@cyanheads/pubmed-mcp-server 2.10.20 → 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 (110) hide show
  1. package/AGENTS.md +3 -3
  2. package/CLAUDE.md +3 -3
  3. package/Dockerfile +3 -3
  4. package/README.md +14 -11
  5. package/changelog/2.10.x/2.10.21.md +42 -0
  6. package/changelog/2.10.x/2.10.22.md +44 -0
  7. package/dist/index.js +1 -1
  8. package/dist/index.js.map +1 -1
  9. package/dist/mcp-server/tools/definitions/_budget.d.ts +35 -6
  10. package/dist/mcp-server/tools/definitions/_budget.d.ts.map +1 -1
  11. package/dist/mcp-server/tools/definitions/_budget.js +26 -3
  12. package/dist/mcp-server/tools/definitions/_budget.js.map +1 -1
  13. package/dist/mcp-server/tools/definitions/_notices.d.ts +33 -0
  14. package/dist/mcp-server/tools/definitions/_notices.d.ts.map +1 -0
  15. package/dist/mcp-server/tools/definitions/_notices.js +35 -0
  16. package/dist/mcp-server/tools/definitions/_notices.js.map +1 -0
  17. package/dist/mcp-server/tools/definitions/_schemas.d.ts +14 -0
  18. package/dist/mcp-server/tools/definitions/_schemas.d.ts.map +1 -1
  19. package/dist/mcp-server/tools/definitions/_schemas.js +9 -0
  20. package/dist/mcp-server/tools/definitions/_schemas.js.map +1 -1
  21. package/dist/mcp-server/tools/definitions/fetch-articles.tool.d.ts +11 -0
  22. package/dist/mcp-server/tools/definitions/fetch-articles.tool.d.ts.map +1 -1
  23. package/dist/mcp-server/tools/definitions/fetch-articles.tool.js +64 -19
  24. package/dist/mcp-server/tools/definitions/fetch-articles.tool.js.map +1 -1
  25. package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts +22 -4
  26. package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts.map +1 -1
  27. package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js +386 -167
  28. package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js.map +1 -1
  29. package/dist/mcp-server/tools/definitions/format-citations.tool.d.ts +12 -0
  30. package/dist/mcp-server/tools/definitions/format-citations.tool.d.ts.map +1 -1
  31. package/dist/mcp-server/tools/definitions/format-citations.tool.js +41 -8
  32. package/dist/mcp-server/tools/definitions/format-citations.tool.js.map +1 -1
  33. package/dist/mcp-server/tools/definitions/lookup-citation.tool.d.ts.map +1 -1
  34. package/dist/mcp-server/tools/definitions/lookup-citation.tool.js +8 -6
  35. package/dist/mcp-server/tools/definitions/lookup-citation.tool.js.map +1 -1
  36. package/dist/mcp-server/tools/definitions/lookup-mesh.tool.d.ts +1 -1
  37. package/dist/mcp-server/tools/definitions/lookup-mesh.tool.d.ts.map +1 -1
  38. package/dist/mcp-server/tools/definitions/lookup-mesh.tool.js +66 -76
  39. package/dist/mcp-server/tools/definitions/lookup-mesh.tool.js.map +1 -1
  40. package/dist/mcp-server/tools/definitions/pubmed-europepmc-fetch.tool.d.ts +6 -5
  41. package/dist/mcp-server/tools/definitions/pubmed-europepmc-fetch.tool.d.ts.map +1 -1
  42. package/dist/mcp-server/tools/definitions/pubmed-europepmc-fetch.tool.js +11 -18
  43. package/dist/mcp-server/tools/definitions/pubmed-europepmc-fetch.tool.js.map +1 -1
