openrxiv-utils 0.0.0

package/dist/biorxiv-parser.d.ts

@@ -0,0 +1,51 @@
+/**
+ * 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/biorxiv-parser.d.ts.map

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package/dist/biorxiv-parser.js

@@ -0,0 +1,127 @@
+/**
+ * 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,
+    };
+}
+//# sourceMappingURL=biorxiv-parser.js.map

package/dist/biorxiv-parser.js.map

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package/dist/biorxiv-parser.spec.d.ts

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=biorxiv-parser.spec.d.ts.map

package/dist/biorxiv-parser.spec.d.ts.map

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

package/dist/biorxiv-parser.spec.js

@@ -0,0 +1,226 @@
+import { describe, it, expect } from 'vitest';
+import { extractDOIFromURL, parseDOI, extractBaseDOI, extractVersion, isValidBiorxivDOI, isValidBiorxivURL, parseBiorxivURL, } from './biorxiv-parser.js';
+describe('BioRxiv URL Parser', () => {
+    describe('extractDOIFromURL', () => {
+        it.each([
+            [
+                'https://www.biorxiv.org/content/10.1101/2024.01.25.577295v3',
+                '10.1101/2024.01.25.577295v3',
+            ],
+            [
+                'https://www.medrxiv.org/content/10.1101/2020.03.19.20039131v2',
+                '10.1101/2020.03.19.20039131v2',
+            ],
+            [
+                'https://www.biorxiv.org/content/10.1101/2024.01.25.577295v3.article-info',
+                '10.1101/2024.01.25.577295v3',
+            ],
+            [
+                'https://www.biorxiv.org/content/10.1101/2024.01.25.577295v3.full',
+                '10.1101/2024.01.25.577295v3',
+            ],
+            [
+                'https://www.biorxiv.org/content/10.1101/2024.01.25.577295v3.abstract',
+                '10.1101/2024.01.25.577295v3',
+            ],
+            [
+                'https://www.biorxiv.org/content/10.1101/2024.01.25.577295v3.pdf',
+                '10.1101/2024.01.25.577295v3',
+            ],
+            [
+                'https://www.biorxiv.org/content/10.1101/2024.01.25.577295v3.suppl',
+                '10.1101/2024.01.25.577295v3',
+            ],
+            ['https://doi.org/10.1101/2024.01.25.577295v3', '10.1101/2024.01.25.577295v3'],
+            ['10.1101/2024.01.25.577295v3', '10.1101/2024.01.25.577295v3'],
+        ])('should extract DOI from standard content URL', (url, expected) => {
+            const result = extractDOIFromURL(url);
+            expect(result).toBe(expected);
+        });
+        it.each([
+            ['https://example.com/not-biorxiv', null],
+            ['https://biorxiv.org/invalid-path', null],
+            ['not-a-url', null],
+            ['', null],
+            ['https://biorxiv.org/', null],
+        ])('should return null for invalid URLs', (url, expected) => {
+            const result = extractDOIFromURL(url);
+            expect(result).toBe(expected);
+        });
+    });
+    describe('parseDOI', () => {
+        it('should parse DOI with version', () => {
+            const doi = '10.1101/2024.01.25.577295v3';
+            const result = parseDOI(doi);
+            expect(result).toEqual({
+                doi: '10.1101/2024.01.25.577295v3',
+                prefix: '10.1101',
+                date: '2024-01-25',
+                identifier: '577295',
+                suffix: '2024.01.25.577295',
+                version: 'v3',
+            });
+        });
+        it('should parse DOI without version', () => {
+            const doi = '10.1101/2024.01.25.577295';
+            const result = parseDOI(doi);
+            expect(result).toEqual({
+                doi: '10.1101/2024.01.25.577295',
+                prefix: '10.1101',
+                date: '2024-01-25',
+                identifier: '577295',
+                suffix: '2024.01.25.577295',
+                version: null,
+            });
+        });
+        it('should parse DOI with single digit month and day', () => {
+            const doi = '10.1101/2024.01.05.123456v1';
+            const result = parseDOI(doi);
+            expect(result).toEqual({
+                doi: '10.1101/2024.01.05.123456v1',
+                prefix: '10.1101',
+                date: '2024-01-05',
+                identifier: '123456',
+                suffix: '2024.01.05.123456',
+                version: 'v1',
+            });
+        });
+        it('should return null for invalid DOI format', () => {
+            const invalidDOIs = [
+                '10.1000/123.456.789',
+                '10.1101/2024.1.25.577295',
+                '10.1101/2024.01.25.57729',
+                '10.1101/2024.01.25.5772955666',
+                '10.1101/2024.01.25.577295v',
+                '10.1101/2024.01.25.577295v',
+                'invalid-doi',
+                '',
+            ];
+            invalidDOIs.forEach((doi) => {
+                const result = parseDOI(doi);
+                expect(result).toBeNull();
+            });
+        });
+    });
+    describe('extractBaseDOI', () => {
+        it.each([
+            ['10.1101/2024.01.25.577295', '10.1101/2024.01.25.577295'], // Same DOI
+            ['10.1101/2024.01.25.577295v3', '10.1101/2024.01.25.577295'], // Remove version
+            ['10.1101/2024.01.25.577295v12', '10.1101/2024.01.25.577295'], // Remove double digit version
+            ['10.1101/2020.03.19.20039131v2', '10.1101/2020.03.19.20039131'], // medrxiv variant
+        ])('should extract base DOI from versioned DOI', (doi, expected) => {
+            const result = extractBaseDOI(doi);
+            expect(result).toBe(expected);
+        });
+    });
+    describe('extractVersion', () => {
+        it.each([
+            ['10.1101/2024.01.25.577295v3', '3'],
+            ['10.1101/2024.01.25.577295', null],
