@morscherlab/mint-sdk 1.3.9 → 1.4.0-beta.1

package/src/templates/doseResponseBuilder.ts

@@ -1,45 +0,0 @@
-import { compoundIdFromName } from './builderIdUtils'
-import {
-  normalizeCompound,
-  normalizeControl,
-} from './calibrationNormalizers'
-import {
-  createTemplateEnvelope,
-  getTemplateData,
-} from './templateEnvelopes'
-import { validateDoseResponseData } from './templateValidators'
-import type {
-  CreateDoseResponseTemplateOptions,
-  DoseResponseTemplate,
-  DoseResponseTemplateData,
-  PlateMapTemplateData,
-} from './types'
-
-/** @deprecated Scheduled for removal from the core SDK in MINT 1.4; the biology templates move to a dedicated package or the owning plugins. */
-export function createDoseResponseTemplate(
-  options: CreateDoseResponseTemplateOptions
-): DoseResponseTemplate {
-  const compounds = Array.isArray(options.compounds)
-    ? options.compounds.map(normalizeCompound)
-    : Object.entries(options.compounds).map(([name, concentrations], index) => normalizeCompound({
-      id: compoundIdFromName(name, index),
-      name,
-      concentrations,
-      metadata: {},
-    }))
-
-  const layout = options.layout
-    ? getTemplateData<PlateMapTemplateData>(options.layout)
-    : undefined
-
-  const data: DoseResponseTemplateData = {
-    compounds,
-    unit: options.unit,
-    replicates: options.replicates ?? 1,
-    controls: (options.controls ?? []).map(normalizeControl),
-    layout,
-    metadata: options.metadata ?? {},
-  }
-  validateDoseResponseData(data)
-  return createTemplateEnvelope('dose-response', data, options.metadata ?? {})
-}

package/src/templates/elisaAssayCollectionBuilder.ts

@@ -1,63 +0,0 @@
-import { createAssayMatrixTemplate } from './assayMatrixBuilder'
-import { SAMPLE_COLOR_SCALE } from '../utils/color'
-import { idFromName } from './builderIdUtils'
-import { createCalibrationCurveTemplate } from './calibrationCurveBuilder'
-import { createPlateMapTemplate } from './plateMapBuilder'
-import { createSampleSheetTemplate } from './sampleSheetBuilder'
-import { presetSampleRecords } from './sampleNormalizers'
-import { createTemplateCollection } from './templateEnvelopes'
-import type {
-  CreateElisaAssayCollectionOptions,
-  TemplateCollectionEnvelope,
-} from './types'
-
-/** @deprecated Scheduled for removal from the core SDK in MINT 1.4; the biology templates move to a dedicated package or the owning plugins. */
-export function createElisaAssayCollection(
-  options: CreateElisaAssayCollectionOptions = {}
-): TemplateCollectionEnvelope {
-  const sampleRecords = presetSampleRecords(options.samples ?? ['Control', 'Treatment'])
-  const analyte = options.analyte ?? 'Analyte'
-  const responseUnit = options.responseUnit ?? 'OD450'
-  const plate = createPlateMapTemplate({
-    name: options.plateName ?? 'ELISA plate',
-    format: options.plateFormat ?? 96,
-    samples: [
-      { id: 'blank', name: 'Blank' },
-      { id: 'standard', name: 'Standards' },
-      { id: 'qc', name: 'QC' },
-      ...sampleRecords.map((sample, index) => ({
-        id: sample.sampleId,
-        name: sample.name ?? sample.sampleId,
-        color: SAMPLE_COLOR_SCALE[index % SAMPLE_COLOR_SCALE.length],
-      })),
-    ],
-  })
-  const sampleSheet = createSampleSheetTemplate({ samples: sampleRecords })
-  const calibrationCurve = createCalibrationCurveTemplate({
-    concentrations: options.standardConcentrations ?? [1000, 100, 10, 1],
-    analyte,
-    unit: options.unit ?? 'pg/mL',
-    responseUnit,
-    model: 'four-parameter-logistic',
-  })
-  const assayMatrix = createAssayMatrixTemplate({
-    samples: sampleRecords.map(sample => ({
-      sampleId: sample.sampleId,
-      name: sample.name,
-      group: sample.group,
-      metadata: sample.metadata ?? {},
-    })),
-    features: [{
-      id: idFromName(analyte, 'analyte'),
-      name: analyte,
-      type: 'protein',
-      unit: responseUnit,
-      metadata: {},
-    }],
-    metadata: { analyte, responseUnit },
-  })
-  return createTemplateCollection(
-    [plate, sampleSheet, calibrationCurve, assayMatrix],
-    { preset: 'elisa-assay', ...(options.metadata ?? {}) }
-  )
-}

