@morscherlab/mint-sdk 1.0.0-beta.7 → 1.0.0-rc.2

package/src/types/index.ts

@@ -43,11 +43,16 @@ export type {
   WellExtendedData,
   WellEditData,
   WellEditField,
+  WellSampleDropData,
+  WellSampleDropContext,
+  WellSampleDropParser,
   WellLegendItem,
   PlateCondition,
   ColumnCondition,
   RowCondition,
   Rack,
+  RackSampleDropContext,
+  RackSampleDropMapper,
   // Sample Legend types
   SampleType,
   // Plate Map Editor types
@@ -111,6 +116,9 @@ export type {
   SettingsModalLayout,
   SettingsGroup,
   SettingsModalSchema,
+  SettingsUserType,
+  SettingsAudience,
+  SettingsAudienceInput,
   // ScientificNumber types
   NumberNotation,
   // UnitInput types
@@ -166,6 +174,33 @@ export type {
   TreeNode,
 } from './components'
 
+export type {
+  InstrumentAlert,
+  InstrumentAlertBody,
+  InstrumentAlertLevel,
+  InstrumentState,
+  InstrumentStatus,
+  SampleInfo,
+  SampleInfo as InstrumentSampleInfo,
+  SequenceProgress,
+} from './instrument'
+
+export type {
+  LcmsContainerType,
+  LcmsPolarity,
+  LcmsSequenceItem,
+  LcmsSequenceTableColumn,
+} from '../lcms'
+
+export type {
+  AccessAudience,
+  AccessAudienceInput,
+  AccessPolicy,
+  AccessControlled,
+  PermissionUser,
+  RoleInfo,
+} from '../permissions'
+
 // FormBuilder types
 export type {
   FormFieldType,

package/src/types/instrument.ts

@@ -0,0 +1,61 @@
+export type InstrumentState = 'idle' | 'running' | 'standby' | 'connected' | 'disconnected' | 'error'
+export type InstrumentAlertLevel = 'info' | 'warning' | 'critical'
+
+export interface SampleInfo {
+  file_name: string
+  sample_id?: string | null
+  sample_name?: string | null
+  vial_position?: string | null
+  injection_volume?: number | null
+}
+
+export interface SequenceProgress {
+  sequence_name?: string | null
+  current_sample: number
+  total_samples: number
+  elapsed_seconds?: number
+  estimated_remaining_seconds?: number | null
+  avg_sample_seconds?: number | null
+  current_sample_name?: string | null
+  current_method?: string | null
+  estimated_finish_time?: string | Date | null
+  sample_durations?: readonly number[]
+}
+
+export interface InstrumentStatus {
+  instrument_id: string
+  instrument_name?: string | null
+  monitor_id?: string | null
+  state: InstrumentState
+  active_method?: string | null
+  current_sample?: SampleInfo | null
+  sequence_progress?: SequenceProgress | null
+  timestamp?: string | Date
+  last_seen?: string | Date | null
+  connected?: boolean
+  sequence_file?: string | null
+  sequence_row_index?: number | null
+  current_raw_file?: string | null
+  method_elapsed_pct?: number | null
+}
+
+export interface InstrumentAlertBody {
+  source?: string | null
+  event?: string | null
+  detail: string
+  code?: number | null
+  raw_file?: string | null
+}
+
+export interface InstrumentAlert {
+  id?: string
+  instrument_id: string
+  instrument_name?: string | null
+  level: InstrumentAlertLevel
+  rule?: string
+  message?: string | null
+  body?: InstrumentAlertBody | null
+  context?: Record<string, unknown>
+  timestamp?: string | Date
+  acknowledged?: boolean
+}

package/src/types/platform.ts

@@ -1,3 +1,5 @@
+import type { RoleInfo } from '../permissions'
+
 // Plugin information provided by the platform
 export interface PluginInfo {
   id: string
@@ -75,6 +77,8 @@ export interface PlatformContext {
     id: string
     username: string
     role: string
+    role_obj?: RoleInfo | null
+    roleObj?: RoleInfo | null
     shortname?: string
   }
 

package/src/utils/rack.ts

@@ -0,0 +1,209 @@
+import type { Rack, SlotPosition, Well, WellEditData, WellPlateFormat } from '../types'
+