  44. package/dist/mcp-server/tools/definitions/pubmed-europepmc-search.tool.d.ts +4 -4
  45. package/dist/mcp-server/tools/definitions/pubmed-europepmc-search.tool.d.ts.map +1 -1
  46. package/dist/mcp-server/tools/definitions/pubmed-europepmc-search.tool.js +9 -8
  47. package/dist/mcp-server/tools/definitions/pubmed-europepmc-search.tool.js.map +1 -1
  48. package/dist/mcp-server/tools/definitions/spell-check.tool.d.ts +4 -4
  49. package/dist/mcp-server/tools/definitions/spell-check.tool.d.ts.map +1 -1
  50. package/dist/mcp-server/tools/definitions/spell-check.tool.js +12 -8
  51. package/dist/mcp-server/tools/definitions/spell-check.tool.js.map +1 -1
  52. package/dist/services/error-contracts.d.ts +1 -1
  53. package/dist/services/error-contracts.d.ts.map +1 -1
  54. package/dist/services/error-contracts.js +1 -1
  55. package/dist/services/error-contracts.js.map +1 -1
  56. package/dist/services/europe-pmc/api-client.d.ts.map +1 -1
  57. package/dist/services/europe-pmc/api-client.js +4 -3
  58. package/dist/services/europe-pmc/api-client.js.map +1 -1
  59. package/dist/services/europe-pmc/europe-pmc-service.d.ts +31 -11
  60. package/dist/services/europe-pmc/europe-pmc-service.d.ts.map +1 -1
  61. package/dist/services/europe-pmc/europe-pmc-service.js +122 -47
  62. package/dist/services/europe-pmc/europe-pmc-service.js.map +1 -1
  63. package/dist/services/europe-pmc/types.d.ts +5 -1
  64. package/dist/services/europe-pmc/types.d.ts.map +1 -1
  65. package/dist/services/fetch-redaction.d.ts +23 -0
  66. package/dist/services/fetch-redaction.d.ts.map +1 -0
  67. package/dist/services/fetch-redaction.js +62 -0
  68. package/dist/services/fetch-redaction.js.map +1 -0
  69. package/dist/services/ncbi/api-client.d.ts +3 -0
  70. package/dist/services/ncbi/api-client.d.ts.map +1 -1
  71. package/dist/services/ncbi/api-client.js +21 -8
  72. package/dist/services/ncbi/api-client.js.map +1 -1
  73. package/dist/services/ncbi/formatting/citation-formatter.d.ts +19 -3
  74. package/dist/services/ncbi/formatting/citation-formatter.d.ts.map +1 -1
  75. package/dist/services/ncbi/formatting/citation-formatter.js +410 -138
  76. package/dist/services/ncbi/formatting/citation-formatter.js.map +1 -1
  77. package/dist/services/ncbi/ncbi-service.d.ts +22 -0
  78. package/dist/services/ncbi/ncbi-service.d.ts.map +1 -1
  79. package/dist/services/ncbi/ncbi-service.js +115 -18
  80. package/dist/services/ncbi/ncbi-service.js.map +1 -1
  81. package/dist/services/ncbi/parsing/article-parser.d.ts.map +1 -1
  82. package/dist/services/ncbi/parsing/article-parser.js +89 -36
  83. package/dist/services/ncbi/parsing/article-parser.js.map +1 -1
  84. package/dist/services/ncbi/parsing/pmc-article-parser.d.ts +13 -8
  85. package/dist/services/ncbi/parsing/pmc-article-parser.d.ts.map +1 -1
  86. package/dist/services/ncbi/parsing/pmc-article-parser.js +326 -72
  87. package/dist/services/ncbi/parsing/pmc-article-parser.js.map +1 -1
  88. package/dist/services/ncbi/parsing/pmc-xml-helpers.d.ts +42 -0
  89. package/dist/services/ncbi/parsing/pmc-xml-helpers.d.ts.map +1 -1
  90. package/dist/services/ncbi/parsing/pmc-xml-helpers.js +275 -12
