openrxiv 0.0.0 → 0.0.3

package/dist/cli/src/utils/months.js

@@ -1,135 +0,0 @@
-/**
- * Month utility functions for batch processing
- */
-/**
- * Generate a range of months to process backwards from current month to 2018-12
- */
-export function generateMonthRange() {
-    const months = [];
-    const now = new Date();
-    const currentDate = new Date(now.getFullYear(), now.getMonth(), 1);
-    // Go back from current month to December 2018
-    while (currentDate.getFullYear() >= 2018) {
-        const year = currentDate.getFullYear();
-        const month = String(currentDate.getMonth() + 1).padStart(2, '0');
-        // Stop at 2018-12 (inclusive)
-        if (year === 2018 && month === '12') {
-            months.push('2018-12');
-            break;
-        }
-        months.push(`${year}-${month}`);
-        // Move to previous month
-        currentDate.setMonth(currentDate.getMonth() - 1);
-    }
-    return months;
-}
-/**
- * Parse month input and return array of months to process
- */
-export function parseMonthInput(monthInput) {
-    // Handle comma-separated list
-    if (monthInput.includes(',')) {
-        const parts = monthInput
-            .split(',')
-            .map((m) => m.trim())
-            .filter((m) => m.length > 0);
-        // Process each part (which may contain wildcards)
-        const result = [];
-        for (const part of parts) {
-            if (part.includes('*')) {
-                // Expand wildcard pattern
-                result.push(...parseWildcardPattern(part));
-            }
-            else {
-                // Single month
-                result.push(part);
-            }
-        }
-        return result;
-    }
-    // Handle wildcard pattern (e.g., "2025-*")
-    if (monthInput.includes('*')) {
-        return parseWildcardPattern(monthInput);
-    }
-    // Single month
-    return [monthInput];
-}
-/**
- * Parse wildcard pattern like "2025-*" to get all months in that year
- */
-export function parseWildcardPattern(pattern) {
-    const months = [];
-    // Extract year from pattern
-    const yearMatch = pattern.match(/^(\d{4})-\*$/);
-    if (!yearMatch) {
-        throw new Error(`Invalid wildcard pattern: ${pattern}. Use format like "2025-*"`);
-    }
-    const year = parseInt(yearMatch[1], 10);
-    const now = new Date();
-    const currentYear = now.getFullYear();
-    const currentMonth = now.getMonth() + 1;
-    // Generate all months in the year, but only up to current month if it's current year
-    for (let month = 1; month <= 12; month++) {
-        if (year === currentYear && month > currentMonth) {
-            break; // Don't process future months
-        }
-        const monthStr = String(month).padStart(2, '0');
-        months.push(`${year}-${monthStr}`);
-    }
-    return months;
-}
-/**
- * Validate month format (YYYY-MM)
- */
-export function validateMonthFormat(month) {
-    const monthRegex = /^\d{4}-\d{2}$/;
-    if (!monthRegex.test(month)) {
-        return false;
-    }
-    const [year, monthNum] = month.split('-');
-    const yearNum = parseInt(year, 10);
-    const monthInt = parseInt(monthNum, 10);
-    return yearNum <= 2100 && monthInt >= 1 && monthInt <= 12;
-}
-/**
- * Sort months chronologically (oldest first)
- */
-export function sortMonthsChronologically(months) {
-    return months.sort((a, b) => {
-        const [yearA, monthA] = a.split('-').map(Number);
-        const [yearB, monthB] = b.split('-').map(Number);
-        if (yearA !== yearB) {
-            return yearA - yearB;
-        }
-        return monthA - monthB;
-    });
-}
-/**
- * Get current month in YYYY-MM format
- */
-export function getCurrentMonth() {
-    const now = new Date();
-    const year = now.getFullYear();
-    const month = String(now.getMonth() + 1).padStart(2, '0');
-    return `${year}-${month}`;
-}
-/**
- * Get previous month in YYYY-MM format
- */
-export function getPreviousMonth() {
-    const now = new Date();
-    now.setMonth(now.getMonth() - 1);
-    const year = now.getFullYear();
-    const month = String(now.getMonth() + 1).padStart(2, '0');
-    return `${year}-${month}`;
-}
-/**
- * Check if a month is in the future
- */
-export function isFutureMonth(month) {
-    const [year, monthNum] = month.split('-').map(Number);
-    const now = new Date();
-    const currentYear = now.getFullYear();
-    const currentMonth = now.getMonth() + 1;
-    return year > currentYear || (year === currentYear && monthNum > currentMonth);
-}

