@cyanheads/pubmed-mcp-server 2.10.18 → 2.10.20
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.
- package/AGENTS.md +16 -15
- package/CLAUDE.md +16 -15
- package/Dockerfile +86 -36
- package/README.md +86 -109
- package/changelog/2.10.x/2.10.19.md +42 -0
- package/changelog/2.10.x/2.10.20.md +63 -0
- package/dist/mcp-server/resources/definitions/database-info.resource.d.ts +43 -1
- package/dist/mcp-server/resources/definitions/database-info.resource.d.ts.map +1 -1
- package/dist/mcp-server/resources/definitions/database-info.resource.js +2 -0
- package/dist/mcp-server/resources/definitions/database-info.resource.js.map +1 -1
- package/dist/mcp-server/tools/definitions/_text.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/_text.js +10 -5
- package/dist/mcp-server/tools/definitions/_text.js.map +1 -1
- package/dist/mcp-server/tools/definitions/_visible-text.d.ts +19 -0
- package/dist/mcp-server/tools/definitions/_visible-text.d.ts.map +1 -0
- package/dist/mcp-server/tools/definitions/_visible-text.js +22 -0
- package/dist/mcp-server/tools/definitions/_visible-text.js.map +1 -0
- package/dist/mcp-server/tools/definitions/convert-ids.tool.d.ts +11 -4
- package/dist/mcp-server/tools/definitions/convert-ids.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/convert-ids.tool.js +1 -1
- package/dist/mcp-server/tools/definitions/convert-ids.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/fetch-articles.tool.d.ts +20 -7
- package/dist/mcp-server/tools/definitions/fetch-articles.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/fetch-articles.tool.js +68 -15
- package/dist/mcp-server/tools/definitions/fetch-articles.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts +37 -12
- package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js +590 -481
- package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/find-related.tool.d.ts +5 -5
- package/dist/mcp-server/tools/definitions/find-related.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/find-related.tool.js +31 -13
- package/dist/mcp-server/tools/definitions/find-related.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/format-citations.tool.d.ts +11 -4
- package/dist/mcp-server/tools/definitions/format-citations.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/lookup-citation.tool.d.ts +26 -21
- package/dist/mcp-server/tools/definitions/lookup-citation.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/lookup-citation.tool.js +109 -55
- package/dist/mcp-server/tools/definitions/lookup-citation.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/lookup-mesh.tool.d.ts +15 -7
- package/dist/mcp-server/tools/definitions/lookup-mesh.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/lookup-mesh.tool.js +19 -11
- package/dist/mcp-server/tools/definitions/lookup-mesh.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/pubmed-europepmc-fetch.tool.d.ts +20 -2
- package/dist/mcp-server/tools/definitions/pubmed-europepmc-fetch.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/pubmed-europepmc-fetch.tool.js +98 -14
- package/dist/mcp-server/tools/definitions/pubmed-europepmc-fetch.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/pubmed-europepmc-search.tool.d.ts +21 -6
- package/dist/mcp-server/tools/definitions/pubmed-europepmc-search.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/pubmed-europepmc-search.tool.js +42 -10
- package/dist/mcp-server/tools/definitions/pubmed-europepmc-search.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/search-articles.tool.d.ts +42 -18
- package/dist/mcp-server/tools/definitions/search-articles.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/search-articles.tool.js +220 -48
- package/dist/mcp-server/tools/definitions/search-articles.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/spell-check.tool.d.ts +15 -7
- package/dist/mcp-server/tools/definitions/spell-check.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/spell-check.tool.js +13 -9
- package/dist/mcp-server/tools/definitions/spell-check.tool.js.map +1 -1
- package/dist/services/error-contracts.d.ts +43 -72
- package/dist/services/error-contracts.d.ts.map +1 -1
- package/dist/services/error-contracts.js +44 -76
- package/dist/services/error-contracts.js.map +1 -1
- package/dist/services/europe-pmc/api-client.d.ts +8 -2
- package/dist/services/europe-pmc/api-client.d.ts.map +1 -1
- package/dist/services/europe-pmc/api-client.js +13 -8
- package/dist/services/europe-pmc/api-client.js.map +1 -1
- package/dist/services/europe-pmc/europe-pmc-service.d.ts +25 -2
- package/dist/services/europe-pmc/europe-pmc-service.d.ts.map +1 -1
- package/dist/services/europe-pmc/europe-pmc-service.js +90 -25
- package/dist/services/europe-pmc/europe-pmc-service.js.map +1 -1
- package/dist/services/europe-pmc/types.d.ts +6 -1
