biorxiv 0.0.0

package/dist/cli/src/api/api-client.d.ts

@@ -0,0 +1,96 @@
+/**
+ * openRxiv API Client
+ * Provides access to bioRxiv and medRxiv APIs for fetching preprint metadata
+ */
+export interface WorkDetails {
+    doi: string;
+    title: string;
+    authors: string;
+    author_corresponding: string;
+    author_corresponding_institution: string;
+    date: string;
+    version: string;
+    type: string;
+    license: string;
+    category: string;
+    jats_xml_path: string;
+    abstract: string;
+    funding: FundingInfo[];
+    published: string;
+    server: 'biorxiv' | 'medrxiv';
+}
+export interface FundingInfo {
+    name: string;
+    id: string;
+    'id-type': string;
+    award: string;
+}
+export interface ApiResponse {
+    collection: WorkDetails[];
+    messages: ApiMessage[];
+}
+export interface ApiMessage {
+    cursor: number;
+    count: number;
+    total: number;
+    limit: number;
+    offset: number;
+}
+export interface ApiOptions {
+    format?: 'json' | 'xml' | 'html';
+    server?: 'biorxiv' | 'medrxiv';
+    timeout?: number;
+}
+export declare class OpenRxivApiClient {
+    private options;
+    private baseUrl;
+    private defaultTimeout;
+    constructor(options?: ApiOptions);
+    /**
+     * Get content details for a specific DOI
+     * Endpoint: /details/[server]/[DOI]/na/[format]
+     * Note: The API expects base DOIs without version numbers
+     */
+    getContentDetail(doi: string, options?: Partial<ApiOptions>): Promise<WorkDetails | null>;
+    /**
+     * Get content details for multiple DOIs
+     */
+    getContentDetails(dois: string[], options?: Partial<ApiOptions>): Promise<(WorkDetails | null)[]>;
+    /**
+     * Get all versions of a preprint
+     * This is useful for versioned preprints where the API returns multiple versions
+     */
+    getAllVersions(doi: string, options?: Partial<ApiOptions>): Promise<WorkDetails[]>;
+    /**
+     * Get content details for a date range
+     * Endpoint: /details/[server]/[start_date]/[end_date]/[cursor]
+     */
+    getContentDetailsByDateRange(startDate: string, endDate: string, cursor?: number, options?: Partial<ApiOptions>): Promise<ApiResponse | null>;
+    /**
+     * Get content details for recent posts
+     * Endpoint: /details/[server]/[count]/[cursor]
+     */
+    getRecentContentDetails(count: number, cursor?: number, options?: Partial<ApiOptions>): Promise<ApiResponse | null>;
+    /**
+     * Get content details for recent days
+     * Endpoint: /details/[server]/[days]d/[cursor]
+     */
+    getContentDetailsByDays(days: number, cursor?: number, options?: Partial<ApiOptions>): Promise<ApiResponse | null>;
+    /**
+     * Get content details with subject category filter
+     */
+    getContentDetailsByCategory(startDate: string, endDate: string, category: string, cursor?: number, options?: Partial<ApiOptions>): Promise<ApiResponse | null>;
+    /**
+     * Make HTTP request with timeout and error handling
+     */
+    private makeRequest;
+}
+/**
+ * Utility function to create a bioRxiv API client
+ */
+export declare function createOpenRxivApiClient(options?: ApiOptions): OpenRxivApiClient;
+/**
+ * Utility function to extract server from DOI
+ */
+export declare function getServerFromDOI(doi: string): 'biorxiv' | 'medrxiv';
+//# sourceMappingURL=api-client.d.ts.map

package/dist/cli/src/api/api-client.d.ts.map

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package/dist/cli/src/api/api-client.js

