@cyanheads/pubmed-mcp-server 2.10.20 → 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.
- package/AGENTS.md +3 -3
- package/CLAUDE.md +3 -3
- package/README.md +7 -6
- package/changelog/2.10.x/2.10.21.md +42 -0
- package/dist/mcp-server/tools/definitions/fetch-articles.tool.d.ts +8 -0
- package/dist/mcp-server/tools/definitions/fetch-articles.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/fetch-articles.tool.js +36 -4
- package/dist/mcp-server/tools/definitions/fetch-articles.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts +21 -4
- package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js +287 -127
- package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/format-citations.tool.d.ts +12 -0
- package/dist/mcp-server/tools/definitions/format-citations.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/format-citations.tool.js +53 -7
- package/dist/mcp-server/tools/definitions/format-citations.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/lookup-citation.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/lookup-citation.tool.js +8 -6
- package/dist/mcp-server/tools/definitions/lookup-citation.tool.js.map +1 -1
- 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 +0 -1
- package/dist/mcp-server/tools/definitions/pubmed-europepmc-fetch.tool.js.map +1 -1
- package/dist/services/europe-pmc/api-client.d.ts.map +1 -1
- package/dist/services/europe-pmc/api-client.js +4 -3
- package/dist/services/europe-pmc/api-client.js.map +1 -1
- package/dist/services/fetch-redaction.d.ts +23 -0
- package/dist/services/fetch-redaction.d.ts.map +1 -0
- package/dist/services/fetch-redaction.js +62 -0
- package/dist/services/fetch-redaction.js.map +1 -0
- package/dist/services/ncbi/api-client.d.ts +3 -0
- package/dist/services/ncbi/api-client.d.ts.map +1 -1
- package/dist/services/ncbi/api-client.js +21 -8
- package/dist/services/ncbi/api-client.js.map +1 -1
- package/dist/services/ncbi/formatting/citation-formatter.d.ts +19 -3
- package/dist/services/ncbi/formatting/citation-formatter.d.ts.map +1 -1
- package/dist/services/ncbi/formatting/citation-formatter.js +224 -46
- package/dist/services/ncbi/formatting/citation-formatter.js.map +1 -1
- package/dist/services/ncbi/ncbi-service.d.ts.map +1 -1
- package/dist/services/ncbi/ncbi-service.js +2 -1
- package/dist/services/ncbi/ncbi-service.js.map +1 -1
- package/dist/services/ncbi/parsing/article-parser.d.ts.map +1 -1
- package/dist/services/ncbi/parsing/article-parser.js +80 -34
- package/dist/services/ncbi/parsing/article-parser.js.map +1 -1
- package/dist/services/ncbi/parsing/pmc-article-parser.d.ts +8 -7
- package/dist/services/ncbi/parsing/pmc-article-parser.d.ts.map +1 -1
- package/dist/services/ncbi/parsing/pmc-article-parser.js +257 -57
- package/dist/services/ncbi/parsing/pmc-article-parser.js.map +1 -1
- package/dist/services/ncbi/parsing/pmc-xml-helpers.d.ts +29 -0
- package/dist/services/ncbi/parsing/pmc-xml-helpers.d.ts.map +1 -1
- package/dist/services/ncbi/parsing/pmc-xml-helpers.js +171 -6
- package/dist/services/ncbi/parsing/pmc-xml-helpers.js.map +1 -1
- package/dist/services/ncbi/response-handler.d.ts.map +1 -1
- package/dist/services/ncbi/response-handler.js +3 -0
- package/dist/services/ncbi/response-handler.js.map +1 -1
- package/dist/services/ncbi/types.d.ts +42 -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 +4 -3
- package/dist/services/openalex/api-client.js.map +1 -1
- package/dist/services/unpaywall/unpaywall-service.d.ts +3 -0
- package/dist/services/unpaywall/unpaywall-service.d.ts.map +1 -1
- package/dist/services/unpaywall/unpaywall-service.js +18 -8
- package/dist/services/unpaywall/unpaywall-service.js.map +1 -1
- package/package.json +5 -5
- package/server.json +3 -3
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@@ -65,6 +65,8 @@ export interface NcbiCallOptions {
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*/
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export interface ParseFullArticleOptions {
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includeGrants?: boolean;
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/** Read `MedlineCitation/InvestigatorList` into `investigators`. (#216) */
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includeInvestigators?: boolean;
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includeMesh?: boolean;
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}
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export interface XmlTextElement {
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@@ -91,6 +93,16 @@ export interface XmlAuthor {
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Initials?: XmlTextElement;
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LastName?: XmlTextElement;
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}
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/**
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* One member of a collective author, from `InvestigatorList`. The DTD gives an
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* investigator an author's person fields but no `CollectiveName`:
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* `(LastName, ForeName?, Initials?, Suffix?, Identifier*, AffiliationInfo*)`. (#216)
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*/
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export type XmlInvestigator = Omit<XmlAuthor, 'CollectiveName'>;
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/** `MedlineCitation/InvestigatorList` — repeatable, one or more `Investigator` each. */
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export interface XmlInvestigatorList {
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Investigator?: XmlInvestigator[] | XmlInvestigator;
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}
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export interface XmlAuthorList {
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'@_CompleteYN'?: 'Y' | 'N';
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/**
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@@ -225,6 +237,7 @@ export interface XmlMedlineCitation {
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GeneralNote?: (XmlTextElement & {
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'@_Owner'?: string;
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})[];
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InvestigatorList?: XmlInvestigatorList[] | XmlInvestigatorList;
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KeywordList?: XmlKeywordList[] | XmlKeywordList;
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MeshHeadingList?: XmlMeshHeadingList;
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PMID: XmlPMID;
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@@ -320,6 +333,20 @@ export interface ParsedArticleAuthor {
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lastName?: string;
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orcid?: string;
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}
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/**
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* A member of a collective author, from `InvestigatorList`. Not an author: kept
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* apart from {@link ParsedArticleAuthor}, and no citation style lists one. A name
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* part the record lacks is omitted, never `""`. `affiliationIndices` point into
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* the article's `affiliations`, where investigator affiliations follow the
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* authors' own. (#216)
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*/
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export interface ParsedInvestigator {
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affiliationIndices?: number[];
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firstName?: string;
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initials?: string;
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lastName?: string;
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orcid?: string;
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}
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export interface ParsedArticleDate {
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dateType?: string;
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day?: string;
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@@ -448,6 +475,12 @@ export interface ParsedArticle {
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commentsCorrections?: ParsedCommentsCorrection[];
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doi?: string;
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grantList?: ParsedGrant[];
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/**
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* Every `InvestigatorList` entry, lists flattened in upstream order, uncapped.