package/src/templates/flowCytometryAssayCollectionBuilder.ts

@@ -1,42 +0,0 @@
-import { createAssayMatrixTemplate } from './assayMatrixBuilder'
-import { createFlowCytometryPanelTemplate } from './flowCytometryPanelBuilder'
-import { createSampleSheetTemplate } from './sampleSheetBuilder'
-import { presetSampleRecords } from './sampleNormalizers'
-import { createTemplateCollection } from './templateEnvelopes'
-import type {
-  CreateFlowCytometryAssayCollectionOptions,
-  TemplateCollectionEnvelope,
-} from './types'
-
-/** @deprecated Scheduled for removal from the core SDK in MINT 1.4; the biology templates move to a dedicated package or the owning plugins. */
-export function createFlowCytometryAssayCollection(
-  options: CreateFlowCytometryAssayCollectionOptions = {}
-): TemplateCollectionEnvelope {
-  const sampleRecords = presetSampleRecords(options.samples ?? ['Control', 'Treatment'])
-  const markers = options.markers ?? ['CD3', 'CD4', 'CD8']
-  const sampleSheet = createSampleSheetTemplate({ samples: sampleRecords })
-  const flowPanel = createFlowCytometryPanelTemplate({
-    markers,
-    instrument: options.instrument ?? 'Flow cytometer',
-    includeDefaultControls: options.includeDefaultControls,
-  })
-  const assayMatrix = createAssayMatrixTemplate({
-    samples: sampleRecords.map(sample => ({
-      sampleId: sample.sampleId,
-      name: sample.name,
-      group: sample.group,
-      metadata: sample.metadata ?? {},
-    })),
-    features: options.features ?? flowPanel.data.markers.map(marker => ({
-      id: marker.id,
-      name: `${marker.marker}+ cells`,
-      type: 'cell',
-      unit: '%',
-      metadata: { marker: marker.marker, fluorophore: marker.fluorophore },
-    })),
-  })
-  return createTemplateCollection(
-    [sampleSheet, flowPanel, assayMatrix],
-    { preset: 'flow-cytometry-assay', ...(options.metadata ?? {}) }
-  )
-}

package/src/templates/flowCytometryPanelBuilder.ts

@@ -1,54 +0,0 @@
-import { idFromName } from './builderIdUtils'
-import {
-  defaultFlowControls,
-  normalizeFlowControl,
-  normalizeFlowMarker,
-} from './flowNormalizers'
-import { createTemplateEnvelope } from './templateEnvelopes'
-import { validateFlowCytometryPanelData } from './templateValidators'
-import type {
-  CreateFlowCytometryPanelTemplateOptions,
-  FlowCytometryPanelTemplate,
-  FlowCytometryPanelTemplateData,
-  FlowPanelControl,
-  FlowPanelMarker,
-} from './types'
-
-/** @deprecated Scheduled for removal from the core SDK in MINT 1.4; the biology templates move to a dedicated package or the owning plugins. */
-export function createFlowCytometryPanelTemplate(
-  options: CreateFlowCytometryPanelTemplateOptions
-): FlowCytometryPanelTemplate {
-  const markers = options.markers.map((marker, index): FlowPanelMarker => {
-    if (typeof marker !== 'string') return normalizeFlowMarker(marker, index)
-    return {
-      id: idFromName(marker, `marker-${index + 1}`),
-      marker,
-      fluorophore: 'unassigned',
-      purpose: 'phenotype',
-      compensationRequired: true,
-      metadata: {},
-    }
-  })
-  const controls = options.controls === undefined
-    ? options.includeDefaultControls === false
-      ? []
-      : defaultFlowControls(markers)
-    : options.controls.map((control, index): FlowPanelControl => {
-        if (typeof control !== 'string') return normalizeFlowControl(control, index)
-        return {
-          id: idFromName(control, `control-${index + 1}`),
-          name: control,
-          kind: 'other',
-          required: true,
-          metadata: {},
-        }
-      })
-  const data: FlowCytometryPanelTemplateData = {
-    markers,
-    controls,
-    instrument: options.instrument,
-    metadata: options.metadata ?? {},
-  }
-  validateFlowCytometryPanelData(data)
-  return createTemplateEnvelope('flow-cytometry-panel', data, options.metadata ?? {})
-}