package/dist/cli/src/utils/months.test.d.ts

@@ -1,2 +0,0 @@
-export {};
-//# sourceMappingURL=months.test.d.ts.map

package/dist/cli/src/utils/months.test.d.ts.map

@@ -1 +0,0 @@
-{"version":3,"file":"months.test.d.ts","sourceRoot":"","sources":["../../../../src/utils/months.test.ts"],"names":[],"mappings":""}

package/dist/cli/src/utils/months.test.js

@@ -1,209 +0,0 @@
-import { describe, it, expect, beforeEach, afterEach, vi } from 'vitest';
-import { generateMonthRange, parseMonthInput, parseWildcardPattern, validateMonthFormat, sortMonthsChronologically, getCurrentMonth, getPreviousMonth, isFutureMonth, } from './months.js';
-import { getFolderStructure, removeDuplicateFolders, sortFoldersChronologically, } from 'biorxiv-utils';
-describe('Month Utilities', () => {
-    beforeEach(() => {
-        // Mock the current date to 2025-01-15 for consistent testing
-        const mockDate = new Date('2025-01-15T12:00:00Z');
-        vi.useFakeTimers();
-        vi.setSystemTime(mockDate);
-    });
-    afterEach(() => {
-        vi.useRealTimers();
-    });
-    describe('generateMonthRange', () => {
-        it('should generate months from current month back to 2018-12', () => {
-            const months = generateMonthRange();
-            // Should start from current month (2025-01)
-            expect(months[0]).toBe('2025-01');
-            // Should end at 2018-12
-            expect(months[months.length - 1]).toBe('2018-12');
-            // Should include 2018-12
-            expect(months).toContain('2018-12');
-            // Should not include 2018-11 or earlier
-            expect(months).not.toContain('2018-11');
-            expect(months).not.toContain('2017-12');
-            // Should have correct number of months
-            // From 2025-01 to 2018-12: (2025-2018+1) * 12 = 8 * 12 = 96 months
-            // But we stop at 2018-12, so it's actually 74 months
-            expect(months).toHaveLength(74);
-        });
-        it('should generate months in descending order (newest first)', () => {
-            const months = generateMonthRange();
-            // First few months should be newest
-            expect(months[0]).toBe('2025-01');
-            expect(months[1]).toBe('2024-12');
-            expect(months[2]).toBe('2024-11');
-            // Last few months should be oldest
-            expect(months[months.length - 3]).toBe('2019-02');
-            expect(months[months.length - 2]).toBe('2019-01');
-            expect(months[months.length - 1]).toBe('2018-12');
-        });
-    });
-    describe('parseMonthInput', () => {
-        it('should handle single month', () => {
-            const result = parseMonthInput('2025-01');
-            expect(result).toEqual(['2025-01']);
-        });
-        it('should handle comma-separated months', () => {
-            const result = parseMonthInput('2025-01,2024-12,2024-11');
-            expect(result).toEqual(['2025-01', '2024-12', '2024-11']);
-        });
-        it('should handle comma-separated months with spaces', () => {
-            const result = parseMonthInput(' 2025-01 , 2024-12 , 2024-11 ');
-            expect(result).toEqual(['2025-01', '2024-12', '2024-11']);
-        });
-        it('should handle wildcard pattern', () => {
-            const result = parseMonthInput('2024-*');
-            expect(result).toHaveLength(12);
-            expect(result).toContain('2024-01');
-            expect(result).toContain('2024-12');
-        });
-        it('should filter out empty strings', () => {
-            const result = parseMonthInput('2025-01,,2024-12,');
-            expect(result).toEqual(['2025-01', '2024-12']);
-        });
-    });
-    describe('parseWildcardPattern', () => {
-        it('should parse valid wildcard pattern', () => {
-            const result = parseWildcardPattern('2024-*');
-            expect(result).toHaveLength(12);
-            expect(result).toContain('2024-01');
-            expect(result).toContain('2024-06');
-            expect(result).toContain('2024-12');
-        });
-        it('should handle current year and stop at current month', () => {
-            const result = parseWildcardPattern('2025-*');
-            // Since we're mocking 2025-01, should only include January
-            expect(result).toHaveLength(1);
-            expect(result).toEqual(['2025-01']);
-        });
-        it('should throw error for invalid wildcard pattern', () => {
-            expect(() => parseWildcardPattern('2024-')).toThrow('Invalid wildcard pattern');
-            expect(() => parseWildcardPattern('2024-*x')).toThrow('Invalid wildcard pattern');
-            expect(() => parseWildcardPattern('*-2024')).toThrow('Invalid wildcard pattern');
-        });
-        it('should handle past years correctly', () => {
-            const result = parseWildcardPattern('2020-*');
-            expect(result).toHaveLength(12);
-            expect(result).toContain('2020-01');
-            expect(result).toContain('2020-12');
-        });
-    });
-    describe('validateMonthFormat', () => {
-        it('should validate correct month formats', () => {
-            expect(validateMonthFormat('2025-01')).toBe(true);
-            expect(validateMonthFormat('2024-12')).toBe(true);
-            expect(validateMonthFormat('2018-12')).toBe(true);
-            expect(validateMonthFormat('2020-06')).toBe(true);
-        });
-        it('should reject invalid month formats', () => {
