paper-search-cli - npm Package Compare versions

Comparing version 0.3.0 to 0.3.1

dist/cli.js

@@ -627,2 +627,6 @@ #!/usr/bin/env node
         {
+            name: 'citation_expansion uses Semantic Scholar Graph API',
+            ok: capabilityProfile.entries.find(entry => entry.id === 'citation_expansion')?.configured.includes('semantic_scholar_graph') === true
+        },
+        {
             name: 'pdf_discovery has source groups',
@@ -629,0 +633,0 @@ ok: Boolean(capabilityProfile.entries.find(entry => entry.id === 'pdf_discovery')?.sourceGroups?.open_access_sources) &&

dist/cli.js.map

@@ -1,1 +0,1 @@
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dist/core/capabilityProfile.d.ts

 export type CapabilityStatus = 'available' | 'degraded' | 'unavailable';
 export interface CapabilityEntry {
-    id: 'metadata_search' | 'body_snippet_search' | 'journal_metrics' | 'pdf_discovery' | 'entitled_access';
+    id: 'metadata_search' | 'citation_expansion' | 'body_snippet_search' | 'journal_metrics' | 'pdf_discovery' | 'entitled_access';
     status: CapabilityStatus;
@@ -5,0 +5,0 @@ reason: string;

dist/core/capabilityProfile.d.ts.map

@@ -1,1 +0,1 @@
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+{"version":3,"file":"capabilityProfile.d.ts","sourceRoot":"","sources":["../../src/core/capabilityProfile.ts"],"names":[],"mappings":"AAEA,MAAM,MAAM,gBAAgB,GAAG,WAAW,GAAG,UAAU,GAAG,aAAa,CAAC;AAExE,MAAM,WAAW,eAAe;IAC9B,EAAE,EACE,iBAAiB,GACjB,oBAAoB,GACpB,qBAAqB,GACrB,iBAAiB,GACjB,eAAe,GACf,iBAAiB,CAAC;IACtB,MAAM,EAAE,gBAAgB,CAAC;IACzB,MAAM,EAAE,MAAM,CAAC;IACf,UAAU,EAAE,MAAM,EAAE,CAAC;IACrB,OAAO,EAAE,MAAM,EAAE,CAAC;IAClB,YAAY,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,EAAE,CAAC,CAAC;IACxC,YAAY,CAAC,EAAE,MAAM,EAAE,CAAC;IACxB,YAAY,CAAC,EAAE,MAAM,EAAE,CAAC;CACzB;AAED,MAAM,WAAW,iBAAiB;IAChC,EAAE,EAAE,OAAO,CAAC;IACZ,OAAO,EAAE,eAAe,EAAE,CAAC;IAC3B,OAAO,EAAE,MAAM,CAAC,MAAM,EAAE,gBAAgB,CAAC,CAAC;CAC3C;AAmDD,wBAAgB,sBAAsB,IAAI,iBAAiB,CAe1D"}

dist/core/capabilityProfile.js

@@ -52,2 +52,3 @@ import { CONFIG_KEYS, listConfigEntries } from '../config/ConfigService.js';
         metadataSearchEntry(configuredKeys),
+        citationExpansionEntry(),
         bodySnippetSearchEntry(configuredKeys),
@@ -81,2 +82,15 @@ journalMetricsEntry(configuredKeys),
 }
+function citationExpansionEntry() {
+    return {
+        id: 'citation_expansion',
+        status: 'available',
+        reason: 'Semantic Scholar Graph API citation expansion is available; SEMANTIC_SCHOLAR_API_KEY is optional for higher quota.',
+        configured: ['semantic_scholar_graph'],
+        missing: [],
+        sourceGroups: {
+            citation_sources: ['semantic_scholar_graph']
+        },
+        optionalKeys: ['SEMANTIC_SCHOLAR_API_KEY']
+    };
+}
 function bodySnippetSearchEntry(configuredKeys) {
@@ -83,0 +97,0 @@ const hasKey = configuredKeys.has('SEMANTIC_SCHOLAR_API_KEY');

dist/core/capabilityProfile.js.map

@@ -1,1 +0,1 @@
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dist/core/handleToolCall.d.ts.map

@@ -1,1 +0,1 @@
-{"version":3,"file":"handleToolCall.d.ts","sourceRoot":"","sources":["../../src/core/handleToolCall.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,gBAAgB,CAAC;AAiFhD,wBAAsB,cAAc,CAClC,WAAW,EAAE,MAAM,EACnB,OAAO,EAAE,OAAO,EAChB,SAAS,EAAE,SAAS;;;;;GAwpBrB"}
+{"version":3,"file":"handleToolCall.d.ts","sourceRoot":"","sources":["../../src/core/handleToolCall.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,gBAAgB,CAAC;AAmGhD,wBAAsB,cAAc,CAClC,WAAW,EAAE,MAAM,EACnB,OAAO,EAAE,OAAO,EAChB,SAAS,EAAE,SAAS;;;;;GAwqBrB"}

dist/core/handleToolCall.js

@@ -8,2 +8,3 @@ import { parseToolArgs } from './schemas.js';
 import { queryJournalMetrics } from '../services/JournalMetricsService.js';
+import CitationService from '../services/CitationService.js';
 import { withTimeout } from '../utils/SecurityUtils.js';
@@ -51,2 +52,20 @@ import { getGenericSearchToolPlatform, getPlatformMetadata, isPlatformAlias, resolvePlatformId } from './platformMetadata.js';
 }
+function resolveCitationTarget(args) {
+    if (args.paperId)
+        return args.paperId;
+    if (args.doi)
+        return `DOI:${args.doi}`;
+    if (args.arxivId)
+        return `ARXIV:${args.arxivId}`;
+    throw new Error('Provide paperId, doi, or arxivId');
+}
+function citationResponse(target, relation, papers) {
+    return {
+        target,
+        relation,
+        provider: 'semantic_scholar',
+        total: papers.length,
+        papers
+    };
+}
 async function handleGenericSearch(platform, args, searchers) {
@@ -184,2 +203,16 @@ const resolvedPlatform = resolvePlatformId(platform);
         }
+        case 'get_paper_citations': {
+            const target = resolveCitationTarget(args);
+            const service = new CitationService();
+            const papers = await service.getCitations(target, args.limit);
+            const result = citationResponse(target, 'citations', papers);
+            return jsonTextResponse(`Found ${papers.length} citing paper(s).\n\n${JSON.stringify(result, null, 2)}`);
+        }
+        case 'get_paper_references': {
+            const target = resolveCitationTarget(args);
+            const service = new CitationService();
+            const papers = await service.getReferences(target, args.limit);
+            const result = citationResponse(target, 'references', papers);
+            return jsonTextResponse(`Found ${papers.length} cited reference(s).\n\n${JSON.stringify(result, null, 2)}`);
+        }
         case 'search_iacr': {
@@ -186,0 +219,0 @@ const { query, maxResults, fetchDetails } = args;

dist/core/handleToolCall.js.map

@@ -1,1 +0,1 @@
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dist/core/schemas.d.ts