+export type LcmsPlateType = '96well' | '54vial'
+export type LcmsControlSampleType = 'blank' | 'qc' | 'iqc'
+
+export interface LcmsPlateCell {
+  row: string
+  column: number
+  sample_name: string
+  sample_type?: string | null
+  injection_volume?: number | null
+  injection_count?: number | null
+  custom_method?: string | null
+  slot?: SlotPosition | null
+}
+
+export interface LcmsPlateCellsToRackOptions {
+  rackId?: string
+  rackName?: string
+  format?: WellPlateFormat
+  plateType?: LcmsPlateType
+  slot?: SlotPosition
+  injectionVolume?: number
+}
+
+export interface LcmsPlateCellsToRacksOptions extends Omit<LcmsPlateCellsToRackOptions, 'rackId' | 'rackName' | 'slot'> {
+  defaultSlot?: SlotPosition
+  rackId?: (slot: SlotPosition, index: number) => string
+  rackName?: (slot: SlotPosition, index: number) => string
+}
+
+export const LCMS_DEFAULT_CONTROL_POSITIONS: Record<LcmsPlateType, Record<LcmsControlSampleType, { row: string; column: number }>> = {
+  '96well': {
+    blank: { row: 'H', column: 12 },
+    qc: { row: 'H', column: 11 },
+    iqc: { row: 'H', column: 10 },
+  },
+  '54vial': {
+    blank: { row: 'F', column: 9 },
+    qc: { row: 'F', column: 8 },
+    iqc: { row: 'F', column: 7 },
+  },
+}
+
+const SLOT_ORDER: SlotPosition[] = ['R', 'G', 'B', 'Y']
+
+export function lcmsPlateTypeToRackFormat(plateType: LcmsPlateType): WellPlateFormat {
+  return plateType === '96well' ? 96 : 54
+}
+
+export function rackFormatToLcmsPlateType(format: WellPlateFormat): LcmsPlateType {
+  if (format === 96) return '96well'
+  if (format === 54) return '54vial'
+  throw new Error(`LCMS plate cells support only 54-vial racks and 96-well plates; received format ${format}.`)
+}
+
+export function lcmsWellId(row: string, column: number): string {
+  return `${row.toUpperCase()}${column}`
+}
+
+export function parseLcmsWellId(wellId: string): { row: string; column: number } {
+  const match = /^([A-Za-z]+)(\d+)$/.exec(wellId.trim())
+  if (!match) {
+    throw new Error(`Invalid well id "${wellId}". Expected a row letter followed by a column number, e.g. A1.`)
+  }
+
+  return {
+    row: match[1].toUpperCase(),
+    column: Number(match[2]),
+  }
+}
+
+export function lcmsPlateCellsToRack(cells: LcmsPlateCell[], options: LcmsPlateCellsToRackOptions = {}): Rack {
+  const format = options.format ?? (options.plateType ? lcmsPlateTypeToRackFormat(options.plateType) : inferRackFormat(cells))
+  const slot = options.slot ?? cells.find(cell => cell.slot)?.slot ?? 'R'
+  const injectionVolume = options.injectionVolume ?? inferInjectionVolume(cells) ?? 5
+
+  return {
+    id: options.rackId ?? `rack-${slot}`,
+    name: options.rackName ?? `Rack ${slot}`,
+    format,
+    slot,
+    injectionVolume,
+    wells: Object.fromEntries(
+      cells
+        .filter(cell => cell.sample_name.trim())
+        .map((cell) => {
+          const wellId = lcmsWellId(cell.row, cell.column)
+          const well: Partial<Well> = {
+            id: wellId,
+            row: rowIndex(cell.row),
+            col: cell.column - 1,
+            state: 'filled',
+            sampleType: cell.sample_type ?? 'sample',
+            metadata: {
+              label: cell.sample_name.trim(),
+              injectionVolume: cell.injection_volume ?? injectionVolume,
+              injectionCount: cell.injection_count ?? 1,
+              customMethod: cell.custom_method ?? null,
+            },
+          }
+          return [wellId, well]
+        }),
+    ),
+  }
+}
+
+export function lcmsPlateCellsToRacks(cells: LcmsPlateCell[], options: LcmsPlateCellsToRacksOptions = {}): Rack[] {
+  const bySlot = new Map<SlotPosition, LcmsPlateCell[]>()
