@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/parsing/pmc-article-parser.js.map CHANGED
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package/dist/services/ncbi/parsing/pmc-xml-helpers.d.ts CHANGED
@@ -40,6 +40,35 @@ export declare function textOf(node: JatsNode): string;
40
40
  * Foundation of China`) alike, so no reader takes its text. (#196, #208)
41
41
  */
42
42
  export declare const IDENTIFIER_TAGS: ReadonlySet<string>;
43
+ /**
44
+ * True for a MathML `<math>` element, matched by local name whatever its
45
+ * namespace prefix — `<mml:math>` in PMC deposits, `<math>` elsewhere. (#207)
46
+ */
47
+ export declare function isMathTag(tag: string): boolean;
48
+ /**
49
+ * A MathML `<math>` element in a TeX-style linear form — the notation a
50
+ * formula deposited as `<tex-math>` already reads in — so a formula keeps the
51
+ * structure that carries its meaning instead of reading as the run of its
52
+ * leaves (`∑j=1Nlij`, a matrix's numeric cells fused into `−4.401.20`). (#207)
53
+ *
54
+ * | MathML | Linear form |
55
+ * |:--|:--|
56
+ * | `mi`, `mn`, `mo`, `mtext`, `ms` | their text as deposited (`−` stays U+2212) |
57
+ * | `msub`, `munder` / `msup`, `mover` | base`_{…}` / base`^{…}` |
58
+ * | `msubsup`, `munderover`, `mmultiscripts` | base`_{…}^{…}`, per script pair; `mmultiscripts` prescripts as `{}_{…}^{…}` before the base |
59
+ * | `mfrac` / `msqrt` / `mroot` | `\frac{…}{…}` / `\sqrt{…}` / `\sqrt[index]{…}` |
60
+ * | `mfenced` | `open`, the children split by `separators`, `close` (defaults `(`, `,`, `)`) |
61
+ * | `mtable` | cells split by ` & `, rows by ` \\ ` |
62
+ * | `mspace` / `mphantom` | one space / nothing |
63
+ * | anything else | its children in order |
64
+ *
65
+ * An empty script slot is left out (`x^{2}`, not `x_{}^{2}`). Whitespace-only
66
+ * text between elements contributes nothing; any other text reads verbatim.
67
+ * Elements match by local name, whatever their prefix. Pieces are written to
68
+ * one buffer rather than returned and concatenated level by level, so the cost
69
+ * stays linear in the size of the formula however deeply it nests.
70
+ */
71
+ export declare function linearMath(math: JatsNode): string;
43
72
  /**
44
73
  * The single child of an `<alternatives>` whose text stands for the whole
45
74
  * element.
package/dist/services/ncbi/parsing/pmc-xml-helpers.d.ts.map CHANGED
@@ -1 +1 @@
1
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package/dist/services/ncbi/parsing/pmc-xml-helpers.js CHANGED
@@ -87,6 +87,166 @@ const TEX_DOCUMENT_BODY = /\\begin\{document\}([\s\S]*?)(?:\\end\{document\}|$)/
87
87
  function texMathExpression(raw) {
88
88
  return TEX_DOCUMENT_BODY.exec(raw)?.[1] ?? raw;
89
89
  }
90
+ /** An element's tag without its namespace prefix: `math` for `mml:math`. */
91
+ const localName = (tag) => tag.slice(tag.indexOf(':') + 1);
92
+ /**
93
+ * True for a MathML `<math>` element, matched by local name whatever its
94
+ * namespace prefix — `<mml:math>` in PMC deposits, `<math>` elsewhere. (#207)
95
+ */
96
+ export function isMathTag(tag) {
97
+ return localName(tag) === 'math';
98
+ }
99
+ /** MathML token elements, which contribute their text as deposited. */
100
+ const MATH_TOKEN_TAGS = new Set(['mi', 'mn', 'mo', 'mtext', 'ms']);
101
+ /**
102
+ * A MathML `<math>` element in a TeX-style linear form — the notation a
103
+ * formula deposited as `<tex-math>` already reads in — so a formula keeps the
104
+ * structure that carries its meaning instead of reading as the run of its
105
+ * leaves (`∑j=1Nlij`, a matrix's numeric cells fused into `−4.401.20`). (#207)
106
+ *
107
+ * | MathML | Linear form |
108
+ * |:--|:--|
109
+ * | `mi`, `mn`, `mo`, `mtext`, `ms` | their text as deposited (`−` stays U+2212) |
110
+ * | `msub`, `munder` / `msup`, `mover` | base`_{…}` / base`^{…}` |
111
+ * | `msubsup`, `munderover`, `mmultiscripts` | base`_{…}^{…}`, per script pair; `mmultiscripts` prescripts as `{}_{…}^{…}` before the base |
112
+ * | `mfrac` / `msqrt` / `mroot` | `\frac{…}{…}` / `\sqrt{…}` / `\sqrt[index]{…}` |
113
+ * | `mfenced` | `open`, the children split by `separators`, `close` (defaults `(`, `,`, `)`) |
114
+ * | `mtable` | cells split by ` & `, rows by ` \\ ` |
115
+ * | `mspace` / `mphantom` | one space / nothing |
116
+ * | anything else | its children in order |
117
+ *
118
+ * An empty script slot is left out (`x^{2}`, not `x_{}^{2}`). Whitespace-only
119
+ * text between elements contributes nothing; any other text reads verbatim.
