@cyanheads/pubmed-mcp-server 2.10.10 → 2.10.12
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.
- package/AGENTS.md +1 -1
- package/CLAUDE.md +1 -1
- package/README.md +10 -3
- package/dist/mcp-server/resources/definitions/database-info.resource.js +6 -6
- package/dist/mcp-server/resources/definitions/database-info.resource.js.map +1 -1
- package/dist/mcp-server/tools/definitions/_schemas.d.ts +16 -0
- package/dist/mcp-server/tools/definitions/_schemas.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/_schemas.js +20 -0
- package/dist/mcp-server/tools/definitions/_schemas.js.map +1 -1
- package/dist/mcp-server/tools/definitions/convert-ids.tool.d.ts +6 -0
- package/dist/mcp-server/tools/definitions/convert-ids.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/convert-ids.tool.js +28 -3
- package/dist/mcp-server/tools/definitions/convert-ids.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/fetch-articles.tool.d.ts +27 -0
- package/dist/mcp-server/tools/definitions/fetch-articles.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/fetch-articles.tool.js +166 -24
- package/dist/mcp-server/tools/definitions/fetch-articles.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts +1 -0
- package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js +10 -6
- package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/find-related.tool.d.ts +4 -0
- package/dist/mcp-server/tools/definitions/find-related.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/find-related.tool.js +40 -4
- package/dist/mcp-server/tools/definitions/find-related.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/format-citations.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/format-citations.tool.js +11 -13
- package/dist/mcp-server/tools/definitions/format-citations.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/lookup-citation.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/lookup-citation.tool.js +42 -8
- package/dist/mcp-server/tools/definitions/lookup-citation.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/search-articles.tool.d.ts +4 -0
- package/dist/mcp-server/tools/definitions/search-articles.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/search-articles.tool.js +37 -2
- package/dist/mcp-server/tools/definitions/search-articles.tool.js.map +1 -1
- package/dist/services/error-contracts.d.ts +17 -0
- package/dist/services/error-contracts.d.ts.map +1 -1
- package/dist/services/error-contracts.js +19 -0
- package/dist/services/error-contracts.js.map +1 -1
- package/dist/services/ncbi/formatting/citation-formatter.d.ts +4 -20
- package/dist/services/ncbi/formatting/citation-formatter.d.ts.map +1 -1
- package/dist/services/ncbi/formatting/citation-formatter.js +406 -31
- package/dist/services/ncbi/formatting/citation-formatter.js.map +1 -1
- package/dist/services/ncbi/ncbi-service.d.ts +3 -2
- package/dist/services/ncbi/ncbi-service.d.ts.map +1 -1
- package/dist/services/ncbi/ncbi-service.js +22 -10
- package/dist/services/ncbi/ncbi-service.js.map +1 -1
- package/dist/services/ncbi/parsing/article-parser.d.ts +45 -2
- package/dist/services/ncbi/parsing/article-parser.d.ts.map +1 -1
- package/dist/services/ncbi/parsing/article-parser.js +201 -2
- package/dist/services/ncbi/parsing/article-parser.js.map +1 -1
- package/dist/services/ncbi/parsing/esummary-parser.d.ts +11 -1
- package/dist/services/ncbi/parsing/esummary-parser.d.ts.map +1 -1
- package/dist/services/ncbi/parsing/esummary-parser.js +48 -8
- package/dist/services/ncbi/parsing/esummary-parser.js.map +1 -1
- package/dist/services/ncbi/parsing/pmc-article-parser.d.ts.map +1 -1
- package/dist/services/ncbi/parsing/pmc-article-parser.js +33 -4
- package/dist/services/ncbi/parsing/pmc-article-parser.js.map +1 -1
- package/dist/services/ncbi/parsing/pmc-xml-helpers.d.ts +19 -0
- package/dist/services/ncbi/parsing/pmc-xml-helpers.d.ts.map +1 -1
- package/dist/services/ncbi/parsing/pmc-xml-helpers.js +81 -2
- package/dist/services/ncbi/parsing/pmc-xml-helpers.js.map +1 -1
- package/dist/services/ncbi/parsing/xml-helpers.d.ts +29 -3
- package/dist/services/ncbi/parsing/xml-helpers.d.ts.map +1 -1
- package/dist/services/ncbi/parsing/xml-helpers.js +46 -0
- package/dist/services/ncbi/parsing/xml-helpers.js.map +1 -1
- package/dist/services/ncbi/response-handler.d.ts.map +1 -1
- package/dist/services/ncbi/response-handler.js +96 -28
- package/dist/services/ncbi/response-handler.js.map +1 -1
- package/dist/services/ncbi/types.d.ts +172 -2
- package/dist/services/ncbi/types.d.ts.map +1 -1
- package/package.json +1 -1
- package/server.json +3 -3
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1
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+
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@@ -33,8 +33,9 @@ export declare class NcbiService {
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*
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* Results come back one per submitted citation, in submission order, carrying
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* the caller's `key`. Correlation runs on the wire key (see
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-
* {@link wireKeysFor}), never on `key` itself — that label is caller-supplied
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-
* and may
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+
* {@link wireKeysFor}), never on `key` itself — that label is caller-supplied,
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+
* so it may repeat and may carry characters that break the wire format.
