@cyanheads/pubmed-mcp-server 2.10.8 → 2.10.10

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 (67) hide show
  1. package/AGENTS.md +1 -1
  2. package/CLAUDE.md +1 -1
  3. package/README.md +6 -4
  4. package/dist/mcp-server/tools/definitions/_text.d.ts +23 -1
  5. package/dist/mcp-server/tools/definitions/_text.d.ts.map +1 -1
  6. package/dist/mcp-server/tools/definitions/_text.js +25 -1
  7. package/dist/mcp-server/tools/definitions/_text.js.map +1 -1
  8. package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts +35 -0
  9. package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts.map +1 -1
  10. package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js +657 -44
  11. package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js.map +1 -1
  12. package/dist/mcp-server/tools/definitions/find-related.tool.d.ts +8 -0
  13. package/dist/mcp-server/tools/definitions/find-related.tool.d.ts.map +1 -1
  14. package/dist/mcp-server/tools/definitions/find-related.tool.js +131 -23
  15. package/dist/mcp-server/tools/definitions/find-related.tool.js.map +1 -1
  16. package/dist/mcp-server/tools/definitions/lookup-mesh.tool.d.ts +6 -0
  17. package/dist/mcp-server/tools/definitions/lookup-mesh.tool.d.ts.map +1 -1
  18. package/dist/mcp-server/tools/definitions/lookup-mesh.tool.js +14 -3
  19. package/dist/mcp-server/tools/definitions/lookup-mesh.tool.js.map +1 -1
  20. package/dist/mcp-server/tools/definitions/search-articles.tool.d.ts +6 -0
  21. package/dist/mcp-server/tools/definitions/search-articles.tool.d.ts.map +1 -1
  22. package/dist/mcp-server/tools/definitions/search-articles.tool.js +15 -3
  23. package/dist/mcp-server/tools/definitions/search-articles.tool.js.map +1 -1
  24. package/dist/mcp-server/tools/definitions/spell-check.tool.d.ts +6 -0
  25. package/dist/mcp-server/tools/definitions/spell-check.tool.d.ts.map +1 -1
  26. package/dist/mcp-server/tools/definitions/spell-check.tool.js +15 -3
  27. package/dist/mcp-server/tools/definitions/spell-check.tool.js.map +1 -1
  28. package/dist/services/error-contracts.d.ts +22 -2
  29. package/dist/services/error-contracts.d.ts.map +1 -1
  30. package/dist/services/error-contracts.js +24 -2
  31. package/dist/services/error-contracts.js.map +1 -1
  32. package/dist/services/europe-pmc/europe-pmc-service.d.ts +3 -3
  33. package/dist/services/europe-pmc/europe-pmc-service.d.ts.map +1 -1
  34. package/dist/services/europe-pmc/europe-pmc-service.js +8 -16
  35. package/dist/services/europe-pmc/europe-pmc-service.js.map +1 -1
  36. package/dist/services/ncbi/parsing/ordered-xml-parser-options.d.ts +44 -0
  37. package/dist/services/ncbi/parsing/ordered-xml-parser-options.d.ts.map +1 -0
  38. package/dist/services/ncbi/parsing/ordered-xml-parser-options.js +41 -0
  39. package/dist/services/ncbi/parsing/ordered-xml-parser-options.js.map +1 -0
  40. package/dist/services/ncbi/parsing/pmc-article-parser.d.ts +70 -10
  41. package/dist/services/ncbi/parsing/pmc-article-parser.d.ts.map +1 -1
  42. package/dist/services/ncbi/parsing/pmc-article-parser.js +795 -79
  43. package/dist/services/ncbi/parsing/pmc-article-parser.js.map +1 -1
  44. package/dist/services/ncbi/parsing/pmc-xml-helpers.d.ts +18 -0
  45. package/dist/services/ncbi/parsing/pmc-xml-helpers.d.ts.map +1 -1
  46. package/dist/services/ncbi/parsing/pmc-xml-helpers.js +39 -3
  47. package/dist/services/ncbi/parsing/pmc-xml-helpers.js.map +1 -1
  48. package/dist/services/ncbi/response-handler.d.ts +3 -9
  49. package/dist/services/ncbi/response-handler.d.ts.map +1 -1
  50. package/dist/services/ncbi/response-handler.js +6 -29
  51. package/dist/services/ncbi/response-handler.js.map +1 -1
  52. package/dist/services/ncbi/types.d.ts +82 -0
  53. package/dist/services/ncbi/types.d.ts.map +1 -1
  54. package/dist/services/openalex/api-client.d.ts +13 -4
  55. package/dist/services/openalex/api-client.d.ts.map +1 -1
  56. package/dist/services/openalex/api-client.js +19 -8
  57. package/dist/services/openalex/api-client.js.map +1 -1
  58. package/dist/services/openalex/openalex-service.d.ts +34 -17
  59. package/dist/services/openalex/openalex-service.d.ts.map +1 -1
  60. package/dist/services/openalex/openalex-service.js +119 -35
  61. package/dist/services/openalex/openalex-service.js.map +1 -1
  62. package/dist/services/openalex/types.d.ts +34 -1
  63. package/dist/services/openalex/types.d.ts.map +1 -1
  64. package/dist/services/openalex/types.js +20 -0
  65. package/dist/services/openalex/types.js.map +1 -1
  66. package/package.json +1 -1
  67. 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
@@ -45,8 +45,26 @@ export declare function rawTextContent(input: JatsNode | JatsNodeList | undefine
45
45
  * children must read back in the order they appear in the source.