@@ -230,2 +230,28 @@ import { z } from 'zod';
 }>;
+export declare const CitationLookupSchema: z.ZodEffects<z.ZodObject<{
+    paperId: z.ZodOptional<z.ZodString>;
+    doi: z.ZodOptional<z.ZodString>;
+    arxivId: z.ZodOptional<z.ZodString>;
+    limit: z.ZodDefault<z.ZodOptional<z.ZodNumber>>;
+}, "strip", z.ZodTypeAny, {
+    limit: number;
+    paperId?: string | undefined;
+    doi?: string | undefined;
+    arxivId?: string | undefined;
+}, {
+    paperId?: string | undefined;
+    doi?: string | undefined;
+    limit?: number | undefined;
+    arxivId?: string | undefined;
+}>, {
+    limit: number;
+    paperId?: string | undefined;
+    doi?: string | undefined;
+    arxivId?: string | undefined;
+}, {
+    paperId?: string | undefined;
+    doi?: string | undefined;
+    limit?: number | undefined;
+    arxivId?: string | undefined;
+}>;
 export declare const SearchIACRSchema: z.ZodObject<{
@@ -562,4 +588,4 @@ query: z.ZodString;
 }>;
-export type ToolName = string | 'search_papers' | 'search_arxiv' | 'search_webofscience' | 'search_pubmed' | 'search_biorxiv' | 'search_medrxiv' | 'search_semantic_scholar' | 'search_semantic_snippets' | 'search_iacr' | 'download_paper' | 'search_google_scholar' | 'get_paper_by_doi' | 'search_scihub' | 'check_scihub_mirrors' | 'get_platform_status' | 'search_sciencedirect' | 'search_springer' | 'search_wiley' | 'search_scopus' | 'search_crossref' | 'search_openalex' | 'search_unpaywall' | 'search_pmc' | 'search_europepmc' | 'search_core' | 'search_openaire' | 'download_with_fallback' | 'query_journal_metrics';
+export type ToolName = string | 'search_papers' | 'search_arxiv' | 'search_webofscience' | 'search_pubmed' | 'search_biorxiv' | 'search_medrxiv' | 'search_semantic_scholar' | 'search_semantic_snippets' | 'get_paper_citations' | 'get_paper_references' | 'search_iacr' | 'download_paper' | 'search_google_scholar' | 'get_paper_by_doi' | 'search_scihub' | 'check_scihub_mirrors' | 'get_platform_status' | 'search_sciencedirect' | 'search_springer' | 'search_wiley' | 'search_scopus' | 'search_crossref' | 'search_openalex' | 'search_unpaywall' | 'search_pmc' | 'search_europepmc' | 'search_core' | 'search_openaire' | 'download_with_fallback' | 'query_journal_metrics';
 export declare function parseToolArgs(toolName: ToolName, args: unknown): any;
 //# sourceMappingURL=schemas.d.ts.map

dist/core/schemas.d.ts.map

@@ -1,1 +0,1 @@
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+{"version":3,"file":"schemas.d.ts","sourceRoot":"","sources":["../../src/core/schemas.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,CAAC,EAAE,MAAM,KAAK,CAAC;AAaxB,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAmC3B,CAAC;AAEL,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;EAUpB,CAAC;AAEX,eAAO,MAAM,wBAAwB;;;;;;;;;;;;;;;;;;;;;;;;EAY3B,CAAC;AAEX,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;EAUrB,CAAC;AAEX,eAAO,MAAM,mBAAmB;;;;;;;;;;;;;;;EAOtB,CAAC;AAEX,eAAO,MAAM,mBAAmB;;;;;;;;;;;;;;;EAAsB,CAAC;AAEvD,eAAO,MAAM,2BAA2B;;;;;;;;;;;;;;;EAO9B,CAAC;AAEX,eAAO,MAAM,4BAA4B;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAa/B,CAAC;AAEX,eAAO,MAAM,oBAAoB;;;;;;;;;;;;;;;;;;;;;;;;;EAU7B,CAAC;AAEL,eAAO,MAAM,gBAAgB;;;;;;;;;;;;EAMnB,CAAC;AAEX,eAAO,MAAM,mBAAmB;;;;;;;;;;;;EAQtB,CAAC;AAEX,eAAO,MAAM,yBAAyB;;;;;;;;;;;;;;;;;;EAQ5B,CAAC;AAEX,eAAO,MAAM,mBAAmB;;;;;;;;;EAmBtB,CAAC;AAEX,eAAO,MAAM,kBAAkB;;;;;;;;;;;;EAMrB,CAAC;AAEX,eAAO,MAAM,wBAAwB;;;;;;EAI3B,CAAC;AAEX,eAAO,MAAM,yBAAyB;;;;;;;;;;;;;;;;;;;;;EAS5B,CAAC;AAEX,eAAO,MAAM,oBAAoB;;;;;;;;;;;;;;;;;;;;;;;;;;;EAWvB,CAAC;AAEX,eAAO,MAAM,iBAAiB;;;;;;EAIpB,CAAC;AAEX,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAYrB,CAAC;AAEX,eAAO,MAAM,oBAAoB;;;;;;;;;;;;;;;;;;;;;EASvB,CAAC;AAEX,eAAO,MAAM,oBAAoB;;;;;;;;;;;;EAMvB,CAAC;AAEX,eAAO,MAAM,qBAAqB;;;;;;;;;EAKxB,CAAC;AAEX,eAAO,MAAM,oBAAoB;;;;;;;;;;;;EAMvB,CAAC;AAEX,eAAO,MAAM,gBAAgB;;;;;;;;;;;;;;;;;;;;EASzB,CAAC;AAEL,eAAO,MAAM,2BAA2B;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAa9B,CAAC;AAEX,eAAO,MAAM,0BAA0B;;;;;;;;;;;;;;;;;;;;;EAS7B,CAAC;AAEX,eAAO,MAAM,uBAAuB;;;;;;EAI1B,CAAC;AAEX,eAAO,MAAM,yBAAyB;;;;;;;;;;;;;;;;;;;;;;;;;EAUlC,CAAC;AAEL,MAAM,MAAM,QAAQ,GAChB,MAAM,GACN,eAAe,GACf,cAAc,GACd,qBAAqB,GACrB,eAAe,GACf,gBAAgB,GAChB,gBAAgB,GAChB,yBAAyB,GACzB,0BAA0B,GAC1B,qBAAqB,GACrB,sBAAsB,GACtB,aAAa,GACb,gBAAgB,GAChB,uBAAuB,GACvB,kBAAkB,GAClB,eAAe,GACf,sBAAsB,GACtB,qBAAqB,GACrB,sBAAsB,GACtB,iBAAiB,GACjB,cAAc,GACd,eAAe,GACf,iBAAiB,GACjB,iBAAiB,GACjB,kBAAkB,GAClB,YAAY,GACZ,kBAAkB,GAClB,aAAa,GACb,iBAAiB,GACjB,wBAAwB,GACxB,uBAAuB,CAAC;AAE5B,wBAAgB,aAAa,CAAC,QAAQ,EAAE,QAAQ,EAAE,IAAI,EAAE,OAAO,GAAG,GAAG,CAkEpE"}

dist/core/schemas.js

@@ -114,2 +114,13 @@ import { z } from 'zod';
     .strip();
+export const CitationLookupSchema = z
+    .object({
+    paperId: z.coerce.string().min(1).optional(),
+    doi: z.coerce.string().min(1).optional(),
+    arxivId: z.coerce.string().min(1).optional(),
+    limit: z.number().int().min(1).max(100).optional().default(100)
+})
+    .strip()
+    .refine(value => Boolean(value.paperId || value.doi || value.arxivId), {
+    message: 'Provide paperId, doi, or arxivId'
+});
 export const SearchIACRSchema = z
@@ -313,2 +324,5 @@ .object({
             return SearchSemanticSnippetsSchema.parse(args);
+        case 'get_paper_citations':
+        case 'get_paper_references':
+            return CitationLookupSchema.parse(args);
         case 'search_iacr':
@@ -315,0 +329,0 @@ return SearchIACRSchema.parse(args);

dist/core/schemas.js.map

@@ -1,1 +0,1 @@
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dist/core/tools.d.ts.map

@@ -1,1 +0,1 @@
-{"version":3,"file":"tools.d.ts","sourceRoot":"","sources":["../../src/core/tools.ts"],"names":[],"mappings":"AAEA,MAAM,WAAW,OAAO;IACtB,IAAI,EAAE,MAAM,CAAC;IACb,WAAW,EAAE,MAAM,CAAC;IACpB,WAAW,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;CACtC;AAusBD,eAAO,MAAM,KAAK,EAAE,OAAO,EAAoD,CAAC"}
+{"version":3,"file":"tools.d.ts","sourceRoot":"","sources":["../../src/core/tools.ts"],"names":[],"mappings":"AAEA,MAAM,WAAW,OAAO;IACtB,IAAI,EAAE,MAAM,CAAC;IACb,WAAW,EAAE,MAAM,CAAC;IACpB,WAAW,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;CACtC;AA+vBD,eAAO,MAAM,KAAK,EAAE,OAAO,EAAoD,CAAC"}