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+
* (#113, #125)
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*/
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eCitMatch(citations: ECitMatchCitation[], options?: NcbiCallOptions): Promise<ECitMatchResult[]>;
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/**
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"ncbi-service.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/ncbi-service.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAeH,OAAO,EAAE,aAAa,EAAE,MAAM,iBAAiB,CAAC;AAChD,OAAO,EAAE,gBAAgB,EAAE,MAAM,oBAAoB,CAAC;AACtD,OAAO,EAAE,mBAAmB,EAAE,MAAM,uBAAuB,CAAC;AAC5D,OAAO,EACL,KAAK,iBAAiB,EACtB,KAAK,eAAe,EAGpB,KAAK,aAAa,EAGlB,KAAK,YAAY,EAEjB,KAAK,cAAc,EACnB,KAAK,eAAe,EAGpB,KAAK,eAAe,EACpB,KAAK,kBAAkB,EACvB,KAAK,iBAAiB,EACtB,KAAK,mBAAmB,EACzB,MAAM,YAAY,CAAC;
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1
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+
{"version":3,"file":"ncbi-service.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/ncbi-service.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAeH,OAAO,EAAE,aAAa,EAAE,MAAM,iBAAiB,CAAC;AAChD,OAAO,EAAE,gBAAgB,EAAE,MAAM,oBAAoB,CAAC;AACtD,OAAO,EAAE,mBAAmB,EAAE,MAAM,uBAAuB,CAAC;AAC5D,OAAO,EACL,KAAK,iBAAiB,EACtB,KAAK,eAAe,EAGpB,KAAK,aAAa,EAGlB,KAAK,YAAY,EAEjB,KAAK,cAAc,EACnB,KAAK,eAAe,EAGpB,KAAK,eAAe,EACpB,KAAK,kBAAkB,EACvB,KAAK,iBAAiB,EACtB,KAAK,mBAAmB,EACzB,MAAM,YAAY,CAAC;AAgFpB;;;GAGG;AACH,qBAAa,WAAW;IAEpB,OAAO,CAAC,QAAQ,CAAC,SAAS;IAC1B,OAAO,CAAC,QAAQ,CAAC,KAAK;IACtB,OAAO,CAAC,QAAQ,CAAC,eAAe;IAChC,OAAO,CAAC,QAAQ,CAAC,UAAU;IAC3B,OAAO,CAAC,QAAQ,CAAC,eAAe;IALlC,YACmB,SAAS,EAAE,aAAa,EACxB,KAAK,EAAE,gBAAgB,EACvB,eAAe,EAAE,mBAAmB,EACpC,UAAU,EAAE,MAAM,EAClB,eAAe,EAAE,MAAM,EACtC;IAEE,OAAO,CAAC,MAAM,EAAE,iBAAiB,EAAE,OAAO,CAAC,EAAE,eAAe,GAAG,OAAO,CAAC,aAAa,CAAC,CAoB1F;IAEK,QAAQ,CAAC,MAAM,EAAE,iBAAiB,EAAE,OAAO,CAAC,EAAE,eAAe,GAAG,OAAO,CAAC,cAAc,CAAC,CAO5F;IAED,MAAM,CAAC,CAAC,GAAG;QAAE,gBAAgB,CAAC,EAAE,mBAAmB,CAAA;KAAE,EACnD,MAAM,EAAE,iBAAiB,EACzB,OAAO,GAAE,kBAAuC,GAC/C,OAAO,CAAC,CAAC,CAAC,CAIZ;IAED,KAAK,CAAC,CAAC,GAAG,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC/B,MAAM,EAAE,iBAAiB,EACzB,OAAO,CAAC,EAAE,eAAe,GACxB,OAAO,CAAC,CAAC,CAAC,CAKZ;IAEK,MAAM,CAAC,MAAM,EAAE,iBAAiB,EAAE,OAAO,CAAC,EAAE,eAAe,GAAG,OAAO,CAAC,YAAY,CAAC,CA+BxF;IAED,KAAK,CAAC,MAAM,EAAE,iBAAiB,EAAE,OAAO,CAAC,EAAE,eAAe,GAAG,OAAO,CAAC,OAAO,CAAC,CAK5E;IAED;;;;;;;;;OASG;IACG,SAAS,CACb,SAAS,EAAE,iBAAiB,EAAE,EAC9B,OAAO,CAAC,EAAE,eAAe,GACxB,OAAO,CAAC,eAAe,EAAE,CAAC,CAmE5B;IAED;;;OAGG;IACG,SAAS,CACb,GAAG,EAAE,MAAM,EAAE,EACb,MAAM,CAAC,EAAE,MAAM,EACf,OAAO,CAAC,EAAE,eAAe,GACxB,OAAO,CAAC,eAAe,EAAE,CAAC,CA+E5B;IAED,sEAAsE;IACtE,OAAO,CAAC,MAAM,CAAC,QAAQ,CAAC,eAAe,CAIpC;IAEH,6FAA6F;IAC7F,OAAO,CAAC,MAAM,CAAC,QAAQ,CAAC,cAAc,CAAU;IAEhD;;;;;OAKG;YACW,eAAe;IAkC7B;;;;;OAKG;YACW,SAAS;IAgEvB;;;;;;;;OAQG;IACH,OAAO,CAAC,cAAc;CA2BvB;AAMD,qEAAqE;AACrE,wBAAgB,eAAe,IAAI,IAAI,CA8BtC;AAED,mEAAmE;AACnE,wBAAgB,cAAc,IAAI,WAAW,CAG5C"}
|
|
@@ -43,15 +43,16 @@ function normalizeDiagnosticList(list) {
|
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|
43
43
|
* The tracking token each citation is submitted to ECitMatch under — echoed
|
|
44
44
|
* back verbatim on that citation's response row, and unique within the request.