-            expect(validateMonthFormat('2025-1')).toBe(false); // Missing leading zero
-            expect(validateMonthFormat('2025-13')).toBe(false); // Invalid month
-            expect(validateMonthFormat('2025-00')).toBe(false); // Invalid month
-            expect(validateMonthFormat('2025-1a')).toBe(false); // Non-numeric
-            expect(validateMonthFormat('2025')).toBe(false); // Missing month
-            expect(validateMonthFormat('2025-01-01')).toBe(false); // Too many parts
-        });
-        it('should reject months outside valid year range', () => {
-            expect(validateMonthFormat('2101-01')).toBe(false); // After 2100
-        });
-        it('should accept boundary years', () => {
-            expect(validateMonthFormat('2018-01')).toBe(true);
-            expect(validateMonthFormat('2018-12')).toBe(true);
-            expect(validateMonthFormat('2100-01')).toBe(true);
-            expect(validateMonthFormat('2100-12')).toBe(true);
-        });
-    });
-    describe('sortMonthsChronologically', () => {
-        it('should sort months in chronological order (oldest first)', () => {
-            const months = ['2025-01', '2024-12', '2024-01', '2025-02'];
-            const sorted = sortMonthsChronologically(months);
-            expect(sorted).toEqual(['2024-01', '2024-12', '2025-01', '2025-02']);
-        });
-        it('should handle months within same year', () => {
-            const months = ['2024-12', '2024-01', '2024-06'];
-            const sorted = sortMonthsChronologically(months);
-            expect(sorted).toEqual(['2024-01', '2024-06', '2024-12']);
-        });
-        it('should handle single month', () => {
-            const months = ['2024-06'];
-            const sorted = sortMonthsChronologically(months);
-            expect(sorted).toEqual(['2024-06']);
-        });
-        it('should handle empty array', () => {
-            const months = [];
-            const sorted = sortMonthsChronologically(months);
-            expect(sorted).toEqual([]);
-        });
-    });
-    describe('getCurrentMonth', () => {
-        it('should return current month in YYYY-MM format', () => {
-            const currentMonth = getCurrentMonth();
-            expect(currentMonth).toBe('2025-01');
-        });
-    });
-    describe('getPreviousMonth', () => {
-        it('should return previous month in YYYY-MM format', () => {
-            const previousMonth = getPreviousMonth();
-            expect(previousMonth).toBe('2024-12');
-        });
-        it('should handle year boundary correctly', () => {
-            // Mock to January 2024 to test year boundary
-            vi.setSystemTime(new Date('2024-01-15T12:00:00Z'));
-            const previousMonth = getPreviousMonth();
-            expect(previousMonth).toBe('2023-12');
-        });
-    });
-    describe('isFutureMonth', () => {
-        it('should identify future months correctly', () => {
-            expect(isFutureMonth('2025-02')).toBe(true);
-            expect(isFutureMonth('2025-12')).toBe(true);
-            expect(isFutureMonth('2026-01')).toBe(true);
-        });
-        it('should identify current and past months correctly', () => {
-            expect(isFutureMonth('2025-01')).toBe(false); // Current month
-            expect(isFutureMonth('2024-12')).toBe(false); // Past month
-            expect(isFutureMonth('2024-01')).toBe(false); // Past month
-            expect(isFutureMonth('2018-12')).toBe(false); // Past month
-        });
-        it('should handle year boundaries correctly', () => {
-            expect(isFutureMonth('2024-12')).toBe(false); // Past year
-            expect(isFutureMonth('2026-01')).toBe(true); // Future year
-        });
-    });
-    describe('Integration tests', () => {
-        it('should handle complete workflow: parse, validate, sort, deduplicate', () => {
-            const input = '2025-01,2024-12,2025-01,2024-11,2024-12';
-            // Parse input
-            const parsed = parseMonthInput(input);
-            expect(parsed).toEqual(['2025-01', '2024-12', '2025-01', '2024-11', '2024-12']);
-            // Validate all months
-            const valid = parsed.filter(validateMonthFormat);
-            expect(valid).toEqual(['2025-01', '2024-12', '2025-01', '2024-11', '2024-12']);
-            // Remove duplicates
-            const folders = valid.map((month) => getFolderStructure({ month }));
-            const unique = removeDuplicateFolders(folders);
-            expect(unique.length).toEqual(3);
-            // Sort chronologically
-            const sorted = sortFoldersChronologically(unique);
-            expect(sorted.length).toEqual(3);
-            expect(sorted[0].batch).toEqual('November_2024');
-            expect(sorted[1].batch).toEqual('December_2024');
-            expect(sorted[2].batch).toEqual('January_2025');
-        });
-        it('should handle wildcard with validation and sorting', () => {
-            const input = '2024-*';
-            // Parse wildcard
-            const parsed = parseMonthInput(input);
-            expect(parsed).toHaveLength(12);
-            // Validate all months
-            const valid = parsed.filter(validateMonthFormat);
-            expect(valid).toHaveLength(12);
-            // Sort chronologically
-            const sorted = sortMonthsChronologically(valid);
-            expect(sorted[0]).toBe('2024-01');
-            expect(sorted[11]).toBe('2024-12');
-        });
-    });
-});

