openrxiv-utils 0.0.0

package/dist/folder-structure.test.js

@@ -0,0 +1,419 @@
+import { describe, it, expect } from 'vitest';
+import { getFolderStructure, normalizeBatch } from './folder-structure.js';
+describe('Content Structure Utilities', () => {
+    describe('normalizeBatch', () => {
+        describe('bioRxiv server (default)', () => {
+            it.each([
+                // Number inputs
+                [1, 'Batch_01'],
+                [5, 'Batch_05'],
+                [10, 'Batch_10'],
+                [25, 'Batch_25'],
+                [100, 'Batch_100'],
+                // String inputs with various formats
+                ['1', 'Batch_01'],
+                ['5', 'Batch_05'],
+                ['10', 'Batch_10'],
+                ['01', 'Batch_01'],
+                ['05', 'Batch_05'],
+                // With "batch" prefix
+                ['batch1', 'Batch_01'],
+                ['batch-1', 'Batch_01'],
+                ['batch_1', 'Batch_01'],
+                ['Batch1', 'Batch_01'],
+                ['BATCH-1', 'Batch_01'],
+                ['BATCH_1', 'Batch_01'],
+                // With leading zeros
+                ['001', 'Batch_01'],
+                ['005', 'Batch_05'],
+                ['010', 'Batch_10'],
+                ['batch001', 'Batch_01'],
+                ['batch-001', 'Batch_01'],
+                ['batch_001', 'Batch_01'],
+                // Edge cases
+                ['batch-01', 'Batch_01'],
+                ['batch_01', 'Batch_01'],
+                ['Batch_01', 'Batch_01'],
+                ['BATCH_01', 'Batch_01'],
+            ])('should normalize "%s" to "%s" for bioRxiv', (input, expected) => {
+                expect(normalizeBatch(input, 'biorxiv')).toBe(expected);
+            });
+            it.each([
+                ['0', 'Invalid batch format: 0. Expected a positive number or batch identifier.'],
+                ['-1', 'Invalid batch format: -1. Expected a positive number or batch identifier.'],
+                ['abc', 'Invalid batch format: abc. Expected a positive number or batch identifier.'],
+                [
+                    'batch-abc',
+                    'Invalid batch format: batch-abc. Expected a positive number or batch identifier.',
+                ],
+                ['', 'Invalid batch format: . Expected a positive number or batch identifier.'],
+                ['batch-', 'Invalid batch format: batch-. Expected a positive number or batch identifier.'],
+                ['batch_', 'Invalid batch format: batch_. Expected a positive number or batch identifier.'],
+            ])('should throw error for invalid input "%s" for bioRxiv', (input, expectedError) => {
+                expect(() => normalizeBatch(input, 'biorxiv')).toThrow(expectedError);
+            });
+            it.each([
+                [0, 'Invalid batch format: 0. Expected a positive number or batch identifier.'],
+                [-1, 'Invalid batch format: -1. Expected a positive number or batch identifier.'],
+                [-100, 'Invalid batch format: -100. Expected a positive number or batch identifier.'],
+            ])('should throw error for invalid number input %d for bioRxiv', (input, expectedError) => {
+                expect(() => normalizeBatch(input, 'biorxiv')).toThrow(expectedError);
+            });
+        });
+        describe('medRxiv server', () => {
+            it.each([
+                // Number inputs
+                [1, 'medRxiv_Batch_01'],
+                [5, 'medRxiv_Batch_05'],
+                [10, 'medRxiv_Batch_10'],
+                [25, 'medRxiv_Batch_25'],
+                [100, 'medRxiv_Batch_100'],
+                // String inputs with various formats
+                ['1', 'medRxiv_Batch_01'],
+                ['5', 'medRxiv_Batch_05'],
+                ['10', 'medRxiv_Batch_10'],
+                ['01', 'medRxiv_Batch_01'],
+                ['05', 'medRxiv_Batch_05'],
+                // With "batch" prefix
+                ['batch1', 'medRxiv_Batch_01'],
+                ['batch-1', 'medRxiv_Batch_01'],
+                ['batch_1', 'medRxiv_Batch_01'],
+                ['Batch1', 'medRxiv_Batch_01'],
+                ['BATCH-1', 'medRxiv_Batch_01'],
+                ['BATCH_1', 'medRxiv_Batch_01'],
+                // With "medrxiv" prefix
+                ['medrxiv-batch1', 'medRxiv_Batch_01'],
+                ['medrxiv-batch-1', 'medRxiv_Batch_01'],
+                ['medrxiv_batch_1', 'medRxiv_Batch_01'],
+                ['MedRxiv-Batch1', 'medRxiv_Batch_01'],
+                ['MEDRXIV-BATCH-1', 'medRxiv_Batch_01'],
+                ['MEDRXIV_BATCH_1', 'medRxiv_Batch_01'],
+                // With leading zeros
+                ['001', 'medRxiv_Batch_01'],
+                ['005', 'medRxiv_Batch_05'],
+                ['010', 'medRxiv_Batch_10'],
+                ['batch001', 'medRxiv_Batch_01'],
+                ['batch-001', 'medRxiv_Batch_01'],
+                ['batch_001', 'medRxiv_Batch_01'],