+  const defaultSlot = options.defaultSlot ?? 'R'
+
+  for (const cell of cells) {
+    const slot = cell.slot ?? defaultSlot
+    const slotCells = bySlot.get(slot) ?? []
+    slotCells.push(cell)
+    bySlot.set(slot, slotCells)
+  }
+
+  return Array.from(bySlot.entries())
+    .sort(([a], [b]) => SLOT_ORDER.indexOf(a) - SLOT_ORDER.indexOf(b))
+    .map(([slot, slotCells], index) => lcmsPlateCellsToRack(slotCells, {
+      ...options,
+      slot,
+      rackId: options.rackId?.(slot, index) ?? `rack-${slot}`,
+      rackName: options.rackName?.(slot, index) ?? `Rack ${slot}`,
+    }))
+}
+
+export function rackToLcmsPlateCells(rack: Rack): LcmsPlateCell[] {
+  return Object.entries(rack.wells)
+    .map(([wellId, well]) => wellToLcmsPlateCell(rack, wellId, well))
+    .filter((cell): cell is LcmsPlateCell => cell !== null)
+    .sort(comparePlateCells)
+}
+
+export function racksToLcmsPlateCells(racks: Rack[]): LcmsPlateCell[] {
+  return racks.flatMap(rackToLcmsPlateCells)
+}
+
+export function getLcmsDefaultControlWellId(plateType: LcmsPlateType, sampleType: LcmsControlSampleType): string {
+  const position = LCMS_DEFAULT_CONTROL_POSITIONS[plateType][sampleType]
+  return lcmsWellId(position.row, position.column)
+}
+
+export function createLcmsControlWellEditData(
+  sampleType: LcmsControlSampleType,
+  options: {
+    wellId?: string
+    plateType?: LcmsPlateType
+    injectionVolume?: number
+  } = {},
+): WellEditData {
+  const plateType = options.plateType ?? '54vial'
+  return {
+    wellId: options.wellId ?? getLcmsDefaultControlWellId(plateType, sampleType),
+    label: sampleType === 'blank' ? 'Blank' : sampleType.toUpperCase(),
+    sampleType,
+    injectionVolume: options.injectionVolume ?? 5,
+    injectionCount: 1,
+    customMethod: '',
+  }
+}
+
+function wellToLcmsPlateCell(rack: Rack, wellId: string, well: Partial<Well>): LcmsPlateCell | null {
+  const metadata = well.metadata ?? {}
+  const label = getString(metadata.label)
+  if (!label) return null
+
+  const parsed = parseLcmsWellId(well.id ?? wellId)
+  return {
+    row: parsed.row,
+    column: parsed.column,
+    sample_name: label,
+    sample_type: well.sampleType ?? null,
+    injection_volume: getNumber(metadata.injectionVolume) ?? rack.injectionVolume,
+    injection_count: getNumber(metadata.injectionCount) ?? 1,
+    custom_method: getNullableString(metadata.customMethod),
+    slot: rack.slot,
+  }
+}
+
+function inferRackFormat(cells: LcmsPlateCell[]): WellPlateFormat {
+  return cells.some(cell => rowIndex(cell.row) > 5 || cell.column > 9) ? 96 : 54
+}
+
+function inferInjectionVolume(cells: LcmsPlateCell[]): number | undefined {
+  return cells.find(cell => typeof cell.injection_volume === 'number')?.injection_volume ?? undefined
+}
+
+function rowIndex(row: string): number {
+  return row.toUpperCase().charCodeAt(0) - 65
+}
+
+function getString(value: unknown): string | undefined {
+  return typeof value === 'string' && value.trim() ? value.trim() : undefined
+}
+
+function getNullableString(value: unknown): string | null {
+  return typeof value === 'string' && value.trim() ? value.trim() : null
+}
+
+function getNumber(value: unknown): number | undefined {
+  return typeof value === 'number' && Number.isFinite(value) ? value : undefined
+}
+
+function comparePlateCells(a: LcmsPlateCell, b: LcmsPlateCell): number {
+  const rowDiff = rowIndex(a.row) - rowIndex(b.row)
+  return rowDiff === 0 ? a.column - b.column : rowDiff
+}