120
+ * Elements match by local name, whatever their prefix. Pieces are written to
121
+ * one buffer rather than returned and concatenated level by level, so the cost
122
+ * stays linear in the size of the formula however deeply it nests.
123
+ */
124
+ export function linearMath(math) {
125
+ const out = [];
126
+ const emit = (text) => {
127
+ if (text)
128
+ out.push(text);
129
+ };
130
+ /** Element children only: text between MathML arguments is never one of them. */
131
+ const argsOf = (node) => childrenOf(node).filter((child) => !isTextNode(child));
132
+ /** Write `pieces` after `open`, or nothing at all when they write nothing. */
133
+ const unlessEmpty = (open, pieces, close = '') => {
134
+ const start = out.length;
135
+ out.push(open);
136
+ pieces();
137
+ if (out.length === start + 1)
138
+ out.length = start;
139
+ else
140
+ emit(close);
141
+ };
142
+ const script = (mark, node) => unlessEmpty(`${mark}{`, () => write(node), '}');
143
+ /** Script pairs — subscript, then superscript — in document order. */
144
+ const scriptPairs = (scripts) => {
145
+ for (let i = 0; i < scripts.length; i += 2) {
146
+ script('_', scripts[i]);
147
+ script('^', scripts[i + 1]);
148
+ }
149
+ };
150
+ const write = (node) => {
151
+ if (!node)
152
+ return;
153
+ if (isTextNode(node)) {
154
+ const text = textOf(node);
155
+ if (VISIBLE_CHAR.test(text))
156
+ emit(text);
157
+ return;
158
+ }
159
+ const name = localName(tagNameOf(node) ?? '');
160
+ if (MATH_TOKEN_TAGS.has(name)) {
161
+ for (const child of childrenOf(node)) {
162
+ if (isTextNode(child))
163
+ emit(textOf(child));
164
+ else
165
+ write(child);
166
+ }
167
+ return;
168
+ }
169
+ const args = argsOf(node);
170
+ switch (name) {
171
+ case 'msub':
172
+ case 'munder':
173
+ write(args[0]);
174
+ script('_', args[1]);
175
+ return;
176
+ case 'msup':
177
+ case 'mover':
178
+ write(args[0]);
179
+ script('^', args[1]);
180
+ return;
181
+ case 'msubsup':
182
+ case 'munderover':
183
+ write(args[0]);
184
+ script('_', args[1]);
185
+ script('^', args[2]);
186
+ return;
187
+ case 'mmultiscripts': {
188
+ const split = args.findIndex((arg) => localName(tagNameOf(arg) ?? '') === 'mprescripts');
189
+ if (split !== -1)
190
+ unlessEmpty('{}', () => scriptPairs(args.slice(split + 1)));
191
+ write(args[0]);
192
+ scriptPairs(args.slice(1, split === -1 ? undefined : split));
193
+ return;
194
+ }
195
+ case 'mfrac':
196
+ emit('\\frac{');
197
+ write(args[0]);
198
+ emit('}{');
199
+ write(args[1]);
200
+ emit('}');
201
+ return;
202
+ case 'msqrt':
203
+ emit('\\sqrt{');
204
+ for (const arg of args)
205
+ write(arg);
206
+ emit('}');
207
+ return;
208
+ case 'mroot':
209
+ emit('\\sqrt[');
210
+ write(args[1]);
211
+ emit(']{');
212
+ write(args[0]);
213
+ emit('}');
214
+ return;
215
+ case 'mfenced': {
216
+ const separators = [...(attrOf(node, 'separators') ?? ',').replace(/\s/g, '')];
217
+ emit(attrOf(node, 'open') ?? '(');
218
+ for (const [i, arg] of args.entries()) {
219
+ if (i > 0)
220
+ emit(separators[Math.min(i - 1, separators.length - 1)] ?? '');
221
+ write(arg);
222
+ }
223
+ emit(attrOf(node, 'close') ?? ')');
224
+ return;
225
+ }
226
+ case 'mtable':
227
+ for (const [r, row] of args.entries()) {
228
+ if (r > 0)
229
+ emit(' \\\\ ');
230
+ for (const [c, cell] of argsOf(row).entries()) {
231
+ if (c > 0)
232
+ emit(' & ');
233
+ write(cell);
234
+ }
235
+ }
236
+ return;
237
+ case 'mspace':
238
+ emit(' ');
239
+ return;
240
+ case 'mphantom':
241
+ return;
242
+ default:
243
+ for (const child of childrenOf(node))
244
+ write(child);
245
+ }
246
+ };
247
+ write(math);
248
+ return out.join('');
249
+ }
90
250
  /**
91
251
  * The single child of an `<alternatives>` whose text stands for the whole
92
252
  * element.
