@ncukondo/reference-manager 0.22.2 → 0.22.3

package/dist/chunks/index-CNr_FIip.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index-CNr_FIip.js","sources":["../../src/features/attachments/filename.ts","../../src/features/attachments/types.ts","../../src/utils/path.ts","../../src/features/attachments/directory.ts","../../src/features/attachments/directory-manager.ts","../../src/features/operations/attachments/add.ts","../../src/features/operations/fulltext-adapter/fulltext-adapter.ts","../../src/features/operations/fulltext/attach.ts","../../src/features/operations/fulltext/get.ts","../../node_modules/@ncukondo/academic-fulltext/dist/discovery/arxiv.js","../../node_modules/@ncukondo/academic-fulltext/dist/discovery/core.js","../../node_modules/@ncukondo/academic-fulltext/dist/discovery/pmc.js","../../node_modules/@ncukondo/academic-fulltext/dist/discovery/unpaywall.js","../../node_modules/@ncukondo/academic-fulltext/dist/discovery/index.js","../../node_modules/@ncukondo/academic-fulltext/dist/download/downloader.js","../../node_modules/@ncukondo/academic-fulltext/dist/download/pmc-xml.js","../../node_modules/fast-xml-parser/src/util.js","../../node_modules/fast-xml-parser/src/validator.js","../../node_modules/fast-xml-parser/src/xmlparser/OptionsBuilder.js","../../node_modules/fast-xml-parser/src/xmlparser/xmlNode.js","../../node_modules/fast-xml-parser/src/xmlparser/DocTypeReader.js","../../node_modules/strnum/strnum.js","../../node_modules/fast-xml-parser/src/ignoreAttributes.js","../../node_modules/fast-xml-parser/src/xmlparser/OrderedObjParser.js","../../node_modules/fast-xml-parser/src/xmlparser/node2json.js","../../node_modules/fast-xml-parser/src/xmlparser/XMLParser.js","../../node_modules/@ncukondo/academic-fulltext/dist/convert/jats-parser.js","../../node_modules/@ncukondo/academic-fulltext/dist/convert/markdown-writer.js","../../node_modules/@ncukondo/academic-fulltext/dist/convert/index.js","../../src/features/operations/fulltext/discover.ts","../../src/features/operations/fulltext/fetch.ts","../../src/features/operations/fulltext/convert.ts","../../src/features/format/citation-fallback.ts","../../src/features/format/citation-csl.ts","../../src/features/pagination/sorter.ts","../../src/features/pagination/paginate.ts","../../src/config/csl-styles.ts","../../src/features/operations/remove.ts","../../src/features/import/cache.ts","../../src/features/import/normalizer.ts","../../src/features/import/detector.ts","../../src/features/import/rate-limiter.ts","../../src/features/import/fetcher.ts","../../src/features/import/parser.ts","../../src/features/import/importer.ts","../../src/features/operations/add.ts","../../src/server/routes/add.ts","../../src/features/operations/cite.ts","../../src/server/routes/cite.ts","../../src/server/routes/health.ts","../../src/features/operations/list.ts","../../src/server/routes/list.ts","../../src/features/operations/update.ts","../../src/server/routes/references.ts","../../src/features/operations/search.ts","../../src/server/routes/search.ts","../../src/server/index.ts"],"sourcesContent":["import path from \"node:path\";\n\n/**\n * Filename utilities for attachments\n *\n * File format: {role}[-{label-slug}].{ext}\n * Examples:\n *   - fulltext.pdf\n *   - supplement-table-s1.xlsx\n *   - notes-reading-analysis.md\n */\n\ninterface ParsedFilename {\n  role: string;\n  ext: string;\n  label?: string;\n}\n\n/**\n * Convert a human-readable label to a filesystem-safe slug\n */\nexport function slugifyLabel(label: string): string {\n  return label\n    .toLowerCase()\n    .replace(/[^a-z0-9]+/g, \"-\") // Replace non-alphanumeric with hyphen\n    .replace(/-+/g, \"-\") // Collapse multiple hyphens\n    .replace(/^-|-$/g, \"\"); // Trim leading/trailing hyphens\n}\n\n/**\n * Generate filename from role, extension, and optional label\n */\nexport function generateFilename(role: string, ext: string, label?: string): string {\n  if (label) {\n    const slug = slugifyLabel(label);\n    return `${role}-${slug}.${ext}`;\n  }\n  return `${role}.${ext}`;\n}\n\n/**\n * Parse filename to extract role, extension, and label\n *\n * Returns null for empty filenames\n */\nexport function parseFilename(filename: string): ParsedFilename | null {\n  if (!filename) {\n    return null;\n  }\n\n  const ext = path.extname(filename);\n  const extWithoutDot = ext.startsWith(\".\") ? ext.slice(1) : ext;\n  const basename = ext ? filename.slice(0, -ext.length) : filename;\n\n  // Split basename by first hyphen to get role and potential label\n  const firstHyphenIndex = basename.indexOf(\"-\");\n\n  if (firstHyphenIndex === -1) {\n    // No hyphen: just role, no label\n    return {\n      role: basename,\n      ext: extWithoutDot,\n    };\n  }\n\n  const role = basename.slice(0, firstHyphenIndex);\n  const label = basename.slice(firstHyphenIndex + 1);\n\n  if (label) {\n    return {\n      role,\n      ext: extWithoutDot,\n      label,\n    };\n  }\n\n  return {\n    role,\n    ext: extWithoutDot,\n  };\n}\n","import path from \"node:path\";\n\n/**\n * Attachment file metadata stored in reference's custom field\n */\nexport interface AttachmentFile {\n  /** Filename without path (e.g., \"fulltext.pdf\") */\n  filename: string;\n  /** Role identifier (e.g., \"fulltext\", \"supplement\", \"notes\") */\n  role: string;\n  /** Human-readable label (optional) */\n  label?: string;\n}\n\n/**\n * Attachments container stored in reference's custom.attachments field\n */\nexport interface Attachments {\n  /** Directory name relative to attachments base (e.g., \"Smith-2024-PMID12345678-123e4567\") */\n  directory: string;\n  /** List of attached files */\n  files: AttachmentFile[];\n}\n\n/**\n * Reserved role identifiers with special constraints\n */\nexport const RESERVED_ROLES = [\"fulltext\", \"supplement\", \"notes\", \"draft\"] as const;\n\nexport type ReservedRole = (typeof RESERVED_ROLES)[number];\n\n/**\n * Check if a role is a reserved role\n */\nexport function isReservedRole(role: string): role is ReservedRole {\n  return RESERVED_ROLES.includes(role as ReservedRole);\n}\n\n/**\n * Get file extension from filename (without leading dot)\n */\nexport function getExtension(filename: string): string {\n  const ext = path.extname(filename);\n  return ext.startsWith(\".\") ? ext.slice(1).toLowerCase() : ext.toLowerCase();\n}\n\n/**\n * Check if fulltext files satisfy the constraint: max 2 files (1 PDF + 1 Markdown)\n */\nexport function isValidFulltextFiles(files: AttachmentFile[]): boolean {\n  const fulltextFiles = files.filter((f) => f.role === \"fulltext\");\n\n  if (fulltextFiles.length > 2) {\n    return false;\n  }\n\n  if (fulltextFiles.length <= 1) {\n    return true;\n  }\n\n  // Exactly 2 files: must be 1 PDF and 1 Markdown\n  const extensions = fulltextFiles.map((f) => getExtension(f.filename));\n  const pdfCount = extensions.filter((ext) => ext === \"pdf\").length;\n  const mdCount = extensions.filter((ext) => ext === \"md\").length;\n\n  return pdfCount === 1 && mdCount === 1;\n}\n","/**\n * Cross-platform path utilities\n *\n * IMPORTANT: Path handling conventions in this codebase:\n *\n * 1. File system operations (fs.readFile, fs.writeFile, etc.)\n *    → Use NATIVE paths (path.join result as-is)\n *\n * 2. User-facing output (CLI output, API responses, result.path)\n *    → Use NORMALIZED paths (forward slashes via normalizePathForOutput)\n *\n * 3. Test expectations for output paths\n *    → Use NORMALIZED paths to match actual output\n */\n\n/**\n * Normalize path separators to forward slashes for consistent cross-platform output.\n *\n * Use this function ONLY for user-facing output, NOT for file system operations.\n *\n * @example\n * // In operation result\n * return { success: true, path: normalizePathForOutput(filePath) };\n *\n * // NOT for fs operations - use native path directly\n * await fs.readFile(filePath); // filePath from path.join, NOT normalized\n */\nexport function normalizePathForOutput(p: string): string {\n  return p.replace(/\\\\/g, \"/\");\n}\n","/**\n * Directory name utilities for attachments\n *\n * Directory format: {id}[-PMID{pmid}]-{uuid-prefix}\n * Examples:\n *   - With PMID: Smith-2024-PMID12345678-123e4567\n *   - Without PMID: Smith-2024-123e4567\n */\n\ninterface ReferenceForDirectory {\n  id: string;\n  PMID?: string;\n  custom?: { uuid?: string };\n}\n\ninterface ParsedDirectoryName {\n  id: string;\n  pmid?: string;\n  uuidPrefix: string;\n}\n\n/**\n * Extract first 8 characters of UUID as prefix\n */\nexport function extractUuidPrefix(uuid: string): string {\n  // Remove dashes and take first 8 chars\n  const normalized = uuid.replace(/-/g, \"\");\n  return normalized.slice(0, 8);\n}\n\n/**\n * Generate directory name for a reference\n */\nexport function generateDirectoryName(ref: ReferenceForDirectory): string {\n  const uuid = ref.custom?.uuid;\n  if (!uuid) {\n    throw new Error(\"Reference must have custom.uuid\");\n  }\n\n  const uuidPrefix = extractUuidPrefix(uuid);\n  const pmid = ref.PMID?.trim();\n\n  if (pmid) {\n    return `${ref.id}-PMID${pmid}-${uuidPrefix}`;\n  }\n  return `${ref.id}-${uuidPrefix}`;\n}\n\n/**\n * Parse directory name to extract components\n *\n * Returns null if the directory name doesn't match expected format\n */\nexport function parseDirectoryName(name: string): ParsedDirectoryName | null {\n  if (!name) {\n    return null;\n  }\n\n  // Pattern: {id}-PMID{pmid}-{uuidPrefix} or {id}-{uuidPrefix}\n  // uuidPrefix is always 8 hex characters at the end\n  const uuidPrefixPattern = /^[0-9a-f]{8}$/i;\n\n  // Split by '-' and check last part is uuid prefix\n  const parts = name.split(\"-\");\n  if (parts.length < 2) {\n    return null;\n  }\n\n  const lastPart = parts[parts.length - 1];\n  if (!lastPart || !uuidPrefixPattern.test(lastPart)) {\n    return null;\n  }\n\n  const uuidPrefix = lastPart;\n\n  // Check for PMID pattern in second-to-last position\n  const remainingParts = parts.slice(0, -1);\n  const lastRemaining = remainingParts[remainingParts.length - 1];\n  const pmidMatch = lastRemaining?.match(/^PMID(\\d+)$/);\n\n  if (pmidMatch?.[1]) {\n    // Has PMID\n    const id = remainingParts.slice(0, -1).join(\"-\");\n    if (!id) {\n      return null;\n    }\n    return {\n      id,\n      pmid: pmidMatch[1],\n      uuidPrefix,\n    };\n  }\n\n  // No PMID\n  const id = remainingParts.join(\"-\");\n  if (!id) {\n    return null;\n  }\n  return {\n    id,\n    uuidPrefix,\n  };\n}\n","import fs from \"node:fs/promises\";\nimport path from \"node:path\";\nimport { normalizePathForOutput } from \"../../utils/path.js\";\nimport { generateDirectoryName } from \"./directory.js\";\nimport type { Attachments } from \"./types.js\";\n\n/**\n * Reference with attachment-related fields\n */\ninterface ReferenceForAttachments {\n  id: string;\n  PMID?: string;\n  custom?: {\n    uuid?: string;\n    attachments?: Attachments;\n  };\n}\n\n/**\n * Get the full directory path for a reference's attachments\n *\n * Uses existing directory name from metadata if available,\n * otherwise generates a new one.\n */\nexport function getDirectoryPath(ref: ReferenceForAttachments, baseDir: string): string {\n  const existingDir = ref.custom?.attachments?.directory;\n  if (existingDir) {\n    // Normalize to forward slashes for consistent cross-platform output\n    return normalizePathForOutput(path.join(baseDir, existingDir));\n  }\n\n  // Generate new directory name\n  const dirName = generateDirectoryName(ref as Parameters<typeof generateDirectoryName>[0]);\n  // Normalize to forward slashes for consistent cross-platform output\n  return normalizePathForOutput(path.join(baseDir, dirName));\n}\n\n/**\n * Ensure the attachments directory exists for a reference\n *\n * Creates the directory if it doesn't exist.\n * Returns the full directory path.\n */\nexport async function ensureDirectory(\n  ref: ReferenceForAttachments,\n  baseDir: string\n): Promise<string> {\n  const dirPath = getDirectoryPath(ref, baseDir);\n\n  try {\n    await fs.mkdir(dirPath, { recursive: true });\n  } catch (error) {\n    // Ignore if directory already exists\n    if ((error as NodeJS.ErrnoException).code !== \"EEXIST\") {\n      throw error;\n    }\n  }\n\n  return dirPath;\n}\n\n/**\n * Delete a directory if it's empty\n *\n * Does nothing if the directory is not empty or doesn't exist.\n */\nexport async function deleteDirectoryIfEmpty(dirPath: string): Promise<void> {\n  try {\n    const files = await fs.readdir(dirPath);\n    if (files.length === 0) {\n      await fs.rmdir(dirPath);\n    }\n  } catch (error) {\n    // Ignore if directory doesn't exist\n    if ((error as NodeJS.ErrnoException).code !== \"ENOENT\") {\n      throw error;\n    }\n  }\n}\n\n/**\n * Rename a directory\n *\n * Does nothing if the paths are the same or old directory doesn't exist.\n */\nexport async function renameDirectory(oldPath: string, newPath: string): Promise<void> {\n  if (oldPath === newPath) {\n    return;\n  }\n\n  try {\n    await fs.rename(oldPath, newPath);\n  } catch (error) {\n    // Ignore if old directory doesn't exist\n    if ((error as NodeJS.ErrnoException).code !== \"ENOENT\") {\n      throw error;\n    }\n  }\n}\n","/**\n * Attachment add operation\n */\n\nimport { copyFile, rename, stat } from \"node:fs/promises\";\nimport { extname, join } from \"node:path\";\nimport type { CslItem } from \"../../../core/csl-json/types.js\";\nimport type { ILibrary, IdentifierType } from \"../../../core/library-interface.js\";\nimport { ensureDirectory } from \"../../attachments/directory-manager.js\";\nimport { generateDirectoryName } from \"../../attachments/directory.js\";\nimport { generateFilename } from \"../../attachments/filename.js\";\nimport {\n  type AttachmentFile,\n  type Attachments,\n  getExtension,\n  isValidFulltextFiles,\n} from \"../../attachments/types.js\";\n\n/**\n * Options for addAttachment operation\n */\nexport interface AddAttachmentOptions {\n  /** Reference identifier (id or uuid) */\n  identifier: string;\n  /** Path to the file to attach */\n  filePath: string;\n  /** Role for the attachment */\n  role: string;\n  /** Human-readable label (optional) */\n  label?: string;\n  /** Move file instead of copy */\n  move?: boolean;\n  /** Force overwrite existing file */\n  force?: boolean;\n  /** Identifier type */\n  idType?: IdentifierType;\n  /** Base directory for attachments */\n  attachmentsDirectory: string;\n}\n\n/**\n * Result of addAttachment operation\n */\nexport interface AddAttachmentResult {\n  success: boolean;\n  filename?: string;\n  directory?: string;\n  overwritten?: boolean;\n  existingFile?: string;\n  requiresConfirmation?: boolean;\n  error?: string;\n}\n\n/**\n * Reference with attachment-related fields\n */\ninterface ReferenceForAttachments {\n  id: string;\n  PMID?: string;\n  custom?: {\n    uuid?: string;\n    attachments?: Attachments;\n  };\n}\n\n/**\n * Check if source file exists\n */\nasync function checkSourceFile(filePath: string): Promise<string | null> {\n  try {\n    await stat(filePath);\n    return null;\n  } catch {\n    return `Source file not found: ${filePath}`;\n  }\n}\n\n/**\n * Validate fulltext constraints\n */\nfunction validateFulltextConstraint(\n  existingFiles: AttachmentFile[],\n  newFile: AttachmentFile\n): string | null {\n  if (newFile.role !== \"fulltext\") {\n    return null;\n  }\n\n  const newExt = getExtension(newFile.filename);\n  const existingFulltexts = existingFiles.filter((f) => f.role === \"fulltext\");\n\n  // Check if same format already exists\n  for (const existing of existingFulltexts) {\n    const existingExt = getExtension(existing.filename);\n    if (existingExt === newExt) {\n      return `A fulltext ${newExt.toUpperCase()} already exists. Use --force to overwrite.`;\n    }\n  }\n\n  // Check total count constraint\n  const testFiles = [...existingFiles, newFile];\n  if (!isValidFulltextFiles(testFiles)) {\n    return \"fulltext role allows max 2 files (1 PDF + 1 Markdown)\";\n  }\n\n  return null;\n}\n\n/**\n * Check if file with same name already exists\n */\nfunction findExistingFile(files: AttachmentFile[], filename: string): AttachmentFile | undefined {\n  return files.find((f) => f.filename === filename);\n}\n\n/**\n * Copy or move file to destination\n */\nasync function copyOrMoveFile(\n  sourcePath: string,\n  destPath: string,\n  move: boolean\n): Promise<string | null> {\n  try {\n    if (move) {\n      await rename(sourcePath, destPath);\n    } else {\n      await copyFile(sourcePath, destPath);\n    }\n    return null;\n  } catch (error) {\n    return `Failed to ${move ? \"move\" : \"copy\"} file: ${error instanceof Error ? error.message : String(error)}`;\n  }\n}\n\n/**\n * Update library with new attachment metadata\n */\nasync function updateAttachmentMetadata(\n  library: ILibrary,\n  item: CslItem,\n  updatedAttachments: Attachments\n): Promise<void> {\n  await library.update(item.id, {\n    custom: {\n      ...item.custom,\n      attachments: updatedAttachments,\n    },\n  } as Partial<CslItem>);\n}\n\n/**\n * Build updated files list\n */\nfunction buildUpdatedFiles(\n  existingFiles: AttachmentFile[],\n  newFile: AttachmentFile,\n  existingFile: AttachmentFile | undefined\n): AttachmentFile[] {\n  if (existingFile) {\n    return existingFiles.map((f) => (f.filename === newFile.filename ? newFile : f));\n  }\n  return [...existingFiles, newFile];\n}\n\n/**\n * Add an attachment to a reference\n */\nexport async function addAttachment(\n  library: ILibrary,\n  options: AddAttachmentOptions\n): Promise<AddAttachmentResult> {\n  const {\n    identifier,\n    filePath,\n    role,\n    label,\n    move = false,\n    force = false,\n    idType = \"id\",\n    attachmentsDirectory,\n  } = options;\n\n  // Find reference\n  const item = await library.find(identifier, { idType });\n  if (!item) {\n    return { success: false, error: `Reference '${identifier}' not found` };\n  }\n\n  // Check UUID\n  const uuid = (item as CslItem).custom?.uuid;\n  if (!uuid) {\n    return { success: false, error: \"Reference has no UUID. Cannot create attachment directory.\" };\n  }\n\n  // Check source file exists\n  const sourceError = await checkSourceFile(filePath);\n  if (sourceError) {\n    return { success: false, error: sourceError };\n  }\n\n  // Generate filename\n  const ext = extname(filePath).slice(1).toLowerCase();\n  const filename = generateFilename(role, ext, label);\n\n  // Get existing attachments\n  const existingAttachments = (item as CslItem).custom?.attachments as Attachments | undefined;\n  const existingFiles = existingAttachments?.files ?? [];\n\n  // Create new attachment file entry\n  const newFile: AttachmentFile = {\n    filename,\n    role,\n    ...(label && { label }),\n  };\n\n  // Check if file with same name exists\n  const existingFile = findExistingFile(existingFiles, filename);\n\n  // Validate fulltext constraints first (provides better error messages)\n  if (!existingFile || !force) {\n    const constraintError = validateFulltextConstraint(existingFiles, newFile);\n    if (constraintError) {\n      return { success: false, error: constraintError };\n    }\n  }\n\n  // Check if file with same name exists (non-fulltext case)\n  if (existingFile && !force) {\n    return {\n      success: false,\n      existingFile: filename,\n      requiresConfirmation: true,\n    };\n  }\n\n  // Ensure directory exists\n  const ref = item as ReferenceForAttachments;\n  const dirPath = await ensureDirectory(ref, attachmentsDirectory);\n  const dirName =\n    existingAttachments?.directory ??\n    generateDirectoryName(ref as Parameters<typeof generateDirectoryName>[0]);\n\n  // Copy or move file\n  const destPath = join(dirPath, filename);\n  const copyError = await copyOrMoveFile(filePath, destPath, move);\n  if (copyError) {\n    return { success: false, error: copyError };\n  }\n\n  // Update metadata\n  const updatedFiles = buildUpdatedFiles(existingFiles, newFile, existingFile);\n  const updatedAttachments: Attachments = {\n    directory: dirName,\n    files: updatedFiles,\n  };\n\n  await updateAttachmentMetadata(library, item as CslItem, updatedAttachments);\n  await library.save();\n\n  return {\n    success: true,\n    filename,\n    directory: dirName,\n    overwritten: !!existingFile,\n  };\n}\n","/**\n * Fulltext-to-attachments adapter utilities\n *\n * Maps fulltext command options and data to the new attachments system.\n * This adapter enables the fulltext command to use attachments backend\n * while maintaining backward-compatible interface.\n */\n\nimport type { AttachmentFile, Attachments } from \"../../attachments/types.js\";\nimport { getExtension } from \"../../attachments/types.js\";\n\n/**\n * The role used for fulltext files in the attachments system\n */\nexport const FULLTEXT_ROLE = \"fulltext\" as const;\n\n/**\n * Fulltext format type (matching existing FulltextType)\n */\nexport type FulltextFormat = \"pdf\" | \"markdown\";\n\n/**\n * Convert fulltext format to file extension\n */\nexport function formatToExtension(format: FulltextFormat): string {\n  return format === \"markdown\" ? \"md\" : format;\n}\n\n/**\n * Convert file extension to fulltext format\n * Returns undefined if extension is not a valid fulltext format\n */\nexport function extensionToFormat(ext: string): FulltextFormat | undefined {\n  const normalized = ext.toLowerCase();\n  if (normalized === \"pdf\") return \"pdf\";\n  if (normalized === \"md\" || normalized === \"markdown\") return \"markdown\";\n  return undefined;\n}\n\n/**\n * Get the standard filename for a fulltext file\n * Following the naming convention: fulltext.{ext}\n */\nexport function getFulltextFilename(format: FulltextFormat): string {\n  const ext = formatToExtension(format);\n  return `fulltext.${ext}`;\n}\n\n/**\n * Find a fulltext file of specific format in attachments\n */\nexport function findFulltextFile(\n  attachments: Attachments | undefined,\n  format: FulltextFormat\n): AttachmentFile | undefined {\n  if (!attachments?.files) {\n    return undefined;\n  }\n\n  const targetExt = formatToExtension(format);\n\n  return attachments.files.find((file) => {\n    if (file.role !== FULLTEXT_ROLE) {\n      return false;\n    }\n    const fileExt = getExtension(file.filename);\n    return fileExt === targetExt;\n  });\n}\n\n/**\n * Find all fulltext files in attachments\n */\nexport function findFulltextFiles(attachments: Attachments | undefined): AttachmentFile[] {\n  if (!attachments?.files) {\n    return [];\n  }\n\n  return attachments.files.filter((file) => file.role === FULLTEXT_ROLE);\n}\n","/**\n * Fulltext attach operation\n *\n * Uses attachments system internally with role='fulltext'.\n */\n\nimport { mkdtempSync, writeFileSync } from \"node:fs\";\nimport { rm } from \"node:fs/promises\";\nimport { tmpdir } from \"node:os\";\nimport { extname, join } from \"node:path\";\nimport type { ILibrary, IdentifierType } from \"../../../core/library-interface.js\";\nimport { type AddAttachmentResult, addAttachment } from \"../attachments/add.js\";\nimport {\n  FULLTEXT_ROLE,\n  type FulltextFormat,\n  formatToExtension,\n} from \"../fulltext-adapter/index.js\";\n\n/**\n * Fulltext type (matches existing FulltextType for backward compatibility)\n */\nexport type FulltextType = FulltextFormat;\n\n/**\n * Options for fulltextAttach operation\n */\nexport interface FulltextAttachOptions {\n  /** Reference identifier (id or uuid) */\n  identifier: string;\n  /** Path to the file to attach */\n  filePath?: string | undefined;\n  /** Explicit file type (pdf or markdown) */\n  type?: FulltextType | undefined;\n  /** Move file instead of copy */\n  move?: boolean | undefined;\n  /** Force overwrite existing file */\n  force?: boolean | undefined;\n  /** Identifier type: 'id' (default), 'uuid', 'doi', 'pmid', or 'isbn' */\n  idType?: IdentifierType | undefined;\n  /** Directory for attachments (replaces fulltextDirectory) */\n  fulltextDirectory: string;\n  /** Content from stdin */\n  stdinContent?: Buffer | undefined;\n}\n\n/**\n * Result of fulltextAttach operation\n */\nexport interface FulltextAttachResult {\n  success: boolean;\n  filename?: string | undefined;\n  type?: FulltextType | undefined;\n  overwritten?: boolean | undefined;\n  existingFile?: string | undefined;\n  requiresConfirmation?: boolean | undefined;\n  error?: string | undefined;\n}\n\n/**\n * Detect fulltext type from file extension\n */\nfunction detectType(filePath: string): FulltextType | undefined {\n  const ext = extname(filePath).toLowerCase();\n  if (ext === \".pdf\") return \"pdf\";\n  if (ext === \".md\" || ext === \".markdown\") return \"markdown\";\n  return undefined;\n}\n\n/**\n * Resolve file type from options\n */\nfunction resolveFileType(\n  explicitType: FulltextType | undefined,\n  filePath: string | undefined,\n  stdinContent: Buffer | undefined\n): FulltextType | { error: string } {\n  let fileType = explicitType;\n  if (!fileType && filePath) {\n    fileType = detectType(filePath);\n  }\n\n  if (stdinContent && !fileType) {\n    return {\n      error: \"File type must be specified with --pdf or --markdown when reading from stdin.\",\n    };\n  }\n\n  if (!fileType) {\n    return { error: \"Cannot detect file type. Use --pdf or --markdown to specify the type.\" };\n  }\n\n  return fileType;\n}\n\n/**\n * Prepare source path from stdin content\n */\nfunction prepareStdinSource(\n  stdinContent: Buffer,\n  fileType: FulltextType\n): { sourcePath: string; tempDir: string } | { error: string } {\n  try {\n    const tempDir = mkdtempSync(join(tmpdir(), \"refmgr-\"));\n    const ext = formatToExtension(fileType);\n    const sourcePath = join(tempDir, `stdin.${ext}`);\n    writeFileSync(sourcePath, stdinContent);\n    return { sourcePath, tempDir };\n  } catch (error) {\n    return {\n      error: `Failed to write stdin content: ${error instanceof Error ? error.message : String(error)}`,\n    };\n  }\n}\n\n/**\n * Clean up temp directory\n */\nasync function cleanupTempDir(tempDir: string | undefined): Promise<void> {\n  if (tempDir) {\n    await rm(tempDir, { recursive: true, force: true }).catch(() => {});\n  }\n}\n\n/**\n * Prepare source path from options\n */\nfunction prepareSourcePath(\n  filePath: string | undefined,\n  stdinContent: Buffer | undefined,\n  fileType: FulltextType\n): { sourcePath: string; tempDir?: string } | { error: string } {\n  if (stdinContent) {\n    return prepareStdinSource(stdinContent, fileType);\n  }\n\n  if (!filePath) {\n    return { error: \"No file path or stdin content provided.\" };\n  }\n\n  return { sourcePath: filePath };\n}\n\n/**\n * Convert AddAttachmentResult to FulltextAttachResult\n */\nfunction convertResult(result: AddAttachmentResult, fileType: FulltextType): FulltextAttachResult {\n  if (result.success) {\n    return {\n      success: true,\n      filename: result.filename,\n      type: fileType,\n      overwritten: result.overwritten,\n    };\n  }\n\n  if (result.requiresConfirmation) {\n    return {\n      success: false,\n      existingFile: result.existingFile,\n      requiresConfirmation: true,\n    };\n  }\n\n  return {\n    success: false,\n    error: result.error,\n  };\n}\n\n/**\n * Attach a fulltext file to a reference.\n *\n * @param library - The library containing the reference\n * @param options - Attach options\n * @returns Result of the attach operation\n */\nexport async function fulltextAttach(\n  library: ILibrary,\n  options: FulltextAttachOptions\n): Promise<FulltextAttachResult> {\n  const {\n    identifier,\n    filePath,\n    type: explicitType,\n    move,\n    force,\n    idType = \"id\",\n    fulltextDirectory,\n    stdinContent,\n  } = options;\n\n  // Resolve file type first\n  const fileTypeResult = resolveFileType(explicitType, filePath, stdinContent);\n  if (typeof fileTypeResult === \"object\" && \"error\" in fileTypeResult) {\n    // Check if reference exists (for consistent error messages)\n    const item = await library.find(identifier, { idType });\n    if (!item) {\n      return { success: false, error: `Reference '${identifier}' not found` };\n    }\n    return { success: false, error: fileTypeResult.error };\n  }\n  const fileType = fileTypeResult;\n\n  // Prepare source path\n  const sourceResult = prepareSourcePath(filePath, stdinContent, fileType);\n  if (\"error\" in sourceResult) {\n    // Check if reference exists (for consistent error messages)\n    const item = await library.find(identifier, { idType });\n    if (!item) {\n      return { success: false, error: `Reference '${identifier}' not found` };\n    }\n    return { success: false, error: sourceResult.error };\n  }\n  const { sourcePath, tempDir } = sourceResult;\n\n  try {\n    // Use attachments system with fulltext role\n    const result = await addAttachment(library, {\n      identifier,\n      filePath: sourcePath,\n      role: FULLTEXT_ROLE,\n      move: move ?? false,\n      force: force ?? false,\n      idType,\n      attachmentsDirectory: fulltextDirectory,\n    });\n\n    await cleanupTempDir(tempDir);\n\n    return convertResult(result, fileType);\n  } catch (error) {\n    await cleanupTempDir(tempDir);\n    throw error;\n  }\n}\n","/**\n * Fulltext get operation\n *\n * Uses attachments system internally with role='fulltext'.\n */\n\nimport { readFile } from \"node:fs/promises\";\nimport { join } from \"node:path\";\nimport type { CslItem } from \"../../../core/csl-json/types.js\";\nimport type { ILibrary, IdentifierType } from \"../../../core/library-interface.js\";\nimport { normalizePathForOutput } from \"../../../utils/path.js\";\nimport type { AttachmentFile, Attachments } from \"../../attachments/types.js\";\nimport {\n  type FulltextFormat,\n  extensionToFormat,\n  findFulltextFile,\n  findFulltextFiles,\n} from \"../fulltext-adapter/index.js\";\n\n/**\n * Fulltext type (matches existing FulltextType for backward compatibility)\n */\nexport type FulltextType = FulltextFormat;\n\n/**\n * Options for fulltextGet operation\n */\nexport interface FulltextGetOptions {\n  /** Reference identifier (id or uuid) */\n  identifier: string;\n  /** Specific type to get (pdf or markdown) */\n  type?: FulltextType | undefined;\n  /** Preferred type ordering when type is not specified (pdf or markdown) */\n  preferredType?: FulltextType | undefined;\n  /** If true, return file content instead of path */\n  stdout?: boolean | undefined;\n  /** Identifier type: 'id' (default), 'uuid', 'doi', 'pmid', or 'isbn' */\n  idType?: IdentifierType | undefined;\n  /** Directory for attachments (replaces fulltextDirectory) */\n  fulltextDirectory: string;\n}\n\n/**\n * Result of fulltextGet operation\n */\nexport interface FulltextGetResult {\n  success: boolean;\n  paths?: {\n    pdf?: string;\n    markdown?: string;\n  };\n  content?: Buffer;\n  error?: string;\n}\n\n/**\n * Build file path from attachments metadata\n */\nfunction buildFilePath(attachmentsDirectory: string, directory: string, filename: string): string {\n  return normalizePathForOutput(join(attachmentsDirectory, directory, filename));\n}\n\n/**\n * Get file content for stdout mode\n */\nasync function getFileContent(filePath: string): Promise<FulltextGetResult> {\n  const content = await readFile(filePath);\n  return { success: true, content };\n}\n\n/**\n * Handle stdout mode - get file content\n */\nasync function handleStdoutMode(\n  attachments: Attachments | undefined,\n  type: FulltextType,\n  identifier: string,\n  fulltextDirectory: string\n): Promise<FulltextGetResult> {\n  const file = findFulltextFile(attachments, type);\n  if (!file || !attachments?.directory) {\n    return { success: false, error: `No ${type} fulltext attached to '${identifier}'` };\n  }\n  const filePath = buildFilePath(fulltextDirectory, attachments.directory, file.filename);\n  try {\n    return await getFileContent(filePath);\n  } catch {\n    return { success: false, error: `No ${type} fulltext attached to '${identifier}'` };\n  }\n}\n\n/**\n * Get single type path\n */\nfunction getSingleTypePath(\n  attachments: Attachments | undefined,\n  type: FulltextType,\n  identifier: string,\n  fulltextDirectory: string\n): FulltextGetResult {\n  const file = findFulltextFile(attachments, type);\n  if (!file || !attachments?.directory) {\n    return { success: false, error: `No ${type} fulltext attached to '${identifier}'` };\n  }\n  const filePath = buildFilePath(fulltextDirectory, attachments.directory, file.filename);\n  const paths: { pdf?: string; markdown?: string } = {};\n  paths[type] = filePath;\n  return { success: true, paths };\n}\n\n/**\n * Get all fulltext paths\n */\nfunction getAllFulltextPaths(\n  attachments: Attachments,\n  fulltextFiles: AttachmentFile[],\n  fulltextDirectory: string,\n  identifier: string,\n  preferredType?: FulltextType\n): FulltextGetResult {\n  const paths: { pdf?: string; markdown?: string } = {};\n  for (const file of fulltextFiles) {\n    const ext = file.filename.split(\".\").pop() || \"\";\n    const format = extensionToFormat(ext);\n    if (format) {\n      const filePath = buildFilePath(fulltextDirectory, attachments.directory, file.filename);\n      paths[format] = filePath;\n    }\n  }\n\n  if (Object.keys(paths).length === 0) {\n    return { success: false, error: `No fulltext attached to '${identifier}'` };\n  }\n\n  // Reorder paths based on preferredType\n  if (preferredType && paths[preferredType]) {\n    const ordered: { pdf?: string; markdown?: string } = {};\n    ordered[preferredType] = paths[preferredType];\n    for (const key of Object.keys(paths) as FulltextType[]) {\n      if (key !== preferredType && paths[key]) {\n        ordered[key] = paths[key];\n      }\n    }\n    return { success: true, paths: ordered };\n  }\n\n  return { success: true, paths };\n}\n\n/**\n * Get fulltext file paths or content for a reference.\n *\n * @param library - The library containing the reference\n * @param options - Get options\n * @returns Result with file paths or content\n */\nexport async function fulltextGet(\n  library: ILibrary,\n  options: FulltextGetOptions\n): Promise<FulltextGetResult> {\n  const { identifier, type, preferredType, stdout, idType = \"id\", fulltextDirectory } = options;\n\n  // Find reference\n  const item = await library.find(identifier, { idType });\n  if (!item) {\n    return { success: false, error: `Reference '${identifier}' not found` };\n  }\n\n  // Get attachments metadata\n  const attachments = (item as CslItem).custom?.attachments as Attachments | undefined;\n\n  // Stdout mode with specific type\n  if (stdout && type) {\n    return handleStdoutMode(attachments, type, identifier, fulltextDirectory);\n  }\n\n  // Path mode - find all fulltext files\n  const fulltextFiles = findFulltextFiles(attachments);\n  if (fulltextFiles.length === 0) {\n    return { success: false, error: `No fulltext attached to '${identifier}'` };\n  }\n\n  // If specific type requested, filter to that type\n  if (type) {\n    return getSingleTypePath(attachments, type, identifier, fulltextDirectory);\n  }\n\n  // Return all fulltext paths\n  if (!attachments) {\n    return { success: false, error: `No fulltext attached to '${identifier}'` };\n  }\n\n  return getAllFulltextPaths(\n    attachments,\n    fulltextFiles,\n    fulltextDirectory,\n    identifier,\n    preferredType\n  );\n}\n","/**\n * arXiv OA discovery client.\n * Generates PDF download URLs for arXiv articles.\n *\n * URL pattern: https://arxiv.org/pdf/{id}.pdf\n * No API call needed — arXiv is always open access.\n */\n/** Strip common prefixes from arXiv IDs */\nfunction normalizeArxivId(id) {\n    return id.replace(/^arXiv:/i, \"\");\n}\n/**\n * Check arXiv availability for an article.\n * Since all arXiv articles are freely available, this simply\n * generates the PDF URL from the arXiv ID.\n *\n * @param arxivId - arXiv identifier (e.g., \"2401.12345\", \"hep-ph/9901234\")\n * @returns Array with a single PDF OALocation, or null if no ID\n */\nexport function checkArxiv(arxivId) {\n    if (!arxivId)\n        return null;\n    const id = normalizeArxivId(arxivId);\n    return [\n        {\n            source: \"arxiv\",\n            url: `https://arxiv.org/pdf/${id}.pdf`,\n            urlType: \"pdf\",\n            version: \"submitted\",\n        },\n    ];\n}\n//# sourceMappingURL=arxiv.js.map","/**\n * CORE API OA discovery client.\n * Checks Open Access availability via the CORE API.\n *\n * API: https://api.core.ac.uk/v3/search/works?q=doi:\"{doi}\"\n * Auth: Bearer token (API key, free registration)\n * Rate limit: 10 req/sec\n */\nconst CORE_API_BASE = \"https://api.core.ac.uk/v3\";\n/**\n * Check CORE API for Open Access availability of an article.\n *\n * @param doi - The article's DOI\n * @param apiKey - CORE API key (required; returns null if empty)\n * @returns Array of OALocations if found, null if not found or no key\n * @throws On rate limit (429) or network errors\n */\nexport async function checkCore(doi, apiKey) {\n    if (!doi)\n        return null;\n    if (!apiKey)\n        return null;\n    const url = `${CORE_API_BASE}/search/works?q=doi:\"${doi}\"&limit=1`;\n    const response = await fetch(url, {\n        headers: {\n            Authorization: `Bearer ${apiKey}`,\n        },\n    });\n    if (!response.ok) {\n        if (response.status === 429) {\n            throw new Error(\"CORE API rate limit exceeded\");\n        }\n        throw new Error(`CORE API error: HTTP ${response.status} ${response.statusText}`);\n    }\n    const data = (await response.json());\n    if (!data.totalHits || !data.results || data.results.length === 0) {\n        return null;\n    }\n    const firstResult = data.results[0];\n    if (!firstResult)\n        return null;\n    // Prefer downloadUrl (direct PDF from CORE)\n    if (firstResult.downloadUrl) {\n        return [\n            {\n                source: \"core\",\n                url: firstResult.downloadUrl,\n                urlType: \"pdf\",\n                version: \"accepted\",\n            },\n        ];\n    }\n    // Fall back to sourceFulltextUrls (repository links)\n    if (firstResult.sourceFulltextUrls && firstResult.sourceFulltextUrls.length > 0) {\n        const repoUrl = firstResult.sourceFulltextUrls[0];\n        if (repoUrl) {\n            return [\n                {\n                    source: \"core\",\n                    url: repoUrl,\n                    urlType: \"repository\",\n                    version: \"accepted\",\n                },\n            ];\n        }\n    }\n    return null;\n}\n//# sourceMappingURL=core.js.map","/**\n * PMC OA discovery client.