import {
  readBoolean,
  readInteger,
  readNumber,
  readNumberList,
  readOptionalString,
  readString,
  readStringList,
} from './builderReadUtils'
import { readPlateFormat } from '../components/WellPlate.geometry'
import { getBioTemplatePresetInfo } from './presets'
import type {
  CreateElisaAssayCollectionOptions,
  CreateFlowCytometryAssayCollectionOptions,
  CreateLcmsBatchCollectionOptions,
  CreateQpcrExpressionCollectionOptions,
  CreateQpcrPlateTemplateOptions,
  CreateSamplePrepTemplateOptions,
  CreateTargetedMetabolomicsCollectionOptions,
  CreateWellPlateScreenCollectionOptions,
  CreateWesternBlotAssayCollectionOptions,
  TemplatePresetId,
} from './types'

export type BioTemplateControlValues = Record<string, unknown>

/** @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 bioTemplatePresetControlValuesToOptions(
  name: 'wellplate-screen',
  values: BioTemplateControlValues
): CreateWellPlateScreenCollectionOptions
export function bioTemplatePresetControlValuesToOptions(
  name: 'qpcr-expression',
  values: BioTemplateControlValues
): CreateQpcrExpressionCollectionOptions
export function bioTemplatePresetControlValuesToOptions(
  name: 'lcms-batch',
  values: BioTemplateControlValues
): CreateLcmsBatchCollectionOptions
export function bioTemplatePresetControlValuesToOptions(
  name: 'targeted-metabolomics',
  values: BioTemplateControlValues
): CreateTargetedMetabolomicsCollectionOptions
export function bioTemplatePresetControlValuesToOptions(
  name: 'elisa-assay',
  values: BioTemplateControlValues
): CreateElisaAssayCollectionOptions
export function bioTemplatePresetControlValuesToOptions(
  name: 'flow-cytometry-assay',
  values: BioTemplateControlValues
): CreateFlowCytometryAssayCollectionOptions
export function bioTemplatePresetControlValuesToOptions(
  name: 'western-blot-assay',
  values: BioTemplateControlValues
): CreateWesternBlotAssayCollectionOptions
export function bioTemplatePresetControlValuesToOptions(
  name: TemplatePresetId | string,
  values: BioTemplateControlValues
):
  | CreateWellPlateScreenCollectionOptions
  | CreateQpcrExpressionCollectionOptions
  | CreateLcmsBatchCollectionOptions
  | CreateTargetedMetabolomicsCollectionOptions
  | CreateElisaAssayCollectionOptions
  | CreateFlowCytometryAssayCollectionOptions
  | CreateWesternBlotAssayCollectionOptions
export function bioTemplatePresetControlValuesToOptions(
  name: TemplatePresetId | string,
  values: BioTemplateControlValues
):
  | CreateWellPlateScreenCollectionOptions
  | CreateQpcrExpressionCollectionOptions
  | CreateLcmsBatchCollectionOptions
  | CreateTargetedMetabolomicsCollectionOptions
  | CreateElisaAssayCollectionOptions
  | CreateFlowCytometryAssayCollectionOptions
  | CreateWesternBlotAssayCollectionOptions {
  const preset = getBioTemplatePresetInfo(name)
  if (!preset) {
    throw new Error(`Unknown template preset '${name}'.`)
  }

  if (preset.name === 'wellplate-screen') {
    return {
      samples: readStringList(values.sampleNames, ['Control', 'Treatment']),
      plateName: readString(values.plateName, 'Screen plate'),
      plateFormat: readPlateFormat(values.plateFormat, 96),
      unit: readString(values.unit, 'uM'),
      replicates: readInteger(values.replicates, 3),
    }
  }

  if (preset.name === 'qpcr-expression') {
    return {
      samples: readStringList(values.sampleNames, ['Control', 'Treatment']),
      targets: readStringList(values.targets, ['ACTB', 'GAPDH']),
      chemistry: readString(values.chemistry, 'sybr') as CreateQpcrPlateTemplateOptions['chemistry'],
      format: readPlateFormat(values.plateFormat, 96),
      includeNoTemplateControls: readBoolean(values.includeNoTemplateControls, true),
      replicates: readInteger(values.replicates, 3),
      instrument: readOptionalString(values.instrument),
    }
  }

  if (preset.name === 'lcms-batch') {
    return {
      samples: readStringList(values.sampleNames, ['S001', 'S002']),
      features: readStringList(values.featureNames, ['Glucose', 'Lactate']),
      instrument: readString(values.instrument, 'LC-MS'),
      method: readString(values.method, 'Default method'),
      includeQc: readBoolean(values.includeQc, true),
    }
  }

  if (preset.name === 'targeted-metabolomics') {
    return {
      samples: readStringList(values.sampleNames, ['S001', 'S002']),
      metabolites: readStringList(values.metaboliteNames, ['Glucose', 'Lactate', 'Pyruvate']),
      internalStandards: readStringList(
        values.internalStandards,
        ['Stable isotope internal standard mix'],
      ),
      standardConcentrations: readNumberList(values.standardConcentrations, [0.1, 1, 10, 100]),
      concentrationUnit: readString(values.concentrationUnit, 'uM'),
      responseUnit: readString(values.responseUnit, 'peak area ratio'),
      calibrationAnalyte: readOptionalString(values.calibrationAnalyte),
      instrument: readString(values.instrument, 'LC-MS'),
      method: readString(values.method, 'Targeted metabolomics'),
      prepType: readString(values.prepType, 'extraction') as CreateSamplePrepTemplateOptions['prepType'],
      outputVolume: readNumber(values.outputVolume, 50),
      includeQc: readBoolean(values.includeQc, true),
    }
  }

  if (preset.name === 'elisa-assay') {
    return {
      samples: readStringList(values.sampleNames, ['Control', 'Treatment']),
      analyte: readString(values.analyte, 'Analyte'),
      standardConcentrations: readNumberList(values.standardConcentrations, [1000, 100, 10, 1]),
      unit: readString(values.unit, 'pg/mL'),
      responseUnit: readString(values.responseUnit, 'OD450'),
      plateName: readString(values.plateName, 'ELISA plate'),
      plateFormat: readPlateFormat(values.plateFormat, 96),
    }
  }

  if (preset.name === 'flow-cytometry-assay') {
    return {
      samples: readStringList(values.sampleNames, ['Control', 'Treatment']),
      markers: readStringList(values.markers, ['CD3', 'CD4', 'CD8']),
      features: readStringList(values.featureNames, ['CD3+ cells', 'CD4+ cells', 'CD8+ cells']),
      instrument: readString(values.instrument, 'Flow cytometer'),
      includeDefaultControls: readBoolean(values.includeDefaultControls, true),
    }
  }

  if (preset.name === 'western-blot-assay') {
    return {
      samples: readStringList(values.sampleNames, ['Control', 'Treatment']),
      targets: readStringList(values.targets, ['Target protein']),
      loadingControl: readString(values.loadingControl, 'ACTB'),
    }
  }

  throw new Error(`Unknown template preset '${name}'.`)
}