paper-search-cli 0.1.0

package/dist/platforms/CrossrefSearcher.js

@@ -0,0 +1,339 @@
+/**
+ * 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 axios from 'axios';
+import { PaperFactory } from '../models/Paper.js';
+import { PaperSource } from './PaperSource.js';
+import { sanitizeDoi, withTimeout } from '../utils/SecurityUtils.js';
+import { API_ENDPOINTS, DEFAULT_MAILTO, 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 { RequestCache } from '../utils/RequestCache.js';
+export class CrossrefSearcher extends PaperSource {
+    client;
+    mailto;
+    rateLimiter;
+    cache;
+    constructor(mailto) {
+        super('crossref', 'https://api.crossref.org/works', undefined);
+        this.mailto = mailto || process.env.CROSSREF_MAILTO || DEFAULT_MAILTO;
+        this.client = axios.create({
+            baseURL: this.baseUrl,
+            timeout: TIMEOUTS.DEFAULT,
+            headers: {
+                'Accept': 'application/json',
+                'User-Agent': `${USER_AGENT} paper-search-cli/0.1.0 (mailto:${this.mailto})`
+            }
+        });
+        // Crossref polite pool: 50 req/s with mailto, conservative 3 req/s, burst=5
+        this.rateLimiter = new RateLimiter({
+            requestsPerSecond: 3,
+            burstCapacity: 5
+        });
+        this.cache = new RequestCache({
+            maxSize: 100,
+            ttlMs: 3600000 // 1 hour
+        });
+    }
+    getCapabilities() {
+        return {
+            search: true,
+            download: false,
+            fullText: false,
+            citations: true,
+            requiresApiKey: false,
+            supportedOptions: ['maxResults', 'year', 'author', 'sortBy', 'sortOrder']
+        };
+    }
+    /**
+     * Clean and validate DOI format
+     * @param doi Raw DOI string (may include URL prefixes)
+     * @returns Cleaned DOI or null if invalid
+     */
+    cleanAndValidateDoi(doi) {
+        const result = sanitizeDoi(doi);
+        return result.valid ? result.sanitized : null;
+    }
+    async search(query, options = {}) {
+        const customOptions = options;
+        const forceRefresh = customOptions.forceRefresh === true;
+        // Check cache first
+        if (!forceRefresh) {
+            const cacheKey = this.cache.generateKey('crossref', query, options);
+            const cached = this.cache.get(cacheKey);
+            if (cached) {
+                return cached;
+            }
+        }
+        const maxResults = Math.min(options.maxResults || 10, 1000);
+        const params = {
+            query: query,
+            rows: maxResults,
+            mailto: this.mailto
+        };
+        // Build filters
+        const filters = [];
+        // Year filter
+        if (options.year) {
+            const yearMatch = options.year.match(/^(\d{4})(?:-(\d{4})?)?$/);
+            if (yearMatch) {
+                const startYear = yearMatch[1];
+                const endYear = yearMatch[2] || startYear;
+                if (startYear) {
+                    filters.push(`from-pub-date:${startYear}`);
+                }
+                if (endYear && endYear !== startYear) {
+                    filters.push(`until-pub-date:${endYear}`);
+                }
+            }
+        }
+        // Add filters
+        if (filters.length > 0) {
+            params.filter = filters.join(',');
+        }
+        // Sorting
+        const sortMapping = {
+            'relevance': 'relevance',
+            'date': 'published',
+            'citations': 'is-referenced-by-count'
+        };
+        params.sort = sortMapping[options.sortBy || 'relevance'] || 'relevance';
+        params.order = options.sortOrder === 'asc' ? 'asc' : 'desc';
+        try {
+            await this.rateLimiter.waitForPermission();
+            const response = await ErrorHandler.retryWithBackoff(() => this.client.get('', { params }), { context: 'Crossref search' });
+            if (response.status === 200 && response.data?.message?.items) {
+                const papers = this.parseSearchResponse(response.data);
+                // Cache results
+                const cacheKey = this.cache.generateKey('crossref', query, options);
+                this.cache.set(cacheKey, papers);
+                return papers;
+            }
+            return [];
+        }
+        catch (error) {
+            this.handleHttpError(error, 'search');
+        }
+    }
+    async getPaperByDoi(doi) {
+        const cleanDoi = this.cleanAndValidateDoi(doi);
+        if (!cleanDoi) {
+            return null;
+        }
+        try {
+            // Encode DOI for URL path (DOIs can contain special characters like /)
+            const encodedDoi = encodeURIComponent(cleanDoi);
+            await this.rateLimiter.waitForPermission();
+            const response = await ErrorHandler.retryWithBackoff(() => this.client.get(`/${encodedDoi}`, { params: { mailto: this.mailto } }), { context: 'Crossref getPaperByDoi' });
+            if (response.status === 200 && response.data?.message) {
+                const paper = this.parsePaper(response.data.message);
+                // Extract references
+                if (paper) {
+                    const references = this.extractReferenceDois(response.data.message);
+                    paper.references = references;
+                }
+                return paper;
+            }
+            return null;
+        }
+        catch (error) {
+            // 404 means not found
+            if (error?.response?.status === 404) {
+                return null;
+            }
+            this.handleHttpError(error, 'getPaperByDoi');
+            return null;
+        }
+    }
+    async getCitations(doi) {
+        // Crossref API doesn't directly provide citations
+        // Use OpenCitations COCI API as supplement
+        const cleanDoi = this.cleanAndValidateDoi(doi);
+        if (!cleanDoi) {
+            return [];
+        }
+        try {
+            // Encode DOI for URL path
+            const encodedDoi = encodeURIComponent(cleanDoi);
+            // Wrap with timeout for additional protection
+            const response = await withTimeout(axios.get(`${API_ENDPOINTS.OPENCITATIONS}/citations/${encodedDoi}`, { timeout: TIMEOUTS.DEFAULT }), TIMEOUTS.DEFAULT + TIMEOUTS.BUFFER, 'OpenCitations API request timed out');
