import { createAssayMatrixTemplate } from './assayMatrixBuilder'
import { SAMPLE_COLOR_SCALE } from '../utils/color'
import { idFromName } from './builderIdUtils'
import { createCalibrationCurveTemplate } from './calibrationCurveBuilder'
import { createPlateMapTemplate } from './plateMapBuilder'
import { createSampleSheetTemplate } from './sampleSheetBuilder'
import { presetSampleRecords } from './sampleNormalizers'
import { createTemplateCollection } from './templateEnvelopes'
import type {
  CreateElisaAssayCollectionOptions,
  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 createElisaAssayCollection(
  options: CreateElisaAssayCollectionOptions = {}
): TemplateCollectionEnvelope {
  const sampleRecords = presetSampleRecords(options.samples ?? ['Control', 'Treatment'])
  const analyte = options.analyte ?? 'Analyte'
  const responseUnit = options.responseUnit ?? 'OD450'
  const plate = createPlateMapTemplate({
    name: options.plateName ?? 'ELISA plate',
    format: options.plateFormat ?? 96,
    samples: [
      { id: 'blank', name: 'Blank' },
      { id: 'standard', name: 'Standards' },
      { id: 'qc', name: 'QC' },
      ...sampleRecords.map((sample, index) => ({
        id: sample.sampleId,
        name: sample.name ?? sample.sampleId,
        color: SAMPLE_COLOR_SCALE[index % SAMPLE_COLOR_SCALE.length],
      })),
    ],
  })
  const sampleSheet = createSampleSheetTemplate({ samples: sampleRecords })
  const calibrationCurve = createCalibrationCurveTemplate({
    concentrations: options.standardConcentrations ?? [1000, 100, 10, 1],
    analyte,
    unit: options.unit ?? 'pg/mL',
    responseUnit,
    model: 'four-parameter-logistic',
  })
  const assayMatrix = createAssayMatrixTemplate({
    samples: sampleRecords.map(sample => ({
      sampleId: sample.sampleId,
      name: sample.name,
      group: sample.group,
      metadata: sample.metadata ?? {},
    })),
    features: [{
      id: idFromName(analyte, 'analyte'),
      name: analyte,
      type: 'protein',
      unit: responseUnit,
      metadata: {},
    }],
    metadata: { analyte, responseUnit },
  })
  return createTemplateCollection(
    [plate, sampleSheet, calibrationCurve, assayMatrix],
    { preset: 'elisa-assay', ...(options.metadata ?? {}) }
  )
}