@cyanheads/pubmed-mcp-server 2.10.21 → 2.10.22

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 (86) hide show
  1. package/AGENTS.md +2 -2
  2. package/CLAUDE.md +2 -2
  3. package/Dockerfile +3 -3
  4. package/README.md +8 -6
  5. package/changelog/2.10.x/2.10.22.md +44 -0
  6. package/dist/index.js +1 -1
  7. package/dist/index.js.map +1 -1
  8. package/dist/mcp-server/tools/definitions/_budget.d.ts +35 -6
  9. package/dist/mcp-server/tools/definitions/_budget.d.ts.map +1 -1
  10. package/dist/mcp-server/tools/definitions/_budget.js +26 -3
  11. package/dist/mcp-server/tools/definitions/_budget.js.map +1 -1
  12. package/dist/mcp-server/tools/definitions/_notices.d.ts +33 -0
  13. package/dist/mcp-server/tools/definitions/_notices.d.ts.map +1 -0
  14. package/dist/mcp-server/tools/definitions/_notices.js +35 -0
  15. package/dist/mcp-server/tools/definitions/_notices.js.map +1 -0
  16. package/dist/mcp-server/tools/definitions/_schemas.d.ts +14 -0
  17. package/dist/mcp-server/tools/definitions/_schemas.d.ts.map +1 -1
  18. package/dist/mcp-server/tools/definitions/_schemas.js +9 -0
  19. package/dist/mcp-server/tools/definitions/_schemas.js.map +1 -1
  20. package/dist/mcp-server/tools/definitions/fetch-articles.tool.d.ts +3 -0
  21. package/dist/mcp-server/tools/definitions/fetch-articles.tool.d.ts.map +1 -1
  22. package/dist/mcp-server/tools/definitions/fetch-articles.tool.js +28 -15
  23. package/dist/mcp-server/tools/definitions/fetch-articles.tool.js.map +1 -1
  24. package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts +1 -0
  25. package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts.map +1 -1
  26. package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js +107 -48
  27. package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js.map +1 -1
  28. package/dist/mcp-server/tools/definitions/format-citations.tool.d.ts.map +1 -1
  29. package/dist/mcp-server/tools/definitions/format-citations.tool.js +3 -16
  30. package/dist/mcp-server/tools/definitions/format-citations.tool.js.map +1 -1
  31. package/dist/mcp-server/tools/definitions/lookup-mesh.tool.d.ts +1 -1
  32. package/dist/mcp-server/tools/definitions/lookup-mesh.tool.d.ts.map +1 -1
  33. package/dist/mcp-server/tools/definitions/lookup-mesh.tool.js +66 -76
  34. package/dist/mcp-server/tools/definitions/lookup-mesh.tool.js.map +1 -1
  35. package/dist/mcp-server/tools/definitions/pubmed-europepmc-fetch.tool.d.ts +6 -5
  36. package/dist/mcp-server/tools/definitions/pubmed-europepmc-fetch.tool.d.ts.map +1 -1
  37. package/dist/mcp-server/tools/definitions/pubmed-europepmc-fetch.tool.js +11 -17
  38. package/dist/mcp-server/tools/definitions/pubmed-europepmc-fetch.tool.js.map +1 -1
  39. package/dist/mcp-server/tools/definitions/pubmed-europepmc-search.tool.d.ts +4 -4
  40. package/dist/mcp-server/tools/definitions/pubmed-europepmc-search.tool.d.ts.map +1 -1
  41. package/dist/mcp-server/tools/definitions/pubmed-europepmc-search.tool.js +9 -8
  42. package/dist/mcp-server/tools/definitions/pubmed-europepmc-search.tool.js.map +1 -1
  43. package/dist/mcp-server/tools/definitions/spell-check.tool.d.ts +4 -4
  44. package/dist/mcp-server/tools/definitions/spell-check.tool.d.ts.map +1 -1
  45. package/dist/mcp-server/tools/definitions/spell-check.tool.js +12 -8
  46. package/dist/mcp-server/tools/definitions/spell-check.tool.js.map +1 -1
  47. package/dist/services/error-contracts.d.ts +1 -1
