@cyanheads/pubmed-mcp-server 2.10.19 → 2.10.21
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/AGENTS.md +8 -5
- package/CLAUDE.md +8 -5
- package/Dockerfile +12 -3
- package/README.md +12 -11
- package/changelog/2.10.x/2.10.20.md +63 -0
- package/changelog/2.10.x/2.10.21.md +42 -0
- 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/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 +64 -14
- package/dist/mcp-server/tools/definitions/fetch-articles.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts +44 -9
- package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js +815 -563
- 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 +12 -8
- package/dist/mcp-server/tools/definitions/find-related.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 +11 -7
- package/dist/mcp-server/tools/definitions/lookup-citation.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/lookup-citation.tool.js +72 -34
- package/dist/mcp-server/tools/definitions/lookup-citation.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/lookup-mesh.tool.d.ts +2 -1
- package/dist/mcp-server/tools/definitions/lookup-mesh.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/lookup-mesh.tool.js +11 -3
- 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 +18 -0
- 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 +96 -13
- 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 +4 -3
- 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 +7 -5
- 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 +6 -4
- package/dist/mcp-server/tools/definitions/search-articles.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/search-articles.tool.js +33 -11
- package/dist/mcp-server/tools/definitions/search-articles.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/spell-check.tool.d.ts +2 -1
- package/dist/mcp-server/tools/definitions/spell-check.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/spell-check.tool.js +5 -1
- package/dist/mcp-server/tools/definitions/spell-check.tool.js.map +1 -1
- package/dist/services/error-contracts.d.ts +1 -1
- package/dist/services/error-contracts.d.ts.map +1 -1
- package/dist/services/error-contracts.js +1 -1
- package/dist/services/error-contracts.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 +42 -2
- package/dist/services/ncbi/formatting/citation-formatter.d.ts.map +1 -1
- package/dist/services/ncbi/formatting/citation-formatter.js +370 -91
- package/dist/services/ncbi/formatting/citation-formatter.js.map +1 -1
- package/dist/services/ncbi/ncbi-service.d.ts +16 -1
- package/dist/services/ncbi/ncbi-service.d.ts.map +1 -1
- package/dist/services/ncbi/ncbi-service.js +117 -71
- 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 +116 -61
- 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 +8 -7
- package/dist/services/ncbi/parsing/pmc-article-parser.d.ts.map +1 -1
- package/dist/services/ncbi/parsing/pmc-article-parser.js +633 -185
- package/dist/services/ncbi/parsing/pmc-article-parser.js.map +1 -1
- package/dist/services/ncbi/parsing/pmc-xml-helpers.d.ts +102 -5
- package/dist/services/ncbi/parsing/pmc-xml-helpers.d.ts.map +1 -1
- package/dist/services/ncbi/parsing/pmc-xml-helpers.js +389 -28
- 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 +115 -19
- package/dist/services/ncbi/response-handler.js.map +1 -1
- package/dist/services/ncbi/types.d.ts +44 -4
- 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/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 +13 -9
- package/dist/services/openalex/openalex-service.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 +14 -12
- package/server.json +10 -24
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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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@@ -13,8 +13,10 @@
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13
13
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* serving an unexplained empty window.
|
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*
|
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15
15
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* Transient failures retry with capped exponential backoff. Once retries run
|
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16
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-
* out,
|
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17
|
-
*
|
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16
|
+
* out, the last attempt's `data.reason` is kept (`openalex_invalid_response` for
|
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17
|
+
* a body that is not JSON), and only a `ServiceUnavailable` with no reason is
|
|
18
|
+
* reported as `openalex_unreachable`; a `Timeout` or `RateLimited` keeps its own
|
|
19
|
+
* code and any upstream `retryAfter`.
|
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20
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*
|
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19
21
|
* Uses the NCBI_ADMIN_EMAIL config (adminEmail) as the OpenAlex polite-pool
|
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|
* `mailto=` parameter when set; omits it when unset.
|
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@@ -70,10 +72,12 @@ export declare class OpenAlexService {
|
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private finish;
|
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71
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/**
|
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72
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* Retry wrapper for transient errors. On exhaustion the last error keeps its
|
|
73
|
-
* code and an upstream `retryAfter`, so a 429 still tells the
|
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74
|
-
*
|
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75
|
-
*
|
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76
|
-
*
|
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75
|
+
* code, its `data.reason`, and an upstream `retryAfter`, so a 429 still tells the
|
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76
|
+
* caller how long to wait and an unparseable body stays
|
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77
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+
* `openalex_invalid_response`. Only a `ServiceUnavailable` carrying no reason
|
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78
|
+
* gains `openalex_unreachable` — the one code that reason is declared for; a
|
|
79
|
+
* `Timeout` or `RateLimited` keeps its code with no reason, as the Europe PMC
|
|
80
|
+
* service reports them.
