC;KAC3E,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,mCAAmC,EAAE,EAAE,KAAK,EAAE,KAAK,CAAC,KAAK,EAAE,CAAC,CAAC;QAC1E,4EAA4E;QAC5E,4EAA4E;QAC5E,wEAAwE;QACxE,gDAAgD;QAChD,IAAI,KAAK,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YACpC,MAAM,GAAG,CAAC,IAAI,CAAC,aAAa,EAAE,yDAAyD,EAAE;gBACvF,GAAG,GAAG,CAAC,WAAW,CAAC,aAAa,CAAC;aAClC,CAAC,CAAC;QACL,CAAC;QACD,MAAM,MAAM,GAAG,MAAM,cAAc,EAAE,CAAC,MAAM,CAC1C,EAAE,EAAE,EAAE,QAAQ,EAAE,IAAI,EAAE,KAAK,CAAC,KAAK,EAAE,EACnC,EAAE,MAAM,EAAE,GAAG,CAAC,MAAM,EAAE,CACvB,CAAC;QACF,OAAO;YACL,QAAQ,EAAE,MAAM,CAAC,QAAQ;YACzB,SAAS,EAAE,MAAM,CAAC,SAAS;YAC3B,aAAa,EAAE,MAAM,CAAC,aAAa;SACpC,CAAC;IACJ,CAAC;IAED,MAAM,EAAE,CAAC,MAAM,EAAE,EAAE;QACjB,IAAI,MAAM,CAAC,aAAa,EAAE,CAAC;YACzB,OAAO;gBACL;oBACE,IAAI,EAAE,MAAM;oBACZ,IAAI,EAAE,oBAAoB,MAAM,CAAC,SAAS,iBAAiB,MAAM,CAAC,QAAQ,IAAI;iBAC/E;aACF,CAAC;QACJ,CAAC;QACD,OAAO;YACL;gBACE,IAAI,EAAE,MAAM;gBACZ,IAAI,EAAE,0BAA0B,MAAM,CAAC,QAAQ,+BAA+B;aAC/E;SACF,CAAC;IACJ,CAAC;CACF,CAAC,CAAC"}

package/dist/services/error-contracts.d.ts CHANGED Viewed

@@ -1,6 +1,8 @@
 /**
- * @fileoverview Canonical service-layer error contracts. Single source of truth
- * for the failure modes both services throw and tools declare in `errors[]`.
+ * @fileoverview Canonical error contracts. Single source of truth for the
+ * failure modes services throw and tools declare in `errors[]`, plus the
+ * input rejections shared by the tools that forward a free-text query
+ * upstream.
  *
  * Service-layer code can't reach `ctx.recoveryFor` (no Context), so it spreads
  * `recoveryFor(reason)` from this module into the error factory's `data` arg.
@@ -50,6 +52,24 @@ export declare const NCBI_SERVICE_ERRORS: readonly [{
     readonly recovery: 'Verify the ID exists in PubMed; the resource was not found in NCBI and retrying will not help.';
     readonly retryable: false;
 }];
+/**
+ * Input failure the NCBI query tools reject before any call is made. Declared
+ * here rather than inside `NCBI_SERVICE_ERRORS` so only the tools that actually
+ * throw it advertise it — a tool that takes no free-text query can never
+ * produce it, and declaring it there would advertise a failure mode that
+ * cannot happen.
+ *
+ * Unlike the service arrays in this module, this one is thrown from a tool
+ * handler via `ctx.fail('blank_query', …)`, so its recovery hint resolves
+ * through `ctx.recoveryFor` and it stays out of {@link ServiceErrorReason}.
+ */
+export declare const NCBI_QUERY_INPUT_ERRORS: readonly [{
+    readonly reason: 'blank_query';
+    readonly code: JsonRpcErrorCode.ValidationError;
+    readonly when: 'The query holds no search term once whitespace, and any markup the tool strips first, are removed — so NCBI would receive a blank term.';
+    readonly recovery: 'Supply a nonblank search term; NCBI cannot search a blank term and retrying the same input will not help.';
+    readonly retryable: false;
+}];
 /**
  * Failure modes the Unpaywall service layer can surface. Tools that consume
  * `getUnpaywallService()` (currently `pubmed_fetch_fulltext`) should spread

package/dist/services/error-contracts.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/services/error-contracts.js CHANGED Viewed

