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

package/src/templates/samplePrepBuilder.ts

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+import { idFromName } from './builderIdUtils'
+import { normalizeSamplePrepStep } from './sampleNormalizers'
+import { createTemplateEnvelope } from './templateEnvelopes'
+import { validateSamplePrepData } from './templateValidators'
+import type {
+  CreateSamplePrepTemplateOptions,
+  SamplePrepStep,
+  SamplePrepTemplate,
+  SamplePrepTemplateData,
+} from './types'
+
+export function createSamplePrepTemplate(
+  options: CreateSamplePrepTemplateOptions
+): SamplePrepTemplate {
+  const prepType = options.prepType ?? 'extraction'
+  const volumeUnit = options.volumeUnit ?? 'uL'
+  const steps: SamplePrepStep[] = []
+  let order = 1
+
+  for (const [index, sample] of options.samples.entries()) {
+    if (typeof sample !== 'string') {
+      const step = normalizeSamplePrepStep(sample, prepType, volumeUnit, order, index)
+      steps.push(step)
+      order = Math.max(order, step.order + 1)
+      continue
+    }
+    const sourceSampleId = idFromName(sample, `sample-${index + 1}`)
+    steps.push({
+      id: `${sourceSampleId}-prep`,
+      order,
+      type: prepType,
+      name: `Prepare ${sample}`,
+      sourceSampleId,
+      destinationSampleId: `${sourceSampleId}-prepared`,
+      inputVolume: options.inputVolume,
+      outputVolume: options.outputVolume,
+      volumeUnit,
+      status: 'planned',
+      metadata: {},
+    })
+    order += 1
+  }
+
+  const data: SamplePrepTemplateData = {
+    protocolName: options.protocolName ?? 'Sample preparation',
+    steps,
+    metadata: options.metadata ?? {},
+  }
+  validateSamplePrepData(data)
+  return createTemplateEnvelope('sample-prep', data, options.metadata ?? {})
+}

package/src/templates/sampleSheetAdapters.ts

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+import type {
+  DataFrameColumn,
+  SelectOption,
+} from '../types'
+import { getTemplateData } from './templateEnvelopes'
+import { validateSampleSheetData } from './templateValidators'
+import type {
+  SampleColumnsAdapterResult,
+  SampleDataFrameAdapterResult,
+  SampleOptionsAdapterResult,
+  SampleRowsAdapterResult,
+  SampleSheetTemplate,
+  SampleSheetTemplateData,
+} from './types'
+
+export function toSampleRows(
+  template: SampleSheetTemplate | SampleSheetTemplateData
+): SampleRowsAdapterResult {
+  const data = getTemplateData(template, 'sample-sheet')
+  validateSampleSheetData(data)
+  return data.samples.map(sample => ({
+    sampleId: sample.sampleId,
+    name: sample.name,
+    group: sample.group,
+    batch: sample.batch,
+    replicate: sample.replicate,
+    plateId: sample.plateId,
+    wellId: sample.wellId,
+    ...(sample.metadata ?? {}),
+  }))
+}
+
+export function toSampleColumns(
+  template: SampleSheetTemplate | SampleSheetTemplateData
+): SampleColumnsAdapterResult {
+  const data = getTemplateData(template, 'sample-sheet')
+  validateSampleSheetData(data)
+  return data.columns.map((column): DataFrameColumn<Record<string, unknown>> => ({
+    key: sampleColumnKey(column.id),
+    label: column.label,
+    sortable: true,
+    align: column.type === 'number' || column.type === 'integer' ? 'right' : 'left',
+  }))
+}
+
+export function toSampleDataFrame(
+  template: SampleSheetTemplate | SampleSheetTemplateData
+): SampleDataFrameAdapterResult {
+  return {
+    data: toSampleRows(template),
+    columns: toSampleColumns(template),
+    rowKey: 'sampleId',
+  }
+}
+
+export function toSampleOptions(
+  template: SampleSheetTemplate | SampleSheetTemplateData
+): SampleOptionsAdapterResult {
+  const data = getTemplateData(template, 'sample-sheet')
+  validateSampleSheetData(data)
+  return data.samples.map((sample): SelectOption<string> => ({
+    value: sample.sampleId,
+    label: sample.name ?? sample.sampleId,
+    description: [sample.group, sample.batch].filter(Boolean).join(' / ') || undefined,
+  }))
+}
+
+function sampleColumnKey(columnId: string): string {
+  const aliases: Record<string, string> = {
+    sample_id: 'sampleId',
+    plate_id: 'plateId',
+    well_id: 'wellId',
+  }
+  return aliases[columnId] ?? columnId
+}