46
46
  */
47
47
  export declare function textContent(input: JatsNode | JatsNodeList | undefined): string;
48
+ /**
49
+ * {@link textContent}, with the subtree of any element named in `excludedTags`
50
+ * left out. Block content a publisher nests inside a `<p>` — a `<table-wrap>` in
51
+ * particular — would otherwise be flattened into the paragraph, running every
52
+ * cell together into values that never existed. Such content is extracted
53
+ * separately and must not appear in the prose twice.
54
+ */
55
+ export declare function textContentExcluding(input: JatsNode | JatsNodeList | undefined, excludedTags: ReadonlySet<string>): string;
48
56
  /** First direct child with the given tag name. */
49
57
  export declare function findOne(input: JatsNode | JatsNodeList | undefined, tagName: string): JatsNode | undefined;
50
58
  /** All direct children with the given tag name. */
51
59
  export declare function findAll(input: JatsNode | JatsNodeList | undefined, tagName: string): JatsNode[];
60
+ /**
61
+ * Every descendant element with the given tag name, in document order.
62
+ * {@link findAll} matches direct children only, which is right for reading a
63
+ * known JATS shape; this is for containers publishers place at varying depths
64
+ * (a `<ref-list>` under `<back>` in one deposit and under `body/sec/sec` in the
65
+ * next). The walk keeps descending through a match, so a container nested
66
+ * inside another of the same tag is reported too. Each node is visited once, so
67
+ * the result never repeats a node.
68
+ */
69
+ export declare function findAllDescendants(input: JatsNode | JatsNodeList | undefined, tagName: string): JatsNode[];
52
70
  //# sourceMappingURL=pmc-xml-helpers.d.ts.map
package/dist/services/ncbi/parsing/pmc-xml-helpers.d.ts.map CHANGED
@@ -1 +1 @@
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;AAmBD;;;;;;GAMG;AACH,wBAAgB,cAAc,CAAC,KAAK,EAAE,QAAQ,GAAG,YAAY,GAAG,SAAS,GAAG,MAAM,CAEjF;AAED;;;;;GAKG;AACH,wBAAgB,WAAW,CAAC,KAAK,EAAE,QAAQ,GAAG,YAAY,GAAG,SAAS,GAAG,MAAM,CAG9E;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"}
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;AAoBD;;;;;;GAMG;AACH,wBAAgB,cAAc,CAAC,KAAK,EAAE,QAAQ,GAAG,YAAY,GAAG,SAAS,GAAG,MAAM,CAEjF;AAED;;;;;GAKG;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,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
@@ -44,16 +44,17 @@ export function textOf(node) {
44
44
  /**
45
45
  * Concatenate text content in document order without normalizing whitespace.
46
46
  * Internal helper so recursion preserves the original spacing between siblings.
47
+ * `excluded` skips a whole subtree by tag name; omitting it reads everything.
47
48
  */
48
- function concatText(input) {
49
+ function concatText(input, excluded) {
49
50
  const nodes = Array.isArray(input) ? input : [input];
50
51
  const parts = [];
51
52
  for (const node of nodes) {
52
53
  if (isTextNode(node)) {
53
54
  parts.push(textOf(node));
54
55
  }
55
- else {
56
- parts.push(concatText(childrenOf(node)));
56
+ else if (!excluded?.has(tagNameOf(node) ?? '')) {
57
+ parts.push(concatText(childrenOf(node), excluded));
57
58
  }
58
59
  }
59
60
  return parts.join('');
@@ -79,6 +80,18 @@ export function textContent(input) {
79
80
  return '';
80
81
  return concatText(input).replace(/\s+/g, ' ').trim();
81
82
  }
83
+ /**
84
+ * {@link textContent}, with the subtree of any element named in `excludedTags`
85
+ * left out. Block content a publisher nests inside a `<p>` — a `<table-wrap>` in
86
+ * particular — would otherwise be flattened into the paragraph, running every
87
+ * cell together into values that never existed. Such content is extracted
88
+ * separately and must not appear in the prose twice.