@@ -281,12 +441,13 @@ export class TextAssembler {
281
441
  * Drive `sink` through a node or sibling list in document order. `excluded`
282
442
  * skips a whole subtree by tag name; omitting it reads everything else.
283
443
  *
284
- * Three JATS elements do not contribute the plain concatenation of their
285
- * subtree: a `<tex-math>` contributes only its LaTeX document body, an
286
- * `<alternatives>` exactly one child, and an {@link IDENTIFIER_TAGS} element
287
- * nothing. The rules live here, beside the boundary rules {@link TextAssembler}
288
- * applies, so every consumer inherits them — table cells, footnotes, titles,
289
- * affiliations, references. (#135, #185, #208)
444
+ * Four JATS elements do not contribute the plain concatenation of their
445
+ * subtree: a `<tex-math>` contributes only its LaTeX document body, a MathML
446
+ * `<math>` its {@link linearMath} form, an `<alternatives>` exactly one child,
447
+ * and an {@link IDENTIFIER_TAGS} element nothing. The rules live here, beside
448
+ * the boundary rules {@link TextAssembler} applies, so every consumer inherits
449
+ * them — table cells, footnotes, titles, affiliations, references. (#135, #185,
450
+ * #207, #208)
290
451
  */
291
452
  function readInto(input, sink, excluded) {
292
453
  for (const node of Array.isArray(input) ? input : [input]) {
@@ -301,6 +462,10 @@ function readInto(input, sink, excluded) {
301
462
  sink.text(texMathExpression(readText(childrenOf(node))));
302
463
  continue;
303
464
  }
465
+ if (isMathTag(tag)) {
466
+ sink.text(linearMath(node));
467
+ continue;
468
+ }
304
469
  if (tag === ALTERNATIVES_TAG) {
305
470
  const chosen = selectAlternative(node, excluded);
306
471
  if (chosen)
package/dist/services/ncbi/parsing/pmc-xml-helpers.js.map CHANGED
@@ -1 +1 @@
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package/dist/services/ncbi/response-handler.d.ts.map CHANGED
@@ -1 +1 @@
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package/dist/services/ncbi/response-handler.js CHANGED
@@ -52,6 +52,9 @@ const NCBI_ARRAY_JPATHS = new Set([
52
52
  'PubmedArticleSet.PubmedArticle.MedlineCitation.Article.GrantList.Grant',
53
53
  'PubmedArticleSet.PubmedArticle.MedlineCitation.Article.PublicationTypeList.PublicationType',
54
54
  'PubmedArticleSet.PubmedArticle.MedlineCitation.CommentsCorrectionsList.CommentsCorrections',
55
+ 'PubmedArticleSet.PubmedArticle.MedlineCitation.InvestigatorList',
56
+ 'PubmedArticleSet.PubmedArticle.MedlineCitation.InvestigatorList.Investigator',
57
+ 'PubmedArticleSet.PubmedArticle.MedlineCitation.InvestigatorList.Investigator.AffiliationInfo',
55
58
  'PubmedArticleSet.PubmedArticle.MedlineCitation.KeywordList.Keyword',
56
59
  'PubmedArticleSet.PubmedArticle.MedlineCitation.MeshHeadingList.MeshHeading',
57
60
  'PubmedArticleSet.PubmedArticle.MedlineCitation.MeshHeadingList.MeshHeading.QualifierName',
package/dist/services/ncbi/response-handler.js.map CHANGED
@@ -1 +1 @@
1
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