- package/dist/services/europe-pmc/types.d.ts.map +1 -1
- package/dist/services/ncbi/api-client.d.ts.map +1 -1
- package/dist/services/ncbi/api-client.js +2 -3
- package/dist/services/ncbi/api-client.js.map +1 -1
- package/dist/services/ncbi/formatting/citation-formatter.d.ts +24 -0
- package/dist/services/ncbi/formatting/citation-formatter.d.ts.map +1 -1
- package/dist/services/ncbi/formatting/citation-formatter.js +147 -46
- package/dist/services/ncbi/formatting/citation-formatter.js.map +1 -1
- package/dist/services/ncbi/ncbi-service.d.ts +18 -2
- package/dist/services/ncbi/ncbi-service.d.ts.map +1 -1
- package/dist/services/ncbi/ncbi-service.js +182 -90
- package/dist/services/ncbi/ncbi-service.js.map +1 -1
- package/dist/services/ncbi/parsing/article-parser.d.ts +15 -1
- package/dist/services/ncbi/parsing/article-parser.d.ts.map +1 -1
- package/dist/services/ncbi/parsing/article-parser.js +67 -29
- package/dist/services/ncbi/parsing/article-parser.js.map +1 -1
- package/dist/services/ncbi/parsing/esummary-parser.d.ts +9 -0
- package/dist/services/ncbi/parsing/esummary-parser.d.ts.map +1 -1
- package/dist/services/ncbi/parsing/esummary-parser.js +26 -2
- package/dist/services/ncbi/parsing/esummary-parser.js.map +1 -1
- package/dist/services/ncbi/parsing/pmc-article-parser.d.ts.map +1 -1
- package/dist/services/ncbi/parsing/pmc-article-parser.js +395 -147
- package/dist/services/ncbi/parsing/pmc-article-parser.js.map +1 -1
- package/dist/services/ncbi/parsing/pmc-xml-helpers.d.ts +73 -5
- package/dist/services/ncbi/parsing/pmc-xml-helpers.d.ts.map +1 -1
- package/dist/services/ncbi/parsing/pmc-xml-helpers.js +223 -27
- package/dist/services/ncbi/parsing/pmc-xml-helpers.js.map +1 -1
- package/dist/services/ncbi/parsing/text-helpers.d.ts +8 -6
- package/dist/services/ncbi/parsing/text-helpers.d.ts.map +1 -1
- package/dist/services/ncbi/parsing/text-helpers.js +95 -19
- package/dist/services/ncbi/parsing/text-helpers.js.map +1 -1
- package/dist/services/ncbi/response-handler.d.ts +20 -12
- package/dist/services/ncbi/response-handler.d.ts.map +1 -1
- package/dist/services/ncbi/response-handler.js +134 -38
- package/dist/services/ncbi/response-handler.js.map +1 -1
- package/dist/services/ncbi/types.d.ts +35 -2
- package/dist/services/ncbi/types.d.ts.map +1 -1
- package/dist/services/openalex/api-client.d.ts.map +1 -1
- package/dist/services/openalex/api-client.js +6 -7
- package/dist/services/openalex/api-client.js.map +1 -1
- package/dist/services/openalex/openalex-service.d.ts +10 -6
- package/dist/services/openalex/openalex-service.d.ts.map +1 -1
- package/dist/services/openalex/openalex-service.js +14 -12
- package/dist/services/openalex/openalex-service.js.map +1 -1
- package/dist/services/unpaywall/unpaywall-service.d.ts.map +1 -1
- package/dist/services/unpaywall/unpaywall-service.js +1 -3
- package/dist/services/unpaywall/unpaywall-service.js.map +1 -1
- package/package.json +16 -13
- package/server.json +10 -24
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1
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/**
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* Elements whose text identifies the element around them and is never prose:
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* the `<institution-id>` (a ROR URL, a GRID or ISNI id, a Crossref Funder DOI)
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* an `<institution-wrap>` carries beside the `<institution>` name. Read as text
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* it fuses onto that name, in an affiliation
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* (`1https://ror.org/034t3zs45grid.454711.2School of …`) and in a funding
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* statement (`sponsored by the 10.13039/501100001809National Natural Science
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* Foundation of China`) alike, so no reader takes its text. (#196, #208)
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*/
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export declare const IDENTIFIER_TAGS: ReadonlySet<string>;
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* The single child of an `<alternatives>` whose text stands for the whole
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export declare function selectAlternative(node: JatsNode, excluded?: ReadonlySet<string>): JatsNode | undefined;
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* Accumulates JATS text in document order and decides every separator the
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* markup implies in the same pass, from state it carries rather than by
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* re-reading text already emitted — so the cost stays linear in the size of the