+            if (response.status !== 200) {
+                return [];
+            }
+            const citingDois = [];
+            for (const item of response.data || []) {
+                if (item.citing) {
+                    citingDois.push(item.citing);
+                }
+            }
+            if (citingDois.length === 0) {
+                return [];
+            }
+            // Fetch citing papers (limit to 50)
+            const papers = [];
+            for (const citingDoi of citingDois.slice(0, 50)) {
+                try {
+                    const paper = await this.getPaperByDoi(citingDoi);
+                    if (paper) {
+                        papers.push(paper);
+                    }
+                }
+                catch (error) {
+                    // Skip failed DOIs
+                }
+            }
+            return papers;
+        }
+        catch (error) {
+            this.handleHttpError(error, 'getCitations');
+        }
+    }
+    async getReferences(doi) {
+        try {
+            const paper = await this.getPaperByDoi(doi);
+            if (!paper || !paper.references || paper.references.length === 0) {
+                return [];
+            }
+            // Fetch reference papers (limit to 50)
+            const papers = [];
+            for (const refDoi of paper.references.slice(0, 50)) {
+                try {
+                    const refPaper = await this.getPaperByDoi(refDoi);
+                    if (refPaper) {
+                        papers.push(refPaper);
+                    }
+                }
+                catch (error) {
+                    // Skip failed DOIs
+                }
+            }
+            return papers;
+        }
+        catch (error) {
+            this.handleHttpError(error, 'getReferences');
+        }
+    }
+    async downloadPdf(paperId, options) {
+        throw new Error('Crossref does not support direct PDF download');
+    }
+    async readPaper(paperId, options) {
+        throw new Error('Crossref does not support full text extraction');
+    }
+    parseSearchResponse(data) {
+        const papers = [];
+        const items = data.message?.items || [];
+        for (const item of items) {
+            const paper = this.parsePaper(item);
+            if (paper) {
+                papers.push(paper);
+            }
+        }
+        return papers;
+    }
+    parsePaper(data) {
+        try {
+            const doi = data.DOI || '';
+            // Extract title
+            const titleList = data.title || [];
+            const title = titleList[0] || 'No title';
+            // Extract authors
+            const authors = [];
+            for (const author of data.author || []) {
+                const given = author.given || '';
+                const family = author.family || '';
+                const fullName = `${given} ${family}`.trim();
+                if (fullName) {
+                    authors.push(fullName);
+                }
+            }
+            // Extract abstract - may contain HTML tags
+            let abstract = data.abstract || '';
+            if (abstract) {
+                // Remove HTML tags
+                abstract = abstract.replace(/<[^>]+>/g, '');
+            }
+            // Extract publication date
+            let publishedDate = null;
+            let year;
+            const dateData = data['published-print'] ||
+                data['published-online'] ||
+                data['published'] ||
+                data['created'];
+            if (dateData && dateData['date-parts']?.[0]) {
+                const dateParts = dateData['date-parts'][0];
+                if (dateParts.length > 0 && typeof dateParts[0] === 'number') {
+                    year = dateParts[0];
+                    const month = dateParts[1] || 1;
+                    const day = dateParts[2] || 1;
+                    try {
+                        publishedDate = new Date(year, month - 1, day);
+                    }
+                    catch {
+                        // Ignore date parsing errors
+                    }
+                }
+            }
+            // Extract journal name
+            const containerTitleList = data['container-title'] || [];
+            const journal = containerTitleList[0] || undefined;
+            // Extract publisher
+            const publisher = data.publisher || '';
+            // Extract citation count
+            const citationCount = data['is-referenced-by-count'] || 0;
+            // Extract URL
+            const url = data.URL || (doi ? `https://doi.org/${doi}` : '');
+            // Extract pages, volume, issue
+            const pages = data.page || undefined;
+            const volume = data.volume || undefined;
+            const issue = data.issue || undefined;
+            // Document type
+            const docType = data.type || '';
+            return PaperFactory.create({
+                paperId: doi,
+                title: title,
+                authors: authors,
+                abstract: abstract,
+                source: 'crossref',
+                publishedDate: publishedDate,
+                year: year,
+                journal: journal,
+                doi: doi,
+                url: url,
+                pdfUrl: '',
+                volume: volume,
+                issue: issue,
+                pages: pages,
+                citationCount: citationCount,
+                extra: {
+                    publisher: publisher,
+                    type: docType,
+                    issn: data.ISSN || [],
+                    isbn: data.ISBN || [],
+                    subjects: data.subject || []
+                }
+            });
+        }
+        catch (error) {
+            logDebug('Error parsing Crossref paper:', error.message);
+            return null;
+        }
+    }
+    extractReferenceDois(data) {
+        const references = [];
+        const referenceData = data.reference || [];
+        for (const ref of referenceData) {
+            const doi = ref.DOI;
+            if (doi) {
+                references.push(doi);
+            }
+        }
+        return references;
+    }
+}
+//# sourceMappingURL=CrossrefSearcher.js.map

