@morscherlab/mint-sdk 1.0.0-rc.2 → 1.0.0-rc.5

package/src/types/auto-group.ts

@@ -1,5 +1,6 @@
 import type { SampleGroup } from './components'
 
+// ---- Legacy (kept for source-compatibility) ----
 export type OutlierAction = 'include' | 'exclude' | 'qc'
 export type InputMode = 'paste' | 'csv' | 'experiment'
 
@@ -10,31 +11,128 @@ export interface OutlierInfo {
   action: OutlierAction
 }
 
+export interface MetadataRow {
+  sampleName: string
+  fields: Record<string, string>
+  group: string
+}
+
+export interface ParsedCsvData {
+  columns: string[]
+  rows: Record<string, string>[]
+  sampleColumn: string
+  delimiter: string
+}
+
+// ---- Class detection ----
+
+export type SampleClassKind =
+  | 'biological'
+  | 'iqc'
+  | 'eqc'
+  | 'standard'
+  | 'spike-in'
+  | 'stock'
+  | 'blank'
+  | 'unknown'
+
+export type ClassDisposition = 'group' | 'overlay' | 'exclude'
+
+export interface SampleClass {
+  kind: SampleClassKind
+  label: string
+  subKind?: string
+  members: number[]
+  classTagPositions: number[]
+  disposition: ClassDisposition
+}
+
+// ---- Column / role classifier ----
+
+export type ColumnRole =
+  | 'constant'
+  | 'factor'
+  | 'replicate'
+  | 'run-order'
+  | 'numeric'
+  | 'class-tag'
+  | 'ignore'
+
+export interface NumericParse {
+  value: number
+  unit: string
+  raw: string
+}
+
+export interface NumericBinning {
+  mode: 'discrete' | 'binned'
+  edges?: number[]
+  labels?: string[]
+}
+
+export interface ValueOps {
+  alias?: Record<string, string>
+  exclude?: string[]
+}
+
 export interface ColumnInfo {
   index: number
   name: string
+  sourceIndices: number[]
   uniqueValues: string[]
   cardinality: number
+  /** Legacy field, retained alongside `role` during the shim window. */
   type?: 'prefix' | 'suffix'
+  role?: ColumnRole
+  numeric?: { byValue: Record<string, NumericParse> }
+  binning?: NumericBinning
+  ops?: ValueOps
   /** Original CSV column header — used for row lookups when name is renamed */
   originalName?: string
+  displayName?: string
 }
 
-export interface MetadataRow {
-  sampleName: string
-  fields: Record<string, string>
-  group: string
+export interface ClassSchema {
+  classKind: SampleClassKind
+  subKind?: string
+  columns: ColumnInfo[]
+  groupBy: number[]
+  replicateColumn?: number
+}
+
+export interface MergeSuggestion {
+  classKind: SampleClassKind
+  subKind?: string
+  columnIndices: number[]
+  proposedName: string
+  confidence: number
 }
 
 export interface AutoGroupResult {
+  /** All emitted groups, experimental + overlay concatenated for source compat. */
   groups: SampleGroup[]
+  /** Class disposition === 'group' only. */
+  experimentalGroups?: SampleGroup[]
+  /** Class disposition === 'overlay' only. */
+  qcGroups?: SampleGroup[]
   metadata: MetadataRow[]
   excludedSamples: string[]
+  schemas?: ClassSchema[]
+  fingerprint?: SchemaFingerprint
 }
 
-export interface ParsedCsvData {
-  columns: string[]
-  rows: Record<string, string>[]
-  sampleColumn: string
-  delimiter: string
+export interface SchemaFingerprint {
+  version: 1
+  classes: Array<{
+    kind: SampleClassKind
+    subKind?: string
+    columns: Array<{
+      name: string
+      role: ColumnRole
+      sourceIndices: number[]
+      binning?: NumericBinning
+      ops?: ValueOps
+    }>
+    groupBy: number[]
+  }>
 }