|
|
45
45
|
*
|
|
46
|
-
*
|
|
47
|
-
* reconciling response rows on it collapses two
|
|
48
|
-
*
|
|
49
|
-
*
|
|
50
|
-
*
|
|
46
|
+
* Always the citation's 1-based position, never `ECitMatchCitation.key`. That
|
|
47
|
+
* label is caller-supplied, so reconciling response rows on it collapses two
|
|
48
|
+
* citations carrying the same label onto one row and hands the second
|
|
49
|
+
* citation's PMID to the first (#113); and a `|` inside it shifts the
|
|
50
|
+
* pipe-delimited field layout of the submitted line, so NCBI's echoed row no
|
|
51
|
+
* longer reconciles and a citation it matched comes back as not_found (#125).
|
|
52
|
+
* Keeping the label off the wire entirely removes both.
|
|
51
53
|
*/
|
|
52
54
|
function wireKeysFor(citations) {
|
|
53
|
-
|
|
54
|
-
return new Set(keys).size === keys.length ? keys : citations.map((_, i) => String(i + 1));
|
|
55
|
+
return citations.map((_, i) => String(i + 1));
|
|
55
56
|
}
|
|
56
57
|
/** Sentinel reason used when the service-level deadline expires. */
|
|
57
58
|
class NcbiDeadlineExceeded extends Error {
|
|
@@ -174,8 +175,9 @@ export class NcbiService {
|
|
|
174
175
|
*
|
|
175
176
|
* Results come back one per submitted citation, in submission order, carrying
|
|
176
177
|
* the caller's `key`. Correlation runs on the wire key (see
|
|
177
|
-
* {@link wireKeysFor}), never on `key` itself — that label is caller-supplied
|
|
178
|
-
* and may
|
|
178
|
+
* {@link wireKeysFor}), never on `key` itself — that label is caller-supplied,
|
|
179
|
+
* so it may repeat and may carry characters that break the wire format.
|
|
180
|
+
* (#113, #125)
|
|
179
181
|
*/
|
|
180
182
|
async eCitMatch(citations, options) {
|
|
181
183
|
const wireKeys = wireKeysFor(citations);
|
|
@@ -223,7 +225,7 @@ export class NcbiService {
|
|
|
223
225
|
// one row can never stand in for a second citation — then restore the
|
|
224
226
|
// caller's label on the way out. Every input gets a result row, so callers
|
|
225
227
|
// can rely on results.length === citations.length and on results[i]
|
|
226
|
-
// describing citations[i]. (#54, #113)
|
|
228
|
+
// describing citations[i]. (#54, #113, #125)
|
|
227
229
|
const parsedByWireKey = new Map(parsed.map((r) => [r.key, r]));
|
|
228
230
|
return citations.map((c, i) => {
|
|
229
231
|
const row = parsedByWireKey.get(wireKeys[i] ?? '');
|
|
@@ -237,6 +239,16 @@ export class NcbiService {
|
|
|
237
239
|
* Accepts up to 200 IDs in a single request. Only works for articles in PMC.
|
|
238
240
|
*/
|
|
239
241
|
async idConvert(ids, idtype, options) {
|
|
242
|
+
// A comma is the ID Converter's list delimiter in every encoding, so an
|
|
243
|
+
// element carrying one is indistinguishable from two submitted IDs: the
|
|
244
|
+
// upstream answers 200 with more records than were submitted and the
|
|
245
|
+
// one-record-per-input contract breaks. Reject at the service boundary so
|
|
246
|
+
// no caller can reach the splitting behavior, whichever tool built the
|
|
247
|
+
// input. (#120)
|
|
248
|
+
const packed = ids.find((id) => id.includes(','));
|
|
249
|
+
if (packed !== undefined) {
|
|
250
|
+
throw validationError(`PMC ID Converter identifier "${packed}" contains a comma, which the API reads as a list delimiter. Submit one identifier per array element.`, { idType: idtype, idCount: ids.length });
|
|
251
|
+
}
|
|
240
252
|
// The PMC ID Converter rejects an entire batch (HTTP 400) when PMC-prefixed
|
|
241
253
|
// and bare-digit PMCIDs are mixed, even though it accepts each form on its
|
|
242
254
|
// own. Canonicalize bare digits to "PMC"+digits so every pmcid batch is
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
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@@ -3,7 +3,7 @@
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* typically from EFetch results.