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* Set only when requested and the record carries at least one; journal
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* articles only, as a Bookshelf record's list is never read. (#216)
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*/
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investigators?: ParsedInvestigator[];
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/**
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* Absent on `book-chapter` and `book` records — a Bookshelf record has no
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* journal, and the book title is never promoted into one.
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@@ -682,6 +715,13 @@ export interface ParsedPmcArticle {
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/** Figures and supplementary material, in document order. Absent when the article carries none. */
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assets?: ParsedPmcAsset[];
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authors?: ParsedPmcAuthor[];
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/**
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* Back-matter sections — every `<back>` child but `<ref-list>`, in source
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* order. Kept apart from `sections` so a record with back matter and no body
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* still reads as bodyless; the tool appends them after the body. Absent when
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* `<back>` carries none. (#206)
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*/
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backSections?: ParsedPmcSection[];
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doi?: string;
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journal?: ParsedPmcJournal;
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keywords?: string[];
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/** Display label, e.g. `Fig. 1`. */
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label?: string;
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/**
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* Title of the innermost enclosing
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* Title of the innermost enclosing section wherever it sits — body, back
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* matter, or appendix. Absent for a `<floats-group>` deposit, which sits in no
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* section at all.
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*/
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/** Cell text by grid column, spans expanded. Empty when unextractable. */
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rows: string[][];
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/**
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* Title of the innermost enclosing section wherever it sits — body, back
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* matter, or appendix. Absent only for a table inside no section at all.
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*/
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sectionTitle?: string;
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@@ -1 +1 @@
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1
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-
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1
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+
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@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"api-client.d.ts","sourceRoot":"","sources":["../../../src/services/openalex/api-client.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;
|
|
1
|
+
{"version":3,"file":"api-client.d.ts","sourceRoot":"","sources":["../../../src/services/openalex/api-client.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAOH,OAAO,EAGL,KAAK,YAAY,EAElB,MAAM,YAAY,CAAC;AAIpB,MAAM,WAAW,uBAAuB;IACtC,sEAAsE;IACtE,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,SAAS,EAAE,MAAM,CAAC;CACnB;AAED;;;;;;;;GAQG;AACH,qBAAa,iBAAiB;IAChB,OAAO,CAAC,QAAQ,CAAC,MAAM;IAAnC,YAA6B,MAAM,EAAE,uBAAuB,EAAI;IAEhE;;;;;;;;;OASG;IACG,aAAa,CAAC,IAAI,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,YAAY,GAAG,IAAI,CAAC,CA0CpF;IAED;;;;;;;;;OASG;IACH,mBAAmB,CAAC,KAAK,EAAE,MAAM,EAAE,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,YAAY,EAAE,CAAC,CAiBlF;IAED;;;;;;;OAOG;IACG,UAAU,CACd,IAAI,EAAE,MAAM,EACZ,OAAO,EAAE,MAAM,EACf,IAAI,EAAE,MAAM,EACZ,MAAM,CAAC,EAAE,WAAW,GACnB,OAAO,CAAC;QAAE,KAAK,EAAE,YAAY,EAAE,CAAC;QAAC,UAAU,EAAE,MAAM,CAAA;KAAE,CAAC,CAiExD;IAED,gEAAgE;YAClD,cAAc;CAqC7B"}