@@ -0,0 +1,257 @@
+/**
+ * openRxiv API Client
+ * Provides access to bioRxiv and medRxiv APIs for fetching preprint metadata
+ */
+import version from '../version.js';
+export class OpenRxivApiClient {
+    constructor(options = {}) {
+        this.options = options;
+        this.baseUrl = 'https://api.biorxiv.org';
+        this.defaultTimeout = 10000; // 10 seconds
+        this.options = {
+            format: 'json',
+            server: 'biorxiv',
+            timeout: this.defaultTimeout,
+            ...options,
+        };
+    }
+    /**
+     * Get content details for a specific DOI
+     * Endpoint: /details/[server]/[DOI]/na/[format]
+     * Note: The API expects base DOIs without version numbers
+     */
+    async getContentDetail(doi, options) {
+        const opts = { ...this.options, ...options };
+        const server = opts.server || 'biorxiv';
+        const format = opts.format || 'json';
+        try {
+            // Remove version number from DOI for API query
+            const baseDOI = doi.replace(/v\d+$/, '');
+            // Don't encode the DOI - the API expects literal forward slashes
+            const url = `${this.baseUrl}/details/${server}/${baseDOI}/na/${format}`;
+            console.log(`🔍 Fetching content details from: ${url}`);
+            const response = await this.makeRequest(url, opts.timeout);
+            if (!response) {
+                return null;
+            }
+            // Parse response based on format
+            let data;
+            if (format === 'json') {
+                data = response;
+            }
+            else {
+                // For XML/HTML, we'd need to parse differently
+                throw new Error(`Format ${format} not yet implemented`);
+            }
+            // Return the first (and should be only) item in the collection
+            if (data.collection && data.collection.length > 0) {
+                return data.collection[0];
+            }
+            return null;
+        }
+        catch (error) {
+            console.error(`❌ Error fetching content details for DOI ${doi}:`, error);
+            throw new Error(`Failed to fetch content details: ${error instanceof Error ? error.message : 'Unknown error'}`);
+        }
+    }
+    /**
+     * Get content details for multiple DOIs
+     */
+    async getContentDetails(dois, options) {
+        const results = await Promise.allSettled(dois.map((doi) => this.getContentDetail(doi, options)));
+        return results.map((result) => {
+            if (result.status === 'fulfilled') {
+                return result.value;
+            }
+            else {
+                console.error('Failed to fetch DOI:', result.reason);
+                return null;
+            }
+        });
+    }
+    /**
+     * Get all versions of a preprint
+     * This is useful for versioned preprints where the API returns multiple versions
+     */
+    async getAllVersions(doi, options) {
+        const opts = { ...this.options, ...options };
+        const server = opts.server || 'biorxiv';
+        const format = opts.format || 'json';
+        try {
+            // Remove version number from DOI for API query
+            const baseDOI = doi.replace(/v\d+$/, '');
+            // Don't encode the DOI - the API expects literal forward slashes
+            const url = `${this.baseUrl}/details/${server}/${baseDOI}/na/${format}`;
+            console.log(`🔍 Fetching all versions from: ${url}`);
+            const response = await this.makeRequest(url, opts.timeout);
+            if (!response) {
+                return [];
+            }
+            // Parse response based on format
+            let data;
+            if (format === 'json') {
+                data = response;
+            }
+            else {
+                // For XML/HTML, we'd need to parse differently
+                throw new Error(`Format ${format} not yet implemented`);
+            }
+            // Return all versions in the collection
+            if (data.collection && data.collection.length > 0) {
+                return data.collection;
+            }
+            return [];
+        }
+        catch (error) {
+            console.error(`❌ Error fetching all versions for DOI ${doi}:`, error);
+            throw new Error(`Failed to fetch all versions: ${error instanceof Error ? error.message : 'Unknown error'}`);
+        }
+    }
+    /**
+     * Get content details for a date range
+     * Endpoint: /details/[server]/[start_date]/[end_date]/[cursor]
+     */
+    async getContentDetailsByDateRange(startDate, endDate, cursor = 0, options) {
+        const opts = { ...this.options, ...options };
+        const server = opts.server || 'biorxiv';
+        const format = opts.format || 'json';
+        try {
+            const url = `${this.baseUrl}/details/${server}/${startDate}/${endDate}/${cursor}/${format}`;
+            console.log(`🔍 Fetching content details for date range: ${startDate} to ${endDate}`);
+            const response = await this.makeRequest(url, opts.timeout);
+            if (!response) {
+                return null;
+            }
+            return response;
+        }
+        catch (error) {
+            console.error(`❌ Error fetching content details for date range:`, error);
