@cyanheads/pubmed-mcp-server 2.10.20 → 2.10.21

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 (65) hide show
  1. package/AGENTS.md +3 -3
  2. package/CLAUDE.md +3 -3
  3. package/README.md +7 -6
  4. package/changelog/2.10.x/2.10.21.md +42 -0
  5. package/dist/mcp-server/tools/definitions/fetch-articles.tool.d.ts +8 -0
  6. package/dist/mcp-server/tools/definitions/fetch-articles.tool.d.ts.map +1 -1
  7. package/dist/mcp-server/tools/definitions/fetch-articles.tool.js +36 -4
  8. package/dist/mcp-server/tools/definitions/fetch-articles.tool.js.map +1 -1
  9. package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts +21 -4
  10. package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts.map +1 -1
  11. package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js +287 -127
  12. package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js.map +1 -1
  13. package/dist/mcp-server/tools/definitions/format-citations.tool.d.ts +12 -0
  14. package/dist/mcp-server/tools/definitions/format-citations.tool.d.ts.map +1 -1
  15. package/dist/mcp-server/tools/definitions/format-citations.tool.js +53 -7
  16. package/dist/mcp-server/tools/definitions/format-citations.tool.js.map +1 -1
  17. package/dist/mcp-server/tools/definitions/lookup-citation.tool.d.ts.map +1 -1
  18. package/dist/mcp-server/tools/definitions/lookup-citation.tool.js +8 -6
  19. package/dist/mcp-server/tools/definitions/lookup-citation.tool.js.map +1 -1
  20. package/dist/mcp-server/tools/definitions/pubmed-europepmc-fetch.tool.d.ts.map +1 -1
  21. package/dist/mcp-server/tools/definitions/pubmed-europepmc-fetch.tool.js +0 -1
  22. package/dist/mcp-server/tools/definitions/pubmed-europepmc-fetch.tool.js.map +1 -1
  23. package/dist/services/europe-pmc/api-client.d.ts.map +1 -1
  24. package/dist/services/europe-pmc/api-client.js +4 -3
  25. package/dist/services/europe-pmc/api-client.js.map +1 -1
  26. package/dist/services/fetch-redaction.d.ts +23 -0
  27. package/dist/services/fetch-redaction.d.ts.map +1 -0
  28. package/dist/services/fetch-redaction.js +62 -0
  29. package/dist/services/fetch-redaction.js.map +1 -0
  30. package/dist/services/ncbi/api-client.d.ts +3 -0
  31. package/dist/services/ncbi/api-client.d.ts.map +1 -1
  32. package/dist/services/ncbi/api-client.js +21 -8
  33. package/dist/services/ncbi/api-client.js.map +1 -1
  34. package/dist/services/ncbi/formatting/citation-formatter.d.ts +19 -3
  35. package/dist/services/ncbi/formatting/citation-formatter.d.ts.map +1 -1
  36. package/dist/services/ncbi/formatting/citation-formatter.js +224 -46
  37. package/dist/services/ncbi/formatting/citation-formatter.js.map +1 -1
  38. package/dist/services/ncbi/ncbi-service.d.ts.map +1 -1
  39. package/dist/services/ncbi/ncbi-service.js +2 -1
  40. package/dist/services/ncbi/ncbi-service.js.map +1 -1
  41. package/dist/services/ncbi/parsing/article-parser.d.ts.map +1 -1
  42. package/dist/services/ncbi/parsing/article-parser.js +80 -34
  43. package/dist/services/ncbi/parsing/article-parser.js.map +1 -1
  44. package/dist/services/ncbi/parsing/pmc-article-parser.d.ts +8 -7
  45. package/dist/services/ncbi/parsing/pmc-article-parser.d.ts.map +1 -1
  46. package/dist/services/ncbi/parsing/pmc-article-parser.js +257 -57
  47. package/dist/services/ncbi/parsing/pmc-article-parser.js.map +1 -1
  48. package/dist/services/ncbi/parsing/pmc-xml-helpers.d.ts +29 -0
  49. package/dist/services/ncbi/parsing/pmc-xml-helpers.d.ts.map +1 -1
  50. package/dist/services/ncbi/parsing/pmc-xml-helpers.js +171 -6
  51. package/dist/services/ncbi/parsing/pmc-xml-helpers.js.map +1 -1