|
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@@ -6,6 +6,7 @@
|
|
|
6
6
|
*/
|
|
7
7
|
import { JsonRpcErrorCode, McpError, serviceUnavailable } from '@cyanheads/mcp-ts-core/errors';
|
|
8
8
|
import { fetchWithTimeout, logger, requestContextService } from '@cyanheads/mcp-ts-core/utils';
|
|
9
|
+
import { readBody } from '../fetch-redaction.js';
|
|
9
10
|
import { OPENALEX_API_BASE, OPENALEX_MAX_PAGE_SIZE, } from './types.js';
|
|
10
11
|
const USER_AGENT = 'pubmed-mcp-server (+https://github.com/cyanheads/pubmed-mcp-server)';
|
|
11
12
|
/**
|
|
@@ -60,7 +61,7 @@ export class OpenAlexApiClient {
|
|
|
60
61
|
const msg = error instanceof Error ? error.message : String(error);
|
|
61
62
|
throw serviceUnavailable(`OpenAlex request failed: ${msg}`, { reason: 'openalex_unreachable' }, { cause: error });
|
|
62
63
|
}
|
|
63
|
-
const text = await response.text();
|
|
64
|
+
const text = await readBody(response.text());
|
|
64
65
|
try {
|
|
65
66
|
return JSON.parse(text);
|
|
66
67
|
}
|
|
@@ -132,7 +133,7 @@ export class OpenAlexApiClient {
|
|
|
132
133
|
const msg = error instanceof Error ? error.message : String(error);
|
|
133
134
|
throw serviceUnavailable(`OpenAlex request failed: ${msg}`, { reason: 'openalex_unreachable' }, { cause: error });
|
|
134
135
|
}
|
|
135
|
-
const text = await response.text();
|
|
136
|
+
const text = await readBody(response.text());
|
|
136
137
|
let parsed;
|
|
137
138
|
try {
|
|
138
139
|
parsed = JSON.parse(text);
|
|
@@ -170,7 +171,7 @@ export class OpenAlexApiClient {
|
|
|
170
171
|
const msg = error instanceof Error ? error.message : String(error);
|
|
171
172
|
throw serviceUnavailable(`OpenAlex request failed: ${msg}`, { reason: 'openalex_unreachable' }, { cause: error });
|
|
172
173
|
}
|
|
173
|
-
const text = await response.text();
|
|
174
|
+
const text = await readBody(response.text());
|
|
174
175
|
let parsed;
|
|
175
176
|
try {
|
|
176
177
|
parsed = JSON.parse(text);
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"api-client.js","sourceRoot":"","sources":["../../../src/services/openalex/api-client.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAAE,gBAAgB,EAAE,QAAQ,EAAE,kBAAkB,EAAE,MAAM,+BAA+B,CAAC;AAC/F,OAAO,EAAE,gBAAgB,EAAE,MAAM,EAAE,qBAAqB,EAAE,MAAM,8BAA8B,CAAC;AAE/F,OAAO,EACL,iBAAiB,EACjB,sBAAsB,GAGvB,MAAM,YAAY,CAAC;AAEpB,MAAM,UAAU,GAAG,qEAAqE,CAAC;AAQzF;;;;;;;;GAQG;AACH,MAAM,OAAO,iBAAiB;IACC,MAAM;IAAnC,YAA6B,MAA+B;sBAA/B,MAAM;IAA4B,CAAC;IAEhE;;;;;;;;;OASG;IACH,KAAK,CAAC,aAAa,CAAC,IAAY,EAAE,MAAoB;QACpD,MAAM,MAAM,GAAG,IAAI,eAAe,CAAC;YACjC,MAAM,EAAE,mCAAmC;SAC5C,CAAC,CAAC;QACH,IAAI,IAAI,CAAC,MAAM,CAAC,KAAK;YAAE,MAAM,CAAC,GAAG,CAAC,QAAQ,EAAE,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC;QAE/D,MAAM,GAAG,GAAG,GAAG,iBAAiB,eAAe,kBAAkB,CAAC,IAAI,CAAC,IAAI,MAAM,CAAC,QAAQ,EAAE,EAAE,CAAC;QAC/F,MAAM,GAAG,GAAG,qBAAqB,CAAC,oBAAoB,CAAC;YACrD,SAAS,EAAE,uBAAuB;YAClC,iBAAiB,EAAE,EAAE,IAAI,EAAE;SAC5B,CAAC,CAAC;QAEH,IAAI,QAAkB,CAAC;QACvB,IAAI,CAAC;YACH,QAAQ,GAAG,MAAM,gBAAgB,CAAC,GAAG,EAAE,IAAI,CAAC,MAAM,CAAC,SAAS,EAAE,GAAG,EAAE;gBACjE,OAAO,EAAE,EAAE,MAAM,EAAE,kBAAkB,EAAE,YAAY,EAAE,UAAU,EAAE;gBACjE,gBAAgB,EAAE,CAAC,GAAG,CAAC;gBACvB,GAAG,CAAC,MAAM,IAAI,EAAE,MAAM,EAAE,CAAC;aAC1B,CAAC,CAAC;QACL,CAAC;QAAC,OAAO,KAAc,EAAE,CAAC;YACxB,IAAI,KAAK,YAAY,QAAQ,EAAE,CAAC;gBAC9B,IAAI,KAAK,CAAC,IAAI,KAAK,gBAAgB,CAAC,QAAQ;oBAAE,OAAO,IAAI,CAAC;gBAC1D,MAAM,KAAK,CAAC;YACd,CAAC;YACD,MAAM,GAAG,GAAG,KAAK,YAAY,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC;YACnE,MAAM,kBAAkB,CACtB,4BAA4B,GAAG,EAAE,EACjC,EAAE,MAAM,EAAE,sBAAsB,EAAE,EAClC,EAAE,KAAK,EAAE,KAAK,EAAE,CACjB,CAAC;QACJ,CAAC;QAED,MAAM,IAAI,GAAG,MAAM,QAAQ,CAAC,IAAI,EAAE,CAAC;
|
|
1
|
+
{"version":3,"file":"api-client.js","sourceRoot":"","sources":["../../../src/services/openalex/api-client.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAAE,gBAAgB,EAAE,QAAQ,EAAE,kBAAkB,EAAE,MAAM,+BAA+B,CAAC;AAC/F,OAAO,EAAE,gBAAgB,EAAE,MAAM,EAAE,qBAAqB,EAAE,MAAM,8BAA8B,CAAC;AAE/F,OAAO,EAAE,QAAQ,EAAE,MAAM,+BAA+B,CAAC;AAEzD,OAAO,EACL,iBAAiB,EACjB,sBAAsB,GAGvB,MAAM,YAAY,CAAC;AAEpB,MAAM,UAAU,GAAG,qEAAqE,CAAC;AAQzF;;;;;;;;GAQG;AACH,MAAM,OAAO,iBAAiB;IACC,MAAM;IAAnC,YAA6B,MAA+B;sBAA/B,MAAM;IAA4B,CAAC;IAEhE;;;;;;;;;OASG;IACH,KAAK,CAAC,aAAa,CAAC,IAAY,EAAE,MAAoB;QACpD,MAAM,MAAM,GAAG,IAAI,eAAe,CAAC;YACjC,MAAM,EAAE,mCAAmC;SAC5C,CAAC,CAAC;QACH,IAAI,IAAI,CAAC,MAAM,CAAC,KAAK;YAAE,MAAM,CAAC,GAAG,CAAC,QAAQ,EAAE,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC;QAE/D,MAAM,GAAG,GAAG,GAAG,iBAAiB,eAAe,kBAAkB,CAAC,IAAI