@morscherlab/mint-sdk 1.0.0-beta.1 → 1.0.0-beta.3

package/src/templates/types.ts

@@ -0,0 +1,668 @@
+import type {
+  DataFrameColumn,
+  PlateCondition,
+  PlateMap,
+  PlateMapEditorState,
+  ProtocolStep,
+  Reagent,
+  SampleType,
+  SelectOption,
+  Well,
+  WellPlateFormat,
+} from '../types'
+
+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'
+  | 'elisa-assay'
+  | 'flow-cytometry-assay'
+  | 'western-blot-assay'
+
+export type TemplatePackId =
+  | 'cell-culture-screen'
+  | 'omics-assay'
+  | 'longitudinal-study'
+  | 'molecular-assay'
+
+export interface CreateBioTemplatePackCollectionOptions {
+  metadata?: Record<string, unknown>
+}
+
+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 QpcrChemistry = 'sybr' | 'taqman' | 'probe' | 'evagreen' | 'other'
+export type QpcrControlKind = 'sample' | 'no-template' | 'no-rt' | 'positive' | 'standard' | 'calibrator'
+
+export interface QpcrSample {
+  sampleId: string
+  name?: string
+  group?: string
+  metadata?: Record<string, unknown>
+}
+
+export interface QpcrTarget {
+  id: string
+  name: string
+  assayId?: string
+  reporter?: string
+  quencher?: string
+  ampliconBp?: number
+  metadata?: Record<string, unknown>
+}
+
+export interface QpcrReaction {
+  id: string
+  wellId: string
+  sampleId?: string
+  targetId: string
+  replicate: number
+  controlKind: QpcrControlKind
+  cq?: number | null
+  quantity?: number | null
+  flags: string[]
+  metadata?: Record<string, unknown>
+}
+
+export interface QpcrPlateTemplateData {
+  plateId: string
+  format: WellPlateFormat
+  samples: QpcrSample[]
+  targets: QpcrTarget[]
+  reactions: QpcrReaction[]
+  instrument?: string
+  chemistry: QpcrChemistry
+  metadata: Record<string, unknown>
+}
+
+export type QpcrPlateTemplate = BioTemplateEnvelope<QpcrPlateTemplateData>
+
+export type DataFrameTemplate =
+  | SampleSheetTemplate
+  | SamplePrepTemplate
+  | CalibrationCurveTemplate
+  | TimeCourseTemplate
+  | ProtocolStepsTemplate
+  | AssayMatrixTemplate
+  | ReagentListTemplate
+  | FlowCytometryPanelTemplate
+  | InstrumentRunTemplate
+  | QpcrPlateTemplate
+
+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 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>
+}
+
+export type PlateMapEditorAdapterResult = PlateMapEditorState
+export type WellMapAdapterResult = Record<string, Well>
+export type SampleRowsAdapterResult = Array<Record<string, unknown>>
+export type SampleColumnsAdapterResult = DataFrameColumn<Record<string, unknown>>[]
+export interface DataFrameAdapterResult {
+  data: Array<Record<string, unknown>>
+  columns: DataFrameColumn<Record<string, unknown>>[]
+  rowKey?: string
+}
+export type SampleDataFrameAdapterResult = DataFrameAdapterResult
+export type SampleOptionsAdapterResult = SelectOption<string>[]
+export type SamplePrepRowsAdapterResult = Array<Record<string, unknown>>
+export type SamplePrepColumnsAdapterResult = DataFrameColumn<Record<string, unknown>>[]
+export type SamplePrepDataFrameAdapterResult = DataFrameAdapterResult
+export type DoseConditionsAdapterResult = PlateCondition[]
+export type CalibrationCurveRowsAdapterResult = Array<Record<string, unknown>>
+export type CalibrationCurveColumnsAdapterResult = DataFrameColumn<Record<string, unknown>>[]
+export type CalibrationCurveDataFrameAdapterResult = DataFrameAdapterResult
+export type TimeCourseRowsAdapterResult = Array<Record<string, unknown>>
+export type TimeCourseColumnsAdapterResult = DataFrameColumn<Record<string, unknown>>[]
+export type TimeCourseDataFrameAdapterResult = DataFrameAdapterResult
+export type TimeCourseStepsAdapterResult = ProtocolStep[]
+export type ProtocolStepsAdapterResult = ProtocolStep[]
+export type ProtocolRowsAdapterResult = Array<Record<string, unknown>>
+export type ProtocolColumnsAdapterResult = DataFrameColumn<Record<string, unknown>>[]
+export type ProtocolDataFrameAdapterResult = DataFrameAdapterResult
+export type AssayMatrixRowsAdapterResult = Array<Record<string, unknown>>
+export type AssayMatrixColumnsAdapterResult = DataFrameColumn<Record<string, unknown>>[]
+export type AssayMatrixDataFrameAdapterResult = DataFrameAdapterResult
+export type ReagentListItemsAdapterResult = Reagent[]
+export type ReagentRowsAdapterResult = Array<Record<string, unknown>>
+export type ReagentColumnsAdapterResult = DataFrameColumn<Record<string, unknown>>[]
+export type ReagentDataFrameAdapterResult = DataFrameAdapterResult
+export type FlowPanelRowsAdapterResult = Array<Record<string, unknown>>
+export type FlowPanelColumnsAdapterResult = DataFrameColumn<Record<string, unknown>>[]
+export type FlowPanelDataFrameAdapterResult = DataFrameAdapterResult
+export type InstrumentRunRowsAdapterResult = Array<Record<string, unknown>>
+export type InstrumentRunColumnsAdapterResult = DataFrameColumn<Record<string, unknown>>[]
+export type InstrumentRunDataFrameAdapterResult = DataFrameAdapterResult
+export type QpcrRowsAdapterResult = Array<Record<string, unknown>>
+export type QpcrColumnsAdapterResult = DataFrameColumn<Record<string, unknown>>[]
+export type QpcrDataFrameAdapterResult = DataFrameAdapterResult
+export type QpcrWellMapAdapterResult = Record<string, Well>
+export type TemplateDataFrameAdapterResult = DataFrameAdapterResult