dist/core/tools.js

@@ -261,2 +261,56 @@ import { PLATFORM_METADATA, SEARCH_PLATFORM_VALUES } from './platformMetadata.js';
     {
+        name: 'get_paper_citations',
+        description: 'Get citing papers for a target paper using Semantic Scholar Graph API. Provide one of paperId, doi, or arxivId.',
+        inputSchema: {
+            type: 'object',
+            properties: {
+                paperId: {
+                    type: 'string',
+                    description: 'Semantic Scholar paper id or external id such as DOI:10.xxxx/xxxxx'
+                },
+                doi: {
+                    type: 'string',
+                    description: 'DOI for the target paper; converted to DOI:<doi>'
+                },
+                arxivId: {
+                    type: 'string',
+                    description: 'arXiv id for the target paper; converted to ARXIV:<id>'
+                },
+                limit: {
+                    type: 'number',
+                    minimum: 1,
+                    maximum: 100,
+                    description: 'Maximum number of citing papers to return. Default: 100'
+                }
+            }
+        }
+    },
+    {
+        name: 'get_paper_references',
+        description: 'Get cited references for a target paper using Semantic Scholar Graph API. Provide one of paperId, doi, or arxivId.',
+        inputSchema: {
+            type: 'object',
+            properties: {
+                paperId: {
+                    type: 'string',
+                    description: 'Semantic Scholar paper id or external id such as DOI:10.xxxx/xxxxx'
+                },
+                doi: {
+                    type: 'string',
+                    description: 'DOI for the target paper; converted to DOI:<doi>'
+                },
+                arxivId: {
+                    type: 'string',
+                    description: 'arXiv id for the target paper; converted to ARXIV:<id>'
+                },
+                limit: {
+                    type: 'number',
+                    minimum: 1,
+                    maximum: 100,
+                    description: 'Maximum number of cited references to return. Default: 100'
+                }
+            }
+        }
+    },
+    {
         name: 'search_iacr',
@@ -263,0 +317,0 @@ description: 'Search IACR ePrint Archive for cryptography papers',

dist/core/tools.js.map

@@ -1,1 +0,1 @@
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dist/platforms/BioRxivSearcher.d.ts.map

@@ -1,1 +0,1 @@
-{"version":3,"file":"BioRxivSearcher.d.ts","sourceRoot":"","sources":["../../src/platforms/BioRxivSearcher.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAKH,OAAO,EAAE,KAAK,EAAgB,MAAM,oBAAoB,CAAC;AACzD,OAAO,EAAE,WAAW,EAAE,aAAa,EAAE,eAAe,EAAE,oBAAoB,EAAE,MAAM,kBAAkB,CAAC;AAOrG,UAAU,oBAAqB,SAAQ,aAAa;IAClD,aAAa;IACb,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,YAAY;IACZ,MAAM,CAAC,EAAE,SAAS,GAAG,SAAS,CAAC;CAChC;AA2BD,qBAAa,eAAgB,SAAQ,WAAW;IAC9C,OAAO,CAAC,QAAQ,CAAC,UAAU,CAAwB;IACnD,OAAO,CAAC,QAAQ,CAAC,WAAW,CAAc;gBAE9B,UAAU,GAAE,SAAS,GAAG,SAAqB;IAUzD,eAAe,IAAI,oBAAoB;IAWvC;;OAEG;IACG,MAAM,CAAC,KAAK,EAAE,MAAM,EAAE,OAAO,GAAE,oBAAyB,GAAG,OAAO,CAAC,KAAK,EAAE,CAAC;IA+CjF;;OAEG;IACG,WAAW,CAAC,OAAO,EAAE,MAAM,EAAE,OAAO,GAAE,eAAoB,GAAG,OAAO,CAAC,MAAM,CAAC;IAgClF;;OAEG;IACG,SAAS,CAAC,OAAO,EAAE,MAAM,EAAE,OAAO,GAAE,eAAoB,GAAG,OAAO,CAAC,MAAM,CAAC;IAgBhF;;OAEG;IACH,OAAO,CAAC,mBAAmB;IAqB3B,OAAO,CAAC,gBAAgB;IAWxB;;OAEG;IACH,OAAO,CAAC,iBAAiB;CAyC1B;AAED;;GAEG;AACH,qBAAa,eAAgB,SAAQ,eAAe;;CAInD"}
+{"version":3,"file":"BioRxivSearcher.d.ts","sourceRoot":"","sources":["../../src/platforms/BioRxivSearcher.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAKH,OAAO,EAAE,KAAK,EAAgB,MAAM,oBAAoB,CAAC;AACzD,OAAO,EAAE,WAAW,EAAE,aAAa,EAAE,eAAe,EAAE,oBAAoB,EAAE,MAAM,kBAAkB,CAAC;AAOrG,UAAU,oBAAqB,SAAQ,aAAa;IAClD,aAAa;IACb,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,YAAY;IACZ,MAAM,CAAC,EAAE,SAAS,GAAG,SAAS,CAAC;CAChC;AA4BD,qBAAa,eAAgB,SAAQ,WAAW;IAC9C,OAAO,CAAC,QAAQ,CAAC,UAAU,CAAwB;IACnD,OAAO,CAAC,QAAQ,CAAC,WAAW,CAAc;gBAE9B,UAAU,GAAE,SAAS,GAAG,SAAqB;IAUzD,eAAe,IAAI,oBAAoB;IAWvC;;OAEG;IACG,MAAM,CAAC,KAAK,EAAE,MAAM,EAAE,OAAO,GAAE,oBAAyB,GAAG,OAAO,CAAC,KAAK,EAAE,CAAC;IA4DjF;;OAEG;IACG,WAAW,CAAC,OAAO,EAAE,MAAM,EAAE,OAAO,GAAE,eAAoB,GAAG,OAAO,CAAC,MAAM,CAAC;IAgClF;;OAEG;IACG,SAAS,CAAC,OAAO,EAAE,MAAM,EAAE,OAAO,GAAE,eAAoB,GAAG,OAAO,CAAC,MAAM,CAAC;IAgBhF;;OAEG;IACH,OAAO,CAAC,mBAAmB;IA4B3B,OAAO,CAAC,gBAAgB;IAWxB;;OAEG;IACH,OAAO,CAAC,iBAAiB;CAyC1B;AAED;;GAEG;AACH,qBAAa,eAAgB,SAAQ,eAAe;;CAInD"}

dist/platforms/BioRxivSearcher.js

@@ -46,25 +46,40 @@ /**
             const startDate = new Date(Date.now() - days * 24 * 60 * 60 * 1000).toISOString().split('T')[0];
-            // 构建搜索URL
-            const searchUrl = `${this.baseUrl}/${startDate}/${endDate}`;
-            const params = {
-                cursor: 0
-            };
-            // 添加分类过滤
-            if (query && query !== '*') {
-                // 将查询转换为分类格式
-                const category = query.toLowerCase().replace(/\s+/g, '_');
-                params.category = category;
+            const maxResults = options.maxResults || 10;
+            const maxPages = Math.max(1, Math.min(25, Math.ceil(maxResults / 30) + 10));
+            const papers = [];
+            const seen = new Set();
+            let cursor = 0;
+            let total;
+            let pages = 0;
+            while (papers.length < maxResults && pages < maxPages && (total === undefined || cursor < total)) {
+                const searchUrl = `${this.baseUrl}/${startDate}/${endDate}/${cursor}`;
+                logDebug(`${this.serverType} API Request: GET ${searchUrl}`);
+                await this.rateLimiter.waitForPermission();
+                const response = await ErrorHandler.retryWithBackoff(() => axios.get(searchUrl, {
+                    timeout: TIMEOUTS.DEFAULT,
+                    headers: { 'User-Agent': USER_AGENT }
+                }), { context: `${this.serverType} search` });
+                logDebug(`${this.serverType} API Response: ${response.status} ${response.statusText}`);
+                const collection = Array.isArray(response.data?.collection) ? response.data.collection : [];
+                const message = Array.isArray(response.data?.messages) ? response.data.messages[0] : undefined;
+                const parsedTotal = Number(message?.total);
+                if (Number.isFinite(parsedTotal))
+                    total = parsedTotal;
+                const pagePapers = this.parseSearchResponse(response.data, query, options);
+                for (const paper of pagePapers) {
+                    const key = paper.doi || paper.paperId || paper.title;
+                    if (!seen.has(key)) {
+                        seen.add(key);
+                        papers.push(paper);
+                        if (papers.length >= maxResults)
+                            break;
+                    }
+                }
+                if (collection.length === 0)
+                    break;
+                cursor += collection.length;
+                pages += 1;
             }
-            logDebug(`${this.serverType} API Request: GET ${searchUrl}`);
-            logDebug(`${this.serverType} Request params:`, params);
-            await this.rateLimiter.waitForPermission();
-            const response = await ErrorHandler.retryWithBackoff(() => axios.get(searchUrl, {
-                params,
-                timeout: TIMEOUTS.DEFAULT,
-                headers: { 'User-Agent': USER_AGENT }
-            }), { context: `${this.serverType} search` });
-            logDebug(`${this.serverType} API Response: ${response.status} ${response.statusText}`);
-            const papers = this.parseSearchResponse(response.data, query, options);
             logDebug(`${this.serverType} Parsed ${papers.length} papers`);
-            return papers.slice(0, options.maxResults || 10);
+            return papers.slice(0, maxResults);
         }
@@ -133,2 +148,6 @@ catch (error) {
         }
+        if (options.category && options.category.trim()) {
+            const categoryLower = options.category.toLowerCase().replace(/_/g, ' ');
+            filteredCollection = filteredCollection.filter(item => item.category.toLowerCase().replace(/_/g, ' ').includes(categoryLower));
+        }
         return filteredCollection.map(item => this.parseBioRxivPaper(item))
@@ -135,0 +154,0 @@ .filter(paper => paper !== null);

dist/platforms/BioRxivSearcher.js.map

@@ -1,1 +0,1 @@
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dist/platforms/GoogleScholarSearcher.d.ts.map

