paper-search-cli 0.1.0

package/dist/platforms/PubMedSearcher.js

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+/**
+ * PubMed E-utilities API集成模块
+ * 支持无API密钥的免费使用（3 req/s）和有API密钥的增强使用（10 req/s）
+ */
+import axios from 'axios';
+import * as xml2js from 'xml2js';
+import { PaperFactory } from '../models/Paper.js';
+import { PaperSource } from './PaperSource.js';
+import { RateLimiter } from '../utils/RateLimiter.js';
+import { ErrorHandler } from '../utils/ErrorHandler.js';
+import { TIMEOUTS, USER_AGENT } from '../config/constants.js';
+import { logDebug } from '../utils/Logger.js';
+export class PubMedSearcher extends PaperSource {
+    baseApiUrl;
+    rateLimiter;
+    retMax = 20; // 每次批量获取的最大数量
+    constructor(apiKey) {
+        super('pubmed', 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils', apiKey);
+        this.baseApiUrl = this.baseUrl;
+        // 根据是否有API密钥设置不同的速率限制
+        const requestsPerSecond = apiKey ? 10 : 3;
+        this.rateLimiter = new RateLimiter({
+            requestsPerSecond,
+            burstCapacity: requestsPerSecond,
+            debug: process.env.NODE_ENV === 'development'
+        });
+    }
+    getCapabilities() {
+        return {
+            search: true,
+            download: false, // PubMed不提供直接PDF下载
+            fullText: false, // 只有摘要，不是全文
+            citations: false, // 基础版本不提供被引统计
+            requiresApiKey: false, // 无API密钥也可以使用，但有限制
+            supportedOptions: ['maxResults', 'year', 'author', 'journal', 'sortBy']
+        };
+    }
+    /**
+     * 搜索PubMed文献
+     */
+    async search(query, options = {}) {
+        try {
+            logDebug(`PubMed Search Starting: query="${query}"`, options);
+            // 第一步：使用ESearch获取PMID列表
+            const pmids = await this.searchPMIDs(query, options);
+            if (pmids.length === 0) {
+                return [];
+            }
+            // 第二步：批量获取详细信息
+            const papers = [];
+            for (let i = 0; i < pmids.length; i += this.retMax) {
+                const batch = pmids.slice(i, i + this.retMax);
+                const batchPapers = await this.fetchPaperDetails(batch);
+                papers.push(...batchPapers);
+            }
+            return papers;
+        }
+        catch (error) {
+            logDebug('PubMed Search Error:', error.message);
+            this.handleHttpError(error, 'search');
+        }
+    }
+    /**
+     * 搜索获取PMID列表
+     */
+    async searchPMIDs(query, options) {
+        await this.rateLimiter.waitForPermission();
+        const searchQuery = this.buildSearchQuery(query, options);
+        const params = {
+            db: 'pubmed',
+            term: searchQuery,
+            retmax: (options.maxResults || 10).toString(),
+            retmode: 'xml',
+            sort: this.mapSortField(options.sortBy || 'relevance')
+        };
+        // 添加API密钥（如果有）
+        if (this.apiKey) {
+            params.api_key = this.apiKey;
+        }
+        const url = `${this.baseApiUrl}/esearch.fcgi`;
+        logDebug(`PubMed ESearch Request: GET ${url}`);
+        logDebug('PubMed ESearch params:', params);
+        const response = await ErrorHandler.retryWithBackoff(() => axios.get(url, {
+            params,
+            timeout: TIMEOUTS.DEFAULT,
+            headers: { 'User-Agent': USER_AGENT }
+        }), { context: 'PubMed ESearch' });
+        logDebug(`PubMed ESearch Response: ${response.status} ${response.statusText}`);
+        logDebug('PubMed ESearch Response data:', response.data.substring(0, 500));
+        const result = await this.parseXmlResponse(response.data);
+        let pmids = result.eSearchResult.IdList?.Id || [];
+        // 处理单个ID vs ID数组
+        if (typeof pmids === 'string') {
+            pmids = [pmids];
+        }
+        logDebug(`PubMed Found ${pmids.length} PMIDs:`, pmids.slice(0, 5));
+        return pmids;
+    }
+    /**
+     * 获取论文详细信息
+     */
+    async fetchPaperDetails(pmids) {
+        await this.rateLimiter.waitForPermission();
+        const params = {
+            db: 'pubmed',
+            id: pmids.join(','),
+            retmode: 'xml'
+        };
+        // 添加API密钥（如果有）
+        if (this.apiKey) {
+            params.api_key = this.apiKey;
+        }
+        const url = `${this.baseApiUrl}/efetch.fcgi`;
+        const response = await ErrorHandler.retryWithBackoff(() => axios.get(url, {
+            params,
+            timeout: TIMEOUTS.DEFAULT,
+            headers: { 'User-Agent': USER_AGENT }
+        }), { context: 'PubMed EFetch' });
+        const result = await this.parseXmlResponse(response.data);
+        // 处理xml2js的单个元素vs数组问题
+        let articles = result.PubmedArticleSet?.PubmedArticle || [];
+        if (!Array.isArray(articles)) {
+            articles = [articles]; // 将单个对象转换为数组
+        }
+        return this.parsePubMedArticles(articles);
+    }
+    /**
+     * 构建搜索查询
+     */
+    buildSearchQuery(query, options) {
