@morscherlab/mint-sdk 1.2.0-beta.3 → 1.2.0-beta.4

package/src/templates/targetedMetabolomicsHelpers.ts

@@ -0,0 +1,102 @@
+import type {
+  AssayFeature,
+  CalibrationPoint,
+  InstrumentRunItemInput,
+  ReagentTemplateInput,
+  SampleRecord,
+} from './types'
+import {
+  normalizeAssayFeature,
+  normalizeReagent,
+} from './assayNormalizers'
+import { idFromName } from './builderIdUtils'
+
+export function normalizeMetaboliteFeatures(
+  metabolites: Array<string | AssayFeature>,
+  responseUnit: string,
+): AssayFeature[] {
+  return metabolites.map((metabolite, index) => {
+    if (typeof metabolite === 'string') {
+      return {
+        id: idFromName(metabolite, `metabolite-${index + 1}`),
+        name: metabolite,
+        type: 'metabolite',
+        unit: responseUnit,
+        metadata: { quantitation: 'targeted' },
+      }
+    }
+
+    const feature = normalizeAssayFeature(metabolite)
+    return {
+      ...feature,
+      type: feature.type ?? 'metabolite',
+      unit: feature.unit ?? responseUnit,
+      metadata: {
+        quantitation: 'targeted',
+        ...feature.metadata,
+      },
+    }
+  })
+}
+
+export function normalizeInternalStandardReagents(
+  internalStandards: Array<string | ReagentTemplateInput>,
+): ReagentTemplateInput[] {
+  return internalStandards.map((standard, index) => {
+    if (typeof standard === 'string') {
+      return {
+        id: idFromName(standard, `internal-standard-${index + 1}`),
+        name: standard,
+        kind: 'compound',
+        metadata: { role: 'internal-standard' },
+      }
+    }
+
+    const reagent = normalizeReagent(standard)
+    return {
+      ...reagent,
+      kind: standard.kind ?? 'compound',
+      metadata: {
+        role: 'internal-standard',
+        ...reagent.metadata,
+      },
+    }
+  })
+}
+
+export function targetedMetabolomicsRunItems(
+  samples: SampleRecord[],
+  calibrationPoints: CalibrationPoint[],
+  includeQc: boolean,
+): InstrumentRunItemInput[] {
+  const calibrationItems = calibrationPoints
+    .filter(point => point.role !== 'qc' || includeQc)
+    .filter(point => point.role === 'blank' || point.role === 'standard' || point.role === 'qc')
+    .map((point): InstrumentRunItemInput => ({
+      id: `${point.id}-run`,
+      kind: calibrationRunItemKind(point.role),
+      name: point.level,
+      metadata: {
+        concentration: point.concentration,
+        unit: point.unit,
+        role: point.role,
+      },
+    }))
+
+  const sampleItems = samples.map((sample): InstrumentRunItemInput => ({
+    sampleId: sample.sampleId,
+    name: sample.name ?? sample.sampleId,
+    kind: 'sample',
+  }))
+
+  return [...calibrationItems, ...sampleItems]
+}
+
+export function firstFeatureName(features: AssayFeature[], fallback: string): string {
+  return features.find(feature => feature.name)?.name ?? fallback
+}
+
+function calibrationRunItemKind(role: CalibrationPoint['role']): 'blank' | 'standard' | 'qc' {
+  if (role === 'blank' || role === 'standard' || role === 'qc') return role
+  return 'standard'
+}

package/src/templates/templateAdapterTypes.ts

@@ -0,0 +1,58 @@
+import type {
+  DataFrameColumn,
+  PlateCondition,
+  PlateMapEditorState,
+  ProtocolStep,
+  Reagent,
+  ScheduleEvent,
+  SelectOption,
+  Well,
+} from '../types'
+
+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 AssayMatrixSampleOptionsAdapterResult = SelectOption<string>[]
+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 InstrumentRunStepsAdapterResult = ProtocolStep[]
+export type InstrumentRunScheduleEventsAdapterResult = ScheduleEvent[]
+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

