@cyanheads/pubmed-mcp-server 2.10.16 → 2.10.18
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 +2 -2
- package/CLAUDE.md +2 -2
- package/README.md +7 -5
- package/changelog/2.10.x/2.10.17.md +19 -0
- package/changelog/2.10.x/2.10.18.md +14 -0
- package/dist/config/server-config.d.ts.map +1 -1
- package/dist/config/server-config.js +7 -3
- package/dist/config/server-config.js.map +1 -1
- package/dist/mcp-server/tools/definitions/_text.d.ts +20 -3
- package/dist/mcp-server/tools/definitions/_text.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/_text.js +35 -3
- package/dist/mcp-server/tools/definitions/_text.js.map +1 -1
- package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts +23 -31
- package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js +349 -130
- package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/find-related.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/find-related.tool.js +22 -7
- package/dist/mcp-server/tools/definitions/find-related.tool.js.map +1 -1
- package/dist/services/error-contracts.d.ts +5 -3
- package/dist/services/error-contracts.d.ts.map +1 -1
- package/dist/services/error-contracts.js +5 -3
- package/dist/services/error-contracts.js.map +1 -1
- package/dist/services/europe-pmc/europe-pmc-service.d.ts +18 -12
- package/dist/services/europe-pmc/europe-pmc-service.d.ts.map +1 -1
- package/dist/services/europe-pmc/europe-pmc-service.js +82 -67
- package/dist/services/europe-pmc/europe-pmc-service.js.map +1 -1
- package/dist/services/europe-pmc/request-queue.d.ts +11 -27
- package/dist/services/europe-pmc/request-queue.d.ts.map +1 -1
- package/dist/services/europe-pmc/request-queue.js +17 -104
- package/dist/services/europe-pmc/request-queue.js.map +1 -1
- package/dist/services/ncbi/parsing/pmc-article-parser.d.ts +8 -0
- package/dist/services/ncbi/parsing/pmc-article-parser.d.ts.map +1 -1
- package/dist/services/ncbi/parsing/pmc-article-parser.js +159 -16
- package/dist/services/ncbi/parsing/pmc-article-parser.js.map +1 -1
- package/dist/services/openalex/openalex-service.d.ts +11 -1
- package/dist/services/openalex/openalex-service.d.ts.map +1 -1
- package/dist/services/openalex/openalex-service.js +19 -10
- package/dist/services/openalex/openalex-service.js.map +1 -1
- package/dist/services/unpaywall/types.d.ts +16 -2
- package/dist/services/unpaywall/types.d.ts.map +1 -1
- package/dist/services/unpaywall/unpaywall-service.d.ts +4 -3
- package/dist/services/unpaywall/unpaywall-service.d.ts.map +1 -1
- package/dist/services/unpaywall/unpaywall-service.js +15 -4
- package/dist/services/unpaywall/unpaywall-service.js.map +1 -1
- package/package.json +1 -1
- package/server.json +3 -3
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-
{"version":3,"file":"error-contracts.d.ts","sourceRoot":"","sources":["../../src/services/error-contracts.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;GAqBG;AAEH,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAEjE;;;;GAIG;AACH,eAAO,MAAM,mBAAmB;aAE5B,MAAM,EAAE,YAAY;aACpB,IAAI;aACJ,IAAI,EAAE,gLAAgL;aACtL,QAAQ,EACN,iIAAiI;aACnI,SAAS;aACT,QAAQ,EAAE,SAAS;;aAGnB,MAAM,EAAE,kBAAkB;aAC1B,IAAI;aACJ,IAAI,EAAE,2DAA2D;aACjE,QAAQ,EAAE,4EAA4E;aACtF,SAAS;aACT,QAAQ,EAAE,SAAS;;aAGnB,MAAM,EAAE,wBAAwB;aAChC,IAAI;aACJ,IAAI,EAAE,iEAAiE;aACvE,QAAQ,EAAE,+DAA+D;aACzE,SAAS;aACT,QAAQ,EAAE,SAAS;;aAGnB,MAAM,EAAE,uBAAuB;aAC/B,IAAI;aACJ,IAAI,EAAE,mEAAmE;aACzE,QAAQ,EAAE,iFAAiF;aAC3F,SAAS;aACT,QAAQ,EAAE,SAAS;;aAGnB,MAAM,EAAE,yBAAyB;aACjC,IAAI;aACJ,IAAI,EAAE,uEAAuE;aAC7E,QAAQ,EACN,gGAAgG;aAClG,SAAS;aACT,QAAQ,EAAE,SAAS;EAEb,CAAC;AAEX;;;;;;;;;;GAUG;AACH,eAAO,MAAM,uBAAuB;aAEhC,MAAM,EAAE,aAAa;aACrB,IAAI;aACJ,IAAI,EAAE,oTAAoT;aAC1T,QAAQ,EACN,8JAA8J;aAChK,SAAS;EAEH,CAAC;AAEX;;;;;;;;;GASG;AACH,eAAO,MAAM,oBAAoB;aAE7B,MAAM,EAAE,cAAc;aACtB,IAAI;aACJ,IAAI,EAAE,0LAA0L;aAChM,QAAQ,EACN,uHAAuH;aACzH,SAAS;EAEH,CAAC;AAEX
