import type {
  PlateMap,
  ProtocolStep,
  Reagent,
  SampleType,
  Well,
} from '../types'
import type { QpcrPlateTemplate } from './templateQpcrTypes'

export type TemplateKind = 'experiment-design'
export type TemplateId =
  | 'plate-map'
  | 'sample-sheet'
  | 'sample-prep'
  | 'dose-response'
  | 'calibration-curve'
  | 'time-course'
  | 'protocol-steps'
  | 'assay-matrix'
  | 'reagent-list'
  | 'flow-cytometry-panel'
  | 'instrument-run'
  | 'qpcr-plate'

export type TemplatePresetId =
  | 'wellplate-screen'
  | 'qpcr-expression'
  | 'lcms-batch'
  | 'targeted-metabolomics'
  | 'elisa-assay'
  | 'flow-cytometry-assay'
  | 'western-blot-assay'

export type TemplatePackId =
  | 'cell-culture-screen'
  | 'omics-assay'
  | 'longitudinal-study'
  | 'molecular-assay'

export interface BioTemplateEnvelope<TData = Record<string, unknown>> {
  template_id: TemplateId | string
  template_version: string
  kind: TemplateKind | string
  data: TData
  metadata: Record<string, unknown>
}

export type TemplateCollection = Record<string, BioTemplateEnvelope<unknown>>

export interface TemplateCollectionEnvelope {
  templates: TemplateCollection
  metadata?: Record<string, unknown>
}

export type TemplateWell = Well
export type TemplatePlateMap = PlateMap
export type TemplateSample = SampleType

export interface PlateMapTemplateData {
  plates: TemplatePlateMap[]
  samples: TemplateSample[]
  activePlateId?: string
  selectedWells?: string[]
  activeSampleId?: string
}

export type PlateMapTemplate = BioTemplateEnvelope<PlateMapTemplateData>

export type SampleColumnType = 'string' | 'number' | 'integer' | 'boolean' | 'date' | 'category' | 'unknown'

export interface SampleColumn {
  id: string
  label: string
  type: SampleColumnType
  required: boolean
  groupable: boolean
}

export interface SampleRecord {
  sampleId: string
  name?: string
  group?: string
  batch?: string
  replicate?: number | string
  plateId?: string
  wellId?: string
  metadata?: Record<string, unknown>
}

export interface SampleGroupDefinition {
  name: string
  color: string
  samples: string[]
}

export interface SampleSheetTemplateData {
  samples: SampleRecord[]
  columns: SampleColumn[]
  groups: SampleGroupDefinition[]
}

export type SampleSheetTemplate = BioTemplateEnvelope<SampleSheetTemplateData>

export type SamplePrepStepType =
  | 'extraction'
  | 'dilution'
  | 'normalization'
  | 'transfer'
  | 'incubation'
  | 'centrifugation'
  | 'cleanup'
  | 'digestion'
  | 'labeling'
  | 'other'
export type SamplePrepStatus = 'planned' | 'in-progress' | 'completed' | 'failed' | 'skipped'

export interface SamplePrepStep {
  id: string
  order: number
  type: SamplePrepStepType
  name: string
  sourceSampleId?: string
  sourcePlateId?: string
  sourceWellId?: string
  destinationSampleId?: string
  destinationPlateId?: string
  destinationWellId?: string
  reagentId?: string
  inputVolume?: number
  outputVolume?: number
  volumeUnit: string
  durationMin?: number
  status: SamplePrepStatus
  metadata?: Record<string, unknown>
}

export interface SamplePrepTemplateData {
  protocolName: string
  steps: SamplePrepStep[]
  metadata: Record<string, unknown>
}

export type SamplePrepTemplate = BioTemplateEnvelope<SamplePrepTemplateData>
export type SamplePrepStepInput = Partial<SamplePrepStep> & { name?: string; sourceSampleId?: string }

export interface CompoundDoseSeries {
  id: string
  name: string
  concentrations: number[]
  metadata?: Record<string, unknown>
}

export type ControlRole = 'vehicle' | 'positive' | 'negative' | 'blank' | 'baseline' | 'other'

export interface ControlDefinition {
  id: string
  name: string
  role: ControlRole
  vehicle?: string
  metadata?: Record<string, unknown>
}

