@cyanheads/pubmed-mcp-server 2.10.19 → 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 (110) hide show
  1. package/AGENTS.md +8 -5
  2. package/CLAUDE.md +8 -5
  3. package/Dockerfile +12 -3
  4. package/README.md +12 -11
  5. package/changelog/2.10.x/2.10.20.md +63 -0
  6. package/changelog/2.10.x/2.10.21.md +42 -0
  7. package/dist/mcp-server/tools/definitions/_text.d.ts.map +1 -1
  8. package/dist/mcp-server/tools/definitions/_text.js +10 -5
  9. package/dist/mcp-server/tools/definitions/_text.js.map +1 -1
  10. package/dist/mcp-server/tools/definitions/fetch-articles.tool.d.ts +8 -0
  11. package/dist/mcp-server/tools/definitions/fetch-articles.tool.d.ts.map +1 -1
  12. package/dist/mcp-server/tools/definitions/fetch-articles.tool.js +64 -14
  13. package/dist/mcp-server/tools/definitions/fetch-articles.tool.js.map +1 -1
  14. package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts +44 -9
  15. package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts.map +1 -1
  16. package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js +815 -563
  17. package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js.map +1 -1
  18. package/dist/mcp-server/tools/definitions/find-related.tool.d.ts +5 -5
  19. package/dist/mcp-server/tools/definitions/find-related.tool.d.ts.map +1 -1
  20. package/dist/mcp-server/tools/definitions/find-related.tool.js +12 -8
  21. package/dist/mcp-server/tools/definitions/find-related.tool.js.map +1 -1
  22. package/dist/mcp-server/tools/definitions/format-citations.tool.d.ts +12 -0
  23. package/dist/mcp-server/tools/definitions/format-citations.tool.d.ts.map +1 -1
  24. package/dist/mcp-server/tools/definitions/format-citations.tool.js +53 -7
  25. package/dist/mcp-server/tools/definitions/format-citations.tool.js.map +1 -1
  26. package/dist/mcp-server/tools/definitions/lookup-citation.tool.d.ts +11 -7
  27. package/dist/mcp-server/tools/definitions/lookup-citation.tool.d.ts.map +1 -1
  28. package/dist/mcp-server/tools/definitions/lookup-citation.tool.js +72 -34
  29. package/dist/mcp-server/tools/definitions/lookup-citation.tool.js.map +1 -1
  30. package/dist/mcp-server/tools/definitions/lookup-mesh.tool.d.ts +2 -1
  31. package/dist/mcp-server/tools/definitions/lookup-mesh.tool.d.ts.map +1 -1
  32. package/dist/mcp-server/tools/definitions/lookup-mesh.tool.js +11 -3
  33. package/dist/mcp-server/tools/definitions/lookup-mesh.tool.js.map +1 -1
  34. package/dist/mcp-server/tools/definitions/pubmed-europepmc-fetch.tool.d.ts +18 -0
  35. package/dist/mcp-server/tools/definitions/pubmed-europepmc-fetch.tool.d.ts.map +1 -1
  36. package/dist/mcp-server/tools/definitions/pubmed-europepmc-fetch.tool.js +96 -13
  37. package/dist/mcp-server/tools/definitions/pubmed-europepmc-fetch.tool.js.map +1 -1
  38. package/dist/mcp-server/tools/definitions/pubmed-europepmc-search.tool.d.ts +4 -3
  39. package/dist/mcp-server/tools/definitions/pubmed-europepmc-search.tool.d.ts.map +1 -1
  40. package/dist/mcp-server/tools/definitions/pubmed-europepmc-search.tool.js +7 -5
  41. package/dist/mcp-server/tools/definitions/pubmed-europepmc-search.tool.js.map +1 -1
  42. package/dist/mcp-server/tools/definitions/search-articles.tool.d.ts +6 -4
  43. package/dist/mcp-server/tools/definitions/search-articles.tool.d.ts.map +1 -1
  44. package/dist/mcp-server/tools/definitions/search-articles.tool.js +33 -11
  45. package/dist/mcp-server/tools/definitions/search-articles.tool.js.map +1 -1
  46. package/dist/mcp-server/tools/definitions/spell-check.tool.d.ts +2 -1
  47. package/dist/mcp-server/tools/definitions/spell-check.tool.d.ts.map +1 -1
  48. package/dist/mcp-server/tools/definitions/spell-check.tool.js +5 -1
  49. package/dist/mcp-server/tools/definitions/spell-check.tool.js.map +1 -1
  50. package/dist/services/error-contracts.d.ts +1 -1
  51. package/dist/services/error-contracts.d.ts.map +1 -1
  52. package/dist/services/error-contracts.js +1 -1
  53. package/dist/services/error-contracts.js.map +1 -1
  54. package/dist/services/europe-pmc/api-client.d.ts.map +1 -1
  55. package/dist/services/europe-pmc/api-client.js +4 -3
  56. package/dist/services/europe-pmc/api-client.js.map +1 -1
  57. package/dist/services/fetch-redaction.d.ts +23 -0
  58. package/dist/services/fetch-redaction.d.ts.map +1 -0