+            ['10.1101/2024.01.25.577295v12', '12'],
+        ])('should extract version from DOI', (doi, expected) => {
+            const result = extractVersion(doi);
+            expect(result).toBe(expected);
+        });
+    });
+    describe('isValidBiorxivDOI', () => {
+        it.each([
+            // Valid DOIs
+            ['10.1101/2024.01.25.577295v3', true],
+            ['10.1101/2024.01.25.577295', true],
+            ['10.1101/2020.01.15.123456v2', true],
+            ['10.1101/2018.01.15.789012', true],
+            ['10.1101/789012', true],
+            ['10.1101/789012v12', true],
+            ['10.1101/789012v3', true],
+            ['10.1101/2020.03.19.20039131v2', true],
+            ['10.1101/2024.1.25.577295', false],
+            ['10.1101/2024.01.25.57729', false],
+            ['invalid-doi', false],
+            ['10.1101/78901', false],
+            ['10.1101/78901v3', false],
+            ['', false],
+        ])('should validate correct bioRxiv DOIs %s', (doi, expected) => {
+            const result = isValidBiorxivDOI(doi);
+            expect(result).toBe(expected);
+        });
+    });
+    describe('isValidBiorxivURL', () => {
+        it.each([
+            ['https://www.biorxiv.org/content/10.1101/2024.01.25.577295v3', true],
+            ['https://www.biorxiv.org/content/10.1101/2024.01.25.577295v3.article-info', true],
+            ['https://doi.org/10.1101/2024.01.25.577295v3', true],
+            ['10.1101/2024.01.25.577295v3', true],
+            ['https://www.biorxiv.org/content/10.1101/486050v2.article-info', true],
+            ['https://www.biorxiv.org/content/10.1101/486050', true],
+            // Invalid
+            ['https://example.com/not-biorxiv', false],
+            ['https://biorxiv.org/invalid-path', false],
+            ['10.1000/123.456.789', false],
+            ['invalid-url', false],
+            ['', false],
+        ])('should validate correct bioRxiv URLs', (url, expected) => {
+            const result = isValidBiorxivURL(url);
+            expect(result).toBe(expected);
+        });
+    });
+    describe('parseBiorxivURL', () => {
+        it('should parse valid bioRxiv URL', () => {
+            const url = 'https://www.biorxiv.org/content/10.1101/2024.01.25.577295v3.article-info';
+            const result = parseBiorxivURL(url);
+            expect(result).toEqual({
+                doi: '10.1101/2024.01.25.577295v3',
+                baseDOI: '10.1101/2024.01.25.577295',
+                version: '3',
+                fullURL: url,
+                isValid: true,
+            });
+        });
+        it('should parse URL without version', () => {
+            const url = 'https://www.biorxiv.org/content/10.1101/2024.01.25.577295';
+            const result = parseBiorxivURL(url);
+            expect(result).toEqual({
+                doi: '10.1101/2024.01.25.577295',
+                baseDOI: '10.1101/2024.01.25.577295',
+                version: null,
+                fullURL: url,
+                isValid: true,
+            });
+        });
+        it('should return null for invalid URL', () => {
+            const url = 'https://example.com/not-biorxiv';
+            const result = parseBiorxivURL(url);
+            expect(result).toBeNull();
+        });
+    });
+    describe('Edge Cases', () => {
+        it('should handle DOIs with leading zeros in month/day', () => {
+            const doi = '10.1101/2024.01.05.123456v1';
+            const result = parseDOI(doi);
+            expect(result).toEqual({
+                doi: '10.1101/2024.01.05.123456v1',
+                prefix: '10.1101',
+                date: '2024-01-05',
+                identifier: '123456',
+                suffix: '2024.01.05.123456',
+                version: 'v1',
+            });
+        });
+        it('should handle DOIs with different identifier lengths', () => {
+            const doi = '10.1101/2024.01.25.123456v1';
+            const result = parseDOI(doi);
+            expect(result?.identifier).toBe('123456');
+        });
+        it('should handle URLs with query parameters', () => {
+            const url = 'https://www.biorxiv.org/content/10.1101/2024.01.25.577295v3?query=test';
+            const result = extractDOIFromURL(url);
+            expect(result).toBe('10.1101/2024.01.25.577295v3');
+        });
+        it('should handle URLs with fragments', () => {
+            const url = 'https://www.biorxiv.org/content/10.1101/2024.01.25.577295v3#section';
+            const result = extractDOIFromURL(url);
+            expect(result).toBe('10.1101/2024.01.25.577295v3');
+        });
+    });
+});
+//# sourceMappingURL=biorxiv-parser.spec.js.map

package/dist/biorxiv-parser.spec.js.map

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package/dist/content-structure.d.ts

@@ -0,0 +1,38 @@
+/**
+ * Utility functions for determining bioRxiv content 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 ContentStructure {
+    server: 'biorxiv' | 'medrxiv';
+    type: 'current' | 'back';
+    prefix: string;
+    batch: string;
+}
+export interface ContentStructureOptions {
+    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 content structure for a given month or batch
+ * @param options - Options containing month or batch
+ * @returns ContentStructure with the appropriate prefix and type
+ */
+export declare function getContentStructure(options: ContentStructureOptions): ContentStructure;
+export declare function removeDuplicateFolders(folders: ContentStructure[]): ContentStructure[];
+/**
+ * Sort folders chronologically, putting batches before months
+ */
+export declare function sortFoldersChronologically(folders: ContentStructure[]): ContentStructure[];
+//# sourceMappingURL=content-structure.d.ts.map

package/dist/content-structure.d.ts.map

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