\n * Checks PubMed Central availability and generates download URLs.\n *\n * PDF: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC{id}/pdf/\n * XML: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&id={pmcid}&rettype=xml\n * PMID→PMCID: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&db=pmc&id={pmid}&retmode=json\n */\nconst EUTILS_BASE = \"https://eutils.ncbi.nlm.nih.gov/entrez/eutils\";\n/** Strip \"PMC\" prefix from PMCID, returning just the numeric part */\nfunction stripPmcPrefix(pmcid) {\n    return pmcid.replace(/^PMC/i, \"\");\n}\n/** Ensure PMCID has the \"PMC\" prefix */\nfunction ensurePmcPrefix(pmcid) {\n    return pmcid.startsWith(\"PMC\") ? pmcid : `PMC${pmcid}`;\n}\n/**\n * Generate PMC download URLs from a known PMCID.\n */\nexport function getPmcUrls(pmcid) {\n    const numericId = stripPmcPrefix(pmcid);\n    const fullPmcid = ensurePmcPrefix(pmcid);\n    return [\n        {\n            source: \"pmc\",\n            url: `https://www.ncbi.nlm.nih.gov/pmc/articles/${fullPmcid}/pdf/`,\n            urlType: \"pdf\",\n            version: \"published\",\n        },\n        {\n            source: \"pmc\",\n            url: `${EUTILS_BASE}/efetch.fcgi?db=pmc&id=${numericId}&rettype=xml`,\n            urlType: \"xml\",\n            version: \"published\",\n        },\n    ];\n}\n/**\n * Look up PMCID from PMID via E-utilities elink API.\n * @returns PMCID string or null if not in PMC\n */\nasync function lookupPmcid(pmid, options) {\n    let url = `${EUTILS_BASE}/elink.fcgi?dbfrom=pubmed&db=pmc&id=${pmid}&retmode=json`;\n    if (options?.apiKey) {\n        url += `&api_key=${options.apiKey}`;\n    }\n    const response = await fetch(url);\n    if (!response.ok) {\n        throw new Error(`PMC elink API error: HTTP ${response.status}`);\n    }\n    const data = (await response.json());\n    const linksets = data.linksets;\n    if (!linksets || linksets.length === 0)\n        return null;\n    const firstLinkset = linksets[0];\n    if (!firstLinkset?.linksetdbs)\n        return null;\n    const pmcLink = firstLinkset.linksetdbs.find((db) => db.dbto === \"pmc\");\n    if (!pmcLink?.links || pmcLink.links.length === 0)\n        return null;\n    const pmcNumericId = pmcLink.links[0];\n    return pmcNumericId ? `PMC${pmcNumericId}` : null;\n}\n/**\n * Check PMC availability for an article.\n * If PMCID is known, generates URLs directly.\n * If only PMID is known, looks up PMCID via E-utilities elink.\n */\nexport async function checkPmc(ids, options) {\n    // If PMCID is already known, generate URLs directly\n    if (ids.pmcid) {\n        return getPmcUrls(ids.pmcid);\n    }\n    // If only PMID is known, look up PMCID\n    if (ids.pmid) {\n        const pmcid = await lookupPmcid(ids.pmid, options);\n        if (!pmcid)\n            return null;\n        return getPmcUrls(pmcid);\n    }\n    // No identifiers provided\n    return null;\n}\n//# sourceMappingURL=pmc.js.map","/**\n * Unpaywall OA discovery client.\n * Checks Open Access availability via the Unpaywall API.\n *\n * API: https://api.unpaywall.org/v2/{doi}?email={email}\n * Rate limit: 100,000 requests/day (no per-second limit documented)\n */\nconst UNPAYWALL_BASE_URL = \"https://api.unpaywall.org/v2\";\n/** Map Unpaywall version strings to our OALocation version format */\nfunction mapVersion(version) {\n    switch (version) {\n        case \"publishedVersion\":\n            return \"published\";\n        case \"acceptedVersion\":\n            return \"accepted\";\n        case \"submittedVersion\":\n            return \"submitted\";\n        default:\n            return \"published\";\n    }\n}\n/** Convert an Unpaywall location to our OALocation format */\nfunction toOALocation(loc) {\n    const hasPdf = loc.url_for_pdf != null;\n    const url = hasPdf ? loc.url_for_pdf : loc.url_for_landing_page;\n    if (!url)\n        return null;\n    const result = {\n        source: \"unpaywall\",\n        url,\n        urlType: hasPdf ? \"pdf\" : \"html\",\n        version: mapVersion(loc.version),\n    };\n    if (loc.license) {\n        result.license = loc.license;\n    }\n    return result;\n}\n/**\n * Check Unpaywall for Open Access availability of an article.\n *\n * @param doi - The article's DOI\n * @param email - Email address required by Unpaywall API (free, no registration)\n * @returns Array of OALocations if OA, null if closed/not found\n * @throws On rate limit (429) or network errors\n */\nexport async function checkUnpaywall(doi, email) {\n    if (!doi)\n        return null;\n    if (!email) {\n        throw new Error(\"Unpaywall email is required for API access\");\n    }\n    const url = `${UNPAYWALL_BASE_URL}/${doi}?email=${encodeURIComponent(email)}`;\n    const response = await fetch(url);\n    if (!response.ok) {\n        if (response.status === 404)\n            return null;\n        if (response.status === 429) {\n            throw new Error(\"Unpaywall rate limit exceeded\");\n        }\n        throw new Error(`Unpaywall API error: HTTP ${response.status} ${response.statusText}`);\n    }\n    const data = (await response.json());\n    if (!data.is_oa || !data.oa_locations || data.oa_locations.length === 0) {\n        return null;\n    }\n    const locations = [];\n    for (const loc of data.oa_locations) {\n        const oaLoc = toOALocation(loc);\n        if (oaLoc)\n            locations.push(oaLoc);\n    }\n    return locations.length > 0 ? locations : null;\n}\n//# sourceMappingURL=unpaywall.js.map","/**\n * OA Discovery Aggregator.\n * Combines results from multiple OA discovery sources.\n */\nimport { checkArxiv } from \"./arxiv.js\";\nimport { checkCore } from \"./core.js\";\nimport { checkPmc } from \"./pmc.js\";\nimport { checkUnpaywall } from \"./unpaywall.js\";\n/** Default source order when preferSources is empty or not specified */\nconst DEFAULT_SOURCE_ORDER = [\"pmc\", \"arxiv\", \"unpaywall\", \"core\"];\nasync function checkPmcSource(article) {\n    if (!article.pmid && !article.pmcid)\n        return undefined;\n    const ids = {};\n    if (article.pmid)\n        ids.pmid = article.pmid;\n    if (article.pmcid)\n        ids.pmcid = article.pmcid;\n    return await checkPmc(ids);\n}\nfunction checkArxivSource(article) {\n    if (!article.arxivId)\n        return undefined;\n    return checkArxiv(article.arxivId);\n}\nasync function checkUnpaywallSource(article, config) {\n    if (!config.unpaywallEmail || !article.doi)\n        return undefined;\n    return await checkUnpaywall(article.doi, config.unpaywallEmail);\n}\nasync function checkCoreSource(article, config) {\n    if (!config.coreApiKey || !article.doi)\n        return undefined;\n    return await checkCore(article.doi, config.coreApiKey);\n}\n/** Map of source name to its checker function. */\nconst sourceCheckers = {\n    pmc: checkPmcSource,\n    arxiv: checkArxivSource,\n    unpaywall: checkUnpaywallSource,\n    core: checkCoreSource,\n};\n/** Determine OA status from collected locations and errors. */\nfunction determineOAStatus(locations, errors, sourcesChecked) {\n    if (locations.length > 0)\n        return \"open\";\n    if (errors.length > 0 && errors.length >= sourcesChecked)\n        return \"unknown\";\n    return \"closed\";\n}\n/**\n * Discover OA availability for an article across all configured sources.\n * Checks sources in the order specified by config.preferSources, falling back\n * to the default order. Individual source errors are caught and reported\n * without failing the whole discovery.\n */\nexport async function discoverOA(article, config) {\n    const locations = [];\n    const errors = [];\n    let sourcesChecked = 0;\n    const sourceOrder = config.preferSources.length > 0 ? config.preferSources : DEFAULT_SOURCE_ORDER;\n    for (const source of sourceOrder) {\n        const checker = sourceCheckers[source];\n        if (!checker)\n            continue;\n        const result = await runSourceChecker(checker, article, config);\n        if (result.skipped)\n            continue;\n        sourcesChecked++;\n        if (result.error) {\n            errors.push({ source, error: result.error });\n        }\n        else if (result.locations) {\n            locations.push(...result.locations);\n        }\n    }\n    const oaStatus = determineOAStatus(locations, errors, sourcesChecked);\n    return { oaStatus, locations, errors };\n}\n/** Run a single source checker with error handling. */\nasync function runSourceChecker(checker, article, config) {\n    try {\n        const result = await checker(article, config);\n        if (result === undefined)\n            return { skipped: true };\n        return { skipped: false, locations: result ?? [] };\n    }\n    catch (err) {\n        return { skipped: false, error: String(err) };\n    }\n}\n//# sourceMappingURL=index.js.map","/**\n * PDF downloader with retry and error handling.\n */\nimport { mkdir, writeFile } from \"node:fs/promises\";\nimport { dirname } from \"node:path\";\n/** HTTP status codes that should not be retried */\nconst NON_RETRYABLE_STATUSES = new Set([400, 401, 403, 404, 405, 410]);\n/** Content types accepted as valid PDF responses */\nconst VALID_CONTENT_TYPES = [\"application/pdf\", \"application/octet-stream\"];\nconst USER_AGENT = \"search-hub/0.8.0 (https://github.com/ncukondo/search-hub)\";\nfunction isValidPdfContentType(contentType) {\n    if (!contentType)\n        return false;\n    const base = (contentType.split(\";\")[0] ?? \"\").trim().toLowerCase();\n    return VALID_CONTENT_TYPES.includes(base);\n}\nfunction sleep(ms) {\n    return new Promise((resolve) => setTimeout(resolve, ms));\n}\nasync function attemptDownload(url, destPath) {\n    const response = await fetch(url, {\n        headers: { \"User-Agent\": USER_AGENT },\n    });\n    if (!response.ok) {\n        const error = `HTTP ${response.status} ${response.statusText}`;\n        if (NON_RETRYABLE_STATUSES.has(response.status)) {\n            return { kind: \"fail\", result: { success: false, error } };\n        }\n        return { kind: \"retry\", error };\n    }\n    const contentType = response.headers.get(\"content-type\");\n    if (!isValidPdfContentType(contentType)) {\n        return {\n            kind: \"fail\",\n            result: {\n                success: false,\n                error: `Unexpected Content-Type: ${contentType ?? \"none\"}`,\n            },\n        };\n    }\n    const buffer = await response.arrayBuffer();\n    await mkdir(dirname(destPath), { recursive: true });\n    await writeFile(destPath, Buffer.from(buffer));\n    return { kind: \"success\", result: { success: true, size: buffer.byteLength } };\n}\n/**\n * Download a PDF from a URL to a local file path.\n * Retries on network errors and 429 responses with exponential backoff.\n * Does not retry on 403/404 or other client errors.\n */\nexport async function downloadPdf(url, destPath, options) {\n    const retries = options?.retries ?? 3;\n    const retryDelay = options?.retryDelay ?? 1000;\n    let lastError;\n    for (let attempt = 1; attempt <= retries; attempt++) {\n        try {\n            const outcome = await attemptDownload(url, destPath);\n            if (outcome.kind === \"success\" || outcome.kind === \"fail\") {\n                return outcome.result;\n            }\n            lastError = outcome.error;\n        }\n        catch (err) {\n            lastError = err instanceof Error ? err.message : String(err);\n        }\n        if (attempt < retries) {\n            await sleep(retryDelay * attempt);\n        }\n    }\n    return { success: false, error: lastError ?? \"Download failed\" };\n}\n//# sourceMappingURL=downloader.js.map","/**\n * PMC XML downloader via E-utilities.\n */\nimport { mkdir, writeFile } from \"node:fs/promises\";\nimport { dirname } from \"node:path\";\nconst PMC_EFETCH_URL = \"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi\";\n/** Content types accepted as valid XML responses */\nconst VALID_XML_TYPES = [\"text/xml\", \"application/xml\"];\nconst USER_AGENT = \"search-hub/0.8.0 (https://github.com/ncukondo/search-hub)\";\nfunction isValidXmlContentType(contentType) {\n    if (!contentType)\n        return false;\n    const base = (contentType.split(\";\")[0] ?? \"\").trim().toLowerCase();\n    return VALID_XML_TYPES.includes(base);\n}\n/** Strip \"PMC\" prefix if present, returning numeric ID */\nfunction normalizePmcid(pmcid) {\n    return pmcid.replace(/^PMC/i, \"\");\n}\n/**\n * Download PMC XML for a given PMCID via E-utilities efetch.\n */\nexport async function downloadPmcXml(pmcid, destPath) {\n    const numericId = normalizePmcid(pmcid);\n    const url = `${PMC_EFETCH_URL}?db=pmc&id=${numericId}&rettype=xml`;\n    try {\n        const response = await fetch(url, {\n            headers: { \"User-Agent\": USER_AGENT },\n        });\n        if (!response.ok) {\n            return {\n                success: false,\n                error: `HTTP ${response.status} ${response.statusText}`,\n            };\n        }\n        const contentType = response.headers.get(\"content-type\");\n        if (!isValidXmlContentType(contentType)) {\n            return {\n                success: false,\n                error: `Unexpected Content-Type: ${contentType ?? \"none\"} (expected XML)`,\n            };\n        }\n        const text = await response.text();\n        await mkdir(dirname(destPath), { recursive: true });\n        await writeFile(destPath, text, \"utf-8\");\n        return { success: true, size: Buffer.byteLength(text) };\n    }\n    catch (err) {\n        return {\n            success: false,\n            error: err instanceof Error ? err.message : String(err),\n        };\n    }\n}\n//# sourceMappingURL=pmc-xml.js.map","'use strict';\n\nconst nameStartChar = ':A-Za-z_\\\\u00C0-\\\\u00D6\\\\u00D8-\\\\u00F6\\\\u00F8-\\\\u02FF\\\\u0370-\\\\u037D\\\\u037F-\\\\u1FFF\\\\u200C-\\\\u200D\\\\u2070-\\\\u218F\\\\u2C00-\\\\u2FEF\\\\u3001-\\\\uD7FF\\\\uF900-\\\\uFDCF\\\\uFDF0-\\\\uFFFD';\nconst nameChar = nameStartChar + '\\\\-.\\\\d\\\\u00B7\\\\u0300-\\\\u036F\\\\u203F-\\\\u2040';\nexport const nameRegexp = '[' + nameStartChar + '][' + nameChar + ']*';\nconst regexName = new RegExp('^' + nameRegexp + '$');\n\nexport function getAllMatches(string, regex) {\n  const matches = [];\n  let match = regex.exec(string);\n  while (match) {\n    const allmatches = [];\n    allmatches.startIndex = regex.lastIndex - match[0].length;\n    const len = match.length;\n    for (let index = 0; index < len; index++) {\n      allmatches.push(match[index]);\n    }\n    matches.push(allmatches);\n    match = regex.exec(string);\n  }\n  return matches;\n}\n\nexport const isName = function(string) {\n  const match = regexName.exec(string);\n  return !(match === null || typeof match === 'undefined');\n}\n\nexport function isExist(v) {\n  return typeof v !== 'undefined';\n}\n\nexport function isEmptyObject(obj) {\n  return Object.keys(obj).length === 0;\n}\n\n/**\n * Copy all the properties of a into b.\n * @param {*} target\n * @param {*} a\n */\nexport function merge(target, a, arrayMode) {\n  if (a) {\n    const keys = Object.keys(a); // will return an array of own properties\n    const len = keys.length; //don't make it inline\n    for (let i = 0; i < len; i++) {\n      if (arrayMode === 'strict') {\n        target[keys[i]] = [ a[keys[i]] ];\n      } else {\n        target[keys[i]] = a[keys[i]];\n      }\n    }\n  }\n}\n/* exports.merge =function (b,a){\n  return Object.assign(b,a);\n} */\n\nexport function getValue(v) {\n  if (exports.isExist(v)) {\n    return v;\n  } else {\n    return '';\n  }\n}\n\n// const fakeCall = function(a) {return a;};\n// const fakeCallNoReturn = function() {};","'use strict';\n\nimport {getAllMatches, isName} from './util.js';\n\nconst defaultOptions = {\n  allowBooleanAttributes: false, //A tag can have attributes without any value\n  unpairedTags: []\n};\n\n//const tagsPattern = new RegExp(\"<\\\\/?([\\\\w:\\\\-_\\.]+)\\\\s*\\/?>\",\"g\");\nexport function validate(xmlData, options) {\n  options = Object.assign({}, defaultOptions, options);\n\n  //xmlData = xmlData.replace(/(\\r\\n|\\n|\\r)/gm,\"\");//make it single line\n  //xmlData = xmlData.replace(/(^\\s*<\\?xml.*?\\?>)/g,\"\");//Remove XML starting tag\n  //xmlData = xmlData.replace(/(<!DOCTYPE[\\s\\w\\\"\\.\\/\\-\\:]+(\\[.*\\])*\\s*>)/g,\"\");//Remove DOCTYPE\n  const tags = [];\n  let tagFound = false;\n\n  //indicates that the root tag has been closed (aka. depth 0 has been reached)\n  let reachedRoot = false;\n\n  if (xmlData[0] === '\\ufeff') {\n    // check for byte order mark (BOM)\n    xmlData = xmlData.substr(1);\n  }\n  \n  for (let i = 0; i < xmlData.length; i++) {\n\n    if (xmlData[i] === '<' && xmlData[i+1] === '?') {\n      i+=2;\n      i = readPI(xmlData,i);\n      if (i.err) return i;\n    }else if (xmlData[i] === '<') {\n      //starting of tag\n      //read until you reach to '>' avoiding any '>' in attribute value\n      let tagStartPos = i;\n      i++;\n      \n      if (xmlData[i] === '!') {\n        i = readCommentAndCDATA(xmlData, i);\n        continue;\n      } else {\n        let closingTag = false;\n        if (xmlData[i] === '/') {\n          //closing tag\n          closingTag = true;\n          i++;\n        }\n        //read tagname\n        let tagName = '';\n        for (; i < xmlData.length &&\n          xmlData[i] !== '>' &&\n          xmlData[i] !== ' ' &&\n          xmlData[i] !== '\\t' &&\n          xmlData[i] !== '\\n' &&\n          xmlData[i] !== '\\r'; i++\n        ) {\n          tagName += xmlData[i];\n        }\n        tagName = tagName.trim();\n        //console.log(tagName);\n\n        if (tagName[tagName.length - 1] === '/') {\n          //self closing tag without attributes\n          tagName = tagName.substring(0, tagName.length - 1);\n          //continue;\n          i--;\n        }\n        if (!validateTagName(tagName)) {\n          let msg;\n          if (tagName.trim().length === 0) {\n            msg = \"Invalid space after '<'.\";\n          } else {\n            msg = \"Tag '\"+tagName+\"' is an invalid name.\";\n          }\n          return getErrorObject('InvalidTag', msg, getLineNumberForPosition(xmlData, i));\n        }\n\n        const result = readAttributeStr(xmlData, i);\n        if (result === false) {\n          return getErrorObject('InvalidAttr', \"Attributes for '\"+tagName+\"' have open quote.\", getLineNumberForPosition(xmlData, i));\n        }\n        let attrStr = result.value;\n        i = result.index;\n\n        if (attrStr[attrStr.length - 1] === '/') {\n          //self closing tag\n          const attrStrStart = i - attrStr.length;\n          attrStr = attrStr.substring(0, attrStr.length - 1);\n          const isValid = validateAttributeString(attrStr, options);\n          if (isValid === true) {\n            tagFound = true;\n            //continue; //text may presents after self closing tag\n          } else {\n            //the result from the nested function returns the position of the error within the attribute\n            //in order to get the 'true' error line, we need to calculate the position where the attribute begins (i - attrStr.length) and then add the position within the attribute\n            //this gives us the absolute index in the entire xml, which we can use to find the line at last\n            return getErrorObject(isValid.err.code, isValid.err.msg, getLineNumberForPosition(xmlData, attrStrStart + isValid.err.line));\n          }\n        } else if (closingTag) {\n          if (!result.tagClosed) {\n            return getErrorObject('InvalidTag', \"Closing tag '\"+tagName+\"' doesn't have proper closing.\", getLineNumberForPosition(xmlData, i));\n          } else if (attrStr.trim().length > 0) {\n            return getErrorObject('InvalidTag', \"Closing tag '\"+tagName+\"' can't have attributes or invalid starting.\", getLineNumberForPosition(xmlData, tagStartPos));\n          } else if (tags.length === 0) {\n            return getErrorObject('InvalidTag', \"Closing tag '\"+tagName+\"' has not been opened.\", getLineNumberForPosition(xmlData, tagStartPos));\n          } else {\n            const otg = tags.pop();\n            if (tagName !== otg.tagName) {\n              let openPos = getLineNumberForPosition(xmlData, otg.tagStartPos);\n              return getErrorObject('InvalidTag',\n                \"Expected closing tag '\"+otg.tagName+\"' (opened in line \"+openPos.line+\", col \"+openPos.col+\") instead of closing tag '\"+tagName+\"'.\",\n                getLineNumberForPosition(xmlData, tagStartPos));\n            }\n\n            //when there are no more tags, we reached the root level.\n            if (tags.length == 0) {\n              reachedRoot = true;\n            }\n          }\n        } else {\n          const isValid = validateAttributeString(attrStr, options);\n          if (isValid !== true) {\n            //the result from the nested function returns the position of the error within the attribute\n            //in order to get the 'true' error line, we need to calculate the position where the attribute begins (i - attrStr.length) and then add the position within the attribute\n            //this gives us the absolute index in the entire xml, which we can use to find the line at last\n            return getErrorObject(isValid.err.code, isValid.err.msg, getLineNumberForPosition(xmlData, i - attrStr.length + isValid.err.line));\n          }\n\n          //if the root level has been reached before ...\n          if (reachedRoot === true) {\n            return getErrorObject('InvalidXml', 'Multiple possible root nodes found.', getLineNumberForPosition(xmlData, i));\n          } else if(options.unpairedTags.indexOf(tagName) !== -1){\n            //don't push into stack\n          } else {\n            tags.push({tagName, tagStartPos});\n          }\n          tagFound = true;\n        }\n\n        //skip tag text value\n        //It may include comments and CDATA value\n        for (i++; i < xmlData.length; i++) {\n          if (xmlData[i] === '<') {\n            if (xmlData[i + 1] === '!') {\n              //comment or CADATA\n              i++;\n              i = readCommentAndCDATA(xmlData, i);\n              continue;\n            } else if (xmlData[i+1] === '?') {\n              i = readPI(xmlData, ++i);\n              if (i.err) return i;\n            } else{\n              break;\n            }\n          } else if (xmlData[i] === '&') {\n            const afterAmp = validateAmpersand(xmlData, i);\n            if (afterAmp == -1)\n              return getErrorObject('InvalidChar', \"char '&' is not expected.\", getLineNumberForPosition(xmlData, i));\n            i = afterAmp;\n          }else{\n            if (reachedRoot === true && !isWhiteSpace(xmlData[i])) {\n              return getErrorObject('InvalidXml', \"Extra text at the end\", getLineNumberForPosition(xmlData, i));\n            }\n          }\n        } //end of reading tag text value\n        if (xmlData[i] === '<') {\n          i--;\n        }\n      }\n    } else {\n      if ( isWhiteSpace(xmlData[i])) {\n        continue;\n      }\n      return getErrorObject('InvalidChar', \"char '\"+xmlData[i]+\"' is not expected.\", getLineNumberForPosition(xmlData, i));\n    }\n  }\n\n  if (!tagFound) {\n    return getErrorObject('InvalidXml', 'Start tag expected.', 1);\n  }else if (tags.length == 1) {\n      return getErrorObject('InvalidTag', \"Unclosed tag '\"+tags[0].tagName+\"'.\", getLineNumberForPosition(xmlData, tags[0].tagStartPos));\n  }else if (tags.length > 0) {\n      return getErrorObject('InvalidXml', \"Invalid '\"+\n          JSON.stringify(tags.map(t => t.tagName), null, 4).replace(/\\r?\\n/g, '')+\n          \"' found.\", {line: 1, col: 1});\n  }\n\n  return true;\n};\n\nfunction isWhiteSpace(char){\n  return char === ' ' || char === '\\t' || char === '\\n'  || char === '\\r';\n}\n/**\n * Read Processing insstructions and skip\n * @param {*} xmlData\n * @param {*} i\n */\nfunction readPI(xmlData, i) {\n  const start = i;\n  for (; i < xmlData.length; i++) {\n    if (xmlData[i] == '?' || xmlData[i] == ' ') {\n      //tagname\n      const tagname = xmlData.substr(start, i - start);\n      if (i > 5 && tagname === 'xml') {\n        return getErrorObject('InvalidXml', 'XML declaration allowed only at the start of the document.', getLineNumberForPosition(xmlData, i));\n      } else if (xmlData[i] == '?' && xmlData[i + 1] == '>') {\n        //check if valid attribut string\n        i++;\n        break;\n      } else {\n        continue;\n      }\n    }\n  }\n  return i;\n}\n\nfunction readCommentAndCDATA(xmlData, i) {\n  if (xmlData.length > i + 5 && xmlData[i + 1] === '-' && xmlData[i + 2] === '-') {\n    //comment\n    for (i += 3; i < xmlData.length; i++) {\n      if (xmlData[i] === '-' && xmlData[i + 1] === '-' && xmlData[i + 2] === '>') {\n        i += 2;\n        break;\n      }\n    }\n  } else if (\n    xmlData.length > i + 8 &&\n    xmlData[i + 1] === 'D' &&\n    xmlData[i + 2] === 'O' &&\n    xmlData[i + 3] === 'C' &&\n    xmlData[i + 4] === 'T' &&\n    xmlData[i + 5] === 'Y' &&\n    xmlData[i + 6] === 'P' &&\n    xmlData[i + 7] === 'E'\n  ) {\n    let angleBracketsCount = 1;\n    for (i += 8; i < xmlData.length; i++) {\n      if (xmlData[i] === '<') {\n        angleBracketsCount++;\n      } else if (xmlData[i] === '>') {\n        angleBracketsCount--;\n        if (angleBracketsCount === 0) {\n          break;\n        }\n      }\n    }\n  } else if (\n    xmlData.length > i + 9 &&\n    xmlData[i + 1] === '[' &&\n    xmlData[i + 2] === 'C' &&\n    xmlData[i + 3] === 'D' &&\n    xmlData[i + 4] === 'A' &&\n    xmlData[i + 5] === 'T' &&\n    xmlData[i + 6] === 'A' &&\n    xmlData[i + 7] === '['\n  ) {\n    for (i += 8; i < xmlData.length; i++) {\n      if (xmlData[i] === ']' && xmlData[i + 1] === ']' && xmlData[i + 2] === '>') {\n        i += 2;\n        break;\n      }\n    }\n  }\n\n  return i;\n}\n\nconst doubleQuote = '\"';\nconst singleQuote = \"'\";\n\n/**\n * Keep reading xmlData until '<' is found outside the attribute value.\n * @param {string} xmlData\n * @param {number} i\n */\nfunction readAttributeStr(xmlData, i) {\n  let attrStr = '';\n  let startChar = '';\n  let tagClosed = false;\n  for (; i < xmlData.length; i++) {\n    if (xmlData[i] === doubleQuote || xmlData[i] === singleQuote) {\n      if (startChar === '') {\n        startChar = xmlData[i];\n      } else if (startChar !== xmlData[i]) {\n        //if vaue is enclosed with double quote then single quotes are allowed inside the value and vice versa\n      } else {\n        startChar = '';\n      }\n    } else if (xmlData[i] === '>') {\n      if (startChar === '') {\n        tagClosed = true;\n        break;\n      }\n    }\n    attrStr += xmlData[i];\n  }\n  if (startChar !== '') {\n    return false;\n  }\n\n  return {\n    value: attrStr,\n    index: i,\n    tagClosed: tagClosed\n  };\n}\n\n/**\n * Select all the attributes whether valid or invalid.\n */\nconst validAttrStrRegxp = new RegExp('(\\\\s*)([^\\\\s=]+)(\\\\s*=)?(\\\\s*([\\'\"])(([\\\\s\\\\S])*?)\\\\5)?', 'g');\n\n//attr, =\"sd\", a=\"amit's\", a=\"sd\"b=\"saf\", ab  cd=\"\"\n\nfunction validateAttributeString(attrStr, options) {\n  //console.log(\"start:\"+attrStr+\":end\");\n\n  //if(attrStr.trim().length === 0) return true; //empty string\n\n  const matches = getAllMatches(attrStr, validAttrStrRegxp);\n  const attrNames = {};\n\n  for (let i = 0; i < matches.length; i++) {\n    if (matches[i][1].length === 0) {\n      //nospace before attribute name: a=\"sd\"b=\"saf\"\n      return getErrorObject('InvalidAttr', \"Attribute '\"+matches[i][2]+\"' has no space in starting.\", getPositionFromMatch(matches[i]))\n    } else if (matches[i][3] !== undefined && matches[i][4] === undefined) {\n      return getErrorObject('InvalidAttr', \"Attribute '\"+matches[i][2]+\"' is without value.\", getPositionFromMatch(matches[i]));\n    } else if (matches[i][3] === undefined && !options.allowBooleanAttributes) {\n      //independent attribute: ab\n      return getErrorObject('InvalidAttr', \"boolean attribute '\"+matches[i][2]+\"' is not allowed.\", getPositionFromMatch(matches[i]));\n    }\n    /* else if(matches[i][6] === undefined){//attribute without value: ab=\n                    return { err: { code:\"InvalidAttr\",msg:\"attribute \" + matches[i][2] + \" has no value assigned.\"}};\n                } */\n    const attrName = matches[i][2];\n    if (!validateAttrName(attrName)) {\n      return getErrorObject('InvalidAttr', \"Attribute '\"+attrName+\"' is an invalid name.\", getPositionFromMatch(matches[i]));\n    }\n    if (!attrNames.hasOwnProperty(attrName)) {\n      //check for duplicate attribute.\n      attrNames[attrName] = 1;\n    } else {\n      return getErrorObject('InvalidAttr', \"Attribute '\"+attrName+\"' is repeated.\", getPositionFromMatch(matches[i]));\n    }\n  }\n\n  return true;\n}\n\nfunction validateNumberAmpersand(xmlData, i) {\n  let re = /\\d/;\n  if (xmlData[i] === 'x') {\n    i++;\n    re = /[\\da-fA-F]/;\n  }\n  for (; i < xmlData.length; i++) {\n    if (xmlData[i] === ';')\n      return i;\n    if (!xmlData[i].match(re))\n      break;\n  }\n  return -1;\n}\n\nfunction validateAmpersand(xmlData, i) {\n  // https://www.w3.org/TR/xml/#dt-charref\n  i++;\n  if (xmlData[i] === ';')\n    return -1;\n  if (xmlData[i] === '#') {\n    i++;\n    return validateNumberAmpersand(xmlData, i);\n  }\n  let count = 0;\n  for (; i < xmlData.length; i++, count++) {\n    if (xmlData[i].match(/\\w/) && count < 20)\n      continue;\n    if (xmlData[i] === ';')\n      break;\n    return -1;\n  }\n  return i;\n}\n\nfunction getErrorObject(code, message, lineNumber) {\n  return {\n    err: {\n      code: code,\n      msg: message,\n      line: lineNumber.line || lineNumber,\n      col: lineNumber.col,\n    },\n  };\n}\n\nfunction validateAttrName(attrName) {\n  return isName(attrName);\n}\n\n// const startsWithXML = /^xml/i;\n\nfunction validateTagName(tagname) {\n  return isName(tagname) /* && !tagname.match(startsWithXML) */;\n}\n\n//this function returns the line number for the character at the given index\nfunction getLineNumberForPosition(xmlData, index) {\n  const lines = xmlData.substring(0, index).split(/\\r?\\n/);\n  return {\n    line: lines.length,\n\n    // column number is last line's length + 1, because column numbering starts at 1:\n    col: lines[lines.length - 1].length + 1\n  };\n}\n\n//this function returns the position of the first character of match within attrStr\nfunction getPositionFromMatch(match) {\n  return match.startIndex + match[1].length;\n}\n","\nexport const defaultOptions = {\n    preserveOrder: false,\n    attributeNamePrefix: '@_',\n    attributesGroupName: false,\n    textNodeName: '#text',\n    ignoreAttributes: true,\n    removeNSPrefix: false, // remove NS from tag name or attribute name if true\n    allowBooleanAttributes: false, //a tag can have attributes without any value\n    //ignoreRootElement : false,\n    parseTagValue: true,\n    parseAttributeValue: false,\n    trimValues: true, //Trim string values of tag and attributes\n    cdataPropName: false,\n    numberParseOptions: {\n      hex: true,\n      leadingZeros: true,\n      eNotation: true\n    },\n    tagValueProcessor: function(tagName, val) {\n      return val;\n    },\n    attributeValueProcessor: function(attrName, val) {\n      return val;\n    },\n    stopNodes: [], //nested tags will not be parsed even for errors\n    alwaysCreateTextNode: false,\n    isArray: () => false,\n    commentPropName: false,\n    unpairedTags: [],\n    processEntities: true,\n    htmlEntities: false,\n    ignoreDeclaration: false,\n    ignorePiTags: false,\n    transformTagName: false,\n    transformAttributeName: false,\n    updateTag: function(tagName, jPath, attrs){\n      return tagName\n    },\n    // skipEmptyListItem: false\n    captureMetaData: false,\n};\n   \nexport const buildOptions = function(options) {\n    return Object.assign({}, defaultOptions, options);\n};\n","'use strict';\n\nlet METADATA_SYMBOL;\n\nif (typeof Symbol !== \"function\") {\n  METADATA_SYMBOL = \"@@xmlMetadata\";\n} else {\n  METADATA_SYMBOL = Symbol(\"XML Node Metadata\");\n}\n\nexport default class XmlNode{\n  constructor(tagname) {\n    this.tagname = tagname;\n    this.child = []; //nested tags, text, cdata, comments in order\n    this[\":@\"] = {}; //attributes map\n  }\n  add(key,val){\n    // this.child.push( {name : key, val: val, isCdata: isCdata });\n    if(key === \"__proto__\") key = \"#__proto__\";\n    this.child.push( {[key]: val });\n  }\n  addChild(node, startIndex) {\n    if(node.tagname === \"__proto__\") node.tagname = \"#__proto__\";\n    if(node[\":@\"] && Object.keys(node[\":@\"]).length > 0){\n      this.child.push( { [node.tagname]: node.child, [\":@\"]: node[\":@\"] });\n    }else{\n      this.child.push( { [node.tagname]: node.child });\n    }\n    // if requested, add the startIndex\n    if (startIndex !== undefined) {\n      // Note: for now we just overwrite the metadata. If we had more complex metadata,\n      // we might need to do an object append here:  metadata = { ...metadata, startIndex }\n      this.child[this.child.length - 1][METADATA_SYMBOL] = { startIndex };\n    }\n  }\n  /** symbol used for metadata */\n  static getMetaDataSymbol() {\n    return METADATA_SYMBOL;\n  }\n}\n","import {isName} from '../util.js';\n\nexport default class DocTypeReader{\n    constructor(processEntities){\n        this.suppressValidationErr = !processEntities;\n    }\n    \n    readDocType(xmlData, i){\n    \n        const entities = {};\n        if( xmlData[i + 3] === 'O' &&\n            xmlData[i + 4] === 'C' &&\n            xmlData[i + 5] === 'T' &&\n            xmlData[i + 6] === 'Y' &&\n            xmlData[i + 7] === 'P' &&\n            xmlData[i + 8] === 'E')\n        {    \n            i = i+9;\n            let angleBracketsCount = 1;\n            let hasBody = false, comment = false;\n            let exp = \"\";\n            for(;i<xmlData.length;i++){\n                if (xmlData[i] === '<' && !comment) { //Determine the tag type\n                    if( hasBody && hasSeq(xmlData, \"!ENTITY\",i)){\n                        i += 7; \n                        let entityName, val;\n                        [entityName, val,i] = this.readEntityExp(xmlData,i+1,this.suppressValidationErr);\n                        if(val.indexOf(\"&\") === -1){ //Parameter entities are not supported\n                            const escaped = entityName.replace(/[.\\-+*:]/g, '\\\\.');\n                            entities[ entityName ] = {\n                                regx : RegExp( `&${escaped};`,\"g\"),\n                                val: val\n                            };\n                        }\n                    }\n                    else if( hasBody && hasSeq(xmlData, \"!ELEMENT\",i))  {\n                        i += 8;//Not supported\n                        const {index} = this.readElementExp(xmlData,i+1);\n                        i = index;\n                    }else if( hasBody && hasSeq(xmlData, \"!ATTLIST\",i)){\n                        i += 8;//Not supported\n                        // const {index} = this.readAttlistExp(xmlData,i+1);\n                        // i = index;\n                    }else if( hasBody && hasSeq(xmlData, \"!NOTATION\",i)) {\n                        i += 9;//Not supported\n                        const {index} = this.readNotationExp(xmlData,i+1,this.suppressValidationErr);\n                        i = index;\n                    }else if( hasSeq(xmlData, \"!--\",i) ) comment = true;\n                    else throw new Error(`Invalid DOCTYPE`);\n\n                    angleBracketsCount++;\n                    exp = \"\";\n                } else if (xmlData[i] === '>') { //Read tag content\n                    if(comment){\n                        if( xmlData[i - 1] === \"-\" && xmlData[i - 2] === \"-\"){\n                            comment = false;\n                            angleBracketsCount--;\n                        }\n                    }else{\n                        angleBracketsCount--;\n                    }\n                    if (angleBracketsCount === 0) {\n                    break;\n                    }\n                }else if( xmlData[i] === '['){\n                    hasBody = true;\n                }else{\n                    exp += xmlData[i];\n                }\n            }\n            if(angleBracketsCount !== 0){\n                throw new Error(`Unclosed DOCTYPE`);\n            }\n        }else{\n            throw new Error(`Invalid Tag instead of DOCTYPE`);\n        }\n        return {entities, i};\n    }\n    readEntityExp(xmlData, i) {    \n        //External entities are not supported\n        //    <!ENTITY ext SYSTEM \"http://normal-website.com\" >\n\n        //Parameter entities are not supported\n        //    <!ENTITY entityname \"&anotherElement;\">\n\n        //Internal entities are supported\n        //    <!ENTITY entityname \"replacement text\">\n\n        // Skip leading whitespace after <!ENTITY\n        i = skipWhitespace(xmlData, i);\n\n        // Read entity name\n        let entityName = \"\";\n        while (i < xmlData.length && !/\\s/.test(xmlData[i]) && xmlData[i] !== '\"' && xmlData[i] !== \"'\") {\n            entityName += xmlData[i];\n            i++;\n        }\n        validateEntityName(entityName);\n\n        // Skip whitespace after entity name\n        i = skipWhitespace(xmlData, i);\n\n        // Check for unsupported constructs (external entities or parameter entities)\n        if(!this.suppressValidationErr){\n            if (xmlData.substring(i, i + 6).toUpperCase() === \"SYSTEM\") {\n                throw new Error(\"External entities are not supported\");\n            }else if (xmlData[i] === \"%\") {\n                throw new Error(\"Parameter entities are not supported\");\n            }\n        }\n\n        // Read entity value (internal entity)\n        let entityValue = \"\";\n        [i, entityValue] = this.readIdentifierVal(xmlData, i, \"entity\");\n        i--;\n        return [entityName, entityValue, i ];\n    }\n\n    readNotationExp(xmlData, i) {\n        // Skip leading whitespace after <!NOTATION\n        i = skipWhitespace(xmlData, i);\n\n        // Read notation name\n        let notationName = \"\";\n        while (i < xmlData.length && !