paper-search-cli 0.1.0

package/dist/platforms/BioRxivSearcher.js

@@ -0,0 +1,196 @@
+/**
+ * bioRxiv API集成模块
+ * 支持bioRxiv和medRxiv预印本论文搜索
+ */
+import axios from 'axios';
+import * as fs from 'fs';
+import * as path from 'path';
+import { PaperFactory } from '../models/Paper.js';
+import { PaperSource } from './PaperSource.js';
+import { TIMEOUTS, USER_AGENT } from '../config/constants.js';
+import { logDebug } from '../utils/Logger.js';
+import { RateLimiter } from '../utils/RateLimiter.js';
+import { ErrorHandler } from '../utils/ErrorHandler.js';
+import { downloadPdfFromUrl, safeFilename } from '../utils/PdfDownload.js';
+export class BioRxivSearcher extends PaperSource {
+    serverType;
+    rateLimiter;
+    constructor(serverType = 'biorxiv') {
+        super(serverType, `https://api.biorxiv.org/details/${serverType}`);
+        this.serverType = serverType;
+        // bioRxiv rate limit: 1 req/s, burst=2
+        this.rateLimiter = new RateLimiter({
+            requestsPerSecond: 1,
+            burstCapacity: 2
+        });
+    }
+    getCapabilities() {
+        return {
+            search: true,
+            download: true,
+            fullText: true,
+            citations: false,
+            requiresApiKey: false,
+            supportedOptions: ['maxResults', 'days', 'category']
+        };
+    }
+    /**
+     * 搜索bioRxiv/medRxiv论文
+     */
+    async search(query, options = {}) {
+        try {
+            // 计算日期范围
+            const days = options.days || 30;
+            const endDate = new Date().toISOString().split('T')[0];
+            const startDate = new Date(Date.now() - days * 24 * 60 * 60 * 1000).toISOString().split('T')[0];
+            // 构建搜索URL
+            const searchUrl = `${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;
+            }
+            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 ${papers.length} papers`);
+            return papers.slice(0, options.maxResults || 10);
+        }
+        catch (error) {
+            logDebug(`${this.serverType} Search Error:`, error.message);
+            this.handleHttpError(error, 'search');
+        }
+    }
+    /**
+     * 下载PDF文件
+     */
+    async downloadPdf(paperId, options = {}) {
+        const savePath = options.savePath || './downloads';
+        const candidates = this.pdfUrlCandidates(paperId);
+        let lastError;
+        await this.rateLimiter.waitForPermission();
+        for (const pdfUrl of candidates) {
+            try {
+                return await downloadPdfFromUrl(pdfUrl, savePath, `${this.serverType}_${safeFilename(paperId)}`, {
+                    headers: {
+                        Referer: `https://www.${this.serverType}.org/`,
+                        'User-Agent': 'Mozilla/5.0 (Macintosh; Intel Mac OS X 10_15_7) AppleWebKit/537.36'
+                    }
+                });
+            }
+            catch (error) {
+                lastError = error;
+                logDebug(`${this.serverType} PDF candidate failed: ${pdfUrl}`, error?.message || error);
+            }
+        }
+        throw new Error(`${this.serverType} PDF download failed for ${paperId}. ${lastError?.message || String(lastError)}`);
+    }
+    /**
+     * 读取论文全文内容
+     */
+    async readPaper(paperId, options = {}) {
+        try {
+            const savePath = options.savePath || './downloads';
+            const filePath = path.join(savePath, `${paperId.replace(/\//g, '_')}.pdf`);
+            // 如果PDF不存在，先下载
+            if (!fs.existsSync(filePath)) {
+                await this.downloadPdf(paperId, options);
+            }
+            return `PDF file downloaded at: ${filePath}. Full text extraction requires additional PDF parsing implementation.`;
+        }
+        catch (error) {
+            this.handleHttpError(error, 'read paper');
+        }
+    }
+    /**
+     * 解析搜索响应
+     */
+    parseSearchResponse(data, query, options) {
+        if (!data.collection || !Array.isArray(data.collection)) {
+            return [];
+        }
+        // 如果有查询词，进行文本匹配过滤
+        let filteredCollection = data.collection;
+        if (query && query !== '*' && query.trim()) {
+            const queryLower = query.toLowerCase();
+            filteredCollection = data.collection.filter(item => item.title.toLowerCase().includes(queryLower) ||
+                item.abstract.toLowerCase().includes(queryLower) ||
+                item.authors.toLowerCase().includes(queryLower) ||
+                item.category.toLowerCase().includes(queryLower));
+        }
+        return filteredCollection.map(item => this.parseBioRxivPaper(item))
+            .filter(paper => paper !== null);
+    }
+    pdfUrlCandidates(paperId) {
+        const clean = paperId.trim();
+        if (/v\d+$/i.test(clean)) {
+            return [`https://www.${this.serverType}.org/content/${clean}.full.pdf`];
+        }
+        return [
+            `https://www.${this.serverType}.org/content/${clean}.full.pdf`,
+            `https://www.${this.serverType}.org/content/${clean}v1.full.pdf`
+        ];
+    }
+    /**
+     * 解析单个bioRxiv论文
+     */
+    parseBioRxivPaper(item) {
+        try {
+            // 解析作者
+            const authors = item.authors.split(';').map(author => author.trim());
+            // 解析日期
+            const publishedDate = this.parseDate(item.date);
+            const year = publishedDate?.getFullYear();
+            // 构建URL
+            const paperUrl = `https://www.${this.serverType}.org/content/${item.doi}v${item.version}`;
+            const pdfUrl = `https://www.${this.serverType}.org/content/${item.doi}v${item.version}.full.pdf`;
+            return PaperFactory.create({
+                paperId: item.doi,
+                title: this.cleanText(item.title),
+                authors: authors,
+                abstract: this.cleanText(item.abstract),
+                doi: item.doi,
+                publishedDate: publishedDate,
+                pdfUrl: pdfUrl,
+                url: paperUrl,
+                source: this.serverType,
+                categories: [item.category],
+                keywords: [],
+                citationCount: 0,
+                year: year,
+                extra: {
+                    version: item.version,
+                    type: item.type,
+                    license: item.license,
+                    server: item.server,
+                    corresponding_author: item.author_corresponding,
+                    corresponding_institution: item.author_corresponding_institution
+                }
+            });
+        }
+        catch (error) {
+            logDebug(`Error parsing ${this.serverType} paper:`, error);
+            return null;
+        }
+    }
+}
+/**
+ * medRxiv搜索器 - 继承自BioRxivSearcher
+ */
+export class MedRxivSearcher extends BioRxivSearcher {
+    constructor() {
+        super('medrxiv');
+    }
+}
+//# sourceMappingURL=BioRxivSearcher.js.map