+            throw new Error(`Failed to fetch content details: ${error instanceof Error ? error.message : 'Unknown error'}`);
+        }
+    }
+    /**
+     * Get content details for recent posts
+     * Endpoint: /details/[server]/[count]/[cursor]
+     */
+    async getRecentContentDetails(count, cursor = 0, options) {
+        const opts = { ...this.options, ...options };
+        const server = opts.server || 'biorxiv';
+        const format = opts.format || 'json';
+        try {
+            const url = `${this.baseUrl}/details/${server}/${count}/${cursor}/${format}`;
+            console.log(`🔍 Fetching ${count} recent content details`);
+            const response = await this.makeRequest(url, opts.timeout);
+            if (!response) {
+                return null;
+            }
+            return response;
+        }
+        catch (error) {
+            console.error(`❌ Error fetching recent content details:`, error);
+            throw new Error(`Failed to fetch recent content details: ${error instanceof Error ? error.message : 'Unknown error'}`);
+        }
+    }
+    /**
+     * Get content details for recent days
+     * Endpoint: /details/[server]/[days]d/[cursor]
+     */
+    async getContentDetailsByDays(days, cursor = 0, options) {
+        const opts = { ...this.options, ...options };
+        const server = opts.server || 'biorxiv';
+        const format = opts.format || 'json';
+        try {
+            const url = `${this.baseUrl}/details/${server}/${days}d/${cursor}/${format}`;
+            console.log(`🔍 Fetching content details for last ${days} days`);
+            const response = await this.makeRequest(url, opts.timeout);
+            if (!response) {
+                return null;
+            }
+            return response;
+        }
+        catch (error) {
+            console.error(`❌ Error fetching content details for days:`, error);
+            throw new Error(`Failed to fetch content details: ${error instanceof Error ? error.message : 'Unknown error'}`);
+        }
+    }
+    /**
+     * Get content details with subject category filter
+     */
+    async getContentDetailsByCategory(startDate, endDate, category, cursor = 0, options) {
+        const opts = { ...this.options, ...options };
+        const server = opts.server || 'biorxiv';
+        const format = opts.format || 'json';
+        try {
+            // Encode category (replace spaces with underscores or URL encode)
+            const encodedCategory = category.replace(/\s+/g, '_');
+            const url = `${this.baseUrl}/details/${server}/${startDate}/${endDate}/${cursor}/${format}?category=${encodedCategory}`;
+            console.log(`🔍 Fetching content details for category: ${category}`);
+            const response = await this.makeRequest(url, opts.timeout);
+            if (!response) {
+                return null;
+            }
+            return response;
+        }
+        catch (error) {
+            console.error(`❌ Error fetching content details for category:`, error);
+            throw new Error(`Failed to fetch content details: ${error instanceof Error ? error.message : 'Unknown error'}`);
+        }
+    }
+    /**
+     * Make HTTP request with timeout and error handling
+     */
+    async makeRequest(url, timeout) {
+        const controller = new AbortController();
+        const timeoutId = setTimeout(() => controller.abort(), timeout || this.defaultTimeout);
+        try {
+            const response = await fetch(url, {
+                signal: controller.signal,
+                headers: {
+                    Accept: 'application/json',
+                    'User-Agent': `biorxiv-cli/${version}`,
+                },
+            });
+            clearTimeout(timeoutId);
+            if (!response.ok) {
+                if (response.status === 404) {
+                    console.log(`📭 No content found for the requested DOI`);
+                    return null;
+                }
+                throw new Error(`HTTP ${response.status}: ${response.statusText}`);
+            }
+            const contentType = response.headers.get('content-type');
+            if (contentType && contentType.includes('application/json')) {
+                return await response.json();
+            }
+            else {
+                return await response.text();
+            }
+        }
+        catch (error) {
+            clearTimeout(timeoutId);
+            if (error instanceof Error) {
+                if (error.name === 'AbortError') {
+                    throw new Error('Request timed out');
+                }
+                throw error;
+            }
+            throw new Error('Unknown error occurred');
+        }
+    }
+}
+/**
+ * Utility function to create a bioRxiv API client
+ */
+export function createOpenRxivApiClient(options) {
+    return new OpenRxivApiClient(options);
+}
+/**
+ * Utility function to extract server from DOI
+ */
+export function getServerFromDOI(doi) {
+    // This is a simple heuristic - in practice, you might want to check both servers
+    // or use additional metadata to determine the correct server
+    if (doi.includes('medrxiv')) {
+        return 'medrxiv';
+    }
+    return 'biorxiv';
+}