/\\s/.test(xmlData[i])) {\n            notationName += xmlData[i];\n            i++;\n        }\n        !this.suppressValidationErr && validateEntityName(notationName);\n\n        // Skip whitespace after notation name\n        i = skipWhitespace(xmlData, i);\n\n        // Check identifier type (SYSTEM or PUBLIC)\n        const identifierType = xmlData.substring(i, i + 6).toUpperCase();\n        if (!this.suppressValidationErr && identifierType !== \"SYSTEM\" && identifierType !== \"PUBLIC\") {\n            throw new Error(`Expected SYSTEM or PUBLIC, found \"${identifierType}\"`);\n        }\n        i += identifierType.length;\n\n        // Skip whitespace after identifier type\n        i = skipWhitespace(xmlData, i);\n\n        // Read public identifier (if PUBLIC)\n        let publicIdentifier = null;\n        let systemIdentifier = null;\n\n        if (identifierType === \"PUBLIC\") {\n            [i, publicIdentifier ] = this.readIdentifierVal(xmlData, i, \"publicIdentifier\");\n\n            // Skip whitespace after public identifier\n            i = skipWhitespace(xmlData, i);\n\n            // Optionally read system identifier\n            if (xmlData[i] === '\"' || xmlData[i] === \"'\") {\n                [i, systemIdentifier ] = this.readIdentifierVal(xmlData, i,\"systemIdentifier\");\n            }\n        } else if (identifierType === \"SYSTEM\") {\n            // Read system identifier (mandatory for SYSTEM)\n            [i, systemIdentifier ] = this.readIdentifierVal(xmlData, i, \"systemIdentifier\");\n\n            if (!this.suppressValidationErr && !systemIdentifier) {\n                throw new Error(\"Missing mandatory system identifier for SYSTEM notation\");\n            }\n        }\n        \n        return {notationName, publicIdentifier, systemIdentifier, index: --i};\n    }\n\n    readIdentifierVal(xmlData, i, type) {\n        let identifierVal = \"\";\n        const startChar = xmlData[i];\n        if (startChar !== '\"' && startChar !== \"'\") {\n            throw new Error(`Expected quoted string, found \"${startChar}\"`);\n        }\n        i++;\n\n        while (i < xmlData.length && xmlData[i] !== startChar) {\n            identifierVal += xmlData[i];\n            i++;\n        }\n\n        if (xmlData[i] !== startChar) {\n            throw new Error(`Unterminated ${type} value`);\n        }\n        i++;\n        return [i, identifierVal];\n    }\n\n    readElementExp(xmlData, i) {\n        // <!ELEMENT br EMPTY>\n        // <!ELEMENT div ANY>\n        // <!ELEMENT title (#PCDATA)>\n        // <!ELEMENT book (title, author+)>\n        // <!ELEMENT name (content-model)>\n        \n        // Skip leading whitespace after <!ELEMENT\n        i = skipWhitespace(xmlData, i);\n\n        // Read element name\n        let elementName = \"\";\n        while (i < xmlData.length && !/\\s/.test(xmlData[i])) {\n            elementName += xmlData[i];\n            i++;\n        }\n\n        // Validate element name\n        if (!this.suppressValidationErr && !isName(elementName)) {\n            throw new Error(`Invalid element name: \"${elementName}\"`);\n        }\n\n        // Skip whitespace after element name\n        i = skipWhitespace(xmlData, i);\n        let contentModel = \"\";\n        // Expect '(' to start content model\n        if(xmlData[i] === \"E\" && hasSeq(xmlData, \"MPTY\",i)) i+=4;\n        else if(xmlData[i] === \"A\" && hasSeq(xmlData, \"NY\",i)) i+=2;\n        else if (xmlData[i] === \"(\") {\n            i++; // Move past '('\n\n            // Read content model\n            while (i < xmlData.length && xmlData[i] !== \")\") {\n                contentModel += xmlData[i];\n                i++;\n            }\n            if (xmlData[i] !== \")\") {\n                throw new Error(\"Unterminated content model\");\n            }\n\n        }else if(!this.suppressValidationErr){\n            throw new Error(`Invalid Element Expression, found \"${xmlData[i]}\"`);\n        }\n        \n        return {\n            elementName,\n            contentModel: contentModel.trim(),\n            index: i\n        };\n    }\n\n    readAttlistExp(xmlData, i) {\n        // Skip leading whitespace after <!ATTLIST\n        i = skipWhitespace(xmlData, i);\n\n        // Read element name\n        let elementName = \"\";\n        while (i < xmlData.length && !/\\s/.test(xmlData[i])) {\n            elementName += xmlData[i];\n            i++;\n        }\n\n        // Validate element name\n        validateEntityName(elementName)\n\n        // Skip whitespace after element name\n        i = skipWhitespace(xmlData, i);\n\n        // Read attribute name\n        let attributeName = \"\";\n        while (i < xmlData.length && !/\\s/.test(xmlData[i])) {\n            attributeName += xmlData[i];\n            i++;\n        }\n\n        // Validate attribute name\n        if (!validateEntityName(attributeName)) {\n            throw new Error(`Invalid attribute name: \"${attributeName}\"`);\n        }\n\n        // Skip whitespace after attribute name\n        i = skipWhitespace(xmlData, i);\n\n        // Read attribute type\n        let attributeType = \"\";\n        if (xmlData.substring(i, i + 8).toUpperCase() === \"NOTATION\") {\n            attributeType = \"NOTATION\";\n            i += 8; // Move past \"NOTATION\"\n\n            // Skip whitespace after \"NOTATION\"\n            i = skipWhitespace(xmlData, i);\n\n            // Expect '(' to start the list of notations\n            if (xmlData[i] !== \"(\") {\n                throw new Error(`Expected '(', found \"${xmlData[i]}\"`);\n            }\n            i++; // Move past '('\n\n            // Read the list of allowed notations\n            let allowedNotations = [];\n            while (i < xmlData.length && xmlData[i] !== \")\") {\n                let notation = \"\";\n                while (i < xmlData.length && xmlData[i] !== \"|\" && xmlData[i] !== \")\") {\n                    notation += xmlData[i];\n                    i++;\n                }\n\n                // Validate notation name\n                notation = notation.trim();\n                if (!validateEntityName(notation)) {\n                    throw new Error(`Invalid notation name: \"${notation}\"`);\n                }\n\n                allowedNotations.push(notation);\n\n                // Skip '|' separator or exit loop\n                if (xmlData[i] === \"|\") {\n                    i++; // Move past '|'\n                    i = skipWhitespace(xmlData, i); // Skip optional whitespace after '|'\n                }\n            }\n\n            if (xmlData[i] !== \")\") {\n                throw new Error(\"Unterminated list of notations\");\n            }\n            i++; // Move past ')'\n\n            // Store the allowed notations as part of the attribute type\n            attributeType += \" (\" + allowedNotations.join(\"|\") + \")\";\n        } else {\n            // Handle simple types (e.g., CDATA, ID, IDREF, etc.)\n            while (i < xmlData.length && !/\\s/.test(xmlData[i])) {\n                attributeType += xmlData[i];\n                i++;\n            }\n\n            // Validate simple attribute type\n            const validTypes = [\"CDATA\", \"ID\", \"IDREF\", \"IDREFS\", \"ENTITY\", \"ENTITIES\", \"NMTOKEN\", \"NMTOKENS\"];\n            if (!this.suppressValidationErr && !validTypes.includes(attributeType.toUpperCase())) {\n                throw new Error(`Invalid attribute type: \"${attributeType}\"`);\n            }\n        }\n\n        // Skip whitespace after attribute type\n        i = skipWhitespace(xmlData, i);\n\n        // Read default value\n        let defaultValue = \"\";\n        if (xmlData.substring(i, i + 8).toUpperCase() === \"#REQUIRED\") {\n            defaultValue = \"#REQUIRED\";\n            i += 8;\n        } else if (xmlData.substring(i, i + 7).toUpperCase() === \"#IMPLIED\") {\n            defaultValue = \"#IMPLIED\";\n            i += 7;\n        } else {\n            [i, defaultValue] = this.readIdentifierVal(xmlData, i, \"ATTLIST\");\n        }\n\n        return {\n            elementName,\n            attributeName,\n            attributeType,\n            defaultValue,\n            index: i\n        }\n    }\n}\n\n\n\nconst skipWhitespace = (data, index) => {\n    while (index < data.length && /\\s/.test(data[index])) {\n        index++;\n    }\n    return index;\n};\n\n\n\nfunction hasSeq(data, seq,i){\n    for(let j=0;j<seq.length;j++){\n        if(seq[j]!==data[i+j+1]) return false;\n    }\n    return true;\n}\n\nfunction validateEntityName(name){\n    if (isName(name))\n\t    return name;\n    else\n        throw new Error(`Invalid entity name ${name}`);\n}\n","const hexRegex = /^[-+]?0x[a-fA-F0-9]+$/;\nconst numRegex = /^([\\-\\+])?(0*)([0-9]*(\\.[0-9]*)?)$/;\n// const octRegex = /^0x[a-z0-9]+/;\n// const binRegex = /0x[a-z0-9]+/;\n\n \nconst consider = {\n    hex :  true,\n    // oct: false,\n    leadingZeros: true,\n    decimalPoint: \"\\.\",\n    eNotation: true,\n    //skipLike: /regex/\n};\n\nexport default function toNumber(str, options = {}){\n    options = Object.assign({}, consider, options );\n    if(!str || typeof str !== \"string\" ) return str;\n    \n    let trimmedStr  = str.trim();\n    \n    if(options.skipLike !== undefined && options.skipLike.test(trimmedStr)) return str;\n    else if(str===\"0\") return 0;\n    else if (options.hex && hexRegex.test(trimmedStr)) {\n        return parse_int(trimmedStr, 16);\n    // }else if (options.oct && octRegex.test(str)) {\n    //     return Number.parseInt(val, 8);\n    }else if (trimmedStr.includes('e') || trimmedStr.includes('E')) { //eNotation\n        return resolveEnotation(str,trimmedStr,options);\n    // }else if (options.parseBin && binRegex.test(str)) {\n    //     return Number.parseInt(val, 2);\n    }else{\n        //separate negative sign, leading zeros, and rest number\n        const match = numRegex.exec(trimmedStr);\n        // +00.123 => [ , '+', '00', '.123', ..\n        if(match){\n            const sign = match[1] || \"\";\n            const leadingZeros = match[2];\n            let numTrimmedByZeros = trimZeros(match[3]); //complete num without leading zeros\n            const decimalAdjacentToLeadingZeros = sign ? // 0., -00., 000.\n                str[leadingZeros.length+1] === \".\" \n                : str[leadingZeros.length] === \".\";\n\n            //trim ending zeros for floating number\n            if(!options.leadingZeros //leading zeros are not allowed\n                && (leadingZeros.length > 1 \n                    || (leadingZeros.length === 1 && !decimalAdjacentToLeadingZeros))){\n                // 00, 00.3, +03.24, 03, 03.24\n                return str;\n            }\n            else{//no leading zeros or leading zeros are allowed\n                const num = Number(trimmedStr);\n                const parsedStr = String(num);\n\n                if( num === 0) return num;\n                if(parsedStr.search(/[eE]/) !== -1){ //given number is long and parsed to eNotation\n                    if(options.eNotation) return num;\n                    else return str;\n                }else if(trimmedStr.indexOf(\".\") !== -1){ //floating number\n                    if(parsedStr === \"0\") return num; //0.0\n                    else if(parsedStr === numTrimmedByZeros) return num; //0.456. 0.79000\n                    else if( parsedStr === `${sign}${numTrimmedByZeros}`) return num;\n                    else return str;\n                }\n                \n                let n = leadingZeros? numTrimmedByZeros : trimmedStr;\n                if(leadingZeros){\n                    // -009 => -9\n                    return (n === parsedStr) || (sign+n === parsedStr) ? num : str\n                }else  {\n                    // +9\n                    return (n === parsedStr) || (n === sign+parsedStr) ? num : str\n                }\n            }\n        }else{ //non-numeric string\n            return str;\n        }\n    }\n}\n\nconst eNotationRegx = /^([-+])?(0*)(\\d*(\\.\\d*)?[eE][-\\+]?\\d+)$/;\nfunction resolveEnotation(str,trimmedStr,options){\n    if(!options.eNotation) return str;\n    const notation = trimmedStr.match(eNotationRegx); \n    if(notation){\n        let sign = notation[1] || \"\";\n        const eChar = notation[3].indexOf(\"e\") === -1 ? \"E\" : \"e\";\n        const leadingZeros = notation[2];\n        const eAdjacentToLeadingZeros = sign ? // 0E.\n            str[leadingZeros.length+1] === eChar \n            : str[leadingZeros.length] === eChar;\n\n        if(leadingZeros.length > 1 && eAdjacentToLeadingZeros) return str;\n        else if(leadingZeros.length === 1 \n            && (notation[3].startsWith(`.${eChar}`) || notation[3][0] === eChar)){\n                return Number(trimmedStr);\n        }else if(options.leadingZeros && !eAdjacentToLeadingZeros){ //accept with leading zeros\n            //remove leading 0s\n            trimmedStr = (notation[1] || \"\") + notation[3];\n            return Number(trimmedStr);\n        }else return str;\n    }else{\n        return str;\n    }\n}\n\n/**\n * \n * @param {string} numStr without leading zeros\n * @returns \n */\nfunction trimZeros(numStr){\n    if(numStr && numStr.indexOf(\".\") !== -1){//float\n        numStr = numStr.replace(/0+$/, \"\"); //remove ending zeros\n        if(numStr === \".\")  numStr = \"0\";\n        else if(numStr[0] === \".\")  numStr = \"0\"+numStr;\n        else if(numStr[numStr.length-1] === \".\")  numStr = numStr.substring(0,numStr.length-1);\n        return numStr;\n    }\n    return numStr;\n}\n\nfunction parse_int(numStr, base){\n    //polyfill\n    if(parseInt) return parseInt(numStr, base);\n    else if(Number.parseInt) return Number.parseInt(numStr, base);\n    else if(window && window.parseInt) return window.parseInt(numStr, base);\n    else throw new Error(\"parseInt, Number.parseInt, window.parseInt are not supported\")\n}","export default function getIgnoreAttributesFn(ignoreAttributes) {\n    if (typeof ignoreAttributes === 'function') {\n        return ignoreAttributes\n    }\n    if (Array.isArray(ignoreAttributes)) {\n        return (attrName) => {\n            for (const pattern of ignoreAttributes) {\n                if (typeof pattern === 'string' && attrName === pattern) {\n                    return true\n                }\n                if (pattern instanceof RegExp && pattern.test(attrName)) {\n                    return true\n                }\n            }\n        }\n    }\n    return () => false\n}","'use strict';\n///@ts-check\n\nimport {getAllMatches, isExist} from '../util.js';\nimport xmlNode from './xmlNode.js';\nimport DocTypeReader from './DocTypeReader.js';\nimport toNumber from \"strnum\";\nimport getIgnoreAttributesFn from \"../ignoreAttributes.js\";\n\n// const regx =\n//   '<((!\\\\[CDATA\\\\[([\\\\s\\\\S]*?)(]]>))|((NAME:)?(NAME))([^>]*)>|((\\\\/)(NAME)\\\\s*>))([^<]*)'\n//   .replace(/NAME/g, util.nameRegexp);\n\n//const tagsRegx = new RegExp(\"<(\\\\/?[\\\\w:\\\\-\\._]+)([^>]*)>(\\\\s*\"+cdataRegx+\")*([^<]+)?\",\"g\");\n//const tagsRegx = new RegExp(\"<(\\\\/?)((\\\\w*:)?([\\\\w:\\\\-\\._]+))([^>]*)>([^<]*)(\"+cdataRegx+\"([^<]*))*([^<]+)?\",\"g\");\n\nexport default class OrderedObjParser{\n  constructor(options){\n    this.options = options;\n    this.currentNode = null;\n    this.tagsNodeStack = [];\n    this.docTypeEntities = {};\n    this.lastEntities = {\n      \"apos\" : { regex: /&(apos|#39|#x27);/g, val : \"'\"},\n      \"gt\" : { regex: /&(gt|#62|#x3E);/g, val : \">\"},\n      \"lt\" : { regex: /&(lt|#60|#x3C);/g, val : \"<\"},\n      \"quot\" : { regex: /&(quot|#34|#x22);/g, val : \"\\\"\"},\n    };\n    this.ampEntity = { regex: /&(amp|#38|#x26);/g, val : \"&\"};\n    this.htmlEntities = {\n      \"space\": { regex: /&(nbsp|#160);/g, val: \" \" },\n      // \"lt\" : { regex: /&(lt|#60);/g, val: \"<\" },\n      // \"gt\" : { regex: /&(gt|#62);/g, val: \">\" },\n      // \"amp\" : { regex: /&(amp|#38);/g, val: \"&\" },\n      // \"quot\" : { regex: /&(quot|#34);/g, val: \"\\\"\" },\n      // \"apos\" : { regex: /&(apos|#39);/g, val: \"'\" },\n      \"cent\" : { regex: /&(cent|#162);/g, val: \"¢\" },\n      \"pound\" : { regex: /&(pound|#163);/g, val: \"£\" },\n      \"yen\" : { regex: /&(yen|#165);/g, val: \"¥\" },\n      \"euro\" : { regex: /&(euro|#8364);/g, val: \"€\" },\n      \"copyright\" : { regex: /&(copy|#169);/g, val: \"©\" },\n      \"reg\" : { regex: /&(reg|#174);/g, val: \"®\" },\n      \"inr\" : { regex: /&(inr|#8377);/g, val: \"₹\" },\n      \"num_dec\": { regex: /&#([0-9]{1,7});/g, val : (_, str) => fromCodePoint(str, 10, \"&#\") },\n      \"num_hex\": { regex: /&#x([0-9a-fA-F]{1,6});/g, val : (_, str) => fromCodePoint(str, 16, \"&#x\") },\n    };\n    this.addExternalEntities = addExternalEntities;\n    this.parseXml = parseXml;\n    this.parseTextData = parseTextData;\n    this.resolveNameSpace = resolveNameSpace;\n    this.buildAttributesMap = buildAttributesMap;\n    this.isItStopNode = isItStopNode;\n    this.replaceEntitiesValue = replaceEntitiesValue;\n    this.readStopNodeData = readStopNodeData;\n    this.saveTextToParentTag = saveTextToParentTag;\n    this.addChild = addChild;\n    this.ignoreAttributesFn = getIgnoreAttributesFn(this.options.ignoreAttributes)\n\n    if(this.options.stopNodes && this.options.stopNodes.length > 0){\n      this.stopNodesExact = new Set();\n      this.stopNodesWildcard = new Set();\n      for(let i = 0; i < this.options.stopNodes.length; i++){\n        const stopNodeExp = this.options.stopNodes[i];\n        if(typeof stopNodeExp !== 'string') continue;\n        if(stopNodeExp.startsWith(\"*.\")){\n          this.stopNodesWildcard.add(stopNodeExp.substring(2));\n        }else{\n          this.stopNodesExact.add(stopNodeExp);\n        }\n      }\n    }\n  }\n\n}\n\nfunction addExternalEntities(externalEntities){\n  const entKeys = Object.keys(externalEntities);\n  for (let i = 0; i < entKeys.length; i++) {\n    const ent = entKeys[i];\n    const escaped = ent.replace(/[.\\-+*:]/g, '\\\\.');\n    this.lastEntities[ent] = {\n       regex: new RegExp(\"&\"+escaped+\";\",\"g\"),\n       val : externalEntities[ent]\n    }\n  }\n}\n\n/**\n * @param {string} val\n * @param {string} tagName\n * @param {string} jPath\n * @param {boolean} dontTrim\n * @param {boolean} hasAttributes\n * @param {boolean} isLeafNode\n * @param {boolean} escapeEntities\n */\nfunction parseTextData(val, tagName, jPath, dontTrim, hasAttributes, isLeafNode, escapeEntities) {\n  if (val !== undefined) {\n    if (this.options.trimValues && !dontTrim) {\n      val = val.trim();\n    }\n    if(val.length > 0){\n      if(!escapeEntities) val = this.replaceEntitiesValue(val);\n      \n      const newval = this.options.tagValueProcessor(tagName, val, jPath, hasAttributes, isLeafNode);\n      if(newval === null || newval === undefined){\n        //don't parse\n        return val;\n      }else if(typeof newval !== typeof val || newval !== val){\n        //overwrite\n        return newval;\n      }else if(this.options.trimValues){\n        return parseValue(val, this.options.parseTagValue, this.options.numberParseOptions);\n      }else{\n        const trimmedVal = val.trim();\n        if(trimmedVal === val){\n          return parseValue(val, this.options.parseTagValue, this.options.numberParseOptions);\n        }else{\n          return val;\n        }\n      }\n    }\n  }\n}\n\nfunction resolveNameSpace(tagname) {\n  if (this.options.removeNSPrefix) {\n    const tags = tagname.split(':');\n    const prefix = tagname.charAt(0) === '/' ? '/' : '';\n    if (tags[0] === 'xmlns') {\n      return '';\n    }\n    if (tags.length === 2) {\n      tagname = prefix + tags[1];\n    }\n  }\n  return tagname;\n}\n\n//TODO: change regex to capture NS\n//const attrsRegx = new RegExp(\"([\\\\w\\\\-\\\\.\\\\:]+)\\\\s*=\\\\s*(['\\\"])((.|\\n)*?)\\\\2\",\"gm\");\nconst attrsRegx = new RegExp('([^\\\\s=]+)\\\\s*(=\\\\s*([\\'\"])([\\\\s\\\\S]*?)\\\\3)?', 'gm');\n\nfunction buildAttributesMap(attrStr, jPath) {\n  if (this.options.ignoreAttributes !== true && typeof attrStr === 'string') {\n    // attrStr = attrStr.replace(/\\r?\\n/g, ' ');\n    //attrStr = attrStr || attrStr.trim();\n\n    const matches = getAllMatches(attrStr, attrsRegx);\n    const len = matches.length; //don't make it inline\n    const attrs = {};\n    for (let i = 0; i < len; i++) {\n      const attrName = this.resolveNameSpace(matches[i][1]);\n      if (this.ignoreAttributesFn(attrName, jPath)) {\n        continue\n      }\n      let oldVal = matches[i][4];\n      let aName = this.options.attributeNamePrefix + attrName;\n      if (attrName.length) {\n        if (this.options.transformAttributeName) {\n          aName = this.options.transformAttributeName(aName);\n        }\n        if(aName === \"__proto__\") aName  = \"#__proto__\";\n        if (oldVal !== undefined) {\n          if (this.options.trimValues) {\n            oldVal = oldVal.trim();\n          }\n          oldVal = this.replaceEntitiesValue(oldVal);\n          const newVal = this.options.attributeValueProcessor(attrName, oldVal, jPath);\n          if(newVal === null || newVal === undefined){\n            //don't parse\n            attrs[aName] = oldVal;\n          }else if(typeof newVal !== typeof oldVal || newVal !== oldVal){\n            //overwrite\n            attrs[aName] = newVal;\n          }else{\n            //parse\n            attrs[aName] = parseValue(\n              oldVal,\n              this.options.parseAttributeValue,\n              this.options.numberParseOptions\n            );\n          }\n        } else if (this.options.allowBooleanAttributes) {\n          attrs[aName] = true;\n        }\n      }\n    }\n    if (!Object.keys(attrs).length) {\n      return;\n    }\n    if (this.options.attributesGroupName) {\n      const attrCollection = {};\n      attrCollection[this.options.attributesGroupName] = attrs;\n      return attrCollection;\n    }\n    return attrs\n  }\n}\n\nconst parseXml = function(xmlData) {\n  xmlData = xmlData.replace(/\\r\\n?/g, \"\\n\"); //TODO: remove this line\n  const xmlObj = new xmlNode('!xml');\n  let currentNode = xmlObj;\n  let textData = \"\";\n  let jPath = \"\";\n  const docTypeReader = new DocTypeReader(this.options.processEntities);\n  for(let i=0; i< xmlData.length; i++){//for each char in XML data\n    const ch = xmlData[i];\n    if(ch === '<'){\n      // const nextIndex = i+1;\n      // const _2ndChar = xmlData[nextIndex];\n      if( xmlData[i+1] === '/') {//Closing Tag\n        const closeIndex = findClosingIndex(xmlData, \">\", i, \"Closing Tag is not closed.\")\n        let tagName = xmlData.substring(i+2,closeIndex).trim();\n\n        if(this.options.removeNSPrefix){\n          const colonIndex = tagName.indexOf(\":\");\n          if(colonIndex !== -1){\n            tagName = tagName.substr(colonIndex+1);\n          }\n        }\n\n        if(this.options.transformTagName) {\n          tagName = this.options.transformTagName(tagName);\n        }\n\n        if(currentNode){\n          textData = this.saveTextToParentTag(textData, currentNode, jPath);\n        }\n\n        //check if last tag of nested tag was unpaired tag\n        const lastTagName = jPath.substring(jPath.lastIndexOf(\".\")+1);\n        if(tagName && this.options.unpairedTags.indexOf(tagName) !== -1 ){\n          throw new Error(`Unpaired tag can not be used as closing tag: </${tagName}>`);\n        }\n        let propIndex = 0\n        if(lastTagName && this.options.unpairedTags.indexOf(lastTagName) !== -1 ){\n          propIndex = jPath.lastIndexOf('.', jPath.lastIndexOf('.')-1)\n          this.tagsNodeStack.pop();\n        }else{\n          propIndex = jPath.lastIndexOf(\".\");\n        }\n        jPath = jPath.substring(0, propIndex);\n\n        currentNode = this.tagsNodeStack.pop();//avoid recursion, set the parent tag scope\n        textData = \"\";\n        i = closeIndex;\n      } else if( xmlData[i+1] === '?') {\n\n        let tagData = readTagExp(xmlData,i, false, \"?>\");\n        if(!tagData) throw new Error(\"Pi Tag is not closed.\");\n\n        textData = this.saveTextToParentTag(textData, currentNode, jPath);\n        if( (this.options.ignoreDeclaration && tagData.tagName === \"?xml\") || this.options.ignorePiTags){\n          //do nothing\n        }else{\n  \n          const childNode = new xmlNode(tagData.tagName);\n          childNode.add(this.options.textNodeName, \"\");\n          \n          if(tagData.tagName !== tagData.tagExp && tagData.attrExpPresent){\n            childNode[\":@\"] = this.buildAttributesMap(tagData.tagExp, jPath);\n          }\n          this.addChild(currentNode, childNode, jPath, i);\n        }\n\n\n        i = tagData.closeIndex + 1;\n      } else if(xmlData.substr(i + 1, 3) === '!--') {\n        const endIndex = findClosingIndex(xmlData, \"-->\", i+4, \"Comment is not closed.\")\n        if(this.options.commentPropName){\n          const comment = xmlData.substring(i + 4, endIndex - 2);\n\n          textData = this.saveTextToParentTag(textData, currentNode, jPath);\n\n          currentNode.add(this.options.commentPropName, [ { [this.options.textNodeName] : comment } ]);\n        }\n        i = endIndex;\n      } else if( xmlData.substr(i + 1, 2) === '!D') {\n        const result = docTypeReader.readDocType(xmlData, i);\n        this.docTypeEntities = result.entities;\n        i = result.i;\n      }else if(xmlData.substr(i + 1, 2) === '![') {\n        const closeIndex = findClosingIndex(xmlData, \"]]>\", i, \"CDATA is not closed.\") - 2;\n        const tagExp = xmlData.substring(i + 9,closeIndex);\n\n        textData = this.saveTextToParentTag(textData, currentNode, jPath);\n\n        let val = this.parseTextData(tagExp, currentNode.tagname, jPath, true, false, true, true);\n        if(val == undefined) val = \"\";\n\n        //cdata should be set even if it is 0 length string\n        if(this.options.cdataPropName){\n          currentNode.add(this.options.cdataPropName, [ { [this.options.textNodeName] : tagExp } ]);\n        }else{\n          currentNode.add(this.options.textNodeName, val);\n        }\n        \n        i = closeIndex + 2;\n      }else {//Opening tag\n        let result = readTagExp(xmlData,i, this.options.removeNSPrefix);\n        let tagName= result.tagName;\n        const rawTagName = result.rawTagName;\n        let tagExp = result.tagExp;\n        let attrExpPresent = result.attrExpPresent;\n        let closeIndex = result.closeIndex;\n\n        if (this.options.transformTagName) {\n          //console.log(tagExp, tagName)\n          const newTagName = this.options.transformTagName(tagName);\n          if(tagExp === tagName) {\n            tagExp = newTagName\n          }\n          tagName = newTagName;\n        }\n        \n        //save text as child node\n        if (currentNode && textData) {\n          if(currentNode.tagname !== '!xml'){\n            //when nested tag is found\n            textData = this.saveTextToParentTag(textData, currentNode, jPath, false);\n          }\n        }\n\n        //check if last tag was unpaired tag\n        const lastTag = currentNode;\n        if(lastTag && this.options.unpairedTags.indexOf(lastTag.tagname) !== -1 ){\n          currentNode = this.tagsNodeStack.pop();\n          jPath = jPath.substring(0, jPath.lastIndexOf(\".\"));\n        }\n        if(tagName !== xmlObj.tagname){\n          jPath += jPath ? \".\" + tagName : tagName;\n        }\n        const startIndex = i;\n        if (this.isItStopNode(this.stopNodesExact, this.stopNodesWildcard, jPath, tagName)) {\n          let tagContent = \"\";\n          //self-closing tag\n          if(tagExp.length > 0 && tagExp.lastIndexOf(\"/\") === tagExp.length - 1){\n            if(tagName[tagName.length - 1] === \"/\"){ //remove trailing '/'\n              tagName = tagName.substr(0, tagName.length - 1);\n              jPath = jPath.substr(0, jPath.length - 1);\n              tagExp = tagName;\n            }else{\n              tagExp = tagExp.substr(0, tagExp.length - 1);\n            }\n            i = result.closeIndex;\n          }\n          //unpaired tag\n          else if(this.options.unpairedTags.indexOf(tagName) !== -1){\n            \n            i = result.closeIndex;\n          }\n          //normal tag\n          else{\n            //read until closing tag is found\n            const result = this.readStopNodeData(xmlData, rawTagName, closeIndex + 1);\n            if(!result) throw new Error(`Unexpected end of ${rawTagName}`);\n            i = result.i;\n            tagContent = result.tagContent;\n          }\n\n          const childNode = new xmlNode(tagName);\n\n          if(tagName !== tagExp && attrExpPresent){\n            childNode[\":@\"] = this.buildAttributesMap(tagExp, jPath\n            );\n          }\n          if(tagContent) {\n            tagContent = this.parseTextData(tagContent, tagName, jPath, true, attrExpPresent, true, true);\n          }\n          \n          jPath = jPath.substr(0, jPath.lastIndexOf(\".\"));\n          childNode.add(this.options.textNodeName, tagContent);\n          \n          this.addChild(currentNode, childNode, jPath, startIndex);\n        }else{\n  //selfClosing tag\n          if(tagExp.length > 0 && tagExp.lastIndexOf(\"/\") === tagExp.length - 1){\n            if(tagName[tagName.length - 1] === \"/\"){ //remove trailing '/'\n              tagName = tagName.substr(0, tagName.length - 1);\n              jPath = jPath.substr(0, jPath.length - 1);\n              tagExp = tagName;\n            }else{\n              tagExp = tagExp.substr(0, tagExp.length - 1);\n            }\n            \n            if(this.options.transformTagName) {\n              const newTagName = this.options.transformTagName(tagName);\n              if(tagExp === tagName) {\n                tagExp = newTagName\n              }\n              tagName = newTagName;\n            }\n\n            const childNode = new xmlNode(tagName);\n            if(tagName !== tagExp && attrExpPresent){\n              childNode[\":@\"] = this.buildAttributesMap(tagExp, jPath);\n            }\n            this.addChild(currentNode, childNode, jPath, startIndex);\n            jPath = jPath.substr(0, jPath.lastIndexOf(\".\"));\n          }\n    //opening tag\n          else{\n            const childNode = new xmlNode( tagName);\n            this.tagsNodeStack.push(currentNode);\n            \n            if(tagName !== tagExp && attrExpPresent){\n              childNode[\":@\"] = this.buildAttributesMap(tagExp, jPath);\n            }\n            this.addChild(currentNode, childNode, jPath, startIndex);\n            currentNode = childNode;\n          }\n          textData = \"\";\n          i = closeIndex;\n        }\n      }\n    }else{\n      textData += xmlData[i];\n    }\n  }\n  return xmlObj.child;\n}\n\nfunction addChild(currentNode, childNode, jPath, startIndex){\n  // unset startIndex if not requested\n  if (!this.options.captureMetaData) startIndex = undefined;\n  const result = this.options.updateTag(childNode.tagname, jPath, childNode[\":@\"])\n  if(result === false){\n    //do nothing\n  } else if(typeof result === \"string\"){\n    childNode.tagname = result\n    currentNode.addChild(childNode, startIndex);\n  }else{\n    currentNode.addChild(childNode, startIndex);\n  }\n}\n\nconst replaceEntitiesValue = function(val){\n\n  if(this.options.processEntities){\n    for(let entityName in this.docTypeEntities){\n      const entity = this.docTypeEntities[entityName];\n      val = val.replace( entity.regx, entity.val);\n    }\n    for(let entityName in this.lastEntities){\n      const entity = this.lastEntities[entityName];\n      val = val.replace( entity.regex, entity.val);\n    }\n    if(this.options.htmlEntities){\n      for(let entityName in this.htmlEntities){\n        const entity = this.htmlEntities[entityName];\n        val = val.replace( entity.regex, entity.val);\n      }\n    }\n    val = val.replace( this.ampEntity.regex, this.ampEntity.val);\n  }\n  return val;\n}\nfunction saveTextToParentTag(textData, currentNode, jPath, isLeafNode) {\n  if (textData) { //store previously collected data as textNode\n    if(isLeafNode === undefined) isLeafNode = currentNode.child.length === 0\n    \n    textData = this.parseTextData(textData,\n      currentNode.tagname,\n      jPath,\n      false,\n      currentNode[\":@\"] ? Object.keys(currentNode[\":@\"]).length !== 0 : false,\n      isLeafNode);\n\n    if (textData !== undefined && textData !== \"\")\n      currentNode.add(this.options.textNodeName, textData);\n    textData = \"\";\n  }\n  return textData;\n}\n\n//TODO: use jPath to simplify the logic\n/**\n * @param {Set} stopNodesExact\n * @param {Set} stopNodesWildcard\n * @param {string} jPath\n * @param {string} currentTagName\n */\nfunction isItStopNode(stopNodesExact, stopNodesWildcard, jPath, currentTagName){\n  if(stopNodesWildcard && stopNodesWildcard.has(currentTagName)) return true;\n  if(stopNodesExact && stopNodesExact.has(jPath)) return true;\n  return false;\n}\n\n/**\n * Returns the tag Expression and where it is ending handling single-double quotes situation\n * @param {string} xmlData \n * @param {number} i starting index\n * @returns \n */\nfunction tagExpWithClosingIndex(xmlData, i, closingChar = \">\"){\n  let attrBoundary;\n  let tagExp = \"\";\n  for (let index = i; index < xmlData.length; index++) {\n    let ch = xmlData[index];\n    if (attrBoundary) {\n        if (ch === attrBoundary) attrBoundary = \"\";//reset\n    } else if (ch === '\"' || ch === \"'\") {\n        attrBoundary = ch;\n    } else if (ch === closingChar[0]) {\n      if(closingChar[1]){\n        if(xmlData[index + 1] === closingChar[1]){\n          return {\n            data: tagExp,\n            index: index\n          }\n        }\n      }else{\n        return {\n          data: tagExp,\n          index: index\n        }\n      }\n    } else if (ch === '\\t') {\n      ch = \" \"\n    }\n    tagExp += ch;\n  }\n}\n\nfunction findClosingIndex(xmlData, str, i, errMsg){\n  const closingIndex = xmlData.indexOf(str, i);\n  if(closingIndex === -1){\n    throw new Error(errMsg)\n  }else{\n    return closingIndex + str.length - 1;\n  }\n}\n\nfunction readTagExp(xmlData,i, removeNSPrefix, closingChar = \">\"){\n  const result = tagExpWithClosingIndex(xmlData, i+1, closingChar);\n  if(!result) return;\n  let tagExp = result.data;\n  const closeIndex = result.index;\n  const separatorIndex = tagExp.search(/\\s/);\n  let tagName = tagExp;\n  let attrExpPresent = true;\n  if(separatorIndex !== -1){//separate tag name and attributes expression\n    tagName = tagExp.substring(0, separatorIndex);\n    tagExp = tagExp.substring(separatorIndex + 1).trimStart();\n  }\n\n  const rawTagName = tagName;\n  if(removeNSPrefix){\n    const colonIndex = tagName.indexOf(\":\");\n    if(colonIndex !== -1){\n      tagName = tagName.substr(colonIndex+1);\n      attrExpPresent = tagName !== result.data.substr(colonIndex + 1);\n    }\n  }\n\n  return {\n    tagName: tagName,\n    tagExp: tagExp,\n    closeIndex: closeIndex,\n    attrExpPresent: attrExpPresent,\n    rawTagName: rawTagName,\n  }\n}\n/**\n * find paired tag for a stop node\n * @param {string} xmlData \n * @param {string} tagName \n * @param {number} i \n */\nfunction readStopNodeData(xmlData, tagName, i){\n  const startIndex = i;\n  // Starting at 1 since we already have an open tag\n  let openTagCount = 1;\n\n  for (; i < xmlData.length; i++) {\n    if( xmlData[i] === \"<\"){ \n      if (xmlData[i+1] === \"/\") {//close tag\n          const closeIndex = findClosingIndex(xmlData, \">\", i, `${tagName} is not closed`);\n          let closeTagName = xmlData.substring(i+2,closeIndex).trim();\n          if(closeTagName === tagName){\n            openTagCount--;\n            if (openTagCount === 0) {\n              return {\n                tagContent: xmlData.substring(startIndex, i),\n                i : closeIndex\n              }\n            }\n          }\n          i=closeIndex;\n        } else if(xmlData[i+1] === '?') { \n          const closeIndex = findClosingIndex(xmlData, \"?>\", i+1, \"StopNode is not closed.\")\n          i=closeIndex;\n        } else if(xmlData.substr(i + 1, 3) === '!--') { \n          const closeIndex = findClosingIndex(xmlData, \"-->\", i+3, \"StopNode is not closed.\")\n          i=closeIndex;\n        } else if(xmlData.substr(i + 1, 2) === '![') { \n          const closeIndex = findClosingIndex(xmlData, \"]]>\", i, \"StopNode is not closed.\") - 2;\n          i=closeIndex;\n        } else {\n          const tagData = readTagExp(xmlData, i, '>')\n\n          if (tagData) {\n            const openTagName = tagData && tagData.tagName;\n            if (openTagName === tagName && tagData.tagExp[tagData.tagExp.length-1] !== \"/\") {\n              openTagCount++;\n            }\n            i=tagData.closeIndex;\n          }\n        }\n      }\n  }//end for loop\n}\n\nfunction parseValue(val, shouldParse, options) {\n  if (shouldParse && typeof val === 'string') {\n    //console.log(options)\n    const newval = val.trim();\n    if(newval === 'true' ) return true;\n    else if(newval === 'false' ) return false;\n    else return toNumber(val, options);\n  } else {\n    if (isExist(val)) {\n      return val;\n    } else {\n      return '';\n    }\n  }\n}\n\nfunction fromCodePoint(str, base, prefix){\n  const codePoint = Number.parseInt(str, base);\n\n  if (codePoint >= 0 && codePoint <= 0x10FFFF) {\n      return String.fromCodePoint(codePoint);\n  } else {\n      return prefix +str + \";\";\n  }\n}","'use strict';\n\nimport XmlNode from './xmlNode.js';\n\nconst METADATA_SYMBOL = XmlNode.getMetaDataSymbol();\n\n/**\n * \n * @param {array} node \n * @param {any} options \n * @returns \n */\nexport default function prettify(node, options){\n  return compress( node, options);\n}\n\n/**\n * \n * @param {array} arr \n * @param {object} options \n * @param {string} jPath \n * @returns object\n */\nfunction compress(arr, options, jPath){\n  let text;\n  const compressedObj = {};\n  for (let i = 0; i < arr.length; i++) {\n    const tagObj = arr[i];\n    const property = propName(tagObj);\n    let newJpath = \"\";\n    if(jPath === undefined) newJpath = property;\n    else newJpath = jPath + \".\" + property;\n\n    if(property === options.textNodeName){\n      if(text === undefined) text = tagObj[property];\n      else text += \"\" + tagObj[property];\n    }else if(property === undefined){\n      continue;\n    }else if(tagObj[property]){\n      \n      let val = compress(tagObj[property], options, newJpath);\n      const isLeaf = isLeafTag(val, options);\n      if (tagObj[METADATA_SYMBOL] !