import {
  createAssayFeatureLookup,
  createAssaySampleLookup,
} from './assayLookups'
import {
  normalizeAssayFeature,
  normalizeAssaySample,
} from './assayNormalizers'
import { idFromName } from './builderIdUtils'
import { createTemplateEnvelope } from './templateEnvelopes'
import { validateAssayMatrixData } from './templateValidators'
import type {
  AssayFeature,
  AssayMatrixTemplate,
  AssayMatrixTemplateData,
  AssaySample,
  CreateAssayMatrixTemplateOptions,
} 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 createAssayMatrixTemplate(
  options: CreateAssayMatrixTemplateOptions
): AssayMatrixTemplate {
  const samples = options.samples.map((sample, index): AssaySample => {
    if (typeof sample !== 'string') return normalizeAssaySample(sample)
    return {
      sampleId: idFromName(sample, `sample-${index + 1}`),
      name: sample,
      metadata: {},
    }
  })
  const features = options.features.map((feature, index): AssayFeature => {
    if (typeof feature !== 'string') return normalizeAssayFeature(feature)
    return {
      id: idFromName(feature, `feature-${index + 1}`),
      name: feature,
      type: 'readout',
      metadata: {},
    }
  })
  const sampleLookup = createAssaySampleLookup(samples)
  const featureLookup = createAssayFeatureLookup(features)
  const measurements = Object.entries(options.values ?? {}).flatMap(([sampleId, featureValues]) =>
    Object.entries(featureValues).map(([featureId, value]) => ({
      sampleId: sampleLookup.get(sampleId) ?? sampleId,
      featureId: featureLookup.get(featureId) ?? featureId,
      value,
      metadata: {},
    }))
  )

  const data: AssayMatrixTemplateData = {
    samples,
    features,
    measurements,
    metadata: options.metadata ?? {},
  }
  validateAssayMatrixData(data)
  return createTemplateEnvelope('assay-matrix', data, options.metadata ?? {})
}