package/src/templates/flowNormalizers.ts

@@ -1,58 +0,0 @@
-import type {
-  FlowPanelControl,
-  FlowPanelMarker,
-} from './types'
-import { idFromName } from './builderIdUtils'
-
-export function normalizeFlowMarker(
-  marker: Partial<FlowPanelMarker> & { marker: string },
-  index: number
-): FlowPanelMarker {
-  return {
-    id: marker.id ?? idFromName(marker.marker, `marker-${index + 1}`),
-    marker: marker.marker,
-    fluorophore: marker.fluorophore ?? 'unassigned',
-    detector: marker.detector,
-    clone: marker.clone,
-    reagentId: marker.reagentId,
-    purpose: marker.purpose ?? 'phenotype',
-    compensationRequired: marker.compensationRequired ?? true,
-    metadata: marker.metadata ?? {},
-  }
-}
-
-export function normalizeFlowControl(
-  control: Partial<FlowPanelControl> & { name: string },
-  index: number
-): FlowPanelControl {
-  return {
-    id: control.id ?? idFromName(control.name, `control-${index + 1}`),
-    name: control.name,
-    kind: control.kind ?? 'other',
-    markerId: control.markerId,
-    required: control.required ?? true,
-    metadata: control.metadata ?? {},
-  }
-}
-
-export function defaultFlowControls(markers: FlowPanelMarker[]): FlowPanelControl[] {
-  return [
-    {
-      id: 'unstained',
-      name: 'Unstained',
-      kind: 'unstained',
-      required: true,
-      metadata: {},
-    },
-    ...markers
-      .filter(marker => marker.compensationRequired)
-      .map(marker => ({
-        id: `${marker.id}-single-stain`,
-        name: `${marker.marker} single stain`,
-        kind: 'single-stain' as const,
-        markerId: marker.id,
-        required: true,
-        metadata: {},
-      })),
-  ]
-}

package/src/templates/flowPanelAdapters.ts

@@ -1,61 +0,0 @@
-import { getTemplateData } from './templateEnvelopes'
-import { validateFlowCytometryPanelData } from './templateValidators'
-import type {
-  FlowCytometryPanelTemplate,
-  FlowCytometryPanelTemplateData,
-  FlowPanelColumnsAdapterResult,
-  FlowPanelDataFrameAdapterResult,
-  FlowPanelRowsAdapterResult,
-} from './types'
-
-/** @deprecated Scheduled for removal from the core SDK in MINT 1.4; the biology templates move to a dedicated package or the owning plugins. */
-export function toFlowPanelRows(
-  template: FlowCytometryPanelTemplate | FlowCytometryPanelTemplateData
-): FlowPanelRowsAdapterResult {
-  const data = getTemplateData(template, 'flow-cytometry-panel')
-  validateFlowCytometryPanelData(data)
-  return data.markers.map(marker => {
-    const markerControls = data.controls
-      .filter(control => control.markerId === marker.id)
-      .map(control => control.name)
-      .join(', ')
-    return {
-      id: marker.id,
-      marker: marker.marker,
-      fluorophore: marker.fluorophore,
-      detector: marker.detector,
-      clone: marker.clone,
-      reagentId: marker.reagentId,
-      purpose: marker.purpose,
-      compensationRequired: marker.compensationRequired,
-      controls: markerControls,
-      instrument: data.instrument,
-      ...(marker.metadata ?? {}),
-    }
-  })
-}
-
-/** @deprecated Scheduled for removal from the core SDK in MINT 1.4; the biology templates move to a dedicated package or the owning plugins. */
-export function toFlowPanelColumns(): FlowPanelColumnsAdapterResult {
-  return [
-    { key: 'marker', label: 'Marker', sortable: true },
-    { key: 'fluorophore', label: 'Fluorophore', sortable: true },
-    { key: 'detector', label: 'Detector', sortable: true },
-    { key: 'clone', label: 'Clone', sortable: true },
-    { key: 'purpose', label: 'Purpose', sortable: true },
-    { key: 'compensationRequired', label: 'Compensation', sortable: true },
-    { key: 'controls', label: 'Controls' },
-    { key: 'instrument', label: 'Instrument', sortable: true },
-  ]
-}
-
-/** @deprecated Scheduled for removal from the core SDK in MINT 1.4; the biology templates move to a dedicated package or the owning plugins. */
-export function toFlowPanelDataFrame(
-  template: FlowCytometryPanelTemplate | FlowCytometryPanelTemplateData
-): FlowPanelDataFrameAdapterResult {
-  return {
-    data: toFlowPanelRows(template),
-    columns: toFlowPanelColumns(),
-    rowKey: 'id',
-  }
-}

