paper-search-cli 0.3.1 → 0.3.2

package/dist/capabilities/metadata-search/handler.js

@@ -0,0 +1,163 @@
+import { TIMEOUTS } from '../../config/constants.js';
+import { PaperFactory } from '../../models/Paper.js';
+import { logDebug } from '../../utils/Logger.js';
+import { withTimeout } from '../../utils/SecurityUtils.js';
+import { getPlatformMetadata, resolvePlatformId } from '../../core/platformMetadata.js';
+import { searchMultipleSources } from './MultiSourceSearchService.js';
+const DOI_LOOKUP_SOURCES = [
+    'crossref',
+    'openalex',
+    'unpaywall',
+    'pubmed',
+    'pmc',
+    'europepmc',
+    'core',
+    'webofscience',
+    'arxiv'
+];
+function jsonTextResponse(text) {
+    return {
+        content: [
+            {
+                type: 'text',
+                text
+            }
+        ]
+    };
+}
+function normalizeDoi(value) {
+    return value
+        .trim()
+        .replace(/^https?:\/\/(?:dx\.)?doi\.org\//i, '')
+        .toLowerCase();
+}
+function paperMatchesDoi(paper, doi) {
+    return normalizeDoi(paper.doi || '') === normalizeDoi(doi);
+}
+export async function handleGenericSearch(platform, args, searchers) {
+    const resolvedPlatform = resolvePlatformId(platform);
+    const searcher = searchers[resolvedPlatform];
+    if (!searcher) {
+        throw new Error(`Unsupported platform: ${platform}`);
+    }
+    const { query, ...searchOptions } = args;
+    const results = await searcher.search(query, searchOptions);
+    const displayName = getPlatformMetadata(platform)?.displayName || platform;
+    return jsonTextResponse(`Found ${results.length} ${displayName} papers.\n\n${JSON.stringify(results.map((paper) => PaperFactory.toDict(paper)), null, 2)}`);
+}
+export async function handleSearchPapers(args, searchers) {
+    const { query, platform, sources, maxResults, year, author, journal, category, days, fetchDetails, fieldsOfStudy, sortBy, sortOrder } = args;
+    const results = [];
+    const searchOptions = {
+        maxResults,
+        year,
+        author,
+        journal,
+        category,
+        days,
+        fetchDetails,
+        fieldsOfStudy,
+        sortBy,
+        sortOrder
+    };
+    if (platform === 'all') {
+        const result = await searchMultipleSources(searchers, query, sources || 'all', searchOptions);
+        return jsonTextResponse(`Found ${result.total} papers across ${result.sources_used.length} source(s).\n\n${JSON.stringify(result, null, 2)}`);
+    }
+    else if (sources) {
+        const result = await searchMultipleSources(searchers, query, sources, searchOptions);
+        return jsonTextResponse(`Found ${result.total} papers across ${result.sources_used.length} source(s).\n\n${JSON.stringify(result, null, 2)}`);
+    }
+    else {
+        const resolvedPlatform = resolvePlatformId(platform);
+        const searcher = searchers[resolvedPlatform];
+        if (!searcher) {
+            throw new Error(`Unsupported platform: ${platform}`);
+        }
+        const platformResults = await searcher.search(query, searchOptions);
+        results.push(...platformResults.map((paper) => PaperFactory.toDict(paper)));
+    }
+    return jsonTextResponse(`Found ${results.length} papers.\n\n${JSON.stringify(results, null, 2)}`);
+}
+export async function handleGetPaperByDoi(args, searchers) {
+    const { doi, platform } = args;
+    const results = [];
+    const sourceResults = {};