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* subtree. A reader drives it with {@link text} for text nodes and with
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* {@link open} / {@link close} around each element's children.
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*
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* - A line-boundary element ({@link LINE_BOUNDARY_TAGS}, `<break/>`, `<hr/>`)
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* owes a line boundary before the next content.
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* - A `<label>` that carried text owes one space, and a line boundary arriving
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* before any further content becomes that space: `<fn><label>*</label><p>…`
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* reads `* …`, the marker leading its line rather than standing alone on it.
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{"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;
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{"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;AAqChF;;;;;;;;;;;;;;;;;GAiBG;AACH,wBAAgB,iBAAiB,CAC/B,IAAI,EAAE,QAAQ,EACd,QAAQ,CAAC,EAAE,WAAW,CAAC,MAAM,CAAC,GAC7B,QAAQ,GAAG,SAAS,CAQtB;AAgDD;;;;;;;;;;;;;;;;;;;;;;;;;GAyBG;AACH,qBAAa,aAAa;;IAiBxB,YAAY,OAAO,GAAE;QAAE,KAAK,CAAC,EAAE,OAAO,CAAA;KAAO,EAE5C;IAED,oCAAoC;IACpC,IAAI,CAAC,KAAK,EAAE,MAAM,GAAG,IAAI,CAqBxB;IAED,sDAAsD;IACtD,IAAI,CAAC,GAAG,EAAE,MAAM,GAAG,IAAI,CAStB;IAED;;;;OAIG;IACH,KAAK,CAAC,GAAG,EAAE,MAAM,GAAG,IAAI,CAiBvB;IAED,iCAAiC;IACjC,QAAQ,IAAI,MAAM,CAOjB;CAKF;AAmDD;;;;;;;;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"}
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* Foundation of China`) alike, so no reader takes its text. (#196, #208)
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*
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'def-item',
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'def-list',
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'disp-quote',
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]);
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/** Empty elements that are a line boundary in themselves. (#185) */
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/** No separator owed. */
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|
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*
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|
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|
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|
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* boundary is written as `\n`, replacing whatever spacing the source had there,
|
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|
+
* so the result keeps the source's line structure and nothing else. (#185)
|
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*/
|
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|
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export class TextAssembler {
|
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#lines;
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#out = [];
|
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|
+
/** How many non-whitespace text pieces have been written. */
|
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#written = 0;
|
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|
+
/** The last character written is whitespace. */
|
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|
+
#endsWithSpace = false;
|
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|
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#owed = NO_SEPARATOR;
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/** A `<label>` closed and nothing but whitespace has arrived since. */
|
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#afterLabel = false;
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/** An `<xref>` carrying text closed and no source text has arrived since. */
|
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|
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#afterXref = false;
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|
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/** A comma is owed before the open `<xref>`'s first text. */
|
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|
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#commaOwed = false;
|
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|
+
/** {@link #written} at each open `<label>` and `<xref>`, innermost last. */
|
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|
+
#marks = [];
|
|
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|
+
constructor(options = {}) {
|
|
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|
