import { describe, expect, it } from 'vitest'
import {
  basenameFromWindowsPath,
  extractLcmsCommonPrefix,
  extractLcmsSampleName,
  inferLcmsPlateTypeFromWellIds,
  lcmsWellIdFromPosition,
  reconstructLcmsPlateCellsFromSequenceItems,
} from '../../lcms'

describe('lcms utilities', () => {
  it('extracts common prefixes and sample names from Xcalibur file names', () => {
    const prefix = extractLcmsCommonPrefix([
      'Batch_01_NEG_S1_001',
      'Batch_01_NEG_S2_002',
      'Batch_01_NEG_QC_003',
    ])

    expect(prefix).toBe('Batch_01')
    expect(extractLcmsSampleName('Batch_01_NEG_S1_001', prefix)).toBe('S1')
  })

  it('infers plate type from well geometry', () => {
    expect(lcmsWellIdFromPosition('R:A1')).toBe('A1')
    expect(inferLcmsPlateTypeFromWellIds(['A1', 'F9'])).toBe('54vial')
    expect(inferLcmsPlateTypeFromWellIds(['A1', 'H12'])).toBe('96well')
  })

  it('reconstructs plate cells from sequence items while skipping controls', () => {
    const result = reconstructLcmsPlateCellsFromSequenceItems([
      {
        sample_type: 'Unknown',
        file_name: 'Batch_NEG_S1_001',
        sample_id: 'R:A1',
        path: '',
        instrument_method: 'C:\\Methods\\neg.meth',
        position: 'R:A1',
        injection_volume: 5,
      },
      {
        sample_type: 'Unknown',
        file_name: 'Batch_NEG_S2_002',
        sample_id: 'R:H12',
        path: '',
        instrument_method: 'C:\\Methods\\neg.meth',
        position: 'R:H12',
        injection_volume: 5,
      },
      {
        sample_type: 'Blank',
        file_name: 'Batch_NEG_Blank_003',
        sample_id: 'R:F9',
        path: '',
        instrument_method: 'C:\\Methods\\neg.meth',
        position: 'R:F9',
        injection_volume: 5,
      },
    ])

    expect(result).toEqual({
      plateType: '96well',
      cells: [
        { row: 'A', column: 1, sample_name: 'S1' },
        { row: 'H', column: 12, sample_name: 'S2' },
      ],
    })
  })

  it('extracts basenames from Windows and POSIX paths', () => {
    expect(basenameFromWindowsPath('C:\\Methods\\neg.meth')).toBe('neg.meth')
    expect(basenameFromWindowsPath('/methods/pos.meth')).toBe('pos.meth')
  })
})