@@ -1,6 +1,8 @@
 /**
- * @fileoverview Canonical service-layer error contracts. Single source of truth
- * for the failure modes both services throw and tools declare in `errors[]`.
+ * @fileoverview Canonical error contracts. Single source of truth for the
+ * failure modes services throw and tools declare in `errors[]`, plus the
+ * input rejections shared by the tools that forward a free-text query
+ * upstream.
  *
  * Service-layer code can't reach `ctx.recoveryFor` (no Context), so it spreads
  * `recoveryFor(reason)` from this module into the error factory's `data` arg.
@@ -56,6 +58,26 @@ export const NCBI_SERVICE_ERRORS = [
         retryable: false,
     },
 ];
+/**
+ * Input failure the NCBI query tools reject before any call is made. Declared
+ * here rather than inside `NCBI_SERVICE_ERRORS` so only the tools that actually
+ * throw it advertise it — a tool that takes no free-text query can never
+ * produce it, and declaring it there would advertise a failure mode that
+ * cannot happen.
+ *
+ * Unlike the service arrays in this module, this one is thrown from a tool
+ * handler via `ctx.fail('blank_query', …)`, so its recovery hint resolves
+ * through `ctx.recoveryFor` and it stays out of {@link ServiceErrorReason}.
+ */
+export const NCBI_QUERY_INPUT_ERRORS = [
+    {
+        reason: 'blank_query',
+        code: JsonRpcErrorCode.ValidationError,
+        when: 'The query holds no search term once whitespace, and any markup the tool strips first, are removed — so NCBI would receive a blank term.',
+        recovery: 'Supply a nonblank search term; NCBI cannot search a blank term and retrying the same input will not help.',
+        retryable: false,
+    },
+];
 /**
  * Failure modes the Unpaywall service layer can surface. Tools that consume
  * `getUnpaywallService()` (currently `pubmed_fetch_fulltext`) should spread

package/dist/services/error-contracts.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/services/europe-pmc/europe-pmc-service.d.ts CHANGED Viewed

@@ -3,9 +3,9 @@
  * retries, and JATS XML parsing. `search()` covers keyword discovery across the
  * EPMC corpus (MED/PMC/PPR/PAT/AGR), `fetchRecords()` resolves specific records
  * by `source` + EPMC id, `fullTextXml()` fetches a record's full-text JATS, and
- * `citations()` / `references()` walk EPMC's link graph. The XML parser matches
- * NCBI's ordered config so `parsePmcArticle` consumes the result without
- * modification.
+ * `citations()` / `references()` walk EPMC's link graph. The XML parser is built
+ * from the same `ORDERED_XML_PARSER_OPTIONS` NCBI's ordered parser uses, so
+ * `parsePmcArticle` consumes the result without modification.
  *
  * Optional service: only constructed when `EUROPEPMC_ENABLED=true` (the
  * default). `getEuropePmcService()` returns `undefined` when disabled so

