@morscherlab/mint-sdk 1.2.0-beta.1 → 1.2.0-beta.3

package/src/types/analysisArtifactTypes.ts

@@ -1,176 +0,0 @@
-import type { TreeNode } from './componentLabTypes'
-import type { SummaryData } from './componentWorkflowTypes'
-
-/** Result schema identifier for file-backed analysis artifacts. */
-export const ANALYSIS_FILE_ARTIFACT_SCHEMA = 'mint.analysis_file.v1'
-
-/** Known artifact lifecycle states; kept open for forward compatibility. */
-export type AnalysisArtifactStatus = 'active' | 'archived' | (string & {})
-
-/** Status filter vocabulary for artifact lists. */
-export type AnalysisArtifactStatusFilter = 'active' | 'archived' | 'all'
-
-/** Summary row returned by GET /experiments/{id}/analysis-artifacts. */
-export interface AnalysisArtifactSummary {
-  id: number
-  experiment_id: number
-  plugin_id: string
-  artifact_key: string
-  display_name: string
-  note?: string | null
-  status: AnalysisArtifactStatus
-  result_keys: string[]
-  created_at?: string | null
-  updated_at?: string | null
-  archived_at?: string | null
-  archived_by?: number | null
-}
-
-/** Full artifact returned by GET /experiments/{id}/analysis-artifacts/{artifactId}. */
-export interface AnalysisArtifactDetail extends AnalysisArtifactSummary {
-  result: Record<string, unknown>
-  tree: TreeNode[]
-  summary: SummaryData | null
-}
-
-/** Response of GET /experiments/{id}/analysis-artifacts. */
-export interface AnalysisArtifactListResponse {
-  artifacts: AnalysisArtifactSummary[]
-}
-
-/** Stable identity used when one plugin opens another plugin's artifact. */
-export interface AnalysisArtifactTarget {
-  experimentId: number
-  artifactPluginId: string
-  artifactKey: string
-  /** Optional lookup hint. The stable identity remains the three fields above. */
-  artifactId?: number
-}
-
-/** Body of PATCH /experiments/{id}/analysis-artifacts/{artifactId}. */
-export interface AnalysisArtifactMetadataUpdate {
-  display_name?: string
-  /** undefined = keep, string = set, null = clear. */
-  note?: string | null
-}
-
-/** How a save payload should be applied by the plugin backend. */
-export type ArtifactSaveMode = 'create' | 'upsert' | 'update'
-
-/** Where file content comes from when a plugin uses ArtifactSaveDialog. */
-export type ArtifactFileSource = 'upload' | 'handler'
-
-interface ArtifactSavePayloadBase {
-  experimentId: number
-  artifactKey: string
-}
-
-/**
- * JSON artifact save — handler maps to save_analysis_artifact, which upserts by key.
- * That call only assigns display_name/note when they are provided, and cannot clear
- * either; use the metadata PATCH (useAnalysisArtifacts.updateMetadata) for that.
- */
-export interface JsonArtifactSavePayload extends ArtifactSavePayloadBase {
-  kind: 'json'
-  mode: 'create' | 'upsert'
-  result: Record<string, unknown>
-  displayName?: string
-  note?: string
-}
-
-/** File artifact create — handler maps to save_analysis_file_artifact (create-only: a reused key conflicts). */
-export interface FileArtifactCreatePayload extends ArtifactSavePayloadBase {
-  kind: 'file'
-  mode: 'create'
-  file: File
-  /** Maps to the Python `kind=` argument (defaults to "file" backend-side). */
-  fileKind: string
-  filename?: string
-  displayName?: string
-  note?: string
-  contentType?: string
-  metadata?: Record<string, unknown>
-}
-
-/**
- * File artifact replacement — handler maps to update_analysis_file_artifact
- * (transactional CAS replace). `kind` and `filename` are immutable backend-side, so
- * `fileKind` echoes the artifact's existing kind and no filename is carried. `note`
- * is three-state: omitted preserves, null clears, a string sets. `metadata` REPLACES
- * the previous result metadata rather than merging, so it always carries the full
- * intended map — omitting it clears whatever was there.
- */
-export interface FileArtifactUpdatePayload extends ArtifactSavePayloadBase {
-  kind: 'file'
-  mode: 'update'
-  file: File
-  fileKind: string
-  note?: string | null
-  contentType?: string
-  metadata?: Record<string, unknown>
-}
-
-/**
- * File artifact create where the plugin handler produces the bytes itself.
- * This is intended for server-side serialization of in-memory analysis state;
- * the browser neither fabricates nor uploads a placeholder File.
- */
-export interface HandlerFileArtifactCreatePayload extends ArtifactSavePayloadBase {
-  kind: 'file'
-  mode: 'create'
-  source: 'handler'
-  fileKind: string
-  displayName?: string
-  note?: string
-  metadata?: Record<string, unknown>
-}
-
-/** File artifact replacement where the plugin handler produces the bytes itself. */
-export interface HandlerFileArtifactUpdatePayload extends ArtifactSavePayloadBase {
-  kind: 'file'
-  mode: 'update'
-  source: 'handler'
-  fileKind: string
-  note?: string | null
-  metadata?: Record<string, unknown>
-}
-
-export type ArtifactSavePayload =
-  | JsonArtifactSavePayload
-  | FileArtifactCreatePayload
-  | FileArtifactUpdatePayload
-
-/** Payloads accepted when `ArtifactSaveDialog.fileSource` is `handler`. */
-export type HandlerArtifactSavePayload =
-  | JsonArtifactSavePayload
-  | HandlerFileArtifactCreatePayload
-  | HandlerFileArtifactUpdatePayload
-
-/** Every payload variant the dialog can emit across both file sources. */
-export type ArtifactSaveDialogPayload =
-  | ArtifactSavePayload
-  | HandlerFileArtifactCreatePayload
-  | HandlerFileArtifactUpdatePayload
-
-/** Optional handler result; cleanupPending surfaces AnalysisFileArtifactUpdate.cleanup_pending. */
-export interface ArtifactSaveResult {
-  artifact?: AnalysisArtifactSummary
-  cleanupPending?: boolean
-}
-
-/**
- * Plugin-supplied save handler. The dialog never writes to the platform;
- * the handler forwards the payload to the plugin backend, which calls
- * save_analysis_artifact / save_analysis_file_artifact / update_analysis_file_artifact.
- */
-export type ArtifactSaveHandler = (
-  payload: ArtifactSavePayload,
-) => Promise<ArtifactSaveResult | void>
-
-/** Save handler paired with `ArtifactSaveDialog.fileSource="handler"`. */
-export type HandlerArtifactSaveHandler = (
-  payload: HandlerArtifactSavePayload,
-) => Promise<ArtifactSaveResult | void>
-
-/** Handler accepted by ArtifactSaveDialog; `fileSource` selects the payload family. */
-export type ArtifactSaveDialogHandler = ArtifactSaveHandler | HandlerArtifactSaveHandler