+        let searchQuery = query;
+        // 添加作者过滤
+        if (options.author) {
+            searchQuery += ` AND ${options.author}[Author]`;
+        }
+        // 添加期刊过滤
+        if (options.journal) {
+            searchQuery += ` AND "${options.journal}"[Journal]`;
+        }
+        // 添加年份过滤
+        if (options.year) {
+            if (options.year.includes('-')) {
+                const [startYear, endYear] = options.year.split('-');
+                if (startYear && endYear) {
+                    searchQuery += ` AND ${startYear}:${endYear}[Publication Date]`;
+                }
+                else if (startYear) {
+                    searchQuery += ` AND ${startYear}:3000[Publication Date]`;
+                }
+                else if (endYear) {
+                    searchQuery += ` AND 1900:${endYear}[Publication Date]`;
+                }
+            }
+            else {
+                searchQuery += ` AND ${options.year}[Publication Date]`;
+            }
+        }
+        // 添加文献类型过滤
+        if (options.publicationType && options.publicationType.length > 0) {
+            const typeQuery = options.publicationType
+                .map(type => `"${type}"[Publication Type]`)
+                .join(' OR ');
+            searchQuery += ` AND (${typeQuery})`;
+        }
+        return searchQuery;
+    }
+    /**
+     * 映射排序字段
+     */
+    mapSortField(sortBy) {
+        const fieldMap = {
+            'relevance': 'relevance',
+            'date': 'pub+date',
+            'citations': 'relevance' // PubMed不直接支持按被引排序
+        };
+        return fieldMap[sortBy] || 'relevance';
+    }
+    /**
+     * 解析XML响应
+     */
+    async parseXmlResponse(xmlData) {
+        const parser = new xml2js.Parser({
+            explicitArray: false, // 简化数组处理
+            mergeAttrs: false,
+            normalize: true,
+            normalizeTags: false,
+            trim: true
+        });
+        logDebug('PubMed XML Parsing - Data preview:', xmlData.substring(0, 200));
+        const result = await parser.parseStringPromise(xmlData);
+        logDebug('PubMed XML Parsed result structure:', JSON.stringify(result, null, 2).substring(0, 1000));
+        return result;
+    }
+    /**
+     * 解析PubMed文章列表
+     */
+    parsePubMedArticles(articles) {
+        return articles.map(article => this.parsePubMedArticle(article))
+            .filter(paper => paper !== null);
+    }
+    /**
+     * 解析单个PubMed文章
+     */
+    parsePubMedArticle(article) {
+        try {
+            const medlineCitation = article.MedlineCitation;
+            const articleData = medlineCitation.Article;
+            const pubmedData = article.PubmedData;
+            // 提取PMID
+            const pmid = medlineCitation.PMID._;
+            // 提取标题
+            const title = articleData.ArticleTitle || 'No title available';
+            // 提取作者
+            const authors = this.extractAuthors(articleData.AuthorList?.Author || []);
+            // 提取摘要
+            const abstract = this.extractAbstract(articleData.Abstract);
+            // 提取期刊信息
+            const journal = articleData.Journal.Title || articleData.Journal.ISOAbbreviation || '';
+            // 提取发布日期
+            const publishedDate = this.extractPublishedDate(articleData.Journal.JournalIssue.PubDate);
+            // 提取DOI和其他ID
+            const { doi, pmc } = this.extractArticleIds([
+                ...(articleData.ArticleIdList?.ArticleId || []),
+                ...(pubmedData.ArticleIdList?.ArticleId || [])
+            ]);
+            // 提取页码
+            const pages = articleData.Pagination?.MedlinePgn || '';
+            // 构建URL
+            const url = `https://pubmed.ncbi.nlm.nih.gov/${pmid}/`;
+            const pdfUrl = pmc ? `https://www.ncbi.nlm.nih.gov/pmc/articles/${pmc}/pdf/` : '';
+            return PaperFactory.create({
+                paperId: pmid,
+                title: this.cleanText(title),
+                authors: authors,
+                abstract: this.cleanText(abstract),
+                doi: doi,
+                publishedDate: publishedDate,
+                pdfUrl: pdfUrl,
+                url: url,
+                source: 'pubmed',
+                journal: journal,
+                volume: articleData.Journal.JournalIssue.Volume || undefined,
+                issue: articleData.Journal.JournalIssue.Issue || undefined,
+                pages: pages || undefined,
+                year: publishedDate?.getFullYear(),
+                extra: {
+                    pmid: pmid,
+                    pmc: pmc || undefined
+                }
+            });
+        }
+        catch (error) {
+            logDebug('Error parsing PubMed article:', error);
+            return null;
+        }
+    }
+    /**
+     * 提取作者信息
+     */
+    extractAuthors(authorList) {
+        if (!Array.isArray(authorList)) {
+            return [];
+        }
+        return authorList.map(author => {