+    const errors = {};
+    const failedSources = [];
+    if (platform === 'all') {
+        const selected = DOI_LOOKUP_SOURCES.filter(source => source in searchers);
+        const settled = await Promise.allSettled(selected.map(async (source) => {
+            const searcher = searchers[source];
+            const paper = await withTimeout(searcher.getPaperByDoi(doi), TIMEOUTS.SOURCE_TASK, `${source} DOI lookup timed out after ${TIMEOUTS.SOURCE_TASK}ms`);
+            return { source, paper };
+        }));
+        for (let i = 0; i < settled.length; i += 1) {
+            const source = selected[i];
+            const result = settled[i];
+            if (result.status === 'rejected') {
+                sourceResults[source] = 0;
+                errors[source] = result.reason?.message || String(result.reason);
+                failedSources.push(source);
+                logDebug(`Error getting paper by DOI from ${source}:`, result.reason);
+                continue;
+            }
+            const paper = result.value.paper;
+            if (!paper) {
+                sourceResults[source] = 0;
+                continue;
+            }
+            if (!paperMatchesDoi(paper, doi)) {
+                sourceResults[source] = 0;
+                errors[source] = `Returned DOI ${paper.doi || '(missing)'} did not match requested DOI ${doi}`;
+                failedSources.push(source);
+                continue;
+            }
+            sourceResults[source] = 1;
+            results.push(PaperFactory.toDict(paper));
+        }
+    }
+    else {
+        const searcher = searchers[resolvePlatformId(platform)];
+        if (!searcher) {
+            throw new Error(`Unsupported platform: ${platform}`);
+        }
+        const paper = await searcher.getPaperByDoi(doi);
+        if (paper) {
+            results.push(PaperFactory.toDict(paper));
+        }
+    }
+    if (results.length === 0) {
+        if (platform === 'all') {
+            const result = {
+                doi,
+                sources_requested: 'all',
+                sources_used: DOI_LOOKUP_SOURCES.filter(source => source in searchers),
+                source_results: sourceResults,
+                errors,
+                failed_sources: failedSources,
+                warnings: failedSources.map(source => `${source}: ${errors[source]}`),
+                total: 0,
+                papers: []
+            };
+            return jsonTextResponse(`No paper found with DOI: ${doi}\n\n${JSON.stringify(result, null, 2)}`);
+        }
+        return jsonTextResponse(`No paper found with DOI: ${doi}`);
+    }
+    if (platform === 'all') {
+        const result = {
+            doi,
+            sources_requested: 'all',
+            sources_used: DOI_LOOKUP_SOURCES.filter(source => source in searchers),
+            source_results: sourceResults,
+            errors,
+            failed_sources: failedSources,
+            warnings: failedSources.map(source => `${source}: ${errors[source]}`),
+            total: results.length,
+            papers: results
+        };
+        return jsonTextResponse(`Found ${results.length} paper(s) with DOI ${doi} across ${result.sources_used.length} source(s).\n\n${JSON.stringify(result, null, 2)}`);
+    }
+    return jsonTextResponse(`Found ${results.length} paper(s) with DOI ${doi}:\n\n${JSON.stringify(results, null, 2)}`);
+}
+//# sourceMappingURL=handler.js.map