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* @module src/services/ncbi/parsing/article-parser
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*/
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-
import type { ParsedArticle, ParsedArticleAuthor, ParsedArticleDate, ParsedGrant, ParsedJournalInfo, ParsedMeshTerm, ParseFullArticleOptions, XmlArticle, XmlArticleIdList, XmlAuthorList, XmlGrantList, XmlJournal, XmlKeywordList, XmlMedlineCitation, XmlMeshHeadingList, XmlPublicationTypeList, XmlPubmedArticle } from '../types.js';
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import type { ParsedArticle, ParsedArticleAuthor, ParsedArticleDate, ParsedBookInfo, ParsedGrant, ParsedJournalInfo, ParsedMeshTerm, ParseFullArticleOptions, XmlArticle, XmlArticleIdList, XmlAuthorList, XmlBookDocument, XmlGrantList, XmlJournal, XmlKeywordList, XmlMedlineCitation, XmlMeshHeadingList, XmlPublicationTypeList, XmlPubmedArticle, XmlPubmedArticleSet, XmlPubmedBookArticle } from '../types.js';
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/**
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* Result of extracting authors with deduplicated affiliations.
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*/
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@@ -22,7 +22,7 @@ export declare function extractAuthors(authorListXml?: XmlAuthorList): Extracted
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/**
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* Extracts and formats journal information from XML.
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* @param journalXml - The XML Journal element from an Article.
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-
* @param articleXml - The XML Article element (for Pagination).
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+
* @param articleXml - The XML Article element (for Pagination and ELocationID).
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* @returns Formatted journal information.
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*/
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export declare function extractJournalInfo(journalXml?: XmlJournal, articleXml?: XmlArticle): ParsedJournalInfo | undefined;
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@@ -95,4 +95,47 @@ export declare function extractArticleDates(articleXml?: XmlArticle): ParsedArti
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* @returns A fully parsed article object.
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*/
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export declare function parseFullArticle(xmlArticle: XmlPubmedArticle, options?: ParseFullArticleOptions): ParsedArticle;
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+
/**
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99
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+
* Extract the containing book from a `BookDocument`.
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+
*
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101
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+
* `Book/AuthorList` is split on its `Type` attribute: `editors` is the only
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+
* value that makes a list editors, so an untyped list is read as authors —
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103
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+
* mislabelling real authors as editors would put them in the wrong slot of every
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* citation style.
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105
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+
* @param bookDocumentXml - The XML BookDocument element.
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+
* @returns The parsed book, with absent elements omitted rather than emptied.
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+
*/
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108
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+
export declare function extractBookInfo(bookDocumentXml: XmlBookDocument): ParsedBookInfo;
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+
/**
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110
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+
* Parse a `PubmedBookArticle` — an NCBI Bookshelf record — into the same
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111
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+
* {@link ParsedArticle} shape a journal article produces.
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112
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+
*
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113
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+
* `ArticleTitle` is the discriminator: a record carrying one is a chapter, and
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114
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+
* one without it is the whole book, whose `title` then comes from `BookTitle`.
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115
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+
* `journalInfo` is never populated — a Bookshelf record has no journal, and
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116
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+
* promoting the book title into one would invent a venue that does not exist.
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+
*
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118
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+
* Chapter authors come from `BookDocument/AuthorList`; a book-level author list
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119
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+
* stands in only when the chapter carries none of its own. `Sections`,
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120
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+
* `ReferenceList` and `ItemList` are not read — metadata and abstract only. (#114)
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121
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+
* @param xmlBookArticle - The raw XML PubmedBookArticle element.
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122
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+
* @returns A parsed record with `recordType` set to `book-chapter` or `book`.