,CAAC,IAAI,MAAM,CAAC,QAAQ,EAAE,EAAE,CAAC;QAC/F,MAAM,GAAG,GAAG,qBAAqB,CAAC,oBAAoB,CAAC;YACrD,SAAS,EAAE,uBAAuB;YAClC,iBAAiB,EAAE,EAAE,IAAI,EAAE;SAC5B,CAAC,CAAC;QAEH,IAAI,QAAkB,CAAC;QACvB,IAAI,CAAC;YACH,QAAQ,GAAG,MAAM,gBAAgB,CAAC,GAAG,EAAE,IAAI,CAAC,MAAM,CAAC,SAAS,EAAE,GAAG,EAAE;gBACjE,OAAO,EAAE,EAAE,MAAM,EAAE,kBAAkB,EAAE,YAAY,EAAE,UAAU,EAAE;gBACjE,gBAAgB,EAAE,CAAC,GAAG,CAAC;gBACvB,GAAG,CAAC,MAAM,IAAI,EAAE,MAAM,EAAE,CAAC;aAC1B,CAAC,CAAC;QACL,CAAC;QAAC,OAAO,KAAc,EAAE,CAAC;YACxB,IAAI,KAAK,YAAY,QAAQ,EAAE,CAAC;gBAC9B,IAAI,KAAK,CAAC,IAAI,KAAK,gBAAgB,CAAC,QAAQ;oBAAE,OAAO,IAAI,CAAC;gBAC1D,MAAM,KAAK,CAAC;YACd,CAAC;YACD,MAAM,GAAG,GAAG,KAAK,YAAY,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC;YACnE,MAAM,kBAAkB,CACtB,4BAA4B,GAAG,EAAE,EACjC,EAAE,MAAM,EAAE,sBAAsB,EAAE,EAClC,EAAE,KAAK,EAAE,KAAK,EAAE,CACjB,CAAC;QACJ,CAAC;QAED,MAAM,IAAI,GAAG,MAAM,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,CAAC,CAAC;QAC7C,IAAI,CAAC;YACH,OAAO,IAAI,CAAC,KAAK,CAAC,IAAI,CAAiB,CAAC;QAC1C,CAAC;QAAC,OAAO,KAAc,EAAE,CAAC;YACxB,MAAM,kBAAkB,CACtB,oCAAoC,EACpC,EAAE,MAAM,EAAE,2BAA2B,EAAE,EACvC,EAAE,KAAK,EAAE,KAAK,EAAE,CACjB,CAAC;QACJ,CAAC;IACH,CAAC;IAED;;;;;;;;;OASG;IACH,mBAAmB,CAAC,KAAe,EAAE,MAAoB;QACvD,IAAI,KAAK,CAAC,MAAM,KAAK,CAAC;YAAE,OAAO,OAAO,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC;QAEnD,0EAA0E;QAC1E,MAAM,OAAO,GAAG,KAAK,CAAC,GAAG,CAAC,CAAC,EAAE,EAAE,EAAE,CAC/B,EAAE,CAAC,UAAU,CAAC,uBAAuB,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,KAAK,CAAC,uBAAuB,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,EAAE,CACvF,CAAC;QAEF,MAAM,MAAM,GAAG,IAAI,eAAe,CAAC;YACjC,MAAM,EAAE,YAAY,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE;YACvC,MAAM,EAAE,QAAQ;YAChB,QAAQ,EAAE,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,MAAM,EAAE,sBAAsB,CAAC,CAAC;SACjE,CAAC,CAAC;QACH,IAAI,IAAI,CAAC,MAAM,CAAC,KAAK;YAAE,MAAM,CAAC,GAAG,CAAC,QAAQ,EAAE,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC;QAE/D,MAAM,GAAG,GAAG,GAAG,iBAAiB,UAAU,MAAM,CAAC,QAAQ,EAAE,EAAE,CAAC;QAC9D,OAAO,IAAI,CAAC,cAAc,CAAC,GAAG,EAAE,sBAAsB,EAAE,MAAM,CAAC,CAAC;IAClE,CAAC;IAED;;;;;;;OAOG;IACH,KAAK,CAAC,UAAU,CACd,IAAY,EACZ,OAAe,EACf,IAAY,EACZ,MAAoB;QAEpB,kCAAkC;QAClC,MAAM,MAAM,GAAG,IAAI,CAAC,UAAU,CAAC,uBAAuB,CAAC;YACrD,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,uBAAuB,CAAC,MAAM,CAAC;YAC5C,CAAC,CAAC,IAAI,CAAC;QAET,MAAM,MAAM,GAAG,IAAI,eAAe,CAAC;YACjC,MAAM,EAAE,SAAS,MAAM,EAAE;YACzB,MAAM,EAAE,QAAQ;YAChB,QAAQ,EAAE,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,OAAO,EAAE,sBAAsB,CAAC,CAAC;YAC3D,IAAI,EAAE,MAAM,CAAC,IAAI,CAAC;SACnB,CAAC,CAAC;QACH,IAAI,IAAI,CAAC,MAAM,CAAC,KAAK;YAAE,MAAM,CAAC,GAAG,CAAC,QAAQ,EAAE,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC;QAE/D,MAAM,GAAG,GAAG,GAAG,iBAAiB,UAAU,MAAM,CAAC,QAAQ,EAAE,EAAE,CAAC;QAC9D,MAAM,GAAG,GAAG,qBAAqB,CAAC,oBAAoB,CAAC;YACrD,SAAS,EAAE,oBAAoB;YAC/B,iBAAiB,EAAE,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE;SAC1C,CAAC,CAAC;QAEH,IAAI,QAAkB,CAAC;QACvB,IAAI,CAAC;YACH,QAAQ,GAAG,MAAM,gBAAgB,CAAC,GAAG,EAAE,IAAI,CAAC,MAAM,CAAC,SAAS,EAAE,GAAG,EAAE;gBACjE,OAAO,EAAE,EAAE,MAAM,EAAE,kBAAkB,EAAE,YAAY,EAAE,UAAU,EAAE;gBACjE,GAAG,CAAC,MAAM,IAAI,EAAE,MAAM,EAAE,CAAC;aAC1B,CAAC,CAAC;QACL,CAAC;QAAC,OAAO,KAAc,EAAE,CAAC;YACxB,IAAI,KAAK,YAAY,QAAQ;gBAAE,MAAM,KAAK,CAAC;YAC3C,MAAM,GAAG,GAAG,KAAK,YAAY,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC;YACnE,MAAM,kBAAkB,CACtB,4BAA4B,GAAG,EAAE,EACjC,EAAE,MAAM,EAAE,sBAAsB,EAAE,EAClC,EAAE,KAAK,EAAE,KAAK,EAAE,CACjB,CAAC;QACJ,CAAC;QAED,MAAM,IAAI,GAAG,MAAM,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,CAAC,CAAC;QAC7C,IAAI,MAA6B,CAAC;QAClC,IAAI,CAAC;YACH,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAA0B,CAAC;QACrD,CAAC;QAAC,OAAO,KAAc,EAAE,CAAC;YACxB,MAAM,kBAAkB,CACtB,oCAAoC,EACpC,EAAE,MAAM,EAAE,2BAA2B,EAAE,EACvC,EAAE,KAAK,EAAE,KAAK,EAAE,CACjB,CAAC;QACJ,CAAC;QAED,MAAM,CAAC,KAAK,CACV,4BAA4B,EAC5B,qBAAqB,CAAC,oBAAoB,CAAC;YACzC,SAAS,EAAE,wBAAwB;YACnC,iBAAiB,EAAE;gBACjB,IAAI,EAAE,MAAM;gBACZ,IAAI;gBACJ,UAAU,EAAE,MAAM,CAAC,IAAI,EAAE,KAAK;gBAC9B,WAAW,EAAE,MAAM,CAAC,OAAO,EAAE,MAAM;aACpC;SACF,CAAC,CACH,CAAC;QAEF,OAAO;YACL,KAAK,EAAE,MAAM,CAAC,OAAO,IAAI,EAAE;YAC3B,UAAU,EAAE,MAAM,CAAC,IAAI,EAAE,KAAK,IAAI,CAAC;SACpC,CAAC;IACJ,CAAC;IAED,gEAAgE;IACxD,KAAK,CAAC,cAAc,CAC1B,GAAW,EACX,SAAiB,EACjB,MAAoB;QAEpB,MAAM,GAAG,GAAG,qBAAqB,CAAC,oBAAoB,CAAC,EAAE,SAAS,EAAE,CAAC,CAAC;QAEtE,IAAI,QAAkB,CAAC;QACvB,IAAI,CAAC;YACH,QAAQ,GAAG,MAAM,gBAAgB,CAAC,GAAG,EAAE,IAAI,CAAC,MAAM,CAAC,SAAS,EAAE,GAAG,EAAE;gBACjE,OAAO,EAAE,EAAE,MAAM,EAAE,kBAAkB,EAAE,YAAY,EAAE,UAAU,EAAE;gBACjE,GAAG,CAAC,MAAM,IAAI,EAAE,MAAM,EAAE,CAAC;aAC1B,CAAC,CAAC;QACL,CAAC;QAAC,OAAO,KAAc,EAAE,CAAC;YACxB,IAAI,KAAK,YAAY,QAAQ;gBAAE,MAAM,KAAK,CAAC;YAC3C,MAAM,GAAG,GAAG,KAAK,YAAY,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC;YACnE,MAAM,kBAAkB,CACtB,4BAA4B,GAAG,EAAE,EACjC,EAAE,MAAM,EAAE,sBAAsB,EAAE,EAClC,EAAE,KAAK,EAAE,KAAK,EAAE,CACjB,CAAC;QACJ,CAAC;QAED,MAAM,IAAI,GAAG,MAAM,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,CAAC,CAAC;QAC7C,IAAI,MAA6B,CAAC;QAClC,IAAI,CAAC;YACH,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAA0B,CAAC;QACrD,CAAC;QAAC,OAAO,KAAc,EAAE,CAAC;YACxB,MAAM,kBAAkB,CACtB,oCAAoC,EACpC,EAAE,MAAM,EAAE,2BAA2B,EAAE,EACvC,EAAE,KAAK,EAAE,KAAK,EAAE,CACjB,CAAC;QACJ,CAAC;QAED,OAAO,MAAM,CAAC,OAAO,IAAI,EAAE,CAAC;IAC9B,CAAC;CACF"}