+            if (author.CollectiveName) {
+                return author.CollectiveName;
+            }
+            const lastName = author.LastName || '';
+            const foreName = author.ForeName || author.Initials || '';
+            if (lastName && foreName) {
+                return `${lastName}, ${foreName}`;
+            }
+            else if (lastName) {
+                return lastName;
+            }
+            else if (foreName) {
+                return foreName;
+            }
+            return 'Unknown Author';
+        }).filter(name => name && name !== 'Unknown Author');
+    }
+    /**
+     * 提取摘要
+     */
+    extractAbstract(abstractData) {
+        if (!abstractData) {
+            return '';
+        }
+        if (typeof abstractData.AbstractText === 'string') {
+            return abstractData.AbstractText;
+        }
+        if (Array.isArray(abstractData.AbstractText)) {
+            return abstractData.AbstractText.join(' ');
+        }
+        return '';
+    }
+    /**
+     * 提取发布日期
+     */
+    extractPublishedDate(pubDate) {
+        if (!pubDate) {
+            return null;
+        }
+        const year = pubDate.Year;
+        const month = pubDate.Month;
+        const day = pubDate.Day;
+        if (year) {
+            const monthNum = month ? this.parseMonth(month) : 1;
+            const dayNum = day ? parseInt(day, 10) : 1;
+            return new Date(parseInt(year, 10), monthNum - 1, dayNum);
+        }
+        return null;
+    }
+    /**
+     * 解析月份（支持英文和数字）
+     */
+    parseMonth(month) {
+        const monthMap = {
+            'Jan': 1, 'Feb': 2, 'Mar': 3, 'Apr': 4, 'May': 5, 'Jun': 6,
+            'Jul': 7, 'Aug': 8, 'Sep': 9, 'Oct': 10, 'Nov': 11, 'Dec': 12,
+            'January': 1, 'February': 2, 'March': 3, 'April': 4, 'June': 6,
+            'July': 7, 'August': 8, 'September': 9, 'October': 10, 'November': 11, 'December': 12
+        };
+        const mapped = monthMap[month];
+        if (mapped) {
+            return mapped;
+        }
+        const num = parseInt(month, 10);
+        return (num >= 1 && num <= 12) ? num : 1;
+    }
+    /**
+     * 提取文章ID（DOI、PMC等）
+     */
+    extractArticleIds(articleIds) {
+        let doi = '';
+        let pmc = '';
+        if (Array.isArray(articleIds)) {
+            for (const id of articleIds) {
+                const idType = id.$?.IdType?.toLowerCase();
+                const value = id._;
+                if (idType === 'doi' && !doi) {
+                    doi = value;
+                }
+                else if (idType === 'pmc' && !pmc) {
+                    pmc = value;
+                }
+            }
+        }
+        return { doi, pmc };
+    }
+    /**
+     * PubMed通常不支持直接PDF下载
+     */
+    async downloadPdf(paperId, options) {
+        // 尝试获取PMC链接
+        const paper = await this.getPaperByPmid(paperId);
+        if (paper?.extra?.pmc) {
+            const pmcUrl = `https://www.ncbi.nlm.nih.gov/pmc/articles/${paper.extra.pmc}/pdf/`;
+            throw new Error(`PubMed paper may be available as PDF at PMC: ${pmcUrl}. Direct download not supported through this API.`);
+        }
+        throw new Error('PubMed does not support direct PDF download. Please access the paper through the publisher or PMC.');
+    }
+    /**
+     * PubMed不提供全文内容
+     */
+    async readPaper(paperId, options) {
+        throw new Error('PubMed does not provide full-text content. Only abstracts and metadata are available.');
+    }
+    /**
+     * 根据PMID获取论文信息
+     */
+    async getPaperByPmid(pmid) {
+        try {
+            const papers = await this.fetchPaperDetails([pmid]);
+            return papers.length > 0 ? papers[0] : null;
+        }
+        catch (error) {
+            logDebug('Error getting paper by PMID:', error);
+            return null;
+        }
+    }
+    /**
+     * 根据DOI获取论文信息
+     */
+    async getPaperByDoi(doi) {
+        try {
+            const results = await this.search(`"${doi}"[DOI]`, { maxResults: 1 });
+            return results.length > 0 ? results[0] : null;
+        }
+        catch (error) {
+            logDebug('Error getting paper by DOI from PubMed:', error);
+            return null;
+        }
+    }
+    /**
+     * 获取速率限制器状态
+     */
+    getRateLimiterStatus() {
+        return this.rateLimiter.getStatus();
+    }
+    /**
+     * 验证API密钥（如果提供）
+     */
+    async validateApiKey() {
+        if (!this.apiKey) {
+            return true; // 无API密钥时总是有效（使用免费限制）
+        }
+        try {
+            await this.search('test', { maxResults: 1 });
+            return true;
+        }
+        catch (error) {
+            // API密钥无效通常返回400或403错误
+            if (error.response?.status === 400 || error.response?.status === 403) {
+                return false;
+            }
+            // 其他错误可能是网络问题，认为密钥可能有效
+            return true;
+        }
+    }
+}
+//# sourceMappingURL=PubMedSearcher.js.map

