import { idFromName } from './builderIdUtils'
import {
  defaultFlowControls,
  normalizeFlowControl,
  normalizeFlowMarker,
} from './flowNormalizers'
import { createTemplateEnvelope } from './templateEnvelopes'
import { validateFlowCytometryPanelData } from './templateValidators'
import type {
  CreateFlowCytometryPanelTemplateOptions,
  FlowCytometryPanelTemplate,
  FlowCytometryPanelTemplateData,
  FlowPanelControl,
  FlowPanelMarker,
} 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 createFlowCytometryPanelTemplate(
  options: CreateFlowCytometryPanelTemplateOptions
): FlowCytometryPanelTemplate {
  const markers = options.markers.map((marker, index): FlowPanelMarker => {
    if (typeof marker !== 'string') return normalizeFlowMarker(marker, index)
    return {
      id: idFromName(marker, `marker-${index + 1}`),
      marker,
      fluorophore: 'unassigned',
      purpose: 'phenotype',
      compensationRequired: true,
      metadata: {},
    }
  })
  const controls = options.controls === undefined
    ? options.includeDefaultControls === false
      ? []
      : defaultFlowControls(markers)
    : options.controls.map((control, index): FlowPanelControl => {
        if (typeof control !== 'string') return normalizeFlowControl(control, index)
        return {
          id: idFromName(control, `control-${index + 1}`),
          name: control,
          kind: 'other',
          required: true,
          metadata: {},
        }
      })
  const data: FlowCytometryPanelTemplateData = {
    markers,
    controls,
    instrument: options.instrument,
    metadata: options.metadata ?? {},
  }
  validateFlowCytometryPanelData(data)
  return createTemplateEnvelope('flow-cytometry-panel', data, options.metadata ?? {})
}