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

export type DoseResponseTemplate = BioTemplateEnvelope<DoseResponseTemplateData>

export type CalibrationModel =
  | 'linear'
  | 'linear-weighted-1-x'
  | 'linear-weighted-1-x2'
  | 'quadratic'
  | 'four-parameter-logistic'
export type CalibrationPointRole = 'blank' | 'standard' | 'qc' | 'unknown'
export type CalibrationPointStatus = 'planned' | 'accepted' | 'rejected' | 'warning'

export interface CalibrationAcceptance {
  minRSquared: number
  standardTolerancePercent: number
  qcTolerancePercent: number
  requireBlank: boolean
  metadata?: Record<string, unknown>
}

export interface CalibrationPoint {
  id: string
  order: number
  role: CalibrationPointRole
  level: string
  concentration: number
  unit: string
  expectedResponse?: number
  response?: number
  replicate: number
  include: boolean
  status: CalibrationPointStatus
  metadata?: Record<string, unknown>
}

export interface CalibrationCurveTemplateData {
  analyte: string
  model: CalibrationModel
  xUnit: string
  responseUnit: string
  points: CalibrationPoint[]
  acceptance: CalibrationAcceptance
  metadata: Record<string, unknown>
}

export type CalibrationCurveTemplate = BioTemplateEnvelope<CalibrationCurveTemplateData>
export type CalibrationAcceptanceInput = Partial<CalibrationAcceptance>
export type CalibrationPointInput = Partial<CalibrationPoint> & { concentration?: number; level?: string }

export type TimeUnit = 'second' | 'minute' | 'hour' | 'day' | 'week'

export interface TimePoint {
  id: string
  label: string
  value: number
  unit: TimeUnit
  metadata?: Record<string, unknown>
}

export interface TimeCourseCondition {
  id: string
  name: string
  color?: string
  description?: string
  metadata?: Record<string, unknown>
}

export interface TimeCourseSample {
  sampleId: string
  conditionId: string
  timepointId: string
  replicate: number
  metadata?: Record<string, unknown>
}

export interface TimeCourseTemplateData {
  timepoints: TimePoint[]
  conditions: TimeCourseCondition[]
  samples: TimeCourseSample[]
  metadata: Record<string, unknown>
}

export type TimeCourseTemplate = BioTemplateEnvelope<TimeCourseTemplateData>

export type AssayFeatureType = 'metabolite' | 'protein' | 'gene' | 'cell' | 'compound' | 'readout' | 'other'

export interface AssaySample {
  sampleId: string
  name?: string
  group?: string
  metadata?: Record<string, unknown>
}

export interface AssayFeature {
  id: string
  name: string
  type: AssayFeatureType
  unit?: string
  metadata?: Record<string, unknown>
}

export interface AssayMeasurement {
  sampleId: string
  featureId: string
  value?: number | null
  metadata?: Record<string, unknown>
}

export interface AssayMatrixTemplateData {
  samples: AssaySample[]
  features: AssayFeature[]
  measurements: AssayMeasurement[]
  metadata: Record<string, unknown>
}

export type AssayMatrixTemplate = BioTemplateEnvelope<AssayMatrixTemplateData>

export type ProtocolStepRecord = ProtocolStep & {
  metadata?: Record<string, unknown>
}

export interface ProtocolStepsTemplateData {
  steps: ProtocolStepRecord[]
  metadata: Record<string, unknown>
}

export type ProtocolStepsTemplate = BioTemplateEnvelope<ProtocolStepsTemplateData>

export type ReagentKind =
  | 'compound'
  | 'antibody'
  | 'primer'
  | 'enzyme'
  | 'buffer'
  | 'media'
  | 'kit'
  | 'reagent'
  | 'other'

export type ReagentTemplateInput = Omit<Reagent, 'expiryDate'> & {
  expiryDate?: Date | string | null
  kind?: ReagentKind
  concentration?: string
  metadata?: Record<string, unknown>
}

export interface ReagentRecord extends Omit<Reagent, 'expiryDate'> {
  expiryDate?: string
  kind?: ReagentKind
  concentration?: string
  metadata?: Record<string, unknown>
}

export interface ReagentListTemplateData {
  reagents: ReagentRecord[]
  metadata: Record<string, unknown>
}

export type ReagentListTemplate = BioTemplateEnvelope<ReagentListTemplateData>

export type FlowMarkerPurpose = 'phenotype' | 'viability' | 'activation' | 'sorting' | 'control' | 'other'
export type FlowControlKind = 'unstained' | 'single-stain' | 'fmo' | 'isotype' | 'viability' | 'beads' | 'other'

export interface FlowPanelMarker {
  id: string
  marker: string
  fluorophore: string
  detector?: string
  clone?: string
  reagentId?: string
  purpose: FlowMarkerPurpose
  compensationRequired: boolean
  metadata?: Record<string, unknown>
}

export interface FlowPanelControl {
  id: string
  name: string
  kind: FlowControlKind
  markerId?: string
  required: boolean
  metadata?: Record<string, unknown>
}

export interface FlowCytometryPanelTemplateData {
  markers: FlowPanelMarker[]
  controls: FlowPanelControl[]
  instrument?: string
  metadata: Record<string, unknown>
}

export type FlowCytometryPanelTemplate = BioTemplateEnvelope<FlowCytometryPanelTemplateData>