package/dist/cli/src/aws/bucket-explorer.d.ts

@@ -0,0 +1,26 @@
+/**
+ * Get the S3 bucket name based on the server
+ */
+export declare function getBucketName(server?: 'biorxiv' | 'medrxiv'): string;
+export interface ListOptions {
+    month?: string;
+    batch?: string;
+    limit?: number;
+    server?: 'biorxiv' | 'medrxiv';
+}
+export interface SearchOptions {
+    type?: 'pdf' | 'xml' | 'all';
+    limit?: number;
+}
+export interface ContentItem {
+    key: string;
+    size: number;
+    lastModified: Date;
+    type: 'meca' | 'pdf' | 'xml' | 'other';
+}
+export declare function listBucketContent(options: ListOptions): Promise<void>;
+export declare function getContentInfo(path: string, options?: {
+    detailed?: boolean;
+    server?: 'biorxiv' | 'medrxiv';
+}): Promise<void>;
+//# sourceMappingURL=bucket-explorer.d.ts.map

package/dist/cli/src/aws/bucket-explorer.d.ts.map

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package/dist/cli/src/aws/bucket-explorer.js

@@ -0,0 +1,220 @@
+import { ListObjectsV2Command, HeadObjectCommand } from '@aws-sdk/client-s3';
+import chalk from 'chalk';
+import { getS3Client } from './config.js';
+import { getFolderStructure } from 'biorxiv-utils';
+import { getDefaultServer } from '../utils/default-server.js';
+/**
+ * Get the S3 bucket name based on the server
+ */
+export function getBucketName(server = getDefaultServer()) {
+    switch (server.toLowerCase()) {
+        case 'medrxiv':
+            return 'medrxiv-src-monthly';
+        case 'biorxiv':
+            return 'biorxiv-src-monthly';
+        default:
+            console.error(`❌ Error: Invalid server ${server}, must be "biorxiv" or "medrxiv"`);
+            process.exit(1);
+    }
+}
+export async function listBucketContent(options) {
+    const client = await getS3Client();
+    const { month, batch, limit = 50, server = getDefaultServer() } = options;
+    const bucketName = getBucketName(server);
+    console.log(chalk.blue(`Listing ${server} bucket content...`));
+    console.log(chalk.blue('===================================='));
+    try {
+        // If no month or batch specified, show the available content structure
+        if (!month && !batch) {
+            await listFolder(client, server);
+            return;
+        }
+        let prefix = '';
+        let folder = null;
+        if (month || batch) {
+            // Use folder structure utility to determine the correct prefix
+            folder = getFolderStructure({ month, batch, server });
+            prefix = folder.prefix;
+            console.log(chalk.gray(`🔍 Content Type: ${folder.type === 'current' ? 'Current Content' : 'Back Content'}`));
+            if (folder.batch) {
+                console.log(chalk.gray(`🔍 Batch: ${folder.batch}`));
+            }
+        }
+        const commandOptions = {
+            Bucket: bucketName,
+            Prefix: prefix,
+            MaxKeys: parseInt(limit.toString()),
+            RequestPayer: 'requester',
+        };
+        const command = new ListObjectsV2Command(commandOptions);
+        const response = await client.send(command);
+        if (!response.Contents || response.Contents.length === 0) {
+            console.log(chalk.yellow('No content found'));
+            return;
+        }
+        console.log(chalk.green(`Found ${response.Contents.length} items:`));
+        console.log('');
+        for (const item of response.Contents) {
+            if (!item.Key)
+                continue;
+            const type = getContentType(item.Key);
+            const size = formatFileSize(item.Size || 0);
+            const date = item.LastModified ? item.LastModified.toLocaleDateString() : 'Unknown';
+            console.log(`${chalk.cyan(item.Key)}`);