package/dist/services/europe-pmc/europe-pmc-service.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"europe-pmc-service.d.ts","sourceRoot":"","sources":["../../../src/services/europe-pmc/europe-pmc-service.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;GAcG;AAgBH,OAAO,KAAK,EAAE,QAAQ,EAAgB,MAAM,4CAA4C,CAAC;AAGzF,OAAO,EAAE,kBAAkB,EAAE,MAAM,iBAAiB,CAAC;AACrD,OAAO,EAAE,qBAAqB,EAAE,MAAM,oBAAoB,CAAC;AAC3D,OAAO,KAAK,EACV,uBAAuB,EAEvB,kBAAkB,EAElB,sBAAsB,EACtB,kBAAkB,EAClB,qBAAqB,EAErB,qBAAqB,EACrB,eAAe,EAChB,MAAM,YAAY,CAAC;AAkDpB;;;;;;;;;GASG;AACH,qBAAa,gBAAgB;IAIzB,OAAO,CAAC,QAAQ,CAAC,MAAM;IACvB,OAAO,CAAC,QAAQ,CAAC,KAAK;IACtB,OAAO,CAAC,QAAQ,CAAC,UAAU;IAL7B,OAAO,CAAC,QAAQ,CAAC,gBAAgB,CAAY;IAE7C,YACmB,MAAM,EAAE,kBAAkB,EAC1B,KAAK,EAAE,qBAAqB,EAC5B,UAAU,EAAE,MAAM,EAQpC;IAED;;;OAGG;IACG,MAAM,CAAC,MAAM,EAAE,qBAAqB,GAAG,OAAO,CAAC,qBAAqB,CAAC,CA6F1E;IAED;;;;;;;;;;OAUG;IACG,YAAY,CAChB,IAAI,EAAE,SAAS,kBAAkB,EAAE,EACnC,MAAM,CAAC,EAAE,WAAW,GACnB,OAAO,CAAC,kBAAkB,EAAE,CAAC,CAQ/B;IAED;;;;;;;OAOG;IACG,WAAW,CACf,MAAM,EAAE,MAAM,EACd,MAAM,EAAE,eAAe,EACvB,MAAM,CAAC,EAAE,WAAW,GACnB,OAAO,CAAC,uBAAuB,CAAC,CAgBlC;IAED;;;;;;;;;;OAUG;IACH,SAAS,CACP,IAAI,EAAE,MAAM,EACZ,QAAQ,EAAE,MAAM,EAChB,IAAI,EAAE,MAAM,EACZ,MAAM,CAAC,EAAE,WAAW,GACnB,OAAO,CAAC,sBAAsB,CAAC,CAQjC;IAED;;;;;;;;;;OAUG;IACH,UAAU,CACR,IAAI,EAAE,MAAM,EACZ,QAAQ,EAAE,MAAM,EAChB,IAAI,EAAE,MAAM,EACZ,MAAM,CAAC,EAAE,WAAW,GACnB,OAAO,CAAC,sBAAsB,CAAC,CAQjC;IAED;;;;;OAKG;YACW,iBAAiB;IAsE/B;;;;;;;;OAQG;IACH,gBAAgB,CAAC,GAAG,EAAE,MAAM,GAAG,QAAQ,GAAG,SAAS,CA8BlD;IAED;;;;OAIG;YACW,SAAS;CAoDxB;AAMD;;;;GAIG;AACH,wBAAgB,oBAAoB,IAAI,IAAI,CAyB3C;AAED,6EAA6E;AAC7E,wBAAgB,mBAAmB,IAAI,gBAAgB,GAAG,SAAS,CAElE"}

package/dist/services/europe-pmc/europe-pmc-service.js CHANGED Viewed

@@ -3,9 +3,9 @@
  * retries, and JATS XML parsing. `search()` covers keyword discovery across the
  * EPMC corpus (MED/PMC/PPR/PAT/AGR), `fetchRecords()` resolves specific records
  * by `source` + EPMC id, `fullTextXml()` fetches a record's full-text JATS, and
- * `citations()` / `references()` walk EPMC's link graph. The XML parser matches
- * NCBI's ordered config so `parsePmcArticle` consumes the result without
- * modification.
+ * `citations()` / `references()` walk EPMC's link graph. The XML parser is built
+ * from the same `ORDERED_XML_PARSER_OPTIONS` NCBI's ordered parser uses, so
+ * `parsePmcArticle` consumes the result without modification.
  *
  * Optional service: only constructed when `EUROPEPMC_ENABLED=true` (the
  * default). `getEuropePmcService()` returns `undefined` when disabled so
@@ -19,6 +19,7 @@ import { logger, requestContextService } from '@cyanheads/mcp-ts-core/utils';
 import { XMLParser, XMLValidator } from 'fast-xml-parser';
 import { getServerConfig } from '../../config/server-config.js';
 import { recoveryFor } from '../error-contracts.js';
+import { ORDERED_XML_PARSER_OPTIONS } from '../ncbi/parsing/ordered-xml-parser-options.js';
 import { ensureArray } from '../ncbi/parsing/xml-helpers.js';
 import { isTransient } from '../retry-policy.js';
 import { EuropePmcApiClient } from './api-client.js';
@@ -89,20 +90,11 @@ export class EuropePmcService {
         this.queue = queue;
         this.maxRetries = maxRetries;
         /**
-         * EPMC's fullTextXML is JATS Z39.96 — same DTD PMC uses — so the parser
-         * config mirrors `NcbiResponseHandler.orderedXmlParser`. `preserveOrder`
-         * keeps inline mixed content readable; `trimValues: false` retains spaces
-         * between text and inline children.
+         * EPMC's fullTextXML is JATS Z39.96 — the same DTD PMC uses, consumed by
+         * the same `parsePmcArticle` — so it is built from the one shared options
+         * constant rather than a second copy that can drift. (#127)
          */
-        this.orderedXmlParser = new XMLParser({
-            preserveOrder: true,
-            ignoreAttributes: false,
-            attributeNamePrefix: '@_',
-            parseTagValue: true,
-            trimValues: false,
-            processEntities: true,
-            htmlEntities: true,
-        });
+        this.orderedXmlParser = new XMLParser(ORDERED_XML_PARSER_OPTIONS);
     }
     /**
      * Search Europe PMC. Cursor-based pagination — pass `cursorMark: '*'` (or