  91. package/dist/services/ncbi/parsing/pmc-xml-helpers.js.map +1 -1
  92. package/dist/services/ncbi/parsing/text-helpers.d.ts +10 -0
  93. package/dist/services/ncbi/parsing/text-helpers.d.ts.map +1 -1
  94. package/dist/services/ncbi/parsing/text-helpers.js +19 -0
  95. package/dist/services/ncbi/parsing/text-helpers.js.map +1 -1
  96. package/dist/services/ncbi/response-handler.d.ts +0 -11
  97. package/dist/services/ncbi/response-handler.d.ts.map +1 -1
  98. package/dist/services/ncbi/response-handler.js +24 -33
  99. package/dist/services/ncbi/response-handler.js.map +1 -1
  100. package/dist/services/ncbi/types.d.ts +72 -32
  101. package/dist/services/ncbi/types.d.ts.map +1 -1
  102. package/dist/services/openalex/api-client.d.ts.map +1 -1
  103. package/dist/services/openalex/api-client.js +4 -3
  104. package/dist/services/openalex/api-client.js.map +1 -1
  105. package/dist/services/unpaywall/unpaywall-service.d.ts +3 -0
  106. package/dist/services/unpaywall/unpaywall-service.d.ts.map +1 -1
  107. package/dist/services/unpaywall/unpaywall-service.js +18 -8
  108. package/dist/services/unpaywall/unpaywall-service.js.map +1 -1
  109. package/package.json +7 -7
  110. 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 +40,36 @@ 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
+ *
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+ * | MathML | Linear form |
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+ * |:--|:--|
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
+ * | `semantics` | one rendering of its expression, never an annotation (see `semanticsRendering`) |
64
+ * | anything else | its children in order |
65
+ *
66
+ * An empty script slot is left out (`x^{2}`, not `x_{}^{2}`). Whitespace-only
67
+ * text between elements contributes nothing; any other text reads verbatim.
68
+ * Elements match by local name, whatever their prefix. Pieces are written to
69
+ * one buffer rather than returned and concatenated level by level, so the cost
70
+ * stays linear in the size of the formula however deeply it nests.
71
+ */
72
+ export declare function linearMath(math: JatsNode): string;
43
73
  /**
44
74
  * The single child of an `<alternatives>` whose text stands for the whole
45
75
  * element.
@@ -59,6 +89,12 @@ export declare const IDENTIFIER_TAGS: ReadonlySet<string>;
59
89
  * resolve their own `<alternatives>` children by tag.
60
90
  */
61
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>;
62
98
  /**
63
99
  * Accumulates JATS text in document order and decides every separator the
64
100
  * markup implies in the same pass, from state it carries rather than by
@@ -75,6 +111,12 @@ export declare function selectAlternative(node: JatsNode, excluded?: ReadonlySet
75
111
  * between them is preceded by a comma: `[1,2,3,4]`, not `[1234]`, which reads
76
112
  * as one reference. Any source text between them, whitespace included, means
77
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>`
117
+ * reads `L<0.`, not `L<0 .`. A gap with no line break, one before `(` or a
118
+ * word, and a line boundary owed there are kept, and so is a line break