package/src/types/componentLabTypes.ts

@@ -0,0 +1,235 @@
+// Well Plate types
+export type WellPlateFormat = 6 | 12 | 24 | 48 | 54 | 96 | 384
+export type WellState = 'empty' | 'filled' | 'selected' | 'disabled'
+export type WellPlateSelectionMode = 'none' | 'single' | 'multiple' | 'rectangle' | 'drag'
+export type WellPlateSize = 'sm' | 'md' | 'lg' | 'xl' | 'fill'
+export type WellShape = 'circle' | 'rounded'
+
+export interface Well {
+  id: string
+  row: number
+  col: number
+  state: WellState
+  sampleType?: string
+  value?: number
+  metadata?: Record<string, unknown>
+}
+
+export type HeatmapColorScale = 'viridis' | 'plasma' | 'turbo' | 'custom'
+
+export interface HeatmapConfig {
+  enabled: boolean
+  min?: number
+  max?: number
+  colorScale?: HeatmapColorScale
+  customColors?: string[]
+  showLegend?: boolean
+}
+
+// Slot position for rack color coding
+export type SlotPosition = 'R' | 'G' | 'B' | 'Y'
+
+// Extended well data stored in Well.metadata
+export interface WellExtendedData {
+  label?: string
+  injectionVolume?: number
+  injectionCount?: number
+  customMethod?: string | null
+}
+
+// Data emitted when editing a well
+export interface WellEditData {
+  wellId: string
+  label: string
+  sampleType: string
+  injectionVolume: number
+  injectionCount: number
+  customMethod: string
+}
+
+// Fields shown in the edit popup
+export type WellEditField = 'label' | 'sampleType' | 'injectionVolume' | 'injectionCount' | 'customMethod'
+
+// External sample drop payloads for WellPlate / RackEditor
+export interface WellSampleDropData {
+  id?: string
+  sampleName?: string
+  label?: string
+  sampleType?: string
+  injectionVolume?: number
+  injectionCount?: number
+  customMethod?: string | null
+  metadata?: Record<string, unknown>
+  raw?: unknown
+}
+
+export interface WellSampleDropContext {
+  wellId: string
+  event: DragEvent
+}
+
+export type WellSampleDropParser = (
+  event: DragEvent,
+  context: WellSampleDropContext
+) => WellSampleDropData | null | undefined
+
+// Legend item for sample type display
+export interface WellLegendItem {
+  type: string
+  label: string
+  color: string
+}
+
+// Condition headers for dose-response / drug treatment plates
+export interface PlateCondition {
+  label: string
+  color: string
+  concentrations: number[]
+  unit?: string
+}
+
+export interface ColumnCondition extends PlateCondition {
+  cols: number[]
+}
+
+export interface RowCondition extends PlateCondition {
+  rows: string[]
+}
+
+// Rack for RackEditor
+export interface Rack {
+  id: string
+  name: string
+  format: WellPlateFormat
+  slot: SlotPosition
+  injectionVolume: number
+  wells: Record<string, Partial<Well>>
+}
+
+export interface RackSampleDropContext {
+  rack: Rack
+  rackId: string
+  wellId: string
+  event: DragEvent
+}
+
+export type RackSampleDropMapper = (
+  data: WellSampleDropData,
+  context: RackSampleDropContext
+) => WellEditData | null | undefined
+
+// Sample Legend types
+export interface SampleType {
+  id: string
+  name: string
+  color?: string
+  count?: number
+  description?: string
+}
+
+// Plate Map Editor types
+export interface PlateMap {
+  id: string
+  name: string
+  format: WellPlateFormat
+  wells: Record<string, Well>
+}
+
+export interface PlateMapEditorState {
+  plates: PlateMap[]
+  activePlateId: string
+  samples: SampleType[]
+  selectedWells: string[]
+  activeSampleId?: string
+}
+
+// Experiment Timeline types
+export type ProtocolStepType = 'incubation' | 'wash' | 'addition' | 'measurement' | 'transfer' | 'centrifuge' | 'mix' | 'custom'
+export type ProtocolStepStatus = 'pending' | 'in_progress' | 'completed' | 'failed' | 'skipped'
+
+export interface ProtocolStep {
+  id: string
+  type: ProtocolStepType
+  name: string
+  description?: string
+  duration?: number
+  status: ProtocolStepStatus
+  parameters?: Record<string, unknown>
+  order: number
+}
+
+// Sample Selector types
+export interface SampleGroup {
+  name: string
+  color: string
+  samples: string[]
+}
+
+// Group Assigner types
+export interface GroupItem {
+  name: string
+  color: string
+  count: number
+}
+
+// FileUploader types
+export type FileUploaderMode = 'file' | 'folder'
+
+// MoleculeInput types
+export interface MoleculeData {
+  smiles: string
+  molfile: string
+}
+
+// ReagentList types
+export type StorageCondition = 'RT' | '4C' | '-20C' | '-80C'
+
+export type ReagentColumn =
+  | 'name'
+  | 'catalog'
+  | 'lot'
+  | 'expiry'
+  | 'storage'
+  | 'location'
+  | 'stock'
+  | 'supplier'
+
+export interface Reagent {
+  id: string
+  name: string
+  catalogNumber?: string
+  lotNumber?: string
+  expiryDate?: Date | string
+  storageCondition?: StorageCondition
+  location?: string
+  stockLevel?: number
+  stockUnit?: string
+  supplier?: string
+  url?: string
+}
+
+// SampleHierarchyTree types
+export type TreeNodeType =
+  | 'study'
+  | 'experiment'
+  | 'plate'
+  | 'sample'
+  | 'cell_line'
+  | 'passage'
+  | 'clone'
+  | 'treatment'
+  | 'folder'
+  | 'custom'
+
+export type BadgeVariant = 'default' | 'success' | 'warning' | 'error'
+
+export interface TreeNode {
+  id: string
+  label: string
+  type?: TreeNodeType
+  icon?: string
+  children?: TreeNode[]
+  metadata?: Record<string, unknown>
+  badge?: string | number
+  badgeVariant?: BadgeVariant
+}

