import { describe, it, expect } from 'vitest'
import { readFileSync } from 'node:fs'
import { resolve } from 'node:path'
import {
  pickPrimaryDelimiter,
  splitMulti,
  detectClass,
  buildClassSchema,
  composeGroups,
} from '../../../composables/autoGroup'

const FIXTURE = resolve(__dirname, '../../fixtures/auto-group/mixed-lc-ms-batch.txt')

describe('mixed LC-MS batch integration', () => {
  const samples = readFileSync(FIXTURE, 'utf-8').trim().split('\n')
  const delim = pickPrimaryDelimiter(samples)
  const tokenized = samples.map(s => splitMulti(s, delim))
  const classes = detectClass(tokenized, {})

  it('detects exactly 81 Biological/Tissues samples', () => {
    const c = classes.find(c => c.kind === 'biological' && c.subKind === 'Tissues')
    expect(c?.members.length).toBe(81)
  })

  it('detects exactly 81 Biological/Plasma samples', () => {
    const c = classes.find(c => c.kind === 'biological' && c.subKind === 'Plasma')
    expect(c?.members.length).toBe(81)
  })

  it('detects exactly 3 IQC and 3 EQC samples', () => {
    const iqc = classes.find(c => c.kind === 'iqc')
    const eqc = classes.find(c => c.kind === 'eqc')
    expect(iqc?.members.length).toBe(3)
    expect(eqc?.members.length).toBe(3)
  })

  it('totals biological + QC overlay + excluded === 187', () => {
    const tissues = classes.find(c => c.kind === 'biological' && c.subKind === 'Tissues')
    const plasma = classes.find(c => c.kind === 'biological' && c.subKind === 'Plasma')
    const overlayKinds = ['iqc', 'eqc', 'standard', 'spike-in', 'stock', 'blank']
    const overlayCount = classes
      .filter(c => overlayKinds.includes(c.kind))
      .reduce((acc, c) => acc + c.members.length, 0)
    const unknownCount = classes
      .filter(c => c.kind === 'unknown')
      .reduce((acc, c) => acc + c.members.length, 0)
    expect((tissues?.members.length ?? 0) + (plasma?.members.length ?? 0) + overlayCount + unknownCount).toBe(187)
  })

  it('default workspace produces 3 Kidney/Liver/Tumor groups of 27 each', () => {
    const tissuesClass = classes.find(c => c.kind === 'biological' && c.subKind === 'Tissues')!
    const tissuesTokens = tissuesClass.members.map(i => tokenized[i])
    const schema = buildClassSchema(
      tissuesTokens,
      'biological',
      'Tissues',
      tissuesClass.classTagPositions,
    )
    // The Tissue column should be a factor with 3 unique values.
    const tissueCol = schema.columns.find(c => c.uniqueValues.length === 3 && c.role === 'factor')
    expect(tissueCol).toBeDefined()
    const result = composeGroups({
      tokenizedSamples: tokenized,
      sampleNames: samples,
      schemas: { 'biological:Tissues': { ...schema, groupBy: [tissueCol!.index] } },
      classes: [tissuesClass],
    })
    expect(result.experimentalGroups!.length).toBe(3)
    expect(result.experimentalGroups!.every(g => g.samples.length === 27)).toBe(true)
    const names = result.experimentalGroups!.map(g => g.name).sort()
    // Only the Tissues class is passed here, so no disambiguating class prefix
    // is applied: the organ factor is the first (major) hierarchy layer.
    expect(names).toEqual(['Kidney', 'Liver', 'Tumor'])
  })
})