package/dist/cli/src/utils/requester-pays-error.d.ts

@@ -1,6 +0,0 @@
-/**
- * Utility function to display the requester-pays error message
- * Used when S3 operations fail due to requester-pays bucket requirements
- */
-export declare function displayRequesterPaysError(): void;
-//# sourceMappingURL=requester-pays-error.d.ts.map

package/dist/cli/src/utils/requester-pays-error.d.ts.map

@@ -1 +0,0 @@
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package/dist/cli/src/utils/requester-pays-error.js

@@ -1,20 +0,0 @@
-/**
- * Utility function to display the requester-pays error message
- * Used when S3 operations fail due to requester-pays bucket requirements
- */
-export function displayRequesterPaysError() {
-    console.error(`
-❌ Operation failed: S3 bucket requires requester-pays
-💡 This bucket has requester-pays enabled, which means:
-   • You need to pay for data transfer costs
-   • Your AWS credentials must be configured
-   • The bucket policy must allow your account
-
-🔧 To fix this:
-   1. Ensure your AWS credentials are configured
-   2. Verify you have permission to access the bucket
-   3. Add the --requester-pays flag to your command
-
-📚 For more help, see: https://docs.aws.amazon.com/AmazonS3/latest/userguide/RequesterPaysBuckets.html
-`);
-}

package/dist/cli/src/version.d.ts

@@ -1,3 +0,0 @@
-declare const version = "0.0.0";
-export default version;
-//# sourceMappingURL=version.d.ts.map

package/dist/cli/src/version.d.ts.map

@@ -1 +0,0 @@
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package/dist/cli/src/version.js