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@@ -46,6 +46,9 @@ export declare class UnpaywallService {
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46
46
|
* `application/octet-stream`, and an HTML interstitial is sometimes served as
|
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47
47
|
* `application/pdf`. Bytes opening with `%PDF-` are a PDF whatever the header
|
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48
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|
* says; everything else is treated as text. (#104)
|
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+
*
|
|
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|
+
* Records and error data name the URL's host, never the URL: a publisher's
|
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+
* PDF link can carry an access token in its path or query.
|
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|
*/
|
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|
private fetchAs;
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|
}
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@@ -1 +1 @@
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|
|
1
|
-
{"version":3,"file":"unpaywall-service.d.ts","sourceRoot":"","sources":["../../../src/services/unpaywall/unpaywall-service.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;
|
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1
|
+
{"version":3,"file":"unpaywall-service.d.ts","sourceRoot":"","sources":["../../../src/services/unpaywall/unpaywall-service.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAYH,OAAO,EAEL,KAAK,gBAAgB,EACrB,KAAK,iBAAiB,EACtB,KAAK,mBAAmB,EAEzB,MAAM,YAAY,CAAC;AAIpB;;;GAGG;AACH,qBAAa,gBAAgB;IAEzB,OAAO,CAAC,QAAQ,CAAC,KAAK;IACtB,OAAO,CAAC,QAAQ,CAAC,SAAS;IAF5B,YACmB,KAAK,EAAE,MAAM,EACb,SAAS,EAAE,MAAM,EAChC;IAEJ;;;;OAIG;IACG,OAAO,CAAC,GAAG,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,mBAAmB,CAAC,CAqE7E;IAED;;;;;;;;;;;;OAYG;IACG,YAAY,CAAC,QAAQ,EAAE,iBAAiB,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,gBAAgB,CAAC,CA6C/F;IAED;;;;;;;;;;;;OAYG;YACW,OAAO;CAgDtB;AAqCD;;;;GAIG;AACH,wBAAgB,oBAAoB,IAAI,IAAI,CAc3C;AAED,qFAAqF;AACrF,wBAAgB,mBAAmB,IAAI,gBAAgB,GAAG,SAAS,CAElE"}
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@@ -11,6 +11,7 @@
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11
11
|
import { JsonRpcErrorCode, McpError, serviceUnavailable } from '@cyanheads/mcp-ts-core/errors';
|
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12
12
|
import { fetchWithTimeout, httpErrorFromResponse, logger, requestContextService, } from '@cyanheads/mcp-ts-core/utils';
|
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13
13
|
import { getServerConfig } from '../../config/server-config.js';
|
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14
|
+
import { readBody } from '../fetch-redaction.js';
|
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14
15
|
import { UNPAYWALL_API_BASE, } from './types.js';
|
|
15
16
|
const USER_AGENT = 'pubmed-mcp-server (+https://github.com/cyanheads/pubmed-mcp-server)';
|
|
16
17
|
/**
|
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@@ -66,7 +67,7 @@ export class UnpaywallService {
|
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|
66
67
|
doi: normalized,
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|
67
68
|
}, { cause: error });
|
|
68
69
|
}
|
|
69
|
-
const data = (await response.json());
|
|
70
|
+
const data = (await readBody(response.json()));
|
|
70
71
|
if (!data.is_oa)
|
|
71
72
|
return { kind: 'no-oa', reason: 'No open-access copy indexed' };
|
|
72
73
|
const location = data.best_oa_location ?? data.oa_locations?.[0];
|
|
@@ -78,7 +79,8 @@ export class UnpaywallService {
|
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|
78
79
|
doi: normalized,
|
|
79
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|
hostType: location.host_type ?? null,
|
|
80
81
|
license: location.license ?? null,
|
|
81
|
-
|
|
82
|
+
// The logger writes a caller's `version` key as `data_version`.