package/dist/platforms/CrossrefSearcher.js.map

@@ -0,0 +1 @@
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package/dist/platforms/EuropePMCSearcher.d.ts

@@ -0,0 +1,20 @@
+import { Paper } from '../models/Paper.js';
+import { PaperSource, SearchOptions, DownloadOptions, PlatformCapabilities } from './PaperSource.js';
+export declare class EuropePMCSearcher extends PaperSource {
+    private readonly client;
+    constructor();
+    getCapabilities(): PlatformCapabilities;
+    search(query: string, options?: SearchOptions): Promise<Paper[]>;
+    downloadPdf(paperId: string, options?: DownloadOptions): Promise<string>;
+    readPaper(paperId: string, options?: DownloadOptions): Promise<string>;
+    private parseItem;
+    private getDetails;
+    private normalizeId;
+    private parseAuthors;
+    private parsePublicationDate;
+    private findPdfUrl;
+    private findPdfUrls;
+    private isEuropePmcRenderUrl;
+    private findLandingUrl;
+}
+//# sourceMappingURL=EuropePMCSearcher.d.ts.map

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

@@ -0,0 +1 @@
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package/dist/platforms/EuropePMCSearcher.js

@@ -0,0 +1,173 @@
+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 EuropePMCSearcher extends PaperSource {
+    client;
+    constructor() {
+        super('europepmc', 'https://www.ebi.ac.uk/europepmc/webservices/rest');
+        this.client = axios.create({
+            baseURL: this.baseUrl,
+            timeout: TIMEOUTS.DEFAULT,
+            headers: {
+                Accept: 'application/json',
+                'User-Agent': USER_AGENT
+            }
+        });
+    }
+    getCapabilities() {
+        return {
+            search: true,
+            download: true,
+            fullText: true,
+            citations: true,
+            requiresApiKey: false,
+            supportedOptions: ['maxResults', 'year']
+        };
+    }
+    async search(query, options = {}) {
+        try {
+            const response = await this.client.get('/search', {
+                params: {
+                    query,
+                    pageSize: Math.min(options.maxResults || 10, 100),
+                    format: 'json',
+                    resultType: 'core',
+                    ...(options.year ? { year: options.year } : {})
+                }
+            });
+            const results = response.data?.resultList?.result || [];
+            return results.map((item) => this.parseItem(item)).filter(Boolean);
+        }
+        catch (error) {
+            this.handleHttpError(error, 'search');
+        }
+    }
+    async downloadPdf(paperId, options = {}) {
+        const details = await this.getDetails(paperId);
+        const pdfUrls = details ? this.findPdfUrls(details) : [];
+        if (pdfUrls.length === 0) {
+            throw new Error(`Europe PMC paper ${paperId} does not expose an accessible PDF URL`);
+        }
+        const errors = [];
+        for (const pdfUrl of pdfUrls) {
+            try {
+                return await downloadPdfFromUrl(pdfUrl, options.savePath || './downloads', `europepmc_${safeFilename(paperId)}`);
+            }
+            catch (error) {
+                errors.push(`${pdfUrl}: ${error?.message || String(error)}`);
+            }
+        }
+        throw new Error(`Europe PMC paper ${paperId} PDF candidates failed. ${errors.join(' | ')}`);
+    }
+    async readPaper(paperId, options = {}) {
+        const pdfPath = await this.downloadPdf(paperId, options);
+        const result = await new PDFExtractor().extractFromFile(pdfPath);
+        return result.text || `PDF downloaded to ${pdfPath}, but no text could be extracted.`;
+    }
+    parseItem(item) {
+        if (!item.id || !item.title)
+            return null;
+        const paperId = this.normalizeId(item);
+        const doi = item.doi || item.doiId || '';
+        const pdfUrl = this.findPdfUrl(item);
+        const landingUrl = this.findLandingUrl(item, paperId, doi);
+        const keywords = item.keywordList?.keyword;
+        return PaperFactory.create({
+            paperId,