package/dist/services/europe-pmc/europe-pmc-service.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/services/ncbi/parsing/ordered-xml-parser-options.d.ts ADDED Viewed

@@ -0,0 +1,44 @@
+/**
+ * @fileoverview fast-xml-parser options shared by every JATS parser instance in
+ * this server. PMC EFetch and Europe PMC both serve JATS Z39.96 and both feed
+ * `parsePmcArticle`, so their parsers must agree field-for-field: a divergence
+ * makes the same article render differently depending on which upstream
+ * answered. Dependency-free leaf — it imports a type and nothing else — so any
+ * service can import it without introducing a cycle.
+ * @module src/services/ncbi/parsing/ordered-xml-parser-options
+ */
+/**
+ * NCBI and Europe PMC responses routinely carry numeric character references
+ * for punctuation and diacritics, especially in page ranges and author names.
+ * Keep entity processing enabled, but cap aggregate expansion so a hostile or
+ * malformed payload cannot turn entity resolution into a denial of service. The
+ * ceiling is high enough for trusted bibliographic payloads.
+ */
+export declare const XML_PROCESS_ENTITIES_OPTIONS: {
+    readonly enabled: true;
+    readonly maxTotalExpansions: 100000;
+};
+/**
+ * Options for the JATS mixed-content parsers. `preserveOrder` keeps document
+ * order so inline markup in `<p>`, `<abstract>`, `<title>` doesn't collapse into
+ * reordered text. `trimValues: false` retains spacing between text nodes and
+ * adjacent inline children. `parseTagValue: false` keeps bibliographic tokens
+ * verbatim — page ranges like `4002.e26`, zero-padded pages, and reference
+ * labels like `1.` would otherwise coerce to `Number` (→ `4.002e+29`, `123`,
+ * `1`); every value on this path is `String()`-ed downstream, so coercion is
+ * pure downside. Entity decoding is unaffected (governed by `processEntities` /
+ * `htmlEntities`), so page-range en-dashes still resolve. (#69, #127)
+ */
+export declare const ORDERED_XML_PARSER_OPTIONS: {
+    readonly preserveOrder: true;
+    readonly ignoreAttributes: false;
+    readonly attributeNamePrefix: '@_';
+    readonly parseTagValue: false;
+    readonly trimValues: false;
+    readonly processEntities: {
+        readonly enabled: true;
+        readonly maxTotalExpansions: 100000;
+    };
+    readonly htmlEntities: true;
+};
+//# sourceMappingURL=ordered-xml-parser-options.d.ts.map

package/dist/services/ncbi/parsing/ordered-xml-parser-options.d.ts.map ADDED Viewed

	@@ -0,0 +1 @@
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package/dist/services/ncbi/parsing/ordered-xml-parser-options.js ADDED Viewed