|
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123
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+
*/
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124
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+
export declare function parseFullBookArticle(xmlBookArticle: XmlPubmedBookArticle): ParsedArticle;
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125
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+
/**
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126
|
+
* Parse a whole `PubmedArticleSet` — every `PubmedArticle` and every
|
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127
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*/
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export declare function parseArticleSet(articleSet: XmlPubmedArticleSet | undefined, options?: ParseFullArticleOptions): ParsedArticle[];
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{"version":3,"file":"article-parser.d.ts","sourceRoot":"","sources":["../../../../src/services/ncbi/parsing/article-parser.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,KAAK,EACV,aAAa,EACb,mBAAmB,EACnB,iBAAiB,
|
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{"version":3,"file":"article-parser.d.ts","sourceRoot":"","sources":["../../../../src/services/ncbi/parsing/article-parser.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,KAAK,EACV,aAAa,EACb,mBAAmB,EACnB,iBAAiB,EAEjB,cAAc,EACd,WAAW,EACX,iBAAiB,EAEjB,cAAc,EACd,uBAAuB,EAEvB,UAAU,EAEV,gBAAgB,EAEhB,aAAa,EACb,eAAe,EAEf,YAAY,EAEZ,UAAU,EAEV,cAAc,EACd,kBAAkB,EAElB,kBAAkB,EAGlB,sBAAsB,EACtB,gBAAgB,EAChB,mBAAmB,EACnB,oBAAoB,EACrB,MAAM,aAAa,CAAC;AAUrB;;GAEG;AACH,MAAM,WAAW,gBAAgB;IAC/B,YAAY,EAAE,MAAM,EAAE,CAAC;IACvB,OAAO,EAAE,mBAAmB,EAAE,CAAC;CAChC;AAED;;;;;;GAMG;AACH,wBAAgB,cAAc,CAAC,aAAa,CAAC,EAAE,aAAa,GAAG,gBAAgB,CAqD9E;AA2BD;;;;;GAKG;AACH,wBAAgB,kBAAkB,CAChC,UAAU,CAAC,EAAE,UAAU,EACvB,UAAU,CAAC,EAAE,UAAU,GACtB,iBAAiB,GAAG,SAAS,CAmC/B;AAED;;;;GAIG;AACH,wBAAgB,gBAAgB,CAAC,kBAAkB,CAAC,EAAE,kBAAkB,GAAG,cAAc,EAAE,CA8B1F;AAED;;;;GAIG;AACH,wBAAgB,aAAa,CAAC,YAAY,CAAC,EAAE,YAAY,GAAG,WAAW,EAAE,CAmBxE;AAED;;;;;;;GAOG;AACH,wBAAgB,UAAU,CACxB,UAAU,CAAC,EAAE,UAAU,EACvB,uBAAuB,CAAC,EAAE,gBAAgB,GACzC,MAAM,GAAG,SAAS,CAyCpB;AAED;;;;;;GAMG;AACH,wBAAgB,YAAY,CAC1B,UAAU,CAAC,EAAE,UAAU,EACvB,uBAAuB,CAAC,EAAE,gBAAgB,GACzC,MAAM,GAAG,SAAS,CAsBpB;AAED;;;;GAIG;AACH,wBAAgB,uBAAuB,CAAC,sBAAsB,CAAC,EAAE,sBAAsB,GAAG,MAAM,EAAE,CAIjG;AAED;;;;GAIG;AACH,wBAAgB,eAAe,CAAC,eAAe,CAAC,EAAE,cAAc,EAAE,GAAG,cAAc,GAAG,MAAM,EAAE,CAa7F;AAED;;;;;;GAMG;AACH,wBAAgB,mBAAmB,CAAC,WAAW,CAAC,EAAE,UAAU,CAAC,UAAU,CAAC,GAAG,MAAM,GAAG,SAAS,CAyB5F;AAED;;;;GAIG;AACH,wBAAgB,WAAW,CAAC,kBAAkB,CAAC,EAAE,kBAAkB,GAAG,MAAM,GAAG,SAAS,CAGvF;AAED;;;;GAIG;AACH,wBAAgB,mBAAmB,CAAC,UAAU,CAAC,EAAE,UAAU,GAAG,iBAAiB,EAAE,CAShF;AAED;;;;;;GAMG;AACH,wBAAgB,gBAAgB,CAC9B,UAAU,EAAE,gBAAgB,EAC5B,OAAO,GAAE,uBAA4B,GACpC,aAAa,CAkCf;AAkCD;;;;;;;;;GASG;AACH,wBAAgB,eAAe,CAAC,eAAe,EAAE,eAAe,GAAG,cAAc,CAgDhF;AAED;;;;;;;;;;;;;;GAcG;AACH,wBAAgB,oBAAoB,CAAC,cAAc,EAAE,oBAAoB,GAAG,aAAa,CAsDxF;AAED;;;;;;;;;;;;;;GAcG;AACH,wBAAgB,eAAe,CAC7B,UAAU,EAAE,mBAAmB,GAAG,SAAS,EAC3C,OAAO,GAAE,uBAA4B,GACpC,aAAa,EAAE,CAejB"}
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* @module src/services/ncbi/parsing/article-parser
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*/
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import { decodeHtmlEntities } from './text-helpers.js';
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import { ensureArray, getAttribute, getText } from './xml-helpers.js';
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import { ensureArray, getAttribute, getOptionalAttribute, getOptionalText, getText, } from './xml-helpers.js';
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/**
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* Extracts and formats author information from XML, deduplicating affiliations.
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* Affiliations are collected into a single array; each author references them by index.
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});
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return { authors, affiliations: affiliationList };
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}
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/**
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* Picks the electronic article locator from an Article's `ELocationID` list —
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* the publisher-assigned article number carried by journals that do not
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* paginate (`<ELocationID EIdType="pii" ValidYN="Y">2400512</ELocationID>`).