package/src/templates/templateControlSchemas.ts

@@ -0,0 +1,320 @@
+import {
+  CONCENTRATION_UNITS,
+  ICONS,
+  PLATE_FORMAT_OPTIONS,
+} from './controlSchemaConstants'
+import type {
+  BioTemplateControlSchema,
+} from './controlSchemaTypes'
+import type {
+  TemplateId,
+} from './types'
+
+export const templateControlSchemas = {
+  'plate-map': {
+    plateName: {
+      label: 'Plate name',
+      default: 'Plate 1',
+      section: 'layout',
+      sectionLabel: 'Layout',
+      sectionSubtitle: 'Plate geometry',
+      view: 'design',
+      sidebar: { icon: ICONS.plate, iconColor: '#6366f1', iconBg: '#e0e7ff' },
+    },
+    plateFormat: {
+      label: 'Format',
+      default: 96,
+      options: PLATE_FORMAT_OPTIONS,
+      section: 'layout',
+      view: 'design',
+    },
+    sampleNames: {
+      type: 'tags',
+      label: 'Samples',
+      default: ['Control', 'Treatment'],
+      section: 'samples',
+      sectionLabel: 'Samples',
+      sectionSubtitle: 'Groups and legend',
+      view: 'design',
+      sidebar: { icon: ICONS.samples, iconColor: '#10b981', iconBg: '#d1fae5' },
+    },
+  },
+  'sample-sheet': {
+    sampleCount: {
+      type: 'number',
+      label: 'Sample count',
+      default: 2,
+      min: 1,
+      max: 10000,
+      section: 'samples',
+      sectionLabel: 'Samples',
+      sectionSubtitle: 'Metadata table',
+      view: 'design',
+      sidebar: { icon: ICONS.samples, iconColor: '#10b981', iconBg: '#d1fae5' },
+    },
+    includeGroups: {
+      label: 'Include groups',
+      default: true,
+      section: 'samples',
+      view: 'design',
+    },
+    includeBatch: {
+      label: 'Include batch',
+      default: false,
+      section: 'columns',
+      sectionLabel: 'Columns',
+      view: 'design',
+      sidebar: { icon: ICONS.table, iconColor: '#0ea5e9', iconBg: '#e0f2fe' },
+    },
+  },
+  'sample-prep': {
+    prepType: {
+      label: 'Prep type',
+      default: 'extraction',
+      options: ['extraction', 'dilution', 'normalization', 'transfer', 'quench', 'custom'],
+      section: 'protocol',
+      sectionLabel: 'Protocol',
+      sectionSubtitle: 'Prep workflow',
+      view: 'design',
+      sidebar: { icon: ICONS.run, iconColor: '#f97316', iconBg: '#ffedd5' },
+    },
+    volumeUnit: {
+      label: 'Volume unit',
+      default: 'uL',
+      options: ['uL', 'mL'],
+      section: 'protocol',
+      view: 'design',
+    },
+    outputVolume: {
+      type: 'number',
+      label: 'Output volume',
+      default: 50,
+      min: 0,
+      section: 'protocol',
+      view: 'design',
+    },
+  },
+  'dose-response': {
+    unit: {
+      label: 'Dose unit',
+      default: 'uM',
+      options: CONCENTRATION_UNITS,
+      section: 'dose',
+      sectionLabel: 'Dose Design',
+      sectionSubtitle: 'Concentration series',
+      view: 'design',
+      sidebar: { icon: ICONS.dose, iconColor: '#8b5cf6', iconBg: '#ede9fe' },
+    },
+    replicates: {
+      type: 'number',
+      label: 'Replicates',
+      default: 3,
+      min: 1,
+      max: 24,
+      section: 'dose',
+      view: 'design',
+    },
+    includePlateLayout: {
+      label: 'Create plate layout',
+      default: true,
+      section: 'layout',
+      sectionLabel: 'Layout',
+      sectionSubtitle: 'Well assignment',
+      view: 'design',
+      sidebar: { icon: ICONS.plate, iconColor: '#6366f1', iconBg: '#e0e7ff', defaultOpen: false },
+    },
+  },
+  'calibration-curve': {
+    analyte: {
+      label: 'Analyte',
+      default: 'Analyte',
+      section: 'standards',
+      sectionLabel: 'Standards',
+      sectionSubtitle: 'Curve setup',
+      view: 'analysis',
+      sidebar: { icon: ICONS.dose, iconColor: '#8b5cf6', iconBg: '#ede9fe' },
+    },
+    model: {
+      label: 'Model',
+      default: 'linear',
+      options: ['linear', 'linear-weighted-1-x', 'linear-weighted-1-x2', 'quadratic', 'four-parameter-logistic'],
+      section: 'fit',
+      sectionLabel: 'Fit',
+      view: 'analysis',
+      sidebar: { icon: ICONS.settings, iconColor: '#6366f1', iconBg: '#e0e7ff' },
+    },
+    minRSquared: {
+      type: 'number',
+      label: 'Minimum R squared',
+      default: 0.99,
+      min: 0,
+      max: 1,
+      props: { step: 0.001 },
+      section: 'fit',
+      view: 'analysis',
+    },
+  },
+  'time-course': {
+    timeUnit: {
+      label: 'Time unit',
+      default: 'hour',
+      options: ['second', 'minute', 'hour', 'day', 'week'],
+      section: 'schedule',
+      sectionLabel: 'Schedule',
+      sectionSubtitle: 'Sampling timeline',
+      view: 'design',