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{"version":3,"file":"error-contracts.d.ts","sourceRoot":"","sources":["../../src/services/error-contracts.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;GAqBG;AAEH,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAEjE;;;;GAIG;AACH,eAAO,MAAM,mBAAmB;aAE5B,MAAM,EAAE,YAAY;aACpB,IAAI;aACJ,IAAI,EAAE,gLAAgL;aACtL,QAAQ,EACN,iIAAiI;aACnI,SAAS;aACT,QAAQ,EAAE,SAAS;;aAGnB,MAAM,EAAE,kBAAkB;aAC1B,IAAI;aACJ,IAAI,EAAE,2DAA2D;aACjE,QAAQ,EAAE,4EAA4E;aACtF,SAAS;aACT,QAAQ,EAAE,SAAS;;aAGnB,MAAM,EAAE,wBAAwB;aAChC,IAAI;aACJ,IAAI,EAAE,iEAAiE;aACvE,QAAQ,EAAE,+DAA+D;aACzE,SAAS;aACT,QAAQ,EAAE,SAAS;;aAGnB,MAAM,EAAE,uBAAuB;aAC/B,IAAI;aACJ,IAAI,EAAE,mEAAmE;aACzE,QAAQ,EAAE,iFAAiF;aAC3F,SAAS;aACT,QAAQ,EAAE,SAAS;;aAGnB,MAAM,EAAE,yBAAyB;aACjC,IAAI;aACJ,IAAI,EAAE,uEAAuE;aAC7E,QAAQ,EACN,gGAAgG;aAClG,SAAS;aACT,QAAQ,EAAE,SAAS;EAEb,CAAC;AAEX;;;;;;;;;;GAUG;AACH,eAAO,MAAM,uBAAuB;aAEhC,MAAM,EAAE,aAAa;aACrB,IAAI;aACJ,IAAI,EAAE,oTAAoT;aAC1T,QAAQ,EACN,8JAA8J;aAChK,SAAS;EAEH,CAAC;AAEX;;;;;;;;;GASG;AACH,eAAO,MAAM,oBAAoB;aAE7B,MAAM,EAAE,cAAc;aACtB,IAAI;aACJ,IAAI,EAAE,0LAA0L;aAChM,QAAQ,EACN,uHAAuH;aACzH,SAAS;EAEH,CAAC;AAEX;;;;;;GAMG;AACH,eAAO,MAAM,wBAAwB;aAEjC,MAAM,EAAE,uBAAuB;aAC/B,IAAI;aACJ,IAAI,EAAE,qEAAqE;aAC3E,QAAQ,EACN,gGAAgG;aAClG,SAAS;aACT,QAAQ,EAAE,SAAS;EAEb,CAAC;AAEX;;;;GAIG;AACH,eAAO,MAAM,uBAAuB;aAEhC,MAAM,EAAE,sBAAsB;aAC9B,IAAI;aACJ,IAAI,EAAE,oDAAoD;aAC1D,QAAQ,EACN,4FAA4F;aAC9F,SAAS;aACT,QAAQ,EAAE,SAAS;;aAGnB,MAAM,EAAE,2BAA2B;aACnC,IAAI;aACJ,IAAI,EAAE,mEAAmE;aACzE,QAAQ,EAAE,qFAAqF;aAC/F,SAAS;aACT,QAAQ,EAAE,SAAS;EAEb,CAAC;AAEX;;;;GAIG;AACH,eAAO,MAAM,wBAAwB;aAEjC,MAAM,EAAE,uBAAuB;aAC/B,IAAI;aACJ,IAAI,EAAE,qKAAqK;aAC3K,QAAQ,EACN,iGAAiG;aACnG,SAAS;aACT,QAAQ,EAAE,SAAS;;aAGnB,MAAM,EAAE,4BAA4B;aACpC,IAAI;aACJ,IAAI,EAAE,4EAA4E;aAClF,QAAQ,EACN,uFAAuF;aACzF,SAAS;aACT,QAAQ,EAAE,SAAS;;aAGnB,MAAM,EAAE,yBAAyB;aACjC,IAAI;aACJ,IAAI,EAAE,iOAAiO;aACvO,QAAQ,EACN,qHAAqH;aACvH,SAAS;aACT,QAAQ,EAAE,SAAS;EAEb,CAAC;AAEX;;;;GAIG;AACH,MAAM,MAAM,kBAAkB,GAC1B,CAAC,OAAO,mBAAmB,CAAC,CAAC,MAAM,CAAC,CAAC,QAAQ,CAAC,GAC9C,CAAC,OAAO,wBAAwB,CAAC,CAAC,MAAM,CAAC,CAAC,QAAQ,CAAC,GACnD,CAAC,OAAO,wBAAwB,CAAC,CAAC,MAAM,CAAC,CAAC,QAAQ,CAAC,GACnD,CAAC,OAAO,uBAAuB,CAAC,CAAC,MAAM,CAAC,CAAC,QAAQ,CAAC,CAAC;AAWvD;;;;;;;;;;;;GAYG;AACH,wBAAgB,WAAW,CAAC,MAAM,EAAE,kBAAkB,GAAG;IAAE,QAAQ,EAAE;QAAE,IAAI,EAAE,MAAM,CAAA;KAAE,CAAA;CAAE,CAMtF"}
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@@ -108,9 +108,11 @@ export const NCBI_ID_INPUT_ERRORS = [
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},
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];
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/**
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* Failure modes the Unpaywall service layer can surface.
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* `getUnpaywallService()`
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*
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* Failure modes the Unpaywall service layer can surface. A tool whose handler
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* lets `getUnpaywallService()` failures propagate spreads these into its
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* `errors[]`. None does today: `pubmed_fetch_fulltext`, the only consumer,
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* folds every Unpaywall failure into its tier chain, so the entries serve the
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* service's own `recoveryFor` hints.