119
+ * between a word and punctuation with no element closing between them. (#225)
78
120
  *
79
121
  * An owed separator is only written between two pieces of content, so a reader
80
122
  * adds nothing at the edges of what it reads. By default the source text is
package/dist/services/ncbi/parsing/pmc-xml-helpers.d.ts.map CHANGED
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1
+ {"version":3,"file":"pmc-xml-helpers.d.ts","sourceRoot":"","sources":["../../../../src/services/ncbi/parsing/pmc-xml-helpers.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAEH;;;;GAIG;AACH,MAAM,MAAM,QAAQ,GAAG,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;AAE/C;;;;GAIG;AACH,MAAM,MAAM,YAAY,GAAG,QAAQ,EAAE,CAAC;AAKtC,uFAAuF;AACvF,wBAAgB,SAAS,CAAC,IAAI,EAAE,QAAQ,GAAG,MAAM,GAAG,SAAS,CAK5D;AAED,iFAAiF;AACjF,wBAAgB,UAAU,CAAC,IAAI,EAAE,QAAQ,GAAG,YAAY,CAKvD;AAED,sDAAsD;AACtD,wBAAgB,MAAM,CAAC,IAAI,EAAE,QAAQ,EAAE,IAAI,EAAE,MAAM,GAAG,MAAM,GAAG,SAAS,CAIvE;AAED,yCAAyC;AACzC,wBAAgB,UAAU,CAAC,IAAI,EAAE,QAAQ,GAAG,OAAO,CAElD;AAED,6CAA6C;AAC7C,wBAAgB,MAAM,CAAC,IAAI,EAAE,QAAQ,GAAG,MAAM,CAG7C;AAQD;;;;;;;;GAQG;AACH,eAAO,MAAM,eAAe,EAAE,WAAW,CAAC,MAAM,CAA+B,CAAC;AAwChF;;;GAGG;AACH,wBAAgB,SAAS,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAE9C;AA4DD;;;;;;;;;;;;;;;;;;;;;;;GAuBG;AACH,wBAAgB,UAAU,CAAC,IAAI,EAAE,QAAQ,GAAG,MAAM,CAqHjD;AAED;;;;;;;;;;;;;;;;;GAiBG;AACH,wBAAgB,iBAAiB,CAC/B,IAAI,EAAE,QAAQ,EACd,QAAQ,CAAC,EAAE,WAAW,CAAC,MAAM,CAAC,GAC7B,QAAQ,GAAG,SAAS,CAQtB;AAgDD;;;;GAIG;AACH,eAAO,MAAM,mBAAmB,EAAE,WAAW,CAAC,MAAM,CAA2C,CAAC;AAEhG;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA+BG;AACH,qBAAa,aAAa;;IAuBxB,YAAY,OAAO,GAAE;QAAE,KAAK,CAAC,EAAE,OAAO,CAAA;KAAO,EAE5C;IAED,oCAAoC;IACpC,IAAI,CAAC,KAAK,EAAE,MAAM,GAAG,IAAI,CAoCxB;IAED,sDAAsD;IACtD,IAAI,CAAC,GAAG,EAAE,MAAM,GAAG,IAAI,CAStB;IAED;;;;OAIG;IACH,KAAK,CAAC,GAAG,EAAE,MAAM,GAAG,IAAI,CAkBvB;IAED,iCAAiC;IACjC,QAAQ,IAAI,MAAM,CAOjB;CAmBF;AAwDD;;;;;;;;GAQG;AACH,wBAAgB,cAAc,CAAC,KAAK,EAAE,QAAQ,GAAG,YAAY,GAAG,SAAS,GAAG,MAAM,CAEjF;AAED;;;;;;;GAOG;AACH,wBAAgB,WAAW,CAAC,KAAK,EAAE,QAAQ,GAAG,YAAY,GAAG,SAAS,GAAG,MAAM,CAG9E;AAED;;;;;;GAMG;AACH,wBAAgB,oBAAoB,CAClC,KAAK,EAAE,QAAQ,GAAG,YAAY,GAAG,SAAS,EAC1C,YAAY,EAAE,WAAW,CAAC,MAAM,CAAC,GAChC,MAAM,CAGR;AAED;;;;;;;;GAQG;AACH,wBAAgB,eAAe,CAAC,KAAK,EAAE,QAAQ,GAAG,YAAY,GAAG,SAAS,GAAG,MAAM,CAElF;AAED,kDAAkD;AAClD,wBAAgB,OAAO,CACrB,KAAK,EAAE,QAAQ,GAAG,YAAY,GAAG,SAAS,EAC1C,OAAO,EAAE,MAAM,GACd,QAAQ,GAAG,SAAS,CAItB;AAED,mDAAmD;AACnD,wBAAgB,OAAO,CAAC,KAAK,EAAE,QAAQ,GAAG,YAAY,GAAG,SAAS,EAAE,OAAO,EAAE,MAAM,GAAG,QAAQ,EAAE,CAI/F;AAED;;;;;;;;GAQG;AACH,wBAAgB,kBAAkB,CAChC,KAAK,EAAE,QAAQ,GAAG,YAAY,GAAG,SAAS,EAC1C,OAAO,EAAE,MAAM,GACd,QAAQ,EAAE,CAWZ"}
package/dist/services/ncbi/parsing/pmc-xml-helpers.js CHANGED
@@ -87,6 +87,217 @@ 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
+ /** The alternate renderings a `<semantics>` carries after its expression. (#230) */
102
+ const MATH_ANNOTATION_TAGS = new Set(['annotation', 'annotation-xml']);
103
+ /**
104
+ * Content MathML elements that can stand as a whole expression: the strict
105
+ * set plus the containers pragmatic markup writes directly. Read as
106