package/dist/capabilities/metadata-search/handler.js.map

@@ -0,0 +1 @@
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package/dist/capabilities/metadata-search/index.d.ts

@@ -0,0 +1,6 @@
+export { dedupePapers, parseSourceList, searchMultipleSources } from './MultiSourceSearchService.js';
+export { handleGenericSearch, handleGetPaperByDoi, handleSearchPapers } from './handler.js';
+export { GetPaperByDoiSchema, SearchPapersSchema } from './schemas.js';
+export { GET_PAPER_BY_DOI_TOOL, METADATA_SEARCH_TOOLS, SEARCH_PAPERS_TOOL } from './tools.js';
+export type { MultiSourceSearchResult } from './types.js';
+//# sourceMappingURL=index.d.ts.map

package/dist/capabilities/metadata-search/index.d.ts.map

@@ -0,0 +1 @@
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package/dist/capabilities/metadata-search/index.js

@@ -0,0 +1,5 @@
+export { dedupePapers, parseSourceList, searchMultipleSources } from './MultiSourceSearchService.js';
+export { handleGenericSearch, handleGetPaperByDoi, handleSearchPapers } from './handler.js';
+export { GetPaperByDoiSchema, SearchPapersSchema } from './schemas.js';
+export { GET_PAPER_BY_DOI_TOOL, METADATA_SEARCH_TOOLS, SEARCH_PAPERS_TOOL } from './tools.js';
+//# sourceMappingURL=index.js.map

package/dist/capabilities/metadata-search/index.js.map

@@ -0,0 +1 @@
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package/dist/capabilities/metadata-search/schemas.d.ts

@@ -0,0 +1,83 @@
+import { z } from 'zod';
+export declare const SearchPapersSchema: z.ZodEffects<z.ZodObject<{
+    query: z.ZodString;
+    platform: z.ZodDefault<z.ZodOptional<z.ZodUnion<[z.ZodEffects<z.ZodString, string, string>, z.ZodLiteral<"all">]>>>;
+    sources: z.ZodOptional<z.ZodString>;
+    maxResults: z.ZodDefault<z.ZodOptional<z.ZodNumber>>;
+    year: z.ZodOptional<z.ZodString>;
+    author: z.ZodOptional<z.ZodString>;
+    journal: z.ZodOptional<z.ZodString>;
+    category: z.ZodOptional<z.ZodString>;
+    days: z.ZodOptional<z.ZodNumber>;
+    fetchDetails: z.ZodOptional<z.ZodBoolean>;
+    fieldsOfStudy: z.ZodOptional<z.ZodArray<z.ZodString, "many">>;
+    sortBy: z.ZodDefault<z.ZodOptional<z.ZodEnum<["relevance", "date", "citations"]>>>;
+    sortOrder: z.ZodDefault<z.ZodOptional<z.ZodEnum<["asc", "desc"]>>>;
+}, "strip", z.ZodTypeAny, {
+    maxResults: number;
+    sortBy: "relevance" | "date" | "citations";
+    sortOrder: "asc" | "desc";
+    query: string;
+    platform: string;
+    journal?: string | undefined;
+    year?: string | undefined;
+    author?: string | undefined;
+    category?: string | undefined;
+    days?: number | undefined;
+    fetchDetails?: boolean | undefined;
+    fieldsOfStudy?: string[] | undefined;
+    sources?: string | undefined;
+}, {
+    query: string;
+    journal?: string | undefined;
+    year?: string | undefined;
+    maxResults?: number | undefined;
+    author?: string | undefined;
+    category?: string | undefined;
+    sortBy?: "relevance" | "date" | "citations" | undefined;
+    sortOrder?: "asc" | "desc" | undefined;
+    days?: number | undefined;
+    fetchDetails?: boolean | undefined;
+    fieldsOfStudy?: string[] | undefined;
+    platform?: string | undefined;
+    sources?: string | undefined;
+}>, {
+    maxResults: number;
+    sortBy: "relevance" | "date" | "citations";
+    sortOrder: "asc" | "desc";
+    query: string;
+    platform: string;
+    journal?: string | undefined;
+    year?: string | undefined;
+    author?: string | undefined;
+    category?: string | undefined;
+    days?: number | undefined;
+    fetchDetails?: boolean | undefined;
+    fieldsOfStudy?: string[] | undefined;
+    sources?: string | undefined;
+}, {
+    query: string;
+    journal?: string | undefined;
+    year?: string | undefined;
+    maxResults?: number | undefined;
+    author?: string | undefined;
+    category?: string | undefined;
+    sortBy?: "relevance" | "date" | "citations" | undefined;
+    sortOrder?: "asc" | "desc" | undefined;
+    days?: number | undefined;
+    fetchDetails?: boolean | undefined;
+    fieldsOfStudy?: string[] | undefined;
+    platform?: string | undefined;
+    sources?: string | undefined;
+}>;
+export declare const GetPaperByDoiSchema: z.ZodObject<{
+    doi: z.ZodString;
+    platform: z.ZodDefault<z.ZodOptional<z.ZodEnum<["arxiv", "webofscience", "pubmed", "crossref", "openalex", "unpaywall", "pmc", "europepmc", "core", "all"]>>>;
+}, "strip", z.ZodTypeAny, {
+    doi: string;
+    platform: "arxiv" | "webofscience" | "pubmed" | "core" | "crossref" | "openalex" | "unpaywall" | "pmc" | "europepmc" | "all";
+}, {
+    doi: string;
+    platform?: "arxiv" | "webofscience" | "pubmed" | "core" | "crossref" | "openalex" | "unpaywall" | "pmc" | "europepmc" | "all" | undefined;
+}>;
+//# sourceMappingURL=schemas.d.ts.map