package/src/types/componentWorkflowTypes.ts

@@ -0,0 +1,190 @@
+import type { UserSummary } from './platform'
+
+// ScientificNumber types
+export type NumberNotation = 'auto' | 'scientific' | 'engineering' | 'compact'
+
+// UnitInput types
+export interface UnitOption {
+  value: string
+  label: string
+  factor?: number
+  group?: string
+}
+
+// StepWizard types
+export interface WizardStep {
+  id: string
+  label: string
+  description?: string
+  icon?: string
+  optional?: boolean
+}
+
+export type WizardStepState = 'pending' | 'active' | 'completed' | 'disabled'
+
+// AuditTrail types
+export type AuditEntryType = 'create' | 'update' | 'delete' | 'system'
+
+export interface AuditEntry {
+  id: string
+  type: AuditEntryType
+  action: string
+  detail?: string
+  user?: string
+  timestamp: Date | string
+  metadata?: Record<string, unknown>
+}
+
+// BatchProgressList types
+export type BatchItemStatus = 'pending' | 'processing' | 'completed' | 'error' | 'skipped'
+
+export interface BatchItem {
+  id: string
+  label: string
+  status: BatchItemStatus
+  progress?: number
+  message?: string
+}
+
+export interface BatchSummary {
+  total: number
+  completed: number
+  processing: number
+  error: number
+  pending: number
+  skipped: number
+  percent: number
+}
+
+// TimePicker types
+export type TimePickerFormat = '12h' | '24h'
+
+export interface TimeRange {
+  start: string  // "HH:mm"
+  end: string    // "HH:mm"
+}
+
+// Schedule types
+export type ScheduleView = 'day' | 'week' | 'month'
+export type ScheduleEventStatus = 'confirmed' | 'pending' | 'cancelled' | 'in-progress'
+
+export interface ScheduleEvent {
+  id: string
+  start: string          // ISO 8601 datetime
+  end: string            // ISO 8601 datetime
+  title: string
+  color?: string
+  status?: ScheduleEventStatus
+  draggable?: boolean
+  resizable?: boolean
+  metadata?: Record<string, unknown>
+}
+
+export interface ScheduleBlockedSlot {
+  start: string
+  end: string
+  label?: string
+}
+
+export interface ScheduleSlotContext {
+  date: Date
+  hour: number
+  minute: number
+}
+
+export interface ScheduleEventCreateContext {
+  start: Date
+  end: Date
+}
+
+export interface ScheduleEventUpdateContext {
+  event: ScheduleEvent
+  newStart: Date
+  newEnd: Date
+}
+
+// Summary data types (for ExperimentDataViewer compact mode)
+export interface SummarySectionItem {
+  label: string
+  metadata?: Record<string, unknown>
+  item_count: number
+  item_key: string
+  columns: string[]
+  rows: Record<string, unknown>[]
+}
+
+export interface SummarySection {
+  key: string
+  label: string
+  type: 'table' | 'group'
+  /** Group sections: list of group items with embedded tables */
+  items?: SummarySectionItem[]
+  /** Table sections: flat table columns and rows */
+  columns?: string[]
+  rows?: Record<string, unknown>[]
+  row_count?: number
+}
+
+export interface SummaryData {
+  metadata: Record<string, unknown>
+  sections: SummarySection[]
+}
+
+// Resource types
+export type ResourceStatus = 'available' | 'in-use' | 'maintenance' | 'offline'
+
+export interface ResourceSpec {
+  label: string
+  value: string
+}
+
+// Experiment selector types
+export type ExperimentStatus = 'planned' | 'ongoing' | 'completed' | 'cancelled'
+export type DatePreset = 'last_7_days' | 'last_30_days' | 'last_90_days'
+export type ExperimentSortField = 'created_at' | 'updated_at' | 'name' | 'status'
+
+export interface ExperimentTypeOption {
+  value: string
+  label: string
+  color?: string
+}
+
+export interface ExperimentSummary {
+  id: number
+  experiment_code?: string
+  name: string
+  status: ExperimentStatus
+  experiment_type: string
+  project?: string
+  project_id?: number
+  project_name?: string
+  notes?: string
+  tags?: Record<string, unknown>
+  created_at: string
+  updated_at: string
+  created_by?: number
+  created_by_user?: UserSummary
+  has_design_data: boolean
+}
+
+export interface ExperimentListResponse {
+  experiments: ExperimentSummary[]
+  total: number
+}
+
+export interface ExperimentFilters {
+  search?: string
+  status?: ExperimentStatus | null
+  project?: string | null
+  experimentType?: string | null
+  datePreset?: DatePreset | null
+}
+
+// FitPanel types
+export type FitState = 'idle' | 'running' | 'completed' | 'error'
+
+export interface FitResultSummary {
+  label: string
+  value: string | number
+  variant?: 'default' | 'success' | 'warning' | 'error'
+}