@morscherlab/mint-sdk 1.2.0-beta.1 → 1.2.0-beta.3

package/dist/templates-DsP51i-S.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"templates-DsP51i-S.js","names":[],"sources":["../src/templates/builderReadUtils.ts","../src/templates/templateEnvelopes.ts","../src/templates/lookup.ts","../src/templates/catalog.ts","../src/templates/packs.ts","../src/templates/presets.ts","../src/templates/componentTargetResolvers.ts","../src/templates/componentBindingHelpers.ts","../src/templates/componentBindingCatalog.ts","../src/templates/plateGeometry.ts","../src/templates/templateValidators.ts","../src/templates/assayMatrixAdapters.ts","../src/templates/calibrationCurveAdapters.ts","../src/templates/flowPanelAdapters.ts","../src/templates/instrumentRunAdapterHelpers.ts","../src/templates/instrumentRunAdapters.ts","../src/templates/protocolAdapters.ts","../src/templates/qpcrAdapters.ts","../src/templates/reagentAdapters.ts","../src/templates/samplePrepAdapters.ts","../src/templates/sampleSheetAdapters.ts","../src/templates/timeCourseAdapters.ts","../src/templates/plateMapAdapters.ts","../src/templates/doseResponseAdapters.ts","../src/templates/adapters.ts","../src/templates/componentPlateHelpers.ts","../src/templates/componentPropsFactory.ts","../src/templates/componentDoseResponseProps.ts","../src/templates/componentGenericProps.ts","../src/templates/componentPlateMapProps.ts","../src/templates/componentQpcrPlateProps.ts","../src/templates/componentTemplateProps.ts","../src/templates/componentBindings.ts","../src/templates/builderPresetControls.ts","../src/templates/builderDefaults.ts","../src/templates/builderIdUtils.ts","../src/templates/plateMapBuilder.ts","../src/templates/sampleNormalizers.ts","../src/templates/sampleSheetBuilder.ts","../src/templates/samplePrepBuilder.ts","../src/templates/calibrationNormalizers.ts","../src/templates/doseResponseBuilder.ts","../src/templates/calibrationCurveBuilder.ts","../src/templates/protocolNormalizers.ts","../src/templates/timeCourseBuilder.ts","../src/templates/protocolStepsBuilder.ts","../src/templates/assayLookups.ts","../src/templates/assayNormalizers.ts","../src/templates/assayMatrixBuilder.ts","../src/templates/reagentListBuilder.ts","../src/templates/flowNormalizers.ts","../src/templates/flowCytometryPanelBuilder.ts","../src/templates/runNormalizers.ts","../src/templates/instrumentRunBuilder.ts","../src/templates/qpcrPlateBuilder.ts","../src/templates/qpcrExpressionCollectionBuilder.ts","../src/templates/lcmsBatchCollectionBuilder.ts","../src/templates/targetedMetabolomicsHelpers.ts","../src/templates/targetedMetabolomicsCollectionBuilder.ts","../src/templates/elisaAssayCollectionBuilder.ts","../src/templates/flowCytometryAssayCollectionBuilder.ts","../src/templates/westernBlotAssayCollectionBuilder.ts","../src/templates/defaultBioTemplateBuilder.ts","../src/templates/templatePackCollectionBuilder.ts","../src/templates/wellPlateScreenCollectionBuilder.ts","../src/templates/templatePresetCollectionBuilder.ts","../src/templates/controlSchemaClone.ts","../src/templates/controlSchemaMerge.ts","../src/templates/controlSchemaTargets.ts","../src/templates/controlSchemaConstants.ts","../src/templates/templateControlSchemas.ts","../src/templates/presetControlSchemas.ts","../src/templates/controlSchemas.ts"],"sourcesContent":["export function isRecord(value: unknown): value is Record<string, unknown> {\n  return typeof value === 'object' && value !