@@ -1,1 +0,1 @@
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+{"version":3,"file":"GoogleScholarSearcher.d.ts","sourceRoot":"","sources":["../../src/platforms/GoogleScholarSearcher.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAIH,OAAO,EAAE,KAAK,EAAgB,MAAM,oBAAoB,CAAC;AACzD,OAAO,EAAE,WAAW,EAAE,aAAa,EAAE,eAAe,EAAE,oBAAoB,EAAE,MAAM,kBAAkB,CAAC;AAKrG,UAAU,oBAAqB,SAAQ,aAAa;IAClD,WAAW;IACX,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,eAAe;IACf,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,QAAQ,CAAC,EAAE,MAAM,CAAC;CACnB;AAID,qBAAa,qBAAsB,SAAQ,WAAW;IACpD,OAAO,CAAC,QAAQ,CAAC,UAAU,CAAwC;IACnE,OAAO,CAAC,QAAQ,CAAC,UAAU,CAIzB;;IAMF,eAAe,IAAI,oBAAoB;IAWvC;;OAEG;IACG,MAAM,CAAC,KAAK,EAAE,MAAM,EAAE,OAAO,GAAE,oBAAyB,GAAG,OAAO,CAAC,KAAK,EAAE,CAAC;IAoDjF;;OAEG;IACG,WAAW,CAAC,OAAO,EAAE,MAAM,EAAE,OAAO,CAAC,EAAE,eAAe,GAAG,OAAO,CAAC,MAAM,CAAC;IAI9E;;OAEG;IACG,SAAS,CAAC,OAAO,EAAE,MAAM,EAAE,OAAO,CAAC,EAAE,eAAe,GAAG,OAAO,CAAC,MAAM,CAAC;IAI5E;;OAEG;IACH,OAAO,CAAC,iBAAiB;IAuBzB;;OAEG;YACW,kBAAkB;IAyBhC;;OAEG;IACH,OAAO,CAAC,kBAAkB;IAiE1B;;OAEG;IACH,OAAO,CAAC,cAAc;IAStB;;OAEG;IACH,OAAO,CAAC,WAAW;IAKnB;;OAEG;IACH,OAAO,CAAC,cAAc;IAStB;;OAEG;IACH,OAAO,CAAC,oBAAoB;IAK5B;;OAEG;IACH,OAAO,CAAC,eAAe;IAMvB;;OAEG;IACH,OAAO,CAAC,UAAU;IAUlB;;OAEG;IACH,OAAO,CAAC,kBAAkB;IAI1B;;OAEG;YACW,WAAW;CAI1B"}

dist/platforms/GoogleScholarSearcher.js

@@ -12,2 +12,3 @@ /**
 import { ErrorHandler } from '../utils/ErrorHandler.js';
+const SCHOLAR_REQUEST_TIMEOUT_MS = 10000;
 export class GoogleScholarSearcher extends PaperSource {
@@ -126,7 +127,7 @@ scholarUrl = 'https://scholar.google.com/scholar';
             },
-            timeout: TIMEOUTS.DEFAULT
+            timeout: Math.min(TIMEOUTS.DEFAULT, SCHOLAR_REQUEST_TIMEOUT_MS)
         };
         logDebug(`Google Scholar Request: GET ${this.scholarUrl}`);
         logDebug('Scholar params:', params);
-        return await ErrorHandler.retryWithBackoff(() => axios.get(this.scholarUrl, config), { context: 'Google Scholar search' });
+        return await ErrorHandler.retryWithBackoff(() => axios.get(this.scholarUrl, config), { context: 'Google Scholar search', maxRetries: 0 });
     }
@@ -133,0 +134,0 @@ /**

dist/platforms/GoogleScholarSearcher.js.map

@@ -1,1 +0,1 @@
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dist/services/CitationService.d.ts.map

@@ -1,1 +0,1 @@
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dist/services/CitationService.js

@@ -153,5 +153,8 @@ import axios from 'axios';
                 'citationCount',
+                'referenceCount',
                 'year',
                 'authors',
-                'venue'
+                'venue',
+                'externalIds',
+                'url'
             ].join(',');
@@ -184,5 +187,8 @@ const response = await ErrorHandler.retryWithBackoff(() => this.client.get(`/paper/${paperId}/references`, {
                 'citationCount',
+                'referenceCount',
                 'year',
                 'authors',
-                'venue'
+                'venue',
+                'externalIds',
+                'url'
             ].join(',');
@@ -189,0 +195,0 @@ const response = await ErrorHandler.retryWithBackoff(() => this.client.get(`/paper/${paperId}/citations`, {

dist/services/CitationService.js.map

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dist/services/OpenAccessFallbackService.d.ts

@@ -20,3 +20,23 @@ import type { Searchers } from '../core/searchers.js';
 }
+export interface DownloadTier {
+    id: string;
+    stage: string;
+    run(context: DownloadTierContext): Promise<DownloadTierResult>;
+}
+export interface DownloadTierContext {
+    searchers: Searchers;
+    source: string;
+    paperId: string;
+    doi?: string;
+    title?: string;
+    savePath: string;
+    useSciHub: boolean;
+}
+export interface DownloadTierResult {
+    status: 'ok' | 'error' | 'skipped';
+    path?: string;
+    message: string;
+}
+export declare const INSTITUTIONAL_ACCESS_TIER_ID = "institutional_access";
 export declare function downloadWithFallback(searchers: Searchers, options: DownloadWithFallbackOptions): Promise<DownloadWithFallbackResult>;
 //# sourceMappingURL=OpenAccessFallbackService.d.ts.map

dist/services/OpenAccessFallbackService.d.ts.map

@@ -1,1 +0,1 @@
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+{"version":3,"file":"OpenAccessFallbackService.d.ts","sourceRoot":"","sources":["../../src/services/OpenAccessFallbackService.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,sBAAsB,CAAC;AAKtD,MAAM,WAAW,2BAA2B;IAC1C,MAAM,EAAE,MAAM,CAAC;IACf,OAAO,EAAE,MAAM,CAAC;IAChB,GAAG,CAAC,EAAE,MAAM,CAAC;IACb,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,wEAAwE;IACxE,SAAS,CAAC,EAAE,OAAO,CAAC;CACrB;AAED,MAAM,WAAW,0BAA0B;IACzC,MAAM,EAAE,IAAI,GAAG,OAAO,CAAC;IACvB,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,QAAQ,EAAE,KAAK,CAAC;QAAE,KAAK,EAAE,MAAM,CAAC;QAAC,MAAM,EAAE,IAAI,GAAG,OAAO,GAAG,SAAS,CAAC;QAAC,OAAO,EAAE,MAAM,CAAA;KAAE,CAAC,CAAC;CACzF;AAED,MAAM,WAAW,YAAY;IAC3B,EAAE,EAAE,MAAM,CAAC;IACX,KAAK,EAAE,MAAM,CAAC;IACd,GAAG,CAAC,OAAO,EAAE,mBAAmB,GAAG,OAAO,CAAC,kBAAkB,CAAC,CAAC;CAChE;AAED,MAAM,WAAW,mBAAmB;IAClC,SAAS,EAAE,SAAS,CAAC;IACrB,MAAM,EAAE,MAAM,CAAC;IACf,OAAO,EAAE,MAAM,CAAC;IAChB,GAAG,CAAC,EAAE,MAAM,CAAC;IACb,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,QAAQ,EAAE,MAAM,CAAC;IACjB,SAAS,EAAE,OAAO,CAAC;CACpB;AAED,MAAM,WAAW,kBAAkB;IACjC,MAAM,EAAE,IAAI,GAAG,OAAO,GAAG,SAAS,CAAC;IACnC,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,OAAO,EAAE,MAAM,CAAC;CACjB;AAED,eAAO,MAAM,4BAA4B,yBAAyB,CAAC;AAgCnE,wBAAsB,oBAAoB,CACxC,SAAS,EAAE,SAAS,EACpB,OAAO,EAAE,2BAA2B,GACnC,OAAO,CAAC,0BAA0B,CAAC,CAsBrC"}