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*
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* DOI-typed entries are skipped: the DOI has its own field and its own
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* selection rules in {@link extractDoi}, and a DOI is not pagination. A locator
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* explicitly marked `ValidYN="N"` is never surfaced, and a valid one wins over
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* an entry with no `ValidYN` attribute at all.
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* @param articleXml - The XML Article element.
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* @returns The locator value and its `EIdType`, or undefined when none applies.
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*/
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function extractELocationId(articleXml) {
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const candidates = ensureArray(articleXml?.ELocationID).filter((eloc) => getAttribute(eloc, 'EIdType') !== 'doi' &&
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getAttribute(eloc, 'ValidYN') !== 'N' &&
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getOptionalText(eloc));
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const locator = candidates.find((eloc) => getAttribute(eloc, 'ValidYN') === 'Y') ?? candidates[0];
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if (!locator)
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return;
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const type = getOptionalAttribute(locator, 'EIdType');
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return { value: getText(locator), ...(type && { type }) };
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}
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/**
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* @param journalXml - The XML Journal element from an Article.
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* @param articleXml - The XML Article element (for Pagination).
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* @param articleXml - The XML Article element (for Pagination and ELocationID).
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* @returns Formatted journal information.
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*/
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export function extractJournalInfo(journalXml, articleXml) {
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@@ -82,6 +104,7 @@ export function extractJournalInfo(journalXml, articleXml) {
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const month = getText(pubDate?.Month);
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const day = getText(pubDate?.Day);
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const medlineDate = getText(pubDate?.MedlineDate);
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const locator = extractELocationId(articleXml);
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return {
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title: getText(journalXml.Title),
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isoAbbreviation: getText(journalXml.ISOAbbreviation),
|
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@@ -90,6 +113,8 @@ export function extractJournalInfo(journalXml, articleXml) {
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volume: getText(journalXml.JournalIssue?.Volume),
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issue: getText(journalXml.JournalIssue?.Issue),
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pages: getText(articleXml?.Pagination?.MedlinePgn),
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...(locator && { elocationId: locator.value }),
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...(locator?.type && { elocationIdType: locator.type }),
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publicationDate: {
|
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...(year && { year }),
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...(month && { month }),
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@@ -352,6 +377,7 @@ export function parseFullArticle(xmlArticle, options = {}) {
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const meshTerms = includeMesh ? extractMeshTerms(medlineCitation?.MeshHeadingList) : undefined;
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const grantList = includeGrants ? extractGrants(article?.GrantList) : undefined;
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return {
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recordType: 'journal-article',
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|
pmid: extractPmid(medlineCitation) ?? '',
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title: getText(article?.ArticleTitle),
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...(abstractText !== undefined && { abstractText }),
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|
@@ -367,4 +393,177 @@ export function parseFullArticle(xmlArticle, options = {}) {
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...(articleDates.length > 0 && { articleDates }),
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};
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}
|
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|
+
// ─── Bookshelf records (PubmedBookArticle) ──────────────────────────────────
|
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|
+
/** Year text from a `PubDate`-shaped element, falling back to a `MedlineDate` span. */
|
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|
+
function extractYear(dateXml) {
|
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|
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if (!dateXml)
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return;
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return getOptionalText(dateXml.Year) ?? getText(dateXml.MedlineDate).match(/\d{4}/)?.[0];
|
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|
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}
|
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|
+
/** First `ArticleId` of the given `IdType`, or undefined. */
|
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|
+
function findArticleId(idListXml, idType) {
|
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|
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for (const articleId of ensureArray(idListXml?.ArticleId)) {
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if (getAttribute(articleId, 'IdType') === idType) {
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|
+
const value = getOptionalText(articleId);
|
|
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|
+
if (value)
|
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|
+
return value;
|
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|
+
}
|
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|
+
}
|
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|
+
return;
|
|
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|
+
}
|
|
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|
+
/**
|
|
415
|
+
* Flatten repeatable `AuthorList` elements into the single list
|
|
416
|
+
* {@link extractAuthors} expects, so affiliation indices stay consistent across
|
|
417
|
+
* them instead of each list restarting its own numbering.
|
|
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|
+
*/
|
|
419
|
+
function mergeAuthorLists(lists) {
|
|
420
|
+
const authors = lists.flatMap((list) => ensureArray(list.Author));
|
|
421
|
+
return authors.length > 0 ? { Author: authors } : undefined;
|
|
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|
+
}
|
|
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|
+
/**
|
|
424
|
+
* Extract the containing book from a `BookDocument`.
|
|
425
|
+
*
|
|
426
|
+
* `Book/AuthorList` is split on its `Type` attribute: `editors` is the only
|
|
427
|
+
* value that makes a list editors, so an untyped list is read as authors —
|
|
428
|
+
* mislabelling real authors as editors would put them in the wrong slot of every
|
|
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|
+
* citation style.