|
|
83
|
+
oaVersion: location.version ?? null,
|
|
82
84
|
},
|
|
83
85
|
}));
|
|
84
86
|
return {
|
|
@@ -115,14 +117,14 @@ export class UnpaywallService {
|
|
|
115
117
|
servedHtml = content;
|
|
116
118
|
logger.debug('Unpaywall PDF URL served non-PDF bytes; falling back to HTML URL', requestContextService.createRequestContext({
|
|
117
119
|
operation: 'UnpaywallPdfNotPdf',
|
|
118
|
-
additionalContext: {
|
|
120
|
+
additionalContext: { host: hostOf(pdfUrl), fetchedHost: hostOf(content.fetchedUrl) },
|
|
119
121
|
}));
|
|
120
122
|
}
|
|
121
123
|
catch (pdfErr) {
|
|
122
124
|
logger.debug('Unpaywall PDF fetch failed; falling back to HTML URL', requestContextService.createRequestContext({
|
|
123
125
|
operation: 'UnpaywallPdfFallback',
|
|
124
126
|
additionalContext: {
|
|
125
|
-
|
|
127
|
+
host: hostOf(pdfUrl),
|
|
126
128
|
error: pdfErr instanceof Error ? pdfErr.message : String(pdfErr),
|
|
127
129
|
},
|
|
128
130
|
}));
|
|
@@ -151,11 +153,15 @@ export class UnpaywallService {
|
|
|
151
153
|
* `application/octet-stream`, and an HTML interstitial is sometimes served as
|
|
152
154
|
* `application/pdf`. Bytes opening with `%PDF-` are a PDF whatever the header
|
|
153
155
|
* says; everything else is treated as text. (#104)
|
|
156
|
+
*
|
|
157
|
+
* Records and error data name the URL's host, never the URL: a publisher's
|
|
158
|
+
* PDF link can carry an access token in its path or query.
|
|
154
159
|
*/
|
|
155
160
|
async fetchAs(url, expected, signal) {
|
|
161
|
+
const host = hostOf(url);
|
|
156
162
|
const ctx = requestContextService.createRequestContext({
|
|
157
163
|
operation: 'UnpaywallFetch',
|
|
158
|
-
additionalContext: {
|
|
164
|
+
additionalContext: { expected, host },
|
|
159
165
|
});
|
|
160
166
|
const accept = expected === 'pdf'
|
|
161
167
|
? 'application/pdf,*/*;q=0.5'
|
|
@@ -170,23 +176,27 @@ export class UnpaywallService {
|
|
|
170
176
|
}
|
|
171
177
|
catch (error) {
|
|
172
178
|
const msg = error instanceof Error ? error.message : String(error);
|
|
173
|
-
throw serviceUnavailable(`Unpaywall content fetch failed: ${msg}`, { reason: 'unpaywall_unreachable',
|
|
179
|
+
throw serviceUnavailable(`Unpaywall content fetch failed: ${msg}`, { reason: 'unpaywall_unreachable', host }, { cause: error });
|
|
174
180
|
}
|
|
175
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|
if (!response.ok) {
|
|
176
182
|
throw await httpErrorFromResponse(response, {
|
|
177
183
|
service: 'Unpaywall content fetch',
|
|
178
|
-
data: {
|
|
184
|
+
data: { host },
|
|
179
185
|
});
|
|
180
186
|
}
|
|
181
187
|
const fetchedUrl = response.url || url;
|
|
182
188
|
// Read the body once — a Response body can only be consumed once, and the
|
|
183
189
|
// bytes are what the classification reads.
|
|
184
|
-
const bytes = new Uint8Array(await response.arrayBuffer());
|
|
190
|
+
const bytes = new Uint8Array(await readBody(response.arrayBuffer()));
|
|
185
191
|
if (hasPdfMagic(bytes))
|
|
186
192
|
return { kind: 'pdf', fetchedUrl, body: bytes };
|
|
187
193
|
return { kind: 'html', fetchedUrl, body: new TextDecoder().decode(bytes) };
|
|
188
194
|
}
|
|
189
195
|
}
|
|
196
|
+
/** The host a URL names, for log and error labels — `undefined` when it does not parse. */
|
|
197
|
+
function hostOf(url) {
|
|
198
|
+
return URL.parse(url)?.host;
|
|
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|
+
}
|
|
190
200
|
/** True for a string carrying more than whitespace — Unpaywall sends `null` for a field it has no value for. */
|
|
191
201
|
function nonBlank(value) {
|
|
192
202
|
return typeof value === 'string' && value.trim().length > 0;
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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|
|
1
|
+