  48. package/dist/services/error-contracts.d.ts.map +1 -1
  49. package/dist/services/error-contracts.js +1 -1
  50. package/dist/services/error-contracts.js.map +1 -1
  51. package/dist/services/europe-pmc/europe-pmc-service.d.ts +31 -11
  52. package/dist/services/europe-pmc/europe-pmc-service.d.ts.map +1 -1
  53. package/dist/services/europe-pmc/europe-pmc-service.js +122 -47
  54. package/dist/services/europe-pmc/europe-pmc-service.js.map +1 -1
  55. package/dist/services/europe-pmc/types.d.ts +5 -1
  56. package/dist/services/europe-pmc/types.d.ts.map +1 -1
  57. package/dist/services/ncbi/formatting/citation-formatter.d.ts.map +1 -1
  58. package/dist/services/ncbi/formatting/citation-formatter.js +204 -110
  59. package/dist/services/ncbi/formatting/citation-formatter.js.map +1 -1
  60. package/dist/services/ncbi/ncbi-service.d.ts +22 -0
  61. package/dist/services/ncbi/ncbi-service.d.ts.map +1 -1
  62. package/dist/services/ncbi/ncbi-service.js +113 -17
  63. package/dist/services/ncbi/ncbi-service.js.map +1 -1
  64. package/dist/services/ncbi/parsing/article-parser.d.ts.map +1 -1
  65. package/dist/services/ncbi/parsing/article-parser.js +11 -4
  66. package/dist/services/ncbi/parsing/article-parser.js.map +1 -1
  67. package/dist/services/ncbi/parsing/pmc-article-parser.d.ts +5 -1
  68. package/dist/services/ncbi/parsing/pmc-article-parser.d.ts.map +1 -1
  69. package/dist/services/ncbi/parsing/pmc-article-parser.js +85 -31
  70. package/dist/services/ncbi/parsing/pmc-article-parser.js.map +1 -1
  71. package/dist/services/ncbi/parsing/pmc-xml-helpers.d.ts +13 -0
  72. package/dist/services/ncbi/parsing/pmc-xml-helpers.d.ts.map +1 -1
  73. package/dist/services/ncbi/parsing/pmc-xml-helpers.js +108 -10
  74. package/dist/services/ncbi/parsing/pmc-xml-helpers.js.map +1 -1
  75. package/dist/services/ncbi/parsing/text-helpers.d.ts +10 -0
  76. package/dist/services/ncbi/parsing/text-helpers.d.ts.map +1 -1
  77. package/dist/services/ncbi/parsing/text-helpers.js +19 -0
  78. package/dist/services/ncbi/parsing/text-helpers.js.map +1 -1
  79. package/dist/services/ncbi/response-handler.d.ts +0 -11
  80. package/dist/services/ncbi/response-handler.d.ts.map +1 -1
  81. package/dist/services/ncbi/response-handler.js +21 -33
  82. package/dist/services/ncbi/response-handler.js.map +1 -1
  83. package/dist/services/ncbi/types.d.ts +30 -30
  84. package/dist/services/ncbi/types.d.ts.map +1 -1
  85. package/package.json +5 -5
  86. package/server.json +3 -3
package/dist/services/ncbi/parsing/article-parser.js.map CHANGED
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package/dist/services/ncbi/parsing/pmc-article-parser.d.ts CHANGED
@@ -9,7 +9,11 @@
9
9
  */
10
10
  import type { ParsedPmcArticle, ParsedPmcAsset, ParsedPmcAuthor, ParsedPmcReference, ParsedPmcSection, ParsedPmcTable } from '../types.js';
11
11
  import { type JatsNode } from './pmc-xml-helpers.js';
12
- /** Extract authors from a single `<contrib-group>` node. Non-author contributors are skipped. */
12
+ /**
13
+ * Extract authors from a single `<contrib-group>` node. Non-author contributors
14
+ * are skipped. A name part the deposit lacks is omitted; a `<suffix>` is kept
15
+ * verbatim (`IV`, never rewritten to `4th`). (#226)
16
+ */
13
17
  export declare function extractJatsAuthors(contribGroup: JatsNode | undefined): ParsedPmcAuthor[];
14
18
  /**
15
19
  * Extract body sections from a `<body>` node, walking children in document order.