dist/services/OpenAccessFallbackService.js

 import { downloadPdfFromUrl, safeFilename } from '../utils/PdfDownload.js';
+export const INSTITUTIONAL_ACCESS_TIER_ID = 'institutional_access';
 const REPOSITORY_SOURCES = ['pmc', 'europepmc', 'core', 'openaire'];
+const DEFAULT_DOWNLOAD_TIERS = [
+    {
+        id: 'primary',
+        stage: 'primary',
+        run: tryPrimaryDownload
+    },
+    {
+        id: 'direct_pdf_url',
+        stage: 'direct_pdf_url',
+        run: tryDirectMetadataUrl
+    },
+    {
+        id: 'repositories',
+        stage: 'repositories',
+        run: tryRepositoryFallback
+    },
+    {
+        id: 'unpaywall',
+        stage: 'unpaywall',
+        run: tryUnpaywall
+    },
+    {
+        id: 'scihub',
+        stage: 'scihub',
+        run: trySciHub
+    }
+];
 export async function downloadWithFallback(searchers, options) {
     const savePath = options.savePath || './downloads';
     const attempts = [];
-    const source = normalizeSource(options.source);
-    const primary = searchers[source];
-    if (primary?.getCapabilities().download) {
-        try {
-            const path = await primary.downloadPdf(options.paperId, { savePath });
-            attempts.push({ stage: 'primary', status: 'ok', message: path });
-            return { status: 'ok', path, attempts };
+    const context = {
+        searchers,
+        source: normalizeSource(options.source),
+        paperId: options.paperId,
+        doi: options.doi,
+        title: options.title,
+        savePath,
+        useSciHub: options.useSciHub !== false
+    };
+    for (const tier of DEFAULT_DOWNLOAD_TIERS) {
+        const result = await tier.run(context);
+        attempts.push({ stage: tier.stage, status: result.status, message: result.message });
+        if (result.status === 'ok' && result.path) {
+            return { status: 'ok', path: result.path, attempts };
         }
-        catch (error) {
-            attempts.push({ stage: 'primary', status: 'error', message: error?.message || String(error) });
-        }
     }
-    else {
-        attempts.push({ stage: 'primary', status: 'skipped', message: `No primary downloader for ${source}` });
+    return { status: 'error', attempts };
+}
+async function tryPrimaryDownload(context) {
+    const primary = context.searchers[context.source];
+    if (!primary?.getCapabilities().download) {
+        return { status: 'skipped', message: `No primary downloader for ${context.source}` };
     }
-    const directResult = await tryDirectMetadataUrl(searchers, source, options.paperId, savePath, attempts);
-    if (directResult)
-        return { status: 'ok', path: directResult, attempts };
-    const repositoryResult = await tryRepositoryFallback(searchers, options, savePath, attempts);
-    if (repositoryResult)
-        return { status: 'ok', path: repositoryResult, attempts };
-    const unpaywallResult = await tryUnpaywall(searchers, options.doi || '', savePath, attempts);
-    if (unpaywallResult)
-        return { status: 'ok', path: unpaywallResult, attempts };
-    if (options.useSciHub !== false) {
-        const identifier = options.doi || options.title || options.paperId;
-        try {
-            const path = await searchers.scihub.downloadPdf(identifier, { savePath });
-            attempts.push({ stage: 'scihub', status: 'ok', message: path });
-            return { status: 'ok', path, attempts };
-        }
-        catch (error) {
-            attempts.push({ stage: 'scihub', status: 'error', message: error?.message || String(error) });
-        }
+    try {
+        const path = await primary.downloadPdf(context.paperId, { savePath: context.savePath });
+        return { status: 'ok', path, message: path };
     }
-    else {
-        attempts.push({ stage: 'scihub', status: 'skipped', message: 'Sci-Hub fallback disabled by useSciHub=false.' });
+    catch (error) {
+        return { status: 'error', message: error?.message || String(error) };
     }
-    return { status: 'error', attempts };
 }
-async function tryDirectMetadataUrl(searchers, source, paperId, savePath, attempts) {
-    const searcher = searchers[source];
-    if (!searcher)
-        return '';
+async function tryDirectMetadataUrl(context) {
+    const searcher = context.searchers[context.source];
+    if (!searcher) {
+        return { status: 'skipped', message: `No metadata searcher for ${context.source}.` };
+    }
     try {
-        const paper = await searcher.getPaperByDoi(paperId);
+        const paper = await searcher.getPaperByDoi(context.paperId);
         if (!paper?.pdfUrl) {
-            attempts.push({ stage: 'direct_pdf_url', status: 'skipped', message: 'No pdf_url found in source metadata.' });
-            return '';
+            return { status: 'skipped', message: 'No pdf_url found in source metadata.' };
         }
-        const path = await downloadPdfFromUrl(paper.pdfUrl, savePath, `${source}_${safeFilename(paper.paperId)}`);
-        attempts.push({ stage: 'direct_pdf_url', status: 'ok', message: path });
-        return path;
+        const path = await downloadPdfFromUrl(paper.pdfUrl, context.savePath, `${context.source}_${safeFilename(paper.paperId)}`);
+        return { status: 'ok', path, message: path };
     }
     catch (error) {
-        attempts.push({ stage: 'direct_pdf_url', status: 'error', message: error?.message || String(error) });
-        return '';
+        return { status: 'error', message: error?.message || String(error) };
     }
 }
-async function tryRepositoryFallback(searchers, options, savePath, attempts) {
-    const queries = [options.doi || '', options.title || ''].filter(Boolean);
+async function tryRepositoryFallback(context) {
+    const queries = [context.doi || '', context.title || ''].filter(Boolean);
     if (queries.length === 0) {
-        attempts.push({ stage: 'repositories', status: 'skipped', message: 'No DOI/title provided for repository discovery.' });
-        return '';
+        return { status: 'skipped', message: 'No DOI/title provided for repository discovery.' };
     }
     for (const source of REPOSITORY_SOURCES) {
-        const searcher = searchers[source];
+        const searcher = context.searchers[source];
         if (!searcher)
@@ -81,35 +97,42 @@ continue;
                     continue;
-                const path = await downloadPdfFromUrl(paper.pdfUrl, savePath, `${source}_${safeFilename(paper.paperId)}`);
-                attempts.push({ stage: `repository:${source}`, status: 'ok', message: path });
-                return path;
+                const path = await downloadPdfFromUrl(paper.pdfUrl, context.savePath, `${source}_${safeFilename(paper.paperId)}`);
+                return { status: 'ok', path, message: path };
             }
-            catch (error) {
-                attempts.push({ stage: `repository:${source}`, status: 'error', message: error?.message || String(error) });
+            catch {
+                continue;
             }
         }
     }
-    attempts.push({ stage: 'repositories', status: 'skipped', message: 'No repository PDF candidate succeeded.' });
-    return '';
+    return { status: 'skipped', message: 'No repository PDF candidate succeeded.' };
 }
-async function tryUnpaywall(searchers, doi, savePath, attempts) {
-    if (!doi) {
-        attempts.push({ stage: 'unpaywall', status: 'skipped', message: 'DOI not provided.' });
-        return '';
+async function tryUnpaywall(context) {
+    if (!context.doi) {
+        return { status: 'skipped', message: 'DOI not provided.' };
     }
     try {
-        const unpaywall = searchers.unpaywall;
-        const pdfUrl = await unpaywall.resolveBestPdfUrl(doi);
+        const unpaywall = context.searchers.unpaywall;
+        const pdfUrl = await unpaywall.resolveBestPdfUrl(context.doi);
         if (!pdfUrl) {
-            attempts.push({ stage: 'unpaywall', status: 'skipped', message: 'No OA PDF URL found or email not configured.' });
-            return '';
+            return { status: 'skipped', message: 'No OA PDF URL found or email not configured.' };
         }
-        const path = await downloadPdfFromUrl(pdfUrl, savePath, `unpaywall_${safeFilename(doi)}`);
-        attempts.push({ stage: 'unpaywall', status: 'ok', message: path });
-        return path;
+        const path = await downloadPdfFromUrl(pdfUrl, context.savePath, `unpaywall_${safeFilename(context.doi)}`);
+        return { status: 'ok', path, message: path };
     }
     catch (error) {
-        attempts.push({ stage: 'unpaywall', status: 'error', message: error?.message || String(error) });
-        return '';
+        return { status: 'error', message: error?.message || String(error) };
     }
 }
+async function trySciHub(context) {
+    if (!context.useSciHub) {
+        return { status: 'skipped', message: 'Sci-Hub fallback disabled by useSciHub=false.' };
+    }
+    const identifier = context.doi || context.title || context.paperId;
+    try {
+        const path = await context.searchers.scihub.downloadPdf(identifier, { savePath: context.savePath });
+        return { status: 'ok', path, message: path };
+    }
+    catch (error) {
+        return { status: 'error', message: error?.message || String(error) };
+    }
+}
 function normalizeSource(source) {
@@ -116,0 +139,0 @@ const normalized = source.trim().toLowerCase();