package/dist/capabilities/metadata-search/schemas.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"schemas.d.ts","sourceRoot":"","sources":["../../../src/capabilities/metadata-search/schemas.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,CAAC,EAAE,MAAM,KAAK,CAAC;AA2BxB,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAmC3B,CAAC;AAEL,eAAO,MAAM,mBAAmB;;;;;;;;;EAmBtB,CAAC"}

package/dist/capabilities/metadata-search/schemas.js

@@ -0,0 +1,81 @@
+import { z } from 'zod';
+import { HARD_CORE_MAX_RESULTS_CAP, getCoreMaxResultsCap } from '../../config/ResultCaps.js';
+import { isKnownSearchPlatform } from '../../core/platformMetadata.js';
+const SortBySchema = z.enum(['relevance', 'date', 'citations']);
+const SortOrderSchema = z.enum(['asc', 'desc']);
+const SearchPlatformSchema = z
+    .string()
+    .min(1)
+    .refine(value => value === 'all' || isKnownSearchPlatform(value), {
+    message: 'Unsupported search platform'
+});
+function assertCoreMaxResults(value, ctx) {
+    const cap = getCoreMaxResultsCap();
+    if (value > cap) {
+        ctx.addIssue({
+            code: z.ZodIssueCode.too_big,
+            maximum: cap,
+            type: 'number',
+            inclusive: true,
+            message: `Number must be less than or equal to ${cap}`,
+            path: ['maxResults']
+        });
+    }
+}
+export const SearchPapersSchema = z
+    .object({
+    query: z.string().min(1),
+    platform: z
+        .union([SearchPlatformSchema, z.literal('all')])
+        .optional()
+        .default('crossref'),
+    sources: z.string().optional(),
+    maxResults: z.number().int().min(1).max(HARD_CORE_MAX_RESULTS_CAP).optional().default(10),
+    year: z.string().optional(),
+    author: z.string().optional(),
+    journal: z.string().optional(),
+    category: z.string().optional(),
+    days: z.number().int().min(1).max(3650).optional(),
+    fetchDetails: z.boolean().optional(),
+    fieldsOfStudy: z.array(z.string()).optional(),
+    sortBy: SortBySchema.optional().default('relevance'),
+    sortOrder: SortOrderSchema.optional().default('desc')
+})
+    .strip()
+    .superRefine((value, ctx) => {
+    if (!value.sources && value.platform === 'core') {
+        assertCoreMaxResults(value.maxResults, ctx);
+        return;
+    }
+    if (value.maxResults > 100) {
+        ctx.addIssue({
+            code: z.ZodIssueCode.too_big,
+            maximum: 100,
+            type: 'number',
+            inclusive: true,
+            message: 'Number must be less than or equal to 100',
+            path: ['maxResults']
+        });
+    }
+});
+export const GetPaperByDoiSchema = z
+    .object({
+    doi: z.coerce.string().min(1),
+    platform: z
+        .enum([
+        'arxiv',
+        'webofscience',
+        'pubmed',
+        'crossref',
+        'openalex',
+        'unpaywall',
+        'pmc',
+        'europepmc',
+        'core',
+        'all'
+    ])
+        .optional()
+        .default('all')
+})
+    .strip();
+//# sourceMappingURL=schemas.js.map

package/dist/capabilities/metadata-search/schemas.js.map

@@ -0,0 +1 @@
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package/dist/capabilities/metadata-search/tools.d.ts