package/dist/services/ncbi/parsing/pmc-article-parser.d.ts.map CHANGED
@@ -1 +1 @@
1
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+ {"version":3,"file":"pmc-article-parser.d.ts","sourceRoot":"","sources":["../../../../src/services/ncbi/parsing/pmc-article-parser.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,KAAK,EACV,gBAAgB,EAChB,cAAc,EAEd,eAAe,EAEf,kBAAkB,EAClB,gBAAgB,EAChB,cAAc,EAEf,MAAM,aAAa,CAAC;AACrB,OAAO,EAUL,KAAK,QAAQ,EAWd,MAAM,sBAAsB,CAAC;AAkI9B;;;;GAIG;AACH,wBAAgB,kBAAkB,CAAC,YAAY,EAAE,QAAQ,GAAG,SAAS,GAAG,eAAe,EAAE,CA4BxF;AA4wBD;;;;;;;;;;;;;;;;;;;;GAoBG;AACH,wBAAgB,mBAAmB,CAAC,IAAI,EAAE,QAAQ,GAAG,SAAS,GAAG,gBAAgB,EAAE,CAElF;AA6SD;;;;;;;;;;;;;;;;;;GAkBG;AACH,wBAAgB,gBAAgB,CAAC,IAAI,EAAE,QAAQ,GAAG,SAAS,GAAG,cAAc,EAAE,CAO7E;AAgGD;;;;;;;;GAQG;AACH,eAAO,MAAM,iBAAiB,MAAM,CAAC;AAoGrC;;;;;;;;;;;;GAYG;AACH,wBAAgB,gBAAgB,CAAC,IAAI,EAAE,QAAQ,GAAG,SAAS,GAAG,cAAc,EAAE,CAQ7E;AA8TD;;;;;;;;;;;;;;;;GAgBG;AACH,wBAAgB,iBAAiB,CAAC,IAAI,EAAE,QAAQ,GAAG,SAAS,GAAG,kBAAkB,EAAE,CAsClF;AAID;;;;;GAKG;AACH,wBAAgB,eAAe,CAAC,WAAW,EAAE,QAAQ,GAAG,gBAAgB,CAkDvE"}
package/dist/services/ncbi/parsing/pmc-article-parser.js CHANGED
@@ -7,7 +7,7 @@
7
7
  * inline children and drops body sections for markup-heavy articles.
8
8
  * @module src/services/ncbi/parsing/pmc-article-parser
9
9
  */
10
- import { attrOf, childrenOf, findAll, findAllDescendants, findOne, IDENTIFIER_TAGS, isMathTag, isTextNode, linearMath, lineTextContent, rawTextContent, selectAlternative, TextAssembler, tagNameOf, textContent, textContentExcluding, textOf, } from './pmc-xml-helpers.js';
10
+ import { attrOf, CLOSING_PUNCTUATION, childrenOf, findAll, findAllDescendants, findOne, IDENTIFIER_TAGS, isMathTag, isTextNode, linearMath, lineTextContent, rawTextContent, selectAlternative, TextAssembler, tagNameOf, textContent, textContentExcluding, textOf, } from './pmc-xml-helpers.js';
11
11
  /**
12
12
  * Block content extracted into a field of its own and therefore left out of the
13
13
  * prose a section contributes. Each one nested inside a `<p>` would otherwise be
@@ -125,7 +125,11 @@ function isAuthorContrib(contrib) {
125
125
  const contribType = attrOf(contrib, 'contrib-type');
126
126
  return !contribType || contribType === 'author';
127
127
  }
128
- /** Extract authors from a single `<contrib-group>` node. Non-author contributors are skipped. */
128
+ /**
129
+ * Extract authors from a single `<contrib-group>` node. Non-author contributors
130
+ * are skipped. A name part the deposit lacks is omitted; a `<suffix>` is kept
131
+ * verbatim (`IV`, never rewritten to `4th`). (#226)
132
+ */
129
133
  export function extractJatsAuthors(contribGroup) {
130
134
  if (!contribGroup)
131
135
  return [];
@@ -144,9 +148,11 @@ export function extractJatsAuthors(contribGroup) {
144
148
  if (nameNode) {
145
149
  const lastName = textContent(findOne(nameNode, 'surname')) || undefined;
146
150
  const givenNames = textContent(findOne(nameNode, 'given-names')) || undefined;
151
+ const suffix = textContent(findOne(nameNode, 'suffix')) || undefined;
147
152
  authors.push({
148
153
  ...(lastName && { lastName }),
149
154
  ...(givenNames && { givenNames }),