dist/services/OpenAccessFallbackService.js.map

@@ -1,1 +0,1 @@
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dist/utils/RateLimiter.d.ts.map

@@ -1,1 +0,1 @@
-{"version":3,"file":"RateLimiter.d.ts","sourceRoot":"","sources":["../../src/utils/RateLimiter.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAIH,MAAM,WAAW,kBAAkB;IACjC,cAAc;IACd,iBAAiB,EAAE,MAAM,CAAC;IAC1B,aAAa;IACb,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,eAAe;IACf,KAAK,CAAC,EAAE,OAAO,CAAC;CACjB;AAED,qBAAa,WAAW;IACtB,OAAO,CAAC,QAAQ,CAAC,iBAAiB,CAAS;IAC3C,OAAO,CAAC,QAAQ,CAAC,UAAU,CAAS;IACpC,OAAO,CAAC,QAAQ,CAAC,aAAa,CAAS;IACvC,OAAO,CAAC,QAAQ,CAAC,KAAK,CAAU;IAEhC,OAAO,CAAC,MAAM,CAAS;IACvB,OAAO,CAAC,UAAU,CAAS;IAC3B,OAAO,CAAC,cAAc,CAAiB;IACvC,OAAO,CAAC,QAAQ,CAAC,eAAe,CAGxB;gBAEI,OAAO,EAAE,kBAAkB;IAevC;;OAEG;IACG,iBAAiB,IAAI,OAAO,CAAC,IAAI,CAAC;IAwBxC;;OAEG;IACH,OAAO,CAAC,YAAY;IAepB;;OAEG;IACH,OAAO,CAAC,sBAAsB;IAiB9B;;OAEG;IACH,SAAS,IAAI;QACX,eAAe,EAAE,MAAM,CAAC;QACxB,SAAS,EAAE,MAAM,CAAC;QAClB,iBAAiB,EAAE,MAAM,CAAC;QAC1B,eAAe,EAAE,MAAM,CAAC;KACzB;IAUD;;OAEG;IACH,OAAO,IAAI,IAAI;IAsBf,OAAO,IAAI,IAAI;CAGhB"}
+{"version":3,"file":"RateLimiter.d.ts","sourceRoot":"","sources":["../../src/utils/RateLimiter.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAIH,MAAM,WAAW,kBAAkB;IACjC,cAAc;IACd,iBAAiB,EAAE,MAAM,CAAC;IAC1B,aAAa;IACb,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,eAAe;IACf,KAAK,CAAC,EAAE,OAAO,CAAC;CACjB;AAED,qBAAa,WAAW;IACtB,OAAO,CAAC,QAAQ,CAAC,iBAAiB,CAAS;IAC3C,OAAO,CAAC,QAAQ,CAAC,UAAU,CAAS;IACpC,OAAO,CAAC,QAAQ,CAAC,aAAa,CAAS;IACvC,OAAO,CAAC,QAAQ,CAAC,KAAK,CAAU;IAEhC,OAAO,CAAC,MAAM,CAAS;IACvB,OAAO,CAAC,UAAU,CAAS;IAC3B,OAAO,CAAC,cAAc,CAAiB;IACvC,OAAO,CAAC,QAAQ,CAAC,eAAe,CAGxB;gBAEI,OAAO,EAAE,kBAAkB;IAevC;;OAEG;IACG,iBAAiB,IAAI,OAAO,CAAC,IAAI,CAAC;IAyBxC;;OAEG;IACH,OAAO,CAAC,YAAY;IAepB;;OAEG;IACH,OAAO,CAAC,sBAAsB;IAqB9B;;OAEG;IACH,SAAS,IAAI;QACX,eAAe,EAAE,MAAM,CAAC;QACxB,SAAS,EAAE,MAAM,CAAC;QAClB,iBAAiB,EAAE,MAAM,CAAC;QAC1B,eAAe,EAAE,MAAM,CAAC;KACzB;IAUD;;OAEG;IACH,OAAO,IAAI,IAAI;IA0Bf,OAAO,IAAI,IAAI;CAGhB"}

dist/utils/RateLimiter.js

@@ -45,2 +45,3 @@ /**
             });
+            this.intervalHandle.ref?.();
             if (this.debug) {
@@ -82,2 +83,5 @@ logDebug(`RateLimiter: Request queued, ${this.pendingRequests.length} waiting`);
         }
+        if (this.pendingRequests.length === 0) {
+            this.intervalHandle.unref?.();
+        }
     }
@@ -115,2 +119,5 @@ /**
         }
+        if (this.pendingRequests.length === 0) {
+            this.intervalHandle.unref?.();
+        }
         if (this.debug && removedCount > 0) {
@@ -117,0 +124,0 @@ logDebug(`RateLimiter: Cleaned up ${removedCount} expired requests`);

dist/utils/RateLimiter.js.map

@@ -1,1 +0,1 @@
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package.json

 {
   "name": "paper-search-cli",
-  "version": "0.3.0",
+  "version": "0.3.1",
   "description": "Agent-friendly CLI for searching and downloading academic papers from multiple sources.",
@@ -5,0 +5,0 @@ "main": "dist/cli.js",

README.md

@@ -5,3 +5,3 @@ # Paper Search CLI
 
-Paper Search CLI is an agent-facing Skill + CLI package built on a standalone Node.js command line tool for academic literature work. It gives AI agents, terminal users, and scripts one reproducible command layer with agent-friendly JSON output for literature metadata search, journal metrics lookup, PDF discovery/download, and paper body snippet search.
+Paper Search CLI is an agent-facing Skill + CLI package built on a standalone Node.js command line tool for academic literature work. It gives AI agents, terminal users, and scripts one reproducible command layer with agent-friendly JSON output for literature metadata search, citation expansion, journal metrics lookup, PDF discovery/download, and paper body snippet search.
 
@@ -22,2 +22,3 @@ ![Node.js](https://img.shields.io/badge/node.js->=18.0.0-green.svg)
 | Literature metadata search | `paper-search search`, `paper-search run search_*` | Paper title, authors, year, journal, DOI, PMID/PMCID, arXiv ID, URL, abstract, and source metadata |
+| Citation expansion | `paper-search run get_paper_citations`, `paper-search run get_paper_references` | Citing papers and cited references for a known Semantic Scholar paper ID, DOI, or arXiv ID |
 | Journal metrics lookup | `paper-search journal-metrics`, `paper-search run query_journal_metrics` | Impact factor, 5-year IF, JCR/SSCI quartile, CAS zone, JCI, ESI, warning flags, and rank fields |
@@ -33,7 +34,7 @@ | PDF discovery and download | `paper-search download`, `paper-search run download_with_fallback` | Verified PDF download paths through native sources, open access, configured entitlement, and Sci-Hub fallback when enabled |
 | --- | --- |
-| CLI package body | Executes literature search, journal metrics lookup, PDF discovery/download, body snippet search, and stable JSON output |
+| CLI package body | Executes literature search, citation expansion, journal metrics lookup, PDF discovery/download, body snippet search, and stable JSON output |
 | Bundled Skill | Ships `skills/paper-search` with agent routing rules and focused references; it does not store API keys, cookies, or account credentials |
-| Friendly Management Layer | Provides `doctor`, `smoke`, `skills`, `config`, and `tools` around the four main capabilities: `metadata_search`, `journal_metrics`, `pdf_discovery`, and `body_snippet_search`. `doctor` health reports include masked configuration, Capability Profile, platform/source status, and missing or degraded items; `smoke` checks command wiring and live readiness; `skills` syncs the bundled Skill |
+| Friendly Management Layer | Provides `doctor`, `smoke`, `skills`, `config`, and `tools` around the five main capabilities: `metadata_search`, `citation_expansion`, `journal_metrics`, `pdf_discovery`, and `body_snippet_search`. `doctor` health reports include masked configuration, Capability Profile, platform/source status, and missing or degraded items; `smoke` checks command wiring and live readiness; `skills` syncs the bundled Skill |
 