|
|
430
|
+
* @param bookDocumentXml - The XML BookDocument element.
|
|
431
|
+
* @returns The parsed book, with absent elements omitted rather than emptied.
|
|
432
|
+
*/
|
|
433
|
+
export function extractBookInfo(bookDocumentXml) {
|
|
434
|
+
const book = bookDocumentXml.Book;
|
|
435
|
+
const editorLists = ensureArray(book?.AuthorList).filter((list) => getAttribute(list, 'Type') === 'editors');
|
|
436
|
+
const editors = extractAuthors(mergeAuthorLists(editorLists)).authors.map(({ lastName, firstName, initials, collectiveName }) => ({
|
|
437
|
+
...(lastName && { lastName }),
|
|
438
|
+
...(firstName && { firstName }),
|
|
439
|
+
...(initials && { initials }),
|
|
440
|
+
...(collectiveName && { collectiveName }),
|
|
441
|
+
}));
|
|
442
|
+
const isbns = ensureArray(book?.Isbn)
|
|
443
|
+
.map(getOptionalText)
|
|
444
|
+
.filter((isbn) => isbn !== undefined);
|
|
445
|
+
const bookDoi = ensureArray(book?.ELocationID)
|
|
446
|
+
.filter((eloc) => getAttribute(eloc, 'EIdType') === 'doi')
|
|
447
|
+
.map(getOptionalText)
|
|
448
|
+
.find(Boolean);
|
|
449
|
+
const title = getOptionalText(book?.BookTitle);
|
|
450
|
+
const publisher = getOptionalText(book?.Publisher?.PublisherName);
|
|
451
|
+
const publisherLocation = getOptionalText(book?.Publisher?.PublisherLocation);
|
|
452
|
+
const pubDate = extractYear(book?.PubDate);
|
|
453
|
+
const beginningDate = extractYear(book?.BeginningDate);
|
|
454
|
+
const endingDate = extractYear(book?.EndingDate);
|
|
455
|
+
const medium = getOptionalText(book?.Medium);
|
|
456
|
+
const edition = getOptionalText(book?.Edition);
|
|
457
|
+
const collectionTitle = getOptionalText(book?.CollectionTitle);
|
|
458
|
+
const accession = findArticleId(bookDocumentXml.ArticleIdList, 'bookaccession');
|
|
459
|
+
return {
|
|
460
|
+
...(title && { title }),
|
|
461
|
+
...(publisher && { publisher }),
|
|
462
|
+
...(publisherLocation && { publisherLocation }),
|
|
463
|
+
...(pubDate && { pubDate }),
|
|
464
|
+
...(beginningDate && { beginningDate }),
|
|
465
|
+
...(endingDate && { endingDate }),
|
|
466
|
+
...(medium && { medium }),
|
|
467
|
+
...(edition && { edition }),
|
|
468
|
+
...(collectionTitle && { collectionTitle }),
|
|
469
|
+
...(isbns.length > 0 && { isbns }),
|
|
470
|
+
...(bookDoi && { doi: bookDoi }),
|
|
471
|
+
...(editors.length > 0 && { editors }),
|
|
472
|
+
...(accession && { accession }),
|
|
473
|
+
};
|
|
474
|
+
}
|
|
475
|
+
/**
|
|
476
|
+
* Parse a `PubmedBookArticle` — an NCBI Bookshelf record — into the same
|
|
477
|
+
* {@link ParsedArticle} shape a journal article produces.
|
|
478
|
+
*
|
|
479
|
+
* `ArticleTitle` is the discriminator: a record carrying one is a chapter, and
|
|
480
|
+
* one without it is the whole book, whose `title` then comes from `BookTitle`.
|
|
481
|
+
* `journalInfo` is never populated — a Bookshelf record has no journal, and
|
|
482
|
+
* promoting the book title into one would invent a venue that does not exist.
|
|
483
|
+
*
|
|
484
|
+
* Chapter authors come from `BookDocument/AuthorList`; a book-level author list
|
|
485
|
+
* stands in only when the chapter carries none of its own. `Sections`,
|
|
486
|
+
* `ReferenceList` and `ItemList` are not read — metadata and abstract only. (#114)
|
|
487
|
+
* @param xmlBookArticle - The raw XML PubmedBookArticle element.
|
|
488
|
+
* @returns A parsed record with `recordType` set to `book-chapter` or `book`.
