import type { WellPlateFormat } from '../types'
import type {
  AssayFeature,
  AssaySample,
  CalibrationAcceptanceInput,
  CalibrationModel,
  CalibrationPointInput,
  CompoundDoseSeries,
  ControlDefinition,
  FlowPanelControl,
  FlowPanelMarker,
  InstrumentMethodInput,
  InstrumentRunItemInput,
  PlateMapTemplate,
  PlateMapTemplateData,
  ProtocolStepRecord,
  ReagentTemplateInput,
  SampleColumn,
  SampleGroupDefinition,
  SamplePrepStepInput,
  SamplePrepStepType,
  SampleRecord,
  TemplateSample,
  TimeCourseCondition,
  TimePoint,
  TimeUnit,
} from './types'
import type {
  QpcrChemistry,
  QpcrSample,
  QpcrTarget,
} from './templateQpcrTypes'

export interface CreateBioTemplatePackCollectionOptions {
  metadata?: Record<string, unknown>
}

export interface CreatePlateMapTemplateOptions {
  name?: string
  id?: string
  format?: WellPlateFormat
  samples?: Array<string | TemplateSample>
  metadata?: Record<string, unknown>
}

export interface CreateSampleSheetTemplateOptions {
  samples: SampleRecord[]
  columns?: SampleColumn[]
  groups?: SampleGroupDefinition[]
  metadata?: Record<string, unknown>
}

export interface CreateSamplePrepTemplateOptions {
  samples: Array<string | SamplePrepStepInput>
  prepType?: SamplePrepStepType
  protocolName?: string
  volumeUnit?: string
  inputVolume?: number
  outputVolume?: number
  metadata?: Record<string, unknown>
}

export interface CreateDoseResponseTemplateOptions {
  compounds: Record<string, number[]> | CompoundDoseSeries[]
  unit: string
  replicates?: number
  controls?: ControlDefinition[]
  layout?: PlateMapTemplate | PlateMapTemplateData
  metadata?: Record<string, unknown>
}

export interface CreateCalibrationCurveTemplateOptions {
  concentrations: Array<number | CalibrationPointInput>
  analyte?: string
  unit?: string
  responseUnit?: string
  model?: CalibrationModel
  includeBlank?: boolean
  includeQc?: boolean
  acceptance?: CalibrationAcceptanceInput
  metadata?: Record<string, unknown>
}

export interface CreateTimeCourseTemplateOptions {
  timepoints: Array<number | TimePoint>
  unit: TimeUnit
  conditions: Array<string | TimeCourseCondition>
  replicates?: number
  metadata?: Record<string, unknown>
}

export interface CreateAssayMatrixTemplateOptions {
  samples: Array<string | AssaySample>
  features: Array<string | AssayFeature>
  values?: Record<string, Record<string, number | null | undefined>>
  metadata?: Record<string, unknown>
}

export interface CreateProtocolStepsTemplateOptions {
  steps: Array<string | (Partial<ProtocolStepRecord> & { name: string })>
  metadata?: Record<string, unknown>
}

export interface CreateReagentListTemplateOptions {
  reagents: Array<string | ReagentTemplateInput>
  metadata?: Record<string, unknown>
}

export interface CreateFlowCytometryPanelTemplateOptions {
  markers: Array<string | (Partial<FlowPanelMarker> & { marker: string })>
  controls?: Array<string | (Partial<FlowPanelControl> & { name: string })>
  instrument?: string
  includeDefaultControls?: boolean
  metadata?: Record<string, unknown>
}

export interface CreateInstrumentRunTemplateOptions {
  items: Array<string | InstrumentRunItemInput>
  method?: string | InstrumentMethodInput
  instrument?: string
  includeBlanks?: boolean
  includeQc?: boolean
  metadata?: Record<string, unknown>
}

export interface CreateQpcrPlateTemplateOptions {
  samples: Array<string | QpcrSample>
  targets: Array<string | QpcrTarget>
  format?: WellPlateFormat
  replicates?: number
  includeNoTemplateControls?: boolean
  instrument?: string
  chemistry?: QpcrChemistry
  metadata?: Record<string, unknown>
}

export interface CreateWellPlateScreenCollectionOptions {
  samples?: Array<string | SampleRecord>
  compounds?: Record<string, number[]> | CompoundDoseSeries[]
  unit?: string
  replicates?: number
  plateName?: string
  plateFormat?: WellPlateFormat
  metadata?: Record<string, unknown>
}

export interface CreateQpcrExpressionCollectionOptions {
  samples?: Array<string | SampleRecord>
  targets?: Array<string | QpcrTarget>
  chemistry?: QpcrChemistry
  includeNoTemplateControls?: boolean
  format?: WellPlateFormat
  replicates?: number
  instrument?: string
  metadata?: Record<string, unknown>
}

export interface CreateLcmsBatchCollectionOptions {
  samples?: Array<string | SampleRecord>
  features?: Array<string | AssayFeature>
  instrument?: string
  method?: string | InstrumentMethodInput
  includeQc?: boolean
  metadata?: Record<string, unknown>
}

export interface CreateTargetedMetabolomicsCollectionOptions {
  samples?: Array<string | SampleRecord>
  metabolites?: Array<string | AssayFeature>
  internalStandards?: Array<string | ReagentTemplateInput>
  standardConcentrations?: number[]
  concentrationUnit?: string
  responseUnit?: string
  calibrationAnalyte?: string
  instrument?: string
  method?: string | InstrumentMethodInput
  prepType?: SamplePrepStepType
  outputVolume?: number
  includeQc?: boolean
  metadata?: Record<string, unknown>
}

export interface CreateElisaAssayCollectionOptions {
  samples?: Array<string | SampleRecord>
  analyte?: string
  standardConcentrations?: number[]
  unit?: string
  responseUnit?: string
  plateName?: string
  plateFormat?: WellPlateFormat
  metadata?: Record<string, unknown>
}

export interface CreateFlowCytometryAssayCollectionOptions {
  samples?: Array<string | SampleRecord>
  markers?: CreateFlowCytometryPanelTemplateOptions['markers']
  features?: Array<string | AssayFeature>
  instrument?: string
  includeDefaultControls?: boolean
  metadata?: Record<string, unknown>
}

export interface CreateWesternBlotAssayCollectionOptions {
  samples?: Array<string | SampleRecord>
  targets?: Array<string | AssayFeature>
  loadingControl?: string
  metadata?: Record<string, unknown>
}