+            console.log(`  Type: ${chalk.yellow(type)} | Size: ${chalk.blue(size)} | Modified: ${chalk.gray(date)}`);
+            console.log('');
+        }
+    }
+    catch (error) {
+        if (error instanceof Error) {
+            throw new Error(`Failed to list bucket content: ${error.message}`);
+        }
+        throw error;
+    }
+}
+/**
+ * Lists the available content structure in the specified server bucket
+ * Shows available months and batches
+ */
+async function listFolder(client, server = getDefaultServer()) {
+    console.log(chalk.cyan('📁 Available Content Structure'));
+    console.log(chalk.cyan('=============================='));
+    console.log('');
+    try {
+        // List Current_Content folders (monthly content)
+        console.log(chalk.blue('📅 Current Content (Monthly):'));
+        console.log(chalk.gray('   Recent content organized by month'));
+        console.log('');
+        const bucketName = getBucketName(server);
+        const currentContentCommand = new ListObjectsV2Command({
+            Bucket: bucketName,
+            Prefix: 'Current_Content/',
+            Delimiter: '/',
+            MaxKeys: 1000,
+            RequestPayer: 'requester',
+        });
+        const currentResponse = await client.send(currentContentCommand);
+        if (currentResponse.CommonPrefixes && currentResponse.CommonPrefixes.length > 0) {
+            const months = currentResponse.CommonPrefixes.map((prefix) => { var _a; return (_a = prefix.Prefix) === null || _a === void 0 ? void 0 : _a.replace('Current_Content/', '').replace('/', ''); })
+                .filter(Boolean)
+                .sort((a, b) => {
+                // Sort by year first, then by month
+                const [monthA, yearA] = a.split('_');
+                const [monthB, yearB] = b.split('_');
+                if (yearA !== yearB)
+                    return parseInt(yearB) - parseInt(yearA); // Newest year first
+                const monthOrder = [
+                    'January',
+                    'February',
+                    'March',
+                    'April',
+                    'May',
+                    'June',
+                    'July',
+                    'August',
+                    'September',
+                    'October',
+                    'November',
+                    'December',
+                ];
+                return monthOrder.indexOf(monthB) - monthOrder.indexOf(monthA);
+            });
+            for (const month of months) {
+                console.log(`   ${chalk.green('📁')} ${chalk.cyan(month)}`);
+            }
+        }
+        else {
+            console.log(chalk.gray('   No monthly content found'));
+        }
+        console.log('');
+        // List Back_Content batches
+        console.log(chalk.blue('📦 Back Content (Historical Batches):'));
+        console.log(chalk.gray('   Legacy content organized in batches'));
+        console.log('');
+        const backContentCommand = new ListObjectsV2Command({
+            Bucket: bucketName,
+            Prefix: 'Back_Content/',
+            Delimiter: '/',
+            MaxKeys: 1000,
+            RequestPayer: 'requester',
+        });
+        const backResponse = await client.send(backContentCommand);
+        if (backResponse.CommonPrefixes && backResponse.CommonPrefixes.length > 0) {
+            const batches = backResponse.CommonPrefixes.map((prefix) => { var _a; return (_a = prefix.Prefix) === null || _a === void 0 ? void 0 : _a.replace('Back_Content/', '').replace('/', ''); })
+                .filter(Boolean)
+                .sort();
+            for (const batch of batches) {
+                console.log(`   ${chalk.green('📁')} ${chalk.cyan(batch)}`);
+            }
+        }