89
+ */
90
+ export function textContentExcluding(input, excludedTags) {
91
+ if (!input)
92
+ return '';
93
+ return concatText(input, excludedTags).replace(/\s+/g, ' ').trim();
94
+ }
82
95
  /** First direct child with the given tag name. */
83
96
  export function findOne(input, tagName) {
84
97
  if (!input)
@@ -93,4 +106,27 @@ export function findAll(input, tagName) {
93
106
  const children = Array.isArray(input) ? input : childrenOf(input);
94
107
  return children.filter((c) => tagNameOf(c) === tagName);
95
108
  }
109
+ /**
110
+ * Every descendant element with the given tag name, in document order.
111
+ * {@link findAll} matches direct children only, which is right for reading a
112
+ * known JATS shape; this is for containers publishers place at varying depths
113
+ * (a `<ref-list>` under `<back>` in one deposit and under `body/sec/sec` in the
114
+ * next). The walk keeps descending through a match, so a container nested
115
+ * inside another of the same tag is reported too. Each node is visited once, so
116
+ * the result never repeats a node.
117
+ */
118
+ export function findAllDescendants(input, tagName) {
119
+ if (!input)
120
+ return [];
121
+ const found = [];
122
+ const visit = (nodes) => {
123
+ for (const node of nodes) {
124
+ if (tagNameOf(node) === tagName)
125
+ found.push(node);
126
+ visit(childrenOf(node));
127
+ }
128
+ };
129
+ visit(Array.isArray(input) ? input : childrenOf(input));
130
+ return found;
131
+ }
96
132
  //# sourceMappingURL=pmc-xml-helpers.js.map
package/dist/services/ncbi/parsing/pmc-xml-helpers.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"pmc-xml-helpers.js","sourceRoot":"","sources":["../../../../src/services/ncbi/parsing/pmc-xml-helpers.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAgBH,MAAM,QAAQ,GAAG,IAAI,CAAC;AACtB,MAAM,QAAQ,GAAG,OAAO,CAAC;AAEzB,uFAAuF;AACvF,MAAM,UAAU,SAAS,CAAC,IAAc;IACtC,KAAK,MAAM,GAAG,IAAI,IAAI,EAAE,CAAC;QACvB,IAAI,GAAG,KAAK,QAAQ,IAAI,GAAG,KAAK,QAAQ;YAAE,OAAO,GAAG,CAAC;IACvD,CAAC;IACD,OAAO;AACT,CAAC;AAED,iFAAiF;AACjF,MAAM,UAAU,UAAU,CAAC,IAAc;IACvC,MAAM,GAAG,GAAG,SAAS,CAAC,IAAI,CAAC,CAAC;IAC5B,IAAI,CAAC,GAAG;QAAE,OAAO,EAAE,CAAC;IACpB,MAAM,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC;IACxB,OAAO,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAE,KAAsB,CAAC,CAAC,CAAC,EAAE,CAAC;AAC7D,CAAC;AAED,sDAAsD;AACtD,MAAM,UAAU,MAAM,CAAC,IAAc,EAAE,IAAY;IACjD,MAAM,KAAK,GAAG,IAAI,CAAC,QAAQ,CAAwC,CAAC;IACpE,MAAM,GAAG,GAAG,KAAK,EAAE,CAAC,KAAK,IAAI,EAAE,CAAC,CAAC;IACjC,OAAO,GAAG,IAAI,IAAI,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;AAC/C,CAAC;AAED,yCAAyC;AACzC,MAAM,UAAU,UAAU,CAAC,IAAc;IACvC,OAAO,QAAQ,IAAI,IAAI,CAAC;AAC1B,CAAC;AAED,6CAA6C;AAC7C,MAAM,UAAU,MAAM,CAAC,IAAc;IACnC,MAAM,CAAC,GAAG,IAAI,CAAC,QAAQ,CAAC,CAAC;IACzB,OAAO,CAAC,IAAI,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC;AACpC,CAAC;AAED;;;GAGG;AACH,SAAS,UAAU,CAAC,KAA8B;IAChD,MAAM,KAAK,GAAG,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC;IACrD,MAAM,KAAK