@@ -0,0 +1,41 @@
+/**
+ * @fileoverview fast-xml-parser options shared by every JATS parser instance in
+ * this server. PMC EFetch and Europe PMC both serve JATS Z39.96 and both feed
+ * `parsePmcArticle`, so their parsers must agree field-for-field: a divergence
+ * makes the same article render differently depending on which upstream
+ * answered. Dependency-free leaf — it imports a type and nothing else — so any
+ * service can import it without introducing a cycle.
+ * @module src/services/ncbi/parsing/ordered-xml-parser-options
+ */
+/**
+ * NCBI and Europe PMC responses routinely carry numeric character references
+ * for punctuation and diacritics, especially in page ranges and author names.
+ * Keep entity processing enabled, but cap aggregate expansion so a hostile or
+ * malformed payload cannot turn entity resolution into a denial of service. The
+ * ceiling is high enough for trusted bibliographic payloads.
+ */
+export const XML_PROCESS_ENTITIES_OPTIONS = {
+    enabled: true,
+    maxTotalExpansions: 100_000,
+};
+/**
+ * Options for the JATS mixed-content parsers. `preserveOrder` keeps document
+ * order so inline markup in `<p>`, `<abstract>`, `<title>` doesn't collapse into
+ * reordered text. `trimValues: false` retains spacing between text nodes and
+ * adjacent inline children. `parseTagValue: false` keeps bibliographic tokens
+ * verbatim — page ranges like `4002.e26`, zero-padded pages, and reference
+ * labels like `1.` would otherwise coerce to `Number` (→ `4.002e+29`, `123`,
+ * `1`); every value on this path is `String()`-ed downstream, so coercion is
+ * pure downside. Entity decoding is unaffected (governed by `processEntities` /
+ * `htmlEntities`), so page-range en-dashes still resolve. (#69, #127)
+ */
+export const ORDERED_XML_PARSER_OPTIONS = {
+    preserveOrder: true,
+    ignoreAttributes: false,
+    attributeNamePrefix: '@_',
+    parseTagValue: false,
+    trimValues: false,
+    processEntities: XML_PROCESS_ENTITIES_OPTIONS,
+    htmlEntities: true,
+};
+//# sourceMappingURL=ordered-xml-parser-options.js.map

package/dist/services/ncbi/parsing/ordered-xml-parser-options.js.map ADDED Viewed

@@ -0,0 +1 @@

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package/dist/services/ncbi/parsing/pmc-article-parser.d.ts CHANGED Viewed