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*/
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export const UNPAYWALL_SERVICE_ERRORS = [
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{
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{"version":3,"file":"error-contracts.js","sourceRoot":"","sources":["../../src/services/error-contracts.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;GAqBG;AAEH,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAEjE;;;;GAIG;AACH,MAAM,CAAC,MAAM,mBAAmB,GAAG;IACjC;QACE,MAAM,EAAE,YAAY;QACpB,IAAI,EAAE,gBAAgB,CAAC,WAAW;QAClC,IAAI,EAAE,gLAAgL;QACtL,QAAQ,EACN,iIAAiI;QACnI,SAAS,EAAE,IAAI;QACf,QAAQ,EAAE,SAAS;KACpB;IACD;QACE,MAAM,EAAE,kBAAkB;QAC1B,IAAI,EAAE,gBAAgB,CAAC,kBAAkB;QACzC,IAAI,EAAE,2DAA2D;QACjE,QAAQ,EAAE,4EAA4E;QACtF,SAAS,EAAE,IAAI;QACf,QAAQ,EAAE,SAAS;KACpB;IACD;QACE,MAAM,EAAE,wBAAwB;QAChC,IAAI,EAAE,gBAAgB,CAAC,OAAO;QAC9B,IAAI,EAAE,iEAAiE;QACvE,QAAQ,EAAE,+DAA+D;QACzE,SAAS,EAAE,IAAI;QACf,QAAQ,EAAE,SAAS;KACpB;IACD;QACE,MAAM,EAAE,uBAAuB;QAC/B,IAAI,EAAE,gBAAgB,CAAC,kBAAkB;QACzC,IAAI,EAAE,mEAAmE;QACzE,QAAQ,EAAE,iFAAiF;QAC3F,SAAS,EAAE,IAAI;QACf,QAAQ,EAAE,SAAS;KACpB;IACD;QACE,MAAM,EAAE,yBAAyB;QACjC,IAAI,EAAE,gBAAgB,CAAC,QAAQ;QAC/B,IAAI,EAAE,uEAAuE;QAC7E,QAAQ,EACN,gGAAgG;QAClG,SAAS,EAAE,KAAK;QAChB,QAAQ,EAAE,SAAS;KACpB;CACO,CAAC;AAEX;;;;;;;;;;GAUG;AACH,MAAM,CAAC,MAAM,uBAAuB,GAAG;IACrC;QACE,MAAM,EAAE,aAAa;QACrB,IAAI,EAAE,gBAAgB,CAAC,eAAe;QACtC,IAAI,EAAE,oTAAoT;QAC1T,QAAQ,EACN,8JAA8J;QAChK,SAAS,EAAE,KAAK;KACjB;CACO,CAAC;AAEX;;;;;;;;;GASG;AACH,MAAM,CAAC,MAAM,oBAAoB,GAAG;IAClC;QACE,MAAM,EAAE,cAAc;QACtB,IAAI,EAAE,gBAAgB,CAAC,eAAe;QACtC,IAAI,EAAE,0LAA0L;QAChM,QAAQ,EACN,uHAAuH;QACzH,SAAS,EAAE,KAAK;KACjB;CACO,CAAC;AAEX
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{"version":3,"file":"error-contracts.js","sourceRoot":"","sources":["../../src/services/error-contracts.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;GAqBG;AAEH,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAEjE;;;;GAIG;AACH,MAAM,CAAC,MAAM,mBAAmB,GAAG;IACjC;QACE,MAAM,EAAE,YAAY;QACpB,IAAI,EAAE,gBAAgB,CAAC,WAAW;QAClC,IAAI,EAAE,gLAAgL;QACtL,QAAQ,EACN,iIAAiI;QACnI,SAAS,EAAE,IAAI;QACf,QAAQ,EAAE,SAAS;KACpB;IACD;QACE,MAAM,EAAE,kBAAkB;QAC1B,IAAI,EAAE,gBAAgB,CAAC,kBAAkB;QACzC,IAAI,EAAE,2DAA2D;QACjE,QAAQ,EAAE,4EAA4E;QACtF,SAAS,EAAE,IAAI;QACf,QAAQ,EAAE,SAAS;KACpB;IACD;QACE,MAAM,EAAE,wBAAwB;QAChC,IAAI,EAAE,gBAAgB,CAAC,OAAO;QAC9B,IAAI,EAAE,iEAAiE;QACvE,QAAQ,EAAE,+DAA+D;QACzE,SAAS,EAAE,IAAI;QACf,QAAQ,EAAE,SAAS;KACpB;IACD;QACE,MAAM,EAAE,uBAAuB;QAC/B,IAAI,EAAE,gBAAgB,CAAC,kBAAkB;QACzC,IAAI,EAAE,mEAAmE;QACzE,QAAQ,EAAE,iFAAiF;QAC3F,SAAS,EAAE,IAAI;QACf,QAAQ,EAAE,SAAS;KACpB;IACD;QACE,MAAM,EAAE,yBAAyB;QACjC,IAAI,EAAE,gBAAgB,CAAC,QAAQ;QAC/B,IAAI,EAAE,uEAAuE;QAC7E,QAAQ,EACN,gGAAgG;QAClG,SAAS,EAAE,KAAK;QAChB,QAAQ,EAAE,SAAS;KACpB;CACO,CAAC;AAEX;;;;;;;;;;GAUG;AACH,MAAM,CAAC,MAAM,uBAAuB,GAAG;IACrC;QACE,MAAM,EAAE,aAAa;QACrB,IAAI,EAAE,gBAAgB,CAAC,eAAe;QACtC,IAAI,EAAE,oTAAoT;QAC1T,QAAQ,EACN,8JAA8J;QAChK,SAAS,EAAE,KAAK;KACjB;CACO,CAAC;AAEX;;;;;;;;;GASG;AACH,MAAM,CAAC,MAAM,oBAAoB,GAAG;IAClC;QACE,MAAM,EAAE,cAAc;QACtB,IAAI,EAAE,gBAAgB,CAAC,eAAe;QACtC,IAAI,EAAE,0LAA0L;QAChM,QAAQ,EACN,uHAAuH;QACzH,SAAS,EAAE,KAAK;KACjB;CACO,CAAC;AAEX;;;;;;GAMG;AACH,MAAM,CAAC,MAAM,wBAAwB,GAAG;IACtC;QACE,MAAM,EAAE,uBAAuB;QAC/B,IAAI,EAAE,gBAAgB,CAAC,kBAAkB;QACzC,IAAI,EAAE,qEAAqE;QAC3E,QAAQ,EACN,gGAAgG;QAClG,SAAS,EAAE,IAAI;QACf,QAAQ,EAAE,SAAS;KACpB;CACO,CAAC;AAEX;;;;GAIG;AACH,MAAM,CAAC,MAAM,uBAAuB,GAAG;IACrC;QACE,MAAM,EAAE,sBAAsB;QAC9B,IAAI,EAAE,gBAAgB,CAAC,kBAAkB;QACzC,IAAI,EAAE,oDAAoD;QAC1D,QAAQ,EACN,4FAA4F;QAC9F,SAAS,EAAE,IAAI;QACf,QAAQ,EAAE,SAAS;KACpB;IACD;QACE,MAAM,EAAE,2BAA2B;QACnC,IAAI,EAAE,gBAAgB,CAAC,kBAAkB;QACzC,IAAI,EAAE,mEAAmE;QACzE,QAAQ,EAAE,qFAAqF;QAC/F,SAAS,EAAE,IAAI;QACf,QAAQ,EAAE,SAAS;KACpB;CACO,CAAC;AAEX;;;;GAIG;AACH,MAAM,CAAC,MAAM,wBAAwB,GAAG;IACtC;QACE,MAAM,EAAE,uBAAuB;QAC/B,IAAI,EAAE,gBAAgB,CAAC,kBAAkB;QACzC,IAAI,EAAE,qKAAqK;QAC3K,QAAQ,EACN,iGAAiG;QACnG,SAAS,EAAE,IAAI;QACf,QAAQ,EAAE,SAAS;KACpB;IACD;QACE,MAAM,EAAE,4BAA4B;QACpC,IAAI,EAAE,gBAAgB,CAAC,kBAAkB;QACzC,IAAI,EAAE,4EAA4E;QAClF,QAAQ,EACN,uFAAuF;QACzF,SAAS,EAAE,IAAI;QACf,QAAQ,EAAE,SAAS;KACpB;IACD;QACE,MAAM,EAAE,yBAAyB;QACjC,IAAI,EAAE,gBAAgB,CAAC,eAAe;QACtC,IAAI,EAAE,iOAAiO;QACvO,QAAQ,EACN,qHAAqH;QACvH,SAAS,EAAE,KAAK;QAChB,QAAQ,EAAE,SAAS;KACpB;CACO,CAAC;AAaX,MAAM,kBAAkB,GAAG,IAAI,GAAG,CAChC;IACE,GAAG,mBAAmB;IACtB,GAAG,wBAAwB;IAC3B,GAAG,wBAAwB;IAC3B,GAAG,uBAAuB;CAC3B,CAAC,GAAG,CAAC,CAAC,KAAK,EAAE,EAAE,CAAC,CAAC,KAAK,CAAC,MAAM,EAAE,KAAK,CAAC,QAAQ,CAAC,CAAC,CACjD,CAAC;AAEF;;;;;;;;;;;;GAYG;AACH,MAAM,UAAU,WAAW,CAAC,MAA0B;IACpD,MAAM,IAAI,GAAG,kBAAkB,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC;IAC5C,IAAI,IAAI,KAAK,SAAS,EAAE,CAAC;QACvB,MAAM,IAAI,KAAK,CAAC,wDAAwD,MAAM,GAAG,CAAC,CAAC;IACrF,CAAC;IACD,OAAO,EAAE,QAAQ,EAAE,EAAE,IAAI,EAAE,EAAE,CAAC;AAChC,CAAC"}
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* from the same `ORDERED_XML_PARSER_OPTIONS` NCBI's ordered parser uses, so
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*
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* Europe PMC's intermittent empty `{ version }` envelope is retried like an
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* @module src/services/europe-pmc/europe-pmc-service
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import { type Pacer } from '@cyanheads/mcp-ts-core/utils';
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import type { JatsNode } from '../ncbi/parsing/pmc-xml-helpers.js';
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import { EuropePmcApiClient } from './api-client.js';
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import { EuropePmcRequestQueue } from './request-queue.js';
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import type { EuropePmcFullTextResult, EuropePmcRecordRef, EuropePmcRelatedResult, EuropePmcSearchHit, EuropePmcSearchParams, EuropePmcSearchResult, EuropePmcSource } from './types.js';
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* - `citations()` / `references()` — EPMC's link graph for a PubMed article.