,GAAa,EAAE,CAAC;IAC3B,KAAK,MAAM,IAAI,IAAI,KAAK,EAAE,CAAC;QACzB,IAAI,UAAU,CAAC,IAAI,CAAC,EAAE,CAAC;YACrB,KAAK,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC;QAC3B,CAAC;aAAM,CAAC;YACN,KAAK,CAAC,IAAI,CAAC,UAAU,CAAC,UAAU,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;QAC3C,CAAC;IACH,CAAC;IACD,OAAO,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;AACxB,CAAC;AAED;;;;;;GAMG;AACH,MAAM,UAAU,cAAc,CAAC,KAA0C;IACvE,OAAO,KAAK,CAAC,CAAC,CAAC,UAAU,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC;AACxC,CAAC;AAED;;;;;GAKG;AACH,MAAM,UAAU,WAAW,CAAC,KAA0C;IACpE,IAAI,CAAC,KAAK;QAAE,OAAO,EAAE,CAAC;IACtB,OAAO,UAAU,CAAC,KAAK,CAAC,CAAC,OAAO,CAAC,MAAM,EAAE,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC;AACvD,CAAC;AAED,kDAAkD;AAClD,MAAM,UAAU,OAAO,CACrB,KAA0C,EAC1C,OAAe;IAEf,IAAI,CAAC,KAAK;QAAE,OAAO;IACnB,MAAM,QAAQ,GAAG,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,UAAU,CAAC,KAAK,CAAC,CAAC;IAClE,OAAO,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,SAAS,CAAC,CAAC,CAAC,KAAK,OAAO,CAAC,CAAC;AACxD,CAAC;AAED,mDAAmD;AACnD,MAAM,UAAU,OAAO,CAAC,KAA0C,EAAE,OAAe;IACjF,IAAI,CAAC,KAAK;QAAE,OAAO,EAAE,CAAC;IACtB,MAAM,QAAQ,GAAG,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,UAAU,CAAC,KAAK,CAAC,CAAC;IAClE,OAAO,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,SAAS,CAAC,CAAC,CAAC,KAAK,OAAO,CAAC,CAAC;AAC1D,CAAC"}
1
+ {"version":3,"file":"pmc-xml-helpers.js","sourceRoot":"","sources":["../../../../src/services/ncbi/parsing/pmc-xml-helpers.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAgBH,MAAM,QAAQ,GAAG,IAAI,CAAC;AACtB,MAAM,QAAQ,GAAG,OAAO,CAAC;AAEzB,uFAAuF;AACvF,MAAM,UAAU,SAAS,CAAC,IAAc;IACtC,KAAK,MAAM,GAAG,IAAI,IAAI,EAAE,CAAC;QACvB,IAAI,GAAG,KAAK,QAAQ,IAAI,GAAG,KAAK,QAAQ;YAAE,OAAO,GAAG,CAAC;IACvD,CAAC;IACD,OAAO;AACT,CAAC;AAED,iFAAiF;AACjF,MAAM,UAAU,UAAU,CAAC,IAAc;IACvC,MAAM,GAAG,GAAG,SAAS,CAAC,IAAI,CAAC,CAAC;IAC5B,IAAI,CAAC,GAAG;QAAE,OAAO,EAAE,CAAC;IACpB,MAAM,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC;IACxB,OAAO,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAE,KAAsB,CAAC,CAAC,CAAC,EAAE,CAAC;AAC7D,CAAC;AAED,sDAAsD;AACtD,MAAM,UAAU,MAAM,CAAC,IAAc,EAAE,IAAY;IACjD,MAAM,KAAK,GAAG,IAAI,CAAC,QAAQ,CAAwC,CAAC;IACpE,MAAM,GAAG,GAAG,KAAK,EAAE,CAAC,KAAK,IAAI,EAAE,CAAC,CAAC;IACjC,OAAO,GAAG,IAAI,IAAI,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;AAC/C,CAAC;AAED,yCAAyC;AACzC,MAAM,UAAU,UAAU,CAAC,IAAc;IACvC,OAAO,QAAQ,IAAI,IAAI,CAAC;AAC1B,CAAC;AAED,6CAA6C;AAC7C,MAAM,UAAU,MAAM,CAAC,IAAc;IACnC,MAAM,CAAC,GAAG,IAAI,CAAC,QAAQ,CAAC,CAAC;IACzB,OAAO,CAAC,IAAI,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC;AACpC,CAAC;AAED;;;;GAIG;AACH,SAAS,UAAU,CAAC,KAA8B,EAAE,QAA8B;IAChF,MAAM,KAAK,GAAG,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC;IACrD,MAAM,KAAK,GAAa,EAAE,CAAC;IAC3B,KAAK,MAAM,IAAI,IAAI,KAAK,EAAE,CAAC;QACzB,IAAI,UAAU,CAAC,IAAI,CAAC,EAAE,CAAC;YACrB,KAAK,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC;QAC3B,CAAC;aAAM,IAAI,CAAC,QAAQ,EAAE,GAAG,CAAC,SAAS,CAAC,IAAI,CAAC,IAAI,EAAE,CAAC,EAAE,CAAC;YACjD,KAAK,CAAC,IAAI,CAAC,UAAU,CAAC,UAAU,CAAC,IAAI,CAAC,EAAE,QAAQ,CAAC,CAAC,CAAC;QACrD,CAAC;IACH,CAAC;IACD,OAAO,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;AACxB,CAAC;AAED;;;;;;GAMG;AACH,MAAM,UAAU,cAAc,CAAC,KAA0C;IACvE,OAAO,KAAK,CAAC,CAAC,CAAC,UAAU,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC;AACxC,CAAC;AAED;;;;;GAKG;AACH,MAAM,UAAU,WAAW,CAAC,KAA0C;IACpE,IAAI,CAAC,KAAK;QAAE,OAAO,EAAE,CAAC;IACtB,OAAO,UAAU,CAAC,KAAK,CAAC,CAAC,OAAO,CAAC,MAAM,EAAE,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC;AACvD,CAAC;AAED;;;;;;GAMG;AACH,MAAM,UAAU,oBAAoB,CAClC,KAA0C,EAC1C,YAAiC;IAEjC,IAAI,CAAC,KAAK;QAAE,OAAO,EAAE,CAAC;IACtB,OAAO,UAAU,CAAC,KAAK,EAAE,YAAY,CAAC,CAAC,OAAO,CAAC,MAAM,EAAE,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC;AACrE,CAAC;AAED,kDAAkD;AAClD,MAAM,UAAU,OAAO,CACrB,KAA0C,EAC1C,OAAe;IAEf,IAAI,CAAC,KAAK;QAAE,OAAO;IACnB,MAAM,QAAQ,GAAG,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,UAAU,CAAC,KAAK,CAAC,CAAC;IAClE,OAAO,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,SAAS,CAAC,CAAC,CAAC,KAAK,OAAO,CAAC,CAAC;AACxD,CAAC;AAED,mDAAmD;AACnD,MAAM,UAAU,OAAO,CAAC,KAA0C,EAAE,OAAe;IACjF,IAAI,CAAC,KAAK;QAAE,OAAO,EAAE,CAAC;IACtB,MAAM,QAAQ,GAAG,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,UAAU,CAAC,KAAK,CAAC,CAAC;IAClE,OAAO,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,SAAS,CAAC,CAAC,CAAC,KAAK,OAAO,CAAC,CAAC;AAC1D,CAAC;AAED;;;;;;;;GAQG;AACH,MAAM,UAAU,kBAAkB,CAChC,KAA0C,EAC1C,OAAe;IAEf,IAAI,CAAC,KAAK;QAAE,OAAO,EAAE,CAAC;IACtB,MAAM,KAAK,GAAe,EAAE,CAAC;IAC7B,MAAM,KAAK,GAAG,CAAC,KAAmB,EAAQ,EAAE;QAC1C,KAAK,MAAM,IAAI,IAAI,KAAK,EAAE,CAAC;YACzB,IAAI,SAAS,CAAC,IAAI,CAAC,KAAK,OAAO;gBAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;YAClD,KAAK,CAAC,UAAU,CAAC,IAAI,CAAC,CAAC,CAAC;QAC1B,CAAC;IACH,CAAC,CAAC;IACF,KAAK,CAAC,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,UAAU,CAAC,KAAK,CAAC,CAAC,CAAC;IACxD,OAAO,KAAK,CAAC;AACf,CAAC"}
package/dist/services/ncbi/response-handler.d.ts CHANGED
@@ -30,15 +30,9 @@ export declare function flattenInlineMarkup(xml: string): string;
30
30
  export declare class NcbiResponseHandler {
31
31
  private readonly xmlParser;
32
32
  /**
33
- * Parser configured for JATS mixed content (PMC full-text). `preserveOrder`
34
- * keeps document order so inline markup in `<p>`, `<abstract>`, `<title>`
35
- * doesn't collapse into reordered text. `trimValues: false` retains spacing
36
- * between text nodes and adjacent inline children. `parseTagValue: false`
37
- * keeps bibliographic tokens verbatim — page ranges like `4002.e26` and
38
- * zero-padded pages would otherwise coerce to `Number` (→ `4.002e+29`, `123`);
39
- * every value on this path is `String()`-ed downstream, so coercion is pure
40
- * downside. Entity decoding is unaffected (it's governed by `processEntities`/
41
- * `htmlEntities`), so page-range en-dashes still resolve. (#69)
33
+ * Parser configured for JATS mixed content (PMC full-text), built from
34