package/dist/auth-QQj2kkze.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"auth-QQj2kkze.js","names":[],"sources":["../src/stores/settings.ts","../src/stores/auth.ts"],"sourcesContent":["import { defineStore } from 'pinia'\nimport { ref, watch } from 'vue'\nimport type { ThemeMode, ColorPalette, TableDensity } from '../types'\n\ndeclare global {\n  interface ImportMetaEnv {\n    readonly VITE_API_PREFIX?: string\n  }\n\n  interface ImportMeta {\n    readonly env: ImportMetaEnv\n  }\n}\n\nexport interface SettingsState {\n  serverHost: string\n  serverPort: number\n  requestTimeout: number\n  wsAutoReconnect: boolean\n  wsReconnectInterval: number\n  theme: ThemeMode\n  colorPalette: ColorPalette\n  tableDensity: TableDensity\n}\n\nconst STORAGE_KEY = 'mint-settings'\n\nfunction getDefaultServerHost(): string {\n  if (typeof window !== 'undefined' && window.location.hostname !== 'localhost') {\n    return window.location.hostname\n  }\n  return 'localhost'\n}\n\nfunction getDefaultServerPort(): number {\n  if (typeof window !== 'undefined') {\n    if (window.location.port) {\n      return parseInt(window.location.port, 10)\n    }\n    // Standard ports: 443 for HTTPS, 80 for HTTP (browser omits from location.port)\n    return window.location.protocol === 'https:' ? 443 : 80\n  }\n  return 8000\n}\n\nconst defaultSettings: SettingsState = {\n  serverHost: getDefaultServerHost(),\n  serverPort: getDefaultServerPort(),\n  requestTimeout: 120000,\n  wsAutoReconnect: true,\n  wsReconnectInterval: 5000,\n  theme: 'system',\n  colorPalette: 'default',\n  tableDensity: 'normal',\n}\n\nexport const colorPalettes: Record<ColorPalette, { name: string; hues: [number, number] }> = {\n  default: { name: 'Default (Cyan-Pink)', hues: [180, 320] },\n  colorblind: { name: 'Colorblind-friendly', hues: [45, 260] },\n  viridis: { name: 'Viridis', hues: [280, 80] },\n  pastel: { name: 'Pastel', hues: [200, 340] },\n}\n\nfunction loadSettings(): SettingsState {\n  try {\n    const stored = localStorage.getItem(STORAGE_KEY)\n    if (stored) {\n      const parsed = JSON.parse(stored)\n      return { ...defaultSettings, ...parsed }\n    }\n  } catch (e) {\n    console.warn('Failed to load settings from localStorage:', e)\n  }\n  return { ...defaultSettings }\n}\n\nfunction saveSettings(settings: SettingsState): void {\n  try {\n    localStorage.setItem(STORAGE_KEY, JSON.stringify(settings))\n  } catch (e) {\n    console.warn('Failed to save settings to localStorage:', e)\n  }\n}\n\nfunction getSystemPrefersDark(): boolean {\n  if (typeof window === 'undefined' || typeof window.matchMedia !== 'function') return false\n  return window.matchMedia('(prefers-color-scheme: dark)').matches\n}\n\nexport const useSettingsStore = defineStore('mint-settings', () => {\n  // State\n  const serverHost = ref(defaultSettings.serverHost)\n  const serverPort = ref(defaultSettings.serverPort)\n  const requestTimeout = ref(defaultSettings.requestTimeout)\n  const wsAutoReconnect = ref(defaultSettings.wsAutoReconnect)\n  const wsReconnectInterval = ref(defaultSettings.wsReconnectInterval)\n  const theme = ref<ThemeMode>(defaultSettings.theme)\n  const systemPrefersDark = ref(getSystemPrefersDark())\n  const colorPalette = ref<ColorPalette>(defaultSettings.colorPalette)\n  const tableDensity = ref<TableDensity>(defaultSettings.tableDensity)\n\n  // API prefix - can be configured via env variable VITE_API_PREFIX\n  const apiPrefix: string = (import.meta.env?.VITE_API_PREFIX as string | undefined) ?? '/api'\n\n  function _isSameOrigin(): { same: boolean; currentHost: string; currentPort: string } {\n    const currentHost = typeof window !== 'undefined' ? window.location.hostname : 'localhost'\n    const currentPort = typeof window !