@@ -0,0 +1,178 @@
+export declare const SEARCH_PAPERS_TOOL: {
+    name: string;
+    description: string;
+    inputSchema: {
+        type: string;
+        properties: {
+            query: {
+                type: string;
+                description: string;
+            };
+            platform: {
+                type: string;
+                enum: string[];
+                description: string;
+            };
+            sources: {
+                type: string;
+                description: string;
+            };
+            maxResults: {
+                type: string;
+                minimum: number;
+                maximum: number;
+                description: string;
+            };
+            year: {
+                type: string;
+                description: string;
+            };
+            author: {
+                type: string;
+                description: string;
+            };
+            journal: {
+                type: string;
+                description: string;
+            };
+            category: {
+                type: string;
+                description: string;
+            };
+            days: {
+                type: string;
+                description: string;
+            };
+            fetchDetails: {
+                type: string;
+                description: string;
+            };
+            fieldsOfStudy: {
+                type: string;
+                items: {
+                    type: string;
+                };
+                description: string;
+            };
+            sortBy: {
+                type: string;
+                enum: string[];
+                description: string;
+            };
+            sortOrder: {
+                type: string;
+                enum: string[];
+                description: string;
+            };
+        };
+        required: string[];
+    };
+};
+export declare const GET_PAPER_BY_DOI_TOOL: {
+    name: string;
+    description: string;
+    inputSchema: {
+        type: string;
+        properties: {
+            doi: {
+                type: string;
+                description: string;
+            };
+            platform: {
+                type: string;
+                enum: string[];
+                description: string;
+            };
+        };
+        required: string[];
+    };
+};
+export declare const METADATA_SEARCH_TOOLS: ({
+    name: string;
+    description: string;
+    inputSchema: {
+        type: string;
+        properties: {
+            query: {
+                type: string;
+                description: string;
+            };
+            platform: {
+                type: string;
+                enum: string[];
+                description: string;
+            };
+            sources: {
+                type: string;
+                description: string;
+            };
+            maxResults: {
+                type: string;
+                minimum: number;
+                maximum: number;
+                description: string;
+            };
+            year: {
+                type: string;
+                description: string;
+            };
+            author: {
+                type: string;
+                description: string;
+            };
+            journal: {
+                type: string;
+                description: string;
+            };
+            category: {
+                type: string;
+                description: string;
+            };
+            days: {
+                type: string;
+                description: string;
+            };
+            fetchDetails: {
+                type: string;
+                description: string;
+            };
+            fieldsOfStudy: {
+                type: string;
+                items: {
+                    type: string;
+                };
+                description: string;
+            };
+            sortBy: {
+                type: string;
+                enum: string[];
+                description: string;
+            };
+            sortOrder: {
+                type: string;
+                enum: string[];
+                description: string;
+            };
+        };
+        required: string[];
+    };
+} | {
+    name: string;
+    description: string;
+    inputSchema: {
+        type: string;
+        properties: {
+            doi: {
+                type: string;
+                description: string;
+            };
+            platform: {
+                type: string;
+                enum: string[];
+                description: string;
+            };
+        };
+        required: string[];
+    };
+})[];
+//# sourceMappingURL=tools.d.ts.map

package/dist/capabilities/metadata-search/tools.d.ts.map

@@ -0,0 +1 @@
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package/dist/capabilities/metadata-search/tools.js