== undefined) {\n        val[METADATA_SYMBOL] = tagObj[METADATA_SYMBOL]; // copy over metadata\n      }\n\n      if(tagObj[\":@\"]){\n        assignAttributes( val, tagObj[\":@\"], newJpath, options);\n      }else if(Object.keys(val).length === 1 && val[options.textNodeName] !== undefined && !options.alwaysCreateTextNode){\n        val = val[options.textNodeName];\n      }else if(Object.keys(val).length === 0){\n        if(options.alwaysCreateTextNode) val[options.textNodeName] = \"\";\n        else val = \"\";\n      }\n\n      if(compressedObj[property] !== undefined && compressedObj.hasOwnProperty(property)) {\n        if(!Array.isArray(compressedObj[property])) {\n            compressedObj[property] = [ compressedObj[property] ];\n        }\n        compressedObj[property].push(val);\n      }else{\n        //TODO: if a node is not an array, then check if it should be an array\n        //also determine if it is a leaf node\n        if (options.isArray(property, newJpath, isLeaf )) {\n          compressedObj[property] = [val];\n        }else{\n          compressedObj[property] = val;\n        }\n      }\n    }\n    \n  }\n  // if(text && text.length > 0) compressedObj[options.textNodeName] = text;\n  if(typeof text === \"string\"){\n    if(text.length > 0) compressedObj[options.textNodeName] = text;\n  }else if(text !== undefined) compressedObj[options.textNodeName] = text;\n  return compressedObj;\n}\n\nfunction propName(obj){\n  const keys = Object.keys(obj);\n  for (let i = 0; i < keys.length; i++) {\n    const key = keys[i];\n    if(key !== \":@\") return key;\n  }\n}\n\nfunction assignAttributes(obj, attrMap, jpath, options){\n  if (attrMap) {\n    const keys = Object.keys(attrMap);\n    const len = keys.length; //don't make it inline\n    for (let i = 0; i < len; i++) {\n      const atrrName = keys[i];\n      if (options.isArray(atrrName, jpath + \".\" + atrrName, true, true)) {\n        obj[atrrName] = [ attrMap[atrrName] ];\n      } else {\n        obj[atrrName] = attrMap[atrrName];\n      }\n    }\n  }\n}\n\nfunction isLeafTag(obj, options){\n  const { textNodeName } = options;\n  const propCount = Object.keys(obj).length;\n  \n  if (propCount === 0) {\n    return true;\n  }\n\n  if (\n    propCount === 1 &&\n    (obj[textNodeName] || typeof obj[textNodeName] === \"boolean\" || obj[textNodeName] === 0)\n  ) {\n    return true;\n  }\n\n  return false;\n}\n","import { buildOptions} from './OptionsBuilder.js';\nimport OrderedObjParser from './OrderedObjParser.js';\nimport prettify from './node2json.js';\nimport {validate} from \"../validator.js\";\nimport XmlNode from './xmlNode.js';\n\nexport default class XMLParser{\n    \n    constructor(options){\n        this.externalEntities = {};\n        this.options = buildOptions(options);\n        \n    }\n    /**\n     * Parse XML dats to JS object \n     * @param {string|Uint8Array} xmlData \n     * @param {boolean|Object} validationOption \n     */\n    parse(xmlData,validationOption){\n        if(typeof xmlData !== \"string\" && xmlData.toString){\n            xmlData = xmlData.toString();\n        }else if(typeof xmlData !== \"string\"){\n            throw new Error(\"XML data is accepted in String or Bytes[] form.\")\n        }\n        \n        if( validationOption){\n            if(validationOption === true) validationOption = {}; //validate with default options\n            \n            const result = validate(xmlData, validationOption);\n            if (result !== true) {\n              throw Error( `${result.err.msg}:${result.err.line}:${result.err.col}` )\n            }\n          }\n        const orderedObjParser = new OrderedObjParser(this.options);\n        orderedObjParser.addExternalEntities(this.externalEntities);\n        const orderedResult = orderedObjParser.parseXml(xmlData);\n        if(this.options.preserveOrder || orderedResult === undefined) return orderedResult;\n        else return prettify(orderedResult, this.options);\n    }\n\n    /**\n     * Add Entity which is not by default supported by this library\n     * @param {string} key \n     * @param {string} value \n     */\n    addEntity(key, value){\n        if(value.indexOf(\"&\") !== -1){\n            throw new Error(\"Entity value can't have '&'\")\n        }else if(key.indexOf(\"&\") !== -1 || key.indexOf(\";\") !== -1){\n            throw new Error(\"An entity must be set without '&' and ';'. Eg. use '#xD' for '&#xD;'\")\n        }else if(value === \"&\"){\n            throw new Error(\"An entity with value '&' is not permitted\");\n        }else{\n            this.externalEntities[key] = value;\n        }\n    }\n\n    /**\n     * Returns a Symbol that can be used to access the metadata\n     * property on a node.\n     * \n     * If Symbol is not available in the environment, an ordinary property is used\n     * and the name of the property is here returned.\n     * \n     * The XMLMetaData property is only present when `captureMetaData`\n     * is true in the options.\n     */\n    static getMetaDataSymbol() {\n        return XmlNode.getMetaDataSymbol();\n    }\n}\n","/**\n * JATS XML parser for PMC articles.\n *\n * Parses JATS (Journal Article Tag Suite) XML into an intermediate\n * representation for Markdown conversion.\n *\n * Uses fast-xml-parser with `preserveOrder: true` to maintain document order\n * of interleaved elements (e.g. text, citations, formatting).\n */\nimport { XMLParser } from \"fast-xml-parser\";\nconst parser = new XMLParser({\n    ignoreAttributes: false,\n    attributeNamePrefix: \"@_\",\n    textNodeName: \"#text\",\n    trimValues: false,\n    preserveOrder: true,\n    processEntities: true,\n    htmlEntities: true,\n});\n// ─── Navigation Helpers ──────────────────────────────────────────────\n/** Get the tag name of an ordered node (the first key that isn't \":@\" or \"#text\"). */\nfunction getTagName(node) {\n    for (const key of Object.keys(node)) {\n        if (key !== \":@\" && key !== \"#text\")\n            return key;\n    }\n    return undefined;\n}\n/** Get the children array of an element node. */\nfunction getChildren(node) {\n    const tag = getTagName(node);\n    if (!tag)\n        return [];\n    const children = node[tag];\n    return Array.isArray(children) ? children : [];\n}\n/** Get attributes of an element node. */\nfunction getAttr(node, attrName) {\n    const attrs = node[\":@\"];\n    if (!attrs)\n        return undefined;\n    const val = attrs[`@_${attrName}`];\n    return val != null ? String(val) : undefined;\n}\n/** Get all attributes of an element node (strips @_ prefix for consistency with getAttr). */\nfunction getAttrs(node) {\n    const attrs = node[\":@\"];\n    if (!attrs)\n        return {};\n    const result = {};\n    for (const [key, value] of Object.entries(attrs)) {\n        if (key.startsWith(\"@_\")) {\n            result[key.slice(2)] = String(value);\n        }\n    }\n    return result;\n}\n/** Find the first child element with the given tag name. */\nfunction findChild(children, tagName) {\n    for (const child of children) {\n        if (tagName in child) {\n            const childArr = child[tagName];\n            return {\n                node: child,\n                children: Array.isArray(childArr) ? childArr : [],\n                attrs: getAttrs(child),\n            };\n        }\n    }\n    return undefined;\n}\n/** Find all child elements with the given tag name. */\nfunction findChildren(children, tagName) {\n    const results = [];\n    for (const child of children) {\n        if (tagName in child) {\n            const childArr = child[tagName];\n            results.push({\n                node: child,\n                children: Array.isArray(childArr) ? childArr : [],\n                attrs: getAttrs(child),\n            });\n        }\n    }\n    return results;\n}\n/** Get text content from a #text node. */\nfunction getTextContent(child) {\n    if (\"#text\" in child) {\n        const val = child[\"#text\"];\n        return val != null ? String(val) : undefined;\n    }\n    return undefined;\n}\n/**\n * Find the <article> element, handling optional <pmc-articleset> wrapper\n * that appears in efetch responses.\n */\nfunction findArticle(parsed) {\n    const direct = findChild(parsed, \"article\");\n    if (direct)\n        return direct;\n    const wrapper = findChild(parsed, \"pmc-articleset\");\n    if (wrapper)\n        return findChild(wrapper.children, \"article\");\n    return undefined;\n}\n// ─── Text Extraction ─────────────────────────────────────────────────\n/** Tags whose text content should be followed by a space when adjacent to other content. */\nconst SPACE_AFTER_TAGS = new Set([\"surname\", \"given-names\", \"name\", \"string-name\"]);\n/**\n * Extract plain text from a node that may contain nested elements.\n * Recursively collects all text content from preserveOrder nodes.\n *\n * When extracting text from inline container elements (e.g. `<name>`,\n * `<string-name>`), inserts a space between adjacent child elements\n * that would otherwise concatenate without whitespace (e.g.\n * `<surname>McGuire</surname><given-names>N</given-names>` → `McGuire N`).\n */\nfunction extractAllText(node) {\n    if (node == null)\n        return \"\";\n    if (typeof node === \"string\")\n        return node;\n    if (typeof node === \"number\")\n        return String(node);\n    if (Array.isArray(node)) {\n        return joinChildTexts(node);\n    }\n    if (typeof node === \"object\") {\n        const obj = node;\n        // Text node\n        const text = getTextContent(obj);\n        if (text != null)\n            return text;\n        // Element node — recurse into children\n        const tag = getTagName(obj);\n        if (tag) {\n            const children = obj[tag];\n            if (Array.isArray(children)) {\n                return joinChildTexts(children);\n            }\n        }\n    }\n    return \"\";\n}\n/**\n * Join extracted text from an array of child nodes, inserting spaces\n * between adjacent inline elements where no whitespace separator exists.\n */\nfunction joinChildTexts(children) {\n    const parts = [];\n    for (const child of children) {\n        const text = extractAllText(child);\n        if (!text)\n            continue;\n        const tag = getTagName(child);\n        // If this is a space-after tag and there's previous content that doesn't\n        // end with whitespace or punctuation, insert a space before this text.\n        if (tag && SPACE_AFTER_TAGS.has(tag) && parts.length > 0) {\n            const prev = parts.at(-1);\n            if (prev && !/[\\s,;.:()\\-/]$/.test(prev)) {\n                parts.push(\" \");\n            }\n        }\n        parts.push(text);\n        // If this is a space-after tag, check if a space is needed after.\n        // We handle this by peeking: space will be inserted before the next\n        // element if needed (handled above). But we also need to handle\n        // the case where the next sibling is a text node starting without space.\n        // That's already handled since text nodes include their own whitespace.\n    }\n    return parts.join(\"\");\n}\n// ─── Metadata Parsing ────────────────────────────────────────────────\n/** Extract DOI, PMCID, and PMID from article-id elements. */\nfunction parseArticleIds(metaChildren) {\n    const articleIds = findChildren(metaChildren, \"article-id\");\n    const result = {};\n    for (const idEntry of articleIds) {\n        const idType = idEntry.attrs[\"pub-id-type\"];\n        const idText = extractAllText(idEntry.children);\n        if (idType === \"doi\")\n            result.doi = idText;\n        if (idType === \"pmc\" || idType === \"pmcid\") {\n            result.pmcid = idText.replace(/^PMC/, \"\");\n        }\n        if (idType === \"pmid\")\n            result.pmid = idText;\n    }\n    return result;\n}\n/** Extract authors from contrib-group. */\nfunction parseAuthors(metaChildren) {\n    const authors = [];\n    const contribGroup = findChild(metaChildren, \"contrib-group\");\n    if (!contribGroup)\n        return authors;\n    const contribs = findChildren(contribGroup.children, \"contrib\");\n    for (const contrib of contribs) {\n        if (contrib.attrs[\"contrib-type\"] !== \"author\")\n            continue;\n        const nameNode = findChild(contrib.children, \"name\");\n        if (!nameNode)\n            continue;\n        const surnameNode = findChild(nameNode.children, \"surname\");\n        const givenNamesNode = findChild(nameNode.children, \"given-names\");\n        const author = {\n            surname: surnameNode ? extractAllText(surnameNode.children) : \"\",\n        };\n        const givenNames = givenNamesNode ? extractAllText(givenNamesNode.children) : \"\";\n        if (givenNames) {\n            author.givenNames = givenNames;\n        }\n        authors.push(author);\n    }\n    return authors;\n}\n/** Extract abstract text, handling both structured and simple formats. */\nfunction parseAbstract(metaChildren) {\n    const abstractNode = findChild(metaChildren, \"abstract\");\n    if (!abstractNode)\n        return undefined;\n    // Structured abstract with <sec> elements\n    const sections = findChildren(abstractNode.children, \"sec\");\n    if (sections.length > 0) {\n        return parseStructuredAbstract(sections);\n    }\n    // Simple abstract with <p>\n    const paragraphs = findChildren(abstractNode.children, \"p\");\n    if (paragraphs.length > 0) {\n        return paragraphs.map((p) => extractAllText(p.children)).join(\"\\n\\n\");\n    }\n    const text = extractAllText(abstractNode.children);\n    return text || undefined;\n}\n/** Parse a structured abstract with <sec> elements. */\nfunction parseStructuredAbstract(sections) {\n    const parts = [];\n    for (const sec of sections) {\n        const secTitleNode = findChild(sec.children, \"title\");\n        const secTitle = secTitleNode ? extractAllText(secTitleNode.children) : \"\";\n        const secPs = findChildren(sec.children, \"p\");\n        const text = secPs.map((p) => extractAllText(p.children)).join(\" \");\n        parts.push(secTitle ? `${secTitle}: ${text}` : text);\n    }\n    return parts.join(\"\\n\\n\");\n}\n/** Extract a date from a pub-date node. */\nfunction extractDateFromNode(pd) {\n    const yearNode = findChild(pd.children, \"year\");\n    if (!yearNode)\n        return undefined;\n    const year = extractAllText(yearNode.children);\n    const monthNode = findChild(pd.children, \"month\");\n    const dayNode = findChild(pd.children, \"day\");\n    const date = { year };\n    if (monthNode)\n        date.month = extractAllText(monthNode.children);\n    if (dayNode)\n        date.day = extractAllText(dayNode.children);\n    return date;\n}\n/**\n * Extract publication date with priority: epub > ppub > collection > any other.\n * Falls back to first available date if none match priority.\n */\nfunction parsePublicationDate(metaChildren) {\n    const pubDates = findChildren(metaChildren, \"pub-date\");\n    const datePriority = { epub: 0, ppub: 1, collection: 2 };\n    let bestPriority = Number.POSITIVE_INFINITY;\n    let publicationDate;\n    for (const pd of pubDates) {\n        const dateType = pd.attrs[\"pub-type\"] ?? pd.attrs[\"date-type\"] ?? \"\";\n        const priority = datePriority[dateType] ?? 3;\n        if (priority < bestPriority) {\n            bestPriority = priority;\n            publicationDate = extractDateFromNode(pd);\n        }\n    }\n    // If no prioritized date found, take first available\n    if (!publicationDate && pubDates.length > 0) {\n        const pd = pubDates.at(0);\n        if (pd) {\n            publicationDate = extractDateFromNode(pd);\n        }\n    }\n    return publicationDate;\n}\n/** Extract license information from permissions. */\nfunction parseLicense(metaChildren) {\n    const permissions = findChild(metaChildren, \"permissions\");\n    if (!permissions)\n        return undefined;\n    const licenseNode = findChild(permissions.children, \"license\");\n    if (!licenseNode)\n        return undefined;\n    // Prefer @xlink:href (standardized URL) over <license-p> (free-text)\n    const href = licenseNode.attrs[\"xlink:href\"];\n    if (href)\n        return href;\n    const licenseP = findChild(licenseNode.children, \"license-p\");\n    if (licenseP)\n        return extractAllText(licenseP.children).trim();\n    return undefined;\n}\n/** Extract keywords from all kwd-group elements. */\nfunction parseKeywords(metaChildren) {\n    const kwdGroups = findChildren(metaChildren, \"kwd-group\");\n    const keywords = [];\n    for (const kwdGroup of kwdGroups) {\n        const kwds = findChildren(kwdGroup.children, \"kwd\");\n        for (const kwd of kwds) {\n            const text = extractAllText(kwd.children).trim();\n            if (text)\n                keywords.push(text);\n        }\n    }\n    return keywords;\n}\n/** Extract volume, issue, and pages from article meta. */\nfunction parseVolumeAndPages(metaChildren) {\n    const volumeNode = findChild(metaChildren, \"volume\");\n    const volume = volumeNode ? extractAllText(volumeNode.children) : undefined;\n    const issueNode = findChild(metaChildren, \"issue\");\n    const issue = issueNode ? extractAllText(issueNode.children) : undefined;\n    let pages;\n    const fpageNode = findChild(metaChildren, \"fpage\");\n    const lpageNode = findChild(metaChildren, \"lpage\");\n    if (fpageNode) {\n        const fp = extractAllText(fpageNode.children);\n        const lp = lpageNode ? extractAllText(lpageNode.children) : \"\";\n        pages = lp ? `${fp}-${lp}` : fp;\n    }\n    else {\n        const elocationNode = findChild(metaChildren, \"elocation-id\");\n        if (elocationNode)\n            pages = extractAllText(elocationNode.children);\n    }\n    const result = {};\n    if (volume !== undefined)\n        result.volume = volume;\n    if (issue !== undefined)\n        result.issue = issue;\n    if (pages !== undefined)\n        result.pages = pages;\n    return result;\n}\n/** Extract journal name from front matter journal-meta. */\nfunction parseJournalName(frontChildren) {\n    const journalMeta = findChild(frontChildren, \"journal-meta\");\n    if (!journalMeta)\n        return undefined;\n    const titleGroup = findChild(journalMeta.children, \"journal-title-group\");\n    if (titleGroup) {\n        const jTitle = findChild(titleGroup.children, \"journal-title\");\n        if (jTitle)\n            return extractAllText(jTitle.children);\n    }\n    const jTitle = findChild(journalMeta.children, \"journal-title\");\n    if (jTitle)\n        return extractAllText(jTitle.children);\n    return undefined;\n}\n/** Extract article title from title-group. */\nfunction parseArticleTitle(metaChildren) {\n    const titleGroup = findChild(metaChildren, \"title-group\");\n    const articleTitle = titleGroup ? findChild(titleGroup.children, \"article-title\") : undefined;\n    return articleTitle ? extractAllText(articleTitle.children) : \"\";\n}\n/** Assemble optional metadata fields into a JatsMetadata result. */\nfunction assembleMetadata(base, fields) {\n    const result = { ...base };\n    if (fields.doi)\n        result.doi = fields.doi;\n    if (fields.pmcid)\n        result.pmcid = fields.pmcid;\n    if (fields.pmid)\n        result.pmid = fields.pmid;\n    if (fields.journal)\n        result.journal = fields.journal;\n    if (fields.publicationDate)\n        result.publicationDate = fields.publicationDate;\n    if (fields.volume)\n        result.volume = fields.volume;\n    if (fields.issue)\n        result.issue = fields.issue;\n    if (fields.pages)\n        result.pages = fields.pages;\n    if (fields.keywords.length > 0)\n        result.keywords = fields.keywords;\n    if (fields.articleType)\n        result.articleType = fields.articleType;\n    if (fields.license)\n        result.license = fields.license;\n    if (fields.abstract)\n        result.abstract = fields.abstract;\n    return result;\n}\n/**\n * Parse JATS XML front matter to extract article metadata.\n */\nexport function parseJatsMetadata(xml) {\n    const parsed = parser.parse(xml);\n    const article = findArticle(parsed);\n    if (!article)\n        return { title: \"\", authors: [] };\n    const front = findChild(article.children, \"front\");\n    if (!front)\n        return { title: \"\", authors: [] };\n    const articleMeta = findChild(front.children, \"article-meta\");\n    if (!articleMeta)\n        return { title: \"\", authors: [] };\n    const metaChildren = articleMeta.children;\n    const journal = parseJournalName(front.children);\n    const publicationDate = parsePublicationDate(metaChildren);\n    const articleType = article.attrs[\"article-type\"] || undefined;\n    const license = parseLicense(metaChildren);\n    const abstract = parseAbstract(metaChildren);\n    return assembleMetadata({ title: parseArticleTitle(metaChildren), authors: parseAuthors(metaChildren) }, {\n        ...parseArticleIds(metaChildren),\n        ...(journal !== undefined ? { journal } : {}),\n        ...(publicationDate !== undefined ? { publicationDate } : {}),\n        ...parseVolumeAndPages(metaChildren),\n        keywords: parseKeywords(metaChildren),\n        ...(articleType !== undefined ? { articleType } : {}),\n        ...(license !== undefined ? { license } : {}),\n        ...(abstract !== undefined ? { abstract } : {}),\n    });\n}\n// ─── Inline Content Parsing ──────────────────────────────────────────\n/** Handle <inline-formula> tag. */\nfunction handleInlineFormula(innerChildren) {\n    // Try to find <tex-math> directly or inside <alternatives>\n    let texMath = findChild(innerChildren, \"tex-math\");\n    if (!texMath) {\n        const alternatives = findChild(innerChildren, \"alternatives\");\n        if (alternatives) {\n            texMath = findChild(alternatives.children, \"tex-math\");\n        }\n    }\n    const tex = texMath ? extractAllText(texMath.children) : undefined;\n    const text = tex || extractAllText(innerChildren);\n    const entry = {\n        type: \"inline-formula\",\n        text,\n    };\n    if (tex)\n        entry.tex = tex;\n    return entry;\n}\n/** Handle <ext-link> tag. */\nfunction handleExtLink(child, innerChildren) {\n    const href = getAttr(child, \"xlink:href\");\n    if (href) {\n        return { type: \"link\", url: href, children: parseInlineContent(innerChildren) };\n    }\n    const linkText = extractAllText(innerChildren);\n    if (linkText)\n        return { type: \"text\", text: linkText };\n    return null;\n}\n/** Handle <uri> tag. */\nfunction handleUri(child, innerChildren) {\n    const href = getAttr(child, \"xlink:href\");\n    const textContent = extractAllText(innerChildren);\n    const url = href || textContent;\n    if (url) {\n        return { type: \"link\", url, children: parseInlineContent(innerChildren) };\n    }\n    return null;\n}\n/** Handle <xref> tag. */\nfunction handleXref(child, innerChildren) {\n    const refType = getAttr(child, \"ref-type\");\n    if (refType === \"bibr\") {\n        return {\n            type: \"citation\",\n            refId: getAttr(child, \"rid\") ?? \"\",\n            text: extractAllText(innerChildren),\n        };\n    }\n    const xrefText = extractAllText(innerChildren);\n    if (xrefText)\n        return { type: \"text\", text: xrefText };\n    return null;\n}\n/** Map of tag names to their inline content handlers. */\nconst inlineTagHandlers = {\n    bold: (_child, innerChildren) => ({\n        type: \"bold\",\n        children: parseInlineContent(innerChildren),\n    }),\n    italic: (_child, innerChildren) => ({\n        type: \"italic\",\n        children: parseInlineContent(innerChildren),\n    }),\n    sup: (_child, innerChildren) => ({\n        type: \"superscript\",\n        text: extractAllText(innerChildren),\n    }),\n    sub: (_child, innerChildren) => ({\n        type: \"subscript\",\n        text: extractAllText(innerChildren),\n    }),\n    \"inline-formula\": (_child, innerChildren) => handleInlineFormula(innerChildren),\n    monospace: (_child, innerChildren) => ({\n        type: \"code\",\n        text: extractAllText(innerChildren),\n    }),\n    \"ext-link\": (child, innerChildren) => handleExtLink(child, innerChildren),\n    uri: (child, innerChildren) => handleUri(child, innerChildren),\n    underline: (_child, innerChildren) => {\n        const passText = extractAllText(innerChildren);\n        return passText ? { type: \"text\", text: passText } : null;\n    },\n    sc: (_child, innerChildren) => {\n        const passText = extractAllText(innerChildren);\n        return passText ? { type: \"text\", text: passText } : null;\n    },\n    xref: (child, innerChildren) => handleXref(child, innerChildren),\n};\n/** Process a single inline child node into an InlineContent, or return null. */\nfunction processInlineChild(child) {\n    // Text node\n    const text = getTextContent(child);\n    if (text != null) {\n        return text ? { type: \"text\", text } : null;\n    }\n    const tag = getTagName(child);\n    if (!tag)\n        return null;\n    const innerChildren = getChildren(child);\n    const handler = inlineTagHandlers[tag];\n    if (handler)\n        return handler(child, innerChildren);\n    // Unknown inline element -- extract text\n    const unknownText = extractAllText(innerChildren);\n    return unknownText ? { type: \"text\", text: unknownText } : null;\n}\n/**\n * Parse inline content from a paragraph's children array.\n * Iterates in document order to preserve interleaving of text, citations,\n * and formatting elements.\n */\nfunction parseInlineContent(children) {\n    const result = [];\n    for (const child of children) {\n        const content = processInlineChild(child);\n        if (content)\n            result.push(content);\n    }\n    return result;\n}\n// ─── Block Content Parsing ───────────────────────────────────────────\n/**\n * Parse a <list> element into a BlockElement.\n */\nfunction parseList(listNode) {\n    const listType = getAttr(listNode, \"list-type\");\n    const ordered = listType === \"order\";\n    const listChildren = getChildren(listNode);\n    const listItems = findChildren(listChildren, \"list-item\");\n    const items = [];\n    for (const item of listItems) {\n        const pNodes = findChildren(item.children, \"p\");\n        const content = pNodes.flatMap((p) => parseInlineContent(p.children));\n        items.push(content);\n    }\n    return { type: \"list\", ordered, items };\n}\n/**\n * Parse a table row into an array of cell text content.\n */\nfunction parseTableRow(trChildren) {\n    const cells = [];\n    for (const child of trChildren) {\n        const tag = getTagName(child);\n        if (tag === \"th\" || tag === \"td\") {\n            const cellChildren = getChildren(child);\n            // Check if cell contains multiple <p> elements\n            const paragraphs = findChildren(cellChildren, \"p\");\n            if (paragraphs.length > 1) {\n                cells.push(paragraphs.map((p) => extractAllText(p.children)).join(\"<br>\"));\n            }\n            else {\n                cells.push(extractAllText(cellChildren));\n            }\n        }\n    }\n    return cells;\n}\n/**\n * Parse an already-parsed table-wrap node.\n */\nfunction parseTableWrap(tableWrapNode) {\n    const children = getChildren(tableWrapNode);\n    // Caption\n    const labelNode = findChild(children, \"label\");\n    const label = labelNode ? extractAllText(labelNode.children) : \"\";\n    const captionNode = findChild(children, \"caption\");\n    const captionText = captionNode ? extractAllText(captionNode.children) : \"\";\n    const captionStr = [label, captionText].filter(Boolean).join(\". \");\n    const tableNode = findChild(children, \"table\");\n    const result = {\n        headers: [],\n        rows: [],\n    };\n    if (captionStr)\n        result.caption = captionStr;\n    if (!tableNode)\n        return result;\n    // Headers from thead\n    const thead = findChild(tableNode.children, \"thead\");\n    if (thead) {\n        const headRows = findChildren(thead.children, \"tr\");\n        if (headRows.length > 0) {\n            result.headers.push(...parseTableRow(headRows[0]?.children ?? []));\n        }\n    }\n    // Body rows\n    const tbody = findChild(tableNode.children, \"tbody\");\n    if (tbody) {\n        const bodyRows = findChildren(tbody.children, \"tr\");\n        for (const row of bodyRows) {\n            result.rows.push(parseTableRow(row.children));\n        }\n    }\n    return result;\n}\n/**\n * Parse a <table-wrap> element into a table block.\n * Exported for standalone use and used internally by parseBlockContent.\n */\nexport function parseJatsTable(xml) {\n    const parsed = parser.parse(xml);\n    const tableWrap = findChild(parsed, \"table-wrap\");\n    if (tableWrap) {\n        return parseTableWrap(tableWrap.node);\n    }\n    // Fallback: if not wrapped, try to find table directly\n    return { headers: [], rows: [] };\n}\n/**\n * Parse a <boxed-text> element into a boxed-text block.\n * Extracts optional title and recursively parses inner block content.\n */\nfunction parseBoxedText(node) {\n    const children = getChildren(node);\n    const titleNode = findChild(children, \"title\");\n    const title = titleNode ? extractAllText(titleNode.children) : undefined;\n    const content = parseBlockContent(children);\n    const block = { type: \"boxed-text\", content };\n    if (title)\n        block.title = title;\n    return block;\n}\n/**\n * Parse a <def-list> element into a def-list block.\n * Extracts optional title and <def-item> pairs with <term> and <def>.\n */\nfunction parseDefList(node) {\n    const children = getChildren(node);\n    const titleNode = findChild(children, \"title\");\n    const title = titleNode ? extractAllText(titleNode.children) : undefined;\n    const defItems = findChildren(children, \"def-item\");\n    const items = [];\n    for (const item of defItems) {\n        const termNode = findChild(item.children, \"term\");\n        const defNode = findChild(item.children, \"def\");\n        const term = termNode ? extractAllText(termNode.children) : \"\";\n        const definition = defNode ? extractAllText(defNode.children) : \"\";\n        items.push({ term, definition });\n    }\n    const block = { type: \"def-list\", items };\n    if (title)\n        block.title = title;\n    return block;\n}\n/**\n * Parse a <disp-formula> element into a formula block.\n * Extracts TeX content from <tex-math> preferentially (inside <alternatives> or direct),\n * falls back to extractAllText for plain text.\n */\nfunction parseDispFormula(node) {\n    const children = getChildren(node);\n    const id = getAttr(node, \"id\");\n    const labelNode = findChild(children, \"label\");\n    const label = labelNode ? extractAllText(labelNode.children) : undefined;\n    // Try <alternatives> wrapper first\n    const alternatives = findChild(children, \"alternatives\");\n    const searchChildren = alternatives ? alternatives.children : children;\n    const texMath = findChild(searchChildren, \"tex-math\");\n    const block = { type: \"formula\" };\n    if (id)\n        block.id = id;\n    if (label)\n        block.label = label;\n    if (texMath) {\n        block.tex = extractAllText(texMath.children);\n    }\n    else {\n        // Fall back to plain text extraction (skip label)\n        const textChildren = children.filter((c) => !(\"label\" in c));\n        const text = extractAllText(textChildren).trim();\n        if (text)\n            block.text = text;\n    }\n    return block;\n}\n/** Tags that represent block-level elements when nested inside <p>. */\nconst BLOCK_TAGS = new Set([\"table-wrap\", \"fig\", \"disp-quote\", \"boxed-text\"]);\n/**\n * Parse a <disp-quote> element into a blockquote block.\n * Extracts <p> children and concatenates their inline content.\n */\nfunction parseDispQuote(node) {\n    const children = getChildren(node);\n    const paragraphs = findChildren(children, \"p\");\n    const content = [];\n    for (let i = 0; i < paragraphs.length; i++) {\n        if (i > 0)\n            content.push({ type: \"text\", text: \"\\n\\n\" });\n        const para = paragraphs[i];\n        if (para)\n            content.push(...parseInlineContent(para.children));\n    }\n    // If no <p> children, extract inline content directly\n    if (paragraphs.length === 0) {\n        content.push(...parseInlineContent(children));\n    }\n    return { type: \"blockquote\", content };\n}\n/**\n * Parse a <table-wrap> node into a table block element.\n */\nfunction parseTableBlock(node) {\n    const tableResult = parseTableWrap(node);\n    const tableBlock = {\n        type: \"table\",\n        headers: tableResult.headers,\n        rows: tableResult.rows,\n    };\n    if (tableResult.caption)\n        tableBlock.caption = tableResult.caption;\n    return tableBlock;\n}\n/**\n * Parse a <fig> node into a figure block element.\n */\nfunction parseFigBlock(node) {\n    const innerChildren = getChildren(node);\n    const figBlock = { type: \"figure\" };\n    const figId = getAttr(node, \"id\");\n    if (figId)\n        figBlock.id = figId;\n    const figLabel = findChild(innerChildren, \"label\");\n    if (figLabel) {\n        const labelText = extractAllText(figLabel.children);\n        if (labelText)\n            figBlock.label = labelText;\n    }\n    const figCaption = findChild(innerChildren, \"caption\");\n    if (figCaption) {\n        const captionText = extractAllText(figCaption.children);\n        if (captionText)\n            figBlock.caption = captionText;\n    }\n    return figBlock;\n}\n/**\n * Parse a <p> element, splitting it if it contains nested block elements\n * (table-wrap, fig, disp-quote). Returns one or more block elements.\n */\nfunction parseParagraph(pChildren) {\n    // Check if <p> contains any nested block elements\n    const hasNestedBlocks = pChildren.some((child) => {\n        const tag = getTagName(child);\n        return tag != null && BLOCK_TAGS.has(tag);\n    });\n    if (!hasNestedBlocks) {\n        return [{ type: \"paragraph\", content: parseInlineContent(pChildren) }];\n    }\n    // Split into inline runs and block elements\n    const blocks = [];\n    let inlineBuffer = [];\n    const flushInline = () => {\n        if (inlineBuffer.length > 0) {\n            const content = parseInlineContent(inlineBuffer);\n            // Skip whitespace-only paragraphs created by XML formatting\n            const hasNonWhitespace = content.some((c) => c.type !== \"text\" || c.text.trim() !== \"\");\n            if (content.length > 0 && hasNonWhitespace) {\n                blocks.push({ type: \"paragraph\", content });\n            }\n            inlineBuffer = [];\n        }\n    };\n    for (const child of pChildren) {\n        const tag = getTagName(child);\n        if (tag === \"table-wrap\") {\n            flushInline();\n            blocks.push(parseTableBlock(child));\n        }\n        else if (tag === \"fig\") {\n            flushInline();\n            blocks.push(parseFigBlock(child));\n        }\n        else if (tag === \"disp-quote\") {\n            flushInline();\n            blocks.push(parseDispQuote(child));\n        }\n        else if (tag === \"boxed-text\") {\n            flushInline();\n            blocks.push(parseBoxedText(child));\n        }\n        else {\n            inlineBuffer.push(child);\n        }\n    }\n    flushInline();\n    return blocks;\n}\n/** Parse a <supplementary-material> element into a paragraph block. */\nfunction parseSupplementaryMaterial(child) {\n    const innerChildren = getChildren(child);\n    const labelNode = findChild(innerChildren, \"label\");\n    const captionNode = findChild(innerChildren, \"caption\");\n    const labelText = labelNode ? extractAllText(labelNode.children) : \"\";\n    const captionText = captionNode ? extractAllText(captionNode.children) : \"\";\n    const text = [labelText, captionText].filter(Boolean).join(\": \");\n    if (text) {\n        return { type: \"paragraph\", content: [{ type: \"text\", text }] };\n    }\n    return null;\n}\n/** Map of tag names to their block content handlers. */\nconst blockTagHandlers = {\n    p: (child) => parseParagraph(getChildren(child)),\n    list: (child) => parseList(child),\n    \"table-wrap\": (child) => parseTableBlock(child),\n    fig: (child) => parseFigBlock(child),\n    \"disp-quote\": (child) => parseDispQuote(child),\n    \"boxed-text\": (child) => parseBoxedText(child),\n    \"def-list\": (child) => parseDefList(child),\n    \"disp-formula\": (child) => parseDispFormula(child),\n    preformat: (child) => ({ type: \"preformat\", text: extractAllText(getChildren(child)) }),\n    \"supplementary-material\": (child) => parseSupplementaryMaterial(child),\n};\n/**\n * Parse block-level content from a section's children.\n * Iterates in document order to preserve ordering of paragraphs, lists,\n * tables, figures, and blockquotes.\n */\nfunction parseBlockContent(sectionChildren) {\n    const blocks = [];\n    for (const child of sectionChildren) {\n        const tag = getTagName(child);\n        if (!tag)\n            continue;\n        const handler = blockTagHandlers[tag];\n        if (!handler)\n            continue;\n        const result = handler(child);\n        if (result == null)\n            continue;\n        if (Array.isArray(result)) {\n            blocks.push(...result);\n        }\n        else {\n            blocks.push(result);\n        }\n    }\n    return blocks;\n}\n// ─── Section Parsing ─────────────────────────────────────────────────\n/**\n * Parse a <sec> element into a JatsSection, recursively handling subsections.\n */\nfunction parseSection(secChildren, level) {\n    const titleNode = findChild(secChildren, \"title\");\n    const title = titleNode ? extractAllText(titleNode.children) : \"\";\n    const content = parseBlockContent(secChildren);\n    // Nested sections\n    const subsections = [];\n    const nestedSecs = findChildren(secChildren, \"sec\");\n    for (const sub of nestedSecs) {\n        subsections.push(parseSection(sub.children, level + 1));\n    }\n    return { title, level, content, subsections };\n}\n/**\n * Parse JATS XML body to extract sections and content.