import { createQpcrPlateTemplate } from './qpcrPlateBuilder'
import { createSampleSheetTemplate } from './sampleSheetBuilder'
import { presetSampleRecords } from './sampleNormalizers'
import { createTemplateCollection } from './templateEnvelopes'
import type {
  CreateQpcrExpressionCollectionOptions,
  TemplateCollectionEnvelope,
} 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 createQpcrExpressionCollection(
  options: CreateQpcrExpressionCollectionOptions = {}
): TemplateCollectionEnvelope {
  const sampleRecords = presetSampleRecords(options.samples ?? ['Control', 'Treatment'])
  const sampleSheet = createSampleSheetTemplate({ samples: sampleRecords })
  const qpcr = createQpcrPlateTemplate({
    samples: sampleRecords.map(sample => ({
      sampleId: sample.sampleId,
      name: sample.name,
      group: sample.group,
      metadata: sample.metadata ?? {},
    })),
    targets: options.targets ?? ['ACTB', 'GAPDH'],
    chemistry: options.chemistry,
    format: options.format,
    includeNoTemplateControls: options.includeNoTemplateControls,
    replicates: options.replicates ?? 3,
    instrument: options.instrument,
  })
  return createTemplateCollection(
    [sampleSheet, qpcr],
    { preset: 'qpcr-expression', ...(options.metadata ?? {}) }
  )
}