+      sidebar: { icon: ICONS.run, iconColor: '#0ea5e9', iconBg: '#e0f2fe' },
+    },
+    replicates: {
+      type: 'number',
+      label: 'Replicates',
+      default: 3,
+      min: 1,
+      max: 24,
+      section: 'samples',
+      sectionLabel: 'Samples',
+      view: 'design',
+      sidebar: { icon: ICONS.samples, iconColor: '#10b981', iconBg: '#d1fae5' },
+    },
+  },
+  'protocol-steps': {
+    defaultDuration: {
+      type: 'number',
+      label: 'Default duration',
+      default: 30,
+      min: 0,
+      section: 'protocol',
+      sectionLabel: 'Protocol',
+      sectionSubtitle: 'Step defaults',
+      view: 'design',
+      sidebar: { icon: ICONS.run, iconColor: '#f97316', iconBg: '#ffedd5' },
+      props: { suffix: 'min' },
+    },
+    editable: {
+      label: 'Editable timeline',
+      default: true,
+      section: 'protocol',
+      view: 'design',
+    },
+  },
+  'assay-matrix': {
+    featureType: {
+      label: 'Feature type',
+      default: 'metabolite',
+      options: ['metabolite', 'protein', 'gene', 'cell', 'compound', 'readout', 'other'],
+      section: 'features',
+      sectionLabel: 'Features',
+      sectionSubtitle: 'Measurement matrix',
+      view: 'analysis',
+      sidebar: { icon: ICONS.table, iconColor: '#0ea5e9', iconBg: '#e0f2fe' },
+    },
+    normalizeValues: {
+      label: 'Normalize values',
+      default: false,
+      section: 'analysis',
+      sectionLabel: 'Analysis',
+      view: 'analysis',
+      sidebar: { icon: ICONS.settings, iconColor: '#6366f1', iconBg: '#e0e7ff', defaultOpen: false },
+    },
+  },
+  'reagent-list': {
+    reagentKind: {
+      label: 'Reagent kind',
+      default: 'reagent',
+      options: ['compound', 'antibody', 'primer', 'enzyme', 'buffer', 'media', 'kit', 'reagent', 'other'],
+      section: 'inventory',
+      sectionLabel: 'Inventory',
+      sectionSubtitle: 'Reagent metadata',
+      view: 'design',
+      sidebar: { icon: ICONS.table, iconColor: '#10b981', iconBg: '#d1fae5' },
+    },
+    trackStock: {
+      label: 'Track stock level',
+      default: true,
+      section: 'inventory',
+      view: 'design',
+    },
+  },
+  'flow-cytometry-panel': {
+    markers: {
+      type: 'tags',
+      label: 'Markers',
+      default: ['CD3', 'CD4', 'CD8'],
+      section: 'panel',
+      sectionLabel: 'Panel',
+      sectionSubtitle: 'Markers and controls',
+      view: 'design',
+      sidebar: { icon: ICONS.table, iconColor: '#0ea5e9', iconBg: '#e0f2fe' },
+    },
+    instrument: {
+      label: 'Instrument',
+      default: 'Flow cytometer',
+      section: 'panel',
+      sectionLabel: 'Panel',
+      sectionSubtitle: 'Markers and controls',
+      view: 'design',
+      sidebar: { icon: ICONS.settings, iconColor: '#6366f1', iconBg: '#e0e7ff' },
+    },
+    includeDefaultControls: {
+      label: 'Default controls',
+      default: true,
+      section: 'panel',
+      view: 'design',
+    },
+  },
+  'instrument-run': {
+    instrument: {
+      label: 'Instrument',
+      default: 'LC-MS',
+      options: ['LC-MS', 'GC-MS', 'Orbitrap', 'Triple quadrupole', 'Plate reader', 'Other'],
+      section: 'acquisition',
+      sectionLabel: 'Acquisition',
+      sectionSubtitle: 'Run queue',
+      view: 'run',
+      sidebar: { icon: ICONS.run, iconColor: '#ef4444', iconBg: '#fee2e2' },
+    },
+    method: {
+      label: 'Method',
+      default: 'Default method',
+      section: 'acquisition',
+      view: 'run',
+    },
+    includeQc: {
+      label: 'Include QC',
+      default: true,
+      section: 'quality',
+      sectionLabel: 'Quality Control',
+      view: 'run',
+      sidebar: { icon: ICONS.settings, iconColor: '#6366f1', iconBg: '#e0e7ff', defaultOpen: false },
+    },
+  },
+  'qpcr-plate': {
+    chemistry: {
+      label: 'Chemistry',
+      default: 'sybr',
+      options: ['sybr', 'taqman', 'probe', 'evagreen', 'other'],
+      section: 'assay',
+      sectionLabel: 'Assay',
+      sectionSubtitle: 'qPCR setup',
+      view: 'design',
+      sidebar: { icon: ICONS.plate, iconColor: '#6366f1', iconBg: '#e0e7ff' },
+    },
+    replicates: {
+      type: 'number',
+      label: 'Replicates',
+      default: 3,
+      min: 1,
+      max: 12,
+      section: 'assay',
+      view: 'design',
+    },
+    includeNoTemplateControls: {
+      label: 'No-template controls',
+      default: true,
+      section: 'controls',
+      sectionLabel: 'Controls',
+      view: 'design',
+      sidebar: { icon: ICONS.settings, iconColor: '#8b5cf6', iconBg: '#ede9fe', defaultOpen: false },
+    },
+  },
+} satisfies Record<TemplateId, BioTemplateControlSchema>

