import { createAssayMatrixTemplate } from './assayMatrixBuilder'
import { createInstrumentRunTemplate } from './instrumentRunBuilder'
import { createSampleSheetTemplate } from './sampleSheetBuilder'
import { presetSampleRecords } from './sampleNormalizers'
import { createTemplateCollection } from './templateEnvelopes'
import type {
  CreateLcmsBatchCollectionOptions,
  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 createLcmsBatchCollection(
  options: CreateLcmsBatchCollectionOptions = {}
): TemplateCollectionEnvelope {
  const sampleRecords = presetSampleRecords(options.samples ?? ['S001', 'S002'])
  const sampleSheet = createSampleSheetTemplate({ samples: sampleRecords })
  const instrumentRun = createInstrumentRunTemplate({
    items: sampleRecords.map(sample => ({
      sampleId: sample.sampleId,
      name: sample.name ?? sample.sampleId,
    })),
    method: options.method ?? 'Default method',
    instrument: options.instrument ?? 'LC-MS',
    includeQc: options.includeQc,
  })
  const assayMatrix = createAssayMatrixTemplate({
    samples: sampleRecords.map(sample => ({
      sampleId: sample.sampleId,
      name: sample.name,
      group: sample.group,
      metadata: sample.metadata ?? {},
    })),
    features: options.features ?? ['Glucose', 'Lactate'],
  })
  return createTemplateCollection(
    [sampleSheet, instrumentRun, assayMatrix],
    { preset: 'lcms-batch', ...(options.metadata ?? {}) }
  )
}