|
|
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|
*/
|
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|
private withRetry;
|
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79
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|
}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"openalex-service.d.ts","sourceRoot":"","sources":["../../../src/services/openalex/openalex-service.ts"],"names":[],"mappings":"AAAA
|
|
1
|
+
{"version":3,"file":"openalex-service.d.ts","sourceRoot":"","sources":["../../../src/services/openalex/openalex-service.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;GAwBG;AAMH,OAAO,EAAE,iBAAiB,EAAE,MAAM,iBAAiB,CAAC;AACpD,OAAO,EAIL,KAAK,qBAAqB,EAE3B,MAAM,YAAY,CAAC;AA4EpB,gFAAgF;AAChF,qBAAa,eAAe;IAExB,OAAO,CAAC,QAAQ,CAAC,MAAM;IACvB,OAAO,CAAC,QAAQ,CAAC,UAAU;IAF7B,YACmB,MAAM,EAAE,iBAAiB,EACzB,UAAU,EAAE,MAAM,EACjC;IAEJ;;;;OAIG;IACG,OAAO,CAAC,IAAI,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,qBAAqB,CAAC,CAW3F;IAED;;;;;;;;OAQG;IACG,OAAO,CAAC,IAAI,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,qBAAqB,CAAC,CA4B3F;IAED;;;OAGG;IACG,UAAU,CAAC,IAAI,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,qBAAqB,CAAC,CAW9F;IAED,8EAA8E;IAC9E,OAAO,CAAC,SAAS;IAQjB;;;;;;;;;OASG;YACW,iBAAiB;IAiC/B;;;;OAIG;IACH,OAAO,CAAC,MAAM;IAcd;;;;;;;;OAQG;YACW,SAAS;CAkDxB;AAMD,yEAAyE;AACzE,wBAAgB,mBAAmB,IAAI,IAAI,CAmB1C;AAED,uEAAuE;AACvE,wBAAgB,kBAAkB,IAAI,eAAe,CAIpD;AAED,kFAAkF;AAClF,wBAAgB,0BAA0B,IAAI,eAAe,GAAG,SAAS,CAExE"}
|
|
@@ -13,8 +13,10 @@
|
|
|
13
13
|
* serving an unexplained empty window.
|
|
14
14
|
*
|
|
15
15
|
* Transient failures retry with capped exponential backoff. Once retries run
|
|
16
|
-
* out,
|
|
17
|
-
*
|
|
16
|
+
* out, the last attempt's `data.reason` is kept (`openalex_invalid_response` for
|
|
17
|
+
* a body that is not JSON), and only a `ServiceUnavailable` with no reason is
|
|
18
|
+
* reported as `openalex_unreachable`; a `Timeout` or `RateLimited` keeps its own
|
|
19
|
+
* code and any upstream `retryAfter`.
|
|
18
20
|
*
|
|
19
21
|
* Uses the NCBI_ADMIN_EMAIL config (adminEmail) as the OpenAlex polite-pool
|
|
20
22
|
* `mailto=` parameter when set; omits it when unset.
|
|
@@ -203,10 +205,12 @@ export class OpenAlexService {
|
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203
205
|
}
|
|
204
206
|
/**
|
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205
207
|
* Retry wrapper for transient errors. On exhaustion the last error keeps its
|
|
206
|
-
* code and an upstream `retryAfter`, so a 429 still tells the
|
|
207
|
-
*
|
|
208
|
-
*
|
|
209
|
-
*
|
|
208
|
+
* code, its `data.reason`, and an upstream `retryAfter`, so a 429 still tells the
|
|
209
|
+
* caller how long to wait and an unparseable body stays
|
|
210
|
+
* `openalex_invalid_response`. Only a `ServiceUnavailable` carrying no reason
|
|
211
|
+
* gains `openalex_unreachable` — the one code that reason is declared for; a
|
|
212
|
+
* `Timeout` or `RateLimited` keeps its code with no reason, as the Europe PMC
|
|
213
|
+
* service reports them.
|
|
210
214
|
*/
|
|
211
215
|
async withRetry(execute, label, signal) {
|
|
212
216
|
for (let attempt = 0; attempt <= this.maxRetries; attempt++) {
|
|
@@ -234,10 +238,10 @@ export class OpenAlexService {
|
|
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|
continue;
|
|
235
239
|
}
|
|
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|
const attempts = this.maxRetries + 1;
|
|
241
|
+
const reason = error.data?.reason ??