== 'undefined' ? window.location.port : '8000'\n    const effectivePort = currentPort || (window.location.protocol === 'https:' ? '443' : '80')\n    const same =\n      (serverHost.value === currentHost && String(serverPort.value) === effectivePort) ||\n      (serverHost.value === 'localhost' && currentHost !== 'localhost')\n    return { same, currentHost, currentPort }\n  }\n\n  function getApiBaseUrl(): string {\n    const { same } = _isSameOrigin()\n    if (same) return apiPrefix\n    return `http://${serverHost.value}:${serverPort.value}${apiPrefix}`\n  }\n\n  function getWsBaseUrl(): string {\n    const { same, currentHost, currentPort } = _isSameOrigin()\n    const protocol = typeof window !== 'undefined' && window.location.protocol === 'https:' ? 'wss:' : 'ws:'\n    if (same) return `${protocol}//${currentHost}${currentPort ? ':' + currentPort : ''}${apiPrefix}`\n    return `ws://${serverHost.value}:${serverPort.value}${apiPrefix}`\n  }\n\n  let _initialized = false\n\n  function initialize() {\n    if (_initialized) return\n    _initialized = true\n\n    const loaded = loadSettings()\n    serverHost.value = loaded.serverHost\n    serverPort.value = loaded.serverPort\n    requestTimeout.value = loaded.requestTimeout\n    wsAutoReconnect.value = loaded.wsAutoReconnect\n    wsReconnectInterval.value = loaded.wsReconnectInterval\n    theme.value = loaded.theme\n    colorPalette.value = loaded.colorPalette\n    tableDensity.value = loaded.tableDensity\n\n    applyTheme()\n  }\n\n  function applyTheme() {\n    if (typeof document === 'undefined') return\n    const dark = theme.value === 'system' ? systemPrefersDark.value : theme.value === 'dark'\n    document.documentElement.classList.toggle('dark', dark)\n  }\n\n  watch(theme, () => {\n    applyTheme()\n    persistSettings()\n  })\n\n  if (typeof window !== 'undefined' && typeof window.matchMedia === 'function') {\n    window.matchMedia('(prefers-color-scheme: dark)').addEventListener('change', (event) => {\n      systemPrefersDark.value = event.matches\n      if (theme.value === 'system') {\n        applyTheme()\n      }\n    })\n  }\n\n  function persistSettings() {\n    saveSettings({\n      serverHost: serverHost.value,\n      serverPort: serverPort.value,\n      requestTimeout: requestTimeout.value,\n      wsAutoReconnect: wsAutoReconnect.value,\n      wsReconnectInterval: wsReconnectInterval.value,\n      theme: theme.value,\n      colorPalette: colorPalette.value,\n      tableDensity: tableDensity.value,\n    })\n  }\n\n  watch([serverHost, serverPort, requestTimeout, wsAutoReconnect, wsReconnectInterval, colorPalette, tableDensity], () => {\n    persistSettings()\n  })\n\n  function resetToDefaults() {\n    serverHost.value = defaultSettings.serverHost\n    serverPort.value = defaultSettings.serverPort\n    requestTimeout.value = defaultSettings.requestTimeout\n    wsAutoReconnect.value = defaultSettings.wsAutoReconnect\n    wsReconnectInterval.value = defaultSettings.wsReconnectInterval\n    theme.value = defaultSettings.theme\n    colorPalette.value = defaultSettings.colorPalette\n    tableDensity.value = defaultSettings.tableDensity\n  }\n\n  function getPaletteHues(): [number, number] {\n    return colorPalettes[colorPalette.value].hues\n  }\n\n  function isDark(): boolean {\n    return theme.value === 'system' ? systemPrefersDark.value : theme.value === 'dark'\n  }\n\n  return {\n    serverHost,\n    serverPort,\n    requestTimeout,\n    wsAutoReconnect,\n    wsReconnectInterval,\n    theme,\n    systemPrefersDark,\n    colorPalette,\n    tableDensity,\n    initialize,\n    applyTheme,\n    persistSettings,\n    resetToDefaults,\n    getPaletteHues,\n    isDark,\n    getApiBaseUrl,\n    getWsBaseUrl,\n  }\n})\n","import { defineStore } from 'pinia'\nimport { ref, computed } from 'vue'\nimport type { AuthConfig, UserInfo } from '../types'\n\nconst AUTH_TOKEN_KEY = 'mint-auth-token'\nconst AUTH_EXPIRES_KEY = 'mint-auth-expires'\n\nconst hasLocalStorage = typeof localStorage !