+ * {@link ORDERED_XML_PARSER_OPTIONS} — the same constant `EuropePmcService`
35
+ * uses, so the two JATS paths cannot drift apart. (#69, #127)
42
36
  */
43
37
  private readonly orderedXmlParser;
44
38
  /**
package/dist/services/ncbi/response-handler.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"response-handler.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/response-handler.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAiBH,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,YAAY,CAAC;AAkMrD;;;;;;;;;;;;;;;;GAgBG;AACH,wBAAgB,mBAAmB,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,CAMvD;AAED;;;GAGG;AACH,qBAAa,mBAAmB;IAC9B,OAAO,CAAC,QAAQ,CAAC,SAAS,CAAgB;IAC1C;;;;;;;;;;OAUG;IACH,OAAO,CAAC,QAAQ,CAAC,gBAAgB,CAAgB;IACjD;;;;;;;;;OASG;IACH,OAAO,CAAC,QAAQ,CAAC,iBAAiB,CAAgB;IAElD,cAqBC;IAED;;;;;;;;OAQG;IACH,OAAO,CAAC,cAAc;IA2BtB,wBAAwB,CAAC,SAAS,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,MAAM,EAAE,CAoBrE;IAED,sBAAsB,CAAC,CAAC,EACtB,YAAY,EAAE,MAAM,EACpB,QAAQ,EAAE,MAAM,EAChB,OAAO,CAAC,EAAE,kBAAkB,GAC3B,CAAC,CAsOH;CACF"}
1
+ {"version":3,"file":"response-handler.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/response-handler.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAqBH,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,YAAY,CAAC;AAuLrD;;;;;;;;;;;;;;;;GAgBG;AACH,wBAAgB,mBAAmB,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,CAMvD;AAED;;;GAGG;AACH,qBAAa,mBAAmB;IAC9B,OAAO,CAAC,QAAQ,CAAC,SAAS,CAAgB;IAC1C;;;;OAIG;IACH,OAAO,CAAC,QAAQ,CAAC,gBAAgB,CAAgB;IACjD;;;;;;;;;OASG;IACH,OAAO,CAAC,QAAQ,CAAC,iBAAiB,CAAgB;IAElD,cAaC;IAED;;;;;;;;OAQG;IACH,OAAO,CAAC,cAAc;IA2BtB,wBAAwB,CAAC,SAAS,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,MAAM,EAAE,CAoBrE;IAED,sBAAsB,CAAC,CAAC,EACtB,YAAY,EAAE,MAAM,EACpB,QAAQ,EAAE,MAAM,EAChB,OAAO,CAAC,EAAE,kBAAkB,GAC3B,CAAC,CAsOH;CACF"}
package/dist/services/ncbi/response-handler.js CHANGED
@@ -18,6 +18,7 @@ import { logger, requestContextService } from '@cyanheads/mcp-ts-core/utils';
18
18
  // biome-ignore lint/suspicious/noDeprecatedImports: staying on in-tree XMLValidator — see block comment above
19
19
  import { XMLParser as FastXmlParser, XMLValidator } from 'fast-xml-parser';
20
20
  import { recoveryFor } from '../error-contracts.js';
21
+ import { ORDERED_XML_PARSER_OPTIONS, XML_PROCESS_ENTITIES_OPTIONS, } from './parsing/ordered-xml-parser-options.js';
21
22
  /**
22
23
  * jpaths that NCBI may return as either a single value or an array.
23
24
  * The `isArray` callback forces these to always parse as arrays for consistency.
@@ -82,16 +83,6 @@ const WARNING_PATHS = [
82
83
  'eSearchResult.WarningList.QuotedPhraseNotFound',
83
84
  'eSearchResult.WarningList.OutputMessage',
84
85
  ];
85
- /**
86
- * NCBI responses routinely contain numeric character references for punctuation
87
- * and diacritics, especially in page ranges and author names. Keep entity
88
- * processing enabled, but raise the aggregate expansion ceiling high enough for
89
- * trusted PubMed payloads.