  52. package/dist/services/ncbi/response-handler.d.ts.map +1 -1
  53. package/dist/services/ncbi/response-handler.js +3 -0
  54. package/dist/services/ncbi/response-handler.js.map +1 -1
  55. package/dist/services/ncbi/types.d.ts +42 -2
  56. package/dist/services/ncbi/types.d.ts.map +1 -1
  57. package/dist/services/openalex/api-client.d.ts.map +1 -1
  58. package/dist/services/openalex/api-client.js +4 -3
  59. package/dist/services/openalex/api-client.js.map +1 -1
  60. package/dist/services/unpaywall/unpaywall-service.d.ts +3 -0
  61. package/dist/services/unpaywall/unpaywall-service.d.ts.map +1 -1
  62. package/dist/services/unpaywall/unpaywall-service.js +18 -8
  63. package/dist/services/unpaywall/unpaywall-service.js.map +1 -1
  64. package/package.json +5 -5
  65. package/server.json +3 -3
package/dist/services/ncbi/ncbi-service.js.map CHANGED
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package/dist/services/ncbi/parsing/article-parser.d.ts.map CHANGED
@@ -1 +1 @@
1
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package/dist/services/ncbi/parsing/article-parser.js CHANGED
@@ -5,6 +5,46 @@
5
5
  */
6
6
  import { decodeHtmlEntities } from './text-helpers.js';
7
7
  import { ensureArray, getAttribute, getOptionalAttribute, getOptionalText, getText, } from './xml-helpers.js';
8
+ /**
9
+ * An article's deduplicated affiliation list: one index per distinct text, a new
10
+ * text appended at the end. Seeded with an existing list, it continues that
11
+ * list's numbering, so the seed's indices never move.
12
+ */
13
+ function affiliationIndex(seed = []) {
14
+ const list = [...seed];
15
+ const indexOf = new Map(list.map((text, index) => [text, index]));
16
+ return {
17
+ list,
18
+ /** Indices of one contributor's `AffiliationInfo` texts, in order. */
19
+ of(infos) {
20
+ const indices = [];
21
+ for (const info of ensureArray(infos)) {
22
+ const text = getText(info?.Affiliation);
23
+ if (!text)
24
+ continue;
25
+ let index = indexOf.get(text);
26
+ if (index === undefined) {
27
+ index = list.length;
28
+ list.push(text);
29
+ indexOf.set(text, index);
30
+ }
31
+ indices.push(index);
32
+ }
33
+ return indices;
34
+ },
35
+ };
36
+ }
37
+ /** The first ORCID among a contributor's `Identifier` elements (`Source="ORCID"`). */
38
+ function extractOrcid(identifiers) {
39
+ for (const id of ensureArray(identifiers)) {
40
+ if (getAttribute(id, 'Source') === 'ORCID') {
41
+ const value = getText(id);
42
+ if (value)
43
+ return value;
44
+ }
45
+ }
46
+ return;
47
+ }
8
48
  /**
9
49
  * Extracts and formats author information from XML, deduplicating affiliations.
10
50
  * Affiliations are collected into a single array; each author references them by index.
@@ -15,40 +55,12 @@ import { ensureArray, getAttribute, getOptionalAttribute, getOptionalText, getTe
15
55
  export function extractAuthors(authorListXml) {
16
56
  if (!authorListXml)
17
57
  return { authors: [], affiliations: [] };
18
- const affiliationMap = new Map();
19
- const affiliationList = [];
20
- function getAffiliationIndex(text) {
21
- const existing = affiliationMap.get(text);
22
- if (existing !== undefined)
23
- return existing;
24
- const idx = affiliationList.length;
25
- affiliationList.push(text);
26
- affiliationMap.set(text, idx);
27
- return idx;
28
- }
58
+ const affiliations = affiliationIndex();
29
59
  const xmlAuthors = ensureArray(authorListXml.Author);
30
60
  const authors = xmlAuthors.map((auth) => {
31
- // Collect all affiliations for this author, deduplicated at article level.