  59. package/dist/services/fetch-redaction.js +62 -0
  60. package/dist/services/fetch-redaction.js.map +1 -0
  61. package/dist/services/ncbi/api-client.d.ts +3 -0
  62. package/dist/services/ncbi/api-client.d.ts.map +1 -1
  63. package/dist/services/ncbi/api-client.js +21 -8
  64. package/dist/services/ncbi/api-client.js.map +1 -1
  65. package/dist/services/ncbi/formatting/citation-formatter.d.ts +42 -2
  66. package/dist/services/ncbi/formatting/citation-formatter.d.ts.map +1 -1
  67. package/dist/services/ncbi/formatting/citation-formatter.js +370 -91
  68. package/dist/services/ncbi/formatting/citation-formatter.js.map +1 -1
  69. package/dist/services/ncbi/ncbi-service.d.ts +16 -1
  70. package/dist/services/ncbi/ncbi-service.d.ts.map +1 -1
  71. package/dist/services/ncbi/ncbi-service.js +117 -71
  72. package/dist/services/ncbi/ncbi-service.js.map +1 -1
  73. package/dist/services/ncbi/parsing/article-parser.d.ts.map +1 -1
  74. package/dist/services/ncbi/parsing/article-parser.js +116 -61
  75. package/dist/services/ncbi/parsing/article-parser.js.map +1 -1
  76. package/dist/services/ncbi/parsing/esummary-parser.d.ts +9 -0
  77. package/dist/services/ncbi/parsing/esummary-parser.d.ts.map +1 -1
  78. package/dist/services/ncbi/parsing/esummary-parser.js +26 -2
  79. package/dist/services/ncbi/parsing/esummary-parser.js.map +1 -1
  80. package/dist/services/ncbi/parsing/pmc-article-parser.d.ts +8 -7
  81. package/dist/services/ncbi/parsing/pmc-article-parser.d.ts.map +1 -1
  82. package/dist/services/ncbi/parsing/pmc-article-parser.js +633 -185
  83. package/dist/services/ncbi/parsing/pmc-article-parser.js.map +1 -1
  84. package/dist/services/ncbi/parsing/pmc-xml-helpers.d.ts +102 -5
  85. package/dist/services/ncbi/parsing/pmc-xml-helpers.d.ts.map +1 -1
  86. package/dist/services/ncbi/parsing/pmc-xml-helpers.js +389 -28
  87. package/dist/services/ncbi/parsing/pmc-xml-helpers.js.map +1 -1
  88. package/dist/services/ncbi/parsing/text-helpers.d.ts +8 -6
  89. package/dist/services/ncbi/parsing/text-helpers.d.ts.map +1 -1
  90. package/dist/services/ncbi/parsing/text-helpers.js +95 -19
  91. package/dist/services/ncbi/parsing/text-helpers.js.map +1 -1
  92. package/dist/services/ncbi/response-handler.d.ts +20 -12
  93. package/dist/services/ncbi/response-handler.d.ts.map +1 -1
  94. package/dist/services/ncbi/response-handler.js +115 -19
  95. package/dist/services/ncbi/response-handler.js.map +1 -1
  96. package/dist/services/ncbi/types.d.ts +44 -4
  97. package/dist/services/ncbi/types.d.ts.map +1 -1
  98. package/dist/services/openalex/api-client.d.ts.map +1 -1
  99. package/dist/services/openalex/api-client.js +4 -3
  100. package/dist/services/openalex/api-client.js.map +1 -1
  101. package/dist/services/openalex/openalex-service.d.ts +10 -6
  102. package/dist/services/openalex/openalex-service.d.ts.map +1 -1
  103. package/dist/services/openalex/openalex-service.js +13 -9
  104. package/dist/services/openalex/openalex-service.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 +14 -12
  110. package/server.json +10 -24
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
@@ -30,6 +30,45 @@ export declare function attrOf(node: JatsNode, name: string): string | undefined
30
30
  export declare function isTextNode(node: JatsNode): boolean;
31
31
  /** Stringified text value of a text node. */
32
32
  export declare function textOf(node: JatsNode): string;
33
+ /**
34
+ * Elements whose text identifies the element around them and is never prose:
35
+ * the `<institution-id>` (a ROR URL, a GRID or ISNI id, a Crossref Funder DOI)
36
+ * an `<institution-wrap>` carries beside the `<institution>` name. Read as text
37
+ * it fuses onto that name, in an affiliation
38
+ * (`1https://ror.org/034t3zs45grid.454711.2School of …`) and in a funding
39
+ * statement (`sponsored by the 10.13039/501100001809National Natural Science
40
+ * Foundation of China`) alike, so no reader takes its text. (#196, #208)
41
+ */
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;
33
72
  /**
34
73
  * The single child of an `<alternatives>` whose text stands for the whole
35
74
  * element.
@@ -49,19 +88,67 @@ export declare function textOf(node: JatsNode): string;
49
88
  * resolve their own `<alternatives>` children by tag.