\n */\nexport function parseJatsBody(xml) {\n    const parsed = parser.parse(xml);\n    const article = findArticle(parsed);\n    if (!article)\n        return [];\n    const body = findChild(article.children, \"body\");\n    if (!body)\n        return [];\n    const sections = [];\n    const secs = findChildren(body.children, \"sec\");\n    if (secs.length > 0) {\n        for (const sec of secs) {\n            sections.push(parseSection(sec.children, 2));\n        }\n    }\n    else {\n        // Body has paragraphs without sections\n        const content = parseBlockContent(body.children);\n        if (content.length > 0) {\n            sections.push({ title: \"\", level: 2, content, subsections: [] });\n        }\n    }\n    return sections;\n}\n// ─── Reference Parsing ───────────────────────────────────────────────\n/** Extract authors from a <person-group> element. */\nfunction extractCitationAuthors(children) {\n    const personGroup = findChild(children, \"person-group\");\n    if (!personGroup)\n        return undefined;\n    const names = findChildren(personGroup.children, \"name\");\n    const authorParts = [];\n    for (const name of names) {\n        const surname = findChild(name.children, \"surname\");\n        const givenNames = findChild(name.children, \"given-names\");\n        const surnameText = surname ? extractAllText(surname.children) : \"\";\n        const givenText = givenNames ? extractAllText(givenNames.children) : \"\";\n        if (surnameText && givenText) {\n            authorParts.push(`${surnameText} ${givenText}`);\n        }\n        else if (surnameText) {\n            authorParts.push(surnameText);\n        }\n    }\n    return authorParts.length > 0 ? authorParts.join(\", \") : undefined;\n}\n/** Format year, volume, and pages into a citation string part. */\nfunction formatYearVolumePage(children) {\n    const year = findChild(children, \"year\");\n    if (!year)\n        return undefined;\n    let yearStr = extractAllText(year.children);\n    const volume = findChild(children, \"volume\");\n    if (volume) {\n        yearStr += `;${extractAllText(volume.children)}`;\n    }\n    const fpage = findChild(children, \"fpage\");\n    if (fpage) {\n        const fpageText = extractAllText(fpage.children);\n        const lpage = findChild(children, \"lpage\");\n        const lpageText = lpage ? extractAllText(lpage.children) : \"\";\n        yearStr += `:${fpageText}${lpageText ? `-${lpageText}` : \"\"}`;\n    }\n    return yearStr;\n}\n/**\n * Format a structured <element-citation> into a readable reference string.\n * Produces: \"Author1, Author2. Title. Source. Year;Volume:FirstPage-LastPage.\"\n */\nfunction formatElementCitation(children) {\n    const parts = [];\n    const authorsStr = extractCitationAuthors(children);\n    if (authorsStr)\n        parts.push(authorsStr);\n    // Article title\n    const articleTitle = findChild(children, \"article-title\");\n    if (articleTitle) {\n        parts.push(extractAllText(articleTitle.children));\n    }\n    // Source (journal name)\n    const source = findChild(children, \"source\");\n    if (source) {\n        parts.push(extractAllText(source.children));\n    }\n    // Year, volume, pages\n    const yearVolumePage = formatYearVolumePage(children);\n    if (yearVolumePage)\n        parts.push(yearVolumePage);\n    return `${parts.join(\". \")}.`;\n}\n/**\n * Extract text from a <mixed-citation>'s children, deduplicating any\n * <pub-id> content that also appears as inline text.\n *\n * Some publishers include the DOI/PMID both as a text node and inside\n * a <pub-id> element, causing duplication like \"10.1234/x 10.1234/x\".\n */\nfunction extractMixedCitationText(children) {\n    // Collect pub-id values\n    const pubIds = findChildren(children, \"pub-id\");\n    const pubIdValues = pubIds.map((p) => extractAllText(p.children).trim()).filter(Boolean);\n    if (pubIdValues.length === 0) {\n        return extractAllText(children).trim();\n    }\n    // Extract full text\n    const fullText = extractAllText(children).trim();\n    // For each pub-id value, if it appears more than once, remove extra occurrences\n    let result = fullText;\n    for (const val of pubIdValues) {\n        // Escape regex special characters\n        const escaped = val.replace(/[.*+?^${}()|[\\]\\\\]/g, \"\\\\$&\");\n        const matches = result.match(new RegExp(escaped, \"g\"));\n        if (matches && matches.length > 1) {\n            // Remove the first occurrence (typically the inline text), keep the last (pub-id element)\n            result = result.replace(val, \"\");\n            // Clean up any leftover extra whitespace\n            result = result.replace(/\\s{2,}/g, \" \").trim();\n        }\n    }\n    return result;\n}\n/**\n * Extract structured pub-id values (DOI, PMID, PMCID) from children nodes.\n */\nfunction extractPubIds(children) {\n    const pubIds = findChildren(children, \"pub-id\");\n    const result = {};\n    for (const p of pubIds) {\n        const idType = p.attrs[\"pub-id-type\"];\n        const value = extractAllText(p.children).trim();\n        if (!value)\n            continue;\n        if (idType === \"doi\")\n            result.doi = value;\n        if (idType === \"pmid\")\n            result.pmid = value;\n        if (idType === \"pmc\" || idType === \"pmcid\") {\n            result.pmcid = value.replace(/^PMC/, \"\");\n        }\n    }\n    return result;\n}\n/**\n * Strip extracted pub-id values from reference text to avoid duplication\n * when pub-ids are rendered separately as links.\n */\nfunction stripPubIdValues(text, pubIds) {\n    let result = text;\n    const values = [pubIds.doi, pubIds.pmid, pubIds.pmcid].filter(Boolean);\n    for (const val of values) {\n        // Strip common label prefixes (e.g. \"doi: \", \"PMID: \", \"DOI:\", \"pmid:\") followed by the value\n        const escaped = val.replace(/[.*+?^${}()|[\\]\\\\]/g, \"\\\\$&\");\n        result = result.replace(new RegExp(`(?:doi|PMID|pmid|PMC|pmc)[:\\\\s]*${escaped}`, \"gi\"), \"\");\n        // Also strip the bare value itself\n        result = result.replace(new RegExp(escaped, \"g\"), \"\");\n    }\n    // Also strip PMC-prefixed form of pmcid\n    if (pubIds.pmcid) {\n        const pmcFull = `PMC${pubIds.pmcid}`;\n        const escaped = pmcFull.replace(/[.*+?^${}()|[\\]\\\\]/g, \"\\\\$&\");\n        result = result.replace(new RegExp(`(?:pmc|pmcid)[:\\\\s]*${escaped}`, \"gi\"), \"\");\n        result = result.replace(new RegExp(escaped, \"g\"), \"\");\n    }\n    // Clean up trailing/leading whitespace and extra spaces\n    result = result.replace(/\\s{2,}/g, \" \").trim();\n    // Clean up trailing period after stripped content (e.g. \"Title. .\" -> \"Title.\")\n    result = result.replace(/\\.\\s*\\.$/, \".\");\n    return result;\n}\n/** Parse a single <ref> element into a JatsReference, or return null if invalid. */\nfunction parseSingleReference(ref) {\n    const id = getAttr(ref.node, \"id\") ?? \"\";\n    // Determine the search scope: if <citation-alternatives> exists, search within it;\n    // otherwise search direct children of <ref>\n    const citationAlternatives = findChild(ref.children, \"citation-alternatives\");\n    const searchChildren = citationAlternatives ? citationAlternatives.children : ref.children;\n    // Try mixed-citation first (already formatted), then element-citation (structured)\n    const mixedCitation = findChild(searchChildren, \"mixed-citation\");\n    if (mixedCitation) {\n        const rawText = extractMixedCitationText(mixedCitation.children);\n        const pubIds = extractPubIds(mixedCitation.children);\n        const text = stripPubIdValues(rawText, pubIds);\n        if (id && text)\n            return { id, text, ...pubIds };\n        return null;\n    }\n    const elementCitation = findChild(searchChildren, \"element-citation\");\n    if (elementCitation) {\n        const rawText = formatElementCitation(elementCitation.children);\n        const pubIds = extractPubIds(elementCitation.children);\n        const text = stripPubIdValues(rawText, pubIds);\n        if (id && text)\n            return { id, text, ...pubIds };\n        return null;\n    }\n    // Fallback: extract all text from ref, skipping <label>\n    const childrenWithoutLabel = ref.children.filter((c) => !(\"label\" in c));\n    const text = extractAllText(childrenWithoutLabel).trim();\n    if (id && text)\n        return { id, text };\n    return null;\n}\n/**\n * Parse JATS XML back matter to extract references.\n */\nexport function parseJatsReferences(xml) {\n    const parsed = parser.parse(xml);\n    const article = findArticle(parsed);\n    if (!article)\n        return [];\n    const back = findChild(article.children, \"back\");\n    if (!back)\n        return [];\n    const refList = findChild(back.children, \"ref-list\");\n    if (!refList)\n        return [];\n    const refs = findChildren(refList.children, \"ref\");\n    const references = [];\n    for (const ref of refs) {\n        const reference = parseSingleReference(ref);\n        if (reference)\n            references.push(reference);\n    }\n    return references;\n}\n/** Parse acknowledgments from <ack> element. */\nfunction parseAcknowledgments(backChildren) {\n    const ack = findChild(backChildren, \"ack\");\n    if (!ack)\n        return undefined;\n    const paragraphs = findChildren(ack.children, \"p\");\n    if (paragraphs.length > 0) {\n        return paragraphs.map((p) => extractAllText(p.children)).join(\"\\n\\n\");\n    }\n    return undefined;\n}\n/** Parse appendices from <app-group>/<app> elements. */\nfunction parseAppendices(backChildren) {\n    const appGroup = findChild(backChildren, \"app-group\");\n    if (!appGroup)\n        return undefined;\n    const apps = findChildren(appGroup.children, \"app\");\n    if (apps.length === 0)\n        return undefined;\n    return apps.map((app) => parseSection(app.children, 2));\n}\n/** Parse a single footnote element into a JatsFootnote. */\nfunction parseSingleFootnote(fn) {\n    const parts = [];\n    // Include <title> if present\n    const titleNode = findChild(fn.children, \"title\");\n    if (titleNode) {\n        const titleText = extractAllText(titleNode.children).trim();\n        if (titleText)\n            parts.push(titleText);\n    }\n    // Extract text from each <p> separately and join with space\n    const paragraphs = findChildren(fn.children, \"p\");\n    for (const p of paragraphs) {\n        const pText = extractAllText(p.children).trim();\n        if (pText)\n            parts.push(pText);\n    }\n    return {\n        id: getAttr(fn.node, \"id\") ?? \"\",\n        text: parts.join(\" \"),\n    };\n}\n/** Parse footnotes from <fn-group>/<fn> elements. */\nfunction parseFootnotes(backChildren) {\n    const fnGroup = findChild(backChildren, \"fn-group\");\n    if (!fnGroup)\n        return undefined;\n    const fns = findChildren(fnGroup.children, \"fn\");\n    if (fns.length === 0)\n        return undefined;\n    return fns.map(parseSingleFootnote);\n}\n/** Parse a single notes element into BackMatterNote entries. */\nfunction parseSingleNotesElement(note) {\n    const notes = [];\n    // Check if this <notes> contains <sec> or nested <notes> children\n    const secs = findChildren(note.children, \"sec\");\n    const nestedNotes = findChildren(note.children, \"notes\");\n    const subItems = secs.length > 0 ? secs : nestedNotes;\n    if (subItems.length > 0) {\n        for (const sub of subItems) {\n            const subTitleNode = findChild(sub.children, \"title\");\n            const subTitle = subTitleNode ? extractAllText(subTitleNode.children) : \"\";\n            const subParagraphs = findChildren(sub.children, \"p\");\n            const subText = subParagraphs.map((p) => extractAllText(p.children)).join(\"\\n\\n\");\n            if (subTitle || subText) {\n                notes.push({ title: subTitle, text: subText });\n            }\n        }\n        return notes;\n    }\n    const titleNode = findChild(note.children, \"title\");\n    const title = titleNode ? extractAllText(titleNode.children) : \"\";\n    const paragraphs = findChildren(note.children, \"p\");\n    const text = paragraphs.map((p) => extractAllText(p.children)).join(\"\\n\\n\");\n    if (title || text) {\n        notes.push({ title, text });\n    }\n    return notes;\n}\n/** Parse notes from <notes> elements (author contributions, funding, etc.). */\nfunction parseNotes(backChildren) {\n    const notesElements = findChildren(backChildren, \"notes\");\n    if (notesElements.length === 0)\n        return undefined;\n    const notes = [];\n    for (const note of notesElements) {\n        notes.push(...parseSingleNotesElement(note));\n    }\n    return notes.length > 0 ? notes : undefined;\n}\n/** Parse glossary elements into BackMatterNote entries. */\nfunction parseGlossary(backChildren) {\n    const glossaryElements = findChildren(backChildren, \"glossary\");\n    const notes = [];\n    for (const glossary of glossaryElements) {\n        const titleNode = findChild(glossary.children, \"title\");\n        const title = titleNode ? extractAllText(titleNode.children) : \"Glossary\";\n        const defList = findChild(glossary.children, \"def-list\");\n        if (!defList)\n            continue;\n        const defItems = findChildren(defList.children, \"def-item\");\n        const lines = [];\n        for (const item of defItems) {\n            const termNode = findChild(item.children, \"term\");\n            const defNode = findChild(item.children, \"def\");\n            const term = termNode ? extractAllText(termNode.children) : \"\";\n            const definition = defNode ? extractAllText(defNode.children) : \"\";\n            lines.push(`${term}: ${definition}`);\n        }\n        notes.push({ title, text: lines.join(\"\\n\") });\n    }\n    return notes;\n}\n/** Parse <floats-group> into block elements. */\nfunction parseFloatsGroup(articleChildren) {\n    const floatsGroup = findChild(articleChildren, \"floats-group\");\n    if (!floatsGroup)\n        return undefined;\n    const blocks = [];\n    for (const child of floatsGroup.children) {\n        const tag = getTagName(child);\n        if (tag === \"fig\") {\n            blocks.push(parseFigBlock(child));\n        }\n        else if (tag === \"table-wrap\") {\n            blocks.push(parseTableBlock(child));\n        }\n    }\n    return blocks.length > 0 ? blocks : undefined;\n}\n/**\n * Parse JATS XML back matter sections (ack, app-group, fn-group)\n * and top-level floats-group.\n */\nexport function parseJatsBackMatter(xml) {\n    const parsed = parser.parse(xml);\n    const article = findArticle(parsed);\n    if (!article)\n        return {};\n    const result = {};\n    // Parse <back> children\n    const back = findChild(article.children, \"back\");\n    if (back) {\n        const ack = parseAcknowledgments(back.children);\n        if (ack)\n            result.acknowledgments = ack;\n        const app = parseAppendices(back.children);\n        if (app)\n            result.appendices = app;\n        const fn = parseFootnotes(back.children);\n        if (fn)\n            result.footnotes = fn;\n        const notes = parseNotes(back.children);\n        const glossaryNotes = parseGlossary(back.children);\n        if (notes || glossaryNotes.length > 0) {\n            result.notes = [...(notes ?? []), ...glossaryNotes];\n        }\n    }\n    // Floats-group: <floats-group> (sibling of <body> and <back>)\n    const floats = parseFloatsGroup(article.children);\n    if (floats)\n        result.floats = floats;\n    return result;\n}\n//# sourceMappingURL=jats-parser.js.map","/**\n * Markdown writer for JATS XML conversion.\n *\n * Converts the intermediate JatsDocument representation to Markdown text.\n */\n/**\n * Format an author's name in abbreviated form (e.g., \"Smith J\").\n */\nfunction formatAuthor(author) {\n    if (!author.givenNames)\n        return author.surname;\n    const initials = author.givenNames\n        .split(/[\\s.]+/)\n        .filter(Boolean)\n        .map((n) => n[0])\n        .join(\"\");\n    return `${author.surname} ${initials}`;\n}\n/**\n * Render inline content to Markdown string.\n */\nfunction renderInline(content) {\n    return content\n        .map((node) => {\n        switch (node.type) {\n            case \"text\":\n                return node.text;\n            case \"bold\":\n                return `**${renderInline(node.children)}**`;\n            case \"italic\":\n                return `*${renderInline(node.children)}*`;\n            case \"superscript\":\n                return `^${node.text}^`;\n            case \"subscript\":\n                return `~${node.text}~`;\n            case \"citation\":\n                return node.text;\n            case \"code\":\n                return `\\`${node.text}\\``;\n            case \"inline-formula\":\n                return node.tex ? `$${node.tex}$` : node.text;\n            case \"link\": {\n                const linkText = renderInline(node.children);\n                if (linkText === node.url)\n                    return node.url;\n                return `[${linkText}](${node.url})`;\n            }\n        }\n    })\n        .join(\"\");\n}\n/**\n * Render a table block to Markdown.\n */\nfunction renderTable(block) {\n    const lines = [];\n    if (block.caption) {\n        lines.push(`*${block.caption}*`);\n        lines.push(\"\");\n    }\n    if (block.headers.length > 0) {\n        lines.push(`| ${block.headers.join(\" | \")} |`);\n        lines.push(`| ${block.headers.map(() => \"---\").join(\" | \")} |`);\n    }\n    else if (block.rows.length > 0) {\n        const colCount = block.rows[0]?.length ?? 0;\n        lines.push(`| ${Array.from({ length: colCount }, () => \"\").join(\" | \")} |`);\n        lines.push(`| ${Array.from({ length: colCount }, () => \"---\").join(\" | \")} |`);\n    }\n    for (const row of block.rows) {\n        lines.push(`| ${row.join(\" | \")} |`);\n    }\n    return lines.join(\"\\n\");\n}\n/**\n * Render a formula block to Markdown.\n */\nfunction renderFormula(block) {\n    const lines = [];\n    if (block.tex) {\n        lines.push(`$$${block.tex}$$`);\n    }\n    else if (block.text) {\n        lines.push(\"```\");\n        lines.push(block.text);\n        lines.push(\"```\");\n    }\n    if (block.label) {\n        lines.push(block.label);\n    }\n    return lines.join(\"\\n\");\n}\n/**\n * Render a definition list block to Markdown.\n */\nfunction renderDefList(block) {\n    const lines = [];\n    if (block.title) {\n        lines.push(`**${block.title}**`);\n        lines.push(\"\");\n    }\n    for (const item of block.items) {\n        lines.push(`**${item.term}**: ${item.definition}`);\n    }\n    return lines.join(\"\\n\");\n}\n/**\n * Render a boxed-text block to Markdown.\n */\nfunction renderBoxedText(block) {\n    const lines = [];\n    if (block.title) {\n        lines.push(`> **${block.title}**`);\n        lines.push(\">\");\n    }\n    for (const inner of block.content) {\n        const rendered = renderBlock(inner);\n        for (const line of rendered.split(\"\\n\")) {\n            lines.push(line === \"\" ? \">\" : `> ${line}`);\n        }\n    }\n    return lines.join(\"\\n\");\n}\n/**\n * Render a block element to Markdown lines.\n */\nfunction renderBlock(block) {\n    switch (block.type) {\n        case \"paragraph\":\n            return renderInline(block.content);\n        case \"blockquote\": {\n            const text = renderInline(block.content);\n            return text\n                .split(\"\\n\")\n                .map((line) => (line === \"\" ? \">\" : `> ${line}`))\n                .join(\"\\n\");\n        }\n        case \"list\": {\n            return block.items\n                .map((item, i) => {\n                const prefix = block.ordered ? `${i + 1}. ` : \"- \";\n                return `${prefix}${renderInline(item)}`;\n            })\n                .join(\"\\n\");\n        }\n        case \"table\":\n            return renderTable(block);\n        case \"figure\": {\n            const label = block.label ?? \"Figure\";\n            const altText = block.caption ? `${label}. ${block.caption}` : label;\n            return `![${altText}]()`;\n        }\n        case \"preformat\":\n            return `\\`\\`\\`\\n${block.text}\\n\\`\\`\\``;\n        case \"formula\":\n            return renderFormula(block);\n        case \"def-list\":\n            return renderDefList(block);\n        case \"boxed-text\":\n            return renderBoxedText(block);\n    }\n}\n/**\n * Render a section and its subsections to Markdown.\n */\nfunction renderSection(section) {\n    const lines = [];\n    const heading = \"#\".repeat(section.level);\n    if (section.title.trim()) {\n        lines.push(`${heading} ${section.title}`);\n        lines.push(\"\");\n    }\n    for (const block of section.content) {\n        lines.push(renderBlock(block));\n        lines.push(\"\");\n    }\n    for (const sub of section.subsections) {\n        lines.push(renderSection(sub));\n    }\n    return lines.join(\"\\n\");\n}\n/**\n * Render references section.\n */\nfunction formatRefPubIds(ref) {\n    const links = [];\n    if (ref.doi) {\n        links.push(`[doi:${ref.doi}](https://doi.org/${ref.doi})`);\n    }\n    if (ref.pmid) {\n        links.push(`[pmid:${ref.pmid}](https://pubmed.ncbi.nlm.nih.gov/${ref.pmid}/)`);\n    }\n    if (ref.pmcid) {\n        links.push(`[pmcid:PMC${ref.pmcid}](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC${ref.pmcid}/)`);\n    }\n    return links.join(\" \");\n}\nfunction renderReferences(references) {\n    if (references.length === 0)\n        return \"\";\n    const lines = [\"## References\", \"\"];\n    references.forEach((ref, i) => {\n        const pubIdLinks = formatRefPubIds(ref);\n        const line = pubIdLinks ? `${i + 1}. ${ref.text} ${pubIdLinks}` : `${i + 1}. ${ref.text}`;\n        lines.push(line);\n    });\n    lines.push(\"\");\n    return lines.join(\"\\n\");\n}\n/**\n * Render footnotes section.\n */\nfunction renderFootnotes(footnotes) {\n    if (footnotes.length === 0)\n        return \"\";\n    const lines = [\"## Footnotes\", \"\"];\n    footnotes.forEach((fn, i) => {\n        lines.push(`${i + 1}. ${fn.text}`);\n    });\n    lines.push(\"\");\n    return lines.join(\"\\n\");\n}\n/**\n * Render floats (figures and tables) section.\n */\nfunction renderFloats(floats) {\n    if (floats.length === 0)\n        return \"\";\n    const lines = [\"## Figures and Tables\", \"\"];\n    for (const block of floats) {\n        lines.push(renderBlock(block));\n        lines.push(\"\");\n    }\n    return lines.join(\"\\n\");\n}\n/**\n * Format a publication date as a string (e.g., \"2024\", \"2024-01\", \"2024-01-15\").\n */\nfunction formatPublicationDate(date) {\n    let dateStr = date.year;\n    if (date.month) {\n        dateStr += `-${date.month.padStart(2, \"0\")}`;\n        if (date.day)\n            dateStr += `-${date.day.padStart(2, \"0\")}`;\n    }\n    return dateStr;\n}\n/**\n * Format a citation string from volume, issue, and pages.\n */\nfunction formatCitation(meta) {\n    if (meta.volume && meta.issue) {\n        let citation = `Vol. ${meta.volume}(${meta.issue})`;\n        if (meta.pages)\n            citation += `, pp. ${meta.pages}`;\n        return citation;\n    }\n    const parts = [];\n    if (meta.volume)\n        parts.push(`Vol. ${meta.volume}`);\n    if (meta.issue)\n        parts.push(`(${meta.issue})`);\n    if (meta.pages)\n        parts.push(`pp. ${meta.pages}`);\n    return parts.join(\", \");\n}\n/**\n * Render document metadata (authors, DOI, journal, etc.) to Markdown lines.\n */\nfunction renderMetadata(doc) {\n    const lines = [];\n    const meta = doc.metadata;\n    // Title\n    lines.push(`# ${meta.title}`);\n    lines.push(\"\");\n    // Track position after title to detect if any metadata fields were added\n    const posAfterTitle = lines.length;\n    // Authors\n    if (meta.authors.length > 0) {\n        const authorStr = meta.authors.map(formatAuthor).join(\", \");\n        lines.push(`**Authors**: ${authorStr}`);\n    }\n    if (meta.doi)\n        lines.push(`**DOI**: ${meta.doi}`);\n    if (meta.pmcid)\n        lines.push(`**PMC**: PMC${meta.pmcid}`);\n    if (meta.pmid)\n        lines.push(`**PMID**: ${meta.pmid}`);\n    if (meta.journal)\n        lines.push(`**Journal**: ${meta.journal}`);\n    if (meta.publicationDate) {\n        lines.push(`**Published**: ${formatPublicationDate(meta.publicationDate)}`);\n    }\n    if (meta.volume || meta.issue || meta.pages) {\n        lines.push(`**Citation**: ${formatCitation(meta)}`);\n    }\n    if (meta.articleType)\n        lines.push(`**Article Type**: ${meta.articleType}`);\n    if (meta.keywords && meta.keywords.length > 0) {\n        lines.push(`**Keywords**: ${meta.keywords.join(\", \")}`);\n    }\n    if (meta.license)\n        lines.push(`**License**: ${meta.license}`);\n    if (lines.length > posAfterTitle) {\n        lines.push(\"\");\n    }\n    // Abstract\n    if (meta.abstract) {\n        lines.push(\"## Abstract\");\n        lines.push(\"\");\n        lines.push(meta.abstract);\n        lines.push(\"\");\n    }\n    return lines;\n}\n/**\n * Render trailing sections (acknowledgments, notes, references, appendices,\n * footnotes, floats) to Markdown lines.\n */\nfunction renderTrailingSections(doc) {\n    const lines = [];\n    // Acknowledgments (before References)\n    if (doc.acknowledgments) {\n        lines.push(\"## Acknowledgments\");\n        lines.push(\"\");\n        lines.push(doc.acknowledgments);\n        lines.push(\"\");\n    }\n    // Notes (between Acknowledgments and References)\n    if (doc.notes && doc.notes.length > 0) {\n        for (const note of doc.notes) {\n            lines.push(`## ${note.title}`);\n            lines.push(\"\");\n            lines.push(note.text);\n            lines.push(\"\");\n        }\n    }\n    // References\n    if (doc.references.length > 0) {\n        lines.push(renderReferences(doc.references));\n    }\n    // Appendices (after References)\n    if (doc.appendices && doc.appendices.length > 0) {\n        for (const appendix of doc.appendices) {\n            lines.push(renderSection(appendix));\n        }\n    }\n    // Footnotes\n    if (doc.footnotes && doc.footnotes.length > 0) {\n        lines.push(renderFootnotes(doc.footnotes));\n    }\n    // Floats (Figures and Tables from floats-group)\n    if (doc.floats && doc.floats.length > 0) {\n        lines.push(renderFloats(doc.floats));\n    }\n    return lines;\n}\n/**\n * Convert a parsed JATS document to Markdown string.\n */\nexport function writeMarkdown(doc) {\n    const lines = [];\n    lines.push(...renderMetadata(doc));\n    // Sections\n    for (const section of doc.sections) {\n        lines.push(renderSection(section));\n    }\n    lines.push(...renderTrailingSections(doc));\n    return `${lines.join(\"\\n\").trimEnd()}\\n`;\n}\n//# sourceMappingURL=markdown-writer.js.map","/**\n * Conversion orchestrator for PMC XML to Markdown.\n *\n * Ties together the JATS parser and Markdown writer with file I/O.\n */\nimport { readFile, stat, writeFile } from \"node:fs/promises\";\nimport { parseJatsBackMatter, parseJatsBody, parseJatsMetadata, parseJatsReferences, } from \"./jats-parser.js\";\nimport { writeMarkdown } from \"./markdown-writer.js\";\n/**\n * Convert a PMC JATS XML file to Markdown.\n *\n * Reads the XML, parses it into a JatsDocument, writes Markdown,\n * and optionally updates meta.json.\n */\nexport async function convertPmcXmlToMarkdown(xmlPath, mdPath, metaPath) {\n    try {\n        const xml = await readFile(xmlPath, \"utf-8\");\n        // Parse\n        const metadata = parseJatsMetadata(xml);\n        const sections = parseJatsBody(xml);\n        const references = parseJatsReferences(xml);\n        const backMatter = parseJatsBackMatter(xml);\n        const doc = { metadata, sections, references };\n        if (backMatter.acknowledgments)\n            doc.acknowledgments = backMatter.acknowledgments;\n        if (backMatter.appendices)\n            doc.appendices = backMatter.appendices;\n        if (backMatter.footnotes)\n            doc.footnotes = backMatter.footnotes;\n        if (backMatter.floats)\n            doc.floats = backMatter.floats;\n        if (backMatter.notes)\n            doc.notes = backMatter.notes;\n        // Write Markdown\n        const md = writeMarkdown(doc);\n        await writeFile(mdPath, md, \"utf-8\");\n        // Update meta.json if path provided and file exists\n        if (metaPath) {\n            try {\n                await stat(metaPath);\n                const metaRaw = await readFile(metaPath, \"utf-8\");\n                const meta = JSON.parse(metaRaw);\n                const mdStat = await stat(mdPath);\n                meta.files.markdown = {\n                    filename: \"fulltext.md\",\n                    source: \"conversion\",\n                    retrievedAt: new Date().toISOString(),\n                    size: mdStat.size,\n                    convertedFrom: \"fulltext.xml\",\n                };\n                await writeFile(metaPath, `${JSON.stringify(meta, null, 2)}\\n`, \"utf-8\");\n            }\n            catch {\n                // meta.json doesn't exist or can't be read, skip update\n            }\n        }\n        const result = { success: true };\n        result.title = metadata.title;\n        result.sections = sections.length;\n        result.references = references.length;\n        return result;\n    }\n    catch (err) {\n        const result = { success: false };\n        result.error = err instanceof Error ? err.message : String(err);\n        return result;\n    }\n}\n//# sourceMappingURL=index.js.map","/**\n * Fulltext OA discovery operation.\n *\n * Discovers open access availability for a reference by checking\n * multiple sources (Unpaywall, PMC, arXiv, CORE).\n */\n\nimport {\n  type DiscoveryArticle,\n  type DiscoveryConfig,\n  type OALocation,\n  type OAStatus,\n  discoverOA,\n} from \"@ncukondo/academic-fulltext\";\nimport type { FulltextConfig } from \"../../../config/schema.js\";\nimport type { IdentifierType } from \"../../../core/library-interface.js\";\nimport type { ILibrary } from \"../../../core/library-interface.js\";\n\nexport interface FulltextDiscoverOptions {\n  /** Reference identifier (id or uuid) */\n  identifier: string;\n  /** Identifier type: 'id' (default), 'uuid', 'doi', 'pmid', or 'isbn' */\n  idType?: IdentifierType | undefined;\n  /** Fulltext configuration */\n  fulltextConfig: FulltextConfig;\n}\n\nexport interface FulltextDiscoverResult {\n  success: boolean;\n  error?: string;\n  /** The reference ID used for display */\n  referenceId?: string;\n  /** OA status */\n  oaStatus?: OAStatus;\n  /** Discovered OA locations */\n  locations?: OALocation[];\n  /** Source-level errors (non-fatal) */\n  errors?: Array<{ source: string; error: string }>;\n}\n\nexport async function fulltextDiscover(\n  library: ILibrary,\n  options: FulltextDiscoverOptions\n): Promise<FulltextDiscoverResult> {\n  const { identifier, idType = \"id\", fulltextConfig } = options;\n\n  // Resolve reference\n  const item = await library.find(identifier, { idType });\n  if (!item) {\n    return { success: false, error: `Reference '${identifier}' not found` };\n  }\n\n  // Extract identifiers\n  const doi = item.DOI;\n  const pmid = item.PMID;\n  const pmcid = item.PMCID;\n\n  if (!doi && !pmid) {\n    return {\n      success: false,\n      error: `No DOI or PMID found for ${identifier}. Cannot discover OA sources.`,\n    };\n  }\n\n  // Build article object for discovery\n  const article: DiscoveryArticle = {};\n  if (doi) article.doi = doi;\n  if (pmid) article.pmid = pmid;\n  if (pmcid) article.pmcid = pmcid;\n\n  // Build discovery config\n  const config: DiscoveryConfig = {\n    unpaywallEmail: fulltextConfig.sources.unpaywallEmail ?? \"\",\n    coreApiKey: fulltextConfig.sources.coreApiKey ?? \"\",\n    preferSources: fulltextConfig.preferSources,\n  };\n\n  const result = await discoverOA(article, config);\n\n  const discoverResult: FulltextDiscoverResult = {\n    success: true,\n    referenceId: item.id,\n    oaStatus: result.oaStatus,\n    locations: result.locations,\n  };\n  if (result.errors.length > 0) {\n    discoverResult.errors = result.errors;\n  }\n  return discoverResult;\n}\n","/**\n * Fulltext fetch operation.\n *\n * Discovers OA sources, downloads full-text files (PDF, PMC XML),\n * converts XML to Markdown, and attaches them to references.\n */\n\nimport { mkdtemp, rm } from \"node:fs/promises\";\nimport { tmpdir } from \"node:os\";\nimport { join } from \"node:path\";\nimport {\n  type DiscoveryArticle,\n  type DiscoveryConfig,\n  type OALocation,\n  convertPmcXmlToMarkdown,\n  discoverOA,\n  downloadPdf,\n  downloadPmcXml,\n} from \"@ncukondo/academic-fulltext\";\nimport type { FulltextConfig, FulltextSource } from \"../../../config/schema.js\";\nimport type { CslItem } from \"../../../core/csl-json/types.js\";\nimport type { ILibrary, IdentifierType } from \"../../../core/library-interface.js\";\nimport { fulltextAttach } from \"./attach.js\";\nimport { fulltextGet } from \"./get.js\";\n\nexport interface FulltextFetchOptions {\n  /** Reference identifier (id or uuid) */\n  identifier: string;\n  /** Identifier type: 'id' (default), 'uuid', 'doi', 'pmid', or 'isbn' */\n  idType?: IdentifierType | undefined;\n  /** Fulltext configuration */\n  fulltextConfig: FulltextConfig;\n  /** Directory for fulltext attachments */\n  fulltextDirectory: string;\n  /** Preferred source to fetch from */\n  source?: FulltextSource | undefined;\n  /** Force overwrite existing fulltext */\n  force?: boolean | undefined;\n}\n\nexport interface FulltextFetchResult {\n  success: boolean;\n  error?: string;\n  /** The reference ID used for display */\n  referenceId?: string;\n  /** Which source was used */\n  source?: string;\n  /** Which file types were attached */\n  attachedFiles?: string[];\n}\n\ninterface AttachContext {\n  library: ILibrary;\n  identifier: string;\n  idType: IdentifierType;\n  fulltextDirectory: string;\n  force: boolean;\n}\n\nfunction buildDiscoveryArticle(item: CslItem): DiscoveryArticle {\n  const article: DiscoveryArticle = {};\n  if (item.DOI) article.doi = item.DOI;\n  if (item.PMID) article.pmid = item.PMID;\n  if (item.PMCID) article.pmcid = item.PMCID;\n  return article;\n}\n\nfunction buildDiscoveryConfig(fulltextConfig: FulltextConfig): DiscoveryConfig {\n  return {\n    unpaywallEmail: fulltextConfig.sources.unpaywallEmail ?? \"\",\n    coreApiKey: fulltextConfig.sources.coreApiKey ?? \"\",\n    preferSources: fulltextConfig.preferSources,\n  };\n}\n\nasync function tryDownloadPdf(\n  locations: OALocation[],\n  tempDir: string,\n  ctx: AttachContext\n): Promise<{ attached: boolean; source: string }> {\n  const pdfLocation = locations.find((loc) => loc.urlType === \"pdf\");\n  if (!pdfLocation) return { attached: false, source: \"\" };\n\n  const pdfPath = join(tempDir, \"fulltext.pdf\");\n  const pdfResult = await downloadPdf(pdfLocation.url, pdfPath);\n  if (!pdfResult.success) return { attached: false, source: pdfLocation.source };\n\n  const attachResult = await fulltextAttach(ctx.library, {\n    identifier: ctx.identifier,\n    idType: ctx.idType,\n    filePath: pdfPath,\n    type: \"pdf\",\n    force: ctx.force,\n    move: true,\n    fulltextDirectory: ctx.fulltextDirectory,\n  });\n\n  return { attached: attachResult.success, source: pdfLocation.source };\n}\n\nasync function tryDownloadPmcXmlAndConvert(\n  pmcid: string,\n  tempDir: string,\n  ctx: AttachContext\n): Promise<boolean> {\n  const xmlPath = join(tempDir, \"fulltext.xml\");\n  const xmlResult = await downloadPmcXml(pmcid, xmlPath);\n  if (!xmlResult.success) return false;\n\n  const mdPath = join(tempDir, \"fulltext.md\");\n  const convertResult = await convertPmcXmlToMarkdown(xmlPath, mdPath);\n  if (!convertResult.success) return false;\n\n  const attachResult = await fulltextAttach(ctx.library, {\n    identifier: ctx.identifier,\n    idType: ctx.idType,\n    filePath: mdPath,\n    type: \"markdown\",\n    force: ctx.force,\n    move: true,\n    fulltextDirectory: ctx.fulltextDirectory,\n  });\n\n  return attachResult.success;\n}\n\nasync function checkExistingFulltext(\n  library: ILibrary,\n  identifier: string,\n  idType: IdentifierType,\n  fulltextDirectory: string\n): Promise<boolean> {\n  const existing = await fulltextGet(library, { identifier, idType, fulltextDirectory });\n  return existing.success && existing.paths !== undefined;\n}\n\nexport async function fulltextFetch(\n  library: ILibrary,\n  options: FulltextFetchOptions\n): Promise<FulltextFetchResult> {\n  const { identifier, idType = \"id\", fulltextConfig, fulltextDirectory, source, force } = options;\n\n  const item = await library.find(identifier, { idType });\n  if (!item) {\n    return { success: false, error: `Reference '${identifier}' not found` };\n  }\n\n  if (!item.DOI && !item.PMID) {\n    return {\n      success: false,\n      error: `No DOI or PMID found for ${identifier}. Cannot discover OA sources.`,\n    };\n  }\n\n  if (!force && (await checkExistingFulltext(library, identifier, idType, fulltextDirectory))) {\n    return {\n      success: false,\n      error: `Fulltext already attached to ${identifier}. Use --force to overwrite.`,\n    };\n  }\n\n  const discovery = await discoverOA(\n    buildDiscoveryArticle(item),\n    buildDiscoveryConfig(fulltextConfig)\n  );\n\n  let locations = discovery.locations;\n  if (source) {\n    locations = locations.filter((loc) => loc.source === source);\n  }\n\n  if (locations.length === 0) {\n    return { success: false, error: `No OA sources found for ${identifier}` };\n  }\n\n  const tempDir = await mkdtemp(join(tmpdir(), \"ref-fulltext-\"));\n  const ctx: AttachContext = {\n    library,\n    identifier,\n    idType,\n    fulltextDirectory,\n    force: force ?? false,\n  };\n\n  try {\n    return await downloadAndAttach(locations, item.PMCID, tempDir, ctx, item.id, identifier);\n  } finally {\n    await rm(tempDir, { recursive: true, force: true }).catch(() => {});\n  }\n}\n\nasync function downloadAndAttach(\n  locations: OALocation[],\n  pmcid: string | undefined,\n  tempDir: string,\n  ctx: AttachContext,\n  referenceId: string,\n  identifier: string\n): Promise<FulltextFetchResult> {\n  const attachedFiles: string[] = [];\n  let usedSource = \"\";\n\n  const pdfResult = await tryDownloadPdf(locations, tempDir, ctx);\n  if (pdfResult.attached) {\n    attachedFiles.push(\"pdf\");\n    usedSource = pdfResult.source;\n  }\n\n  if (pmcid) {\n    const mdAttached = await tryDownloadPmcXmlAndConvert(pmcid, tempDir, ctx);\n    if (mdAttached) {\n      attachedFiles.push(\"markdown\");\n      if (!usedSource) usedSource = \"pmc\";\n    }\n  }\n\n  if (attachedFiles.length === 0) {\n    const pdfLocation = locations.find((loc) => loc.urlType === \"pdf\");\n    if (pdfLocation) {\n      return {\n        success: false,\n        error: `Failed to download from ${pdfLocation.source}: download failed`,\n      };\n    }\n    return { success: false, error: `Failed to download fulltext for ${identifier}` };\n  }\n\n  return {\n    success: true,\n    referenceId,\n    source: usedSource,\n    attachedFiles,\n  };\n}\n","/**\n * Fulltext convert operation.