155
+ ...(suffix && { suffix }),
150
156
  });
151
157
  }
152
158
  }
@@ -415,8 +421,11 @@ function flushRun(flow) {
415
421
  *
416
422
  * The run is a {@link TextAssembler}, so prose follows the separator rules every
417
423
  * other text field does: a `<break/>`, an inline `<fn>` or a `<label>` beside its
418
- * text reads as one space rather than fusing the words on either side, and a run
419
- * of `<xref>` markers with nothing between them reads `[1,2,3,4]`. (#185, #197)
424
+ * text reads as one space rather than fusing the words on either side, a run of
425
+ * `<xref>` markers with nothing between them reads `[1,2,3,4]`, and a line break
426
+ * between a formula — or any element — and the period after it is dropped:
427
+ * `L<0.`, not `L<0 .`. A `<tex-math>` or `<math>` is opened and closed on the
428
+ * run like any element, so that rule sees it. (#185, #197, #225)
420
429
  */
421
430
  function walkFlow(nodes, flow, blockTags) {
422
431
  for (const node of nodes) {
@@ -433,12 +442,10 @@ function walkFlow(nodes, flow, blockTags) {
433
442
  walkFlow([chosen], flow, blockTags);
434
443
  continue;
435
444
  }
436
- if (tag === 'tex-math') {
437
- flow.run.text(rawTextContent(node));
438
- continue;
439
- }
440
- if (isMathTag(tag)) {
441
- flow.run.text(linearMath(node));
445
+ if (tag === 'tex-math' || isMathTag(tag)) {
446
+ flow.run.open(tag);
447
+ flow.run.text(tag === 'tex-math' ? rawTextContent(node) : linearMath(node));
448
+ flow.run.close(tag);
442
449
  continue;
443
450
  }
444
451
  if (blockTags.has(tag)) {
@@ -570,12 +577,28 @@ function alternativePointer(alternatives) {
570
577
  * left in the section text and the `label` reported in `assets[]` cannot
571
578
  * disagree — the tool layer removes the marker by rebuilding it from that label,
572
579
  * so a label resolved one way here and another way there strands the marker in
573
- * the prose under `includeAssets: false`. (#130)
580
+ * the prose under `includeAssets: false`. That is also why the delimiter is
581
+ * stripped here rather than at render (see {@link floatLabel}). (#130, #240)
574
582
  */
575
583
  function assetLabel(node) {
576
- return (textContent(findOne(node, 'label')) ||
577
- textContent(findOne(assetPointer(node), 'label')) ||
578
- undefined);
584
+ return floatLabel(findOne(node, 'label')) ?? floatLabel(findOne(assetPointer(node), 'label'));
585
+ }
586
+ /** Delimiters a deposit may print after a table or asset label. */
587
+ const LABEL_DELIMITERS = new Set(['.', '|', ':']);
588
+ /**
589
+ * A table or asset `<label>`'s text without the one delimiter some deposits
590
+ * print after it — `Table 1.`, `Figure 1 |`, `Figure 1:` read `Table 1`,
591
+ * `Figure 1`. Every surface that names the item puts its own punctuation after
592
+ * the label: a heading's ` — ` before the caption, a list's `, `, a notice's
593
+ * closing period, which read `Table 2..` with the delimiter kept. Only the last
594
+ * character goes, so an internal one stays (`Fig. 1.` reads `Fig. 1`). A label
595
+ * that is nothing but a delimiter reads as no label. Reference labels are not
596