== null && !Array.isArray(value)\n}\n\nexport function readStringList(value: unknown, fallback: string[]): string[] {\n  if (Array.isArray(value)) {\n    const items = value.map(item => String(item).trim()).filter(Boolean)\n    return items.length ? items : fallback\n  }\n  if (typeof value === 'string') {\n    const items = value.split(',').map(item => item.trim()).filter(Boolean)\n    return items.length ? items : fallback\n  }\n  return fallback\n}\n\nexport function readNumberList(value: unknown, fallback: number[]): number[] {\n  const rawItems = Array.isArray(value)\n    ? value\n    : typeof value === 'string'\n      ? value.split(',')\n      : []\n  const items = rawItems\n    .map(item => Number(String(item).trim()))\n    .filter(item => Number.isFinite(item))\n  return items.length ? items : fallback\n}\n\nexport function readString(value: unknown, fallback: string): string {\n  return typeof value === 'string' && value.trim() ? value.trim() : fallback\n}\n\nexport function readOptionalString(value: unknown): string | undefined {\n  return typeof value === 'string' && value.trim() ? value.trim() : undefined\n}\n\nexport function readInteger(value: unknown, fallback: number): number {\n  const parsed = typeof value === 'number'\n    ? value\n    : typeof value === 'string'\n      ? Number(value)\n      : Number.NaN\n  return Number.isFinite(parsed) ? Math.max(1, Math.round(parsed)) : fallback\n}\n\nexport function readNumber(value: unknown, fallback: number): number {\n  const parsed = typeof value === 'number'\n    ? value\n    : typeof value === 'string'\n      ? Number(value)\n      : Number.NaN\n  return Number.isFinite(parsed) ? parsed : fallback\n}\n\nexport function readBoolean(value: unknown, fallback: boolean): boolean {\n  return typeof value === 'boolean' ? value : fallback\n}\n","import type {\n  BioTemplateEnvelope,\n  TemplateCollection,\n  TemplateCollectionEnvelope,\n  TemplateId,\n} from './types'\nimport { isRecord } from './builderReadUtils'\n\nexport const TEMPLATE_COLLECTION_KEY = 'templates'\n\nexport function createTemplateEnvelope<TData>(\n  templateId: TemplateId,\n  data: TData,\n  metadata: Record<string, unknown> = {},\n  templateVersion = '1.0'\n): BioTemplateEnvelope<TData> {\n  return {\n    template_id: templateId,\n    template_version: templateVersion,\n    kind: 'experiment-design',\n    data,\n    metadata,\n  }\n}\n\nexport function createTemplateCollection(\n  templates: Array<BioTemplateEnvelope<unknown>>,\n  metadata?: Record<string, unknown>\n): TemplateCollectionEnvelope {\n  const collection: TemplateCollection = {}\n  for (const template of templates) {\n    assertGenericTemplateEnvelope(template)\n    const templateId = template.template_id\n    if (collection[templateId]) {\n      throw new Error(`Duplicate template_id '${templateId}' in template collection.`)\n    }\n    collection[templateId] = template\n  }\n\n  return metadata === undefined\n    ? { [TEMPLATE_COLLECTION_KEY]: collection }\n    : { [TEMPLATE_COLLECTION_KEY]: collection, metadata }\n}\n\nexport function extractTemplateCollection(value: unknown): TemplateCollection {\n  if (isEnvelope<unknown>(value)) {\n    assertGenericTemplateEnvelope(value)\n    return { [value.template_id]: value }\n  }\n  if (!isRecord(value)) {\n    throw new Error('Template collection payload must be an object.')\n  }\n\n  const rawCollection = value[TEMPLATE_COLLECTION_KEY]\n  if (rawCollection === undefined) {\n    return {}\n  }\n  if (!isRecord(rawCollection)) {\n    throw new Error('Template collection must be an object.')\n  }\n\n  const collection: TemplateCollection = {}\n  for (const [templateId, template] of Object.entries(rawCollection)) {\n    assertGenericTemplateEnvelope(template)\n    if (template.template_id !== templateId) {\n      throw new Error(\n        `Template collection key '${templateId}' does not match envelope template_id '${template.template_id}'.