+                ['medrxiv-batch001', 'medRxiv_Batch_01'],
+                ['medrxiv-batch-001', 'medRxiv_Batch_01'],
+                ['medrxiv_batch_001', 'medRxiv_Batch_01'],
+                // Edge cases
+                ['batch-01', 'medRxiv_Batch_01'],
+                ['batch_01', 'medRxiv_Batch_01'],
+                ['Batch_01', 'medRxiv_Batch_01'],
+                ['BATCH_01', 'medRxiv_Batch_01'],
+                ['medrxiv-batch-01', 'medRxiv_Batch_01'],
+                ['medrxiv_batch_01', 'medRxiv_Batch_01'],
+                ['MedRxiv_Batch_01', 'medRxiv_Batch_01'],
+                ['MEDRXIV_BATCH_01', 'medRxiv_Batch_01'],
+            ])('should normalize "%s" to "%s" for medRxiv', (input, expected) => {
+                expect(normalizeBatch(input, 'medrxiv')).toBe(expected);
+            });
+            it.each([
+                ['0', 'Invalid batch format: 0. Expected a positive number or batch identifier.'],
+                ['-1', 'Invalid batch format: -1. Expected a positive number or batch identifier.'],
+                ['abc', 'Invalid batch format: abc. Expected a positive number or batch identifier.'],
+                [
+                    'batch-abc',
+                    'Invalid batch format: batch-abc. Expected a positive number or batch identifier.',
+                ],
+                [
+                    'medrxiv-batch-abc',
+                    'Invalid batch format: medrxiv-batch-abc. Expected a positive number or batch identifier.',
+                ],
+                ['', 'Invalid batch format: . Expected a positive number or batch identifier.'],
+                ['batch-', 'Invalid batch format: batch-. Expected a positive number or batch identifier.'],
+                ['batch_', 'Invalid batch format: batch_. Expected a positive number or batch identifier.'],
+                [
+                    'medrxiv-batch-',
+                    'Invalid batch format: medrxiv-batch-. Expected a positive number or batch identifier.',
+                ],
+                [
+                    'medrxiv_batch_',
+                    'Invalid batch format: medrxiv_batch_. Expected a positive number or batch identifier.',
+                ],
+            ])('should throw error for invalid input "%s" for medRxiv', (input, expectedError) => {
+                expect(() => normalizeBatch(input, 'medrxiv')).toThrow(expectedError);
+            });
+            it.each([
+                [0, 'Invalid batch format: 0. Expected a positive number or batch identifier.'],
+                [-1, 'Invalid batch format: -1. Expected a positive number or batch identifier.'],
+                [-100, 'Invalid batch format: -100. Expected a positive number or batch identifier.'],
+            ])('should throw error for invalid number input %d for medRxiv', (input, expectedError) => {
+                expect(() => normalizeBatch(input, 'medrxiv')).toThrow(expectedError);
+            });
+        });
+        describe('default behavior (no server specified)', () => {
+            it('should default to bioRxiv format when no server specified', () => {
+                expect(normalizeBatch(1)).toBe('Batch_01');
+                expect(normalizeBatch('5')).toBe('Batch_05');
+                expect(normalizeBatch('batch-10')).toBe('Batch_10');
+            });
+        });
+        describe('case insensitive server names', () => {
+            it('should handle case insensitive server names', () => {
+                expect(normalizeBatch(1, 'BIORXIV')).toBe('Batch_01');
+                expect(normalizeBatch(1, 'BioRxiv')).toBe('Batch_01');
+                expect(normalizeBatch(1, 'MEDRXIV')).toBe('medRxiv_Batch_01');
+                expect(normalizeBatch(1, 'MedRxiv')).toBe('medRxiv_Batch_01');
+            });
+        });
+    });
+    describe('getFolderStructure', () => {
+        describe('with batch option', () => {
+            describe('bioRxiv server', () => {
+                it.each([
+                    ['1', 'Back_Content/Batch_01/'],
+                    ['5', 'Back_Content/Batch_05/'],
+                    ['10', 'Back_Content/Batch_10/'],
+                    ['batch1', 'Back_Content/Batch_01/'],
+                    ['batch-1', 'Back_Content/Batch_01/'],
+                    ['batch_1', 'Back_Content/Batch_01/'],
+                    ['Batch_01', 'Back_Content/Batch_01/'],
+                    ['BATCH_01', 'Back_Content/Batch_01/'],
+                ])('should create Back_Content structure for batch "%s" on bioRxiv', (batch, expectedPrefix) => {
+                    const result = getFolderStructure({ batch, server: 'biorxiv' });
+                    expect(result.type).toBe('back');
+                    expect(result.prefix).toBe(expectedPrefix);
+                    expect(result.batch).toBe(`Batch_${batch.replace(/\D/g, '').padStart(2, '0')}`);
+                });
+            });
+            describe('medRxiv server', () => {
+                it.each([
