@morscherlab/mint-sdk 1.3.11 → 1.4.0-beta.10

package/src/templates/sampleSheetBuilder.ts

@@ -1,24 +0,0 @@
-import { normalizeSampleRecord } from './sampleNormalizers'
-import { createTemplateEnvelope } from './templateEnvelopes'
-import { validateSampleSheetData } from './templateValidators'
-import type {
-  CreateSampleSheetTemplateOptions,
-  SampleSheetTemplate,
-  SampleSheetTemplateData,
-} 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 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

@@ -1,80 +0,0 @@
-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'
-
-/** @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 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

@@ -1,102 +0,0 @@
-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

@@ -1,58 +0,0 @@
-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

@@ -1,320 +0,0 @@
-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: '#0d9488', iconBg: '#ccfbf1' },
-    },
-    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: '#0d9488', iconBg: '#ccfbf1', 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: '#0d9488', iconBg: '#ccfbf1' },
-    },
-    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: '#0d9488', iconBg: '#ccfbf1', 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: '#0d9488', iconBg: '#ccfbf1' },
-    },
-    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: '#0d9488', iconBg: '#ccfbf1', 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: '#0d9488', iconBg: '#ccfbf1' },
-    },
-    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>