import type { SelectOption } from '../types'
import { getTemplateData } from './templateEnvelopes'
import { validateAssayMatrixData } from './templateValidators'
import type {
  AssayMatrixColumnsAdapterResult,
  AssayMatrixDataFrameAdapterResult,
  AssayMatrixRowsAdapterResult,
  AssayMatrixSampleOptionsAdapterResult,
  AssayMatrixTemplate,
  AssayMatrixTemplateData,
} 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 toAssayMatrixRows(
  template: AssayMatrixTemplate | AssayMatrixTemplateData
): AssayMatrixRowsAdapterResult {
  const data = getTemplateData(template, 'assay-matrix')
  validateAssayMatrixData(data)
  const measurements = new Map(
    data.measurements.map(measurement => [
      `${measurement.sampleId}:${measurement.featureId}`,
      measurement.value ?? null,
    ])
  )

  return data.samples.map(sample => {
    const row: Record<string, unknown> = {
      sampleId: sample.sampleId,
      name: sample.name,
      group: sample.group,
      ...(sample.metadata ?? {}),
    }
    for (const feature of data.features) {
      row[feature.id] = measurements.get(`${sample.sampleId}:${feature.id}`) ?? null
    }
    return row
  })
}

/** @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 toAssayMatrixColumns(
  template: AssayMatrixTemplate | AssayMatrixTemplateData
): AssayMatrixColumnsAdapterResult {
  const data = getTemplateData(template, 'assay-matrix')
  validateAssayMatrixData(data)
  return [
    { key: 'sampleId', label: 'Sample ID', sortable: true },
    { key: 'name', label: 'Name', sortable: true },
    { key: 'group', label: 'Group', sortable: true },
    ...data.features.map(feature => ({
      key: feature.id,
      label: feature.unit ? `${feature.name} (${feature.unit})` : feature.name,
      sortable: true,
      align: 'right' as const,
    })),
  ]
}

/** @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 toAssayMatrixDataFrame(
  template: AssayMatrixTemplate | AssayMatrixTemplateData
): AssayMatrixDataFrameAdapterResult {
  return {
    data: toAssayMatrixRows(template),
    columns: toAssayMatrixColumns(template),
    rowKey: 'sampleId',
  }
}

/**
 * Convert an assay-matrix template into SampleSelector options derived from assay samples.
 *
 * @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 toAssayMatrixSampleOptions(
  template: AssayMatrixTemplate | AssayMatrixTemplateData
): AssayMatrixSampleOptionsAdapterResult {
  const data = getTemplateData(template, 'assay-matrix')
  validateAssayMatrixData(data)
  return data.samples.map((sample): SelectOption<string> => ({
    value: sample.sampleId,
    label: sample.name ?? sample.sampleId,
    description: sample.group,
  }))
}