== 'undefined' && typeof localStorage.getItem === 'function'\n\nexport const useAuthStore = defineStore('mint-auth', () => {\n  // State\n  const token = ref<string | null>(null)\n  const tokenExpires = ref<Date | null>(null)\n  const username = ref<string | null>(null)\n  const userInfo = ref<UserInfo | null>(null)\n  const authConfig = ref<AuthConfig>({\n    authRequired: true,\n    passkeyEnabled: false,\n    passkeyRegistered: false,\n    registrationEnabled: false,\n    databaseMode: 'none',\n  })\n  const isInitialized = ref(false)\n  const isLoading = ref(false)\n  const error = ref<string | null>(null)\n\n  // Computed\n  const isAuthenticated = computed(() => {\n    if (!authConfig.value.authRequired) {\n      return true\n    }\n    if (!token.value) {\n      return false\n    }\n    if (tokenExpires.value && tokenExpires.value < new Date()) {\n      return false\n    }\n    return true\n  })\n\n  const needsAuth = computed(() => {\n    return authConfig.value.authRequired && !isAuthenticated.value\n  })\n\n  const isAdmin = computed(() => {\n    return userInfo.value?.role === 'admin'\n  })\n\n  const canRegister = computed(() => {\n    return authConfig.value.registrationEnabled\n  })\n\n  // Actions\n  function initialize() {\n    if (hasLocalStorage) {\n      const storedToken = localStorage.getItem(AUTH_TOKEN_KEY)\n      const storedExpires = localStorage.getItem(AUTH_EXPIRES_KEY)\n\n      if (storedToken) {\n        token.value = storedToken\n\n        if (storedExpires) {\n          const expires = new Date(storedExpires)\n          if (expires > new Date()) {\n            tokenExpires.value = expires\n          } else {\n            clearToken()\n          }\n        }\n      }\n    }\n\n    isInitialized.value = true\n  }\n\n  function setToken(accessToken: string, expiresIn: number) {\n    token.value = accessToken\n    const expires = new Date(Date.now() + expiresIn * 1000)\n    tokenExpires.value = expires\n\n    if (hasLocalStorage) {\n      localStorage.setItem(AUTH_TOKEN_KEY, accessToken)\n      localStorage.setItem(AUTH_EXPIRES_KEY, expires.toISOString())\n    }\n  }\n\n  function clearToken() {\n    token.value = null\n    tokenExpires.value = null\n    username.value = null\n    userInfo.value = null\n\n    if (hasLocalStorage) {\n      localStorage.removeItem(AUTH_TOKEN_KEY)\n      localStorage.removeItem(AUTH_EXPIRES_KEY)\n    }\n  }\n\n  function setUserInfo(info: UserInfo) {\n    userInfo.value = info\n    username.value = info.username\n  }\n\n  function setAuthConfig(config: AuthConfig) {\n    authConfig.value = config\n  }\n\n  function setUsername(name: string) {\n    username.value = name\n  }\n\n  function setError(message: string | null) {\n    error.value = message\n  }\n\n  function setLoading(loading: boolean) {\n    isLoading.value = loading\n  }\n\n  function logout() {\n    clearToken()\n  }\n\n  return {\n    // State\n    token,\n    tokenExpires,\n    username,\n    userInfo,\n    authConfig,\n    isInitialized,\n    isLoading,\n    error,\n\n    // Computed\n    isAuthenticated,\n    needsAuth,\n    isAdmin,\n    canRegister,\n\n    // Actions\n    initialize,\n    setToken,\n    clearToken,\n    setAuthConfig,\n    setUsername,\n    setUserInfo,\n    setError,\n    setLoading,\n    logout,\n  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