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export declare class EuropePmcService {
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constructor(client: EuropePmcApiClient, queue: Pacer, maxRetries: number);
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* Search Europe PMC. Cursor-based pagination — pass `cursorMark: '*'` (or
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{"version":3,"file":"europe-pmc-service.d.ts","sourceRoot":"","sources":["../../../src/services/europe-pmc/europe-pmc-service.ts"],"names":[],"mappings":"AAAA
|
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1
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+
{"version":3,"file":"europe-pmc-service.d.ts","sourceRoot":"","sources":["../../../src/services/europe-pmc/europe-pmc-service.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;GAwBG;AASH,OAAO,EAGL,KAAK,KAAK,EAGX,MAAM,8BAA8B,CAAC;AAOtC,OAAO,KAAK,EAAE,QAAQ,EAAgB,MAAM,4CAA4C,CAAC;AAEzF,OAAO,EAAoB,kBAAkB,EAAE,MAAM,iBAAiB,CAAC;AAEvE,OAAO,KAAK,EACV,uBAAuB,EAEvB,kBAAkB,EAElB,sBAAsB,EACtB,kBAAkB,EAClB,qBAAqB,EAErB,qBAAqB,EACrB,eAAe,EAChB,MAAM,YAAY,CAAC;AA2FpB;;;;;;;;;;GAUG;AACH,qBAAa,gBAAgB;IAIzB,OAAO,CAAC,QAAQ,CAAC,MAAM;IACvB,OAAO,CAAC,QAAQ,CAAC,KAAK;IACtB,OAAO,CAAC,QAAQ,CAAC,UAAU;IAL7B,OAAO,CAAC,QAAQ,CAAC,gBAAgB,CAAY;IAE7C,YACmB,MAAM,EAAE,kBAAkB,EAC1B,KAAK,EAAE,KAAK,EACZ,UAAU,EAAE,MAAM,EAQpC;IAED;;;;;;;OAOG;IACH,MAAM,CAAC,MAAM,EAAE,qBAAqB,GAAG,OAAO,CAAC,qBAAqB,CAAC,CAIpE;IAED;;;;OAIG;YACW,UAAU;IAwHxB;;;;;;;;;;OAUG;IACG,YAAY,CAChB,IAAI,EAAE,SAAS,kBAAkB,EAAE,EACnC,MAAM,CAAC,EAAE,WAAW,GACnB,OAAO,CAAC,kBAAkB,EAAE,CAAC,CAQ/B;IAED;;;;;;;OAOG;IACG,WAAW,CACf,MAAM,EAAE,MAAM,EACd,MAAM,EAAE,eAAe,EACvB,MAAM,CAAC,EAAE,WAAW,GACnB,OAAO,CAAC,uBAAuB,CAAC,CASlC;IAED;;;;;;;;;;OAUG;IACH,SAAS,CACP,IAAI,EAAE,MAAM,EACZ,QAAQ,EAAE,MAAM,EAChB,IAAI,EAAE,MAAM,EACZ,MAAM,CAAC,EAAE,WAAW,GACnB,OAAO,CAAC,sBAAsB,CAAC,CAQjC;IAED;;;;;;;;;;OAUG;IACH,UAAU,CACR,IAAI,EAAE,MAAM,EACZ,QAAQ,EAAE,MAAM,EAChB,IAAI,EAAE,MAAM,EACZ,MAAM,CAAC,EAAE,WAAW,GACnB,OAAO,CAAC,sBAAsB,CAAC,CAQjC;IAED;;;;;OAKG;YACW,iBAAiB;IAkE/B;;;;;;;;OAQG;IACH,gBAAgB,CAAC,GAAG,EAAE,MAAM,GAAG,QAAQ,GAAG,SAAS,CA8BlD;IAED;;;;;;;;;;OAUG;YACW,QAAQ;CA0CvB;AAMD;;;;GAIG;AACH,wBAAgB,oBAAoB,IAAI,IAAI,CAyB3C;AAED,6EAA6E;AAC7E,wBAAgB,mBAAmB,IAAI,gBAAgB,GAAG,SAAS,CAElE"}
|
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@@ -7,6 +7,10 @@
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* from the same `ORDERED_XML_PARSER_OPTIONS` NCBI's ordered parser uses, so
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* `parsePmcArticle` consumes the result without modification.
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*
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* Every call runs as a retry loop around the shared request queue: each attempt
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* concurrency slot, so callers backing off never stall the calls behind them.
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*
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* A search's retry boundary covers fetch and response classification, so
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* Europe PMC's intermittent empty `{ version }` envelope is retried like an
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* HTTP outage; only a sort or cursor that explains it is reported as bad input.
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@@ -19,8 +23,8 @@
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*
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* @module src/services/europe-pmc/europe-pmc-service
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*/
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import {
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import { defaultIsTransient, logger, requestContextService } from '@cyanheads/mcp-ts-core/utils';
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import { JsonRpcErrorCode, McpError, serializationError, serviceUnavailable, validationError, } from '@cyanheads/mcp-ts-core/errors';
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import { defaultIsTransient, logger, requestContextService, withRetry, } from '@cyanheads/mcp-ts-core/utils';
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// biome-ignore lint/suspicious/noDeprecatedImports: staying on in-tree XMLValidator — see ncbi/response-handler.ts
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import { XMLParser, XMLValidator } from 'fast-xml-parser';
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import { getServerConfig } from '../../config/server-config.js';
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@@ -28,24 +32,38 @@ import { recoveryFor } from '../error-contracts.js';
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import { ORDERED_XML_PARSER_OPTIONS } from '../ncbi/parsing/ordered-xml-parser-options.js';
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import { ensureArray } from '../ncbi/parsing/xml-helpers.js';
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import { buildSearchQuery, EuropePmcApiClient } from './api-client.js';
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import {
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import { createEuropePmcRequestQueue } from './request-queue.js';
|
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/** Ceiling on one backoff sleep, so a high retry count cannot grow it without bound. */
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/**
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* Retry gate: the framework's transient set, narrowed to `McpError`s. The client
|
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* classifies every upstream failure, so a plain `Error` reaching the loop is a defect
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* or a response that cannot parse — retrying it only repeats it.
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*/
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const isTransient = (error) => error instanceof McpError && defaultIsTransient(error);
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/**
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* Reshapes an error whose retries ran out: the last attempt's code and message with
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* the attempt count appended, `label`, `attempts`, and the upstream `retryAfter`, so a
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* 429 still tells the caller how long to wait. Only a `ServiceUnavailable` gains
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* `europepmc_unreachable` and its hint; a `Timeout` or `RateLimited` keeps its code
|
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* with no reason, as the NCBI service reports them. Anything never retried — a
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* through unchanged.
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*/
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function toServiceError(error, label) {
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if (!(error instanceof McpError) || typeof error.data?.retryAttempts !== 'number')
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return error;
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const last = error.cause instanceof McpError ? error.cause : error;
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const attempts = error.data.retryAttempts;
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return new McpError(error.code, `${last.message} (failed after ${attempts} attempts)`, {
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reason: 'europepmc_unreachable',
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...recoveryFor('europepmc_unreachable'),
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}),
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label,
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attempts,
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...(last.data?.retryAfter !== undefined && { retryAfter: last.data.retryAfter }),
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}, { cause: last });
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}
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/**
|
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* Europe PMC lookup clause for one record addressed by `source` + EPMC id.