+ * read here and keep their printed form (#209). (#240)
597
+ */
598
+ function floatLabel(label) {
599
+ const text = textContent(label);
600
+ const stripped = LABEL_DELIMITERS.has(text.at(-1) ?? '') ? text.slice(0, -1).trimEnd() : text;
601
+ return stripped || undefined;
579
602
  }
580
603
  /**
581
604
  * The marker a lifted asset leaves at the position it occupied. Prose refers to
@@ -770,7 +793,7 @@ function renderBoxedText(boxedText, { withLabel = true, withTitle = true } = {})
770
793
  blocks.push(...flowBlocks(parts, STATEMENT_BLOCK_TAGS));
771
794
  }
772
795
  else if (withLabel || tag !== 'label')
773
- blocks.push(...flowBlocks([child]));
796
+ blocks.push(...sectionBlocks(child));
774
797
  }
775
798
  return blocks.join('\n\n');
776
799
  }
@@ -820,7 +843,7 @@ function flattenSec(sec) {
820
843
  if (tag === 'sec')
821
844
  nested.push(...flattenSec(child));
822
845
  else
823
- blocks.push(...flowBlocks([child]));
846
+ blocks.push(...sectionBlocks(child));
824
847
  }
825
848
  const head = [heading, blocks.join('\n\n')].filter(Boolean).join('\n');
826
849
  return [...(head ? [head] : []), ...nested];
@@ -925,7 +948,7 @@ function extractSections(children, back) {
925
948
  sections.push({ title, text: renderBlockWithoutTitle(child) });
926
949
  continue;
927
950
  }
928
- pendingBlocks.push(...flowBlocks([child]));
951
+ pendingBlocks.push(...sectionBlocks(child));
929
952
  }
930
953
  flushPending();
931
954
  return sections;
@@ -954,7 +977,9 @@ const BACK_MATTER_TITLES = new Map([
954
977
  * another is a subsection, as a `<sec>` in a `<sec>` is, so a Springer
955
978
  * `Declarations` `<notes>` keeps its inner notes' titles out of its text. In
956
979
  * `<body>` only a `<sec>` forms one: a `<notes>` or `<fn-group>` closing a body
957
- * `<sec>` stays that section's text, as it always read. (#206)
980
+ * `<sec>` stays that section's text, as it always read — a `<fn-group>` one
981
+ * paragraph per footnote, as in back matter (see {@link sectionBlocks}). (#206,
982
+ * #229)
958
983
  */
959
984
  const BACK_SECTION_TAGS = new Set([
960
985
  'sec',
@@ -1000,11 +1025,13 @@ function fallbackTitle(node) {
1000
1025
  return BACK_MATTER_TITLES.get(tagNameOf(node) ?? '');
1001
1026
  }
1002
1027
  /**
1003
- * The paragraphs of a back-matter `<fn>`: each `<p>`, and each block one holds,
1004
- * on its own, with the footnote's `<label>` leading the first. Read as one run,
1005
- * a footnote whose heading sits in a `<p>` of its own fused that heading into
1006
- * the statement after it (`Competing interests The authors declare…`), the
1007
- * fusion a titled `<notes>` is kept from. (#206)
1028
+ * The paragraphs of a `<fn>` that stands as a block — in back matter, or in a
1029
+ * body `<sec>`, `<boxed-text>` or `<fn-group>` (see {@link sectionBlocks}): each
1030
+ * `<p>`, and each block one holds, on its own, with the footnote's `<label>`
1031
+ * leading the first. Read as one run, a footnote whose heading sits in a `<p>`
1032
+ * of its own fused that heading into the statement after it (`Competing
1033
+ * interests The authors declare…`), the fusion a titled `<notes>` is kept from.