|
|
489
|
+
*/
|
|
490
|
+
export function parseFullBookArticle(xmlBookArticle) {
|
|
491
|
+
const bookDocument = xmlBookArticle.BookDocument;
|
|
492
|
+
const book = extractBookInfo(bookDocument);
|
|
493
|
+
const chapterTitle = getOptionalText(bookDocument?.ArticleTitle);
|
|
494
|
+
const bookAuthorLists = ensureArray(bookDocument?.Book?.AuthorList).filter((list) => getAttribute(list, 'Type') !== 'editors');
|
|
495
|
+
const chapterAuthors = extractAuthors(mergeAuthorLists(ensureArray(bookDocument?.AuthorList)));
|
|
496
|
+
const { authors, affiliations } = chapterAuthors.authors.length
|
|
497
|
+
? chapterAuthors
|
|
498
|
+
: extractAuthors(mergeAuthorLists(bookAuthorLists));
|
|
499
|
+
const abstractText = extractAbstractText(bookDocument?.Abstract);
|
|
500
|
+
const keywords = extractKeywords(bookDocument?.KeywordList);
|
|
501
|
+
const publicationTypes = ensureArray(bookDocument?.PublicationType)
|
|
502
|
+
.map((pubType) => getText(pubType))
|
|
503
|
+
.filter(Boolean);
|
|
504
|
+
const articleDates = [
|
|
505
|
+
['ContributionDate', bookDocument?.ContributionDate],
|
|
506
|
+
['DateRevised', bookDocument?.DateRevised],
|
|
507
|
+
].flatMap(([dateType, dateXml]) => dateXml
|
|
508
|
+
? [
|
|
509
|
+
{
|
|
510
|
+
dateType,
|
|
511
|
+
year: getText(dateXml.Year),
|
|
512
|
+
month: getText(dateXml.Month),
|
|
513
|
+
day: getText(dateXml.Day),
|
|
514
|
+
},
|
|
515
|
+
]
|
|
516
|
+
: []);
|
|
517
|
+
const doi = findArticleId(bookDocument?.ArticleIdList, 'doi') ??
|
|
518
|
+
findArticleId(xmlBookArticle.PubmedBookData?.ArticleIdList, 'doi');
|
|
519
|
+
const title = chapterTitle ?? book.title;
|
|
520
|
+
return {
|
|
521
|
+
recordType: chapterTitle ? 'book-chapter' : 'book',
|
|
522
|
+
pmid: getText(bookDocument?.PMID),
|
|
523
|
+
...(title !== undefined && { title }),
|
|
524
|
+
...(abstractText !== undefined && { abstractText }),
|
|
525
|
+
...(affiliations.length > 0 && { affiliations }),
|
|
526
|
+
authors,
|
|
527
|
+
book,
|
|
528
|
+
...(publicationTypes.length > 0 && { publicationTypes }),
|
|
529
|
+
...(keywords.length > 0 && { keywords }),
|
|
530
|
+
...(doi !== undefined && { doi }),
|
|
531
|
+
...(articleDates.length > 0 && { articleDates }),
|
|
532
|
+
};
|
|
533
|
+
}
|
|
534
|
+
/**
|
|
535
|
+
* Parse a whole `PubmedArticleSet` — every `PubmedArticle` and every
|
|
536
|
+
* `PubmedBookArticle` — into one flat record list. This is the entry point every
|
|
537
|
+
* EFetch consumer should use: reading `PubmedArticleSet.PubmedArticle` alone
|
|
538
|
+
* silently discards Bookshelf records, whose PMIDs then look unavailable. (#114)
|
|
539
|
+
*
|
|
540
|
+
* Ordering: records of one kind keep their upstream order, and the two kinds
|
|
541
|
+
* appear in the order they first occur in the response. Exact interleaving is
|
|
542
|
+
* not recoverable — the flat XML parser groups siblings by element name, so a
|
|
543
|
+
* response alternating the two kinds collapses to two runs. A caller that needs
|
|
544
|
+
* records back in the order it asked for them should key on `pmid`.
|
|
545
|
+
* @param articleSet - The parsed `PubmedArticleSet` element.
|
|
546
|
+
* @param options - Options forwarded to journal-article parsing.
|
|
547
|
+
* @returns Parsed records; an empty array when the set holds none.
|
|
548
|
+
*/
|
|
549
|
+
export function parseArticleSet(articleSet, options = {}) {
|
|
550
|
+
if (!articleSet)
|
|
551
|
+
return [];
|
|
552
|
+
const records = [];
|
|
553
|
+
for (const member of Object.keys(articleSet)) {
|
|
554
|
+
if (member === 'PubmedArticle') {
|
|
555
|
+
for (const xmlArticle of ensureArray(articleSet.PubmedArticle)) {
|
|
556
|
+
if (xmlArticle?.MedlineCitation)
|
|
557
|
+
records.push(parseFullArticle(xmlArticle, options));
|
|
558
|
+
}
|
|
559
|
+
}
|
|
560
|
+
else if (member === 'PubmedBookArticle') {
|
|
561
|
+
for (const xmlBookArticle of ensureArray(articleSet.PubmedBookArticle)) {
|
|
562
|
+
if (xmlBookArticle?.BookDocument)
|
|
563
|
+
records.push(parseFullBookArticle(xmlBookArticle));
|
|
564
|
+
}
|
|
565
|
+
}
|
|
566
|
+
}
|
|
567
|
+
return records;
|
|
568
|
+
}
|
|
370
569
|
//# sourceMappingURL=article-parser.js.map
|