-The four main capabilities are executed by the CLI package body and reported by the management layer. The Capability Profile also reports `entitled_access` so users can see whether publisher API keys, database keys, TDM tokens, or institutional entitlements are configured. Missing or degraded configuration for one workflow does not make unrelated workflows unavailable.
+The five main capabilities are executed by the CLI package body and reported by the management layer. The Capability Profile also reports `entitled_access` so users can see whether publisher API keys, database keys, TDM tokens, or institutional entitlements are configured. Missing or degraded configuration for one workflow does not make unrelated workflows unavailable.
 
@@ -50,9 +51,10 @@ ## Quick Start
 
-Try the four main workflows:
+Try the five main workflows:
 
 ```bash
 paper-search search "machine learning clinical prediction" --platform crossref --max-results 3 --pretty
+paper-search run get_paper_citations --arg doi="10.1038/nature12373" --arg limit=5 --pretty
 paper-search journal-metrics "Nature" "BMJ" --pretty
 paper-search download 10.48550/arxiv.1201.0490 --platform arxiv --save-path ./downloads
-paper-search run search_semantic_snippets --arg query="propensity score matching" --arg maxResults=3 --pretty
+paper-search run search_semantic_snippets --arg query="propensity score matching" --arg limit=3 --pretty
 ```
@@ -94,3 +96,3 @@
 | OpenAlex | ✅ Yes | 🟡 Conditional | ❌ No | ✅ Yes | ❌ None | Free metadata; OA links can help PDF fallback |
-| Semantic Scholar | ✅ Yes | 🟡 Conditional | ✅ Body snippets | ✅ Yes | 🟡 Optional; snippets require `SEMANTIC_SCHOLAR_API_KEY` | Good for AI/CS and body snippet clues |
+| Semantic Scholar | ✅ Yes | 🟡 Conditional | ✅ Body snippets | ✅ Yes | 🟡 Optional; snippets require `SEMANTIC_SCHOLAR_API_KEY` | Good for AI/CS, citation expansion, and body snippet clues |
 | Google Scholar | ✅ Yes | ❌ No | ❌ No | ✅ Yes | ❌ None | Broad discovery through page parsing |
@@ -213,3 +215,3 @@
 
-The npm package ships a bundled agent Skill at `skills/paper-search/SKILL.md`. Terminal users can use the CLI directly; AI agent workflows should install or sync the Skill so the agent can route the four main workflows correctly.
+The npm package ships a bundled agent Skill at `skills/paper-search/SKILL.md`. Terminal users can use the CLI directly; AI agent workflows should install or sync the Skill so the agent can route the five main workflows correctly.
 
@@ -216,0 +218,0 @@ ```bash

README.zh.md

@@ -5,3 +5,3 @@ # Paper Search CLI
 
-Paper Search CLI 是一个面向 AI agent 的 Skill + CLI 包，基于独立的 Node.js 命令行工具构建，用于学术文献工作。它为 AI agent、终端用户和脚本提供一个可复现的命令层，并通过 agent 友好的 JSON 输出覆盖文献元数据检索、期刊指标检索、PDF 获取/下载和论文正文片段检索。
+Paper Search CLI 是一个面向 AI agent 的 Skill + CLI 包，基于独立的 Node.js 命令行工具构建，用于学术文献工作。它为 AI agent、终端用户和脚本提供一个可复现的命令层，并通过 agent 友好的 JSON 输出覆盖文献元数据检索、施引/参考文献扩展、期刊指标检索、PDF 获取/下载和论文正文片段检索。
 
@@ -22,2 +22,3 @@ ![Node.js](https://img.shields.io/badge/node.js->=18.0.0-green.svg)
 | 文献元数据检索 | `paper-search search`, `paper-search run search_*` | 题名、作者、年份、期刊、DOI、PMID/PMCID、arXiv ID、URL、摘要和来源元数据 |
+| 引文扩展 | `paper-search run get_paper_citations`, `paper-search run get_paper_references` | 已知 Semantic Scholar paper ID、DOI 或 arXiv ID 对应论文的施引文献和参考文献 |
 | 期刊指标检索 | `paper-search journal-metrics`, `paper-search run query_journal_metrics` | 影响因子、5 年 IF、JCR/SSCI 分区、中科院分区、JCI、ESI、预警和等级字段 |
@@ -33,7 +34,7 @@ | PDF 获取和下载 | `paper-search download`, `paper-search run download_with_fallback` | 通过原生来源、开放获取、已配置权限来源和启用时的 Sci-Hub fallback 获取 PDF |
 | --- | --- |
-| CLI 本体 | 执行文献检索、期刊指标检索、PDF 获取/下载、正文片段检索和稳定 JSON 输出 |
+| CLI 本体 | 执行文献检索、引文扩展、期刊指标检索、PDF 获取/下载、正文片段检索和稳定 JSON 输出 |
 | Bundled Skill | 随包发布 `skills/paper-search`，提供 agent 路由规则和 focused references；不保存密钥、cookie 或账号信息 |
-| Friendly Management Layer | 围绕四个主要能力 `metadata_search`、`journal_metrics`、`pdf_discovery`、`body_snippet_search` 提供 `doctor`、`smoke`、`skills`、`config`、`tools`。`doctor` 健康报告包含脱敏配置、Capability Profile、平台/来源状态、缺失项和降级项；`smoke` 检查命令入口连通性和 live 可用性；`skills` 负责同步随包发布的 Skill |
+| Friendly Management Layer | 围绕五个主要能力 `metadata_search`、`citation_expansion`、`journal_metrics`、`pdf_discovery`、`body_snippet_search` 提供 `doctor`、`smoke`、`skills`、`config`、`tools`。`doctor` 健康报告包含脱敏配置、Capability Profile、平台/来源状态、缺失项和降级项；`smoke` 检查命令入口连通性和 live 可用性；`skills` 负责同步随包发布的 Skill |
 
-四个主要能力由 CLI 本体执行，由管理层报告和检查。Capability Profile 也会报告 `entitled_access`，让用户看到出版商 API key、数据库 key、TDM token 或机构权限是否已配置。某一个能力缺少配置或降级，不会导致其他独立能力不可用。
+五个主要能力由 CLI 本体执行，由管理层报告和检查。Capability Profile 也会报告 `entitled_access`，让用户看到出版商 API key、数据库 key、TDM token 或机构权限是否已配置。某一个能力缺少配置或降级，不会导致其他独立能力不可用。
 
@@ -50,9 +51,10 @@ ## 快速开始
 
-尝试四个主要功能：
+尝试五个主要功能：
 
 ```bash
 paper-search search "machine learning clinical prediction" --platform crossref --max-results 3 --pretty
+paper-search run get_paper_citations --arg doi="10.1038/nature12373" --arg limit=5 --pretty
 paper-search journal-metrics "Nature" "BMJ" --pretty
 paper-search download 10.48550/arxiv.1201.0490 --platform arxiv --save-path ./downloads
-paper-search run search_semantic_snippets --arg query="propensity score matching" --arg maxResults=3 --pretty
+paper-search run search_semantic_snippets --arg query="propensity score matching" --arg limit=3 --pretty
 ```
@@ -94,3 +96,3 @@
 | OpenAlex | ✅ 支持 | 🟡 条件支持 | ❌ 不支持 | ✅ 支持 | ❌ 不需要 | 免费元数据；记录含 OA 链接时可帮助 PDF fallback |
-| Semantic Scholar | ✅ 支持 | 🟡 条件支持 | ✅ 正文片段 | ✅ 支持 | 🟡 可选；正文片段需要 `SEMANTIC_SCHOLAR_API_KEY` | 适合 AI/CS 和正文片段线索 |
+| Semantic Scholar | ✅ 支持 | 🟡 条件支持 | ✅ 正文片段 | ✅ 支持 | 🟡 可选；正文片段需要 `SEMANTIC_SCHOLAR_API_KEY` | 适合 AI/CS、引文扩展和正文片段线索 |
 | Google Scholar | ✅ 支持 | ❌ 不支持 | ❌ 不支持 | ✅ 支持 | ❌ 不需要 | 基于页面解析的广覆盖发现 |
@@ -213,3 +215,3 @@
 