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@@ -99,7 +117,8 @@ function sortExplainsEnvelope(sort) {
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* - `citations()` / `references()` — EPMC's link graph for a PubMed article.
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*
|
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* All honor `ctx.signal` for cancellation and retry transient failures with
|
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* capped exponential backoff plus jitter
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* capped exponential backoff plus jitter, each attempt paced through the shared
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* request queue.
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*/
|
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export class EuropePmcService {
|
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105
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client;
|
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@@ -126,7 +145,7 @@ export class EuropePmcService {
|
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126
145
|
* rather than surfacing after the loop has already returned. (#159)
|
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|
*/
|
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search(params) {
|
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return this.
|
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|
+
return this.runPaced('search', params.signal, (attempt) => this.searchOnce(params, attempt === this.maxRetries + 1));
|
|
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|
}
|
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|
/**
|
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151
|
* One search attempt: fetch, parse, and classify the body. `isLastAttempt`
|
|
@@ -256,7 +275,7 @@ export class EuropePmcService {
|
|
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256
275
|
* publishes no fullTextXML (404 or empty body).
|
|
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|
*/
|
|
258
277
|
async fullTextXml(epmcId, source, signal) {
|
|
259
|
-
const outcome = await this.
|
|
278
|
+
const outcome = await this.runPaced(`fullTextXml(${epmcId})`, signal, () => this.client.fullTextXml(epmcId, signal));
|
|
260
279
|
if (outcome.kind === 'not-available') {
|
|
261
280
|
return { kind: 'not-available', reason: outcome.reason };
|
|
262
281
|
}
|
|
@@ -297,7 +316,7 @@ export class EuropePmcService {
|
|
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297
316
|
* upstream row count and the PubMed-addressable set they actually get back.
|
|
298
317
|
*/
|
|
299
318
|
async fetchRelatedLinks(fetch, kind, pmid, extractRecords, signal) {
|
|
300
|
-
const text = await this.
|
|
319
|
+
const text = await this.runPaced(`${kind}(${pmid})`, signal, fetch);
|
|
301
320
|
let parsed;
|
|
302
321
|
try {
|
|
303
322
|
parsed = JSON.parse(text);
|
|
@@ -385,53 +404,49 @@ export class EuropePmcService {
|
|
|
385
404
|
return nodes.find((n) => 'article' in n);
|
|
386
405
|
}
|
|
387
406
|
/**
|
|
388
|
-
*
|
|
389
|
-
*
|
|
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|
-
*
|
|
391
|
-
* the
|
|
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|
-
*
|
|
393
|
-
*
|
|
394
|
-
*
|
|
395
|
-
*
|
|
407
|
+
* Runs one Europe PMC call: a retry loop around the shared request queue, so
|
|
408
|
+
* every attempt re-queues and is re-paced, and a backoff sleep holds no queue
|
|
409
|
+
* slot. No service-level deadline — Europe PMC requests are cheap individually
|
|
410
|
+
* and the caller's signal (typically `ctx.signal`) bounds the total chain; that
|
|
411
|
+
* signal reaches the queue wait and the backoff sleep. `execute` receives the
|
|
412
|
+
* one-based attempt number.
|
|
413
|
+
*
|
|
414
|
+
* A caller abort rethrows the caller's own reason; an exhausted failure is
|
|
415
|
+
* reshaped by {@link toServiceError}, after the loop.
|
|
396
416
|
*/
|
|
397
|
-
async
|
|
398
|
-
|
|
417
|
+
async runPaced(label, signal, execute) {
|
|
418
|
+
let attempt = 0;
|
|
419
|
+
try {
|
|
420
|
+
return await withRetry(({ signal: attemptSignal }) => {
|
|
421
|
+
const current = ++attempt;
|
|
422
|
+
return this.queue
|
|
423
|
+
.run(() => execute(current), { signal: attemptSignal })
|
|
424
|
+
.catch((error) => {
|
|
425
|
+
if (current <= this.maxRetries && isTransient(error)) {
|
|
426
|
+
logger.warning(`Europe PMC ${label} failed on attempt ${current} of ${this.maxRetries + 1}.`, requestContextService.createRequestContext({
|
|
427
|
+
operation: 'EuropePmcRetry',
|
|
428
|
+
additionalContext: {
|
|
429
|
+
label,
|
|
430
|
+
attempt: current,
|
|
431
|
+
error: error instanceof Error ? error.message : String(error),
|
|
432
|
+
},
|
|
433
|
+
}));
|
|
434
|
+
}
|
|
435
|
+
throw error;
|
|
436
|
+
});
|
|
437
|
+
}, {
|
|
438
|
+
maxRetries: this.maxRetries,
|
|
439
|
+
maxDelayMs: MAX_BACKOFF_MS,
|
|
440
|
+
isTransient,
|
|
441
|
+
operation: `Europe PMC ${label}`,
|
|
442
|
+
...(signal && { signal }),
|
|
443
|
+
});
|
|
444
|
+
}
|
|
445
|
+
catch (error) {
|
|
399
446
|
if (signal?.aborted)
|
|
400
447
|
throw signal.reason;
|
|
401
|
-
|
|
402
|
-
return await execute(attempt);
|
|
403
|
-
}
|
|
404
|
-
catch (error) {
|
|
405
|
-
if (signal?.aborted)
|
|
406
|
-
throw signal.reason;
|
|
407
|
-
if (!(error instanceof McpError))
|
|
408
|
-
throw error;
|
|
409
|
-
if (!defaultIsTransient(error))
|
|
410
|
-
throw error;
|
|
411
|
-
if (attempt < this.maxRetries) {
|
|
412
|
-
const baseDelay = Math.min(1000 * 2 ** attempt, MAX_BACKOFF_MS);
|
|
413
|
-
const jitter = baseDelay * (0.75 + 0.5 * Math.random());
|
|
414
|
-
const retryDelay = Math.round(jitter);
|
|
415
|
-
logger.warning(`Europe PMC ${label} failed. Retrying (${attempt + 1}/${this.maxRetries}) in ${retryDelay}ms.`, requestContextService.createRequestContext({
|
|
416
|
-
operation: 'EuropePmcRetry',
|
|
417
|
-
additionalContext: { label, attempt: attempt + 1, retryDelay },
|
|
418
|
-
}));
|
|
419
|
-
await abortableSleep(retryDelay, signal);
|
|
420
|
-
continue;
|
|
421
|
-
}
|
|
422
|
-
const attempts = this.maxRetries + 1;
|
|
423
|
-
throw new McpError(error.code, `${error.message} (failed after ${attempts} attempts)`, {
|
|
424
|
-
...(error.code === JsonRpcErrorCode.ServiceUnavailable && {
|
|
425
|
-
reason: 'europepmc_unreachable',
|
|
426
|
-
...recoveryFor('europepmc_unreachable'),
|
|
427
|
-
}),
|
|
428
|
-
label,
|
|
429
|
-
attempts,
|
|
430
|
-
...(error.data?.retryAfter !== undefined && { retryAfter: error.data.retryAfter }),
|
|
431
|
-
}, { cause: error });
|
|
432
|
-
}
|
|
448
|
+
throw toServiceError(error, label);
|
|
433
449
|
}
|
|
434
|
-
throw internalError('Europe PMC request failed after all retries.', { label });
|
|
435
450
|
}
|
|
436
451
|
}
|
|
437
452
|
// ─── Init / Accessor ────────────────────────────────────────────────────────
|
|
@@ -451,7 +466,7 @@ export function initEuropePmcService() {
|
|
|
451
466
|
timeoutMs: config.europepmcTimeoutMs,
|
|
452
467
|
...(config.europepmcEmail && { email: config.europepmcEmail }),
|
|
453
468
|
});
|
|
454
|
-
const queue =
|
|
469
|
+
const queue = createEuropePmcRequestQueue(config.europepmcRequestDelayMs);
|
|
455
470
|
_service = new EuropePmcService(client, queue, config.europepmcMaxRetries);
|
|
456
471
|
logger.info('Europe PMC service initialized.', requestContextService.createRequestContext({
|
|
457
472
|
operation: 'EuropePmcInit',
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
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+
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@@ -1,33 +1,17 @@
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1
1
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/**
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2
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* @fileoverview
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3
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-
* concurrent in-flight requests and
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4
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-
*