32
61
  // A collective author carries its own `AffiliationInfo` too. (#212)
33
- const authorAffiliationInfos = ensureArray(auth.AffiliationInfo);
34
- const indices = [];
35
- for (const info of authorAffiliationInfos) {
36
- const text = getText(info?.Affiliation);
37
- if (text)
38
- indices.push(getAffiliationIndex(text));
39
- }
40
- // Extract ORCID from Identifier elements with Source="ORCID"
41
- let orcid;
42
- const identifiers = ensureArray(auth.Identifier);
43
- for (const id of identifiers) {
44
- if (getAttribute(id, 'Source') === 'ORCID') {
45
- const val = getText(id);
46
- if (val) {
47
- orcid = val;
48
- break;
49
- }
50
- }
51
- }
62
+ const indices = affiliations.of(auth.AffiliationInfo);
63
+ const orcid = extractOrcid(auth.Identifier);
52
64
  const collectiveName = getText(auth.CollectiveName);
53
65
  return {
54
66
  ...(collectiveName
@@ -62,7 +74,37 @@ export function extractAuthors(authorListXml) {
62
74
  ...(orcid && { orcid }),
63
75
  };
64
76
  });
65
- return { authors, affiliations: affiliationList };
77
+ return { authors, affiliations: affiliations.list };
78
+ }
79
+ /**
80
+ * Extracts the members of a collective author from every `InvestigatorList`,
81
+ * flattened in upstream order and uncapped. Investigator affiliations join the
82
+ * article's deduplicated list after the authors' entries, so an author's indices
83
+ * never shift. A name part the record lacks is omitted; `Suffix` is not read,
84
+ * as for authors. (#216)
85
+ * @param investigatorListsXml - The record's `InvestigatorList` elements.
86
+ * @param authorAffiliations - The authors' affiliations, from {@link extractAuthors}.
87
+ * @returns The investigators, and the affiliation list extended with theirs.
88
+ */
89
+ function extractInvestigators(investigatorListsXml, authorAffiliations) {
90
+ const affiliations = affiliationIndex(authorAffiliations);
91
+ const investigators = ensureArray(investigatorListsXml)
92
+ .flatMap((list) => ensureArray(list.Investigator))
93
+ .map((inv) => {
94
+ const lastName = getOptionalText(inv.LastName);
95
+ const firstName = getOptionalText(inv.ForeName);
96
+ const initials = getOptionalText(inv.Initials);
97
+ const indices = affiliations.of(inv.AffiliationInfo);
98
+ const orcid = extractOrcid(inv.Identifier);
99
+ return {
100
+ ...(lastName && { lastName }),
101
+ ...(firstName && { firstName }),
102
+ ...(initials && { initials }),
103
+ ...(indices.length > 0 && { affiliationIndices: indices }),
104
+ ...(orcid && { orcid }),
105
+ };
106
+ });
107
+ return { investigators, affiliations: affiliations.list };
66
108
  }
67
109
  /**
68
110
  * Picks the electronic article locator from an Article's `ELocationID` list —
@@ -400,13 +442,16 @@ export function extractArticleDates(articleXml) {
400
442
  export function parseFullArticle(xmlArticle, options = {}) {
401
443
  const medlineCitation = xmlArticle.MedlineCitation;
402
444
  const article = medlineCitation?.Article;
403
- const { includeMesh = true, includeGrants = false } = options;
445
+ const { includeMesh = true, includeGrants = false, includeInvestigators = false } = options;
404
446
  const abstractText = extractAbstractText(article?.Abstract);
405
447
  const journalInfo = extractJournalInfo(article?.Journal, article);
406
448
  const pubmedDataArticleIdList = xmlArticle.PubmedData?.ArticleIdList;
407
449
  const doi = extractDoi(article, pubmedDataArticleIdList);
408
450
  const pmcId = extractPmcId(article, pubmedDataArticleIdList);
409
- const { authors, affiliations } = extractAuthors(article?.AuthorList);
451
+ const { authors, affiliations: authorAffiliations } = extractAuthors(article?.AuthorList);