package/dist/platforms/PubMedSearcher.js.map

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package/dist/platforms/SciHubSearcher.d.ts

@@ -0,0 +1,66 @@
+/**
+ * Sci-Hub 论文搜索和下载器
+ * 支持多镜像站点轮询、自动健康检测和故障转移
+ */
+import { PaperSource, SearchOptions, DownloadOptions, PlatformCapabilities } from './PaperSource.js';
+import { Paper } from '../models/Paper.js';
+export declare class SciHubSearcher extends PaperSource {
+    private mirrorSites;
+    private currentMirrorIndex;
+    private axiosInstance;
+    private readonly maxRetries;
+    private readonly mirrorTestTimeout;
+    private lastHealthCheck;
+    private readonly healthCheckInterval;
+    constructor();
+    getCapabilities(): PlatformCapabilities;
+    /**
+     * 检测所有镜像站点的健康状态
+     */
+    private checkMirrorHealth;
+    /**
+     * 获取当前可用的镜像站点
+     */
+    private getCurrentMirror;
+    /**
+     * 标记镜像站点失败并切换到下一个
+     */
+    private markMirrorFailed;
+    /**
+     * 通过 DOI 或 URL 搜索论文
+     */
+    search(query: string, options?: SearchOptions): Promise<Paper[]>;
+    /**
+     * 验证输入是否为有效的 DOI 或 URL
+     */
+    private isValidDOIOrURL;
+    /**
+     * 从 Sci-Hub 获取论文信息
+     */
+    private fetchPaperInfo;
+    /**
+     * 下载 PDF 文件
+     */
+    downloadPdf(paperId: string, options?: DownloadOptions): Promise<string>;
+    /**
+     * 读取论文内容（Sci-Hub 不提供文本提取）
+     */
+    readPaper(paperId: string, options?: DownloadOptions): Promise<string>;
+    /**
+     * 根据 DOI 获取论文
+     */
+    getPaperByDoi(doi: string): Promise<Paper | null>;
+    /**
+     * 获取镜像站点状态
+     */
+    getMirrorStatus(): {
+        url: string;
+        status: string;
+        responseTime?: number;
+    }[];
+    /**
+     * 手动触发健康检查
+     */
+    forceHealthCheck(): Promise<void>;
+}
+//# sourceMappingURL=SciHubSearcher.d.ts.map

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

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