package/dist/platforms/BioRxivSearcher.js.map

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package/dist/platforms/CORESearcher.d.ts

@@ -0,0 +1,16 @@
+import { Paper } from '../models/Paper.js';
+import { PaperSource, SearchOptions, DownloadOptions, PlatformCapabilities } from './PaperSource.js';
+export declare class CORESearcher extends PaperSource {
+    private readonly client;
+    constructor(apiKey?: string);
+    getCapabilities(): PlatformCapabilities;
+    search(query: string, options?: SearchOptions): Promise<Paper[]>;
+    downloadPdf(paperId: string, options?: DownloadOptions): Promise<string>;
+    readPaper(paperId: string, options?: DownloadOptions): Promise<string>;
+    private getDetails;
+    private requestWithRetry;
+    private parseWork;
+    private findPdfUrl;
+    private nameList;
+}
+//# sourceMappingURL=CORESearcher.d.ts.map

package/dist/platforms/CORESearcher.d.ts.map

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package/dist/platforms/CORESearcher.js

@@ -0,0 +1,148 @@
+import axios from 'axios';
+import { PaperFactory } from '../models/Paper.js';
+import { PaperSource } from './PaperSource.js';
+import { TIMEOUTS, USER_AGENT } from '../config/constants.js';
+import { downloadPdfFromUrl, safeFilename } from '../utils/PdfDownload.js';
+import { PDFExtractor } from '../utils/PDFExtractor.js';
+export class CORESearcher extends PaperSource {
+    client;
+    constructor(apiKey) {
+        const configuredKey = apiKey || process.env.PAPER_SEARCH_CORE_API_KEY || process.env.CORE_API_KEY || '';
+        super('core', 'https://api.core.ac.uk/v3', configuredKey);
+        this.client = axios.create({
+            baseURL: this.baseUrl,
+            timeout: TIMEOUTS.DEFAULT,
+            headers: {
+                Accept: 'application/json',
+                'User-Agent': USER_AGENT,
+                ...(configuredKey ? { Authorization: `Bearer ${configuredKey}` } : {})
+            },
+            validateStatus: status => status < 500 || [500, 502, 503, 504].includes(status)
+        });
+    }
+    getCapabilities() {
+        return {
+            search: true,
+            download: true,
+            fullText: true,
+            citations: true,
+            requiresApiKey: false,
+            supportedOptions: ['maxResults', 'year']
+        };
+    }
+    async search(query, options = {}) {
+        try {
+            const response = await this.requestWithRetry('/search/works', {
+                q: query,
+                limit: Math.min(options.maxResults || 10, 100),
+                offset: 0,
+                ...(options.year ? { year: options.year } : {})
+            });
+            const results = Array.isArray(response?.results) ? response.results : [];
+            return results.map((item) => this.parseWork(item)).filter(Boolean);
+        }
+        catch (error) {
+            this.handleHttpError(error, 'search');
+        }
+    }
+    async downloadPdf(paperId, options = {}) {
+        const details = await this.getDetails(paperId);
+        const pdfUrl = details ? this.findPdfUrl(details) : '';
+        if (!pdfUrl) {
+            throw new Error(`CORE paper ${paperId} does not expose an accessible PDF URL`);
+        }
+        return downloadPdfFromUrl(pdfUrl, options.savePath || './downloads', `core_${safeFilename(paperId)}`);
+    }
+    async readPaper(paperId, options = {}) {
+        const details = await this.getDetails(paperId);
+        if (details?.fullText && details.fullText.length > 500) {
+            return details.fullText;
+        }
+        const pdfPath = await this.downloadPdf(paperId, options);
+        const result = await new PDFExtractor().extractFromFile(pdfPath);
+        return result.text || `PDF downloaded to ${pdfPath}, but no text could be extracted.`;
+    }
+    async getDetails(paperId) {
+        try {
+            const response = await this.client.get(`/works/${encodeURIComponent(paperId)}`);
+            if (response.status >= 400)
+                return null;
+            return response.data;
+        }
+        catch {
+            return null;
+        }
+    }
+    async requestWithRetry(path, params) {
+        let lastError;
+        for (let attempt = 0; attempt < 3; attempt += 1) {
+            try {
+                const response = await this.client.get(path, { params });
+                if ([401, 403, 429].includes(response.status) && !this.apiKey) {
+                    return { results: [] };