@@ -1,2 +0,0 @@
-const version = '0.0.0';
-export default version;

package/dist/utils/src/biorxiv-parser.d.ts

@@ -1,51 +0,0 @@
-/**
- * Utility functions for parsing bioRxiv URLs and DOIs
- */
-export interface ParsedBiorxivURL {
-    doi: string;
-    baseDOI: string;
-    version: string | null;
-    fullURL: string;
-    isValid: boolean;
-}
-export interface DOIParts {
-    doi: string;
-    prefix: string;
-    suffix: string;
-    date: string | null;
-    identifier: string;
-    version: string | null;
-}
-/**
- * Extract DOI from a bioRxiv URL
- */
-export declare function extractDOIFromURL(url: string): string | null;
-/**
- * Parse a bioRxiv DOI into its components
- * Supports both legacy numeric format (2019 and earlier) and current date-based format (2019+)
- */
-export declare function parseDOI(doi: string): DOIParts | null;
-/**
- * Extract base DOI (without version)
- * Works with both legacy numeric and current date-based formats
- */
-export declare function extractBaseDOI(doi: string): string;
-/**
- * Extract version from DOI
- * Works with both legacy numeric and current date-based formats
- */
-export declare function extractVersion(doi: string): string | null;
-/**
- * Check if a DOI is a valid bioRxiv DOI
- * Supports both legacy numeric and current date-based formats
- */
-export declare function isValidBiorxivDOI(doi: string): boolean;
-/**
- * Check if a URL is a valid bioRxiv URL
- */
-export declare function isValidBiorxivURL(url: string): boolean;
-/**
- * Parse a bioRxiv URL and extract all relevant information
- */
-export declare function parseBiorxivURL(url: string): ParsedBiorxivURL | null;
-//# sourceMappingURL=biorxiv-parser.d.ts.map

package/dist/utils/src/biorxiv-parser.d.ts.map

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package/dist/utils/src/biorxiv-parser.js