\n *\n * Converts an attached PMC JATS XML file to Markdown.\n */\n\nimport { access } from \"node:fs/promises\";\nimport { join } from \"node:path\";\nimport { convertPmcXmlToMarkdown } from \"@ncukondo/academic-fulltext\";\nimport type { CslItem } from \"../../../core/csl-json/types.js\";\nimport type { ILibrary, IdentifierType } from \"../../../core/library-interface.js\";\nimport type { Attachments } from \"../../attachments/types.js\";\nimport { fulltextAttach } from \"./attach.js\";\n\nexport interface FulltextConvertOptions {\n  /** Reference identifier (id or uuid) */\n  identifier: string;\n  /** Identifier type: 'id' (default), 'uuid', 'doi', 'pmid', or 'isbn' */\n  idType?: IdentifierType | undefined;\n  /** Directory for fulltext attachments */\n  fulltextDirectory: string;\n}\n\nexport interface FulltextConvertResult {\n  success: boolean;\n  error?: string;\n  /** The converted markdown filename */\n  filename?: string;\n}\n\nfunction findXmlFile(item: CslItem): string | undefined {\n  const attachments = item.custom?.attachments as Attachments | undefined;\n  if (!attachments?.files) return undefined;\n\n  const xmlFile = attachments.files.find(\n    (f) => f.role === \"fulltext\" && f.filename.endsWith(\".xml\")\n  );\n  return xmlFile?.filename;\n}\n\nfunction getXmlPath(item: CslItem, xmlFilename: string, fulltextDirectory: string): string {\n  const attachments = item.custom?.attachments as Attachments | undefined;\n  const directory = attachments?.directory ?? \"\";\n  return join(fulltextDirectory, directory, xmlFilename);\n}\n\nexport async function fulltextConvert(\n  library: ILibrary,\n  options: FulltextConvertOptions\n): Promise<FulltextConvertResult> {\n  const { identifier, idType = \"id\", fulltextDirectory } = options;\n\n  const item = await library.find(identifier, { idType });\n  if (!item) {\n    return { success: false, error: `Reference '${identifier}' not found` };\n  }\n\n  const xmlFilename = findXmlFile(item as CslItem);\n  if (!xmlFilename) {\n    return { success: false, error: `No PMC XML file attached to '${identifier}'` };\n  }\n\n  const xmlPath = getXmlPath(item as CslItem, xmlFilename, fulltextDirectory);\n\n  // Verify file exists on disk\n  try {\n    await access(xmlPath);\n  } catch {\n    return { success: false, error: `XML file not found on disk: ${xmlPath}` };\n  }\n\n  // Convert to temp file then attach\n  const mdPath = xmlPath.replace(/\\.xml$/, \".md\");\n  const convertResult = await convertPmcXmlToMarkdown(xmlPath, mdPath);\n  if (!convertResult.success) {\n    return {\n      success: false,\n      error: `Failed to convert PMC XML to Markdown: ${convertResult.error ?? \"unknown error\"}`,\n    };\n  }\n\n  const attachResult = await fulltextAttach(library, {\n    identifier,\n    idType,\n    filePath: mdPath,\n    type: \"markdown\",\n    force: true,\n    move: true,\n    fulltextDirectory,\n  });\n\n  if (!attachResult.success) {\n    return { success: false, error: attachResult.error ?? \"Attach failed\" };\n  }\n\n  return {\n    success: true,\n    filename: attachResult.filename ?? \"fulltext.md\",\n  };\n}\n","import type { CslItem } from \"../../core/csl-json/types.js\";\n\n/**\n * Extract first author name with initial\n * Returns \"Family G\" or \"Family\" if no given name\n */\nfunction formatFirstAuthor(item: CslItem): string {\n  if (!item.author || item.author.length === 0) {\n    return \"Unknown\";\n  }\n\n  const firstAuthor = item.author[0];\n  if (!firstAuthor) {\n    return \"Unknown\";\n  }\n\n  const family = firstAuthor.family || \"Unknown\";\n  const givenInitial = firstAuthor.given ? firstAuthor.given[0] : \"\";\n\n  if (givenInitial) {\n    return `${family} ${givenInitial}`;\n  }\n  return family;\n}\n\n/**\n * Check if item has multiple authors\n */\nfunction hasMultipleAuthors(item: CslItem): boolean {\n  return (item.author?.length || 0) > 1;\n}\n\n/**\n * Extract year from CSL-JSON issued field\n */\nfunction extractYear(item: CslItem): string {\n  if (item.issued?.[\"date-parts\"]?.[0]?.[0]) {\n    return String(item.issued[\"date-parts\"][0][0]);\n  }\n  return \"n.d.\";\n}\n\n/**\n * Get journal abbreviation (prefer short title)\n */\nfunction getJournalAbbrev(item: CslItem): string {\n  const containerTitleShort = (item as Record<string, unknown>)[\"container-title-short\"];\n  if (typeof containerTitleShort === \"string\") {\n    return containerTitleShort;\n  }\n  return item[\"container-title\"] || \"\";\n}\n\n/**\n * Format volume/issue/pages section\n * Returns formats like: \"10(2):123-145\", \"10:123-145\", \"10(2)\", \"10\", or \"\"\n */\nfunction formatVolumeIssuePage(item: CslItem): string {\n  const volume = item.volume;\n  const issue = item.issue;\n  const page = item.page;\n\n  if (!volume && !issue && !page) {\n    return \"\";\n  }\n\n  let result = \"\";\n\n  if (volume) {\n    result += volume;\n    if (issue) {\n      result += `(${issue})`;\n    }\n    if (page) {\n      result += `:${page}`;\n    }\n  } else if (page) {\n    result += page;\n  }\n\n  return result;\n}\n\n/**\n * Get identifier (PMID > DOI > URL priority)\n */\nfunction getIdentifier(item: CslItem): string {\n  if (item.PMID) {\n    return `PMID:${item.PMID}`;\n  }\n  if (item.DOI) {\n    return `DOI:${item.DOI}`;\n  }\n  if (item.URL) {\n    return item.URL;\n  }\n  return \"\";\n}\n\n/**\n * Format a single bibliography entry\n */\nfunction formatBibliographyEntry(item: CslItem): string {\n  const parts: string[] = [];\n\n  // Author\n  const author = formatFirstAuthor(item);\n  const etAl = hasMultipleAuthors(item) ? \" et al\" : \"\";\n  parts.push(`${author}${etAl}.`);\n\n  // Journal\n  const journal = getJournalAbbrev(item);\n  if (journal) {\n    parts.push(`${journal}.`);\n  }\n\n  // Year and volume/issue/pages\n  const year = extractYear(item);\n  const volumeIssuePage = formatVolumeIssuePage(item);\n\n  if (volumeIssuePage) {\n    parts.push(`${year};${volumeIssuePage}.`);\n  } else {\n    parts.push(`${year}.`);\n  }\n\n  // Identifier\n  const identifier = getIdentifier(item);\n  if (identifier) {\n    parts.push(`${identifier}.`);\n  }\n\n  // Title\n  if (item.title) {\n    parts.push(`${item.title}.`);\n  }\n\n  return parts.join(\" \");\n}\n\n/**\n * Get first author family name only (for in-text citations)\n */\nfunction getFirstAuthorFamilyName(item: CslItem): string {\n  if (!item.author || item.author.length === 0) {\n    return \"Unknown\";\n  }\n\n  const firstAuthor = item.author[0];\n  if (!firstAuthor) {\n    return \"Unknown\";\n  }\n\n  return firstAuthor.family || \"Unknown\";\n}\n\n/**\n * Format a single in-text citation (without parentheses)\n * Returns \"Family et al, YYYY\" or \"Family, YYYY\"\n */\nfunction formatInTextEntry(item: CslItem): string {\n  const author = getFirstAuthorFamilyName(item);\n  const etAl = hasMultipleAuthors(item) ? \" et al\" : \"\";\n  const year = extractYear(item);\n\n  return `${author}${etAl}, ${year}`;\n}\n\n/**\n * Format CSL-JSON items as simplified AMA-like bibliography entries.\n *\n * Format: FirstAuthor [et al]. JournalAbbrev. YYYY;volume(issue):pages. PMID:xxxxx [or DOI:xxxxx]. Title.\n *\n * Multiple items are separated by double newlines.\n *\n * @param items - Array of CSL-JSON items\n * @returns Formatted bibliography entries separated by double newlines\n */\nexport function formatBibliography(items: CslItem[]): string {\n  if (items.length === 0) {\n    return \"\";\n  }\n\n  return items.map(formatBibliographyEntry).join(\"\\n\\n\");\n}\n\n/**\n * Format CSL-JSON items as simplified in-text citations.\n *\n * Format: (FirstAuthor et al, YYYY)\n *\n * Multiple items are separated by semicolons and enclosed in parentheses.\n *\n * @param items - Array of CSL-JSON items\n * @returns Formatted in-text citation(s) enclosed in parentheses\n */\nexport function formatInText(items: CslItem[]): string {\n  if (items.length === 0) {\n    return \"\";\n  }\n\n  const citations = items.map(formatInTextEntry).join(\"; \");\n  return `(${citations})`;\n}\n","import { Cite, plugins } from \"@citation-js/core\";\nimport \"@citation-js/plugin-csl\";\nimport type { CslItem } from \"../../core/csl-json/types.js\";\nimport { formatBibliography, formatInText } from \"./citation-fallback.js\";\n\n/**\n * Options for CSL citation formatting\n */\nexport type CitationFormatOptions = {\n  /**\n   * CSL style name (e.g., 'apa', 'vancouver', 'chicago')\n   * @default 'apa'\n   */\n  style?: string;\n\n  /**\n   * Custom CSL style XML content.\n   * When provided, this XML is registered and used instead of built-in styles.\n   */\n  styleXml?: string;\n\n  /**\n   * Output format: text, html, or rtf\n   * @default 'text'\n   */\n  format?: \"text\" | \"html\" | \"rtf\";\n\n  /**\n   * Locale code (e.g., 'en-US', 'en-GB')\n   * @default 'en-US'\n   */\n  locale?: string;\n};\n\n/**\n * Register a custom CSL style with citation-js.\n * Returns the style name to use for formatting.\n * @throws Error if CSL XML is invalid or malformed\n */\nfunction registerCustomStyle(styleName: string, styleXml: string): string {\n  // Basic XML validation\n  if (!styleXml.includes(\"<style\") || !styleXml.includes(\"</style>\")) {\n    throw new Error(\n      \"Invalid CSL file: Missing <style> element. The file may be malformed or not a valid CSL style.\"\n    );\n  }\n\n  // Check for required CSL sections\n  const hasCitation = styleXml.includes(\"<citation\") || styleXml.includes(\"<citation>\");\n  const hasBibliography = styleXml.includes(\"<bibliography\") || styleXml.includes(\"<bibliography>\");\n  if (!hasCitation && !hasBibliography) {\n    throw new Error(\n      \"Invalid CSL file: Missing <citation> or <bibliography> section. \" +\n        \"A valid CSL style must define at least one of these sections.\"\n    );\n  }\n\n  try {\n    const config = plugins.config.get(\"@csl\");\n    config.templates.add(styleName, styleXml);\n    return styleName;\n  } catch (error) {\n    const message = error instanceof Error ? error.message : String(error);\n    throw new Error(`Failed to register CSL style '${styleName}': ${message}`);\n  }\n}\n\n/**\n * Format CSL-JSON items as bibliography using CSL processor.\n * Falls back to simplified format if CSL processing fails.\n *\n * @param items - Array of CSL-JSON items\n * @param options - Formatting options\n * @returns Formatted bibliography entries\n */\nexport function formatBibliographyCSL(items: CslItem[], options: CitationFormatOptions): string {\n  // Handle empty array\n  if (items.length === 0) {\n    return \"\";\n  }\n\n  // Set defaults\n  let style = options.style || \"apa\";\n  const format = options.format || \"text\";\n  const locale = options.locale || \"en-US\";\n\n  // Register custom style if XML is provided\n  if (options.styleXml) {\n    style = registerCustomStyle(style, options.styleXml);\n  }\n\n  try {\n    // Create Cite instance with CSL-JSON data\n    const cite = new Cite(items);\n\n    // Format as bibliography\n    const result = cite.format(\"bibliography\", {\n      format,\n      template: style,\n      lang: locale,\n    });\n\n    return result;\n  } catch (error) {\n    // Fall back to simplified format on any error\n    const errorMessage = error instanceof Error ? error.message : String(error);\n    process.stderr.write(\n      `Warning: CSL processing failed (style: ${style}), falling back to simplified format: ${errorMessage}\\n`\n    );\n    return formatBibliography(items);\n  }\n}\n\n/**\n * Format CSL-JSON items as in-text citations using CSL processor.\n * Falls back to simplified format if CSL processing fails.\n *\n * @param items - Array of CSL-JSON items\n * @param options - Formatting options\n * @returns Formatted in-text citation(s)\n */\nexport function formatInTextCSL(items: CslItem[], options: CitationFormatOptions): string {\n  // Handle empty array\n  if (items.length === 0) {\n    return \"\";\n  }\n\n  // Set defaults\n  let style = options.style || \"apa\";\n  const format = options.format || \"text\";\n  const locale = options.locale || \"en-US\";\n\n  // Register custom style if XML is provided\n  if (options.styleXml) {\n    style = registerCustomStyle(style, options.styleXml);\n  }\n\n  try {\n    // Create Cite instance with CSL-JSON data\n    const cite = new Cite(items);\n\n    // Format as in-text citation\n    const result = cite.format(\"citation\", {\n      format,\n      template: style,\n      lang: locale,\n    });\n\n    return result;\n  } catch (error) {\n    // Fall back to simplified format on any error\n    const errorMessage = error instanceof Error ? error.message : String(error);\n    process.stderr.write(\n      `Warning: CSL processing failed (style: ${style}), falling back to simplified format: ${errorMessage}\\n`\n    );\n    return formatInText(items);\n  }\n}\n","/**\n * Reference sorter\n */\n\nimport type { CslItem } from \"../../core/csl-json/types.js\";\nimport type { SortField, SortOrder } from \"./types.js\";\n\n/**\n * Extract created_at timestamp from item, returns epoch (0) if missing\n */\nfunction getCreatedAt(item: CslItem): number {\n  const createdAt = item.custom?.created_at;\n  if (!createdAt) return 0;\n  return new Date(createdAt).getTime();\n}\n\n/**\n * Extract updated timestamp from item, falls back to created_at\n */\nfunction getUpdatedAt(item: CslItem): number {\n  const timestamp = item.custom?.timestamp;\n  if (timestamp) return new Date(timestamp).getTime();\n  return getCreatedAt(item);\n}\n\n/**\n * Extract published date as comparable number\n * Returns 0 (epoch) if missing\n */\nfunction getPublishedDate(item: CslItem): number {\n  const dateParts = item.issued?.[\"date-parts\"]?.[0];\n  if (!dateParts || dateParts.length === 0) return 0;\n\n  const year = dateParts[0] ?? 0;\n  const month = dateParts[1] ?? 1;\n  const day = dateParts[2] ?? 1;\n\n  return new Date(year, month - 1, day).getTime();\n}\n\n/**\n * Extract first author's sortable name\n * Returns \"Anonymous\" if no author\n */\nfunction getAuthorName(item: CslItem): string {\n  const firstAuthor = item.author?.[0];\n  if (!firstAuthor) return \"Anonymous\";\n\n  return firstAuthor.family ?? firstAuthor.literal ?? \"Anonymous\";\n}\n\n/**\n * Extract title, returns empty string if missing\n */\nfunction getTitle(item: CslItem): string {\n  return item.title ?? \"\";\n}\n\n/**\n * Get sort value for a given field\n */\nfunction getSortValue(item: CslItem, field: SortField): number | string {\n  switch (field) {\n    case \"created\":\n      return getCreatedAt(item);\n    case \"updated\":\n      return getUpdatedAt(item);\n    case \"published\":\n      return getPublishedDate(item);\n    case \"author\":\n      return getAuthorName(item).toLowerCase();\n    case \"title\":\n      return getTitle(item).toLowerCase();\n  }\n}\n\n/**\n * Compare function for sorting\n */\nfunction compareValues(a: number | string, b: number | string, order: SortOrder): number {\n  const multiplier = order === \"desc\" ? -1 : 1;\n\n  if (typeof a === \"number\" && typeof b === \"number\") {\n    return (a - b) * multiplier;\n  }\n\n  const strA = String(a);\n  const strB = String(b);\n  return strA.localeCompare(strB) * multiplier;\n}\n\n/**\n * Sort references by the specified field and order.\n * Uses secondary sort: created (desc), then id (asc) for stability.\n *\n * @param items - References to sort\n * @param sort - Sort field\n * @param order - Sort order\n * @returns Sorted references (new array, does not mutate input)\n */\nexport function sortReferences(items: CslItem[], sort: SortField, order: SortOrder): CslItem[] {\n  return [...items].sort((a, b) => {\n    // Primary sort\n    const aValue = getSortValue(a, sort);\n    const bValue = getSortValue(b, sort);\n    const primaryCompare = compareValues(aValue, bValue, order);\n\n    if (primaryCompare !== 0) return primaryCompare;\n\n    // Secondary sort: created (desc)\n    const aCreated = getCreatedAt(a);\n    const bCreated = getCreatedAt(b);\n    const createdCompare = bCreated - aCreated; // desc\n\n    if (createdCompare !== 0) return createdCompare;\n\n    // Tertiary sort: id (asc) for stability\n    return a.id.localeCompare(b.id);\n  });\n}\n","/**\n * Pagination applier\n */\n\nexport interface PaginateOptions {\n  limit?: number;\n  offset?: number;\n}\n\nexport interface PaginateResult<T> {\n  items: T[];\n  nextOffset: number | null;\n}\n\n/**\n * Apply pagination to an array of items.\n *\n * @param items - Items to paginate\n * @param options - Pagination options (limit=0 or undefined means unlimited)\n * @returns Paginated items with nextOffset (null if no more items)\n */\nexport function paginate<T>(items: T[], options: PaginateOptions): PaginateResult<T> {\n  const offset = options.offset ?? 0;\n  const limit = options.limit ?? 0;\n\n  // Validate inputs\n  if (limit < 0) {\n    throw new Error(\"limit must be non-negative\");\n  }\n  if (offset < 0) {\n    throw new Error(\"offset must be non-negative\");\n  }\n\n  const isUnlimited = limit === 0;\n\n  // Apply offset\n  const afterOffset = items.slice(offset);\n\n  // Apply limit (0 means unlimited)\n  const paginatedItems = isUnlimited ? afterOffset : afterOffset.slice(0, limit);\n\n  // Calculate nextOffset\n  let nextOffset: number | null = null;\n  if (!isUnlimited && paginatedItems.length > 0) {\n    const nextPosition = offset + paginatedItems.length;\n    if (nextPosition < items.length) {\n      nextOffset = nextPosition;\n    }\n  }\n\n  return {\n    items: paginatedItems,\n    nextOffset,\n  };\n}\n","/**\n * CSL Style Management\n *\n * Handles resolution and loading of CSL (Citation Style Language) style files.\n *\n * Style Resolution Order:\n * 1. --csl-file <path> (exact file path)\n * 2. Built-in style matching --style <name>\n * 3. Search in csl_directory paths (in array order)\n * 4. Default style from config (default_style)\n * 5. \"apa\" (hardcoded default)\n */\n\nimport * as fs from \"node:fs\";\nimport * as path from \"node:path\";\n\n/**\n * Built-in styles available in @citation-js/plugin-csl\n * These can be used directly without loading external files\n */\nexport const BUILTIN_STYLES = [\"apa\", \"vancouver\", \"harvard\"] as const;\n\nexport type BuiltinStyleName = (typeof BUILTIN_STYLES)[number];\n\n/**\n * Check if a style name is a built-in style\n */\nexport function isBuiltinStyle(styleName: string): styleName is BuiltinStyleName {\n  return BUILTIN_STYLES.includes(styleName as BuiltinStyleName);\n}\n\nexport interface StyleResolutionOptions {\n  /**\n   * Exact path to CSL file (from --csl-file option)\n   * Takes highest priority\n   */\n  cslFile?: string;\n\n  /**\n   * Style name to resolve (from --style option)\n   */\n  style?: string;\n\n  /**\n   * Directory or directories to search for custom CSL files\n   * (from csl_directory config)\n   * Can be a single string or array of strings\n   */\n  cslDirectory?: string | string[];\n\n  /**\n   * Default style to use if specified style not found\n   * (from default_style config)\n   */\n  defaultStyle?: string;\n}\n\nexport interface StyleResolution {\n  /**\n   * Type of resolution: \"builtin\" for citation-js built-in styles,\n   * \"custom\" for external CSL files\n   */\n  type: \"builtin\" | \"custom\";\n\n  /**\n   * The resolved style name (for built-in) or identifier (for custom)\n   */\n  styleName: string;\n\n  /**\n   * CSL XML content (only for custom styles)\n   */\n  styleXml?: string;\n}\n\n/**\n * Expand tilde (~) in path to home directory\n */\nfunction expandTilde(filePath: string): string {\n  if (filePath.startsWith(\"~/\")) {\n    const home = process.env.HOME || process.env.USERPROFILE || \"\";\n    return path.join(home, filePath.slice(2));\n  }\n  return filePath;\n}\n\n/**\n * Load CSL style file content from the given path\n *\n * @param stylePath - Path to the CSL style file\n * @returns Content of the CSL style file (XML string)\n * @throws Error if file cannot be read\n */\nexport function loadCSLStyleFile(stylePath: string): string {\n  return fs.readFileSync(stylePath, \"utf-8\");\n}\n\n/**\n * Resolve the style based on resolution options\n *\n * Resolution order:\n * 1. cslFile (exact path) - throws if doesn't exist\n * 2. Built-in style matching style name\n * 3. Search in csl_directory paths (in order)\n * 4. Default style (defaultStyle) - if built-in\n * 5. \"apa\" (hardcoded fallback)\n *\n * @param options - Style resolution options\n * @returns StyleResolution with type, styleName, and optional styleXml\n * @throws Error if cslFile is specified but doesn't exist\n */\nexport function resolveStyle(options: StyleResolutionOptions): StyleResolution {\n  const { cslFile, style, cslDirectory, defaultStyle } = options;\n\n  // 1. If cslFile is specified, use it (highest priority)\n  if (cslFile) {\n    if (!fs.existsSync(cslFile)) {\n      throw new Error(`CSL file '${cslFile}' not found`);\n    }\n    const styleXml = loadCSLStyleFile(cslFile);\n    const styleName = path.basename(cslFile, \".csl\");\n    return {\n      type: \"custom\",\n      styleName,\n      styleXml,\n    };\n  }\n\n  // Determine which style name to try\n  const styleToResolve = style || defaultStyle || \"apa\";\n\n  // 2. Check if it's a built-in style\n  if (isBuiltinStyle(styleToResolve)) {\n    return {\n      type: \"builtin\",\n      styleName: styleToResolve,\n    };\n  }\n\n  // 3. Search in csl_directory paths\n  if (cslDirectory) {\n    const directories = Array.isArray(cslDirectory) ? cslDirectory : [cslDirectory];\n\n    for (const dir of directories) {\n      const expandedDir = expandTilde(dir);\n      const stylePath = path.join(expandedDir, `${styleToResolve}.csl`);\n\n      if (fs.existsSync(stylePath)) {\n        const styleXml = loadCSLStyleFile(stylePath);\n        return {\n          type: \"custom\",\n          styleName: styleToResolve,\n          styleXml,\n        };\n      }\n    }\n  }\n\n  // 4. Fall back to default style if it's built-in\n  if (defaultStyle && isBuiltinStyle(defaultStyle)) {\n    return {\n      type: \"builtin\",\n      styleName: defaultStyle,\n    };\n  }\n\n  // 5. Fall back to apa (hardcoded default)\n  return {\n    type: \"builtin\",\n    styleName: \"apa\",\n  };\n}\n","import { rmdir, unlink } from \"node:fs/promises\";\nimport { join } from \"node:path\";\nimport type { CslItem } from \"../../core/csl-json/types.js\";\nimport type { ILibrary, IdentifierType } from \"../../core/library-interface.js\";\nimport type { Attachments } from \"../attachments/types.js\";\nimport type { FulltextType } from \"../fulltext/index.js\";\nimport { extensionToFormat, findFulltextFiles } from \"./fulltext-adapter/index.js\";\n\n/**\n * Options for removeReference operation\n */\nexport interface RemoveOperationOptions {\n  /** Reference ID or UUID */\n  identifier: string;\n  /** Identifier type: 'id' (default), 'uuid', 'doi', 'pmid', or 'isbn' */\n  idType?: IdentifierType;\n  /** Directory containing fulltext files (required if deleteFulltext is true) */\n  fulltextDirectory?: string;\n  /** Whether to delete associated fulltext files */\n  deleteFulltext?: boolean;\n}\n\n/**\n * Result of removeReference operation\n */\nexport interface RemoveResult {\n  /** Whether the reference was removed */\n  removed: boolean;\n  /** The removed item (if found and removal succeeded) */\n  removedItem?: CslItem;\n  /** Fulltext types that were deleted (only when deleteFulltext=true) */\n  deletedFulltextTypes?: FulltextType[];\n}\n\n/**\n * Get fulltext attachment types from a CSL item.\n */\nexport function getFulltextAttachmentTypes(item: CslItem): FulltextType[] {\n  const types: FulltextType[] = [];\n\n  // Check attachments structure\n  const attachments = item.custom?.attachments as Attachments | undefined;\n  const fulltextFiles = findFulltextFiles(attachments);\n  for (const file of fulltextFiles) {\n    const ext = file.filename.split(\".\").pop()?.toLowerCase();\n    const format = ext ? extensionToFormat(ext) : undefined;\n    if (format && !types.includes(format)) {\n      types.push(format);\n    }\n  }\n\n  return types;\n}\n\n/**\n * Delete fulltext files associated with an item.\n */\nasync function deleteFulltextFiles(item: CslItem, fulltextDirectory: string): Promise<void> {\n  const filesToDelete: string[] = [];\n\n  // Check attachments structure\n  const attachments = item.custom?.attachments as Attachments | undefined;\n  if (attachments?.directory) {\n    const fulltextFiles = findFulltextFiles(attachments);\n    for (const file of fulltextFiles) {\n      filesToDelete.push(join(fulltextDirectory, attachments.directory, file.filename));\n    }\n  }\n\n  // Delete individual files\n  for (const filePath of filesToDelete) {\n    try {\n      await unlink(filePath);\n    } catch {\n      // Ignore errors (file might not exist)\n    }\n  }\n\n  // Try to remove the attachments directory if it's now empty\n  if (attachments?.directory) {\n    try {\n      const dirPath = join(fulltextDirectory, attachments.directory);\n      await rmdir(dirPath); // Only removes if empty\n    } catch {\n      // Ignore - directory might not be empty or not exist\n    }\n  }\n}\n\n/**\n * Remove a reference from the library.\n *\n * @param library - The library to remove from\n * @param options - Remove options including identifier and lookup method\n * @returns Result indicating success and the removed item\n */\nexport async function removeReference(\n  library: ILibrary,\n  options: RemoveOperationOptions\n): Promise<RemoveResult> {\n  const { identifier, idType = \"id\", fulltextDirectory, deleteFulltext = false } = options;\n\n  const result = await library.remove(identifier, { idType });\n\n  if (!result.removed || !result.removedItem) {\n    return { removed: false };\n  }\n\n  // Delete fulltext files if requested\n  let deletedFulltextTypes: FulltextType[] | undefined;\n  if (deleteFulltext && fulltextDirectory) {\n    deletedFulltextTypes = getFulltextAttachmentTypes(result.removedItem);\n    if (deletedFulltextTypes.length > 0) {\n      await deleteFulltextFiles(result.removedItem, fulltextDirectory);\n    }\n  }\n\n  await library.save();\n\n  return {\n    removed: true,\n    removedItem: result.removedItem,\n    ...(deletedFulltextTypes && deletedFulltextTypes.length > 0 && { deletedFulltextTypes }),\n  };\n}\n","/**\n * Response cache for PMID and DOI metadata\n *\n * In-memory cache with TTL to avoid redundant API calls.\n * - Per ADR-001: No persistent cache files on disk\n * - Cache is warm during interactive sessions (server mode)\n * - CLI invocations start fresh\n */\n\nimport type { CslItem } from \"../../core/csl-json/types.js\";\n\n/** Default TTL: 1 hour */\nconst DEFAULT_TTL_MS = 60 * 60 * 1000;\n\n/**\n * Cache configuration\n */\nexport interface CacheConfig {\n  /** Time-to-live in milliseconds (default: 1 hour) */\n  ttlMs?: number;\n}\n\n/**\n * Cache entry with timestamp and TTL\n */\ninterface CacheEntry {\n  item: CslItem;\n  cachedAt: number;\n  ttlMs: number;\n}\n\n/** PMID cache: Map<pmid, CacheEntry> */\nconst pmidCache = new Map<string, CacheEntry>();\n\n/** DOI cache: Map<doi, CacheEntry> */\nconst doiCache = new Map<string, CacheEntry>();\n\n/** ISBN cache: Map<isbn, CacheEntry> */\nconst isbnCache = new Map<string, CacheEntry>();\n\n/**\n * Check if a cache entry is still valid\n */\nfunction isEntryValid(entry: CacheEntry): boolean {\n  const now = Date.now();\n  return now - entry.cachedAt < entry.ttlMs;\n}\n\n/**\n * Get item from cache if valid\n */\nfunction getFromCache(cache: Map<string, CacheEntry>, key: string): CslItem | undefined {\n  const entry = cache.get(key);\n  if (!entry) {\n    return undefined;\n  }\n  if (!isEntryValid(entry)) {\n    cache.delete(key);\n    return undefined;\n  }\n  return entry.item;\n}\n\n/**\n * Store item in cache\n */\nfunction storeInCache(\n  cache: Map<string, CacheEntry>,\n  key: string,\n  item: CslItem,\n  config?: CacheConfig\n): void {\n  const ttlMs = config?.ttlMs ?? DEFAULT_TTL_MS;\n  cache.set(key, {\n    item,\n    cachedAt: Date.now(),\n    ttlMs,\n  });\n}\n\n/**\n * Get cached PMID result\n */\nexport function getPmidFromCache(pmid: string): CslItem | undefined {\n  return getFromCache(pmidCache, pmid);\n}\n\n/**\n * Cache PMID result\n */\nexport function cachePmidResult(pmid: string, item: CslItem, config?: CacheConfig): void {\n  storeInCache(pmidCache, pmid, item, config);\n}\n\n/**\n * Get cached DOI result\n */\nexport function getDoiFromCache(doi: string): CslItem | undefined {\n  return getFromCache(doiCache, doi);\n}\n\n/**\n * Cache DOI result\n */\nexport function cacheDoiResult(doi: string, item: CslItem, config?: CacheConfig): void {\n  storeInCache(doiCache, doi, item, config);\n}\n\n/**\n * Get cached ISBN result\n */\nexport function getIsbnFromCache(isbn: string): CslItem | undefined {\n  return getFromCache(isbnCache, isbn);\n}\n\n/**\n * Cache ISBN result\n */\nexport function cacheIsbnResult(isbn: string, item: CslItem, config?: CacheConfig): void {\n  storeInCache(isbnCache, isbn, item, config);\n}\n\n/**\n * Reset all caches (for test isolation)\n */\nexport function resetCache(): void {\n  pmidCache.clear();\n  doiCache.clear();\n  isbnCache.clear();\n}\n","/**\n * DOI normalizer module\n *\n * Normalizes DOI identifiers by:\n * - Removing URL prefixes (doi.org, dx.doi.org)\n * - Trimming whitespace\n */\n\n/**\n * URL prefixes to remove from DOI\n */\nconst DOI_URL_PREFIXES = [\n  \"https://doi.org/\",\n  \"http://doi.org/\",\n  \"https://dx.doi.org/\",\n  \"http://dx.doi.org/\",\n];\n\n/**\n * Normalize a DOI identifier\n *\n * @param doi - DOI string, possibly with URL prefix\n * @returns Normalized DOI (10.xxx/xxx format)\n */\nexport function normalizeDoi(doi: string): string {\n  // Trim whitespace\n  const trimmed = doi.trim();\n\n  if (!trimmed) {\n    return \"\";\n  }\n\n  // Check for URL prefixes (case-insensitive)\n  const lowerInput = trimmed.toLowerCase();\n\n  for (const prefix of DOI_URL_PREFIXES) {\n    if (lowerInput.startsWith(prefix.toLowerCase())) {\n      // Remove the prefix while preserving the original case of the DOI\n      return trimmed.slice(prefix.length);\n    }\n  }\n\n  // No prefix found, return as-is\n  return trimmed;\n}\n\n/**\n * Normalizes a PMID by removing the optional \"PMID:\" prefix and trimming whitespace.\n *\n * Supported formats:\n * - \"12345678\" -> \"12345678\"\n * - \"PMID:12345678\" -> \"12345678\"\n * - \"pmid:12345678\" -> \"12345678\"\n * - \"PMID: 12345678\" -> \"12345678\" (space after colon)\n *\n * @param pmid - The PMID string to normalize\n * @returns The normalized PMID (digits only) or empty string if invalid\n */\nexport function normalizePmid(pmid: string): string {\n  // Trim whitespace\n  const trimmed = pmid.trim();\n\n  if (!trimmed) {\n    return \"\";\n  }\n\n  // Remove \"PMID:\" prefix (case-insensitive, optional whitespace after colon)\n  const normalized = trimmed.replace(/^pmid:\\s*/i, \"\");\n\n  return normalized.trim();\n}\n\n/**\n * Normalizes an ISBN by removing the \"ISBN:\" prefix, hyphens, spaces, and uppercasing X.\n *\n * Supported formats:\n * - \"ISBN:978-4-00-000000-0\" -> \"9784000000000\"\n * - \"isbn:4-00-000000-0\" -> \"4000000000\"\n * - \"ISBN: 978 4 00 000000 0\" -> \"9784000000000\"\n * - \"ISBN:400000000x\" -> \"400000000X\" (uppercase X)\n *\n * @param isbn - The ISBN string to normalize\n * @returns The normalized ISBN (digits only, X uppercase at end for ISBN-10) or empty string if invalid\n */\nexport function normalizeIsbn(isbn: string): string {\n  // Trim whitespace\n  const trimmed = isbn.trim();\n\n  if (!trimmed) {\n    return \"\";\n  }\n\n  // Check for ISBN: prefix (case-insensitive)\n  if (!/^isbn:/i.test(trimmed)) {\n    return \"\";\n  }\n\n  // Remove \"ISBN:\" prefix (case-insensitive, optional whitespace after colon)\n  let normalized = trimmed.replace(/^isbn:\\s*/i, \"\");\n\n  // Remove hyphens and spaces\n  normalized = normalized.replace(/[-\\s]/g, \"\");\n\n  // Uppercase X (for ISBN-10 check digit)\n  normalized = normalized.toUpperCase();\n\n  return normalized;\n}\n","/**\n * Format detection module for multi-format import\n *\n * Detects input format based on:\n * - File extension (.json, .bib, .ris)\n * - Content patterns (JSON, BibTeX, RIS)\n * - Identifier patterns (PMID, DOI)\n * - Multiple whitespace-separated identifiers\n */\n\nimport { normalizeIsbn, normalizePmid } from \"./normalizer.js\";\n\n/**\n * Supported input formats\n */\nexport type InputFormat =\n  | \"json\"\n  | \"bibtex\"\n  | \"ris\"\n  | \"nbib\"\n  | \"pmid\"\n  | \"doi\"\n  | \"isbn\"\n  | \"identifiers\"\n  | \"unknown\";\n\n/**\n * Extension to format mapping\n */\nconst EXTENSION_MAP: Record<string, InputFormat> = {\n  \".json\": \"json\",\n  \".bib\": \"bibtex\",\n  \".ris\": \"ris\",\n  \".nbib\": \"nbib\",\n};\n\n/**\n * DOI URL prefixes to strip\n */\nconst DOI_URL_PREFIXES = [\n  \"https://doi.org/\",\n  \"http://doi.org/\",\n  \"https://dx.doi.org/\",\n  \"http://dx.doi.org/\",\n];\n\n/**\n * Detect the format of the given input\n *\n * @param input - File path, identifier, or empty string for stdin\n * @param content - Optional content to analyze (for stdin or unknown extension)\n * @returns Detected format\n */\nexport function detectFormat(input: string, content?: string): InputFormat {\n  // 1. Try extension-based detection first\n  const extFormat = detectByExtension(input);\n  if (extFormat !== \"unknown\") {\n    return extFormat;\n  }\n\n  // 2. If content provided, try content-based detection\n  if (content !== undefined) {\n    const contentFormat = detectByContent(content);\n    if (contentFormat !== \"unknown\") {\n      return contentFormat;\n    }\n  }\n\n  // 3. Try identifier detection on input string\n  if (input.length > 0) {\n    const identifierFormat = detectIdentifier(input);\n    if (identifierFormat !== \"unknown\") {\n      return identifierFormat;\n    }\n  }\n\n  return \"unknown\";\n}\n\n/**\n * Detect format based on file extension\n */\nexport function detectByExtension(input: string): InputFormat {\n  if (!input) return \"unknown\";\n\n  // Extract extension (last dot and onwards)\n  const dotIndex = input.lastIndexOf(\".\");\n  if (dotIndex === -1 || dotIndex === input.length - 1) {\n    return \"unknown\";\n  }\n\n  const ext = input.slice(dotIndex).toLowerCase();\n  return EXTENSION_MAP[ext] ?? \"unknown\";\n}\n\n/**\n * Detect format based on content patterns\n */\nexport function detectByContent(content: string): InputFormat {\n  const trimmed = content.trim();\n  if (!trimmed) return \"unknown\";\n\n  // JSON: starts with [ or {\n  if (trimmed.startsWith(\"[\") || trimmed.startsWith(\"{\")) {\n    return \"json\";\n  }\n\n  // BibTeX: starts with @\n  if (trimmed.startsWith(\"@\")) {\n    return \"bibtex\";\n  }\n\n  // RIS: starts with TY  - (tag format)\n  if (trimmed.startsWith(\"TY  -\")) {\n    return \"ris\";\n  }\n\n  // NBIB (PubMed MEDLINE): starts with PMID-\n  if (trimmed.startsWith(\"PMID-\")) {\n    return \"nbib\";\n  }\n\n  // Check if content is multiple identifiers\n  return detectIdentifier(trimmed);\n}\n\n/**\n * Detect if input is an identifier (PMID, DOI, ISBN) or multiple identifiers\n */\nfunction detectIdentifier(input: string): InputFormat {\n  // Split by whitespace\n  const parts = input.split(/\\s+/).filter((p) => p.length > 0);\n\n  if (parts.length === 0) {\n    return \"unknown\";\n  }\n\n  // Check each part\n  const formats: (\"pmid\" | \"doi\" | \"isbn\")[] = [];\n  for (const part of parts) {\n    const format = detectSingleIdentifier(part);\n    if (format === \"unknown\") {\n      // If any part is not a valid identifier, return unknown\n      return \"unknown\";\n    }\n    formats.push(format);\n  }\n\n  // Single identifier returns its specific format\n  if (formats.length === 1) {\n    // formats[0] is guaranteed to exist when length === 1\n    return formats[0] as \"pmid\" | \"doi\" | \"isbn\";\n  }\n\n  // Multiple valid identifiers\n  return \"identifiers\";\n}\n\n/**\n * Detect if a single string is a PMID, DOI, or ISBN\n */\nexport function detectSingleIdentifier(input: string): \"pmid\" | \"doi\" | \"isbn\" | \"unknown\" {\n  // DOI: starts with 10. or is a DOI URL\n  if (isDoi(input)) {\n    return \"doi\";\n  }\n\n  // ISBN: requires ISBN: prefix\n  if (isIsbn(input)) {\n    return \"isbn\";\n  }\n\n  // PMID: numeric only (must be after ISBN check to avoid conflicts)\n  if (isPmid(input)) {\n    return \"pmid\";\n  }\n\n  return \"unknown\";\n}\n\n/**\n * Check if string is a valid DOI\n */\nexport function isDoi(input: string): boolean {\n  // Check DOI URL formats\n  for (const prefix of DOI_URL_PREFIXES) {\n    if (input.toLowerCase().startsWith(prefix.toLowerCase())) {\n      const remainder = input.slice(prefix.length);\n      return isDoiFormat(remainder);\n    }\n  }\n\n  // Check standard DOI format (10.xxx/xxx)\n  return isDoiFormat(input);\n}\n\n/**\n * Check if string is a valid DOI format (10.xxx/xxx)\n */\nfunction isDoiFormat(input: string): boolean {\n  // DOI starts with 10. followed by registrant code and suffix\n  // Pattern: 10.{registrant}/{suffix}\n  if (!input.startsWith(\"10.\")) {\n    return false;\n  }\n\n  // Must have content after 10.