|
|
242
|
+
(error.code === JsonRpcErrorCode.ServiceUnavailable ? 'openalex_unreachable' : undefined);
|
|
237
243
|
throw new McpError(error.code, `${error.message} (failed after ${attempts} attempt${attempts === 1 ? '' : 's'})`, {
|
|
238
|
-
...(
|
|
239
|
-
reason: 'openalex_unreachable',
|
|
240
|
-
}),
|
|
244
|
+
...(reason !== undefined && { reason }),
|
|
241
245
|
label,
|
|
242
246
|
attempts,
|
|
243
247
|
...(error.data?.retryAfter !== undefined && { retryAfter: error.data.retryAfter }),
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"openalex-service.js","sourceRoot":"","sources":["../../../src/services/openalex/openalex-service.ts"],"names":[],"mappings":"AAAA
|
|
1
|
+
{"version":3,"file":"openalex-service.js","sourceRoot":"","sources":["../../../src/services/openalex/openalex-service.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;GAwBG;AAEH,OAAO,EAAE,aAAa,EAAE,gBAAgB,EAAE,QAAQ,EAAE,MAAM,+BAA+B,CAAC;AAC1F,OAAO,EAAE,kBAAkB,EAAE,MAAM,EAAE,qBAAqB,EAAE,MAAM,8BAA8B,CAAC;AAEjG,OAAO,EAAE,eAAe,EAAE,MAAM,2BAA2B,CAAC;AAC5D,OAAO,EAAE,iBAAiB,EAAE,MAAM,iBAAiB,CAAC;AACpD,OAAO,EACL,0BAA0B,EAC1B,sBAAsB,EACtB,8BAA8B,GAG/B,MAAM,YAAY,CAAC;AAEpB,MAAM,cAAc,GAAG,MAAM,CAAC;AAE9B,mEAAmE;AACnE,SAAS,QAAQ,CAAC,EAAU;IAC1B,OAAO,EAAE,CAAC,UAAU,CAAC,uBAAuB,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,KAAK,CAAC,uBAAuB,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC;AAChG,CAAC;AAED,SAAS,cAAc,CAAC,EAAU,EAAE,MAAoB;IACtD,IAAI,CAAC,MAAM;QAAE,OAAO,IAAI,OAAO,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,UAAU,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC;IAC1D,IAAI,MAAM,CAAC,OAAO;QAAE,OAAO,OAAO,CAAC,MAAM,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC;IACzD,OAAO,IAAI,OAAO,CAAO,CAAC,OAAO,EAAE,MAAM,EAAE,EAAE;QAC3C,MAAM,OAAO,GAAG,GAAG,EAAE;YACnB,YAAY,CAAC,KAAK,CAAC,CAAC;YACpB,MAAM,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC;QACxB,CAAC,CAAC;QACF,MAAM,KAAK,GAAG,UAAU,CAAC,GAAG,EAAE;YAC5B,MAAM,CAAC,mBAAmB,CAAC,OAAO,EAAE,OAAO,CAAC,CAAC;YAC7C,OAAO,EAAE,CAAC;QACZ,CAAC,EAAE,EAAE,CAAC,CAAC;QACP,MAAM,CAAC,gBAAgB,CAAC,OAAO,EAAE,OAAO,EAAE,EAAE,IAAI,EAAE,IAAI,EAAE,CAAC,CAAC;IAC5D,CAAC,CAAC,CAAC;AACL,CAAC;AAED;;;;GAIG;AACH,SAAS,WAAW,CAAC,IAAkB;IACrC,MAAM,GAAG,GAAG,IAAI,CAAC,GAAG,EAAE,IAAI,CAAC;IAC3B,IAAI,CAAC,GAAG;QAAE,OAAO,IAAI,CAAC;IACtB,gFAAgF;IAChF,MAAM,KAAK,GAAG,WAAW,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;IACpC,OAAO,KAAK,EAAE,CAAC,CAAC,CAAC,IAAI,IAAI,CAAC;AAC5B,CAAC;AAED;;;;GAIG;AACH,SAAS,WAAW;IAClB,OAAO,EAAE,KAAK,EAAE,EAAE,EAAE,UAAU,EAAE,CAAC,EAAE,aAAa,EAAE,CAAC,EAAE,WAAW,EAAE,KAAK,EAAE,CAAC;AAC5E,CAAC;AAED;;;;;GAKG;AACH,MAAM,aAAa;IAKY,WAAW;IAJ/B,KAAK,GAAa,EAAE,CAAC;IAC9B,aAAa,GAAG,CAAC,CAAC;IACD,IAAI,GAAG,IAAI,GAAG,EAAU,CAAC;IAE1C,YAA6B,WAAmB;2BAAnB,WAAW;IAAW,CAAC;IAEpD;;;OAGG;IACH,GAAG,CAAC,IAA8B;QAChC,MAAM,IAAI,GAAG,IAAI,CAAC,CAAC,CAAC,WAAW,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC;QAC7C,IAAI,CAAC,IAAI,EAAE,CAAC;YACV,IAAI,CAAC,aAAa,EAAE,CAAC;YACrB,OAAO;QACT,CAAC;QACD,IAAI,IAAI,KAAK,IAAI,CAAC,WAAW,IAAI,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC;YAAE,OAAO;QAC7D,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC;QACpB,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;IACxB,CAAC;CACF;AAED,gFAAgF;AAChF,MAAM,OAAO,eAAe;IAEP,MAAM;IACN,UAAU;IAF7B,YACmB,MAAyB,EACzB,UAAkB;sBADlB,MAAM;0BACN,UAAU;IAC1B,CAAC;IAEJ;;;;OAIG;IACH,KAAK,CAAC,OAAO,CAAC,IAAY,EAAE,CAAS,EAAE,MAAoB;QACzD,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,SAAS,CAAC,IAAI,EAAE,MAAM,CAAC,CAAC;QAChD,IAAI,CAAC,IAAI;YAAE,OAAO,WAAW,EAAE,CAAC;QAEhC,OAAO,IAAI,CAAC,iBAAiB,CAC3B,IAAI,EACJ,IAAI,CAAC,aAAa,IAAI,EAAE,EACxB,CAAC,EACD,uBAAuB,IAAI,GAAG,EAC9B,MAAM,CACP,CAAC;IACJ,CAAC;IAED;;;;;;;;OAQG;IACH,KAAK,CAAC,OAAO,CAAC,IAAY,EAAE,CAAS,EAAE,MAAoB;QACzD,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,SAAS,CAAC,IAAI,EAAE,MAAM,CAAC,CAAC;QAChD,IAAI,CAAC,IAAI;YAAE,OAAO,WAAW,EAAE,CAAC;QAEhC,MAAM,OAAO,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,sBAAsB,CAAC,CAAC;QACpD,MAAM,SAAS,GAAG,IAAI,aAAa,CAAC,IAAI,CAAC,CAAC;QAC1C,IAAI,aAAa,GAAG,CAAC,CAAC;QACtB,IAAI,SAAS,GAAG,KAAK,CAAC;QAEtB,KACE,IAAI,IAAI,GAAG,CAAC,EACZ,IAAI,IAAI,8BAA8B,IAAI,SAAS,CAAC,KAAK,CAAC,MAAM,GAAG,CAAC,EACpE,IAAI,EAAE,EACN,CAAC;YACD,MAAM,EAAE,KAAK,EAAE,UAAU,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,CAChD,GAAG,EAAE,CAAC,IAAI,CAAC,MAAM,CAAC,UAAU,CAAC,IAAI,CAAC,EAAE,EAAE,OAAO,EAAE,IAAI,EAAE,MAAM,CAAC,EAC5D,cAAc,IAAI,CAAC,EAAE,UAAU,IAAI,GAAG,EACtC,MAAM,CACP,CAAC;YACF,aAAa,GAAG,UAAU,CAAC;YAC3B,KAAK,MAAM,CAAC,IAAI,KAAK;gBAAE,SAAS,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC;YACxC,IAAI,KAAK,CAAC,MAAM,GAAG,OAAO,IAAI,IAAI,GAAG,OAAO,IAAI,UAAU,EAAE,CAAC;gBAC3D,SAAS,GAAG,IAAI,CAAC;gBACjB,MAAM;YACR,CAAC;QACH,CAAC;QAED,OAAO,IAAI,CAAC,MAAM,CAAC,SAAS,EAAE,SAAS,EAAE,aAAa,EAAE,CAAC,CAAC,CAAC;IAC7D,CAAC;IAED;;;OAGG;IACH,KAAK,CAAC,UAAU,CAAC,IAAY,EAAE,CAAS,EAAE,MAAoB;QAC5D,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,SAAS,CAAC,IAAI,EAAE,MAAM,CAAC,CAAC;QAChD,IAAI,CAAC,IAAI;YAAE,OAAO,WAAW,EAAE,CAAC;QAEhC,OAAO,IAAI,CAAC,iBAAiB,CAC3B,IAAI,EACJ,IAAI,CAAC,gBAAgB,IAAI,EAAE,EAC3B,CAAC,EACD,0BAA0B,IAAI,GAAG,EACjC,MAAM,CACP,CAAC;IACJ,CAAC;IAED,8EAA8E;IACtE,SAAS,CAAC,IAAY,EAAE,MAAoB;QAClD,OAAO,IAAI,CAAC,SAAS,CACnB,GAAG,EAAE,CAAC,IAAI,CAAC,MAAM,CAAC,aAAa,CAAC,IAAI,EAAE,MAAM,CAAC,EAC7C,iBAAiB,IAAI,GAAG,EACxB,MAAM,CACP,CAAC;IACJ,CAAC;IAED;;;;;;;;;OASG;IACK,KAAK,CAAC,iBAAiB,CAC7B,IAAY,EACZ,KAAe,EACf,CAAS,EACT,KAAa,EACb,MAAoB;QAEpB,IAAI,KAAK,CAAC,MAAM,KAAK,CAAC;