+            title: this.cleanText(item.title),
+            authors: this.parseAuthors(item),
+            abstract: item.abstractText || '',
+            doi,
+            publishedDate: this.parsePublicationDate(item),
+            pdfUrl,
+            url: landingUrl,
+            source: 'europepmc',
+            journal: item.journalTitle || '',
+            keywords: Array.isArray(keywords) ? keywords : keywords ? [keywords] : [],
+            citationCount: Number(item.citedByCount || 0),
+            year: item.pubYear ? Number(item.pubYear) || undefined : undefined,
+            extra: {
+                issn: item.journalISSN || '',
+                isOpenAccess: item.isOpenAccess === 'Y',
+                openAccessLicence: item.openAccessLicence || '',
+                pmid: item.pmid || '',
+                pmcid: item.pmcid || ''
+            }
+        });
+    }
+    async getDetails(paperId) {
+        const query = paperId.startsWith('PMID:')
+            ? `ext_id:${paperId.replace('PMID:', '')} src:med`
+            : paperId.startsWith('PMC')
+                ? paperId
+                : paperId.startsWith('10.')
+                    ? `doi:${paperId}`
+                    : `ext_id:${paperId}`;
+        const response = await this.client.get('/search', {
+            params: { query, format: 'json', resultType: 'core', pageSize: 1 }
+        });
+        return response.data?.resultList?.result?.[0] || null;
+    }
+    normalizeId(item) {
+        if (item.source === 'MED')
+            return `PMID:${item.id}`;
+        if (item.source === 'PMC')
+            return item.id?.startsWith('PMC') ? item.id : `PMC${item.id}`;
+        return item.id || item.doi || '';
+    }
+    parseAuthors(item) {
+        const authors = item.authorList?.author || [];
+        if (!Array.isArray(authors))
+            return [];
+        return authors
+            .map(author => (typeof author === 'string' ? author : author.fullName || ''))
+            .filter(Boolean);
+    }
+    parsePublicationDate(item) {
+        if (!item.pubYear)
+            return null;
+        const month = String(item.pubMonth || '1').padStart(2, '0');
+        const day = String(item.pubDay || '1').padStart(2, '0');
+        return this.parseDate(`${item.pubYear}-${month}-${day}`);
+    }
+    findPdfUrl(item) {
+        return this.findPdfUrls(item)[0] || '';
+    }
+    findPdfUrls(item) {
+        const urls = item.fullTextUrlList?.fullTextUrl;
+        const list = Array.isArray(urls) ? urls : urls ? [urls] : [];
+        const pdfs = list.filter(entry => String(entry.documentStyle || '').toLowerCase() === 'pdf' && entry.url);
+        const direct = pdfs
+            .map(entry => entry.url || '')
+            .filter(url => url && !this.isEuropePmcRenderUrl(url) && !url.startsWith('ftp://'));
+        const render = pdfs
+            .map(entry => entry.url || '')
+            .filter(url => this.isEuropePmcRenderUrl(url));
+        const pmcid = item.pmcid || (item.source === 'PMC' ? item.id : '');
+        const ncbiRender = pmcid
+            ? [`https://www.ncbi.nlm.nih.gov/pmc/articles/${pmcid.startsWith('PMC') ? pmcid : `PMC${pmcid}`}/pdf/`]
+            : [];
+        return [...direct, ...render, ...ncbiRender].filter((url, index, urls) => url && urls.indexOf(url) === index);
+    }
+    isEuropePmcRenderUrl(url) {
+        return /europepmc\.org\/articles\/[^?]+\?pdf=render/i.test(url);
+    }
+    findLandingUrl(item, paperId, doi) {
+        const urls = item.fullTextUrlList?.fullTextUrl;
+        const list = Array.isArray(urls) ? urls : urls ? [urls] : [];
+        const html = list.find(entry => entry.documentStyle === 'html' && entry.url)?.url || '';
+        if (html)
+            return html;
+        if (doi)
+            return `https://doi.org/${doi}`;
+        if (paperId.startsWith('PMID:'))
+            return `https://pubmed.ncbi.nlm.nih.gov/${paperId.replace('PMID:', '')}/`;
+        if (paperId.startsWith('PMC'))
+            return `https://www.ncbi.nlm.nih.gov/pmc/articles/${paperId}/`;
+        return '';
+    }
+}
+//# sourceMappingURL=EuropePMCSearcher.js.map