\n  if (input.length <= 3) {\n    return false;\n  }\n\n  // Must have a slash after registrant code\n  const slashIndex = input.indexOf(\"/\");\n  if (slashIndex === -1 || slashIndex <= 3) {\n    return false;\n  }\n\n  return true;\n}\n\n/**\n * Check if string is a valid PMID (numeric only)\n */\nexport function isPmid(input: string): boolean {\n  if (!input || input.length === 0) {\n    return false;\n  }\n\n  // Normalize input (removes PMID: prefix if present)\n  const normalized = normalizePmid(input);\n\n  if (!normalized) {\n    return false;\n  }\n\n  // PMID is all digits\n  return /^\\d+$/.test(normalized);\n}\n\n/**\n * Check if string is a valid ISBN (requires ISBN: prefix)\n *\n * ISBN must have ISBN: prefix and be either:\n * - ISBN-13: 13 digits\n * - ISBN-10: 10 digits (last may be X)\n */\nexport function isIsbn(input: string): boolean {\n  if (!input || input.length === 0) {\n    return false;\n  }\n\n  // Normalize input (removes ISBN: prefix if present, hyphens, spaces)\n  const normalized = normalizeIsbn(input);\n\n  if (!normalized) {\n    return false;\n  }\n\n  // Check length: ISBN-10 (10 chars) or ISBN-13 (13 chars)\n  if (normalized.length !== 10 && normalized.length !== 13) {\n    return false;\n  }\n\n  // ISBN-10: 9 digits + (digit or X)\n  if (normalized.length === 10) {\n    // First 9 must be digits, last can be digit or X\n    if (!/^\\d{9}[\\dX]$/.test(normalized)) {\n      return false;\n    }\n    return true;\n  }\n\n  // ISBN-13: all digits\n  if (!/^\\d{13}$/.test(normalized)) {\n    return false;\n  }\n\n  return true;\n}\n","/**\n * Rate limiter module for API calls\n *\n * Uses factory + lazy initialization singleton pattern:\n * - RateLimiter class: Delay-based rate limiting with configurable requests/second\n * - getRateLimiter(api, config): Returns singleton per API type\n * - resetRateLimiters(): Clears singletons for test isolation\n */\n\n/**\n * API types supported by the rate limiter\n */\nexport type ApiType = \"pubmed\" | \"crossref\" | \"isbn\";\n\n/**\n * Configuration for rate limiter\n */\nexport interface RateLimiterConfig {\n  pubmedApiKey?: string;\n}\n\n/**\n * Rate limiter interface\n */\nexport interface RateLimiter {\n  readonly requestsPerSecond: number;\n  readonly intervalMs: number;\n  readonly lastRequestTime: number;\n  acquire(): Promise<void>;\n}\n\n/**\n * Rate limit settings per API type\n */\nconst RATE_LIMITS = {\n  pubmed: {\n    withoutApiKey: 3, // 3 req/sec\n    withApiKey: 10, // 10 req/sec\n  },\n  crossref: 50, // 50 req/sec\n  isbn: 10, // 10 req/sec (conservative for Google Books API daily limit)\n} as const;\n\n/**\n * Internal rate limiter implementation\n */\nclass RateLimiterImpl implements RateLimiter {\n  readonly requestsPerSecond: number;\n  readonly intervalMs: number;\n  private _lastRequestTime = 0;\n  private _pending: Promise<void> = Promise.resolve();\n\n  constructor(requestsPerSecond: number) {\n    this.requestsPerSecond = requestsPerSecond;\n    this.intervalMs = 1000 / requestsPerSecond;\n  }\n\n  get lastRequestTime(): number {\n    return this._lastRequestTime;\n  }\n\n  async acquire(): Promise<void> {\n    // Chain onto pending promise to ensure sequential processing\n    this._pending = this._pending.then(() => this._acquireInternal());\n    return this._pending;\n  }\n\n  private async _acquireInternal(): Promise<void> {\n    const now = Date.now();\n    const elapsed = now - this._lastRequestTime;\n    const waitTime = Math.max(0, this.intervalMs - elapsed);\n\n    if (waitTime > 0 && this._lastRequestTime > 0) {\n      await this._delay(waitTime);\n    }\n\n    this._lastRequestTime = Date.now();\n  }\n\n  private _delay(ms: number): Promise<void> {\n    return new Promise((resolve) => setTimeout(resolve, ms));\n  }\n}\n\n/**\n * Singleton storage for rate limiters by API type\n */\nconst limiters = new Map<ApiType, RateLimiter>();\n\n/**\n * Create a new rate limiter instance\n */\nexport function createRateLimiter(options: {\n  requestsPerSecond: number;\n}): RateLimiter {\n  return new RateLimiterImpl(options.requestsPerSecond);\n}\n\n/**\n * Get singleton rate limiter for the specified API type\n *\n * Note: Configuration is only used on first call. Subsequent calls\n * return the existing singleton regardless of config changes.\n */\nexport function getRateLimiter(api: ApiType, config: RateLimiterConfig): RateLimiter {\n  const existing = limiters.get(api);\n  if (existing) {\n    return existing;\n  }\n\n  const requestsPerSecond = getRequestsPerSecond(api, config);\n  const limiter = createRateLimiter({ requestsPerSecond });\n  limiters.set(api, limiter);\n\n  return limiter;\n}\n\n/**\n * Determine requests per second based on API type and configuration\n */\nfunction getRequestsPerSecond(api: ApiType, config: RateLimiterConfig): number {\n  switch (api) {\n    case \"pubmed\":\n      return config.pubmedApiKey ? RATE_LIMITS.pubmed.withApiKey : RATE_LIMITS.pubmed.withoutApiKey;\n    case \"crossref\":\n      return RATE_LIMITS.crossref;\n    case \"isbn\":\n      return RATE_LIMITS.isbn;\n  }\n}\n\n/**\n * Reset all rate limiter singletons (for test isolation)\n */\nexport function resetRateLimiters(): void {\n  limiters.clear();\n}\n","/**\n * Fetcher module for PMID and DOI metadata retrieval\n *\n * - PMID: Uses PMC Citation Exporter API (returns CSL-JSON directly)\n * - DOI: Uses citation-js plugin-doi (Cite.async)\n */\n\nimport { Cite } from \"@citation-js/core\";\nimport \"@citation-js/plugin-doi\";\nimport \"@citation-js/plugin-isbn\";\nimport { type CslItem, CslItemSchema } from \"../../core/csl-json/types.js\";\nimport { getRateLimiter } from \"./rate-limiter.js\";\n\n/** PMC Citation Exporter API base URL */\nconst PMC_API_BASE = \"https://pmc.ncbi.nlm.nih.gov/api/ctxp/v1/pubmed/\";\n\n/** Default timeout for API requests (10 seconds) */\nconst DEFAULT_TIMEOUT_MS = 10000;\n\n/** DOI pattern for validation */\nconst DOI_PATTERN = /^10\\.\\d{4,}(?:\\.\\d+)*\\/\\S+$/;\n\n/**\n * PubMed configuration for API requests\n */\nexport interface PubmedConfig {\n  email?: string;\n  apiKey?: string;\n}\n\n/**\n * Categorized failure reasons for JSON output\n */\nexport type FailureReason =\n  | \"not_found\"\n  | \"fetch_error\"\n  | \"parse_error\"\n  | \"validation_error\"\n  | \"unknown\";\n\n/**\n * Result of fetching a single identifier\n */\nexport type FetchResult =\n  | { success: true; item: CslItem }\n  | { success: false; error: string; reason: FailureReason };\n\n/**\n * Result of fetching a PMID (includes pmid for tracking)\n */\nexport type PmidFetchResult =\n  | { pmid: string; success: true; item: CslItem }\n  | { pmid: string; success: false; error: string; reason: FailureReason };\n\n/**\n * Results of fetching multiple PMIDs\n */\nexport type FetchResults = PmidFetchResult[];\n\n/**\n * Build PMC API URL with query parameters\n */\nfunction buildPmcUrl(pmids: string[], config: PubmedConfig): string {\n  const url = new URL(PMC_API_BASE);\n  url.searchParams.set(\"format\", \"csl\");\n\n  // Add each PMID as separate id parameter\n  for (const pmid of pmids) {\n    url.searchParams.append(\"id\", pmid);\n  }\n\n  if (config.email) {\n    url.searchParams.set(\"email\", config.email);\n  }\n  if (config.apiKey) {\n    url.searchParams.set(\"api_key\", config.apiKey);\n  }\n\n  return url.toString();\n}\n\n/**\n * Extract PMID from CSL-JSON item id field\n * PMC API returns id like \"pmid:12345678\"\n */\nfunction extractPmidFromId(id: string | undefined): string | undefined {\n  if (!id) return undefined;\n  const match = id.match(/^pmid:(\\d+)$/);\n  return match?.[1];\n}\n\n/**\n * Fetch metadata for multiple PMIDs from PMC Citation Exporter API\n *\n * Uses batch API endpoint: /api/ctxp/v1/pubmed/?format=csl&id=1&id=2\n */\n\n/**\n * Parse raw API items and build maps of found items and validation errors\n */\nfunction parseRawItems(rawItems: unknown[]): {\n  foundItems: Map<string, CslItem>;\n  validationErrors: Map<string, string>;\n} {\n  const foundItems = new Map<string, CslItem>();\n  const validationErrors = new Map<string, string>();\n\n  for (const rawItem of rawItems) {\n    const parseResult = CslItemSchema.safeParse(rawItem);\n    if (parseResult.success) {\n      const pmid = extractPmidFromId(parseResult.data.id);\n      if (pmid) {\n        foundItems.set(pmid, parseResult.data);\n      }\n    } else {\n      // Try to extract pmid even from invalid data for error reporting\n      const maybeId = (rawItem as { id?: string })?.id;\n      const pmid = extractPmidFromId(maybeId);\n      if (pmid) {\n        validationErrors.set(pmid, parseResult.error.message);\n      }\n    }\n  }\n\n  return { foundItems, validationErrors };\n}\n\n/**\n * Build fetch result for a single PMID\n */\nfunction buildPmidResult(\n  pmid: string,\n  foundItems: Map<string, CslItem>,\n  validationErrors: Map<string, string>\n): PmidFetchResult {\n  const item = foundItems.get(pmid);\n  if (item) {\n    return { pmid, success: true as const, item };\n  }\n  const validationError = validationErrors.get(pmid);\n  if (validationError) {\n    return {\n      pmid,\n      success: false as const,\n      error: `Invalid CSL-JSON data: ${validationError}`,\n      reason: \"validation_error\",\n    };\n  }\n  return {\n    pmid,\n    success: false as const,\n    error: `PMID ${pmid} not found`,\n    reason: \"not_found\",\n  };\n}\n\nexport async function fetchPmids(pmids: string[], config: PubmedConfig): Promise<FetchResults> {\n  // Return empty array for empty input\n  if (pmids.length === 0) {\n    return [];\n  }\n\n  // Apply rate limiting\n  const rateLimiterConfig = config.apiKey ? { pubmedApiKey: config.apiKey } : {};\n  const rateLimiter = getRateLimiter(\"pubmed\", rateLimiterConfig);\n  await rateLimiter.acquire();\n\n  const url = buildPmcUrl(pmids, config);\n\n  try {\n    const response = await fetch(url, {\n      method: \"GET\",\n      signal: AbortSignal.timeout(DEFAULT_TIMEOUT_MS),\n    });\n\n    if (!response.ok) {\n      // Return error for all PMIDs\n      const errorMsg = `HTTP ${response.status}: ${response.statusText}`;\n      return pmids.map((pmid) => ({\n        pmid,\n        success: false as const,\n        error: errorMsg,\n        reason: \"fetch_error\",\n      }));\n    }\n\n    const data = await response.json();\n\n    // Normalize response to array\n    const rawItems: unknown[] = Array.isArray(data) ? data : [data];\n\n    // Parse raw items and build results\n    const { foundItems, validationErrors } = parseRawItems(rawItems);\n\n    // Build results for each requested PMID\n    return pmids.map((pmid) => buildPmidResult(pmid, foundItems, validationErrors));\n  } catch (error) {\n    const errorMsg = error instanceof Error ? error.message : String(error);\n    return pmids.map((pmid) => ({\n      pmid,\n      success: false as const,\n      error: errorMsg,\n      reason: \"fetch_error\",\n    }));\n  }\n}\n\n/**\n * Fetch metadata for a DOI using citation-js\n *\n * Uses @citation-js/plugin-doi for content negotiation\n */\nexport async function fetchDoi(doi: string): Promise<FetchResult> {\n  // Validate DOI format\n  if (!DOI_PATTERN.test(doi)) {\n    return {\n      success: false,\n      error: `Invalid DOI format: ${doi}`,\n      reason: \"validation_error\",\n    };\n  }\n\n  // Apply rate limiting (crossref)\n  const rateLimiter = getRateLimiter(\"crossref\", {});\n  await rateLimiter.acquire();\n\n  try {\n    // Use citation-js Cite.async for DOI resolution\n    const cite = await Cite.async(doi);\n    const rawItems = cite.get({ format: \"real\", type: \"json\" });\n\n    if (!rawItems || !Array.isArray(rawItems) || rawItems.length === 0) {\n      return {\n        success: false,\n        error: `No data returned for DOI ${doi}`,\n        reason: \"not_found\",\n      };\n    }\n\n    // Validate using zod schema\n    const parseResult = CslItemSchema.safeParse(rawItems[0]);\n    if (!parseResult.success) {\n      return {\n        success: false,\n        error: `Invalid CSL-JSON data for DOI ${doi}: ${parseResult.error.message}`,\n        reason: \"validation_error\",\n      };\n    }\n\n    return { success: true, item: parseResult.data };\n  } catch (error) {\n    const errorMsg = error instanceof Error ? error.message : String(error);\n    return {\n      success: false,\n      error: errorMsg,\n      reason: \"fetch_error\",\n    };\n  }\n}\n\n/** ISBN-10 pattern: 9 digits + (digit or X) */\nconst ISBN10_PATTERN = /^\\d{9}[\\dX]$/;\n\n/** ISBN-13 pattern: 13 digits */\nconst ISBN13_PATTERN = /^\\d{13}$/;\n\n/**\n * Fetch metadata for an ISBN using Google Books API via citation-js\n *\n * @param isbn - Normalized ISBN (10 or 13 digits, no hyphens)\n * @returns FetchResult with CSL-JSON item or error\n */\nexport async function fetchIsbn(isbn: string): Promise<FetchResult> {\n  // Validate ISBN format\n  if (!ISBN10_PATTERN.test(isbn) && !ISBN13_PATTERN.test(isbn)) {\n    return {\n      success: false,\n      error: `Invalid ISBN format: ${isbn}`,\n      reason: \"validation_error\",\n    };\n  }\n\n  // Apply rate limiting (google books - daily limit so we use a generic limiter)\n  const rateLimiter = getRateLimiter(\"isbn\", {});\n  await rateLimiter.acquire();\n\n  try {\n    // Use citation-js Cite.async for ISBN resolution\n    const cite = await Cite.async(isbn);\n    const rawItems = cite.get({ format: \"real\", type: \"json\" });\n\n    if (!rawItems || !Array.isArray(rawItems) || rawItems.length === 0) {\n      return {\n        success: false,\n        error: `No data returned for ISBN ${isbn}`,\n        reason: \"not_found\",\n      };\n    }\n\n    // Validate using zod schema\n    const parseResult = CslItemSchema.safeParse(rawItems[0]);\n    if (!parseResult.success) {\n      return {\n        success: false,\n        error: `Invalid CSL-JSON data for ISBN ${isbn}: ${parseResult.error.message}`,\n        reason: \"validation_error\",\n      };\n    }\n\n    return { success: true, item: parseResult.data };\n  } catch (error) {\n    const errorMsg = error instanceof Error ? error.message : String(error);\n    return {\n      success: false,\n      error: errorMsg,\n      reason: \"fetch_error\",\n    };\n  }\n}\n","/**\n * Parser module for BibTeX and RIS formats\n *\n * Uses citation-js plugins for parsing:\n * - @citation-js/plugin-bibtex for BibTeX\n * - @citation-js/plugin-ris for RIS\n */\n\nimport { Cite } from \"@citation-js/core\";\nimport \"@citation-js/plugin-bibtex\";\nimport \"@citation-js/plugin-ris\";\nimport type { CslItem } from \"../../core/csl-json/types.js\";\n\n/**\n * Result of a parse operation\n */\nexport type ParseResult = {\n  success: boolean;\n  items: CslItem[];\n  error?: string;\n};\n\n/**\n * Parse BibTeX content to CSL-JSON\n *\n * @param content - BibTeX content string\n * @returns Parse result with CSL-JSON items\n */\nexport function parseBibtex(content: string): ParseResult {\n  return parseWithCitationJs(content, \"bibtex\");\n}\n\n/**\n * Parse RIS content to CSL-JSON\n *\n * @param content - RIS content string\n * @returns Parse result with CSL-JSON items\n */\nexport function parseRis(content: string): ParseResult {\n  return parseWithCitationJs(content, \"ris\");\n}\n\n/**\n * NBIB to RIS tag mapping\n *\n * Maps PubMed MEDLINE tags to RIS equivalents\n */\nconst NBIB_TO_RIS_TAG_MAP: Record<string, string> = {\n  PMID: \"AN\", // PubMed ID -> Accession Number\n  TI: \"TI\", // Title -> Title\n  FAU: \"AU\", // Full Author -> Author\n  AU: \"AU\", // Author -> Author (short form, use FAU when available)\n  JT: \"JO\", // Journal Title -> Journal Name\n  TA: \"JA\", // Title Abbreviation -> Journal Abbreviation\n  AB: \"AB\", // Abstract -> Abstract\n  VI: \"VL\", // Volume -> Volume\n  IP: \"IS\", // Issue/Part -> Issue Number\n  PG: \"SP\", // Pagination -> Start Page (includes range)\n  DP: \"PY\", // Date of Publication -> Publication Year\n  LA: \"LA\", // Language -> Language\n  MH: \"KW\", // MeSH Headings -> Keywords\n  OT: \"KW\", // Other Terms -> Keywords\n  AD: \"AD\", // Affiliation/Address -> Author Address\n  IS: \"SN\", // ISSN -> Serial Number\n  PT: \"TY\", // Publication Type -> Type of Reference\n};\n\n/**\n * Publication type mapping from NBIB to RIS\n */\nconst NBIB_PUBLICATION_TYPE_MAP: Record<string, string> = {\n  \"Journal Article\": \"JOUR\",\n  Review: \"JOUR\",\n  Book: \"BOOK\",\n  \"Book Chapter\": \"CHAP\",\n  \"Conference Paper\": \"CPAPER\",\n  Thesis: \"THES\",\n  Report: \"RPRT\",\n};\n\n/**\n * Parse a single NBIB entry into tag-value pairs\n */\nfunction parseNbibEntry(entry: string): Array<{ tag: string; value: string }> {\n  const result: Array<{ tag: string; value: string }> = [];\n  const lines = entry.split(\"\\n\");\n\n  let currentTag = \"\";\n  let currentValue = \"\";\n\n  for (const line of lines) {\n    // Check if line starts with a tag (2-4 uppercase letters followed by space(s) and dash)\n    const tagMatch = line.match(/^([A-Z]{2,4})\\s*-\\s*(.*)$/);\n\n    if (tagMatch) {\n      // Save previous tag-value pair\n      if (currentTag) {\n        result.push({ tag: currentTag, value: currentValue.trim() });\n      }\n      currentTag = tagMatch[1] ?? \"\";\n      currentValue = tagMatch[2] ?? \"\";\n    } else if (currentTag && line.match(/^\\s+/)) {\n      // Continuation line (starts with whitespace)\n      currentValue += ` ${line.trim()}`;\n    }\n  }\n\n  // Save the last tag-value pair\n  if (currentTag) {\n    result.push({ tag: currentTag, value: currentValue.trim() });\n  }\n\n  return result;\n}\n\n/**\n * Convert a single NBIB tag-value pair to RIS line\n * @returns RIS line or null if tag should be skipped\n */\nfunction convertNbibTagToRisLine(\n  tag: string,\n  value: string\n): { line: string; isType?: boolean } | null {\n  // Handle DOI specially (AID tag with [doi] suffix)\n  if (tag === \"AID\" && value.includes(\"[doi]\")) {\n    const doi = value.replace(/\\s*\\[doi\\].*$/, \"\").trim();\n    return { line: `DO  - ${doi}` };\n  }\n\n  // Handle PII specially (AID tag with [pii] suffix)\n  if (tag === \"AID\" && value.includes(\"[pii]\")) {\n    const pii = value.replace(/\\s*\\[pii\\].*$/, \"\").trim();\n    return { line: `C1  - ${pii}` }; // C1 = Custom Field 1\n  }\n\n  // Get mapped RIS tag\n  const risTag = NBIB_TO_RIS_TAG_MAP[tag];\n  if (!risTag) {\n    return null; // Skip unmapped tags\n  }\n\n  // Handle publication year (extract year only)\n  if (risTag === \"PY\") {\n    const yearMatch = value.match(/^(\\d{4})/);\n    return yearMatch ? { line: `PY  - ${yearMatch[1]}` } : null;\n  }\n\n  // Handle publication type\n  if (risTag === \"TY\") {\n    const risType = NBIB_PUBLICATION_TYPE_MAP[value] || \"JOUR\";\n    return { line: `TY  - ${risType}`, isType: true };\n  }\n\n  return { line: `${risTag}  - ${value}` };\n}\n\n/**\n * Convert a single NBIB entry to RIS format\n */\nfunction convertSingleNbibEntryToRis(entry: string): string {\n  const parsed = parseNbibEntry(entry);\n\n  if (parsed.length === 0) {\n    return \"\";\n  }\n\n  const risLines: string[] = [];\n  let hasType = false;\n\n  for (const { tag, value } of parsed) {\n    const converted = convertNbibTagToRisLine(tag, value);\n    if (!converted) {\n      continue;\n    }\n\n    if (converted.isType) {\n      risLines.unshift(converted.line); // TY must be first\n      hasType = true;\n    } else {\n      risLines.push(converted.line);\n    }\n  }\n\n  // Add default type if not present\n  if (!hasType) {\n    risLines.unshift(\"TY  - JOUR\");\n  }\n\n  // Add end record tag\n  risLines.push(\"ER  -\");\n\n  return risLines.join(\"\\n\");\n}\n\n/**\n * Convert NBIB (PubMed MEDLINE) format to RIS format\n *\n * @param content - NBIB content string\n * @returns RIS format string\n */\nexport function convertNbibToRis(content: string): string {\n  const trimmed = content.trim();\n\n  if (!trimmed) {\n    return \"\";\n  }\n\n  // Split into entries by blank lines (PMID- starts each entry)\n  const entries = trimmed.split(/\\n\\s*\\n/).filter((e) => e.trim());\n\n  const risEntries = entries.map((entry) => convertSingleNbibEntryToRis(entry)).filter(Boolean);\n\n  return risEntries.join(\"\\n\\n\");\n}\n\n/**\n * Parse NBIB (PubMed MEDLINE) content to CSL-JSON\n *\n * Converts NBIB to RIS format first, then parses with citation-js\n *\n * @param content - NBIB content string\n * @returns Parse result with CSL-JSON items\n */\nexport function parseNbib(content: string): ParseResult {\n  const trimmed = content.trim();\n\n  // Handle empty input\n  if (!trimmed) {\n    return { success: true, items: [] };\n  }\n\n  // Convert NBIB to RIS\n  const risContent = convertNbibToRis(trimmed);\n\n  if (!risContent) {\n    return {\n      success: false,\n      items: [],\n      error: \"Failed to convert NBIB to RIS: No valid entries found\",\n    };\n  }\n\n  // Parse the RIS content\n  return parseRis(risContent);\n}\n\n/**\n * Parse content using citation-js\n */\nfunction parseWithCitationJs(content: string, format: string): ParseResult {\n  const trimmed = content.trim();\n\n  // Handle empty input\n  if (!trimmed) {\n    return { success: true, items: [] };\n  }\n\n  try {\n    // Parse with citation-js (auto-detection works well for bibtex/ris)\n    const cite = new Cite(trimmed);\n\n    // Get CSL-JSON output\n    const items = cite.get({ format: \"real\", type: \"json\" }) as CslItem[];\n\n    // Handle case where parsing produces no results\n    if (!items || items.length === 0) {\n      // Check if input looks like valid format but has no entries\n      if (isEmptyFormat(trimmed, format)) {\n        return { success: true, items: [] };\n      }\n\n      return {\n        success: false,\n        items: [],\n        error: `No valid ${format.toUpperCase()} entries found`,\n      };\n    }\n\n    return { success: true, items };\n  } catch (error) {\n    const errorMessage = error instanceof Error ? error.message : String(error);\n\n    // Check if this is truly empty content (comments only for bibtex)\n    if (isEmptyFormat(trimmed, format)) {\n      return { success: true, items: [] };\n    }\n\n    return {\n      success: false,\n      items: [],\n      error: `Failed to parse ${format.toUpperCase()}: ${errorMessage}`,\n    };\n  }\n}\n\n/**\n * Check if content is \"empty\" for the given format\n * (e.g., only comments for BibTeX)\n */\nfunction isEmptyFormat(content: string, format: string): boolean {\n  if (format === \"bibtex\") {\n    // BibTeX comments start with %\n    const lines = content.split(\"\\n\");\n    return lines.every((line) => {\n      const trimmed = line.trim();\n      return trimmed === \"\" || trimmed.startsWith(\"%\");\n    });\n  }\n\n  return false;\n}\n","/**\n * Importer orchestration module\n *\n * Coordinates format detection, parsing, and fetching to import references\n * from various input formats.\n */\n\nimport { existsSync, readFileSync } from \"node:fs\";\nimport type { CslItem } from \"../../core/csl-json/types.js\";\nimport { CslItemSchema } from \"../../core/csl-json/types.js\";\nimport {\n  cacheDoiResult,\n  cacheIsbnResult,\n  cachePmidResult,\n  getDoiFromCache,\n  getIsbnFromCache,\n  getPmidFromCache,\n} from \"./cache.js\";\nimport { detectByContent, detectByExtension, isDoi, isIsbn, isPmid } from \"./detector.js\";\nimport type { InputFormat } from \"./detector.js\";\nimport { fetchDoi, fetchIsbn, fetchPmids } from \"./fetcher.js\";\nimport type { FailureReason, PubmedConfig } from \"./fetcher.js\";\nimport { normalizeDoi, normalizeIsbn, normalizePmid } from \"./normalizer.js\";\nimport { parseBibtex, parseNbib, parseRis } from \"./parser.js\";\n\n// Re-export FailureReason for external use\nexport type { FailureReason } from \"./fetcher.js\";\n\n/**\n * Result of importing a single item\n */\nexport type ImportItemResult =\n  | { success: true; item: CslItem; source: string }\n  | { success: false; error: string; source: string; reason: FailureReason };\n\n/**\n * Result of an import operation\n */\nexport interface ImportResult {\n  results: ImportItemResult[];\n}\n\n/**\n * Options for import operations\n */\nexport interface ImportOptions {\n  pubmedConfig?: PubmedConfig;\n}\n\n/**\n * Classified identifiers\n */\ninterface ClassifiedIdentifiers {\n  pmids: string[];\n  dois: string[];\n  isbns: string[];\n  unknowns: string[];\n}\n\n/**\n * Classify identifiers into PMIDs, DOIs, and unknowns\n */\nfunction classifyIdentifiers(identifiers: string[]): ClassifiedIdentifiers {\n  const pmids: string[] = [];\n  const dois: string[] = [];\n  const isbns: string[] = [];\n  const unknowns: string[] = [];\n\n  for (const id of identifiers) {\n    if (isPmid(id)) {\n      pmids.push(normalizePmid(id));\n    } else if (isDoi(id)) {\n      dois.push(normalizeDoi(id));\n    } else if (isIsbn(id)) {\n      isbns.push(normalizeIsbn(id));\n    } else {\n      unknowns.push(id);\n    }\n  }\n\n  return { pmids, dois, isbns, unknowns };\n}\n\n/**\n * Build error results for unknown identifiers\n */\nfunction buildUnknownResults(unknowns: string[]): ImportItemResult[] {\n  return unknowns.map((unknown) => ({\n    success: false as const,\n    error: `Cannot interpret '${unknown}' as identifier (not a valid PMID or DOI)`,\n    source: unknown,\n    reason: \"validation_error\" as const,\n  }));\n}\n\n/**\n * Clear the id from a fetched item to force regeneration using author-year format\n * Identifiers (PMID, DOI, ISBN) from APIs may have non-standard IDs that should not be used\n */\nfunction clearItemId(item: CslItem): CslItem {\n  const { id: _ignored, ...rest } = item;\n  return { ...rest, id: \"\" };\n}\n\n/**\n * Fetch PMIDs with cache support\n */\nasync function fetchPmidsWithCache(\n  pmids: string[],\n  pubmedConfig: PubmedConfig\n): Promise<ImportItemResult[]> {\n  const results: ImportItemResult[] = [];\n  const pmidsToFetch: string[] = [];\n\n  // Check cache first\n  for (const pmid of pmids) {\n    const cached = getPmidFromCache(pmid);\n    if (cached) {\n      results.push({ success: true, item: clearItemId(cached), source: pmid });\n    } else {\n      pmidsToFetch.push(pmid);\n    }\n  }\n\n  // Fetch uncached PMIDs\n  if (pmidsToFetch.length > 0) {\n    const fetchResults = await fetchPmids(pmidsToFetch, pubmedConfig);\n    for (const fetchResult of fetchResults) {\n      if (fetchResult.success) {\n        cachePmidResult(fetchResult.pmid, fetchResult.item);\n        results.push({\n          success: true,\n          item: clearItemId(fetchResult.item),\n          source: fetchResult.pmid,\n        });\n      } else {\n        results.push({\n          success: false,\n          error: fetchResult.error,\n          source: fetchResult.pmid,\n          reason: fetchResult.reason,\n        });\n      }\n    }\n  }\n\n  return results;\n}\n\n/**\n * Fetch DOIs with cache support\n */\nasync function fetchDoisWithCache(dois: string[]): Promise<ImportItemResult[]> {\n  const results: ImportItemResult[] = [];\n\n  for (const doi of dois) {\n    const cached = getDoiFromCache(doi);\n    if (cached) {\n      results.push({ success: true, item: clearItemId(cached), source: doi });\n      continue;\n    }\n\n    const fetchResult = await fetchDoi(doi);\n    if (fetchResult.success) {\n      cacheDoiResult(doi, fetchResult.item);\n      results.push({ success: true, item: clearItemId(fetchResult.item), source: doi });\n    } else {\n      results.push({\n        success: false,\n        error: fetchResult.error,\n        source: doi,\n        reason: fetchResult.reason,\n      });\n    }\n  }\n\n  return results;\n}\n\n/**\n * Fetch ISBNs with caching\n */\nasync function fetchIsbnsWithCache(isbns: string[]): Promise<ImportItemResult[]> {\n  const results: ImportItemResult[] = [];\n\n  for (const isbn of isbns) {\n    const cached = getIsbnFromCache(isbn);\n    if (cached) {\n      results.push({ success: true, item: clearItemId(cached), source: isbn });\n      continue;\n    }\n\n    const fetchResult = await fetchIsbn(isbn);\n    if (fetchResult.success) {\n      cacheIsbnResult(isbn, fetchResult.item);\n      results.push({ success: true, item: clearItemId(fetchResult.item), source: isbn });\n    } else {\n      results.push({\n        success: false,\n        error: fetchResult.error,\n        source: isbn,\n        reason: fetchResult.reason,\n      });\n    }\n  }\n\n  return results;\n}\n\n/**\n * Parse JSON content and return import result\n */\nfunction parseJsonContent(content: string): ImportResult {\n  try {\n    const parsed = JSON.parse(content);\n    const items: unknown[] = Array.isArray(parsed) ? parsed : [parsed];\n\n    if (items.length === 0) {\n      return { results: [] };\n    }\n\n    const results: ImportItemResult[] = [];\n    for (const item of items) {\n      const parseResult = CslItemSchema.safeParse(item);\n      if (parseResult.success) {\n        results.push({ success: true, item: parseResult.data, source: \"json\" });\n      } else {\n        results.push({\n          success: false,\n          error: `Invalid CSL-JSON: ${parseResult.error.message}`,\n          source: \"json\",\n          reason: \"validation_error\",\n        });\n      }\n    }\n    return { results };\n  } catch (error) {\n    const message = error instanceof Error ? error.message : String(error);\n    return {\n      results: [\n        {\n          success: false,\n          error: `Failed to parse JSON: ${message}`,\n          source: \"json\",\n          reason: \"parse_error\",\n        },\n      ],\n    };\n  }\n}\n\n/**\n * Parse BibTeX content and return import result\n */\nfunction parseBibtexContent(content: string): ImportResult {\n  const parseResult = parseBibtex(content);\n\n  if (!parseResult.success) {\n    return {\n      results: [\n        {\n          success: false,\n          error: parseResult.error ?? \"Failed to parse BibTeX\",\n          source: \"bibtex\",\n          reason: \"parse_error\",\n        },\n      ],\n    };\n  }\n\n  if (parseResult.items.length === 0) {\n    return { results: [] };\n  }\n\n  return {\n    results: parseResult.items.map((item) => ({\n      success: true as const,\n      item,\n      source: \"bibtex\",\n    })),\n  };\n}\n\n/**\n * Parse RIS content and return import result\n */\nfunction parseRisContent(content: string): ImportResult {\n  const parseResult = parseRis(content);\n\n  if (!parseResult.success) {\n    return {\n      results: [\n        {\n          success: false,\n          error: parseResult.error ?? \"Failed to parse RIS\",\n          source: \"ris\",\n          reason: \"parse_error\",\n        },\n      ],\n    };\n  }\n\n  if (parseResult.items.length === 0) {\n    return { results: [] };\n  }\n\n  return {\n    results: parseResult.items.map((item) => ({\n      success: true as const,\n      item,\n      source: \"ris\",\n    })),\n  };\n}\n\n/**\n * Parse NBIB content and return import result\n */\nfunction parseNbibContent(content: string): ImportResult {\n  const parseResult = parseNbib(content);\n\n  if (!parseResult.success) {\n    return {\n      results: [\n        {\n          success: false,\n          error: parseResult.error ?? \"Failed to parse NBIB\",\n          source: \"nbib\",\n          reason: \"parse_error\",\n        },\n      ],\n    };\n  }\n\n  if (parseResult.items.length === 0) {\n    return { results: [] };\n  }\n\n  return {\n    results: parseResult.items.map((item) => ({\n      success: true as const,\n      item,\n      source: \"nbib\",\n    })),\n  };\n}\n\n/**\n * Import references from content string\n *\n * @param content - The content to parse\n * @param format - The format of the content (or \"auto\" for detection)\n * @param options - Import options\n * @returns Import result with parsed items\n */\nexport async function importFromContent(\n  content: string,\n  format: InputFormat | \"auto\",\n  _options: ImportOptions\n): Promise<ImportResult> {\n  // Determine the actual format\n  let actualFormat: InputFormat;\n  if (format === \"auto\") {\n    actualFormat = detectByContent(content);\n    if (actualFormat === \"unknown\") {\n      return {\n        results: [\n          {\n            success: false,\n            error: \"Cannot detect input format. Use --format to specify explicitly.\",\n            source: \"content\",\n            reason: \"validation_error\",\n          },\n        ],\n      };\n    }\n  } else {\n    actualFormat = format;\n  }\n\n  // Parse based on format\n  switch (actualFormat) {\n    case \"json\":\n      return parseJsonContent(content);\n    case \"bibtex\":\n      return parseBibtexContent(content);\n    case \"ris\":\n      return parseRisContent(content);\n    case \"nbib\":\n      return parseNbibContent(content);\n    default:\n      return {\n        results: [\n          {\n            success: false,\n            error: `Unsupported format for content parsing: ${actualFormat}`,\n            source: \"content\",\n            reason: \"validation_error\",\n          },\n        ],\n      };\n  }\n}\n\n/**\n * Import references from identifier strings (PMID or DOI)\n *\n * @param identifiers - Array of identifier strings\n * @param options - Import options (requires pubmedConfig for PMID fetching)\n * @returns Import result with fetched items\n */\nexport async function importFromIdentifiers(\n  identifiers: string[],\n  options: ImportOptions\n): Promise<ImportResult> {\n  if (identifiers.length === 0) {\n    return { results: [] };\n  }\n\n  // Classify identifiers\n  const { pmids, dois, isbns, unknowns } = classifyIdentifiers(identifiers);\n\n  // Collect results\n  const results: ImportItemResult[] = [];\n\n  // Add errors for unknown identifiers\n  results.push(...buildUnknownResults(unknowns));\n\n  // Fetch PMIDs with cache\n  const pmidResults = await fetchPmidsWithCache(pmids, options.pubmedConfig ?? {});\n  results.push(...pmidResults);\n\n  // Fetch DOIs with cache\n  const doiResults = await fetchDoisWithCache(dois);\n  results.push(...doiResults);\n\n  // Fetch ISBNs with cache\n  const isbnResults = await fetchIsbnsWithCache(isbns);\n  results.push(...isbnResults);\n\n  return { results };\n}\n\n/**\n * Options for importFromInputs\n */\nexport interface ImportInputsOptions extends ImportOptions {\n  /** Explicit format specification (default: auto) */\n  format?: InputFormat | \"auto\";\n  /** Content from stdin (if provided, processed before file/identifier inputs) */\n  stdinContent?: string;\n}\n\n/**\n * Unified entry point for importing references from file paths or identifiers\n *\n * Classifies inputs as files or identifiers:\n * - If path exists as file → read and parse\n * - If path does not exist → interpret as identifier (PMID/DOI)\n *\n * @param inputs - Array of file paths or identifier strings\n * @param options - Import options including format specification\n * @returns Import result with all parsed/fetched items\n */\n\n/**\n * Check if input looks like a file path (has file-like extension)\n */\nfunction looksLikeFilePath(input: string): boolean {\n  const fileExtensions = [\".json\", \".bib\", \".ris\", \".txt\", \".xml\", \".yaml\", \".yml\"];\n  const lowerInput = input.toLowerCase();\n  return fileExtensions.some((ext) => lowerInput.endsWith(ext));\n}\n\n/**\n * Process a single file input\n */\nasync function processFile(\n  filePath: string,\n  options: ImportInputsOptions\n): Promise<ImportItemResult[]> {\n  try {\n    const content = readFileSync(filePath, \"utf-8\");\n\n    // Determine format\n    let format: InputFormat | \"auto\";\n    if (options.format && options.format !== \"auto\") {\n      format = options.format;\n    } else {\n      // Try extension first\n      const extFormat = detectByExtension(filePath);\n      format = extFormat !== \"unknown\" ? extFormat : \"auto\";\n    }\n\n    const result = await importFromContent(content, format, options);\n\n    // Update source to be the file path\n    return result.results.map((r) => ({\n      ...r,\n      source: filePath,\n    }));\n  } catch (error) {\n    const message = error instanceof Error ? error.message : String(error);\n    return [\n      {\n        success: false,\n        error: `Failed to read file: ${message}`,\n        source: filePath,\n        reason: \"fetch_error\",\n      },\n    ];\n  }\n}\n\n/**\n * Process identifier inputs (PMID/DOI)\n */\nasync function processIdentifiers(\n  inputs: string[],\n  options: ImportInputsOptions\n): Promise<ImportItemResult[]> {\n  const results: ImportItemResult[] = [];\n  const validIdentifiers: string[] = [];\n\n  // Separate valid identifiers from invalid inputs\n  for (const input of inputs) {\n    // Check if it's a valid identifier\n    const isValidPmid = isPmid(input);\n    const isValidDoi = isDoi(input);\n    const isValidIsbn = isIsbn(input);\n\n    if (isValidPmid || isValidDoi || isValidIsbn) {\n      validIdentifiers.push(input);\n    } else {\n      // Not a valid identifier\n      const hint = looksLikeFilePath(input)\n        ? \" Hint: If this is a file path, check that the file exists.\"\n        : \"\";\n      results.push({\n        success: false,\n        error: `Cannot interpret '${input}' as identifier (not a valid PMID, DOI, or ISBN).