package/src/templates/index.ts

@@ -1,330 +0,0 @@
-// Biology data templates. Deprecated for removal from the core SDK in MINT 1.4:
-// the @deprecated tags sit on each declaration, because TypeScript ignores them
-// on `export { ... } from` blocks.
-export {
-  assertTemplateEnvelope,
-  bioTemplatePresetControlValuesToOptions,
-  createBioTemplatePackCollection,
-  createBioTemplatePresetCollection,
-  createBioTemplatePresetCollectionFromControls,
-  createAssayMatrixTemplate,
-  createCalibrationCurveTemplate,
-  createDoseResponseTemplate,
-  createElisaAssayCollection,
-  createFlowCytometryAssayCollection,
-  createWesternBlotAssayCollection,
-  createFlowCytometryPanelTemplate,
-  createInstrumentRunTemplate,
-  createLcmsBatchCollection,
-  createPlateMapTemplate,
-  createProtocolStepsTemplate,
-  createQpcrExpressionCollection,
-  createQpcrPlateTemplate,
-  createReagentListTemplate,
-  createSampleSheetTemplate,
-  createSamplePrepTemplate,
-  createTargetedMetabolomicsCollection,
-  createTemplateCollection,
-  createDefaultBioTemplate,
-  createTimeCourseTemplate,
-  createTemplateEnvelope,
-  createWellPlateScreenCollection,
-  ensureTemplateFromCollection,
-  ensureTemplateEnvelope,
-  extractTemplateCollection,
-  getTemplateData,
-  TEMPLATE_COLLECTION_KEY,
-  validateAssayMatrixData,
-  validateCalibrationCurveData,
-  validateDoseResponseData,
-  validateFlowCytometryPanelData,
-  validateInstrumentRunData,
-  validatePlateMapData,
-  validateProtocolStepsData,
-  validateQpcrPlateData,
-  validateReagentListData,
-  validateSampleSheetData,
-  validateSamplePrepData,
-  validateTimeCourseData,
-} from './builders'
-
-export type {
-  BioTemplateControlValues,
-} from './builders'
-
-export {
-  bioTemplateCatalog,
-  getBioTemplateInfo,
-  listBioTemplateCatalog,
-  searchBioTemplateCatalog,
-} from './catalog'
-
-export {
-  bioTemplateControlsToFormSchema,
-  bioTemplateControlsToSectionFormSchemas,
-  bioTemplateControlsToSidebarPanels,
-  createBioTemplateControlToolkit,
-  getBioTemplateControlDefaults,
-  getBioTemplateControlSchema,
-  listBioTemplateControlSchemas,
-  listBioTemplatePresetControlSchemas,
-  requireBioTemplateControlSchema,
-} from './controlSchemas'
-
-export {
-  getBioTemplateComponentProps,
-  getBioTemplateComponentBindings,
-  listBioTemplateComponentBindings,
-  toBioTemplateComponentBindings,
-  toBioTemplateComponentBindingsById,
-  toBioTemplateComponentImports,
-  toBioTemplateComponentProps,
-  toBioTemplateComponentPropsByComponent,
-  toBioTemplateComponentPropsById,
-  toBioTemplateComponentSnippets,
-  toBioTemplateComponentUsage,
-} from './componentBindings'
-
-export type {
-  BioTemplateComponentBindingsById,
-  BioTemplateComponentPropsByComponent,
-  BioTemplateComponentPropsById,
-  BioTemplateComponentPropsLookupOptions,
-} from './componentBindings'
-
-export {
-  bioTemplatePresets,
-  getBioTemplatePresetInfo,
-  listBioTemplatePresets,
-  searchBioTemplatePresets,