50
89
  */
51
90
  export declare function selectAlternative(node: JatsNode, excluded?: ReadonlySet<string>): JatsNode | undefined;
91
+ /**
92
+ * Accumulates JATS text in document order and decides every separator the
93
+ * markup implies in the same pass, from state it carries rather than by
94
+ * re-reading text already emitted — so the cost stays linear in the size of the
95
+ * subtree. A reader drives it with {@link text} for text nodes and with
96
+ * {@link open} / {@link close} around each element's children.
97
+ *
98
+ * - A line-boundary element ({@link LINE_BOUNDARY_TAGS}, `<break/>`, `<hr/>`)
99
+ * owes a line boundary before the next content.
100
+ * - A `<label>` that carried text owes one space, and a line boundary arriving
101
+ * before any further content becomes that space: `<fn><label>*</label><p>…`
102
+ * reads `* …`, the marker leading its line rather than standing alone on it.
103
+ * - An `<xref>` that carries text and follows another with no source text
104
+ * between them is preceded by a comma: `[1,2,3,4]`, not `[1234]`, which reads
105
+ * as one reference. Any source text between them, whitespace included, means
106
+ * the source already separated them. (#197)
107
+ *
108
+ * An owed separator is only written between two pieces of content, so a reader
109
+ * adds nothing at the edges of what it reads. By default the source text is
110
+ * kept verbatim and a separator is written only where neither side carries
111
+ * whitespace — `a<break/>b` gains a `\n`, `a <break/>b` stays as it was — so a
112
+ * caller collapsing whitespace afterwards reads every boundary as one space. In
113
+ * `lines` mode each text node's whitespace collapses to a space and every line
114
+ * boundary is written as `\n`, replacing whatever spacing the source had there,
115
+ * so the result keeps the source's line structure and nothing else. (#185)
116
+ */
117
+ export declare class TextAssembler {
118
+ #private;
119
+ constructor(options?: {
120
+ lines?: boolean;
121
+ });
122
+ /** Append one text node's value. */
123
+ text(value: string): void;
124
+ /** Enter an element, before its children are read. */
125
+ open(tag: string): void;
126
+ /**
127
+ * Leave an element, after its children are read. A close with no matching
128
+ * mark — the run was restarted inside the element, as a prose walk does at a
129
+ * block nested in inline markup — owes nothing.
130
+ */
131
+ close(tag: string): void;
132
+ /** The text assembled so far. */
133
+ toString(): string;
134
+ }
52
135
  /**
53
136
  * Extract all text from a node or sibling list in document order with the
54
- * source spacing intact — no whitespace collapsing, no trimming. Use it when
55
- * the caller assembles several fragments itself and needs to collapse once over
56
- * the joined result; {@link textContent} is the normalizing form for everything
57
- * else.
137
+ * source spacing intact — no whitespace collapsing, no trimming. A line boundary
138
+ * the source marks with an element alone gains a `\n`, and a `<label>` beside
139
+ * its text a space; a boundary the source already spaced is left as it is, and
140
+ * nothing is added at the edges of the node read. Use it when the caller assembles several
141
+ * fragments itself and needs to collapse once over the joined result;
142
+ * {@link textContent} is the normalizing form for everything else.
58
143
  */
59
144
  export declare function rawTextContent(input: JatsNode | JatsNodeList | undefined): string;
60
145
  /**
61
146
  * Extract all text from a node or sibling list in document order, collapsing
62
147
  * runs of whitespace to a single space and trimming the result. Use this for
63
148
  * mixed-content elements (`<p>`, `<title>`, `<abstract>`, …) where inline
64
- * children must read back in the order they appear in the source.
149
+ * children must read back in the order they appear in the source. A structural
150
+ * boundary — `<break/>`, a sibling `<p>` or `<fn>`, a `<label>` beside its text —
151
+ * reads as one space; inline markup never gains one. (#185)
65
152
  */
66
153
  export declare function textContent(input: JatsNode | JatsNodeList | undefined): string;
67
154
  /**
@@ -72,6 +159,16 @@ export declare function textContent(input: JatsNode | JatsNodeList | undefined):
72
159
  * separately and must not appear in the prose twice.
73
160
  */
74
161
  export declare function textContentExcluding(input: JatsNode | JatsNodeList | undefined, excludedTags: ReadonlySet<string>): string;
162
+ /**
163
+ * {@link textContent}, keeping every structural line boundary as `\n`: one line
164
+ * per `<break/>`-separated value, paragraph, footnote, or list item, a
165
+ * `<label>` leading its line by one space. Source whitespace inside a line —
166
+ * pretty-printing newlines included — collapses to one space, and blank lines
167
+ * drop out. For table cells and `<table-wrap-foot>`, whose line structure is
168
+ * part of the value: `1.08<break/>2.44` is two estimates, not `1.082.44`.
169
+ * (#185)
170
+ */
171
+ export declare function lineTextContent(input: JatsNode | JatsNodeList | undefined): string;
75
172
  /** First direct child with the given tag name. */
76
173
  export declare function findOne(input: JatsNode | JatsNodeList | undefined, tagName: string): JatsNode | undefined;
77
174
  /** All direct children with the given tag name. */
package/dist/services/ncbi/parsing/pmc-xml-helpers.d.ts.map CHANGED
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