1034
+ * (#206, #229)
1008
1035
  */
1009
1036
  function footnoteParagraphs(fn) {
1010
1037
  const label = textContent(findOne(fn, 'label'));
@@ -1013,6 +1040,27 @@ function footnoteParagraphs(fn) {
1013
1040
  return label ? [label] : [];
1014
1041
  return [label ? `${label} ${first}` : first, ...rest];
1015
1042
  }
1043
+ /**
1044
+ * The text blocks one child of a section contributes — of a `<sec>`, of
1045
+ * `<body>`, of a `<boxed-text>` or of a `<sec>` one flattens. A `<fn>` reads as
1046
+ * {@link footnoteParagraphs} reads it, and so does each `<fn>` of a
1047
+ * `<fn-group>`, the group's own `<title>` a paragraph ahead of them; anything
1048
+ * else is flow text. Europe PMC moves back matter into `<body>` as
1049
+ * `<sec sec-type="fn-group"><fn-group>…`, and read as flow text there a group's
1050
+ * footnotes ran into one paragraph where the PMC tier, reading the same group
1051
+ * from `<back>`, returned one per statement. A `<fn>` inside a `<p>` is no child
1052
+ * here and still reads inside its sentence. (#229)
1053
+ */
1054
+ function sectionBlocks(child) {
1055
+ switch (tagNameOf(child)) {
1056
+ case 'fn':
1057
+ return footnoteParagraphs(child);
1058
+ case 'fn-group':
1059
+ return childrenOf(child).flatMap(sectionBlocks);
1060
+ default:
1061
+ return flowBlocks([child]);
1062
+ }
1063
+ }
1016
1064
  // ─── Section Reading ────────────────────────────────────────────────────────
1017
1065
  /**
1018
1066
  * The title a block carries of its own, where the JATS content model puts one:
@@ -1089,8 +1137,9 @@ function renderBlockWithoutTitle(node) {
1089
1137
  * reads as a section: the back-matter elements among its children are
1090
1138
  * subsections too, and with neither a title nor a label it takes the title its
1091
1139
  * element names. Each child contributes its own block, so every `<fn>` of a
1092
- * `<fn-group>` is a paragraph of its own, and each `<p>` inside one too (see
1093
- * {@link footnoteParagraphs}). (#206)
1140
+ * `<fn-group>` is a paragraph of its own, and each `<p>` inside one too — in
1141
+ * back matter and, for a `<fn-group>` that stays a body section's text, in
1142
+ * `<body>` alike (see {@link sectionBlocks}). (#206, #229)
1094
1143
  */
1095
1144
  function extractSection(sec, back = false) {
1096
1145
  const lone = loneTitledBlock(sec);
@@ -1117,7 +1166,7 @@ function extractSection(sec, back = false) {
1117
1166
  subsections.push(...nested);
1118
1167
  continue;
1119
1168
  }
1120
- textParts.push(...(back && tag === 'fn' ? footnoteParagraphs(child) : flowBlocks([child])));
1169
+ textParts.push(...sectionBlocks(child));
1121
1170
  }
1122
1171
  title ??= fallbackTitle(sec);
1123
1172
  const text = textParts.join('\n\n');
@@ -1204,7 +1253,7 @@ function collectSectioned(node, sectionTitle, out, take, inBox = false, inBack =
1204
1253
  }
1205
1254
  function parseTableWrap(tableWrap, sectionTitle) {
1206
1255
  const id = attrOf(tableWrap, 'id');
1207
- const label = textContent(findOne(tableWrap, 'label')) || undefined;
1256
+ const label = floatLabel(findOne(tableWrap, 'label'));
1208
1257
  const caption = renderCaption(findOne(tableWrap, 'caption'));
1209
1258
  // One line per footnote or paragraph: a footer is a list of statements, and a
1210
1259
  // marker run into the previous note (`…dose.*No patient…`) misattributes it. (#185)
@@ -1399,13 +1448,20 @@ const PUB_ID_LABELS = {
1399
1448
  doi: 'DOI',
1400
1449
  pmcid: 'PMCID',
1401
1450
  };
1402
- /** Render one `<person-group>` child — a `<name>`, `<collab>`, or `<etal>`. */
1451
+ /**
1452
+ * Render one `<person-group>` child — a `<name>`, `<collab>`, or `<etal>`. A
1453
+ * name reads `Surname Given`, then any `<suffix>` verbatim (`Miller ER III`).