-} from './presets'
-
-export {
-  bioTemplatePacks,
-  getBioTemplatePackInfo,
-  listBioTemplatePacks,
-  searchBioTemplatePacks,
-} from './packs'
-
-export {
-  toAssayMatrixColumns,
-  toAssayMatrixDataFrame,
-  toAssayMatrixRows,
-  toAssayMatrixSampleOptions,
-  toCalibrationCurveColumns,
-  toCalibrationCurveDataFrame,
-  toCalibrationCurveRows,
-  toDoseConditions,
-  toDoseLayoutState,
-  toFlowPanelColumns,
-  toFlowPanelDataFrame,
-  toFlowPanelRows,
-  toInstrumentRunColumns,
-  toInstrumentRunDataFrame,
-  toInstrumentRunRows,
-  toInstrumentRunScheduleEvents,
-  toInstrumentRunSteps,
-  racksFromPlateState,
-  toPlateMapEditorState,
-  toProtocolColumns,
-  toProtocolDataFrame,
-  toProtocolRows,
-  toProtocolSteps,
-  toQpcrColumns,
-  toQpcrDataFrame,
-  toQpcrRows,
-  toQpcrWellPlateWells,
-  toReagentColumns,
-  toReagentDataFrame,
-  toReagentListItems,
-  toReagentRows,
-  toSampleColumns,
-  toSampleDataFrame,
-  toSampleOptions,
-  toSamplePrepColumns,
-  toSamplePrepDataFrame,
-  toSamplePrepRows,
-  toSampleRows,
-  toTemplateDataFrame,
-  toTimeCourseColumns,
-  toTimeCourseDataFrame,
-  toTimeCourseRows,
-  toTimeCourseSteps,
-  toWellMapArray,
-  toWellPlateWells,
-} from './adapters'
-
-export type {
-  AssayFeature,
-  AssayFeatureType,
-  AssayMatrixColumnsAdapterResult,
-  AssayMatrixDataFrameAdapterResult,
-  AssayMatrixRowsAdapterResult,
-  AssayMatrixSampleOptionsAdapterResult,
-  AssayMatrixTemplate,
-  AssayMatrixTemplateData,
-  AssayMeasurement,
-  AssaySample,
-  BioTemplateEnvelope,
-  CalibrationAcceptance,
-  CalibrationAcceptanceInput,
-  CalibrationCurveColumnsAdapterResult,
-  CalibrationCurveDataFrameAdapterResult,
-  CalibrationCurveRowsAdapterResult,
-  CalibrationCurveTemplate,
-  CalibrationCurveTemplateData,
-  CalibrationModel,
-  CalibrationPoint,
-  CalibrationPointInput,
-  CalibrationPointRole,
-  CalibrationPointStatus,
-  CompoundDoseSeries,
-  ControlDefinition,
-  ControlRole,
-  CreateBioTemplatePackCollectionOptions,
-  CreateAssayMatrixTemplateOptions,
-  CreateCalibrationCurveTemplateOptions,
-  CreateDoseResponseTemplateOptions,
-  CreateElisaAssayCollectionOptions,
-  CreateFlowCytometryAssayCollectionOptions,
-  CreateWesternBlotAssayCollectionOptions,
-  CreateFlowCytometryPanelTemplateOptions,
-  CreateInstrumentRunTemplateOptions,
-  CreateLcmsBatchCollectionOptions,
-  CreateTargetedMetabolomicsCollectionOptions,
-  CreatePlateMapTemplateOptions,
-  CreateProtocolStepsTemplateOptions,
-  CreateQpcrExpressionCollectionOptions,
-  CreateQpcrPlateTemplateOptions,
-  CreateReagentListTemplateOptions,
-  CreateSampleSheetTemplateOptions,
-  CreateSamplePrepTemplateOptions,
-  CreateTimeCourseTemplateOptions,
-  CreateWellPlateScreenCollectionOptions,
-  DoseConditionsAdapterResult,
-  DoseResponseTemplate,
-  DoseResponseTemplateData,
-  FlowControlKind,
-  FlowCytometryPanelTemplate,
-  FlowCytometryPanelTemplateData,
-  FlowMarkerPurpose,
-  FlowPanelColumnsAdapterResult,
