import type { Well } from '../types'
import { getTemplateData } from './templateEnvelopes'
import { validateQpcrPlateData } from './templateValidators'
import type {
  QpcrColumnsAdapterResult,
  QpcrDataFrameAdapterResult,
  QpcrPlateTemplate,
  QpcrPlateTemplateData,
  QpcrRowsAdapterResult,
  QpcrWellMapAdapterResult,
} 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 toQpcrRows(
  template: QpcrPlateTemplate | QpcrPlateTemplateData
): QpcrRowsAdapterResult {
  const data = getTemplateData(template, 'qpcr-plate')
  validateQpcrPlateData(data)
  const samples = new Map(data.samples.map(sample => [sample.sampleId, sample]))
  const targets = new Map(data.targets.map(target => [target.id, target]))

  return data.reactions.map(reaction => {
    const sample = reaction.sampleId ? samples.get(reaction.sampleId) : undefined
    const target = targets.get(reaction.targetId)
    return {
      id: reaction.id,
      wellId: reaction.wellId,
      sampleId: reaction.sampleId,
      sample: sample?.name ?? reaction.sampleId ?? reaction.controlKind,
      group: sample?.group,
      targetId: reaction.targetId,
      target: target?.name ?? reaction.targetId,
      replicate: reaction.replicate,
      controlKind: reaction.controlKind,
      cq: reaction.cq ?? null,
      quantity: reaction.quantity ?? null,
      flags: reaction.flags.join(', '),
      instrument: data.instrument,
      chemistry: data.chemistry,
      ...(reaction.metadata ?? {}),
    }
  })
}

/** @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 toQpcrColumns(): QpcrColumnsAdapterResult {
  return [
    { key: 'wellId', label: 'Well', sortable: true },
    { key: 'sample', label: 'Sample', sortable: true },
    { key: 'group', label: 'Group', sortable: true },
    { key: 'target', label: 'Target', sortable: true },
    { key: 'replicate', label: 'Replicate', sortable: true, align: 'right' },
    { key: 'controlKind', label: 'Control', sortable: true },
    { key: 'cq', label: 'Cq', sortable: true, align: 'right' },
    { key: 'quantity', label: 'Quantity', sortable: true, align: 'right' },
    { key: 'flags', label: 'Flags' },
  ]
}

/** @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 toQpcrDataFrame(
  template: QpcrPlateTemplate | QpcrPlateTemplateData
): QpcrDataFrameAdapterResult {
  return {
    data: toQpcrRows(template),
    columns: toQpcrColumns(),
    rowKey: 'id',
  }
}

/** @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 toQpcrWellPlateWells(
  template: QpcrPlateTemplate | QpcrPlateTemplateData
): QpcrWellMapAdapterResult {
  const data = getTemplateData(template, 'qpcr-plate')
  validateQpcrPlateData(data)
  return Object.fromEntries(data.reactions.map(reaction => {
    const [row, col] = wellPositionFromId(reaction.wellId)
    return [
      reaction.wellId,
      {
        id: reaction.wellId,
        row,
        col,
        state: 'filled' as const,
        sampleType: reaction.sampleId ?? reaction.controlKind,
        value: reaction.cq ?? undefined,
        metadata: {
          reactionId: reaction.id,
          sampleId: reaction.sampleId,
          targetId: reaction.targetId,
          replicate: reaction.replicate,
          controlKind: reaction.controlKind,
        },
      } satisfies Well,
    ]
  }))
}

function wellPositionFromId(wellId: string): [number, number] {
  const match = /^([A-Z]+)([1-9][0-9]*)$/.exec(wellId.toUpperCase())
  if (!match) {
    throw new Error(`Invalid well id '${wellId}'.`)
  }
  const row = [...match[1]].reduce((value, char) => value * 26 + char.charCodeAt(0) - 64, 0) - 1
  const col = Number(match[2]) - 1
  return [row, col]
}