import { idFromName } from './builderIdUtils'
import { wellIdsForFormat } from '../components/WellPlate.geometry'
import {
  normalizeQpcrSample,
  normalizeQpcrTarget,
} from './runNormalizers'
import { createTemplateEnvelope } from './templateEnvelopes'
import { validateQpcrPlateData } from './templateValidators'
import type {
  CreateQpcrPlateTemplateOptions,
  QpcrPlateTemplate,
  QpcrPlateTemplateData,
  QpcrReaction,
  QpcrSample,
  QpcrTarget,
} from './types'

/** @deprecated Scheduled for removal from the core SDK in MINT 1.4; the biology templates move to a dedicated package or the owning plugins. */
export function createQpcrPlateTemplate(
  options: CreateQpcrPlateTemplateOptions
): QpcrPlateTemplate {
  const format = options.format ?? 96
  const replicates = options.replicates ?? 3
  if (replicates < 1) {
    throw new Error('qPCR replicates must be at least 1.')
  }

  const samples = options.samples.map((sample, index): QpcrSample => {
    if (typeof sample !== 'string') return normalizeQpcrSample(sample)
    return {
      sampleId: idFromName(sample, `sample-${index + 1}`),
      name: sample,
      metadata: {},
    }
  })
  const targets = options.targets.map((target, index): QpcrTarget => {
    if (typeof target !== 'string') return normalizeQpcrTarget(target)
    return {
      id: idFromName(target, `target-${index + 1}`),
      name: target,
      metadata: {},
    }
  })
  const wells = wellIdsForFormat(format)
  let wellIndex = 0
  const reactions: QpcrReaction[] = []

  for (const sample of samples) {
    for (const target of targets) {
      for (let replicate = 1; replicate <= replicates; replicate += 1) {
        const wellId = wells[wellIndex]
        if (!wellId) throw new Error(`qPCR plate format ${format} does not have enough wells.`)
        reactions.push({
          id: `${sample.sampleId}-${target.id}-r${replicate}`,
          wellId,
          sampleId: sample.sampleId,
          targetId: target.id,
          replicate,
          controlKind: 'sample',
          flags: [],
          metadata: {},
        })
        wellIndex += 1
      }
    }
  }

  if (options.includeNoTemplateControls !== false) {
    for (const target of targets) {
      const wellId = wells[wellIndex]
      if (!wellId) throw new Error(`qPCR plate format ${format} does not have enough wells.`)
      reactions.push({
        id: `ntc-${target.id}`,
        wellId,
        targetId: target.id,
        replicate: 1,
        controlKind: 'no-template',
        flags: [],
        metadata: {},
      })
      wellIndex += 1
    }
  }

  const data: QpcrPlateTemplateData = {
    plateId: 'qpcr-plate-1',
    format,
    samples,
    targets,
    reactions,
    instrument: options.instrument,
    chemistry: options.chemistry ?? 'sybr',
    metadata: options.metadata ?? {},
  }
  validateQpcrPlateData(data)
  return createTemplateEnvelope('qpcr-plate', data, options.metadata ?? {})
}