90
- */
91
- const NCBI_PROCESS_ENTITIES_OPTIONS = {
92
- enabled: true,
93
- maxTotalExpansions: 100_000,
94
- };
95
86
  function resolvePath(obj, path) {
96
87
  let current = obj;
97
88
  for (const part of path.split('.')) {
@@ -228,15 +219,9 @@ export function flattenInlineMarkup(xml) {
228
219
  export class NcbiResponseHandler {
229
220
  xmlParser;
230
221
  /**
231
- * Parser configured for JATS mixed content (PMC full-text). `preserveOrder`
232
- * keeps document order so inline markup in `<p>`, `<abstract>`, `<title>`
233
- * doesn't collapse into reordered text. `trimValues: false` retains spacing
234
- * between text nodes and adjacent inline children. `parseTagValue: false`
235
- * keeps bibliographic tokens verbatim — page ranges like `4002.e26` and
236
- * zero-padded pages would otherwise coerce to `Number` (→ `4.002e+29`, `123`);
237
- * every value on this path is `String()`-ed downstream, so coercion is pure
238
- * downside. Entity decoding is unaffected (it's governed by `processEntities`/
239
- * `htmlEntities`), so page-range en-dashes still resolve. (#69)
222
+ * Parser configured for JATS mixed content (PMC full-text), built from
223
+ * {@link ORDERED_XML_PARSER_OPTIONS} — the same constant `EuropePmcService`
224
+ * uses, so the two JATS paths cannot drift apart. (#69, #127)
240
225
  */
241
226
  orderedXmlParser;
242
227
  /**
@@ -255,21 +240,13 @@ export class NcbiResponseHandler {
255
240
  const flatOptions = {
256
241
  ignoreAttributes: false,
257
242
  attributeNamePrefix: '@_',
258
- processEntities: NCBI_PROCESS_ENTITIES_OPTIONS,
243
+ processEntities: XML_PROCESS_ENTITIES_OPTIONS,
259
244
  htmlEntities: true,
260
245
  isArray: (_name, jpath) => NCBI_ARRAY_JPATHS.has(jpath),
261
246
  };
262
247
  this.xmlParser = new FastXmlParser({ ...flatOptions, parseTagValue: true });
263
248
  this.verbatimXmlParser = new FastXmlParser({ ...flatOptions, parseTagValue: false });
264
- this.orderedXmlParser = new FastXmlParser({
265
- preserveOrder: true,
266
- ignoreAttributes: false,
267
- attributeNamePrefix: '@_',
268
- parseTagValue: false,
269
- trimValues: false,
270
- processEntities: NCBI_PROCESS_ENTITIES_OPTIONS,
271
- htmlEntities: true,
272
- });
249
+ this.orderedXmlParser = new FastXmlParser(ORDERED_XML_PARSER_OPTIONS);
273
250
  }
274
251
  /**
275
252
  * Extract a structured error from a parsed NCBI XML body and throw it as
package/dist/services/ncbi/response-handler.js.map CHANGED
@@ -1 +1 @@
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1
+ 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package/dist/services/ncbi/types.d.ts CHANGED
@@ -481,6 +481,8 @@ export interface ParsedPmcArticle {
481
481
  abstract?: string;
482
482
  affiliations?: string[];
483
483
  articleType?: string;
484
+ /** Figures and supplementary material, in document order. Absent when the article carries none. */
485
+ assets?: ParsedPmcAsset[];
484
486
  authors?: ParsedPmcAuthor[];
485
487
  doi?: string;
486
488
  journal?: ParsedPmcJournal;
@@ -496,8 +498,50 @@ export interface ParsedPmcArticle {
496
498
  pubmedUrl?: string;
497
499
  references?: ParsedPmcReference[];
498
500
  sections: ParsedPmcSection[];
501
+ tables?: ParsedPmcTable[];
499
502
  title?: string;
500
503
  }
504
+ /** Which captioned element an asset came from. */
505
+ export type ParsedPmcAssetType = 'figure' | 'supplementary-material';
506
+ /**
507
+ * A captioned asset lifted out of a PMC full-text article — a `<fig>` or a
508
+ * `<supplementary-material>`. Both are a caption plus a pointer that prose
509
+ * refers to by label, and a sixth of them sit outside `<body>` with no section
510
+ * to hang from, so they are reported at article level the way `tables[]` is,
511
+ * leaving a positional marker in the section text they were lifted from.
512
+ *
513
+ * Scalar leaves only: the tool-layer schema that renders these sits under the
514
+ * framework's `format-parity` walker depth cap.
515
+ *
516
+ * There is no per-asset unextractable reason, and deliberately so. A table
517
+ * promises cells, so a graphic-only deposit has to disclose that it has none; an
518
+ * asset promises a caption, and an uncaptioned supplement is still fully
519
+ * represented by its `id` and `href`, with no re-call that would produce more.
520
+ * There is no media-type field either — `mimetype`/`mime-subtype` are in the
521
+ * JATS model but appear zero times across a 68-record draw. (#130)
522
+ */
523
+ export interface ParsedPmcAsset {
524
+ /** Which element this came from. */
525
+ assetType: ParsedPmcAssetType;
526
+ /** Caption text, without the label. */
527
+ caption?: string;
528
+ /**
529
+ * The `<graphic>`/`<media>` `@xlink:href`, verbatim. A deposit-relative
530
+ * filename (`MOL2-20-1253-g001.jpg`), not a fetchable URL — no absolute form
531
+ * of it resolves. Use `pmcUrl` for the rendered article.
532
+ */
533
+ href?: string;
534
+ /** The `id` attribute, when the deposit carries one. */
535
+ id?: string;
536
+ /** Display label, e.g. `Fig. 1`. */
537
+ label?: string;
538
+ /**
539
+ * Title of the innermost enclosing `<sec>` wherever it sits — body, back
540
+ * matter, or appendix. Absent for a `<floats-group>` deposit, which sits in no
541
+ * section at all.