{"version":3,"file":"unpaywall-service.js","sourceRoot":"","sources":["../../../src/services/unpaywall/unpaywall-service.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAEH,OAAO,EAAE,gBAAgB,EAAE,QAAQ,EAAE,kBAAkB,EAAE,MAAM,+BAA+B,CAAC;AAC/F,OAAO,EACL,gBAAgB,EAChB,qBAAqB,EACrB,MAAM,EACN,qBAAqB,GACtB,MAAM,8BAA8B,CAAC;AAEtC,OAAO,EAAE,eAAe,EAAE,MAAM,2BAA2B,CAAC;AAC5D,OAAO,EAAE,QAAQ,EAAE,MAAM,+BAA+B,CAAC;AACzD,OAAO,EACL,kBAAkB,GAKnB,MAAM,YAAY,CAAC;AAEpB,MAAM,UAAU,GAAG,qEAAqE,CAAC;AAEzF;;;GAGG;AACH,MAAM,OAAO,gBAAgB;IAER,KAAK;IACL,SAAS;IAF5B,YACmB,KAAa,EACb,SAAiB;qBADjB,KAAK;yBACL,SAAS;IACzB,CAAC;IAEJ;;;;OAIG;IACH,KAAK,CAAC,OAAO,CAAC,GAAW,EAAE,MAAoB;QAC7C,MAAM,UAAU,GAAG,YAAY,CAAC,GAAG,CAAC,CAAC;QACrC,IAAI,CAAC,UAAU;YAAE,OAAO,EAAE,IAAI,EAAE,OAAO,EAAE,MAAM,EAAE,aAAa,EAAE,CAAC;QAEjE,MAAM,GAAG,GAAG,GAAG,kBAAkB,IAAI,kBAAkB,CAAC,UAAU,CAAC,UAAU,kBAAkB,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC;QAC9G,MAAM,GAAG,GAAG,qBAAqB,CAAC,oBAAoB,CAAC;YACrD,SAAS,EAAE,kBAAkB;YAC7B,iBAAiB,EAAE,EAAE,GAAG,EAAE;SAC3B,CAAC,CAAC;QAEH,qEAAqE;QACrE,wEAAwE;QACxE,4EAA4E;QAC5E,0EAA0E;QAC1E,uDAAuD;QACvD,IAAI,QAAkB,CAAC;QACvB,IAAI,CAAC;YACH,QAAQ,GAAG,MAAM,gBAAgB,CAAC,GAAG,EAAE,IAAI,CAAC,SAAS,EAAE,GAAG,EAAE;gBAC1D,OAAO,EAAE,EAAE,MAAM,EAAE,kBAAkB,EAAE,YAAY,EAAE,UAAU,EAAE;gBACjE,gBAAgB,EAAE,CAAC,GAAG,EAAE,GAAG,CAAC;gBAC5B,GAAG,CAAC,MAAM,IAAI,EAAE,MAAM,EAAE,CAAC;aAC1B,CAAC,CAAC;QACL,CAAC;QAAC,OAAO,KAAc,EAAE,CAAC;YACxB,IAAI,KAAK,YAAY,QAAQ,EAAE,CAAC;gBAC9B,IAAI,KAAK,CAAC,IAAI,KAAK,gBAAgB,CAAC,QAAQ,EAAE,CAAC;oBAC7C,OAAO,EAAE,IAAI,EAAE,OAAO,EAAE,MAAM,EAAE,0BAA0B,EAAE,CAAC;gBAC/D,CAAC;gBACD,IAAI,KAAK,CAAC,IAAI,KAAK,gBAAgB,CAAC,eAAe,EAAE,CAAC;oBACpD,OAAO,EAAE,IAAI,EAAE,OAAO,EAAE,MAAM,EAAE,oBAAoB,EAAE,CAAC;gBACzD,CAAC;YACH,CAAC;YACD,MAAM,GAAG,GAAG,KAAK,YAAY,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC;YACnE,MAAM,kBAAkB,CACtB,6BAA6B,GAAG,EAAE,EAClC;gBACE,MAAM,EAAE,uBAAuB;gBAC/B,GAAG,EAAE,UAAU;aAChB,EACD,EAAE,KAAK,EAAE,KAAK,EAAE,CACjB,CAAC;QACJ,CAAC;QAED,MAAM,IAAI,GAAG,CAAC,MAAM,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,CAAC,CAAsB,CAAC;QACpE,IAAI,CAAC,IAAI,CAAC,KAAK;YAAE,OAAO,EAAE,IAAI,EAAE,OAAO,EAAE,MAAM,EAAE,6BAA6B,EAAE,CAAC;QAEjF,MAAM,QAAQ,GAAG,IAAI,CAAC,gBAAgB,IAAI,IAAI,CAAC,YAAY,EAAE,CAAC,CAAC,CAAC,CAAC;QACjE,IAAI,CAAC,QAAQ,EAAE,GAAG;YAAE,OAAO,EAAE,IAAI,EAAE,OAAO,EAAE,MAAM,EAAE,uCAAuC,EAAE,CAAC;QAE9F,MAAM,CAAC,KAAK,CACV,wBAAwB,EACxB,qBAAqB,CAAC,oBAAoB,CAAC;YACzC,SAAS,EAAE,mBAAmB;YAC9B,iBAAiB,EAAE;gBACjB,GAAG,EAAE,UAAU;gBACf,QAAQ,EAAE,QAAQ,CAAC,SAAS,IAAI,IAAI;gBACpC,OAAO,EAAE,QAAQ,CAAC,OAAO,IAAI,IAAI;gBACjC,gEAAgE;gBAChE,SAAS,EAAE,QAAQ,CAAC,OAAO,IAAI,IAAI;aACpC;SACF,CAAC,CACH,CAAC;QAEF,OAAO;YACL,IAAI,EAAE,OAAO;YACb,QAAQ;YACR,GAAG,CAAC,QAAQ,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,EAAE,KAAK,EAAE,IAAI,CAAC,KAAK,EAAE,CAAC;YAClD,GAAG,CAAC,QAAQ,CAAC,IAAI,CAAC,YAAY,CAAC,IAAI,EAAE,WAAW,EAAE,IAAI,CAAC,YAAY,EAAE,CAAC;YACtE,GAAG,CAAC,OAAO,IAAI,CAAC,IAAI,KAAK,QAAQ,IAAI,MAAM,CAAC,SAAS,CAAC,IAAI,CAAC,IAAI,CAAC,IAAI,EAAE,IAAI,EAAE,IAAI,CAAC,IAAI,EAAE,CAAC;SACzF,CAAC;IACJ,CAAC;IAED;;;;;;;;;;;;OAYG;IACH,KAAK,CAAC,YAAY,CAAC,QAA2B,EAAE,MAAoB;QAClE,MAAM,MAAM,GAAG,QAAQ,CAAC,WAAW,IAAI,SAAS,CAAC;QACjD,MAAM,OAAO,GAAG,QAAQ,CAAC,GAAG,CAAC;QAE7B,IAAI,MAAM,EAAE,CAAC;YACX,mFAAmF;YACnF,IAAI,UAAwC,CAAC;YAC7C,IAAI,CAAC;gBACH,MAAM,OAAO,GAAG,MAAM,IAAI,CAAC,OAAO,CAAC,MAAM,EAAE,KAAK,EAAE,MAAM,CAAC,CAAC;gBAC1D,IAAI,OAAO,CAAC,IAAI,KAAK,KAAK;oBAAE,OAAO,OAAO,CAAC;gBAC3C,UAAU,GAAG,OAAO,CAAC;gBACrB,MAAM,CAAC,KAAK,CACV,kEAAkE,EAClE,qBAAqB,CAAC,oBAAoB,CAAC;oBACzC,SAAS,EAAE,oBAAoB;oBAC/B,iBAAiB,EAAE,EAAE,IAAI,EAAE,MAAM,CAAC,MAAM,CAAC,EAAE,WAAW,EAAE,MAAM,CAAC,OAAO,CAAC,UAAU,CAAC,EAAE;iBACrF,CAAC,CACH,CAAC;YACJ,CAAC;YAAC,OAAO,MAAe,EAAE,CAAC;gBACzB,MAAM,CAAC,KAAK,CACV,sDAAsD,EACtD,qBAAqB,CAAC,oBAAoB,CAAC;oBACzC,SAAS,EAAE,sBAAsB;oBACjC,iBAAiB,EAAE;wBACjB,IAAI,EAAE,MAAM,CAAC,MAAM,CAAC;wBACpB,KAAK,EAAE,MAAM,YAAY,KAAK,CAAC,CAAC,CAAC,MAAM,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,MAAM,CAAC;qBACjE;iBACF,CAAC,CACH,CAAC;YACJ,CAAC;YAED,gEAAgE;YAChE,IAAI,UAAU,IAAI,CAAC,MAAM,KAAK,OAAO,IAAI,UAAU,CAAC,UAAU,KAAK,OAAO,CAAC,EAAE,CAAC;gBAC5E,OAAO,UAAU,CAAC;YACpB,CAAC;YAED,IAAI,CAAC;gBACH,OAAO,MAAM,IAAI,CAAC,OAAO,CAAC,OAAO,EAAE,MAAM,EAAE,MAAM,CAAC,CAAC;YACrD,CAAC;YAAC,OAAO,OAAgB,EAAE,CAAC;gBAC1B,IAAI,UAAU;oBAAE,OAAO,UAAU,CAAC;gBAClC,MAAM,OAAO,CAAC;YAChB,CAAC;QACH,CAAC;QAED,OAAO,IAAI,CAAC,OAAO,CAAC,OAAO,EAAE,MAAM,EAAE,MAAM,CAAC,CAAC;IAC/C,CAAC;IAED;;;;;;;;;;;;OAYG;IACK,KAAK,CAAC,OAAO,CACnB,GAAW,EACX,QAAwB,EACxB,MAAoB;QAEpB,MAAM,IAAI,GAAG,MAAM,CAAC,GAAG,CAAC,CAAC;QACzB,MAAM,GAAG,GAAG,qBAAqB,CAAC,oBAAoB,CAAC;YACrD,SAAS,EAAE,gBAAgB;YAC3B,iBAAiB,EAAE,EAAE,QAAQ,EAAE,IAAI,EAAE;SACtC,CAAC,CAAC;QAEH,MAAM,MAAM,GACV,QAAQ,KAAK,KAAK;YAChB,CAAC,CAAC,2BAA2B;YAC7B,CAAC,CAAC,2CAA2C,CAAC;QAElD,IAAI,QAAkB,CAAC;QACvB,IAAI,CAAC;YACH,QAAQ,GAAG,MAAM,gBAAgB,CAAC,GAAG,EAAE,IAAI,CAAC,SAAS,EAAE,GAAG,EAAE;gBAC1D,OAAO,EAAE,EAAE,MAAM,EAAE,MAAM,EAAE,YAAY,EAAE,UAAU,EAAE;gBACrD,QAAQ,EAAE,QAAQ;gBAClB,GAAG,CAAC,MAAM,IAAI,EAAE,MAAM,EAAE,CAAC;aAC1B,CAAC,CAAC;QACL,CAAC;QAAC,OAAO,KAAc,EAAE,CAAC;YACxB,MAAM,GAAG,GAAG,KAAK,YAAY,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC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|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@cyanheads/pubmed-mcp-server",
|
|
3
|
-
"version": "2.10.
|
|
3
|
+
"version": "2.10.21",
|
|
4
4
|
"mcpName": "io.github.cyanheads/pubmed-mcp-server",
|
|
5
5
|
"description": "Search PubMed/Europe PMC, fetch articles and full text (PMC/EPMC/Unpaywall), citations, MeSH terms via MCP. STDIO or Streamable HTTP.",
|
|
6
6
|
"type": "module",
|
|
@@ -95,11 +95,11 @@
|
|
|
95
95
|
"access": "public"
|
|
96
96
|
},
|
|
97
97
|
"dependencies": {
|
|
98
|
-
"@cyanheads/mcp-ts-core": "^0.13.
|
|
98
|
+
"@cyanheads/mcp-ts-core": "^0.13.14",
|
|
99
99
|
"defuddle": "^0.19.4",
|
|
100
100
|
"fast-xml-parser": "^5.11.2",
|
|
101
101
|
"linkedom": "^0.18.13",
|
|
102
|
-
"pino-pretty": "^13.
|
|
102
|
+
"pino-pretty": "^13.2.0",
|
|
103
103
|
"sanitize-html": "^2.18.0",
|
|
104
104
|
"unpdf": "^1.8.1",
|
|
105
105
|
"zod": "^4.6.5"
|
|
@@ -107,12 +107,12 @@
|
|
|
107
107
|
"devDependencies": {
|
|
108
108
|
"@biomejs/biome": "^2.5.15",
|
|
109
109
|
"@socketsecurity/bun-security-scanner": "^1.1.3",
|
|
110
|
-
"@types/node": "^26.6.
|
|
110
|
+
"@types/node": "^26.6.4",
|
|
111
111
|
"@types/sanitize-html": "^2.16.2",
|
|
112
112
|
"@vitest/coverage-istanbul": "^5.0.3",
|
|
113
113
|
"depcheck": "^1.4.7",
|
|
114
114
|
"fast-check": "^4.10.2",
|
|
115
|
-
"ignore": "^7.0.
|
|
115
|
+
"ignore": "^7.0.12",
|
|
116
116
|
"tsc-alias": "^1.9.7",
|
|
117
117
|
"typescript": "^7.0.2",
|
|
118
118
|
"vitest": "^5.0.3"
|
package/server.json
CHANGED
|
@@ -6,7 +6,7 @@
|
|
|
6
6
|
"url": "https://github.com/cyanheads/pubmed-mcp-server",
|
|
7
7
|
"source": "github"
|
|
8
8
|
},
|
|
9
|
-
"version": "2.10.
|
|
9
|
+
"version": "2.10.21",
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|
10
10
|
"remotes": [
|
|
11
11
|
{
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12
12
|
"type": "streamable-http",
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@@ -19,7 +19,7 @@
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19
19
|
"registryBaseUrl": "https://registry.npmjs.org",
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|
20
20
|
"identifier": "@cyanheads/pubmed-mcp-server",
|
|
21
21
|
"runtimeHint": "npx",
|
|
22
|
-
"version": "2.10.
|
|
22
|
+
"version": "2.10.21",
|
|
23
23
|
"environmentVariables": [
|
|
24
24
|
{
|
|
25
25
|
"name": "MCP_LOG_LEVEL",
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|
@@ -56,7 +56,7 @@
|
|
|
56
56
|
"registryBaseUrl": "https://registry.npmjs.org",
|
|
57
57
|
"identifier": "@cyanheads/pubmed-mcp-server",
|
|
58
58
|
"runtimeHint": "npx",
|
|
59
|
-
"version": "2.10.
|
|
59
|
+
"version": "2.10.21",
|
|
60
60
|
"environmentVariables": [
|
|
61
61
|
{
|
|
62
62
|
"name": "MCP_TRANSPORT_TYPE",
|