openrxiv-utils 0.0.0

package/src/folder-structure.ts

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+/**
+ * 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 function normalizeBatch(batch: string | number, server: string = 'biorxiv'): string {
+  if (typeof batch === 'number') {
+    if (batch < 1) {
+      throw new Error(
+        `Invalid batch format: ${batch}. Expected a positive number or batch identifier.`,
+      );
+    }
+    const batchNum = batch.toString().padStart(2, '0');
+    return server.toLowerCase() === 'medrxiv' ? `medRxiv_Batch_${batchNum}` : `Batch_${batchNum}`;
+  }
+
+  // Remove common prefixes and normalize
+  const normalized = batch
+    .toLowerCase()
+    .replace(/^batch[-_]?/i, '') // Remove "batch", "batch-", "batch_"
+    .replace(/^medrxiv[-_]?batch[-_]?/i, '') // Remove "medrxiv_batch", "medrxiv-batch", etc.
+    .replace(/^0+/, '') // Remove leading zeros
+    .trim();
+
+  const matchInt = normalized.match(/^\d+$/);
+  if (!matchInt) {
+    throw new Error(
+      `Invalid batch format: ${batch}. Expected a positive number or batch identifier.`,
+    );
+  }
+
+  // Parse the number and format it
+  const batchNum = parseInt(normalized, 10);
+  if (isNaN(batchNum) || batchNum < 1) {
+    throw new Error(
+      `Invalid batch format: ${batch}. Expected a positive number or batch identifier.`,
+    );
+  }
+
+  const formattedBatchNum = batchNum.toString().padStart(2, '0');
+  return server.toLowerCase() === 'medrxiv'
+    ? `medRxiv_Batch_${formattedBatchNum}`
+    : `Batch_${formattedBatchNum}`;
+}
+
+/**
+ * Determines the folder structure for a given month or batch
+ * @param options - Options containing month or batch
+ * @returns FolderStructure with the appropriate prefix and type
+ */
+export function getFolderStructure(options: FolderStructureOptions): FolderStructure {
+  if (options.month && options.batch) {
+    throw new Error('Either month or batch must be specified, not both');
+  }
+  if (!options.month && !options.batch) {
+    throw new Error('Either month or batch must be specified');
+  }
+
+  if (options.batch) {
+    // If batch is specified, use Back_Content structure
+    const normalizedBatch = normalizeBatch(options.batch, options.server);
+    return {
+      server: options.server || 'biorxiv',
+      type: 'back',
+      prefix: `Back_Content/${normalizedBatch}/`,
+      batch: normalizedBatch,
+    };
+  }
+
+  if (options.month) {
+    // Normalize month format to YYYY-MM
+    const normalizedMonth = normalizeMonthToYYYYMM(options.month);
+
+    if (!normalizedMonth) {
+      throw new Error(
+        `Invalid month format: ${options.month}. Expected YYYY-MM or Month_YYYY format.`,
+      );
+    }
+
+    const [year, monthNum] = normalizedMonth.split('-').map(Number);
+
+    // bioRxiv switched from Back_Content to Current_Content in late 2018
+    // We'll use December 2018 as the cutoff point to be safe
+    const cutoffDate = new Date(2018, 11, 1); // December 1, 2018 (0-indexed month)
+    const requestedDate = new Date(year, monthNum - 1, 1);
+
+    if (requestedDate < cutoffDate) {
+      // Use Back_Content structure - but we don't know which batch
+      // User should specify batch explicitly for pre-2019 content
+      throw new Error(
+        `Date ${options.month} is in the Back_Content period. Please specify a batch using --batch option. ` +
+          `Available batches can be listed with 'biorxiv list' command.`,
+      );
+    } else {
+      // Use Current_Content structure
+      const monthName = getMonthName(monthNum);
+      return {
+        server: options.server || 'biorxiv',
+        type: 'current',
+        prefix: `Current_Content/${monthName}_${year}/`,
+        batch: `${monthName}_${year}`,
+      };
+    }
+  }
+  throw new Error('Invalid folder structure options');
+}
+
+export function removeDuplicateFolders(folders: FolderStructure[]): FolderStructure[] {
+  return folders.filter(
+    (folder, index, arr) =>
+      arr.findIndex(
+        (f) =>
+          f.batch === folder.batch &&