542
+ */
543
+ sectionTitle?: string;
544
+ }
501
545
  /** Parsed PMC author. */
502
546
  export interface ParsedPmcAuthor {
503
547
  collectiveName?: string;
@@ -525,6 +569,44 @@ export interface ParsedPmcReference {
525
569
  id?: string;
526
570
  label?: string;
527
571
  }
572
+ /**
573
+ * Why a `<table-wrap>` yielded no rows. Not an error — the table is still
574
+ * returned with its label and caption so a reader is never shown a response
575
+ * that silently omits it.
576
+ * - `graphic-only` — the deposit is a scanned image, with no markup to read.
577
+ * - `cals-tgroup` — a CALS `<tgroup>` body, deliberately not extracted.
578
+ * - `no-rows` — an XHTML `<table>` with no `<tr>` carrying cells.
579
+ */
580
+ export type ParsedPmcTableUnextractableReason = 'cals-tgroup' | 'graphic-only' | 'no-rows';
581
+ /**
582
+ * Parsed `<table-wrap>` from a PMC full-text article. Rows are a plain
583
+ * `string[][]` of cell text, one entry per grid column: `colspan` and `rowspan`
584
+ * are expanded, so a cell covering several columns or rows repeats its text
585
+ * across the cells it covers and a well-formed table comes back rectangular.
586
+ * Nothing deeper than a string hangs off a row — the tool-layer schema that
587
+ * renders these sits at the framework's parity-walker depth cap.
588
+ */
589
+ export interface ParsedPmcTable {
590
+ /** Caption text, without the label. */
591
+ caption?: string;
592
+ /** `<table-wrap-foot>` text, flattened. */
593
+ footnotes?: string;
594
+ /** Leading rows of {@link rows} that came from `<thead>` or are all `<th>`. */
595
+ headerRowCount: number;
596
+ /** The `id` attribute, when the deposit carries one. */
597
+ id?: string;
598
+ /** Display label, e.g. `TABLE 1`. */
599
+ label?: string;
600
+ /** Cell text by grid column, spans expanded. Empty when unextractable. */
601
+ rows: string[][];
602
+ /**
603
+ * Title of the innermost enclosing `<sec>` wherever it sits — body, back
604
+ * matter, or appendix. Absent only for a table inside no section at all.
605
+ */
606
+ sectionTitle?: string;
607
+ /** Set only when {@link rows} is empty. */
608
+ unextractableReason?: ParsedPmcTableUnextractableReason;
609
+ }
528
610
  /** Single citation for ECitMatch lookup. */
529
611
  export interface ECitMatchCitation {
530
612
  /** Author name (e.g., "mann bj") */
package/dist/services/ncbi/types.d.ts.map CHANGED
@@ -1 +1 @@
1
- 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package/dist/services/openalex/api-client.d.ts CHANGED
@@ -36,14 +36,23 @@ export declare class OpenAlexApiClient {
36
36
  /**
37
37
  * Batch-resolve a list of OpenAlex work IDs to their PMIDs.
38
38
  * Uses the filter=openalex:W1|W2|... endpoint with select=id,ids.
39
- * Returns only records that carry a `pmid` field.
39
+ *
40
+ * One call resolves one batch: the OR-filter accepts at most
41
+ * `OPENALEX_MAX_FILTER_VALUES` values and the endpoint serves at most
42
+ * `OPENALEX_MAX_PAGE_SIZE` rows, so splitting a longer list is the caller's
43
+ * job (`OpenAlexService`). Results arrive in OpenAlex's order, not the
44
+ * requested one.
40
45
  */
41
46
  resolveOaIdsToPmids(oaIds: string[], signal?: AbortSignal): Promise<OpenAlexWork[]>;
42
47
  /**
43
- * Fetch works that cite a given OpenAlex work ID (the cited_by relationship).
44
- * Returns up to `perPage` records with PMIDs.
48
+ * Fetch one page of works that cite a given OpenAlex work ID (the cited_by
49
+ * relationship). Returns up to `perPage` records plus OpenAlex's own total.
50
+ *
51
+ * `page` is 1-based. Basic paging is bounded by `page × per_page ≤ 10,000`;
52
+ * past that OpenAlex rejects the request and requires cursor paging, so the
53
+ * caller's page cap must keep the walk inside that ceiling.
45
54
  */
46
- getCitedBy(oaId: string, perPage: number, signal?: AbortSignal): Promise<{
55
+ getCitedBy(oaId: string, perPage: number, page: number, signal?: AbortSignal): Promise<{
47
56
  works: OpenAlexWork[];
48
57
  totalCount: number;
49
58
  }>;
package/dist/services/openalex/api-client.d.ts.map CHANGED
@@ -1 +1 @@
1
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