+
this.#lines = options.lines ?? false;
|
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|
+
}
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+
/** Append one text node's value. */
|
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text(value) {
|
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|
+
if (value === '')
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return;
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+
this.#afterXref = false;
|
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+
if (!VISIBLE_CHAR.test(value)) {
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|
+
this.#out.push(this.#lines ? ' ' : value);
|
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+
this.#endsWithSpace = true;
|
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|
+
return;
|
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|
+
}
|
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|
+
if (this.#written > 0 && this.#owed !== NO_SEPARATOR) {
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|
+
const separator = this.#owed === LINE_SEPARATOR ? '\n' : ' ';
|
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|
+
const sourceSpaced = this.#endsWithSpace || WHITESPACE_CHAR.test(value.charAt(0));
|
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|
+
if (this.#lines || !sourceSpaced)
|
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+
this.#out.push(separator);
|
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+
}
|
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|
+
else if (this.#commaOwed) {
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this.#out.push(',');
|
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|
+
}
|
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|
+
this.#owed = NO_SEPARATOR;
|
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|
+
this.#afterLabel = false;
|
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|
+
this.#commaOwed = false;
|
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|
+
this.#out.push(this.#lines ? value.replace(/\s+/g, ' ') : value);
|
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|
+
this.#endsWithSpace = WHITESPACE_CHAR.test(value.charAt(value.length - 1));
|
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|
+
this.#written += 1;
|
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|
+
}
|
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|
+
/** Enter an element, before its children are read. */
|
|
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|
+
open(tag) {
|
|
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|
+
if (LINE_BREAK_TAGS.has(tag) || LINE_BOUNDARY_TAGS.has(tag)) {
|
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|
+
this.#oweLine();
|
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|
+
}
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|
+
else if (tag === LABEL_TAG) {
|
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|
+
this.#marks.push(this.#written);
|
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|
+
}
|
|
233
|
+
else if (tag === XREF_TAG) {
|
|
234
|
+
this.#marks.push(this.#written);
|
|
235
|
+
this.#commaOwed = this.#afterXref;
|
|
236
|
+
}
|
|
237
|
+
}
|
|
238
|
+
/**
|
|
239
|
+
* Leave an element, after its children are read. A close with no matching
|
|
240
|
+
* mark — the run was restarted inside the element, as a prose walk does at a
|
|
241
|
+
* block nested in inline markup — owes nothing.
|
|
242
|
+
*/
|
|
243
|
+
close(tag) {
|
|
244
|
+
if (LINE_BOUNDARY_TAGS.has(tag)) {
|
|
245
|
+
this.#oweLine();
|
|
246
|
+
return;
|
|
247
|
+
}
|
|
248
|
+
if (tag !== LABEL_TAG && tag !== XREF_TAG)
|
|
249
|
+
return;
|
|
250
|
+
const mark = this.#marks.pop();
|
|
251
|
+
if (mark === undefined)
|
|
252
|
+
return;
|
|
253
|
+
const carriedText = mark !== this.#written;
|
|
254
|
+
if (tag === LABEL_TAG) {
|
|
255
|
+
if (!carriedText)
|
|
256
|
+
return;
|
|
257
|
+
this.#owed = SPACE_SEPARATOR;
|
|
258
|
+
this.#afterLabel = true;
|
|
259
|
+
return;
|
|
260
|
+
}
|
|
261
|
+
this.#commaOwed = false;
|
|
262
|
+
if (carriedText)
|
|
263
|
+
this.#afterXref = true;
|
|
264
|
+
}
|
|
265
|
+
/** The text assembled so far. */
|
|
266
|
+
toString() {
|
|
267
|
+
const text = this.#out.join('');
|
|
268
|
+
if (!this.#lines)
|
|
269
|
+
return text;
|
|
270
|
+
return text
|
|
271
|
+
.replace(/ {2,}/g, ' ')
|
|
272
|
+
.replace(/ ?\n ?/g, '\n')
|
|
273
|
+
.trim();
|
|
274
|
+
}
|
|
275
|
+
#oweLine() {
|
|
276
|
+
if (!this.#afterLabel)
|
|
277
|
+
this.#owed = LINE_SEPARATOR;
|
|
278
|
+
}
|
|
279
|
+
}
|
|
280
|
+
/**
|
|
281
|
+
* Drive `sink` through a node or sibling list in document order. `excluded`
|
|
282
|
+
* skips a whole subtree by tag name; omitting it reads everything else.