+                    ['1', 'Back_Content/medRxiv_Batch_01/'],
+                    ['5', 'Back_Content/medRxiv_Batch_05/'],
+                    ['10', 'Back_Content/medRxiv_Batch_10/'],
+                    ['batch1', 'Back_Content/medRxiv_Batch_01/'],
+                    ['batch-1', 'Back_Content/medRxiv_Batch_01/'],
+                    ['batch_1', 'Back_Content/medRxiv_Batch_01/'],
+                    ['medrxiv-batch1', 'Back_Content/medRxiv_Batch_01/'],
+                    ['medrxiv-batch-1', 'Back_Content/medRxiv_Batch_01/'],
+                    ['medrxiv_batch_1', 'Back_Content/medRxiv_Batch_01/'],
+                    ['MedRxiv_Batch_01', 'Back_Content/medRxiv_Batch_01/'],
+                ])('should create Back_Content structure for batch "%s" on medRxiv', (batch, expectedPrefix) => {
+                    const result = getFolderStructure({ batch, server: 'medrxiv' });
+                    expect(result.type).toBe('back');
+                    expect(result.prefix).toBe(expectedPrefix);
+                    expect(result.batch).toBe(`medRxiv_Batch_${batch.replace(/\D/g, '').padStart(2, '0')}`);
+                });
+            });
+            describe('default server (bioRxiv)', () => {
+                it.each([
+                    ['1', 'Back_Content/Batch_01/'],
+                    ['5', 'Back_Content/Batch_05/'],
+                    ['10', 'Back_Content/Batch_10/'],
+                ])('should create Back_Content structure for batch "%s" with default server', (batch, expectedPrefix) => {
+                    const result = getFolderStructure({ batch });
+                    expect(result.type).toBe('back');
+                    expect(result.prefix).toBe(expectedPrefix);
+                    expect(result.batch).toBe(`Batch_${batch.replace(/\D/g, '').padStart(2, '0')}`);
+                });
+            });
+        });
+        describe('with month option - Current Content period', () => {
+            describe('bioRxiv server', () => {
+                it.each([
+                    ['2019-01', 'Current_Content/January_2019/', 'January_2019'],
+                    ['2019-06', 'Current_Content/June_2019/', 'June_2019'],
+                    ['2019-12', 'Current_Content/December_2019/', 'December_2019'],
+                    ['2020-01', 'Current_Content/January_2020/', 'January_2020'],
+                    ['2024-01', 'Current_Content/January_2024/', 'January_2024'],
+                    ['2025-01', 'Current_Content/January_2025/', 'January_2025'],
+                    ['January_2019', 'Current_Content/January_2019/', 'January_2019'],
+                    ['June_2019', 'Current_Content/June_2019/', 'June_2019'],
+                    ['December_2019', 'Current_Content/December_2019/', 'December_2019'],
+                    ['dec-2019', 'Current_Content/December_2019/', 'December_2019'],
+                    ['December-2019', 'Current_Content/December_2019/', 'December_2019'],
+                ])('should create Current_Content structure for month "%s" on bioRxiv', (month, expectedPrefix, batch) => {
+                    const result = getFolderStructure({ month, server: 'biorxiv' });
+                    expect(result.type).toBe('current');
+                    expect(result.prefix).toBe(expectedPrefix);
+                    expect(result.batch).toBe(batch);
+                });
+            });
+            describe('medRxiv server', () => {
+                it.each([
+                    ['2019-01', 'Current_Content/January_2019/', 'January_2019'],
+                    ['2019-06', 'Current_Content/June_2019/', 'June_2019'],
+                    ['2019-12', 'Current_Content/December_2019/', 'December_2019'],
+                    ['2020-01', 'Current_Content/January_2020/', 'January_2020'],
+                    ['2024-01', 'Current_Content/January_2024/', 'January_2024'],
+                    ['2025-01', 'Current_Content/January_2025/', 'January_2025'],
+                    ['January_2019', 'Current_Content/January_2019/', 'January_2019'],
+                    ['June_2019', 'Current_Content/June_2019/', 'June_2019'],
+                    ['December_2019', 'Current_Content/December_2019/', 'December_2019'],
+                ])('should create Current_Content structure for month "%s" on medRxiv', (month, expectedPrefix, batch) => {
+                    const result = getFolderStructure({ month, server: 'medrxiv' });
+                    expect(result.type).toBe('current');
+                    expect(result.prefix).toBe(expectedPrefix);
+                    expect(result.batch).toBe(batch);
+                });
+            });
+            describe('default server (bioRxiv)', () => {
+                it.each([
+                    ['2019-01', 'Current_Content/January_2019/', 'January_2019'],
+                    ['2024-01', 'Current_Content/January_2024/', 'January_2024'],
+                ])('should create Current_Content structure for month "%s" with default server', (month, expectedPrefix, batch) => {