YAAE,OAAO,WAAW,EAAE,CAAC;QAE7C,MAAM,SAAS,GAAG,IAAI,aAAa,CAAC,IAAI,CAAC,CAAC;QAC1C,IAAI,QAAQ,GAAG,CAAC,CAAC;QAEjB,KACE,IAAI,KAAK,GAAG,CAAC,EACb,KAAK,GAAG,8BAA8B;YACtC,QAAQ,GAAG,KAAK,CAAC,MAAM;YACvB,SAAS,CAAC,KAAK,CAAC,MAAM,GAAG,CAAC,EAC1B,KAAK,EAAE,EACP,CAAC;YACD,MAAM,GAAG,GAAG,KAAK,CAAC,KAAK,CAAC,QAAQ,EAAE,QAAQ,GAAG,0BAA0B,CAAC,CAAC;YACzE,MAAM,QAAQ,GAAG,MAAM,IAAI,CAAC,SAAS,CACnC,GAAG,EAAE,CAAC,IAAI,CAAC,MAAM,CAAC,mBAAmB,CAAC,GAAG,EAAE,MAAM,CAAC,EAClD,KAAK,EACL,MAAM,CACP,CAAC;YACF,MAAM,IAAI,GAAG,IAAI,GAAG,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;YAC/D,KAAK,MAAM,EAAE,IAAI,GAAG;gBAAE,SAAS,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,QAAQ,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC;YAC5D,QAAQ,IAAI,GAAG,CAAC,MAAM,CAAC;QACzB,CAAC;QAED,OAAO,IAAI,CAAC,MAAM,CAAC,SAAS,EAAE,QAAQ,IAAI,KAAK,CAAC,MAAM,EAAE,KAAK,CAAC,MAAM,EAAE,CAAC,CAAC,CAAC;IAC3E,CAAC;IAED;;;;OAIG;IACK,MAAM,CACZ,SAAwB,EACxB,SAAkB,EAClB,aAAqB,EACrB,CAAS;QAET,OAAO;YACL,KAAK,EAAE,SAAS,CAAC,KAAK;YACtB,UAAU,EAAE,SAAS,CAAC,CAAC,CAAC,SAAS,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,aAAa;YAC9D,aAAa,EAAE,SAAS,CAAC,aAAa;YACtC,WAAW,EAAE,CAAC,SAAS,IAAI,SAAS,CAAC,KAAK,CAAC,MAAM,GAAG,CAAC;SACtD,CAAC;IACJ,CAAC;IAED;;;;;;;;OAQG;IACK,KAAK,CAAC,SAAS,CACrB,OAAyB,EACzB,KAAa,EACb,MAAoB;QAEpB,KAAK,IAAI,OAAO,GAAG,CAAC,EAAE,OAAO,IAAI,IAAI,CAAC,UAAU,EAAE,OAAO,EAAE,EAAE,CAAC;YAC5D,IAAI,MAAM,EAAE,OAAO;gBAAE,MAAM,MAAM,CAAC,MAAM,CAAC;YAEzC,IAAI,CAAC;gBACH,OAAO,MAAM,OAAO,EAAE,CAAC;YACzB,CAAC;YAAC,OAAO,KAAc,EAAE,CAAC;gBACxB,IAAI,MAAM,EAAE,OAAO;oBAAE,MAAM,MAAM,CAAC,MAAM,CAAC;gBACzC,IAAI,CAAC,CAAC,KAAK,YAAY,QAAQ,CAAC;oBAAE,MAAM,KAAK,CAAC;gBAC9C,IAAI,CAAC,kBAAkB,CAAC,KAAK,CAAC;oBAAE,MAAM,KAAK,CAAC;gBAE5C,IAAI,OAAO,GAAG,IAAI,CAAC,UAAU,EAAE,CAAC;oBAC9B,MAAM,SAAS,GAAG,IAAI,CAAC,GAAG,CAAC,IAAI,GAAG,CAAC,IAAI,OAAO,EAAE,cAAc,CAAC,CAAC;oBAChE,MAAM,MAAM,GAAG,SAAS,GAAG,CAAC,IAAI,GAAG,GAAG,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC,CAAC;oBACxD,MAAM,UAAU,GAAG,IAAI,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC;oBACtC,MAAM,CAAC,OAAO,CACZ,YAAY,KAAK,sBAAsB,OAAO,GAAG,CAAC,IAAI,IAAI,CAAC,UAAU,QAAQ,UAAU,KAAK,EAC5F,qBAAqB,CAAC,oBAAoB,CAAC;wBACzC,SAAS,EAAE,eAAe;wBAC1B,iBAAiB,EAAE,EAAE,KAAK,EAAE,OAAO,EAAE,OAAO,GAAG,CAAC,EAAE,UAAU,EAAE;qBAC/D,CAAC,CACH,CAAC;oBACF,MAAM,cAAc,CAAC,UAAU,EAAE,MAAM,CAAC,CAAC;oBACzC,SAAS;gBACX,CAAC;gBAED,MAAM,QAAQ,GAAG,IAAI,CAAC,UAAU,GAAG,CAAC,CAAC;gBACrC,MAAM,MAAM,GACV,KAAK,CAAC,IAAI,EAAE,MAAM;oBAClB,CAAC,KAAK,CAAC,IAAI,KAAK,gBAAgB,CAAC,kBAAkB,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC;gBAC5F,MAAM,IAAI,QAAQ,CAChB,KAAK,CAAC,IAAI,EACV,GAAG,KAAK,CAAC,OAAO,kBAAkB,QAAQ,WAAW,QAAQ,KAAK,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,GAAG,EACjF;oBACE,GAAG,CAAC,MAAM,KAAK,SAAS,IAAI,EAAE,MAAM,EAAE,CAAC;oBACvC,KAAK;oBACL,QAAQ;oBACR,GAAG,CAAC,KAAK,CAAC,IAAI,EAAE,UAAU,KAAK,SAAS,IAAI,EAAE,UAAU,EAAE,KAAK,CAAC,IAAI,CAAC,UAAU,EAAE,CAAC;iBACnF,EACD,EAAE,KAAK,EAAE,KAAK,EAAE,CACjB,CAAC;YACJ,CAAC;QACH,CAAC;QAED,MAAM,aAAa,CAAC,4CAA4C,EAAE,EAAE,KAAK,EAAE,CAAC,CAAC;IAC/E,CAAC;CACF;AAED,+EAA+E;AAE/E,IAAI,QAAqC,CAAC;AAE1C,yEAAyE;AACzE,MAAM,UAAU,mBAAmB;IACjC,MAAM,MAAM,GAAG,eAAe,EAAE,CAAC;IACjC,MAAM,MAAM,GAAG,IAAI,iBAAiB,CAAC;QACnC,SAAS,EAAE,MAAM,CAAC,kBAAkB,EAAE,+CAA+C;QACrF,GAAG,CAAC,MAAM,CAAC,UAAU,IAAI,EAAE,KAAK,EAAE,MAAM,CAAC,UAAU,EAAE,CAAC;KACvD,CAAC,CAAC;IACH,2DAA2D;IAC3D,QAAQ,GAAG,IAAI,eAAe,CAAC,MAAM,EAAE,MAAM,CAAC,mBAAmB,CAAC,CAAC;IACnE,MAAM,CAAC,IAAI,CACT,+BAA+B,EAC/B,qBAAqB,CAAC,oBAAoB,CAAC;QACzC,SAAS,EAAE,cAAc;QACzB,iBAAiB,EAAE;YACjB,QAAQ,EAAE,CAAC,CAAC,MAAM,CAAC,UAAU;YAC7B,UAAU,EAAE,MAAM,CAAC,mBAAmB;YACtC,SAAS,EAAE,MAAM,CAAC,kBAAkB;SACrC;KACF,CAAC,CACH,CAAC;AACJ,CAAC;AAED,uEAAuE;AACvE,MAAM,UAAU,kBAAkB;IAChC,IAAI,CAAC,QAAQ;QACX,MAAM,IAAI,KAAK,CAAC,qEAAqE,CAAC,CAAC;IACzF,OAAO,QAAQ,CAAC;AAClB,CAAC;AAED,kFAAkF;AAClF,MAAM,UAAU,0BAA0B;IACxC,OAAO,QAAQ,CAAC;AAClB,CAAC"}
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@@ -46,6 +46,9 @@ export declare class UnpaywallService {
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46
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* `application/octet-stream`, and an HTML interstitial is sometimes served as
|
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47
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* `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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50
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+
* Records and error data name the URL's host, never the URL: a publisher's
|
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51
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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
|
/**
|
|
@@ -66,7 +67,7 @@ export class UnpaywallService {
|
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|
66
67
|
doi: normalized,
|
|
67
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|
}, { 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 {
|
|
|
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
181
|
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;
|
|
199
|
+
}
|
|
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
|
-
{"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,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,IAAI,EAAE,CAAsB,CAAC;
|
|