`\n      )\n    }\n    collection[templateId] = template\n  }\n  return collection\n}\n\nexport function ensureTemplateFromCollection<TTemplate extends BioTemplateEnvelope<unknown>>(\n  value: unknown,\n  templateId: TemplateId | string\n): TTemplate {\n  const collection = extractTemplateCollection(value)\n  const template = collection[templateId]\n  if (!template) {\n    throw new Error(`Template '${templateId}' was not found in template collection.`)\n  }\n  assertTemplateEnvelope(template, templateId)\n  return template as TTemplate\n}\n\nexport function assertTemplateEnvelope<TData>(\n  value: unknown,\n  templateId: TemplateId | string\n): asserts value is BioTemplateEnvelope<TData> {\n  assertGenericTemplateEnvelope(value)\n  if (value.template_id !== templateId) {\n    throw new Error(`Expected template_id '${templateId}', got '${String(value.template_id)}'.`)\n  }\n}\n\nexport function ensureTemplateEnvelope<TTemplate extends BioTemplateEnvelope<unknown>>(\n  value: unknown,\n  templateId: TemplateId | string\n): TTemplate {\n  assertTemplateEnvelope(value, templateId)\n  return value as TTemplate\n}\n\nexport function getTemplateData<TData>(\n  template: BioTemplateEnvelope<TData> | TData,\n  templateId?: TemplateId | string\n): TData {\n  if (isEnvelope<TData>(template)) {\n    if (templateId) assertTemplateEnvelope<TData>(template, templateId)\n    return template.data\n  }\n  return template\n}\n\nfunction assertGenericTemplateEnvelope(value: unknown): asserts value is BioTemplateEnvelope<unknown> {\n  if (!isRecord(value)) {\n    throw new Error('Template envelope must be an object.')\n  }\n  if (typeof value.template_id !== 'string' || value.template_id.length === 0) {\n    throw new Error('Template envelope requires a template_id string.')\n  }\n  if (typeof value.template_version !== 'string' || value.template_version.length === 0) {\n    throw new Error('Template envelope requires a template_version string.')\n  }\n  if (!isRecord(value.data)) {\n    throw new Error('Template envelope data must be an object.')\n  }\n  if ('metadata' in value && !isRecord(value.metadata)) {\n    throw new Error('Template envelope metadata must be an object.')\n  }\n}\n\nfunction isEnvelope<TData>(value: unknown): value is BioTemplateEnvelope<TData> {\n  return isRecord(value) && 'template_id' in value && 'data' in value\n}\n","/** Normalize human-facing template lookup terms so spaces, hyphens, and underscores behave the same. */\nexport function normalizeTemplateLookupKey(value: string): string {\n  return value.trim().toLowerCase().replace(/[\\s_-]+/g, '-')\n}\n\nexport function templateIdentifierMatches(query: string, identifiers: readonly string[]): boolean {\n  const normalizedQuery = normalizeTemplateLookupKey(query)\n  return identifiers.some(value => normalizeTemplateLookupKey(value) === normalizedQuery)\n}\n\nexport function templateSearchMatches(query: string, values: readonly string[]): boolean {\n  const lowerQuery = query.trim().toLowerCase()\n  const normalizedQuery = normalizeTemplateLookupKey(query)\n  return values.some(value =>\n    value.toLowerCase().includes(lowerQuery)\n    || normalizeTemplateLookupKey(value).includes(normalizedQuery),\n  )\n}\n","import type { TemplateId } from './types'\n\nimport { templateIdentifierMatches, templateSearchMatches } from './lookup'\n\nexport interface BioTemplateCatalogEntry {\n  name: TemplateId\n  template_id: TemplateId\n  template_version: string\n  label: string\n  category: 'bio-data'\n  purpose: string\n  aliases: readonly string[]\n  python_import: string\n  python_example: string\n  frontend_import: string\n  frontend_adapters: readonly string[]\n  components: readonly string[]\n  add_command: string\n}\n\nexport const bioTemplateCatalog = [\n  {\n    name: 'plate-map',\n    template_id: 'plate-map',\n    template_version: '1.0',\n    label: 'Plate map',\n    category: 'bio-data',\n    purpose: 'Plate layout, wells, sample assignments, and sample legend