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5
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-
*
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6
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-
*
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2
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+
* @fileoverview Request queue for Europe PMC calls, built on the framework pacer.
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3
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* Caps concurrent in-flight requests and spaces request starts to stay polite with
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4
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* EBI's infrastructure, and releases a waiting caller the moment its signal aborts.
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5
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* Each retry attempt re-enters the queue, so a backoff sleep holds no slot and every
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* @module src/services/europe-pmc/request-queue
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import { type Pacer } from '@cyanheads/mcp-ts-core/utils';
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* Creates the pacer every Europe PMC call runs through. No queue-depth cap and no
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export declare
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private readonly waiters;
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constructor(minStartGapMs: number, maxConcurrent?: number);
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enqueue<T>(task: () => Promise<T>, label: string, signal?: AbortSignal): Promise<T>;
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private tryDispatch;
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export declare function createEuropePmcRequestQueue(minStartGapMs: number): Pacer;
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{"version":3,"file":"request-queue.d.ts","sourceRoot":"","sources":["../../../src/services/europe-pmc/request-queue.ts"],"names":[],"mappings":"AAAA
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{"version":3,"file":"request-queue.d.ts","sourceRoot":"","sources":["../../../src/services/europe-pmc/request-queue.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAe,KAAK,KAAK,EAAE,MAAM,8BAA8B,CAAC;AAQvE;;;;GAIG;AACH,wBAAgB,2BAA2B,CAAC,aAAa,EAAE,MAAM,GAAG,KAAK,CAExE"}
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/**
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* @fileoverview
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* concurrent in-flight requests and
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* @fileoverview Request queue for Europe PMC calls, built on the framework pacer.
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* EBI's infrastructure, and releases a waiting caller the moment its signal aborts.
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* Each retry attempt re-enters the queue, so a backoff sleep holds no slot and every
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import {
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import { createPacer } from '@cyanheads/mcp-ts-core/utils';
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/**
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*
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* requests. Decouples concurrency from rate so slow upstream responses
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* rejects immediately instead of sitting behind a saturated worker.
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* Europe PMC requests in flight at once. `pubmed_fetch_fulltext` fans its Europe PMC
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* tier out over every candidate in parallel and relies on this cap to bound it.
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this.minStartGapMs = minStartGapMs;
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enqueue(task, label, signal) {
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}
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const waiter = {
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resolve,
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reject,
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task,
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label,
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};
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return;
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reject(signal.reason);
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waiter.onAbort = onAbort;
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signal.addEventListener('abort', onAbort, { once: true });
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}
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this.tryDispatch();
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}
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tryDispatch() {
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}, gap);
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return;
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}
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this.lastStartTime = Date.now();
|
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this.inFlight += 1;
|
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|
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logger.debug(`Executing Europe PMC request via queue: ${waiter.label}`, requestContextService.createRequestContext({
|
|
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|
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operation: 'EuropePmcQueueDispatch',
|
|
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|
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additionalContext: {
|
|
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label: waiter.label,
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inFlight: this.inFlight,
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queueDepth: this.waiters.length,
|
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},
|
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}));
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Promise.resolve()
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.then(() => waiter.task())
|
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.then(waiter.resolve, (err) => {
|
|
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|
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logger.error('Error processing Europe PMC request from queue.', requestContextService.createRequestContext({
|
|
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|
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operation: 'EuropePmcQueueProcess',
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additionalContext: {
|
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label: waiter.label,
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errorMessage: err instanceof Error ? err.message : String(err),
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},
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}));
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waiter.reject(err);
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})
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.finally(() => {
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|
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this.inFlight -= 1;
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this.tryDispatch();
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});
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}
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}
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|
+
const MAX_CONCURRENT = 4;
|
|
16
|
+
/**
|
|
17
|
+
* Creates the pacer every Europe PMC call runs through. No queue-depth cap and no
|
|
18
|
+
* wait budget: a caller waits for its turn rather than being shed, so the pacer never
|
|
19
|
+
* rejects on its own — only the caller's signal ends a wait early.