package/src/types/auth.ts

@@ -1,58 +0,0 @@
-import type { RoleInfo } from '../permissions'
-
-// Authentication configuration
-export interface AuthConfig {
-  authRequired: boolean
-  passkeyEnabled: boolean
-  passkeyRegistered: boolean
-  registrationEnabled: boolean
-  experimentVisibilityMode?: 'open' | 'restricted'
-}
-
-// User information
-export interface UserInfo {
-  id: number
-  username: string
-  shortname: string | null
-  email: string | null
-  role: string
-  roleObj?: RoleInfo | null
-  isActive: boolean
-}
-
-// Login response from API
-export interface LoginResponse {
-  access_token: string
-  token_type: string
-  expires_in: number
-}
-
-// Token verification response
-export interface TokenVerifyResponse {
-  valid: boolean
-  username: string | null
-  expires_at: string | null
-}
-
-// Registration request
-export interface RegisterRequest {
-  username: string
-  password: string
-  email?: string
-  shortname?: string
-}
-
-// Profile update request
-export interface UpdateProfileRequest {
-  email?: string
-  shortname?: string
-  current_password?: string
-  new_password?: string
-}
-
-// Passkey credential info
-export interface CredentialInfo {
-  credential_id: string
-  device_name: string | null
-  created_at: string
-}

package/src/types/auto-group.ts

@@ -1,157 +0,0 @@
-import type { SampleGroup } from './components'
-import type { TreeNode } from './componentLabTypes'
-
-// ---- Legacy (kept for source-compatibility) ----
-export type OutlierAction = 'include' | 'exclude' | 'qc'
-export type InputMode = 'paste' | 'csv' | 'experiment'
-
-export interface OutlierInfo {
-  sample: string
-  index: number
-  fieldCount: number
-  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
-  /**
-   * Token count shared by every member of this class. Set by `splitByTokenLength`
-   * after type classification so that samples with different field counts never
-   * share a schema — column index N then means the same field for every member.
-   */
-  tokenLength?: number
-}
-
-// ---- 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 ClassSchema {
-  classKind: SampleClassKind
-  subKind?: string
-  /** Token count of the class this schema describes. Distinguishes schemas that
-   *  share a (kind, subKind) but were split apart by token-length. */
-  tokenLength?: number
-  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
-  /**
-   * Experimental (disposition === 'group') classes as a nested hierarchy:
-   * one root per class, then one level per enabled groupBy column, then the
-   * sample leaves. Parent nodes carry a sample-count `badge`; leaves carry the
-   * sample name plus the detected injection number (`metadata.injection` and as
-   * the leaf badge). Renders directly in `SampleHierarchyTree`.
-   */
-  groupTree?: TreeNode[]
-}
-
-export interface SchemaFingerprint {
-  version: 1
-  classes: Array<{
-    kind: SampleClassKind
-    subKind?: string
-    tokenLength?: number
-    columns: Array<{
-      name: string
-      role: ColumnRole
-      sourceIndices: number[]
-      binning?: NumericBinning
-      ops?: ValueOps
-    }>
-    groupBy: number[]
-  }>
-}

package/src/types/componentLabTypes.ts

@@ -1,235 +0,0 @@
-// 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
-}