import { SAMPLE_COLOR_SCALE } from '../utils/color'
import {
  idFromName,
  timepointId,
} from './builderIdUtils'
import {
  normalizeCondition,
  normalizeTimePoint,
} from './protocolNormalizers'
import { createTemplateEnvelope } from './templateEnvelopes'
import { validateTimeCourseData } from './templateValidators'
import type {
  CreateTimeCourseTemplateOptions,
  TimeCourseCondition,
  TimeCourseTemplate,
  TimeCourseTemplateData,
  TimePoint,
} 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 createTimeCourseTemplate(
  options: CreateTimeCourseTemplateOptions
): TimeCourseTemplate {
  const timepoints = options.timepoints.map((timepoint, index): TimePoint => {
    if (typeof timepoint !== 'number') return normalizeTimePoint(timepoint)
    return {
      id: timepointId(timepoint, options.unit, index),
      label: `${timepoint} ${options.unit}`,
      value: timepoint,
      unit: options.unit,
      metadata: {},
    }
  }).sort((a, b) => a.value - b.value)

  const conditions = options.conditions.map((condition, index): TimeCourseCondition => {
    if (typeof condition !== 'string') return normalizeCondition(condition)
    return {
      id: idFromName(condition, `condition-${index + 1}`),
      name: condition,
      color: SAMPLE_COLOR_SCALE[index % SAMPLE_COLOR_SCALE.length],
      metadata: {},
    }
  })

  const samples = conditions.flatMap(condition =>
    timepoints.flatMap(timepoint =>
      Array.from({ length: options.replicates ?? 1 }, (_, index) => ({
        sampleId: `${condition.id}-${timepoint.id}-r${index + 1}`,
        conditionId: condition.id,
        timepointId: timepoint.id,
        replicate: index + 1,
        metadata: {},
      }))
    )
  )

  const data: TimeCourseTemplateData = {
    timepoints,
    conditions,
    samples,
    metadata: options.metadata ?? {},
  }
  validateTimeCourseData(data)
  return createTemplateEnvelope('time-course', data, options.metadata ?? {})
}