package/src/templates/templateCreateOptions.ts

@@ -0,0 +1,208 @@
+import type { WellPlateFormat } from '../types'
+import type {
+  AssayFeature,
+  AssaySample,
+  CalibrationAcceptanceInput,
+  CalibrationModel,
+  CalibrationPointInput,
+  CompoundDoseSeries,
+  ControlDefinition,
+  FlowPanelControl,
+  FlowPanelMarker,
+  InstrumentMethodInput,
+  InstrumentRunItemInput,
+  PlateMapTemplate,
+  PlateMapTemplateData,
+  ProtocolStepRecord,
+  ReagentTemplateInput,
+  SampleColumn,
+  SampleGroupDefinition,
+  SamplePrepStepInput,
+  SamplePrepStepType,
+  SampleRecord,
+  TemplateSample,
+  TimeCourseCondition,
+  TimePoint,
+  TimeUnit,
+} from './types'
+import type {
+  QpcrChemistry,
+  QpcrSample,
+  QpcrTarget,
+} from './templateQpcrTypes'
+
+export interface CreateBioTemplatePackCollectionOptions {
+  metadata?: Record<string, unknown>
+}
+
+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 CreateTargetedMetabolomicsCollectionOptions {
+  samples?: Array<string | SampleRecord>
+  metabolites?: Array<string | AssayFeature>
+  internalStandards?: Array<string | ReagentTemplateInput>
+  standardConcentrations?: number[]
+  concentrationUnit?: string
+  responseUnit?: string
+  calibrationAnalyte?: string
+  instrument?: string
+  method?: string | InstrumentMethodInput
+  prepType?: SamplePrepStepType
+  outputVolume?: number
+  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>
+}