+ * presentation they contribute only their leaves (`x2` for x²). (#230)
107
+ */
108
+ const CONTENT_MATH_TAGS = new Set([
109
+ 'apply',
110
+ 'bind',
111
+ 'cbytes',
112
+ 'cerror',
113
+ 'ci',
114
+ 'cn',
115
+ 'cs',
116
+ 'csymbol',
117
+ 'interval',
118
+ 'lambda',
119
+ 'list',
120
+ 'matrix',
121
+ 'piecewise',
122
+ 'set',
123
+ 'share',
124
+ 'vector',
125
+ ]);
126
+ /** `<annotation-xml>` encodings that mark a Presentation MathML rendering. (#230) */
127
+ const PRESENTATION_ENCODINGS = new Set([
128
+ 'mathml-presentation',
129
+ 'application/mathml-presentation+xml',
130
+ ]);
131
+ /**
132
+ * The child a MathML `<semantics>` renders through: its expression — the first
133
+ * child that is not an annotation — or, when that expression is Content
134
+ * MathML, a Presentation MathML `<annotation-xml>` beside it (MathML 3
135
+ * §5.1.3, §5.2.1). Every other annotation is an alternate spelling of the same
136
+ * expression (TeX source, MathType data, Content markup) and never reads.
137
+ */
138
+ function semanticsRendering(args) {
139
+ const isAnnotation = (node) => MATH_ANNOTATION_TAGS.has(localName(tagNameOf(node) ?? ''));
140
+ const expression = args.find((arg) => !isAnnotation(arg));
141
+ if (!expression || !CONTENT_MATH_TAGS.has(localName(tagNameOf(expression) ?? ''))) {
142
+ return expression;
143
+ }
144
+ const presentation = args.find((arg) => localName(tagNameOf(arg) ?? '') === 'annotation-xml' &&
145
+ PRESENTATION_ENCODINGS.has(attrOf(arg, 'encoding')?.toLowerCase() ?? ''));
146
+ return presentation ?? expression;
147
+ }
148
+ /**
149
+ * A MathML `<math>` element in a TeX-style linear form — the notation a
150
+ * formula deposited as `<tex-math>` already reads in — so a formula keeps the
151
+ * structure that carries its meaning instead of reading as the run of its
152
+ * leaves (`∑j=1Nlij`, a matrix's numeric cells fused into `−4.401.20`). (#207)
153
+ *
154
+ * | MathML | Linear form |
155
+ * |:--|:--|
156
+ * | `mi`, `mn`, `mo`, `mtext`, `ms` | their text as deposited (`−` stays U+2212) |
157
+ * | `msub`, `munder` / `msup`, `mover` | base`_{…}` / base`^{…}` |
158
+ * | `msubsup`, `munderover`, `mmultiscripts` | base`_{…}^{…}`, per script pair; `mmultiscripts` prescripts as `{}_{…}^{…}` before the base |
159
+ * | `mfrac` / `msqrt` / `mroot` | `\frac{…}{…}` / `\sqrt{…}` / `\sqrt[index]{…}` |
160
+ * | `mfenced` | `open`, the children split by `separators`, `close` (defaults `(`, `,`, `)`) |
161
+ * | `mtable` | cells split by ` & `, rows by ` \\ ` |
162
+ * | `mspace` / `mphantom` | one space / nothing |
163
+ * | `semantics` | one rendering of its expression, never an annotation (see `semanticsRendering`) |
164
+ * | anything else | its children in order |
165
+ *
166
+ * An empty script slot is left out (`x^{2}`, not `x_{}^{2}`). Whitespace-only
167
+ * text between elements contributes nothing; any other text reads verbatim.
168
+ * Elements match by local name, whatever their prefix. Pieces are written to
169
+ * one buffer rather than returned and concatenated level by level, so the cost
170
+ * stays linear in the size of the formula however deeply it nests.