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,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC;YACnE,MAAM,kBAAkB,CACtB,mCAAmC,GAAG,EAAE,EACxC,EAAE,MAAM,EAAE,uBAAuB,EAAE,IAAI,EAAE,EACzC,EAAE,KAAK,EAAE,KAAK,EAAE,CACjB,CAAC;QACJ,CAAC;QAED,IAAI,CAAC,QAAQ,CAAC,EAAE,EAAE,CAAC;YACjB,MAAM,MAAM,qBAAqB,CAAC,QAAQ,EAAE;gBAC1C,OAAO,EAAE,yBAAyB;gBAClC,IAAI,EAAE,EAAE,IAAI,EAAE;aACf,CAAC,CAAC;QACL,CAAC;QAED,MAAM,UAAU,GAAG,QAAQ,CAAC,GAAG,IAAI,GAAG,CAAC;QACvC,0EAA0E;QAC1E,2CAA2C;QAC3C,MAAM,KAAK,GAAG,IAAI,UAAU,CAAC,MAAM,QAAQ,CAAC,QAAQ,CAAC,WAAW,EAAE,CAAC,CAAC,CAAC;QAErE,IAAI,WAAW,CAAC,KAAK,CAAC;YAAE,OAAO,EAAE,IAAI,EAAE,KAAK,EAAE,UAAU,EAAE,IAAI,EAAE,KAAK,EAAE,CAAC;QAExE,OAAO,EAAE,IAAI,EAAE,MAAM,EAAE,UAAU,EAAE,IAAI,EAAE,IAAI,WAAW,EAAE,CAAC,MAAM,CAAC,KAAK,CAAC,EAAE,CAAC;IAC7E,CAAC;CACF;AAED,2FAA2F;AAC3F,SAAS,MAAM,CAAC,GAAW;IACzB,OAAO,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,EAAE,IAAI,CAAC;AAC9B,CAAC;AAED,gHAAgH;AAChH,SAAS,QAAQ,CAAC,KAAc;IAC9B,OAAO,OAAO,KAAK,KAAK,QAAQ,IAAI,KAAK,CAAC,IAAI,EAAE,CAAC,MAAM,GAAG,CAAC,CAAC;AAC9D,CAAC;AAED,yDAAyD;AACzD,MAAM,SAAS,GAAG,UAAU,CAAC,EAAE,CAAC,IAAI,EAAE,IAAI,EAAE,IAAI,EAAE,IAAI,EAAE,IAAI,CAAC,CAAC;AAE9D,8EAA8E;AAC9E,SAAS,WAAW,CAAC,KAAiB;IACpC,OAAO,CACL,KAAK,CAAC,MAAM,IAAI,SAAS,CAAC,MAAM,IAAI,SAAS,CAAC,KAAK,CAAC,CAAC,IAAI,EAAE,KAAK,EAAE,EAAE,CAAC,KAAK,CAAC,KAAK,CAAC,KAAK,IAAI,CAAC,CAC5F,CAAC;AACJ,CAAC;AAED;;;GAGG;AACH,SAAS,YAAY,CAAC,KAAa;IACjC,MAAM,OAAO,GAAG,KAAK,CAAC,IAAI,EAAE,CAAC;IAC7B,IAAI,CAAC,OAAO;QAAE,OAAO;IACrB,MAAM,aAAa,GAAG,OAAO,CAAC,OAAO,CAAC,QAAQ,EAAE,EAAE,CAAC,CAAC,OAAO,CAAC,gCAAgC,EAAE,EAAE,CAAC,CAAC;IAClG,OAAO,aAAa,CAAC,UAAU,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,aAAa,CAAC,CAAC,CAAC,SAAS,CAAC;AACrE,CAAC;AAED,+EAA+E;AAE/E,IAAI,QAAsC,CAAC;AAE3C;;;;GAIG;AACH,MAAM,UAAU,oBAAoB;IAClC,MAAM,MAAM,GAAG,eAAe,EAAE,CAAC;IACjC,IAAI,CAAC,MAAM,CAAC,cAAc,EAAE,CAAC;QAC3B,MAAM,CAAC,IAAI,CAAC,wDAAwD,CAAC,CAAC;QACtE,OAAO;IACT,CAAC;IACD,QAAQ,GAAG,IAAI,gBAAgB,CAAC,MAAM,CAAC,cAAc,EAAE,MAAM,CAAC,kBAAkB,CAAC,CAAC;IAClF,MAAM,CAAC,IAAI,CACT,gCAAgC,EAChC,qBAAqB,CAAC,oBAAoB,CAAC;QACzC,SAAS,EAAE,eAAe;QAC1B,iBAAiB,EAAE,EAAE,SAAS,EAAE,MAAM,CAAC,kBAAkB,EAAE;KAC5D,CAAC,CACH,CAAC;AACJ,CAAC;AAED,qFAAqF;AACrF,MAAM,UAAU,mBAAmB;IACjC,OAAO,QAAQ,CAAC;AAClB,CAAC"}
|
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",
|
|
@@ -30,6 +30,8 @@
|
|
|
30
30
|
"format:unsafe": "biome check --write --unsafe .",
|
|
31
31
|
"test": "bunx vitest run",
|
|
32
32
|
"test:coverage": "bunx vitest run --coverage",
|
|
33
|
+
"test:corpus": "bunx vitest run tests/corpus",
|
|
34
|
+
"corpus:snapshot": "PUBMED_CORPUS_UPDATE=1 bunx vitest run tests/corpus",
|
|
33
35
|
"audit:fix": "bun audit fix",
|
|
34
36
|
"audit:refresh": "rm -f bun.lock && bun install && bun audit",
|
|
35
37
|
"list-skills": "bun run scripts/list-skills.ts",
|
|
@@ -93,27 +95,27 @@
|
|
|
93
95
|
"access": "public"
|
|
94
96
|
},
|
|
95
97
|
"dependencies": {
|
|
96
|
-
"@cyanheads/mcp-ts-core": "^0.13.
