@morscherlab/mint-sdk 1.0.0-rc.1 → 1.0.0-rc.4

package/src/templates/samplePrepAdapters.ts

@@ -0,0 +1,63 @@
+import { getTemplateData } from './templateEnvelopes'
+import { validateSamplePrepData } from './templateValidators'
+import type {
+  SamplePrepColumnsAdapterResult,
+  SamplePrepDataFrameAdapterResult,
+  SamplePrepRowsAdapterResult,
+  SamplePrepTemplate,
+  SamplePrepTemplateData,
+} from './types'
+
+export function toSamplePrepRows(
+  template: SamplePrepTemplate | SamplePrepTemplateData
+): SamplePrepRowsAdapterResult {
+  const data = getTemplateData(template, 'sample-prep')
+  validateSamplePrepData(data)
+  return [...data.steps]
+    .sort((a, b) => a.order - b.order)
+    .map(step => ({
+      id: step.id,
+      order: step.order,
+      type: step.type,
+      name: step.name,
+      sourceSampleId: step.sourceSampleId,
+      sourceWellId: step.sourceWellId,
+      destinationSampleId: step.destinationSampleId,
+      destinationWellId: step.destinationWellId,
+      reagentId: step.reagentId,
+      inputVolume: step.inputVolume,
+      outputVolume: step.outputVolume,
+      volumeUnit: step.volumeUnit,
+      durationMin: step.durationMin,
+      status: step.status,
+      protocolName: data.protocolName,
+      ...(step.metadata ?? {}),
+    }))
+}
+
+export function toSamplePrepColumns(): SamplePrepColumnsAdapterResult {
+  return [
+    { key: 'order', label: 'Order', sortable: true, align: 'right' },
+    { key: 'type', label: 'Type', sortable: true },
+    { key: 'name', label: 'Step', sortable: true },
+    { key: 'sourceSampleId', label: 'Source', sortable: true },
+    { key: 'sourceWellId', label: 'Source well', sortable: true },
+    { key: 'destinationSampleId', label: 'Destination', sortable: true },
+    { key: 'destinationWellId', label: 'Destination well', sortable: true },
+    { key: 'reagentId', label: 'Reagent', sortable: true },
+    { key: 'inputVolume', label: 'Input', sortable: true, align: 'right' },
+    { key: 'outputVolume', label: 'Output', sortable: true, align: 'right' },
+    { key: 'volumeUnit', label: 'Unit', sortable: true },
+    { key: 'status', label: 'Status', sortable: true },
+  ]
+}
+
+export function toSamplePrepDataFrame(
+  template: SamplePrepTemplate | SamplePrepTemplateData
+): SamplePrepDataFrameAdapterResult {
+  return {
+    data: toSamplePrepRows(template),
+    columns: toSamplePrepColumns(),
+    rowKey: 'id',
+  }
+}

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

@@ -0,0 +1,75 @@
+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

@@ -0,0 +1,23 @@
+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

@@ -0,0 +1,79 @@
+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

@@ -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'
+}