171
+ */
172
+ export function linearMath(math) {
173
+ const out = [];
174
+ const emit = (text) => {
175
+ if (text)
176
+ out.push(text);
177
+ };
178
+ /** Element children only: text between MathML arguments is never one of them. */
179
+ const argsOf = (node) => childrenOf(node).filter((child) => !isTextNode(child));
180
+ /** Write `pieces` after `open`, or nothing at all when they write nothing. */
181
+ const unlessEmpty = (open, pieces, close = '') => {
182
+ const start = out.length;
183
+ out.push(open);
184
+ pieces();
185
+ if (out.length === start + 1)
186
+ out.length = start;
187
+ else
188
+ emit(close);
189
+ };
190
+ const script = (mark, node) => unlessEmpty(`${mark}{`, () => write(node), '}');
191
+ /** Script pairs — subscript, then superscript — in document order. */
192
+ const scriptPairs = (scripts) => {
193
+ for (let i = 0; i < scripts.length; i += 2) {
194
+ script('_', scripts[i]);
195
+ script('^', scripts[i + 1]);
196
+ }
197
+ };
198
+ const write = (node) => {
199
+ if (!node)
200
+ return;
201
+ if (isTextNode(node)) {
202
+ const text = textOf(node);
203
+ if (VISIBLE_CHAR.test(text))
204
+ emit(text);
205
+ return;
206
+ }
207
+ const name = localName(tagNameOf(node) ?? '');
208
+ if (MATH_TOKEN_TAGS.has(name)) {
209
+ for (const child of childrenOf(node)) {
210
+ if (isTextNode(child))
211
+ emit(textOf(child));
212
+ else
213
+ write(child);
214
+ }
215
+ return;
216
+ }
217
+ const args = argsOf(node);
218
+ switch (name) {
219
+ case 'msub':
220
+ case 'munder':
221
+ write(args[0]);
222
+ script('_', args[1]);
223
+ return;
224
+ case 'msup':
225
+ case 'mover':
226
+ write(args[0]);
227
+ script('^', args[1]);
228
+ return;
229
+ case 'msubsup':
230
+ case 'munderover':
231
+ write(args[0]);
232
+ script('_', args[1]);
233
+ script('^', args[2]);
234
+ return;
235
+ case 'mmultiscripts': {
236
+ const split = args.findIndex((arg) => localName(tagNameOf(arg) ?? '') === 'mprescripts');
237
+ if (split !== -1)
238
+ unlessEmpty('{}', () => scriptPairs(args.slice(split + 1)));
239
+ write(args[0]);
240
+ scriptPairs(args.slice(1, split === -1 ? undefined : split));
241
+ return;
242
+ }
243
+ case 'mfrac':
244
+ emit('\\frac{');
245
+ write(args[0]);
246
+ emit('}{');
247
+ write(args[1]);
248
+ emit('}');
249
+ return;
250
+ case 'msqrt':
251
+ emit('\\sqrt{');
252
+ for (const arg of args)
253
+ write(arg);
254
+ emit('}');
255
+ return;
256
+ case 'mroot':
257
+ emit('\\sqrt[');
258
+ write(args[1]);
259
+ emit(']{');
260
+ write(args[0]);
261
+ emit('}');
262
+ return;
263
+ case 'mfenced': {
264
+ const separators = [...(attrOf(node, 'separators') ?? ',').replace(/\s/g, '')];
265
+ emit(attrOf(node, 'open') ?? '(');
266
+ for (const [i, arg] of args.entries()) {
267
+ if (i > 0)
268
+ emit(separators[Math.min(i - 1, separators.length - 1)] ?? '');
269
+ write(arg);
270
+ }
271
+ emit(attrOf(node, 'close') ?? ')');
272
+ return;
273
+ }
274
+ case 'mtable':
275
+ for (const [r, row] of args.entries()) {
276
+ if (r > 0)
277
+ emit(' \\\\ ');
278
+ for (const [c, cell] of argsOf(row).entries()) {
279
+ if (c > 0)
280
+ emit(' & ');
281
+ write(cell);
282
+ }
283
+ }
284
+ return;
285
+ case 'mspace':
286
+ emit(' ');
287
+ return;
288
+ case 'mphantom':
289
+ return;
290
+ case 'semantics':
291
+ write(semanticsRendering(args));
292
+ return;
293
+ default:
294
+ for (const child of childrenOf(node))
295
+ write(child);
296
+ }
297
+ };
298
+ write(math);
299
+ return out.join('');
300
+ }
90
301
  /**
91
302
  * The single child of an `<alternatives>` whose text stands for the whole
92
303
  * element.
