import { createAssayMatrixTemplate } from './assayMatrixBuilder'
import { createFlowCytometryPanelTemplate } from './flowCytometryPanelBuilder'
import { createSampleSheetTemplate } from './sampleSheetBuilder'
import { presetSampleRecords } from './sampleNormalizers'
import { createTemplateCollection } from './templateEnvelopes'
import type {
  CreateFlowCytometryAssayCollectionOptions,
  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 createFlowCytometryAssayCollection(
  options: CreateFlowCytometryAssayCollectionOptions = {}
): TemplateCollectionEnvelope {
  const sampleRecords = presetSampleRecords(options.samples ?? ['Control', 'Treatment'])
  const markers = options.markers ?? ['CD3', 'CD4', 'CD8']
  const sampleSheet = createSampleSheetTemplate({ samples: sampleRecords })
  const flowPanel = createFlowCytometryPanelTemplate({
    markers,
    instrument: options.instrument ?? 'Flow cytometer',
    includeDefaultControls: options.includeDefaultControls,
  })
  const assayMatrix = createAssayMatrixTemplate({
    samples: sampleRecords.map(sample => ({
      sampleId: sample.sampleId,
      name: sample.name,
      group: sample.group,
      metadata: sample.metadata ?? {},
    })),
    features: options.features ?? flowPanel.data.markers.map(marker => ({
      id: marker.id,
      name: `${marker.marker}+ cells`,
      type: 'cell',
      unit: '%',
      metadata: { marker: marker.marker, fluorophore: marker.fluorophore },
    })),
  })
  return createTemplateCollection(
    [sampleSheet, flowPanel, assayMatrix],
    { preset: 'flow-cytometry-assay', ...(options.metadata ?? {}) }
  )
}