+                    const result = getFolderStructure({ month });
+                    expect(result.type).toBe('current');
+                    expect(result.prefix).toBe(expectedPrefix);
+                    expect(result.batch).toBe(batch);
+                });
+            });
+        });
+        describe('with month option - Back Content period', () => {
+            describe('bioRxiv server', () => {
+                it.each([
+                    [
+                        '2018-11',
+                        "Date 2018-11 is in the Back_Content period. Please specify a batch using --batch option. Available batches can be listed with 'biorxiv list' command.",
+                    ],
+                    [
+                        '2018-10',
+                        "Date 2018-10 is in the Back_Content period. Please specify a batch using --batch option. Available batches can be listed with 'biorxiv list' command.",
+                    ],
+                    [
+                        '2018-01',
+                        "Date 2018-01 is in the Back_Content period. Please specify a batch using --batch option. Available batches can be listed with 'biorxiv list' command.",
+                    ],
+                    [
+                        '2017-12',
+                        "Date 2017-12 is in the Back_Content period. Please specify a batch using --batch option. Available batches can be listed with 'biorxiv list' command.",
+                    ],
+                    [
+                        '2015-06',
+                        "Date 2015-06 is in the Back_Content period. Please specify a batch using --batch option. Available batches can be listed with 'biorxiv list' command.",
+                    ],
+                    [
+                        'November_2018',
+                        "Date November_2018 is in the Back_Content period. Please specify a batch using --batch option. Available batches can be listed with 'biorxiv list' command.",
+                    ],
+                    [
+                        'October_2018',
+                        "Date October_2018 is in the Back_Content period. Please specify a batch using --batch option. Available batches can be listed with 'biorxiv list' command.",
+                    ],
+                ])('should throw error for Back_Content period month "%s" on bioRxiv', (month, expectedError) => {
+                    expect(() => getFolderStructure({ month, server: 'biorxiv' })).toThrow(expectedError);
+                });
+            });
+            describe('medRxiv server', () => {
+                it.each([
+                    [
+                        '2018-11',
+                        "Date 2018-11 is in the Back_Content period. Please specify a batch using --batch option. Available batches can be listed with 'biorxiv list' command.",
+                    ],
+                    [
+                        '2018-10',
+                        "Date 2018-10 is in the Back_Content period. Please specify a batch using --batch option. Available batches can be listed with 'biorxiv list' command.",
+                    ],
+                    [
+                        '2018-01',
+                        "Date 2018-01 is in the Back_Content period. Please specify a batch using --batch option. Available batches can be listed with 'biorxiv list' command.",
+                    ],
+                ])('should throw error for Back_Content period month "%s" on medRxiv', (month, expectedError) => {
+                    expect(() => getFolderStructure({ month, server: 'medrxiv' })).toThrow(expectedError);
+                });
+            });
+            describe('default server (bioRxiv)', () => {
+                it.each([
+                    [
+                        '2018-11',
+                        "Date 2018-11 is in the Back_Content period. Please specify a batch using --batch option. Available batches can be listed with 'biorxiv list' command.",
+                    ],
+                ])('should throw error for Back_Content period month "%s" with default server', (month, expectedError) => {
+                    expect(() => getFolderStructure({ month })).toThrow(expectedError);
+                });
+            });
+        });
+        describe('with invalid inputs', () => {
+            it.each([
+                [{}, 'Either month or batch must be specified'],
+                [{ month: undefined, batch: undefined }, 'Either month or batch must be specified'],
+                [{ month: '', batch: '' }, 'Either month or batch must be specified'],
+                [
+                    { month: 'invalid-month' },
+                    'Invalid month format: invalid-month. Expected YYYY-MM or Month_YYYY format.',
+                ],
+                [
+                    { month: '2024-13' },
+                    'Invalid month format: 2024-13. Expected YYYY-MM or Month_YYYY format.',
+                ],
+                [
+                    { month: '2024-00' },