-  FlowPanelControl,
-  FlowPanelDataFrameAdapterResult,
-  FlowPanelMarker,
-  FlowPanelRowsAdapterResult,
-  InstrumentMethod,
-  InstrumentMethodInput,
-  InstrumentRunColumnsAdapterResult,
-  InstrumentRunDataFrameAdapterResult,
-  InstrumentRunItem,
-  InstrumentRunItemInput,
-  InstrumentRunItemKind,
-  InstrumentRunRowsAdapterResult,
-  InstrumentRunScheduleEventsAdapterResult,
-  InstrumentRunStepsAdapterResult,
-  InstrumentRunStatus,
-  InstrumentRunTemplate,
-  InstrumentRunTemplateData,
-  DataFrameAdapterResult,
-  DataFrameTemplate,
-  PlateMapEditorAdapterResult,
-  PlateMapTemplate,
-  PlateMapTemplateData,
-  ProtocolColumnsAdapterResult,
-  ProtocolDataFrameAdapterResult,
-  ProtocolRowsAdapterResult,
-  ProtocolStepRecord,
-  ProtocolStepsAdapterResult,
-  ProtocolStepsTemplate,
-  ProtocolStepsTemplateData,
-  QpcrChemistry,
-  QpcrColumnsAdapterResult,
-  QpcrControlKind,
-  QpcrDataFrameAdapterResult,
-  QpcrPlateTemplate,
-  QpcrPlateTemplateData,
-  QpcrReaction,
-  QpcrRowsAdapterResult,
-  QpcrSample,
-  QpcrTarget,
-  QpcrWellMapAdapterResult,
-  ReagentColumnsAdapterResult,
-  ReagentDataFrameAdapterResult,
-  ReagentKind,
-  ReagentListItemsAdapterResult,
-  ReagentListTemplate,
-  ReagentListTemplateData,
-  ReagentRecord,
-  ReagentTemplateInput,
-  ReagentRowsAdapterResult,
-  SampleColumn,
-  SampleColumnType,
-  SampleColumnsAdapterResult,
-  SampleDataFrameAdapterResult,
-  SampleGroupDefinition,
-  SampleOptionsAdapterResult,
-  SamplePrepColumnsAdapterResult,
-  SamplePrepDataFrameAdapterResult,
-  SamplePrepRowsAdapterResult,
-  SamplePrepStatus,
-  SamplePrepStep,
-  SamplePrepStepInput,
-  SamplePrepStepType,
-  SamplePrepTemplate,
-  SamplePrepTemplateData,
-  SampleRecord,
-  SampleRowsAdapterResult,
-  SampleSheetTemplate,
-  SampleSheetTemplateData,
-  TimeCourseColumnsAdapterResult,
-  TimeCourseCondition,
-  TimeCourseDataFrameAdapterResult,
-  TimeCourseRowsAdapterResult,
-  TimeCourseSample,
-  TimeCourseStepsAdapterResult,
-  TimeCourseTemplate,
-  TimeCourseTemplateData,
-  TimePoint,
-  TimeUnit,
-  TemplateId,
-  TemplatePackId,
-  TemplatePresetId,
-  TemplateCollection,
-  TemplateCollectionEnvelope,
-  TemplateDataFrameAdapterResult,
-  TemplateKind,
-  TemplatePlateMap,
-  TemplateSample,
-  TemplateWell,
-  WellMapAdapterResult,
-} from './types'
-
-export type {
-  BioTemplateCatalogEntry,
-} from './catalog'
-
-export type {
-  BioTemplateComponentBinding,
-  BioTemplateComponentImport,
-  BioTemplateComponentPropsBinding,
-  BioTemplateResolvedComponentBinding,
-  BioTemplateComponentSnippet,
-  BioTemplateComponentSnippetOptions,
-  BioTemplateComponentTarget,
-  BioTemplateComponentUsage,
-  BioTemplateComponentUsageOptions,
-} from './componentBindings'
-
-export type {
-  BioTemplateControlSchema,
-  BioTemplateControlTarget,
-} from './controlSchemas'
-
-export type {
-  BioTemplatePresetEntry,
-} from './presets'
-
-export type {
-  BioTemplatePackEntry,
-} from './packs'