+                }
+                if ([429, 500, 502, 503, 504].includes(response.status)) {
+                    await new Promise(resolve => setTimeout(resolve, Math.min(8000, 1000 * 2 ** attempt)));
+                    continue;
+                }
+                if ([401, 403].includes(response.status) && this.apiKey) {
+                    const fallback = await axios.get(`${this.baseUrl}${path}`, {
+                        params,
+                        timeout: TIMEOUTS.DEFAULT,
+                        headers: { Accept: 'application/json', 'User-Agent': USER_AGENT }
+                    });
+                    return fallback.data;
+                }
+                if (response.status >= 400) {
+                    throw new Error(`CORE request failed with HTTP ${response.status}`);
+                }
+                return response.data;
+            }
+            catch (error) {
+                lastError = error;
+                await new Promise(resolve => setTimeout(resolve, Math.min(8000, 1000 * 2 ** attempt)));
+            }
+        }
+        throw lastError instanceof Error ? lastError : new Error('CORE request failed');
+    }
+    parseWork(item) {
+        if (!item.id || !item.title)
+            return null;
+        const categories = this.nameList(item.subjects);
+        const keywords = this.nameList(item.tags);
+        const pdfUrl = this.findPdfUrl(item);
+        return PaperFactory.create({
+            paperId: String(item.id),
+            title: this.cleanText(item.title),
+            authors: this.nameList(item.authors),
+            abstract: item.abstract || '',
+            doi: item.doi || '',
+            publishedDate: item.publishedDate ? this.parseDate(item.publishedDate) : null,
+            pdfUrl,
+            url: item.url || (item.doi ? `https://doi.org/${item.doi}` : ''),
+            source: 'core',
+            categories: categories.slice(0, 10),
+            keywords: keywords.slice(0, 10),
+            citationCount: Number(item.citationCount || 0),
+            year: item.yearPublished,
+            extra: {
+                repository: item.repository?.name || '',
+                language: item.language || '',
+                downloadCount: item.downloadCount || 0
+            }
+        });
+    }
+    findPdfUrl(item) {
+        if (item.downloadUrl?.toLowerCase().includes('pdf'))
+            return item.downloadUrl;
+        return (item.fullTextUrls || []).find(url => url.toLowerCase().includes('pdf')) || '';
+    }
+    nameList(values) {
+        if (!Array.isArray(values))
+            return [];
+        return values
+            .map(value => (typeof value === 'string' ? value : value.name || ''))
+            .filter(Boolean);
+    }
+}
+//# sourceMappingURL=CORESearcher.js.map

package/dist/platforms/CORESearcher.js.map

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package/dist/platforms/CrossrefSearcher.d.ts

@@ -0,0 +1,34 @@
+/**
+ * Crossref API Integration
+ *
+ * Crossref is a DOI registration agency providing free access to scholarly metadata.
+ * No API key required, but providing email (mailto parameter) is recommended for polite pool access.
+ *
+ * Documentation: https://api.crossref.org/
+ */
+import { Paper } from '../models/Paper.js';
+import { PaperSource, SearchOptions, DownloadOptions, PlatformCapabilities } from './PaperSource.js';
+export declare class CrossrefSearcher extends PaperSource {
+    private client;
+    private mailto;
+    private readonly rateLimiter;
+    private readonly cache;
+    constructor(mailto?: string);
+    getCapabilities(): PlatformCapabilities;
+    /**
+     * Clean and validate DOI format
+     * @param doi Raw DOI string (may include URL prefixes)
+     * @returns Cleaned DOI or null if invalid
+     */
+    private cleanAndValidateDoi;
+    search(query: string, options?: SearchOptions): Promise<Paper[]>;
+    getPaperByDoi(doi: string): Promise<Paper | null>;
+    getCitations(doi: string): Promise<Paper[]>;
+    getReferences(doi: string): Promise<Paper[]>;
+    downloadPdf(paperId: string, options?: DownloadOptions): Promise<string>;
+    readPaper(paperId: string, options?: DownloadOptions): Promise<string>;
+    private parseSearchResponse;
+    private parsePaper;
+    private extractReferenceDois;
+}
+//# sourceMappingURL=CrossrefSearcher.d.ts.map

package/dist/platforms/CrossrefSearcher.d.ts.map

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