@@ -7,25 +7,85 @@
  * inline children and drops body sections for markup-heavy articles.
  * @module src/services/ncbi/parsing/pmc-article-parser
  */
-import type { ParsedPmcArticle, ParsedPmcAuthor, ParsedPmcReference, ParsedPmcSection } from '../types.js';
+import type { ParsedPmcArticle, ParsedPmcAsset, ParsedPmcAuthor, ParsedPmcReference, ParsedPmcSection, ParsedPmcTable } from '../types.js';
 import { type JatsNode } from './pmc-xml-helpers.js';
 /** Extract authors from a single `<contrib-group>` node. Non-author contributors are skipped. */
 export declare function extractJatsAuthors(contribGroup: JatsNode | undefined): ParsedPmcAuthor[];
 /**
  * Extract body sections from a `<body>` node, walking children in document order.
- * Consecutive bare `<p>` siblings are collected into an untitled section so
- * articles with mixed structure (direct paragraphs + trailing `<sec>`, common
- * in manuscript-submitted PMC deposits) preserve their main text.
+ * Consecutive bare `<p>` siblings — and any block element sitting directly under
+ * `<body>` — are collected into an untitled section so articles with mixed
+ * structure (direct paragraphs + trailing `<sec>`, common in
+ * manuscript-submitted PMC deposits) preserve their main text.
+ *
+ * A `<body>` whose whole content is one block and no `<sec>` therefore yields a
+ * section carrying that block's text, rather than the empty list the tool layer
+ * reads as an article with no body at all. Legacy
+ * `<preformat preformat-type="pmc-ocr-text">` deposits, which put the entire
+ * article in one such element, are the case that matters. (#130)
  */
 export declare function extractBodySections(body: JatsNode | undefined): ParsedPmcSection[];
 /**
- * Extract references from a `<back>` node. Prefers `<mixed-citation>` over
- * `<element-citation>`, descending into `<citation-alternatives>` when a ref
- * carries both forms there rather than as direct children of `<ref>`. Both
- * forms are rendered child-by-child so adjacent elements stay separable (see
- * `renderMixedCitation` and `renderElementCitation`).
+ * Extract every `<table-wrap>` under `root` in document order — pass the
+ * `<article>` node.
+ *
+ * The walk covers the whole article rather than `<body>` alone: about a quarter
+ * of real tables sit in `<floats-group>`, `<back>/<sec>`, `<table-wrap-group>`
+ * or `<app-group>/<app>`, so a body-scoped extractor drops them. Each table
+ * names the innermost enclosing `<sec>` wherever that sits — a back-matter or
+ * appendix section counts, and naming it is the reader's only positional cue
+ * there. Only a table inside no `<sec>` at all, such as a `<floats-group>`
+ * deposit, carries no section name.
+ *
+ * Only XHTML `<tr>`/`<td>`/`<th>` bodies are read. **Decision, not an
+ * oversight:** across a 283-table survey of open-access records, 276 were XHTML,
+ * 7 were graphic-only deposits and 0 used the CALS `<tgroup>` model. Graphic-only
+ * and CALS bodies therefore take the unextractable path — returned with their
+ * label and caption and a reason — rather than adding a second table model no
+ * observed record needs. Revisit only if CALS shows up in the wild. (#111)
  */
-export declare function extractReferences(back: JatsNode | undefined): ParsedPmcReference[];
+export declare function extractPmcTables(root: JatsNode | undefined): ParsedPmcTable[];
+/**
+ * Widest grid a single table row may occupy, and the ceiling every declared
+ * span is clamped to. Real deposits are far narrower — the widest row observed
+ * across a live sample was 15 columns — so this bounds a malformed or hostile
+ * span rather than limiting any genuine table: `colspan="99999999"` costs a
+ * bounded row instead of an unbounded allocation, and a `rowspan` that large
+ * carries a bounded number of rows down. How many rows a table has is set by its
+ * source `<tr>` elements and needs no cap of its own. (#111)
+ */
+export declare const MAX_TABLE_COLUMNS = 512;
+/**
+ * Extract every `<fig>` and `<supplementary-material>` under `root` in document
+ * order — pass the `<article>` node.
+ *
+ * Whole-article, for the reason the table walk is: 17% of figures and 23% of
+ * supplementary material sit outside `<body>` entirely — `<floats-group>`
+ * deposits, `<back>/<sec>` and `<app-group>/<app>` placements, and figures
+ * hanging off the abstract in `<front>`. Each asset names the innermost
+ * enclosing `<sec>` wherever that sits, an untitled one inheriting its parent's
+ * title, so the reader keeps a positional cue; an asset inside no `<sec>` at all
+ * carries no section name. (#130)
+ */
+export declare function extractPmcAssets(root: JatsNode | undefined): ParsedPmcAsset[];
+/**
+ * Extract references from anywhere under `root` — pass the `<article>` node to
+ * cover a whole document, or a `<back>` node to scope the search to it.
+ *
+ * `<ref-list>` placement is not uniform: roughly 60% of Europe PMC deposits nest
+ * it under `body/sec/sec` and the rest put it directly under `<back>`, so a
+ * search scoped to a direct `<back>` child misses the majority. Every
+ * `<ref-list>` descendant is collected in document order instead, and a `<ref>`
+ * id already seen is skipped so a document exposing the same list under both
+ * containers still yields each reference once. (#116)
+ *
+ * Prefers `<mixed-citation>` over `<element-citation>`, descending into
+ * `<citation-alternatives>` when a ref carries both forms there rather than as
+ * direct children of `<ref>`. Both forms are rendered child-by-child so adjacent
+ * elements stay separable (see `renderMixedCitation` and
+ * `renderElementCitation`).
+ */
+export declare function extractReferences(root: JatsNode | undefined): ParsedPmcReference[];
 /**
  * Parse a single JATS `<article>` node (from PMC EFetch via the ordered parser)
  * into a structured `ParsedPmcArticle`. The input node is the element wrapper

package/dist/services/ncbi/parsing/pmc-article-parser.d.ts.map CHANGED Viewed

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