+                    'Invalid month format: 2024-00. Expected YYYY-MM or Month_YYYY format.',
+                ],
+                [
+                    { month: 'InvalidMonth_2024' },
+                    'Invalid month format: InvalidMonth_2024. Expected YYYY-MM or Month_YYYY format.',
+                ],
+            ])('should throw error for invalid input %o', (input, expectedError) => {
+                expect(() => getFolderStructure(input)).toThrow(expectedError);
+            });
+        });
+        describe('edge cases', () => {
+            describe('bioRxiv server', () => {
+                it('should handle December 2018 as Current Content (cutoff date)', () => {
+                    const result = getFolderStructure({ month: '2018-12', server: 'biorxiv' });
+                    expect(result.type).toBe('current');
+                    expect(result.prefix).toBe('Current_Content/December_2018/');
+                    expect(result.batch).toBe('December_2018');
+                });
+                it('should handle January 2019 as Current Content (after cutoff)', () => {
+                    const result = getFolderStructure({ month: '2019-01', server: 'biorxiv' });
+                    expect(result.type).toBe('current');
+                    expect(result.prefix).toBe('Current_Content/January_2019/');
+                    expect(result.batch).toBe('January_2019');
+                });
+                it('should handle November 2018 as Back Content (before cutoff)', () => {
+                    expect(() => getFolderStructure({ month: '2018-11', server: 'biorxiv' })).toThrow('Date 2018-11 is in the Back_Content period. Please specify a batch using --batch option.');
+                });
+            });
+            describe('medRxiv server', () => {
+                it('should handle December 2018 as Current Content (cutoff date)', () => {
+                    const result = getFolderStructure({ month: '2018-12', server: 'medrxiv' });
+                    expect(result.type).toBe('current');
+                    expect(result.prefix).toBe('Current_Content/December_2018/');
+                    expect(result.batch).toBe('December_2018');
+                });
+                it('should handle January 2019 as Current Content (after cutoff)', () => {
+                    const result = getFolderStructure({ month: '2019-01', server: 'medrxiv' });
+                    expect(result.type).toBe('current');
+                    expect(result.prefix).toBe('Current_Content/January_2019/');
+                    expect(result.batch).toBe('January_2019');
+                });
+                it('should handle November 2018 as Back Content (before cutoff)', () => {
+                    expect(() => getFolderStructure({ month: '2018-11', server: 'medrxiv' })).toThrow('Date 2018-11 is in the Back_Content period. Please specify a batch using --batch option.');
+                });
+            });
+            describe('default server (bioRxiv)', () => {
+                it('should handle December 2018 as Current Content (cutoff date)', () => {
+                    const result = getFolderStructure({ month: '2018-12' });
+                    expect(result.type).toBe('current');
+                    expect(result.prefix).toBe('Current_Content/December_2018/');
+                    expect(result.batch).toBe('December_2018');
+                });
+                it('should handle January 2019 as Current Content (after cutoff)', () => {
+                    const result = getFolderStructure({ month: '2019-01' });
+                    expect(result.type).toBe('current');
+                    expect(result.prefix).toBe('Current_Content/January_2019/');
+                    expect(result.batch).toBe('January_2019');
+                });
+                it('should handle November 2018 as Back Content (before cutoff)', () => {
+                    expect(() => getFolderStructure({ month: '2018-11' })).toThrow('Date 2018-11 is in the Back_Content period. Please specify a batch using --batch option.');
+                });
+            });
+        });
+        describe('server validation', () => {
+            it('should not allow both month and batch to be specified', () => {
+                expect(() => getFolderStructure({ month: '2024-01', batch: '1' })).toThrow('Either month or batch must be specified, not both');
+                expect(() => getFolderStructure({ month: '2024-01', batch: '1', server: 'medrxiv' })).toThrow('Either month or batch must be specified, not both');
+            });
+            it('should require either month or batch', () => {
+                expect(() => getFolderStructure({ server: 'biorxiv' })).toThrow('Either month or batch must be specified');
+                expect(() => getFolderStructure({ server: 'medrxiv' })).toThrow('Either month or batch must be specified');
+            });
+        });
+    });
+});
+//# sourceMappingURL=folder-structure.test.js.map