1454
+ */
1403
1455
  function renderCitationName(node) {
1404
1456
  const tag = tagNameOf(node);
1405
1457
  if (tag === 'name' || tag === 'string-name') {
1406
1458
  const surname = textContent(findOne(node, 'surname'));
1407
1459
  const given = textContent(findOne(node, 'given-names'));
1408
- return [surname, given].filter(Boolean).join(' ') || textContent(node);
1460
+ const name = [surname, given].filter(Boolean).join(' ');
1461
+ if (!name)
1462
+ return textContent(node);
1463
+ const suffix = textContent(findOne(node, 'suffix'));
1464
+ return suffix ? `${name} ${suffix}` : name;
1409
1465
  }
1410
1466
  if (tag === 'collab')
1411
1467
  return textContent(node);
@@ -1477,8 +1533,6 @@ const PERSON_TAGS = new Set(['name', 'string-name', 'collab', 'etal']);
1477
1533
  const SUPPLIED_ETAL = 'et al.';
1478
1534
  /** Any character other than whitespace. */
1479
1535
  const VISIBLE_TEXT = /\S/;
1480
- /** Punctuation that closes the citation field before it: `Henry L.`, `Li X,`, `(2020)`. (#219) */
1481
- const CLOSING_PUNCTUATION = new Set(['.', ',', ';', ':', ')', ']']);
1482
1536
  /**
1483
1537
  * How much of the citation written so far a `<pub-id>` reads for a literal
1484
1538
  * prefix naming its type: the prefix, its `:` or `.`, and the whitespace around
package/dist/services/ncbi/parsing/pmc-article-parser.js.map CHANGED
@@ -1 +1 @@
1
- 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package/dist/services/ncbi/parsing/pmc-xml-helpers.d.ts CHANGED
@@ -60,6 +60,7 @@ export declare function isMathTag(tag: string): boolean;
60
60
  * | `mfenced` | `open`, the children split by `separators`, `close` (defaults `(`, `,`, `)`) |
61
61
  * | `mtable` | cells split by ` & `, rows by ` \\ ` |
62
62
  * | `mspace` / `mphantom` | one space / nothing |
63
+ * | `semantics` | one rendering of its expression, never an annotation (see `semanticsRendering`) |
63
64
  * | anything else | its children in order |
64
65
  *
65
66
  * An empty script slot is left out (`x^{2}`, not `x_{}^{2}`). Whitespace-only
@@ -88,6 +89,12 @@ export declare function linearMath(math: JatsNode): string;
88
89
  * resolve their own `<alternatives>` children by tag.
89
90
  */
90
91
  export declare function selectAlternative(node: JatsNode, excluded?: ReadonlySet<string>): JatsNode | undefined;
92
+ /**
93
+ * Punctuation that closes the text before it — `L<0.`, `Henry L,`, `(2020)` —
94
+ * so whitespace a pretty-printed deposit leaves in front of it is formatting,
95
+ * not spacing. (#219, #225)
96
+ */
97
+ export declare const CLOSING_PUNCTUATION: ReadonlySet<string>;
91
98
  /**
92
99
  * Accumulates JATS text in document order and decides every separator the
93
100
  * markup implies in the same pass, from state it carries rather than by
@@ -104,6 +111,12 @@ export declare function selectAlternative(node: JatsNode, excluded?: ReadonlySet
104
111
  * between them is preceded by a comma: `[1,2,3,4]`, not `[1234]`, which reads
105
112
  * as one reference. Any source text between them, whitespace included, means
106
113
  * the source already separated them. (#197)
114
+ * - Whitespace between an element and the {@link CLOSING_PUNCTUATION} after it
115
+ * is dropped when it holds a line break, whether the punctuation follows in
116
+ * plain text or opens the next element: `</inline-formula>\n<italic>.</italic>`
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+ * reads `L<0.`, not `L<0 .`. A gap with no line break, one before `(` or a
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+ * word, and a line boundary owed there are kept, and so is a line break
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+ * between a word and punctuation with no element closing between them. (#225)
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  *
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  * An owed separator is only written between two pieces of content, so a reader
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  * adds nothing at the edges of what it reads. By default the source text is