452
+ const { investigators, affiliations } = includeInvestigators
453
+ ? extractInvestigators(medlineCitation?.InvestigatorList, authorAffiliations)
454
+ : { investigators: [], affiliations: authorAffiliations };
410
455
  const publicationTypes = extractPublicationTypes(article?.PublicationTypeList);
411
456
  const commentsCorrections = extractCommentsCorrections(medlineCitation?.CommentsCorrectionsList);
412
457
  const keywords = extractKeywords(medlineCitation?.KeywordList ?? article?.KeywordList);
@@ -420,6 +465,7 @@ export function parseFullArticle(xmlArticle, options = {}) {
420
465
  ...(abstractText !== undefined && { abstractText }),
421
466
  ...(affiliations.length > 0 && { affiliations }),
422
467
  authors,
468
+ ...(investigators.length > 0 && { investigators }),
423
469
  ...(journalInfo !== undefined && { journalInfo }),
424
470
  ...(publicationTypes.length > 0 && { publicationTypes }),
425
471
  ...(commentsCorrections.length > 0 && { commentsCorrections }),
package/dist/services/ncbi/parsing/article-parser.js.map CHANGED
@@ -1 +1 @@
1
- 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package/dist/services/ncbi/parsing/pmc-article-parser.d.ts CHANGED
@@ -40,10 +40,10 @@ export declare function extractBodySections(body: JatsNode | undefined): ParsedP
40
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  * The walk covers the whole article rather than `<body>` alone: about a quarter
41
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  * of real tables sit in `<floats-group>`, `<back>/<sec>`, `<table-wrap-group>`
42
42
  * or `<app-group>/<app>`, so a body-scoped extractor drops them. Each table
43
- * names the innermost enclosing `<sec>` wherever that sits — a back-matter or
44
- * appendix section counts, and naming it is the reader's only positional cue
45
- * there. Only a table inside no `<sec>` at all, such as a `<floats-group>`
46
- * deposit, carries no section name.
43
+ * names the innermost enclosing section wherever that sits — a back-matter
44
+ * `<sec>`, `<app>`, `<notes>` or `<fn-group>` counts, and naming it is the
45
+ * reader's only positional cue there. Only a table inside no section at all,
46
+ * such as a `<floats-group>` deposit, carries no section name. (#206)
47
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  *
48
48
  * Only XHTML `<tr>`/`<td>`/`<th>` bodies are read. **Decision, not an
49
49
  * oversight:** across a 283-table survey of open-access records, 276 were XHTML,
@@ -71,9 +71,10 @@ export declare const MAX_TABLE_COLUMNS = 512;
71
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  * supplementary material sit outside `<body>` entirely — `<floats-group>`
72
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  * deposits, `<back>/<sec>` and `<app-group>/<app>` placements, and figures
73
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  * hanging off the abstract in `<front>`. Each asset names the innermost
74
- * enclosing `<sec>` wherever that sits, an untitled one inheriting its parent's
75
- * title, so the reader keeps a positional cue; an asset inside no `<sec>` at all
76
- * carries no section name. (#130)
74
+ * enclosing section wherever that sits — a back-matter element read as one
75
+ * included — an untitled `<sec>` inheriting its parent's title, so the reader
76
+ * keeps a positional cue; an asset inside no section at all carries no section
77
+ * name. (#130, #206)
77
78
  */
78
79
  export declare function extractPmcAssets(root: JatsNode | undefined): ParsedPmcAsset[];
79
80
  /**
package/dist/services/ncbi/parsing/pmc-article-parser.d.ts.map CHANGED
@@ -1 +1 @@
1
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