export type InstrumentRunItemKind = 'sample' | 'blank' | 'qc' | 'standard' | 'calibration' | 'wash' | 'other'
export type InstrumentRunStatus = 'planned' | 'queued' | 'running' | 'completed' | 'failed' | 'skipped'

export interface InstrumentMethod {
  id: string
  name: string
  instrument?: string
  acquisitionMode?: string
  metadata?: Record<string, unknown>
}

export interface InstrumentRunItem {
  id: string
  order: number
  kind: InstrumentRunItemKind
  sampleId?: string
  name?: string
  methodId: string
  vial?: string
  plateId?: string
  wellId?: string
  injectionVolume?: number
  expectedDurationMin?: number
  status: InstrumentRunStatus
  metadata?: Record<string, unknown>
}

export interface InstrumentRunTemplateData {
  runId: string
  instrument?: string
  methods: InstrumentMethod[]
  items: InstrumentRunItem[]
  metadata: Record<string, unknown>
}

export type InstrumentRunTemplate = BioTemplateEnvelope<InstrumentRunTemplateData>

export type InstrumentMethodInput = Partial<InstrumentMethod> & { name?: string }
export type InstrumentRunItemInput = Partial<InstrumentRunItem> & { name?: string; sampleId?: string }

export type DataFrameTemplate =
  | SampleSheetTemplate
  | SamplePrepTemplate
  | CalibrationCurveTemplate
  | TimeCourseTemplate
  | ProtocolStepsTemplate
  | AssayMatrixTemplate
  | ReagentListTemplate
  | FlowCytometryPanelTemplate
  | InstrumentRunTemplate
  | QpcrPlateTemplate

export type {
  QpcrChemistry,
  QpcrControlKind,
  QpcrPlateTemplate,
  QpcrPlateTemplateData,
  QpcrReaction,
  QpcrSample,
  QpcrTarget,
} from './templateQpcrTypes'

export type {
  CreateAssayMatrixTemplateOptions,
  CreateBioTemplatePackCollectionOptions,
  CreateCalibrationCurveTemplateOptions,
  CreateDoseResponseTemplateOptions,
  CreateElisaAssayCollectionOptions,
  CreateFlowCytometryAssayCollectionOptions,
  CreateFlowCytometryPanelTemplateOptions,
  CreateInstrumentRunTemplateOptions,
  CreateLcmsBatchCollectionOptions,
  CreatePlateMapTemplateOptions,
  CreateProtocolStepsTemplateOptions,
  CreateQpcrExpressionCollectionOptions,
  CreateQpcrPlateTemplateOptions,
  CreateReagentListTemplateOptions,
  CreateSamplePrepTemplateOptions,
  CreateSampleSheetTemplateOptions,
  CreateTargetedMetabolomicsCollectionOptions,
  CreateTimeCourseTemplateOptions,
  CreateWellPlateScreenCollectionOptions,
  CreateWesternBlotAssayCollectionOptions,
} from './templateCreateOptions'

export type {
  AssayMatrixColumnsAdapterResult,
  AssayMatrixDataFrameAdapterResult,
  AssayMatrixRowsAdapterResult,
  AssayMatrixSampleOptionsAdapterResult,
  CalibrationCurveColumnsAdapterResult,
  CalibrationCurveDataFrameAdapterResult,
  CalibrationCurveRowsAdapterResult,
  DataFrameAdapterResult,
  DoseConditionsAdapterResult,
  FlowPanelColumnsAdapterResult,
  FlowPanelDataFrameAdapterResult,
  FlowPanelRowsAdapterResult,
  InstrumentRunColumnsAdapterResult,
  InstrumentRunDataFrameAdapterResult,
  InstrumentRunRowsAdapterResult,
  InstrumentRunScheduleEventsAdapterResult,
  InstrumentRunStepsAdapterResult,
  PlateMapEditorAdapterResult,
  ProtocolColumnsAdapterResult,
  ProtocolDataFrameAdapterResult,
  ProtocolRowsAdapterResult,
  ProtocolStepsAdapterResult,
  QpcrColumnsAdapterResult,
  QpcrDataFrameAdapterResult,
  QpcrRowsAdapterResult,
  QpcrWellMapAdapterResult,
  ReagentColumnsAdapterResult,
  ReagentDataFrameAdapterResult,
  ReagentListItemsAdapterResult,
  ReagentRowsAdapterResult,
  SampleColumnsAdapterResult,
  SampleDataFrameAdapterResult,
  SampleOptionsAdapterResult,
  SamplePrepColumnsAdapterResult,
  SamplePrepDataFrameAdapterResult,
  SamplePrepRowsAdapterResult,
  SampleRowsAdapterResult,
  TemplateDataFrameAdapterResult,
  TimeCourseColumnsAdapterResult,
  TimeCourseDataFrameAdapterResult,
  TimeCourseRowsAdapterResult,
  TimeCourseStepsAdapterResult,
  WellMapAdapterResult,
} from './templateAdapterTypes'