+        else {
+            console.log(chalk.gray('   No historical batches found'));
+        }
+        console.log('');
+        console.log(chalk.blue('💡 Usage Examples:'));
+        console.log(chalk.gray(`   List specific month: ${server} list --month 2024-01`));
+        console.log(chalk.gray(`   List specific batch: ${server} list --batch Batch_01`));
+        console.log(chalk.gray(`   List with limit: ${server} list --month 2024-01 --limit 100`));
+        console.log('');
+    }
+    catch (error) {
+        if (error instanceof Error) {
+            console.log(chalk.yellow(`⚠️  Warning: Could not fetch content structure: ${error.message}`));
+            console.log(chalk.gray('   This may be due to AWS permissions or network issues'));
+            console.log('');
+        }
+    }
+}
+export async function getContentInfo(path, options = {}) {
+    var _a;
+    const client = await getS3Client();
+    const { detailed = false, server = getDefaultServer() } = options;
+    const bucketName = getBucketName(server);
+    console.log(chalk.blue(`Getting info for: ${path}`));
+    console.log(chalk.blue('=============================='));
+    try {
+        const commandOptions = {
+            Bucket: bucketName,
+            Key: path,
+            RequestPayer: 'requester',
+        };
+        const command = new HeadObjectCommand(commandOptions);
+        const response = await client.send(command);
+        console.log(chalk.green('✓ Content found'));
+        console.log('');
+        console.log(`Key: ${chalk.cyan(path)}`);
+        console.log(`Size: ${chalk.blue(formatFileSize(response.ContentLength || 0))}`);
+        console.log(`Type: ${chalk.yellow(response.ContentType || 'Unknown')}`);
+        console.log(`Last Modified: ${chalk.gray(((_a = response.LastModified) === null || _a === void 0 ? void 0 : _a.toLocaleString()) || 'Unknown')}`);
+        if (detailed && response.Metadata) {
+            console.log('');
+            console.log(chalk.blue('Metadata:'));
+            for (const [key, value] of Object.entries(response.Metadata)) {
+                console.log(`  ${key}: ${value}`);
+            }
+        }
+    }
+    catch (error) {
+        if (error instanceof Error) {
+            throw new Error(`Failed to get content info: ${error.message}`);
+        }
+        throw error;
+    }
+}
+function getContentType(key) {
+    if (key.endsWith('.meca'))
+        return 'meca';
+    if (key.endsWith('.pdf'))
+        return 'pdf';
+    if (key.endsWith('.xml'))
+        return 'xml';
+    return 'other';
+}
+function formatFileSize(bytes) {
+    if (bytes === 0)
+        return '0 B';
+    const k = 1024;
+    const sizes = ['B', 'KB', 'MB', 'GB', 'TB'];
+    const i = Math.floor(Math.log(bytes) / Math.log(k));
+    return parseFloat((bytes / Math.pow(k, i)).toFixed(2)) + ' ' + sizes[i];
+}

package/dist/cli/src/aws/config.d.ts

@@ -0,0 +1,18 @@
+import { S3Client } from '@aws-sdk/client-s3';
+export declare function setGlobalRequesterPays(enabled: boolean): void;
+export declare function getGlobalRequesterPays(): boolean;
+export interface AWSCredentials {
+    accessKey?: string;
+    secretKey?: string;
+    region?: string;
+}
+export declare function setCredentials(options: AWSCredentials): Promise<void>;
+export declare function testConnection(): Promise<void>;
+export declare function showConfig(): Promise<void>;
+export declare function getCredentials(): Promise<{
+    accessKeyId: string | undefined;
+    secretAccessKey: string | undefined;
+    region: string;
+}>;
+export declare function getS3Client(): Promise<S3Client>;
+//# sourceMappingURL=config.d.ts.map

package/dist/cli/src/aws/config.d.ts.map

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