|
|
20
|
+
*/
|
|
21
|
+
export function createEuropePmcRequestQueue(minStartGapMs) {
|
|
22
|
+
return createPacer({ name: 'europepmc', minStartGapMs, maxConcurrent: MAX_CONCURRENT });
|
|
110
23
|
}
|
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//# sourceMappingURL=request-queue.js.map
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@@ -1 +1 @@
|
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|
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{"version":3,"file":"request-queue.js","sourceRoot":"","sources":["../../../src/services/europe-pmc/request-queue.ts"],"names":[],"mappings":"AAAA
|
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|
+
{"version":3,"file":"request-queue.js","sourceRoot":"","sources":["../../../src/services/europe-pmc/request-queue.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAE,WAAW,EAAc,MAAM,8BAA8B,CAAC;AAEvE;;;GAGG;AACH,MAAM,cAAc,GAAG,CAAC,CAAC;AAEzB;;;;GAIG;AACH,MAAM,UAAU,2BAA2B,CAAC,aAAqB;IAC/D,OAAO,WAAW,CAAC,EAAE,IAAI,EAAE,WAAW,EAAE,aAAa,EAAE,aAAa,EAAE,cAAc,EAAE,CAAC,CAAC;AAC1F,CAAC"}
|
|
@@ -23,6 +23,14 @@ export declare function extractJatsAuthors(contribGroup: JatsNode | undefined):
|
|
|
23
23
|
* reads as an article with no body at all. Legacy
|
|
24
24
|
* `<preformat preformat-type="pmc-ocr-text">` deposits, which put the entire
|
|
25
25
|
* article in one such element, are the case that matters. (#130)
|
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+
*
|
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|
+
* A body-level block that carries a title of its own — a `<def-list>` or
|
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|
+
* `<list>` `<title>`, a `<boxed-text>` `<caption>` title — forms a section of
|
|
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|
+
* its own under that title, and the title leaves the block's text. PMC13546078
|
|
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|
+
* opens its `<body>` with its abbreviations `<def-list>` this way; reporting it
|
|
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|
+
* as an untitled section left `content[]` with no heading to separate the list
|
|
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|
+
* from the abstract above it. Untitled blocks on either side of it are not its
|
|
33
|
+
* content and stay in untitled sections of their own. (#148)
|
|
26
34
|
*/
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|
27
35
|
export declare function extractBodySections(body: JatsNode | undefined): ParsedPmcSection[];
|
|
28
36
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/**
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|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"pmc-article-parser.d.ts","sourceRoot":"","sources":["../../../../src/services/ncbi/parsing/pmc-article-parser.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,KAAK,EACV,gBAAgB,EAChB,cAAc,EAEd,eAAe,EAEf,kBAAkB,EAClB,gBAAgB,EAChB,cAAc,EAEf,MAAM,aAAa,CAAC;AACrB,OAAO,EAOL,KAAK,QAAQ,EAQd,MAAM,sBAAsB,CAAC;AAwH9B,iGAAiG;AACjG,wBAAgB,kBAAkB,CAAC,YAAY,EAAE,QAAQ,GAAG,SAAS,GAAG,eAAe,EAAE,CA2BxF;
|
|
1
|
+
{"version":3,"file":"pmc-article-parser.d.ts","sourceRoot":"","sources":["../../../../src/services/ncbi/parsing/pmc-article-parser.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,KAAK,EACV,gBAAgB,EAChB,cAAc,EAEd,eAAe,EAEf,kBAAkB,EAClB,gBAAgB,EAChB,cAAc,EAEf,MAAM,aAAa,CAAC;AACrB,OAAO,EAOL,KAAK,QAAQ,EAQd,MAAM,sBAAsB,CAAC;AAwH9B,iGAAiG;AACjG,wBAAgB,kBAAkB,CAAC,YAAY,EAAE,QAAQ,GAAG,SAAS,GAAG,eAAe,EAAE,CA2BxF;AA4fD;;;;;;;;;;;;;;;;;;;;GAoBG;AACH,wBAAgB,mBAAmB,CAAC,IAAI,EAAE,QAAQ,GAAG,SAAS,GAAG,gBAAgB,EAAE,CA+BlF;AA4HD;;;;;;;;;;;;;;;;;;GAkBG;AACH,wBAAgB,gBAAgB,CAAC,IAAI,EAAE,QAAQ,GAAG,SAAS,GAAG,cAAc,EAAE,CAO7E;AAoFD;;;;;;;;GAQG;AACH,eAAO,MAAM,iBAAiB,MAAM,CAAC;AAmGrC;;;;;;;;;;;GAWG;AACH,wBAAgB,gBAAgB,CAAC,IAAI,EAAE,QAAQ,GAAG,SAAS,GAAG,cAAc,EAAE,CAQ7E;AAwND;;;;;;;;;;;;;;;;GAgBG;AACH,wBAAgB,iBAAiB,CAAC,IAAI,EAAE,QAAQ,GAAG,SAAS,GAAG,kBAAkB,EAAE,CAsClF;AAID;;;;;GAKG;AACH,wBAAgB,eAAe,CAAC,WAAW,EAAE,QAAQ,GAAG,gBAAgB,CA+CvE"}
|