|
|
109
283
|
*
|
|
110
|
-
*
|
|
111
|
-
* a `<tex-math>` contributes only its LaTeX document body,
|
|
112
|
-
* `<alternatives>`
|
|
113
|
-
*
|
|
114
|
-
*
|
|
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)
|
|
115
290
|
*/
|
|
116
|
-
function
|
|
117
|
-
const
|
|
118
|
-
const parts = [];
|
|
119
|
-
for (const node of nodes) {
|
|
291
|
+
function readInto(input, sink, excluded) {
|
|
292
|
+
for (const node of Array.isArray(input) ? input : [input]) {
|
|
120
293
|
if (isTextNode(node)) {
|
|
121
|
-
|
|
294
|
+
sink.text(textOf(node));
|
|
122
295
|
continue;
|
|
123
296
|
}
|
|
124
297
|
const tag = tagNameOf(node) ?? '';
|
|
125
|
-
if (excluded?.has(tag))
|
|
298
|
+
if (IDENTIFIER_TAGS.has(tag) || excluded?.has(tag))
|
|
126
299
|
continue;
|
|
127
300
|
if (tag === TEX_MATH_TAG) {
|
|
128
|
-
|
|
301
|
+
sink.text(texMathExpression(readText(childrenOf(node))));
|
|
129
302
|
continue;
|
|
130
303
|
}
|
|
131
304
|
if (tag === ALTERNATIVES_TAG) {
|
|
132
305
|
const chosen = selectAlternative(node, excluded);
|
|
133
306
|
if (chosen)
|
|
134
|
-
|
|
307
|
+
readInto(chosen, sink, excluded);
|
|
135
308
|
continue;
|
|
136
309
|
}
|
|
137
|
-
|
|
310
|
+
sink.open(tag);
|
|
311
|
+
readInto(childrenOf(node), sink, excluded);
|
|
312
|
+
sink.close(tag);
|
|
138
313
|
}
|
|
139
|
-
|
|
314
|
+
}
|
|
315
|
+
/** Read a subtree through a fresh {@link TextAssembler}. */
|
|
316
|
+
function readText(input, excluded, lines = false) {
|
|
317
|
+
const sink = new TextAssembler({ lines });
|
|
318
|
+
readInto(input, sink, excluded);
|
|
319
|
+
return sink.toString();
|
|
140
320
|
}
|
|
141
321
|
/**
|
|
142
322
|
* Extract all text from a node or sibling list in document order with the
|
|
143
|
-
* source spacing intact — no whitespace collapsing, no trimming.
|
|
144
|
-
* the
|
|
145
|
-
*
|
|
146
|
-
*
|
|
323
|
+
* source spacing intact — no whitespace collapsing, no trimming. A line boundary
|
|
324
|
+
* the source marks with an element alone gains a `\n`, and a `<label>` beside
|
|
325
|
+
* its text a space; a boundary the source already spaced is left as it is, and
|
|
326
|
+
* nothing is added at the edges of the node read. Use it when the caller assembles several
|
|
327
|
+
* fragments itself and needs to collapse once over the joined result;
|
|
328
|
+
* {@link textContent} is the normalizing form for everything else.
