import type { LcmsPlateCell, LcmsPlateType } from './utils/rack'

/** @deprecated Scheduled for removal in MINT 1.4; no SDK replacement. */
export type LcmsPolarity = 'POS' | 'NEG' | 'BOTH'
/** @deprecated Scheduled for removal in MINT 1.4; no SDK replacement. */
export type LcmsContainerType = 'VIAL' | 'PLATE'

/** @deprecated Scheduled for removal in MINT 1.4; no SDK replacement. */
export interface LcmsSequenceItem {
  sample_type: string
  file_name: string
  sample_id: string
  path: string
  instrument_method: string
  position: string
  injection_volume: number
}

/** @deprecated Scheduled for removal in MINT 1.4; no SDK replacement. */
export interface LcmsSequenceTableColumn {
  key: keyof LcmsSequenceItem | 'index' | 'actions'
  label: string
  align?: 'left' | 'right'
}

/** @deprecated Scheduled for removal in MINT 1.4; no SDK replacement. */
export const DEFAULT_LCMS_SEQUENCE_COLUMNS: LcmsSequenceTableColumn[] = [
  { key: 'index', label: '#' },
  { key: 'sample_type', label: 'Type' },
  { key: 'file_name', label: 'File Name' },
  { key: 'position', label: 'Position' },
  { key: 'instrument_method', label: 'Method' },
  { key: 'injection_volume', label: 'Inj Vol', align: 'right' },
]

/** @deprecated Scheduled for removal in MINT 1.4; no SDK replacement. */
export function extractLcmsCommonPrefix(fileNames: readonly string[]): string {
  if (fileNames.length === 0) return ''
  const stripped = fileNames.map(fileName => fileName.replace(/_\d{3}$/, ''))
  const prefixes = stripped.map((fileName) => {
    const match = fileName.match(/^(.+?)_(POS|NEG)_/i)
    return match ? match[1] : fileName.replace(/_[^_]+$/, '')
  })

  let common = prefixes[0] ?? ''
  for (const prefix of prefixes.slice(1)) {
    while (common && !prefix.startsWith(common)) {
      const index = common.lastIndexOf('_')
      common = index > 0 ? common.substring(0, index) : common.substring(0, common.length - 1)
    }
  }
  return common
}

/** @deprecated Scheduled for removal in MINT 1.4; no SDK replacement. */
export function extractLcmsSampleName(fileName: string, prefix = ''): string {
  let name = fileName.replace(/_\d{3}$/, '')
  if (prefix && name.startsWith(prefix)) {
    name = name.substring(prefix.length).replace(/^_+/, '')
  }
  name = name.replace(/^(POS|NEG)_/i, '')
  return name || fileName
}

/** @deprecated Scheduled for removal in MINT 1.4; no SDK replacement. */
export function lcmsWellIdFromPosition(position: string): string {
  return position.includes(':') ? position.split(':').pop() ?? position : position
}

/** @deprecated Scheduled for removal in MINT 1.4; no SDK replacement. */
export function inferLcmsPlateTypeFromWellIds(wellIds: readonly string[]): LcmsPlateType | null {
  let maxCol = 0
  let maxRow = 0
  for (const wellId of wellIds) {
    const match = wellId.match(/^([A-Z])(\d+)$/i)
    if (!match) continue
    maxRow = Math.max(maxRow, match[1].toUpperCase().charCodeAt(0) - 64)
    maxCol = Math.max(maxCol, Number(match[2]))
  }
  if (maxCol === 0 && maxRow === 0) return null
  return maxCol <= 9 && maxRow <= 6 ? '54vial' : '96well'
}

/** @deprecated Scheduled for removal in MINT 1.4; no SDK replacement. */
export function reconstructLcmsPlateCellsFromSequenceItems(
  items: readonly LcmsSequenceItem[],
): { cells: LcmsPlateCell[]; plateType: LcmsPlateType } | null {
  const unknownItems = items.filter(item => item.sample_type === 'Unknown')
  if (unknownItems.length === 0) return null

  const prefix = extractLcmsCommonPrefix(unknownItems.map(item => item.file_name))
  const seen = new Set<string>()
  const cells: LcmsPlateCell[] = []

  for (const item of unknownItems) {
    const wellId = lcmsWellIdFromPosition(item.position)
    if (seen.has(wellId)) continue
    seen.add(wellId)

    const match = wellId.match(/^([A-Z])(\d+)$/i)
    if (!match) continue
    cells.push({
      row: match[1].toUpperCase(),
      column: Number(match[2]),
      sample_name: extractLcmsSampleName(item.file_name, prefix),
    })
  }

  if (cells.length === 0) return null
  const plateType = inferLcmsPlateTypeFromWellIds(cells.map(cell => `${cell.row}${cell.column}`))
  if (!plateType) return null
  return { cells, plateType }
}

/** @deprecated Scheduled for removal in MINT 1.4; no SDK replacement. */
export function basenameFromWindowsPath(path: string | null | undefined): string {
  if (!path) return ''
  return path.split(/[\\/]/).pop() ?? path
}