@@ -151,6 +362,12 @@ const LINE_SEPARATOR = 2;
151
362
  const WHITESPACE_CHAR = /\s/;
152
363
  /** Any character other than whitespace. */
153
364
  const VISIBLE_CHAR = /\S/;
365
+ /**
366
+ * Punctuation that closes the text before it — `L<0.`, `Henry L,`, `(2020)` —
367
+ * so whitespace a pretty-printed deposit leaves in front of it is formatting,
368
+ * not spacing. (#219, #225)
369
+ */
370
+ export const CLOSING_PUNCTUATION = new Set(['.', ',', ';', ':', ')', ']']);
154
371
  /**
155
372
  * Accumulates JATS text in document order and decides every separator the
156
373
  * markup implies in the same pass, from state it carries rather than by
@@ -167,6 +384,12 @@ const VISIBLE_CHAR = /\S/;
167
384
  * between them is preceded by a comma: `[1,2,3,4]`, not `[1234]`, which reads
168
385
  * as one reference. Any source text between them, whitespace included, means
169
386
  * the source already separated them. (#197)
387
+ * - Whitespace between an element and the {@link CLOSING_PUNCTUATION} after it
388
+ * is dropped when it holds a line break, whether the punctuation follows in
389
+ * plain text or opens the next element: `</inline-formula>\n<italic>.</italic>`
390
+ * reads `L<0.`, not `L<0 .`. A gap with no line break, one before `(` or a
391
+ * word, and a line boundary owed there are kept, and so is a line break
392
+ * between a word and punctuation with no element closing between them. (#225)
170
393
  *
171
394
  * An owed separator is only written between two pieces of content, so a reader
172
395
  * adds nothing at the edges of what it reads. By default the source text is
@@ -193,6 +416,12 @@ export class TextAssembler {
193
416
  #commaOwed = false;
194
417
  /** {@link #written} at each open `<label>` and `<xref>`, innermost last. */
195
418
  #marks = [];
419
+ /** An element closed since the last visible character was written. */
420
+ #elementClosed = false;
421
+ /** The whitespace written since the last visible character holds a line break. */
422
+ #gapHasLineBreak = false;
423
+ /** Where that whitespace starts in {@link #out}: every piece from here on is whitespace. */
424
+ #gapStart = 0;
196
425
  constructor(options = {}) {
197
426
  this.#lines = options.lines ?? false;
198
427
  }
@@ -201,25 +430,44 @@ export class TextAssembler {
201
430
  if (value === '')
202
431
  return;
203
432
  this.#afterXref = false;
204
- if (!VISIBLE_CHAR.test(value)) {
433
+ const lead = value.search(VISIBLE_CHAR);
434
+ if (lead === -1) {
205
435
  this.#out.push(this.#lines ? ' ' : value);
206
436
  this.#endsWithSpace = true;
437
+ if (value.includes('\n'))
438
+ this.#gapHasLineBreak = true;
207
439
  return;
208
440
  }
441
+ let start = 0;
209
442
  if (this.#written > 0 && this.#owed !== NO_SEPARATOR) {
210
443
  const separator = this.#owed === LINE_SEPARATOR ? '\n' : ' ';
211
- const sourceSpaced = this.#endsWithSpace || WHITESPACE_CHAR.test(value.charAt(0));
444
+ const sourceSpaced = this.#endsWithSpace || lead > 0;
212
445
  if (this.#lines || !sourceSpaced)
213
446
  this.#out.push(separator);
214
447
  }
215
448
  else if (this.#commaOwed) {
216
449
  this.#out.push(',');
217
450
  }
451
+ else if (this.#lineBreakBeforePunctuation(value, lead)) {
452
+ this.#out.length = this.#gapStart;
453
+ start = lead;
454
+ }
218
455
  this.#owed = NO_SEPARATOR;
219
456
  this.#afterLabel = false;
220
457
  this.#commaOwed = false;
221
- this.#out.push(this.#lines ? value.replace(/\s+/g, ' ') : value);
222
- this.#endsWithSpace = WHITESPACE_CHAR.test(value.charAt(value.length - 1));
458
+ // The trailing whitespace goes in a piece of its own, so the gap it opens can be dropped whole.