|
|
147
329
|
*/
|
|
148
330
|
export function rawTextContent(input) {
|
|
149
|
-
return input ?
|
|
331
|
+
return input ? readText(input) : '';
|
|
150
332
|
}
|
|
151
333
|
/**
|
|
152
334
|
* Extract all text from a node or sibling list in document order, collapsing
|
|
153
335
|
* runs of whitespace to a single space and trimming the result. Use this for
|
|
154
336
|
* mixed-content elements (`<p>`, `<title>`, `<abstract>`, …) where inline
|
|
155
|
-
* children must read back in the order they appear in the source.
|
|
337
|
+
* children must read back in the order they appear in the source. A structural
|
|
338
|
+
* boundary — `<break/>`, a sibling `<p>` or `<fn>`, a `<label>` beside its text —
|
|
339
|
+
* reads as one space; inline markup never gains one. (#185)
|
|
156
340
|
*/
|
|
157
341
|
export function textContent(input) {
|
|
158
342
|
if (!input)
|
|
159
343
|
return '';
|
|
160
|
-
return
|
|
344
|
+
return readText(input).replace(/\s+/g, ' ').trim();
|
|
161
345
|
}
|
|
162
346
|
/**
|
|
163
347
|
* {@link textContent}, with the subtree of any element named in `excludedTags`
|
|
@@ -169,7 +353,19 @@ export function textContent(input) {
|
|
|
169
353
|
export function textContentExcluding(input, excludedTags) {
|
|
170
354
|
if (!input)
|
|
171
355
|
return '';
|
|
172
|
-
return
|
|
356
|
+
return readText(input, excludedTags).replace(/\s+/g, ' ').trim();
|
|
357
|
+
}
|
|
358
|
+
/**
|
|
359
|
+
* {@link textContent}, keeping every structural line boundary as `\n`: one line
|
|
360
|
+
* per `<break/>`-separated value, paragraph, footnote, or list item, a
|
|
361
|
+
* `<label>` leading its line by one space. Source whitespace inside a line —
|
|
362
|
+
* pretty-printing newlines included — collapses to one space, and blank lines
|
|
363
|
+
* drop out. For table cells and `<table-wrap-foot>`, whose line structure is
|
|
364
|
+
* part of the value: `1.08<break/>2.44` is two estimates, not `1.082.44`.
|
|
365
|
+
* (#185)
|
|
366
|
+
*/
|
|
367
|
+
export function lineTextContent(input) {
|
|
368
|
+
return input ? readText(input, undefined, true) : '';
|
|
173
369
|
}
|
|
174
370
|
/** First direct child with the given tag name. */
|
|
175
371
|
export function findOne(input, tagName) {
|
|
@@ -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,4DAA4D;AAC5D,MAAM,YAAY,GAAG,UAAU,CAAC;AAEhC,kEAAkE;AAClE,MAAM,gBAAgB,GAAG,cAAc,CAAC;AAExC;;;GAGG;AACH,MAAM,YAAY,GAAwB,IAAI,GAAG,CAAC;IAChD,SAAS;IACT,gBAAgB;IAChB,OAAO;IACP,cAAc;CACf,CAAC,CAAC;AAEH;;;;;GAKG;AACH,MAAM,iBAAiB,GAAG,sDAAsD,CAAC;AAEjF;;;;;;;;;;;GAWG;AACH,SAAS,iBAAiB,CAAC,GAAW;IACpC,OAAO,iBAAiB,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,GAAG,CAAC;AACjD,CAAC;AAED;;;;;;;;;;;;;;;;;GAiBG;AACH,MAAM,UAAU,iBAAiB,CAC/B,IAAc,EACd,QAA8B;IAE9B,MAAM,QAAQ,GAAG,UAAU,CAAC,IAAI,CAAC,CAAC;IAClC,MAAM,WAAW,GAAG,CAAC,KAAe,EAAW,EAAE,CAAC,
|
|
1
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+
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