@@ -1,126 +0,0 @@
-/**
- * Utility functions for parsing bioRxiv URLs and DOIs
- */
-/**
- * Extract DOI from a bioRxiv URL
- */
-export function extractDOIFromURL(url) {
-    // Handle various bioRxiv URL formats
-    let doi = null;
-    // Check for bioRxiv content URLs
-    if (url.includes('biorxiv.org/content/')) {
-        const match = url.match(/biorxiv\.org\/content\/([^?#]+)/);
-        if (match && match[1]) {
-            doi = match[1];
-        }
-    }
-    // Check for medRxiv content URLs
-    else if (url.includes('medrxiv.org/content/')) {
-        const match = url.match(/medrxiv\.org\/content\/([^?#]+)/);
-        if (match && match[1]) {
-            doi = match[1];
-        }
-    }
-    // Check for doi.org redirects
-    else if (url.includes('doi.org/')) {
-        const match = url.match(/doi\.org\/([^?#]+)/);
-        if (match && match[1]) {
-            doi = match[1];
-        }
-    }
-    // Check for direct DOI input
-    else if (url.startsWith('10.1101/')) {
-        doi = url;
-    }
-    if (doi) {
-        // Clean up the extracted DOI (remove any trailing extensions)
-        return doi.replace(/\.(article-info|full|abstract|pdf|suppl)$/, '');
-    }
-    return null;
-}
-/**
- * Parse a bioRxiv DOI into its components
- * Supports both legacy numeric format (2019 and earlier) and current date-based format (2019+)
- */
-export function parseDOI(doi) {
-    // Handle current date-based format (2019+): 10.1101/YYYY.MM.DD.XXXXXXvN
-    const currentPattern = /^10\.1101\/(\d{4})\.(\d{2})\.(\d{2})\.(\d{6,8})(v\d+)?$/;
-    const currentMatch = doi.match(currentPattern);
-    if (currentMatch) {
-        const [prefix, suffix] = doi.split('/');
-        const [, year, month, day, identifier, version] = currentMatch;
-        const date = `${year}-${month}-${day}`;
-        return {
-            doi,
-            prefix,
-            suffix: suffix.replace(/(v\d+)$/, ''),
-            date,
-            identifier,
-            version: version || null,
-        };
-    }
-    // Handle legacy numeric format (2019 and earlier): 10.1101/XXXXXX
-    const legacyPattern = /^10\.1101\/(\d{6,8})(v\d+)?$/;
-    const legacyMatch = doi.match(legacyPattern);
-    if (legacyMatch) {
-        const [prefix, suffix] = doi.split('/');
-        const [, identifier, version] = legacyMatch;
-        return {
-            doi,
-            prefix,
-            suffix: suffix.replace(/(v\d+)$/, ''),
-            date: null,
-            identifier,
-            version: version || null,
-        };
-    }
-    return null;
-}
-/**
- * Extract base DOI (without version)
- * Works with both legacy numeric and current date-based formats
- */
-export function extractBaseDOI(doi) {
-    // Remove version suffix if present
-    return doi.replace(/v\d+$/, '');
-}
-/**
- * Extract version from DOI
- * Works with both legacy numeric and current date-based formats
- */
-export function extractVersion(doi) {
-    const match = doi.match(/v(\d+)$/);
-    return match ? match[1] : null;
-}
-/**
- * Check if a DOI is a valid bioRxiv DOI
- * Supports both legacy numeric and current date-based formats
- */
-export function isValidBiorxivDOI(doi) {
-    return parseDOI(doi) !== null;
-}
-/**
- * Check if a URL is a valid bioRxiv URL
- */
-export function isValidBiorxivURL(url) {
-    const doi = extractDOIFromURL(url);
-    return doi !== null && isValidBiorxivDOI(doi);
-}
-/**
- * Parse a bioRxiv URL and extract all relevant information
- */
-export function parseBiorxivURL(url) {
-    const doi = extractDOIFromURL(url);
-    if (!doi || !isValidBiorxivDOI(doi)) {
-        return null;
-    }
-    const baseDOI = extractBaseDOI(doi);
-    const version = extractVersion(doi);
-    return {
-        doi,
-        baseDOI,
-        version,
-        fullURL: url,
-        isValid: true,
-    };
-}

package/dist/utils/src/folder-structure.d.ts

@@ -1,44 +0,0 @@
-/**
- * Utility functions for determining bioRxiv folder structure
- * based on the date requested.
- *
- * The bioRxiv structure is:
- * - Before late 2018: Files are in Back_Content/Batch_[nn]/ folders
- * - After late 2018: Files are in Current_Content/[Month]_[Year]/ folders
- */
-export interface FolderStructure {
-    server: 'biorxiv' | 'medrxiv';
-    type: 'current' | 'back';
-    prefix: string;
-    batch: string;
-}
-export interface FolderStructureOptions {
-    server?: 'biorxiv' | 'medrxiv';
-    month?: string;
-    batch?: string;
-}
-/**
- * Normalizes batch input to the standard "Batch_XX" format
- * @param batch - Batch input in various formats (e.g., "1", "batch-1", "Batch_01", "batch_01")
- * @param server - Server type to determine batch format (e.g., "biorxiv", "medrxiv")
- * @returns Normalized batch string in appropriate format
- */
-export declare function normalizeBatch(batch: string | number, server?: string): string;
-/**
- * Determines the folder structure for a given month or batch
- * @param options - Options containing month or batch
- * @returns FolderStructure with the appropriate prefix and type
- */
-export declare function getFolderStructure(options: FolderStructureOptions): FolderStructure;
-export declare function removeDuplicateFolders(folders: FolderStructure[]): FolderStructure[];
-/**
- * Sort folders chronologically, putting batches before months
- */
-export declare function sortFoldersChronologically(folders: FolderStructure[]): FolderStructure[];
-/**
- * Normalizes various month formats to YYYY-MM
- * @param month - Month in various formats
- * @returns Normalized YYYY-MM format or null if invalid
- */
-export declare function normalizeMonthToYYYYMM(month: string): string | null;
-//# sourceMappingURL=folder-structure.d.ts.map

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