-npm 包会随包发布 agent Skill，位置是 `skills/paper-search/SKILL.md`。终端用户可以只用 CLI；AI agent 工作流应安装或同步 Skill，让 agent 正确路由四个主要功能。
+npm 包会随包发布 agent Skill，位置是 `skills/paper-search/SKILL.md`。终端用户可以只用 CLI；AI agent 工作流应安装或同步 Skill，让 agent 正确路由五个主要功能。
 
@@ -216,0 +218,0 @@ ```bash

skills/paper-search/references/capability-routing.md

 # Capability Routing Reference
 
-Use this reference when mapping a user literature request to one of the four main `paper-search` workflow capabilities.
+Use this reference when mapping a user literature request to one of the five main `paper-search` workflow capabilities.
 
@@ -10,2 +10,3 @@ ## Functional Map
 | Search papers, find related work, verify DOI/PMID, screen literature | `metadata_search` | `paper-search search` integrated entrypoint / `paper-search run search_*` precise tool entrypoint | Returns and verifies paper metadata only; Sci-Hub is not a search source |
+| Expand citation graph for a known paper | `citation_expansion` | `paper-search run get_paper_citations` / `paper-search run get_paper_references` | Requires a known `paperId`, DOI, or arXiv ID; returns citing papers or cited references, not general keyword search |
 | Query impact factor, JCR/SSCI/CAS quartiles, JCI, ESI, warnings, journal rank | `journal_metrics` | `paper-search journal-metrics` / `paper-search run query_journal_metrics` | Journal-level lookup, not paper search; requires `EASYSCHOLAR_KEY` |
@@ -36,3 +37,3 @@ | Get or download a verified paper PDF | `pdf_discovery` | `paper-search download` / `paper-search run download_with_fallback` | Verify identity before download; Sci-Hub is the default enabled final fallback |
 
-It does not call `journal_metrics`, `pdf_discovery`, or `body_snippet_search`.
+It does not call `citation_expansion`, `journal_metrics`, `pdf_discovery`, or `body_snippet_search`.
 
@@ -56,2 +57,13 @@ ```bash
 
+## Citation Expansion
+
+Use `citation_expansion` when the user has a known paper and asks which papers cite it or which references it cites.
+
+```bash
+paper-search run get_paper_citations --arg doi="10.1038/nature12373" --arg limit=5 --pretty
+paper-search run get_paper_references --arg doi="10.1038/nature12373" --arg limit=5 --pretty
+```
+
+Target priority is `paperId` > `doi` > `arxivId`. This capability uses Semantic Scholar Graph API and is separate from keyword-based `metadata_search`.
+
 ## Journal Metrics
@@ -123,2 +135,3 @@
 | Methods/body snippet clues | `search_semantic_snippets` | Use `pubmed`/`semantic` first for titles and synonyms |
+| Citation graph expansion | `get_paper_citations`, `get_paper_references` | Use only after a target paper identifier is known |
 | Computer science, AI, math, physics | `arxiv` | `semantic`, `crossref`, `openalex` |
@@ -125,0 +138,0 @@ | CS bibliographies and conference metadata | `dblp` | `acm`, `usenix`, `openreview`, `ieee` requires key |

skills/paper-search/references/cli-contract.md

@@ -54,2 +54,4 @@ # Paper Search CLI Contract
 - `search_semantic_snippets`
+- `get_paper_citations`
+- `get_paper_references`
 - `search_iacr`
@@ -101,2 +103,19 @@ - `download_paper`
 
+## Citation Expansion Contract
+
+`get_paper_citations` and `get_paper_references` query Semantic Scholar Graph API for citation graph expansion.
+
+- Provide at least one of `paperId`, `doi`, or `arxivId`.
+- Target priority is `paperId`, then `doi`, then `arxivId`.
+- `doi` is converted to `DOI:<doi>`.
+- `arxivId` is converted to `ARXIV:<id>`.
+- `limit` defaults to `100` and accepts values from `1` to `100`.
+
+Examples:
+
+```bash
+paper-search run get_paper_citations --arg doi="10.1038/nature12373" --arg limit=5 --pretty
+paper-search run get_paper_references --arg doi="10.1038/nature12373" --arg limit=5 --pretty
+```
+
 ## Download Command Contract
@@ -103,0 +122,0 @@

skills/paper-search/references/management-layer.md

@@ -38,2 +38,3 @@ # Management Layer Reference
 - `metadata_search`: metadata search through configured/free literature sources. Sci-Hub must not be included in metadata search.
+- `citation_expansion`: citation and reference expansion for a known paper through Semantic Scholar Graph API. `SEMANTIC_SCHOLAR_API_KEY` is optional for higher quota.
 - `body_snippet_search`: Semantic Scholar Open Access snippet search. It requires `SEMANTIC_SCHOLAR_API_KEY`.
@@ -40,0 +41,0 @@ - `journal_metrics`: EasyScholar journal metrics. It requires `EASYSCHOLAR_KEY`.

skills/paper-search/SKILL.md

@@ -8,2 +8,3 @@ ---
   使用 Semantic Scholar Open Access snippet 索引检索论文正文片段中的方法学细节，
+  通过 Semantic Scholar Graph API 查询已知论文的施引文献和参考文献，
   以及通过 EasyScholar 查询期刊影响因子、JCR/SSCI 分区、中科院分区、JCI、ESI、预警和等级指标。
@@ -22,3 +23,3 @@ 当用户提到“搜文献”“找论文”“文献检索”“search papers”“find papers”“literature search”
 
-你是学术文献检索调度器。本 Skill 是 Routing Skill：负责把用户意图路由到 `paper-search` CLI，并维护证据、密钥和下载边界。优先通过 `paper-search` CLI 完成论文检索、元数据核验、正文片段检索、期刊指标查询和 PDF 获取；不要把本 Skill 当作密钥、cookie、账号或下载策略的存储位置。
+你是学术文献检索调度器。本 Skill 是 Routing Skill：负责把用户意图路由到 `paper-search` CLI，并维护证据、密钥和下载边界。优先通过 `paper-search` CLI 完成论文检索、元数据核验、施引/参考文献扩展、正文片段检索、期刊指标查询和 PDF 获取；不要把本 Skill 当作密钥、cookie、账号或下载策略的存储位置。
 
@@ -80,3 +81,3 @@ Reference 读取规则：
 
-本 Skill 只有四个文献主功能。`doctor`、`smoke`、`config`、`skills` 是管理层命令，不属于文献任务本身。
+本 Skill 只有五个文献主功能。`doctor`、`smoke`、`config`、`skills` 是管理层命令，不属于文献任务本身。
 
@@ -86,2 +87,3 @@ | 用户意图 | 能力名 | 首选入口 | 关键边界 |
 | 搜论文、找相关研究、验证 DOI/PMID、做文献初筛 | `metadata_search` | `paper-search search` 集成入口 / `paper-search run search_*` 精确工具入口 | 只返回和核验论文元数据；Sci-Hub 不属于搜索源 |
+| 查询已知论文的施引文献或参考文献 | `citation_expansion` | `paper-search run get_paper_citations` / `paper-search run get_paper_references` | 需要已知 `paperId`、DOI 或 arXiv ID；不是关键词检索 |
 | 查影响因子、JCR/SSCI/中科院分区、JCI、ESI、预警、期刊等级 | `journal_metrics` | `paper-search journal-metrics` / `paper-search run query_journal_metrics` | 这是期刊指标查询，不是论文检索；需要 `EASYSCHOLAR_KEY` |
@@ -88,0 +90,0 @@ | 获取或下载已确认论文的 PDF | `pdf_discovery` | `paper-search download` / `paper-search run download_with_fallback` | 先核验论文身份，再下载；Sci-Hub 是默认开启的最后 fallback |

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