@@ -0,0 +1,75 @@
+import { SEARCH_PLATFORM_VALUES } from '../../core/platformMetadata.js';
+export const SEARCH_PAPERS_TOOL = {
+    name: 'search_papers',
+    description: 'Search academic papers from multiple sources including arXiv, Web of Science, etc.',
+    inputSchema: {
+        type: 'object',
+        properties: {
+            query: { type: 'string', description: 'Search query string' },
+            platform: {
+                type: 'string',
+                enum: [...SEARCH_PLATFORM_VALUES, 'all'],
+                description: 'Platform to search (default: crossref). Use --sources for comma-separated multi-source search. Note: Wiley only supports PDF download by DOI.'
+            },
+            sources: {
+                type: 'string',
+                description: 'Comma-separated source list for multi-source search, or all for every registered search source except DOI-download-only providers. Failed or unconfigured sources are reported in failed_sources/errors. Example: crossref,openalex,pubmed,pmc'
+            },
+            maxResults: {
+                type: 'number',
+                minimum: 1,
+                maximum: 100,
+                description: 'Maximum number of results to return'
+            },
+            year: { type: 'string', description: 'Year filter (e.g., "2023", "2020-2023", "2020-")' },
+            author: { type: 'string', description: 'Author name filter' },
+            journal: { type: 'string', description: 'Journal name filter' },
+            category: { type: 'string', description: 'Category filter (e.g., cs.AI for arXiv)' },
+            days: {
+                type: 'number',
+                description: 'Number of days to search back (bioRxiv/medRxiv only)'
+            },
+            fetchDetails: {
+                type: 'boolean',
+                description: 'Fetch detailed information (IACR only)'
+            },
+            fieldsOfStudy: {
+                type: 'array',
+                items: { type: 'string' },
+                description: 'Fields of study filter (Semantic Scholar only)'
+            },
+            sortBy: {
+                type: 'string',
+                enum: ['relevance', 'date', 'citations'],
+                description: 'Sort results by relevance, date, or citations'
+            },
+            sortOrder: {
+                type: 'string',
+                enum: ['asc', 'desc'],
+                description: 'Sort order: ascending or descending'
+            }
+        },
+        required: ['query']
+    }
+};
+export const GET_PAPER_BY_DOI_TOOL = {
+    name: 'get_paper_by_doi',
+    description: 'Retrieve paper information using DOI from available platforms',
+    inputSchema: {
+        type: 'object',
+        properties: {
+            doi: {
+                type: 'string',
+                description: 'DOI (Digital Object Identifier)'
+            },
+            platform: {
+                type: 'string',
+                enum: ['arxiv', 'webofscience', 'pubmed', 'crossref', 'openalex', 'unpaywall', 'pmc', 'europepmc', 'core', 'all'],
+                description: 'Platform to search'
+            }
+        },
+        required: ['doi']
+    }
+};
+export const METADATA_SEARCH_TOOLS = [SEARCH_PAPERS_TOOL, GET_PAPER_BY_DOI_TOOL];
+//# sourceMappingURL=tools.js.map

package/dist/capabilities/metadata-search/tools.js.map

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package/dist/capabilities/metadata-search/types.d.ts

@@ -0,0 +1,13 @@
+export interface MultiSourceSearchResult {
+    query: string;
+    sources_requested: string;
+    sources_used: string[];
+    source_results: Record<string, number>;
+    errors: Record<string, string>;
+    failed_sources: string[];
+    warnings: string[];
+    total: number;
+    raw_total: number;
+    papers: Record<string, unknown>[];
+}
+//# sourceMappingURL=types.d.ts.map

package/dist/capabilities/metadata-search/types.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"types.d.ts","sourceRoot":"","sources":["../../../src/capabilities/metadata-search/types.ts"],"names":[],"mappings":"AAAA,MAAM,WAAW,uBAAuB;IACtC,KAAK,EAAE,MAAM,CAAC;IACd,iBAAiB,EAAE,MAAM,CAAC;IAC1B,YAAY,EAAE,MAAM,EAAE,CAAC;IACvB,cAAc,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IACvC,MAAM,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IAC/B,cAAc,EAAE,MAAM,EAAE,CAAC;IACzB,QAAQ,EAAE,MAAM,EAAE,CAAC;IACnB,KAAK,EAAE,MAAM,CAAC;IACd,SAAS,EAAE,MAAM,CAAC;IAClB,MAAM,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAAE,CAAC;CACnC"}

package/dist/capabilities/metadata-search/types.js

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=types.js.map

package/dist/capabilities/metadata-search/types.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"types.js","sourceRoot":"","sources":["../../../src/capabilities/metadata-search/types.ts"],"names":[],"mappings":""}