|
|
98
|
+
"@cyanheads/mcp-ts-core": "^0.13.14",
|
|
97
99
|
"defuddle": "^0.19.4",
|
|
98
|
-
"fast-xml-parser": "^5.11.
|
|
100
|
+
"fast-xml-parser": "^5.11.2",
|
|
99
101
|
"linkedom": "^0.18.13",
|
|
100
|
-
"pino-pretty": "^13.
|
|
101
|
-
"sanitize-html": "^2.
|
|
102
|
+
"pino-pretty": "^13.2.0",
|
|
103
|
+
"sanitize-html": "^2.18.0",
|
|
102
104
|
"unpdf": "^1.8.1",
|
|
103
105
|
"zod": "^4.6.5"
|
|
104
106
|
},
|
|
105
107
|
"devDependencies": {
|
|
106
|
-
"@biomejs/biome": "^2.5.
|
|
108
|
+
"@biomejs/biome": "^2.5.15",
|
|
107
109
|
"@socketsecurity/bun-security-scanner": "^1.1.3",
|
|
108
|
-
"@types/node": "^26.6.
|
|
109
|
-
"@types/sanitize-html": "^2.16.
|
|
110
|
-
"@vitest/coverage-istanbul": "^5.0.
|
|
110
|
+
"@types/node": "^26.6.4",
|
|
111
|
+
"@types/sanitize-html": "^2.16.2",
|
|
112
|
+
"@vitest/coverage-istanbul": "^5.0.3",
|
|
111
113
|
"depcheck": "^1.4.7",
|
|
112
114
|
"fast-check": "^4.10.2",
|
|
113
|
-
"ignore": "^7.0.
|
|
114
|
-
"tsc-alias": "^1.9.
|
|
115
|
+
"ignore": "^7.0.12",
|
|
116
|
+
"tsc-alias": "^1.9.7",
|
|
115
117
|
"typescript": "^7.0.2",
|
|
116
|
-
"vitest": "^5.0.
|
|
118
|
+
"vitest": "^5.0.3"
|
|
117
119
|
},
|
|
118
120
|
"overrides": {
|
|
119
121
|
"@hono/node-server": "^2.0.11",
|
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",
|
|
10
10
|
"remotes": [
|
|
11
11
|
{
|
|
12
12
|
"type": "streamable-http",
|
|
@@ -18,18 +18,8 @@
|
|
|
18
18
|
"registryType": "npm",
|
|
19
19
|
"registryBaseUrl": "https://registry.npmjs.org",
|
|
20
20
|
"identifier": "@cyanheads/pubmed-mcp-server",
|
|
21
|
-
"runtimeHint": "
|
|
22
|
-
"version": "2.10.
|
|
23
|
-
"packageArguments": [
|
|
24
|
-
{
|
|
25
|
-
"type": "positional",
|
|
26
|
-
"value": "run"
|
|
27
|
-
},
|
|
28
|
-
{
|
|
29
|
-
"type": "positional",
|
|
30
|
-
"value": "start:stdio"
|
|
31
|
-
}
|
|
32
|
-
],
|
|
21
|
+
"runtimeHint": "npx",
|
|
22
|
+
"version": "2.10.21",
|
|
33
23
|
"environmentVariables": [
|
|
34
24
|
{
|
|
35
25
|
"name": "MCP_LOG_LEVEL",
|
|
@@ -65,19 +55,15 @@
|
|
|
65
55
|
"registryType": "npm",
|
|
66
56
|
"registryBaseUrl": "https://registry.npmjs.org",
|
|
67
57
|
"identifier": "@cyanheads/pubmed-mcp-server",
|
|
68
|
-
"runtimeHint": "
|
|
69
|
-
"version": "2.10.
|
|
70
|
-
"
|
|
58
|
+
"runtimeHint": "npx",
|
|
59
|
+
"version": "2.10.21",
|
|
60
|
+
"environmentVariables": [
|
|
71
61
|
{
|
|
72
|
-
"
|
|
73
|
-
"
|
|
62
|
+
"name": "MCP_TRANSPORT_TYPE",
|
|
63
|
+
"description": "Selects the HTTP transport.",
|
|
64
|
+
"format": "string",
|
|
65
|
+
"value": "http"
|
|
74
66
|
},
|
|
75
|
-
{
|
|
76
|
-
"type": "positional",
|
|
77
|
-
"value": "start:http"
|
|
78
|
-
}
|
|
79
|
-
],
|
|
80
|
-
"environmentVariables": [
|
|
81
67
|
{
|
|
82
68
|
"name": "MCP_HTTP_HOST",
|
|
83
69
|
"description": "The hostname for the HTTP server.",
|