package/dist/platforms/EuropePMCSearcher.js.map

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package/dist/platforms/GoogleScholarSearcher.d.ts

@@ -0,0 +1,77 @@
+/**
+ * Google Scholar搜索器 - 网页抓取实现
+ * 基于HTML解析，包含反检测机制
+ */
+import { Paper } from '../models/Paper.js';
+import { PaperSource, SearchOptions, DownloadOptions, PlatformCapabilities } from './PaperSource.js';
+interface GoogleScholarOptions extends SearchOptions {
+    /** 语言设置 */
+    language?: string;
+    /** 时间范围（年份） */
+    yearLow?: number;
+    yearHigh?: number;
+}
+export declare class GoogleScholarSearcher extends PaperSource {
+    private readonly scholarUrl;
+    private readonly userAgents;
+    constructor();
+    getCapabilities(): PlatformCapabilities;
+    /**
+     * 搜索Google Scholar论文
+     */
+    search(query: string, options?: GoogleScholarOptions): Promise<Paper[]>;
+    /**
+     * Google Scholar不支持直接PDF下载
+     */
+    downloadPdf(paperId: string, options?: DownloadOptions): Promise<string>;
+    /**
+     * Google Scholar不提供全文内容
+     */
+    readPaper(paperId: string, options?: DownloadOptions): Promise<string>;
+    /**
+     * 构建搜索参数
+     */
+    private buildSearchParams;
+    /**
+     * 发起Scholar请求
+     */
+    private makeScholarRequest;
+    /**
+     * 解析单个Scholar搜索结果
+     */
+    private parseScholarResult;
+    /**
+     * 提取作者信息
+     */
+    private extractAuthors;
+    /**
+     * 提取年份
+     */
+    private extractYear;
+    /**
+     * 提取期刊信息
+     */
+    private extractJournal;
+    /**
+     * 提取引用次数
+     */
+    private extractCitationCount;
+    /**
+     * 生成论文ID
+     */
+    private generatePaperId;
+    /**
+     * 简单哈希函数
+     */
+    private simpleHash;
+    /**
+     * 获取随机User-Agent
+     */
+    private getRandomUserAgent;
+    /**
+     * 随机延迟
+     */
+    private randomDelay;
+}
+export {};
+//# sourceMappingURL=GoogleScholarSearcher.d.ts.map

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

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