${hint}`,\n        source: input,\n        reason: \"validation_error\",\n      });\n    }\n  }\n\n  // Fetch valid identifiers\n  if (validIdentifiers.length > 0) {\n    const fetchResult = await importFromIdentifiers(validIdentifiers, options);\n    results.push(...fetchResult.results);\n  }\n\n  return results;\n}\n\nexport async function importFromInputs(\n  inputs: string[],\n  options: ImportInputsOptions\n): Promise<ImportResult> {\n  const allResults: ImportItemResult[] = [];\n\n  // Process stdinContent if provided\n  if (options.stdinContent?.trim()) {\n    const stdinResults = await processStdinContent(options.stdinContent, options);\n    allResults.push(...stdinResults);\n  }\n\n  // Process file/identifier inputs\n  if (inputs.length > 0) {\n    const identifiersToFetch: string[] = [];\n\n    // Process each input\n    for (const input of inputs) {\n      if (existsSync(input)) {\n        // Input is an existing file\n        const fileResults = await processFile(input, options);\n        allResults.push(...fileResults);\n      } else {\n        // Input does not exist as file - treat as potential identifier\n        identifiersToFetch.push(input);\n      }\n    }\n\n    // Process identifiers\n    if (identifiersToFetch.length > 0) {\n      const identifierResults = await processIdentifiers(identifiersToFetch, options);\n      allResults.push(...identifierResults);\n    }\n  }\n\n  return { results: allResults };\n}\n\n/**\n * Process stdin content based on format detection\n * - For file formats (json/bibtex/ris): parse directly\n * - For identifier formats (pmid/doi) or auto with identifiers: split and process\n */\nasync function processStdinContent(\n  content: string,\n  options: ImportInputsOptions\n): Promise<ImportItemResult[]> {\n  const format = options.format || \"auto\";\n\n  // If explicit file format specified, parse as content\n  if (format === \"json\" || format === \"bibtex\" || format === \"ris\" || format === \"nbib\") {\n    const result = await importFromContent(content, format, options);\n    return result.results.map((r) => ({\n      ...r,\n      source: r.source === \"content\" ? \"stdin\" : r.source,\n    }));\n  }\n\n  // If explicit identifier format, split and process\n  if (format === \"pmid\" || format === \"doi\" || format === \"isbn\") {\n    const identifiers = content.split(/\\s+/).filter((s) => s.length > 0);\n    return processIdentifiers(identifiers, options);\n  }\n\n  // Auto-detect format from content\n  const detectedFormat = detectByContent(content);\n\n  if (\n    detectedFormat === \"json\" ||\n    detectedFormat === \"bibtex\" ||\n    detectedFormat === \"ris\" ||\n    detectedFormat === \"nbib\"\n  ) {\n    // File format detected - parse as content\n    const result = await importFromContent(content, detectedFormat, options);\n    return result.results.map((r) => ({\n      ...r,\n      source: r.source === \"content\" ? \"stdin\" : r.source,\n    }));\n  }\n\n  // Not a file format - treat as whitespace-separated identifiers\n  const identifiers = content.split(/\\s+/).filter((s) => s.length > 0);\n  if (identifiers.length === 0) {\n    return [];\n  }\n\n  return processIdentifiers(identifiers, options);\n}\n","import type { CslItem } from \"../../core/csl-json/types.js\";\nimport { generateId } from \"../../core/identifier/generator.js\";\nimport type { ILibrary } from \"../../core/library-interface.js\";\nimport { detectDuplicate } from \"../duplicate/detector.js\";\nimport type { InputFormat } from \"../import/detector.js\";\nimport type { PubmedConfig } from \"../import/fetcher.js\";\nimport {\n  type ImportInputsOptions,\n  type ImportItemResult,\n  importFromInputs,\n} from \"../import/importer.js\";\n\n// Re-export FailureReason for external use\nexport type { FailureReason } from \"../import/importer.js\";\n\n/**\n * Options for adding references\n */\nexport interface AddReferencesOptions {\n  /** Skip duplicate detection */\n  force?: boolean;\n  /** Explicit input format (default: auto) */\n  format?: InputFormat | \"auto\";\n  /** PubMed API configuration */\n  pubmedConfig?: PubmedConfig;\n  /** Content from stdin (if provided, processed before file/identifier inputs) */\n  stdinContent?: string;\n}\n\n/**\n * Information about a successfully added reference\n */\nexport interface AddedItem {\n  source: string;\n  id: string;\n  uuid: string;\n  title: string;\n  /** True if the original ID from source file was changed due to collision */\n  idChanged?: boolean;\n  /** Original ID from source file before collision resolution */\n  originalId?: string;\n}\n\n/**\n * Information about a failed import\n */\nexport interface FailedItem {\n  source: string;\n  error: string;\n  reason: import(\"../import/importer.js\").FailureReason;\n}\n\n/**\n * Information about a skipped duplicate\n */\nexport interface SkippedItem {\n  source: string;\n  existingId: string;\n  duplicateType: import(\"../duplicate/types.js\").DuplicateType;\n}\n\n/**\n * Result of addReferences operation\n */\nexport interface AddReferencesResult {\n  added: AddedItem[];\n  failed: FailedItem[];\n  skipped: SkippedItem[];\n}\n\n/**\n * Add references to a library from various input sources.\n *\n * This function orchestrates:\n * 1. Import from inputs (files or identifiers)\n * 2. Duplicate detection (unless force=true)\n * 3. ID collision resolution\n * 4. Library save\n *\n * @param inputs - File paths or identifiers (PMID, DOI)\n * @param library - Target library\n * @param options - Add options\n * @returns Result with added, failed, and skipped items\n */\nexport async function addReferences(\n  inputs: string[],\n  library: ILibrary,\n  options: AddReferencesOptions\n): Promise<AddReferencesResult> {\n  const added: AddedItem[] = [];\n  const failed: FailedItem[] = [];\n  const skipped: SkippedItem[] = [];\n\n  // 1. Import from inputs\n  const importOptions = buildImportOptions(options);\n  const importResult = await importFromInputs(inputs, importOptions);\n\n  // Get existing items for duplicate/collision checks (getAll now returns CslItem[] directly)\n  const existingItems = await library.getAll();\n\n  // Track IDs we've added in this batch (for collision detection within batch)\n  const addedIds = new Set<string>();\n\n  // 2. Process each import result\n  for (const result of importResult.results) {\n    const processed = await processImportResult(\n      result,\n      existingItems,\n      addedIds,\n      options.force ?? false,\n      library\n    );\n\n    if (processed.type === \"failed\") {\n      failed.push(processed.item);\n    } else if (processed.type === \"skipped\") {\n      skipped.push(processed.item);\n    } else {\n      added.push(processed.item);\n    }\n  }\n\n  // 3. Save library if any items were added\n  if (added.length > 0) {\n    await library.save();\n  }\n\n  return { added, failed, skipped };\n}\n\n/**\n * Build import options from add options\n */\nfunction buildImportOptions(options: AddReferencesOptions): ImportInputsOptions {\n  const importOptions: ImportInputsOptions = {};\n  if (options.format !== undefined) {\n    importOptions.format = options.format;\n  }\n  if (options.pubmedConfig !== undefined) {\n    importOptions.pubmedConfig = options.pubmedConfig;\n  }\n  if (options.stdinContent !== undefined) {\n    importOptions.stdinContent = options.stdinContent;\n  }\n  return importOptions;\n}\n\ntype ProcessResult =\n  | { type: \"added\"; item: AddedItem }\n  | { type: \"failed\"; item: FailedItem }\n  | { type: \"skipped\"; item: SkippedItem };\n\n/**\n * Process a single import result\n */\nasync function processImportResult(\n  result: ImportItemResult,\n  existingItems: CslItem[],\n  addedIds: Set<string>,\n  force: boolean,\n  library: ILibrary\n): Promise<ProcessResult> {\n  if (!result.success) {\n    return {\n      type: \"failed\",\n      item: { source: result.source, error: result.error, reason: result.reason },\n    };\n  }\n\n  const item = result.item;\n\n  // Check for duplicates (unless force=true)\n  if (!force) {\n    const duplicateResult = detectDuplicate(item, existingItems);\n    const existingMatch = duplicateResult.matches[0];\n    if (existingMatch) {\n      return {\n        type: \"skipped\",\n        item: {\n          source: result.source,\n          existingId: existingMatch.existing.id ?? \"\",\n          duplicateType: existingMatch.type,\n        },\n      };\n    }\n  }\n\n  // Resolve ID collision\n  // Prioritize original ID from source file; generate ID only if not present\n  const allExistingIds = new Set([...existingItems.map((i) => i.id), ...addedIds]);\n  const originalId = item.id?.trim() || \"\";\n  const hasOriginalId = originalId.length > 0;\n  const baseId = hasOriginalId ? originalId : generateId(item);\n  const { id, changed } = resolveIdCollision(baseId, allExistingIds);\n\n  const finalItem: CslItem = { ...item, id };\n\n  // Add to library\n  const addedToLibrary = await library.add(finalItem);\n  addedIds.add(id);\n\n  // Build result (uuid comes from the library-added item which has ensured UUID)\n  const uuid = addedToLibrary.custom?.uuid ?? \"\";\n  const addedItem: AddedItem = {\n    source: result.source,\n    id,\n    uuid,\n    title: typeof finalItem.title === \"string\" ? finalItem.title : \"\",\n  };\n\n  // Report idChanged only when original ID from source was changed due to collision\n  // Generated ID collisions are internal and not reported\n  if (hasOriginalId && changed) {\n    addedItem.idChanged = true;\n    addedItem.originalId = originalId;\n  }\n\n  return { type: \"added\", item: addedItem };\n}\n\n/**\n * Generate an alphabetic suffix for ID collision resolution.\n * 0 -> 'a', 1 -> 'b', ..., 25 -> 'z', 26 -> 'aa', etc.\n */\nfunction generateSuffix(index: number): string {\n  const alphabet = \"abcdefghijklmnopqrstuvwxyz\";\n  let suffix = \"\";\n  let n = index;\n\n  do {\n    suffix = alphabet[n % 26] + suffix;\n    n = Math.floor(n / 26) - 1;\n  } while (n >= 0);\n\n  return suffix;\n}\n\n/**\n * Resolve ID collision by appending alphabetic suffix.\n */\nfunction resolveIdCollision(\n  baseId: string,\n  existingIds: Set<string>\n): { id: string; changed: boolean } {\n  if (!existingIds.has(baseId)) {\n    return { id: baseId, changed: false };\n  }\n\n  // Find next available suffix\n  let index = 0;\n  let newId: string;\n\n  do {\n    const suffix = generateSuffix(index);\n    newId = `${baseId}${suffix}`;\n    index++;\n  } while (existingIds.has(newId));\n\n  return { id: newId, changed: true };\n}\n","import { Hono } from \"hono\";\nimport type { Config } from \"../../config/schema.js\";\nimport type { Library } from \"../../core/library.js\";\nimport type { InputFormat } from \"../../features/import/detector.js\";\nimport type { PubmedConfig } from \"../../features/import/fetcher.js\";\nimport { type AddReferencesOptions, addReferences } from \"../../features/operations/add.js\";\n\n/**\n * Build PubmedConfig from config, filtering out undefined values\n * to satisfy exactOptionalPropertyTypes requirements.\n */\nfunction buildPubmedConfig(config: Config): PubmedConfig {\n  const pubmedConfig: PubmedConfig = {};\n  if (config.pubmed.email !== undefined) {\n    pubmedConfig.email = config.pubmed.email;\n  }\n  if (config.pubmed.apiKey !== undefined) {\n    pubmedConfig.apiKey = config.pubmed.apiKey;\n  }\n  return pubmedConfig;\n}\n\n/**\n * Create add route for importing references.\n * @param library - Library instance to use for operations\n * @param config - Configuration with PubMed settings\n * @returns Hono app with add route\n */\nexport function createAddRoute(library: Library, config: Config) {\n  const route = new Hono();\n\n  // POST / - Add references from inputs\n  route.post(\"/\", async (c) => {\n    // Parse request body\n    let body: unknown;\n    try {\n      body = await c.req.json();\n    } catch {\n      return c.json({ error: \"Invalid JSON\" }, 400);\n    }\n\n    // Validate inputs\n    if (!body || typeof body !== \"object\") {\n      return c.json({ error: \"Request body must be an object\" }, 400);\n    }\n\n    const { inputs, options } = body as {\n      inputs?: unknown;\n      options?: { force?: boolean; format?: string };\n    };\n\n    if (!inputs || !Array.isArray(inputs) || inputs.length === 0) {\n      return c.json({ error: \"inputs must be a non-empty array of strings\" }, 400);\n    }\n\n    // Ensure all inputs are strings\n    if (!inputs.every((input) => typeof input === \"string\")) {\n      return c.json({ error: \"All inputs must be strings\" }, 400);\n    }\n\n    // Build options\n    const addOptions: AddReferencesOptions = {\n      force: options?.force ?? false,\n      pubmedConfig: buildPubmedConfig(config),\n    };\n\n    if (options?.format) {\n      addOptions.format = options.format as InputFormat | \"auto\";\n    }\n\n    // Call addReferences\n    const result = await addReferences(inputs as string[], library, addOptions);\n\n    return c.json(result);\n  });\n\n  return route;\n}\n","import { isBuiltinStyle, resolveStyle } from \"../../config/csl-styles.js\";\nimport type { CslItem } from \"../../core/csl-json/types.js\";\nimport type { ILibrary, IdentifierType } from \"../../core/library-interface.js\";\nimport {\n  formatBibliography,\n  formatBibliographyCSL,\n  formatInText,\n  formatInTextCSL,\n} from \"../format/index.js\";\n\n/**\n * Options for citeReferences operation\n */\nexport interface CiteOperationOptions {\n  /** Reference IDs or UUIDs to cite */\n  identifiers: string[];\n  /** Identifier type: 'id' (default), 'uuid', 'doi', 'pmid', or 'isbn' */\n  idType?: IdentifierType;\n  /** CSL style name or path to CSL file */\n  style?: string;\n  /** Path to custom CSL file */\n  cslFile?: string;\n  /** Default style from config (used when style is not specified) */\n  defaultStyle?: string;\n  /** Directory or directories to search for custom CSL files */\n  cslDirectory?: string | string[];\n  /** Locale for citation formatting (default: \"en-US\") */\n  locale?: string;\n  /** Output format (default: \"text\") */\n  format?: \"text\" | \"html\" | \"rtf\";\n  /** If true, generate in-text citation instead of bibliography */\n  inText?: boolean;\n}\n\n/**\n * Result for a single citation\n */\nexport type CiteItemResult =\n  | { success: true; identifier: string; citation: string }\n  | { success: false; identifier: string; error: string };\n\n/**\n * Result of citeReferences operation\n */\nexport interface CiteResult {\n  /** Results for each identifier */\n  results: CiteItemResult[];\n}\n\ninterface FormatOptions {\n  style?: string | undefined;\n  styleXml?: string | undefined;\n  locale?: string | undefined;\n  format?: \"text\" | \"html\" | \"rtf\" | undefined;\n}\n\n/**\n * Check if fallback formatter should be used.\n */\nfunction shouldUseFallback(style: string | undefined, hasCustomXml: boolean): boolean {\n  if (hasCustomXml) {\n    return false;\n  }\n  if (style && !isBuiltinStyle(style)) {\n    return true;\n  }\n  return false;\n}\n\n/**\n * Format a single item as citation.\n */\nfunction formatCitation(item: CslItem, inText: boolean, options: FormatOptions): string {\n  const useFallback = shouldUseFallback(options.style, !!options.styleXml);\n  const style = options.style ?? \"apa\";\n  const locale = options.locale ?? \"en-US\";\n  const format = options.format ?? \"text\";\n  const styleXml = options.styleXml;\n\n  if (useFallback) {\n    return inText ? formatInText([item]) : formatBibliography([item]);\n  }\n\n  const formatOptions = { style, locale, format, ...(styleXml && { styleXml }) };\n  return inText\n    ? formatInTextCSL([item], formatOptions)\n    : formatBibliographyCSL([item], formatOptions);\n}\n\n/**\n * Generate citation for a single identifier.\n */\nasync function generateCitationForIdentifier(\n  library: ILibrary,\n  identifier: string,\n  idType: IdentifierType,\n  inText: boolean,\n  options: FormatOptions\n): Promise<CiteItemResult> {\n  const item = await library.find(identifier, { idType });\n\n  if (!item) {\n    const lookupType = idType === \"uuid\" ? \"UUID\" : idType.toUpperCase();\n    return {\n      success: false,\n      identifier,\n      error: `Reference with ${lookupType} '${identifier}' not found`,\n    };\n  }\n\n  const citation = formatCitation(item, inText, options);\n\n  return {\n    success: true,\n    identifier,\n    citation,\n  };\n}\n\n/**\n * Generate citations for references.\n *\n * @param library - The library to cite from\n * @param options - Citation options including identifiers and style settings\n * @returns Results array with citation or error for each identifier\n */\nexport async function citeReferences(\n  library: ILibrary,\n  options: CiteOperationOptions\n): Promise<CiteResult> {\n  const {\n    identifiers,\n    idType = \"id\",\n    inText = false,\n    style,\n    cslFile,\n    defaultStyle,\n    cslDirectory,\n    locale,\n    format,\n  } = options;\n  const results: CiteItemResult[] = [];\n\n  // Resolve style using the full resolution chain:\n  // 1. cslFile (exact path)\n  // 2. style (if built-in)\n  // 3. Search in cslDirectory\n  // 4. defaultStyle (if built-in or found in cslDirectory)\n  // 5. Fallback to 'apa'\n  const resolution = resolveStyle({\n    ...(cslFile !== undefined && { cslFile }),\n    ...(style !== undefined && { style }),\n    ...(defaultStyle !== undefined && { defaultStyle }),\n    ...(cslDirectory !== undefined && { cslDirectory }),\n  });\n\n  for (const identifier of identifiers) {\n    const result = await generateCitationForIdentifier(library, identifier, idType, inText, {\n      style: resolution.styleName,\n      styleXml: resolution.styleXml,\n      locale,\n      format,\n    });\n    results.push(result);\n  }\n\n  return { results };\n}\n","import { Hono } from \"hono\";\nimport { z } from \"zod\";\nimport type { Library } from \"../../core/library.js\";\nimport {\n  type CiteOperationOptions,\n  type CiteResult,\n  citeReferences,\n} from \"../../features/operations/cite.js\";\n\n/**\n * Zod schema for cite request body\n */\nconst CiteRequestSchema = z.object({\n  identifiers: z.array(z.string()).min(1, \"identifiers must be a non-empty array\"),\n  idType: z.enum([\"id\", \"uuid\", \"doi\", \"pmid\", \"isbn\"]).optional(),\n  inText: z.boolean().optional(),\n  style: z.string().optional(),\n  cslFile: z.string().optional(),\n  locale: z.string().optional(),\n  format: z.enum([\"text\", \"html\"]).optional(),\n});\n\ntype CiteRequestBody = z.infer<typeof CiteRequestSchema>;\n\n/**\n * Build cite operation options from validated request body.\n */\nfunction buildCiteOptions(body: CiteRequestBody): CiteOperationOptions {\n  return {\n    identifiers: body.identifiers,\n    ...(body.idType !== undefined && { idType: body.idType }),\n    ...(body.inText !== undefined && { inText: body.inText }),\n    ...(body.style !== undefined && { style: body.style }),\n    ...(body.cslFile !== undefined && { cslFile: body.cslFile }),\n    ...(body.locale !== undefined && { locale: body.locale }),\n    ...(body.format !== undefined && { format: body.format }),\n  };\n}\n\n/**\n * Create cite route for generating citations.\n * @param library - Library instance to use for operations\n * @returns Hono app with cite route\n */\nexport function createCiteRoute(library: Library) {\n  const route = new Hono();\n\n  // POST / - Generate citations for identifiers\n  route.post(\"/\", async (c) => {\n    // Parse request body\n    let rawBody: unknown;\n    try {\n      rawBody = await c.req.json();\n    } catch {\n      return c.json({ error: \"Invalid JSON\" }, 400);\n    }\n\n    // Validate with zod schema\n    const parseResult = CiteRequestSchema.safeParse(rawBody);\n    if (!parseResult.success) {\n      const errorMessage = parseResult.error.issues[0]?.message ?? \"Invalid request body\";\n      return c.json({ error: errorMessage }, 400);\n    }\n\n    // Call citeReferences operation\n    const result: CiteResult = await citeReferences(library, buildCiteOptions(parseResult.data));\n\n    return c.json(result);\n  });\n\n  return route;\n}\n","import { Hono } from \"hono\";\n\n/**\n * Health check route.\n * Returns a simple status to verify the server is running.\n */\nexport const healthRoute = new Hono();\n\nhealthRoute.get(\"/\", (c) => {\n  return c.json({ status: \"ok\" });\n});\n","import type { CslItem } from \"../../core/csl-json/types.js\";\nimport type { ILibrary } from \"../../core/library-interface.js\";\nimport {\n  type PaginationOptions,\n  type SortField,\n  type SortOptions,\n  type SortOrder,\n  paginate,\n  sortReferences,\n} from \"../pagination/index.js\";\n\n/**\n * Options for listReferences operation\n */\nexport interface ListOptions extends PaginationOptions, SortOptions {}\n\n/**\n * Result of listReferences operation\n */\nexport interface ListResult {\n  /** Raw CslItem array */\n  items: CslItem[];\n  /** Total count before pagination */\n  total: number;\n  /** Applied limit (0 if unlimited) */\n  limit: number;\n  /** Applied offset */\n  offset: number;\n  /** Next page offset, null if no more results */\n  nextOffset: number | null;\n}\n\n/**\n * List all references from the library.\n *\n * @param library - The library to list references from\n * @param options - Pagination and sorting options\n * @returns Raw CslItem[] with pagination metadata\n */\nexport async function listReferences(library: ILibrary, options: ListOptions): Promise<ListResult> {\n  const sort: SortField = options.sort ?? \"updated\";\n  const order: SortOrder = options.order ?? \"desc\";\n  const limit = options.limit ?? 0;\n  const offset = options.offset ?? 0;\n\n  // Get all items\n  const allItems = await library.getAll();\n  const total = allItems.length;\n\n  // Sort\n  const sorted = sortReferences(allItems, sort, order);\n\n  // Paginate\n  const { items: paginatedItems, nextOffset } = paginate(sorted, { limit, offset });\n\n  return {\n    items: paginatedItems,\n    total,\n    limit,\n    offset,\n    nextOffset,\n  };\n}\n","import { Hono } from \"hono\";\nimport { z } from \"zod\";\nimport type { Library } from \"../../core/library.js\";\nimport { type ListOptions, listReferences } from \"../../features/operations/list.js\";\nimport { sortFieldSchema, sortOrderSchema } from \"../../features/pagination/index.js\";\nimport { pickDefined } from \"../../utils/object.js\";\n\n/**\n * Request body schema for list endpoint\n */\nconst listRequestBodySchema = z.object({\n  sort: sortFieldSchema.optional(),\n  order: sortOrderSchema.optional(),\n  limit: z.number().int().min(0).optional(),\n  offset: z.number().int().min(0).optional(),\n});\n\n/**\n * Request body type for list endpoint\n */\nexport type ListRequestBody = z.infer<typeof listRequestBodySchema>;\n\n/**\n * Creates list route for HTTP server\n */\nexport function createListRoute(library: Library) {\n  const route = new Hono();\n\n  // POST / - List all references\n  route.post(\"/\", async (c) => {\n    // Parse request body\n    let body: unknown;\n    try {\n      body = await c.req.json();\n    } catch {\n      return c.json({ error: \"Invalid JSON\" }, 400);\n    }\n\n    // Validate body with zod\n    const parseResult = listRequestBodySchema.safeParse(body);\n    if (!parseResult.success) {\n      const errorMessage = parseResult.error.issues[0]?.message ?? \"Invalid request body\";\n      return c.json({ error: errorMessage }, 400);\n    }\n\n    const requestBody = parseResult.data;\n\n    // Build options for listReferences\n    const options: ListOptions = pickDefined(requestBody, [\n      \"sort\",\n      \"order\",\n      \"limit\",\n      \"offset\",\n    ] as const);\n\n    // Call listReferences operation - always returns raw CslItem[]\n    const result = await listReferences(library, options);\n\n    return c.json(result);\n  });\n\n  return route;\n}\n","import type { CslItem } from \"../../core/csl-json/types.js\";\nimport type { ILibrary, IdentifierType } from \"../../core/library-interface.js\";\n\n/**\n * Options for updateReference operation\n */\nexport interface UpdateOperationOptions {\n  /** Reference ID or UUID */\n  identifier: string;\n  /** Identifier type: 'id' (default), 'uuid', 'doi', 'pmid', or 'isbn' */\n  idType?: IdentifierType;\n  /** Partial updates to apply to the reference */\n  updates: Partial<CslItem>;\n  /** How to handle ID collision: 'fail' (default) or 'suffix' */\n  onIdCollision?: \"fail\" | \"suffix\";\n}\n\n/**\n * Result of updateReference operation\n */\nexport interface UpdateOperationResult {\n  /** Whether the update was successful */\n  updated: boolean;\n  /** The updated item (if successful) */\n  item?: CslItem;\n  /** The original item before update (when item is available) */\n  oldItem?: CslItem;\n  /** Error type when update failed (only when updated=false) */\n  errorType?: \"not_found\" | \"id_collision\";\n  /** True if the ID was changed due to collision resolution */\n  idChanged?: boolean;\n  /** The new ID after collision resolution (only when idChanged=true) */\n  newId?: string;\n}\n\n/**\n * Update a reference in the library.\n *\n * @param library - The library to update\n * @param options - Update options including identifier, updates, and collision handling\n * @returns Result indicating success and the updated item\n */\nexport async function updateReference(\n  library: ILibrary,\n  options: UpdateOperationOptions\n): Promise<UpdateOperationResult> {\n  const { identifier, idType = \"id\", updates, onIdCollision = \"fail\" } = options;\n\n  // Update the reference using unified update() method\n  const updateResult = await library.update(identifier, updates, { idType, onIdCollision });\n\n  if (!updateResult.updated) {\n    const result: UpdateOperationResult = { updated: false };\n    if (updateResult.errorType) {\n      result.errorType = updateResult.errorType;\n    }\n    if (updateResult.item) {\n      result.item = updateResult.item;\n    }\n    if (updateResult.idChanged && updateResult.newId) {\n      result.idChanged = true;\n      result.newId = updateResult.newId;\n    }\n    return result;\n  }\n\n  // Save the library\n  await library.save();\n\n  // Build result from UpdateResult (item is now included)\n  const result: UpdateOperationResult = { updated: true };\n\n  if (updateResult.item) {\n    result.item = updateResult.item;\n  }\n\n  if (updateResult.oldItem) {\n    result.oldItem = updateResult.oldItem;\n  }\n\n  if (updateResult.idChanged && updateResult.newId) {\n    result.idChanged = true;\n    result.newId = updateResult.newId;\n  }\n\n  return result;\n}\n","import { Hono } from \"hono\";\nimport type { Config, FulltextSource } from \"../../config/schema.js\";\nimport type { Library } from \"../../core/library.js\";\nimport {\n  fulltextConvert,\n  fulltextDiscover,\n  fulltextFetch,\n} from \"../../features/operations/fulltext/index.js\";\nimport { removeReference } from \"../../features/operations/remove.js\";\nimport { updateReference } from \"../../features/operations/update.js\";\n\n/**\n * Create references CRUD route with the given library.\n * @param library - Library instance to use for operations\n * @param config - Configuration for fulltext operations\n * @returns Hono app with references routes\n */\nexport function createReferencesRoute(library: Library, config?: Config) {\n  const route = new Hono();\n\n  // GET / - Get all references (getAll now returns Promise<CslItem[]>)\n  route.get(\"/\", async (c) => {\n    const items = await library.getAll();\n    return c.json(items);\n  });\n\n  // GET /uuid/:uuid - Get reference by UUID\n  route.get(\"/uuid/:uuid\", async (c) => {\n    const uuid = c.req.param(\"uuid\");\n    const item = await library.find(uuid, { idType: \"uuid\" });\n\n    if (!item) {\n      return c.json({ error: \"Reference not found\" }, 404);\n    }\n\n    return c.json(item);\n  });\n\n  // GET /id/:id - Get reference by citation ID\n  route.get(\"/id/:id\", async (c) => {\n    const id = c.req.param(\"id\");\n    const item = await library.find(id);\n\n    if (!item) {\n      return c.json({ error: \"Reference not found\" }, 404);\n    }\n\n    return c.json(item);\n  });\n\n  // POST / - Create new reference\n  route.post(\"/\", async (c) => {\n    try {\n      const body = await c.req.json();\n\n      // Create and add reference (library.add handles validation and returns the added item)\n      const addedItem = await library.add(body);\n\n      return c.json(addedItem, 201);\n    } catch (error) {\n      return c.json(\n        {\n          error: \"Invalid request body\",\n          details: error instanceof Error ? error.message : String(error),\n        },\n        400\n      );\n    }\n  });\n\n  // PUT /uuid/:uuid - Update reference by UUID\n  // Request body: { updates: Partial<CslItem>, onIdCollision?: \"fail\" | \"suffix\" }\n  route.put(\"/uuid/:uuid\", async (c) => {\n    const uuid = c.req.param(\"uuid\");\n\n    let body: unknown;\n    try {\n      body = await c.req.json();\n    } catch {\n      return c.json({ error: \"Invalid JSON\" }, 400);\n    }\n\n    if (!body || typeof body !== \"object\") {\n      return c.json({ error: \"Request body must be an object\" }, 400);\n    }\n\n    const { updates, onIdCollision } = body as {\n      updates?: Partial<import(\"../../core/csl-json/types.js\").CslItem>;\n      onIdCollision?: \"fail\" | \"suffix\";\n    };\n\n    if (!updates || typeof updates !== \"object\") {\n      return c.json({ error: \"Request body must contain 'updates' object\" }, 400);\n    }\n\n    // Use updateReference operation\n    const result = await updateReference(library, {\n      identifier: uuid,\n      idType: \"uuid\",\n      updates,\n      onIdCollision: onIdCollision ?? \"suffix\",\n    });\n\n    // Return operation result with appropriate status code\n    if (!result.updated) {\n      const status = result.errorType === \"id_collision\" ? 409 : 404;\n      return c.json(result, status);\n    }\n\n    return c.json(result);\n  });\n\n  // PUT /id/:id - Update reference by citation ID\n  // Request body: { updates: Partial<CslItem>, onIdCollision?: \"fail\" | \"suffix\" }\n  route.put(\"/id/:id\", async (c) => {\n    const id = c.req.param(\"id\");\n\n    let body: unknown;\n    try {\n      body = await c.req.json();\n    } catch {\n      return c.json({ error: \"Invalid JSON\" }, 400);\n    }\n\n    if (!body || typeof body !== \"object\") {\n      return c.json({ error: \"Request body must be an object\" }, 400);\n    }\n\n    const { updates, onIdCollision } = body as {\n      updates?: Partial<import(\"../../core/csl-json/types.js\").CslItem>;\n      onIdCollision?: \"fail\" | \"suffix\";\n    };\n\n    if (!updates || typeof updates !== \"object\") {\n      return c.json({ error: \"Request body must contain 'updates' object\" }, 400);\n    }\n\n    // Use updateReference operation with idType: 'id'\n    const result = await updateReference(library, {\n      identifier: id,\n      updates,\n      onIdCollision: onIdCollision ?? \"suffix\",\n    });\n\n    // Return operation result with appropriate status code\n    if (!result.updated) {\n      const status = result.errorType === \"id_collision\" ? 409 : 404;\n      return c.json(result, status);\n    }\n\n    return c.json(result);\n  });\n\n  // DELETE /uuid/:uuid - Delete reference by UUID\n  route.delete(\"/uuid/:uuid\", async (c) => {\n    const uuid = c.req.param(\"uuid\");\n\n    // Use removeReference operation\n    const result = await removeReference(library, {\n      identifier: uuid,\n      idType: \"uuid\",\n    });\n\n    // Return operation result with appropriate status code\n    if (!result.removed) {\n      return c.json(result, 404);\n    }\n\n    return c.json(result);\n  });\n\n  // DELETE /id/:id - Delete reference by citation ID\n  route.delete(\"/id/:id\", async (c) => {\n    const id = c.req.param(\"id\");\n\n    // Use removeReference operation\n    const result = await removeReference(library, {\n      identifier: id,\n    });\n\n    // Return operation result with appropriate status code\n    if (!result.removed) {\n      return c.json(result, 404);\n    }\n\n    return c.json(result);\n  });\n\n  // Fulltext retrieval routes (require config)\n  if (config) {\n    // GET /uuid/:uuid/fulltext/discover\n    route.get(\"/uuid/:uuid/fulltext/discover\", async (c) => {\n      const uuid = c.req.param(\"uuid\");\n      const result = await fulltextDiscover(library, {\n        identifier: uuid,\n        idType: \"uuid\",\n        fulltextConfig: config.fulltext,\n      });\n\n      if (!result.success) {\n        return c.json({ error: result.error }, 400);\n      }\n\n      return c.json(result);\n    });\n\n    // POST /uuid/:uuid/fulltext/fetch\n    route.post(\"/uuid/:uuid/fulltext/fetch\", async (c) => {\n      const uuid = c.req.param(\"uuid\");\n      let body: { source?: string; force?: boolean } = {};\n      try {\n        body = await c.req.json();\n      } catch {\n        // No body is OK - use defaults\n      }\n\n      const result = await fulltextFetch(library, {\n        identifier: uuid,\n        idType: \"uuid\",\n        fulltextConfig: config.fulltext,\n        fulltextDirectory: config.attachments.directory,\n        source: body.source as FulltextSource | undefined,\n        force: body.force,\n      });\n\n      if (!result.success) {\n        return c.json({ error: result.error }, 400);\n      }\n\n      return c.json(result);\n    });\n\n    // POST /uuid/:uuid/fulltext/convert\n    route.post(\"/uuid/:uuid/fulltext/convert\", async (c) => {\n      const uuid = c.req.param(\"uuid\");\n      const result = await fulltextConvert(library, {\n        identifier: uuid,\n        idType: \"uuid\",\n        fulltextDirectory: config.attachments.directory,\n      });\n\n      if (!result.success) {\n        return c.json({ error: result.error }, 400);\n      }\n\n      return c.json(result);\n    });\n  }\n\n  return route;\n}\n","import type { CslItem } from \"../../core/csl-json/types.js\";\nimport type { ILibrary } from \"../../core/library-interface.js\";\nimport {\n  type PaginationOptions,\n  type SearchSortField,\n  type SortField,\n  type SortOrder,\n  paginate,\n  sortReferences,\n} from \"../pagination/index.js\";\nimport { search } from \"../search/matcher.js\";\nimport { sortResults as sortByRelevance } from \"../search/sorter.js\";\nimport { tokenize } from \"../search/tokenizer.js\";\n\n/**\n * Sort options for search (includes relevance)\n */\nexport interface SearchSortOptions {\n  sort?: SearchSortField;\n  order?: SortOrder;\n}\n\n/**\n * Options for searchReferences operation\n */\nexport interface SearchOperationOptions extends PaginationOptions, SearchSortOptions {\n  /** Search query string */\n  query: string;\n}\n\n/**\n * Result of searchReferences operation\n */\nexport interface SearchResult {\n  /** Raw CslItem array */\n  items: CslItem[];\n  /** Total count before pagination */\n  total: number;\n  /** Applied limit (0 if unlimited) */\n  limit: number;\n  /** Applied offset */\n  offset: number;\n  /** Next page offset, null if no more results */\n  nextOffset: number | null;\n}\n\n/**\n * Search references in the library and return raw CslItem[] results.\n *\n * @param library - The library to search in\n * @param options - Search query and pagination options\n * @returns Raw CslItem[] with pagination metadata\n */\nexport async function searchReferences(\n  library: ILibrary,\n  options: SearchOperationOptions\n): Promise<SearchResult> {\n  const query = options.query;\n  const sort: SearchSortField = options.sort ?? \"updated\";\n  const order: SortOrder = options.order ?? \"desc\";\n  const limit = options.limit ?? 0;\n  const offset = options.offset ?? 0;\n\n  // Get all references\n  const allItems = await library.getAll();\n\n  // Search and get matched items\n  let matchedItems: CslItem[];\n  if (!query.trim()) {\n    matchedItems = allItems;\n  } else {\n    // Tokenize and search\n    const tokens = tokenize(query).tokens;\n    const results = search(allItems, tokens);\n\n    // If sorting 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400);\n    }\n\n    // Validate body with zod\n    const parseResult = searchRequestBodySchema.safeParse(body);\n    if (!parseResult.success) {\n      const errorMessage = parseResult.error.issues[0]?.message ?? \"Invalid request body\";\n      return c.json({ error: errorMessage }, 400);\n    }\n\n    const requestBody = parseResult.data;\n\n    // Build options for searchReferences\n    const options: SearchOperationOptions = {\n      query: requestBody.query,\n      ...pickDefined(requestBody, [\"sort\", \"order\", \"limit\", \"offset\"] as const),\n    };\n\n    // Call searchReferences operation - always returns raw CslItem[]\n    const result = await searchReferences(library, options);\n\n    return c.json(result);\n  });\n\n  return route;\n}\n","import { Hono } from \"hono\";\nimport type { Config } from \"../config/schema.js\";\nimport { Library } from \"../core/library.js\";\nimport { FileWatcher } from \"../features/file-watcher/file-watcher.js\";\nimport { createAddRoute } from \"./routes/add.js\";\nimport { createCiteRoute } from \"./routes/cite.js\";\nimport { healthRoute } from \"./routes/health.js\";\nimport { createListRoute } from \"./routes/list.js\";\nimport { createReferencesRoute } from \"./routes/references.js\";\nimport { createSearchRoute } from \"./routes/search.js\";\n\n/**\n * Result of starting a server with file watcher.\n */\nexport interface ServerWithFileWatcherResult {\n  /** The Hono application */\n  app: Hono;\n  /** The library instance */\n  library: Library;\n  /** The file watcher instance */\n  fileWatcher: FileWatcher;\n  /** Dispose function to clean up resources */\n  dispose: () => Promise<void>;\n}\n\n/**\n * Create the main Hono server application.\n * @param library - Library instance for the references API\n * @param config - Configuration for the server\n * @returns Hono application\n */\nexport function createServer(library: Library, config: Config) {\n  const app = new Hono();\n\n  // Health check route\n  app.route(\"/health\", healthRoute);\n\n  // References API routes\n  const referencesRoute = createReferencesRoute(library, config);\n  app.route(\"/api/references\", referencesRoute);\n\n  // Add references route\n  const addRoute = createAddRoute(library, config);\n  app.route(\"/api/add\", addRoute);\n\n  // Cite route\n  const citeRoute = createCiteRoute(library);\n  app.route(\"/api/cite\", citeRoute);\n\n  // List route\n  const listRoute = createListRoute(library);\n  app.route(\"/api/list\", listRoute);\n\n  // Search route\n  const searchRoute = createSearchRoute(library);\n  app.route(\"/api/search\", searchRoute);\n\n  return app;\n}\n\n/**\n * Start a server with file watcher for automatic library reload.\n * Uses the same pattern as MCP server file monitoring.\n * @param libraryPath - Path to the library file\n * @param config - Configuration for the server\n * @returns Server with file watcher result\n */\nexport async function startServerWithFileWatcher(\n  libraryPath: string,\n  config: Config\n): Promise<ServerWithFileWatcherResult> {\n  // Load library\n  const library = await Library.load(libraryPath);\n\n  // Create the Hono app\n  const app = createServer(library, config);\n\n  // Create and start file watcher\n  const fileWatcher = new FileWatcher(libraryPath, {\n    debounceMs: config.watch.debounceMs,\n    maxRetries: config.watch.maxRetries,\n    retryDelayMs: config.watch.retryIntervalMs,\n    pollIntervalMs: config.watch.pollIntervalMs,\n  });\n\n  // Listen for file changes\n  // Library.reload() handles self-write detection via hash comparison\n  fileWatcher.on(\"change\", () => {\n    library.reload().catch((error) => {\n      // Log error but don't crash - library continues with previous state\n      console.error(\"Failed to reload library:\", error);\n    });\n  });\n\n  await fileWatcher.start();\n\n  // Create dispose function\n  const dispose = async (): Promise<void> => {\n    fileWatcher.close();\n  };\n\n  return {\n    app,\n 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