package/src/templates/sampleSheetBuilder.ts

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+import { normalizeSampleRecord } from './sampleNormalizers'
+import { createTemplateEnvelope } from './templateEnvelopes'
+import { validateSampleSheetData } from './templateValidators'
+import type {
+  CreateSampleSheetTemplateOptions,
+  SampleSheetTemplate,
+  SampleSheetTemplateData,
+} from './types'
+
+export function createSampleSheetTemplate(
+  options: CreateSampleSheetTemplateOptions
+): SampleSheetTemplate {
+  const data: SampleSheetTemplateData = {
+    samples: options.samples.map(normalizeSampleRecord),
+    columns: options.columns ?? [
+      { id: 'sampleId', label: 'Sample ID', type: 'string', required: true, groupable: false },
+      { id: 'name', label: 'Name', type: 'string', required: false, groupable: false },
+    ],
+    groups: options.groups ?? [],
+  }
+  validateSampleSheetData(data)
+  return createTemplateEnvelope('sample-sheet', data, options.metadata ?? {})
+}

package/src/templates/targetedMetabolomicsCollectionBuilder.ts

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+import { createAssayMatrixTemplate } from './assayMatrixBuilder'
+import { createCalibrationCurveTemplate } from './calibrationCurveBuilder'
+import { createInstrumentRunTemplate } from './instrumentRunBuilder'
+import { createReagentListTemplate } from './reagentListBuilder'
+import { createSamplePrepTemplate } from './samplePrepBuilder'
+import { createSampleSheetTemplate } from './sampleSheetBuilder'
+import { presetSampleRecords } from './sampleNormalizers'
+import {
+  firstFeatureName,
+  normalizeInternalStandardReagents,
+  normalizeMetaboliteFeatures,
+  targetedMetabolomicsRunItems,
+} from './targetedMetabolomicsHelpers'
+import { createTemplateCollection } from './templateEnvelopes'
+import type {
+  CreateTargetedMetabolomicsCollectionOptions,
+  TemplateCollectionEnvelope,
+} from './types'
+
+export function createTargetedMetabolomicsCollection(
+  options: CreateTargetedMetabolomicsCollectionOptions = {}
+): TemplateCollectionEnvelope {
+  const sampleRecords = presetSampleRecords(options.samples ?? ['S001', 'S002'])
+  const responseUnit = options.responseUnit ?? 'peak area ratio'
+  const concentrationUnit = options.concentrationUnit ?? 'uM'
+  const metaboliteFeatures = normalizeMetaboliteFeatures(
+    options.metabolites ?? ['Glucose', 'Lactate', 'Pyruvate'],
+    responseUnit,
+  )
+  const sampleSheet = createSampleSheetTemplate({ samples: sampleRecords })
+  const samplePrep = createSamplePrepTemplate({
+    samples: sampleRecords.map(sample => sample.sampleId),
+    prepType: options.prepType ?? 'extraction',
+    protocolName: 'Metabolomics sample preparation',
+    outputVolume: options.outputVolume ?? 50,
+    metadata: { assay: 'targeted-metabolomics' },
+  })
+  const reagents = createReagentListTemplate({
+    reagents: normalizeInternalStandardReagents(
+      options.internalStandards ?? ['Stable isotope internal standard mix'],
+    ),
+    metadata: { assay: 'targeted-metabolomics' },
+  })
+  const calibrationCurve = createCalibrationCurveTemplate({
+    concentrations: options.standardConcentrations ?? [0.1, 1, 10, 100],
+    analyte: options.calibrationAnalyte ?? firstFeatureName(metaboliteFeatures, 'Metabolite panel'),
+    unit: concentrationUnit,
+    responseUnit,
+    model: 'linear-weighted-1-x',
+    includeQc: options.includeQc,
+    metadata: { assay: 'targeted-metabolomics' },
+  })
+  const instrumentRun = createInstrumentRunTemplate({
+    items: targetedMetabolomicsRunItems(
+      sampleRecords,
+      calibrationCurve.data.points,
+      options.includeQc !== false,
+    ),
+    method: options.method ?? 'Targeted metabolomics',
+    instrument: options.instrument ?? 'LC-MS',
+    includeBlanks: false,
+    includeQc: false,
+    metadata: { assay: 'targeted-metabolomics' },
+  })
+  const assayMatrix = createAssayMatrixTemplate({
+    samples: sampleRecords.map(sample => ({
+      sampleId: sample.sampleId,
+      name: sample.name,
+      group: sample.group,
+      metadata: sample.metadata ?? {},
+    })),
+    features: metaboliteFeatures,
+    metadata: { assay: 'targeted-metabolomics', responseUnit },
+  })
+  return createTemplateCollection(
+    [sampleSheet, samplePrep, reagents, instrumentRun, calibrationCurve, assayMatrix],
+    { preset: 'targeted-metabolomics', ...(options.metadata ?? {}) }
+  )
+}

package/src/templates/targetedMetabolomicsHelpers.ts

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+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

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+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