package/dist/folder-structure.test.js.map

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

@@ -0,0 +1,3 @@
+export * from './biorxiv-parser.js';
+export * from './folder-structure.js';
+//# sourceMappingURL=index.d.ts.map

package/dist/index.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AACA,cAAc,qBAAqB,CAAC;AACpC,cAAc,uBAAuB,CAAC"}

package/dist/index.js

@@ -0,0 +1,4 @@
+// Export all utility functions
+export * from './biorxiv-parser.js';
+export * from './folder-structure.js';
+//# sourceMappingURL=index.js.map

package/dist/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,+BAA+B;AAC/B,cAAc,qBAAqB,CAAC;AACpC,cAAc,uBAAuB,CAAC"}

package/package.json

@@ -0,0 +1,42 @@
+{
+  "name": "openrxiv-utils",
+  "version": "0.0.0",
+  "description": "Utility functions for bioRxiv operations including URL parsing and DOI handling",
+  "main": "dist/index.js",
+  "type": "module",
+  "types": "dist/index.d.ts",
+  "exports": {
+    ".": {
+      "types": "./dist/index.d.ts",
+      "import": "./dist/index.js",
+      "default": "./dist/index.js"
+    }
+  },
+  "scripts": {
+    "build": "tsc",
+    "dev": "tsc --watch",
+    "test": "vitest run",
+    "test:watch": "vitest watch"
+  },
+  "keywords": [
+    "biorxiv",
+    "utils",
+    "doi",
+    "url-parsing",
+    "validation"
+  ],
+  "author": "Your Name",
+  "license": "MIT",
+  "engines": {
+    "node": ">=18.0.0"
+  },
+  "devDependencies": {},
+  "repository": {
+    "type": "git",
+    "url": "https://github.com/yourusername/biorxiv-meca.git"
+  },
+  "bugs": {
+    "url": "https://github.com/yourusername/biorxiv-meca/issues"
+  },
+  "homepage": "https://github.com/yourusername/biorxiv-meca#readme"
+}