459
+ let end = value.length;
460
+ while (WHITESPACE_CHAR.test(value.charAt(end - 1)))
461
+ end -= 1;
462
+ const body = value.slice(start, end);
463
+ const trail = value.slice(end);
464
+ this.#out.push(this.#lines ? body.replace(/\s+/g, ' ') : body);
465
+ this.#gapStart = this.#out.length;
466
+ if (trail)
467
+ this.#out.push(this.#lines ? ' ' : trail);
468
+ this.#endsWithSpace = trail !== '';
469
+ this.#gapHasLineBreak = trail.includes('\n');
470
+ this.#elementClosed = false;
223
471
  this.#written += 1;
224
472
  }
225
473
  /** Enter an element, before its children are read. */
@@ -241,6 +489,7 @@ export class TextAssembler {
241
489
  * block nested in inline markup — owes nothing.
242
490
  */
243
491
  close(tag) {
492
+ this.#elementClosed = true;
244
493
  if (LINE_BOUNDARY_TAGS.has(tag)) {
245
494
  this.#oweLine();
246
495
  return;
@@ -276,17 +525,29 @@ export class TextAssembler {
276
525
  if (!this.#afterLabel)
277
526
  this.#owed = LINE_SEPARATOR;
278
527
  }
528
+ /**
529
+ * True when `value`, visible from `lead`, opens with closing punctuation, an
530
+ * element closed since the last visible character, and the whitespace between
531
+ * them holds a line break.
532
+ */
533
+ #lineBreakBeforePunctuation(value, lead) {
534
+ return (this.#written > 0 &&
535
+ this.#elementClosed &&
536
+ CLOSING_PUNCTUATION.has(value.charAt(lead)) &&
537
+ (this.#gapHasLineBreak || value.lastIndexOf('\n', lead) !== -1));
538
+ }
279
539
  }
280
540
  /**
281
541
  * Drive `sink` through a node or sibling list in document order. `excluded`
282
542
  * skips a whole subtree by tag name; omitting it reads everything else.
283
543
  *
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)
544
+ * Four JATS elements do not contribute the plain concatenation of their
545
+ * subtree: a `<tex-math>` contributes only its LaTeX document body, a MathML
546
+ * `<math>` its {@link linearMath} form, an `<alternatives>` exactly one child,
547
+ * and an {@link IDENTIFIER_TAGS} element nothing. The rules live here, beside
548
+ * the boundary rules {@link TextAssembler} applies, so every consumer inherits
549
+ * them — table cells, footnotes, titles, affiliations, references. (#135, #185,
550
+ * #207, #208)
290
551
  */
291
552
  function readInto(input, sink, excluded) {
292
553
  for (const node of Array.isArray(input) ? input : [input]) {
@@ -297,8 +558,10 @@ function readInto(input, sink, excluded) {
297
558
  const tag = tagNameOf(node) ?? '';
298
559
  if (IDENTIFIER_TAGS.has(tag) || excluded?.has(tag))
299
560
  continue;
300
- if (tag === TEX_MATH_TAG) {
301
- sink.text(texMathExpression(readText(childrenOf(node))));
561
+ if (tag === TEX_MATH_TAG || isMathTag(tag)) {
562
+ sink.open(tag);
563
+ sink.text(tag === TEX_MATH_TAG ? texMathExpression(readText(childrenOf(node))) : linearMath(node));
564
+ sink.close(tag);
302
565
  continue;
303
566
  }
304
567
  if (tag === ALTERNATIVES_TAG) {