+          f.server === folder.server &&
+          f.type === folder.type &&
+          f.prefix === folder.prefix,
+      ) === index,
+  );
+}
+
+/**
+ * Sort folders chronologically, putting batches before months
+ */
+export function sortFoldersChronologically(folders: FolderStructure[]): FolderStructure[] {
+  return folders.sort((a, b) => {
+    // Put batches before months
+    if (a.type === 'back' && b.type === 'current') return -1;
+    if (a.type === 'current' && b.type === 'back') return 1;
+
+    // For batches, sort by batch number
+    if (a.type === 'back' && b.type === 'back') {
+      const aNum = parseInt(a.batch.replace(/\D/g, ''));
+      const bNum = parseInt(b.batch.replace(/\D/g, ''));
+      return aNum - bNum;
+    }
+
+    // For months, sort chronologically (newest first)
+    if (a.type === 'current' && b.type === 'current') {
+      const aDate = new Date(a.batch);
+      const bDate = new Date(b.batch);
+      return aDate.getTime() - bDate.getTime();
+    }
+
+    return 0;
+  });
+}
+
+/**
+ * Normalizes various month formats to YYYY-MM
+ * @param month - Month in various formats
+ * @returns Normalized YYYY-MM format or null if invalid
+ */
+export function normalizeMonthToYYYYMM(month: string): string | null {
+  // Already in YYYY-MM format
+  if (month.match(/^\d{4}-\d{2}$/)) {
+    const [, monthNum] = month.split('-').map(Number);
+    if (monthNum < 1 || monthNum > 12) {
+      return null; // Invalid month number
+    }
+    return month;
+  }
+
+  // Month_YYYY format (e.g., "November_2018")
+  const monthYearMatch = month.match(/^([A-Za-z]+)(?:[-_])(\d{4})$/);
+  if (monthYearMatch) {
+    const monthName = monthYearMatch[1];
+    const year = monthYearMatch[2];
+    const monthNum = getMonthNumber(monthName);
+
+    if (monthNum !== null) {
+      return `${year}-${monthNum.toString().padStart(2, '0')}`;
+    }
+  }
+
+  return null;
+}
+
+/**
+ * Gets month number from month name
+ * @param monthName - Month name (case insensitive)
+ * @returns Month number (1-12) or null if invalid
+ */
+function getMonthNumber(monthName: string): number | null {
+  const monthNames = [
+    'january',
+    'february',
+    'march',
+    'april',
+    'may',
+    'june',
+    'july',
+    'august',
+    'september',
+    'october',
+    'november',
+    'december',
+  ];
+
+  const normalizedName = monthName.toLowerCase();
+  let monthIndex = monthNames.indexOf(normalizedName);
+  if (monthIndex === -1) {
+    monthIndex = monthNames.map((m) => m.slice(0, 3).toLowerCase()).indexOf(normalizedName);
+  }
+
+  return monthIndex !== -1 ? monthIndex + 1 : null;
+}
+
+/**
+ * Gets month name from month number
+ * @param monthNum - Month number (1-12)
+ * @returns Month name (e.g., "January")
+ */
+function getMonthName(monthNum: number): string {
+  const monthNames = [
+    'January',
+    'February',
+    'March',
+    'April',
+    'May',
+    'June',
+    'July',
+    'August',
+    'September',
+    'October',
+    'November',
+    'December',
+  ];
+
+  if (monthNum < 1 || monthNum > 12) {
+    throw new Error(`Invalid month number: ${monthNum}. Must be 1-12.`);
+  }
+
+  return monthNames[monthNum - 1];
+}

package/src/index.ts

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+// Export all utility functions
+export * from './biorxiv-parser.js';
+export * from './folder-structure.js';

package/tsconfig.json

@@ -0,0 +1,31 @@
+{
+  "compilerOptions": {
+    "target": "ES2022",
+    "module": "ESNext",
+    "moduleResolution": "node",
+    "allowSyntheticDefaultImports": true,
+    "esModuleInterop": true,
+    "allowJs": true,
+    "strict": true,
+    "skipLibCheck": true,
+    "forceConsistentCasingInFileNames": true,
+    "resolveJsonModule": true,
+    "isolatedModules": true,
+    "declaration": true,
+    "outDir": "./dist",
+    "rootDir": "./src",
+    "sourceMap": true,
+    "declarationMap": true,
+    "baseUrl": ".",
+    "paths": {
+      "@/*": ["./src/*"]
+    }
+  },
+  "include": [
+    "src/**/*"
+  ],
+  "exclude": [
+    "node_modules",
+    "dist"
+  ]
+}