data.',\n    aliases: ['wellplate', 'well-plate', 'plate layout', 'plate-map editor'],\n    python_import: 'from mint_sdk.templates import PlateMapTemplate, save_template',\n    python_example: 'PlateMapTemplate.create_96_well(name=\"Plate 1\", samples=[\"Control\", \"Treatment\"])',\n    frontend_import: \"import { toPlateMapEditorState, toWellPlateWells } from '@morscherlab/mint-sdk/templates'\",\n    frontend_adapters: ['toPlateMapEditorState', 'toWellPlateWells'],\n    components: ['PlateMapEditor', 'WellPlate', 'SampleLegend'],\n    add_command: 'mint add data-template plate-map --page',\n  },\n  {\n    name: 'sample-sheet',\n    template_id: 'sample-sheet',\n    template_version: '1.0',\n    label: 'Sample sheet',\n    category: 'bio-data',\n    purpose: 'Tabular sample metadata, display columns, and group definitions.',\n    aliases: ['sample metadata', 'sample table', 'metadata sheet', 'csv samples'],\n    python_import: 'from mint_sdk.templates import SampleSheetTemplate, save_template',\n    python_example: 'SampleSheetTemplate.from_rows([{\"sample_id\": \"S001\", \"name\": \"Control 1\", \"group\": \"Control\"}])',\n    frontend_import: \"import { toTemplateDataFrame, toSampleOptions } from '@morscherlab/mint-sdk/templates'\",\n    frontend_adapters: ['toTemplateDataFrame', 'toSampleDataFrame', 'toSampleRows', 'toSampleColumns', 'toSampleOptions'],\n    components: ['DataFrame', 'SampleSelector', 'AutoGroupModal', 'GroupAssigner'],\n    add_command: 'mint add data-template sample-sheet --page',\n  },\n  {\n    name: 'sample-prep',\n    template_id: 'sample-prep',\n    template_version: '1.0',\n    label: 'Sample prep',\n    category: 'bio-data',\n    purpose: 'Extraction, dilution, normalization, transfer, source/destination, volume, reagent, and status steps.',\n    aliases: ['sample preparation', 'extraction', 'dilution', 'normalization', 'prep steps'],\n    python_import: 'from mint_sdk.templates import SamplePrepTemplate, save_template',\n    python_example: 'SamplePrepTemplate.create([\"S001\", \"S002\"], prep_type=\"extraction\", output_volume=50)',\n    frontend_import: \"import { toSamplePrepDataFrame, toTemplateDataFrame } from '@morscherlab/mint-sdk/templates'\",\n    frontend_adapters: ['toTemplateDataFrame', 'toSamplePrepDataFrame', 'toSamplePrepRows', 'toSamplePrepColumns'],\n    components: ['DataFrame', 'ProtocolStepEditor', 'SampleSelector', 'WellPlate'],\n    add_command: 'mint add data-template sample-prep --page',\n  },\n  {\n    name: 'dose-response',\n    template_id: 'dose-response',\n    template_version: '1.0',\n    label: 'Dose response',\n    category: 'bio-data',\n    purpose: 'Compounds, concentration series, controls, replicates, and optional plate layout.',\n    aliases: [\n      'drug response',\n      'concentration series',\n      'dose curve',\n      'dose design',\n      'dose planner',\n      'dose calculator',\n      'drp',\n    ],\n    python_import: 'from mint_sdk.templates import ControlDefinition, DoseResponseTemplate, save_template',\n    python_example: 'DoseResponseTemplate.create({\"Compound A\": [10, 1, 0.1]}, unit=\"uM\", replicates=3)',\n    frontend_import: \"import { toDoseConditions, toDoseLayoutState } from '@morscherlab/mint-sdk/templates'\",\n    frontend_adapters: ['toDoseConditions', 'toDoseLayoutState'],\n    components: ['DoseCalculator', 'ReagentEditor', 'WellPlate'],\n    add_command: 'mint add data-template dose-response --page',\n  },\n  {\n    name: 'calibration-curve',\n    template_id: 'calibration-curve',\n    template_version: '1.0',\n    label: 'Calibration curve',\n    category: 'bio-data',\n    purpose: 'Standard curves, blank/QC points, fitted model settings, and acceptance thresholds.',\n    aliases: ['standard curve', 'calibration', 'quantitation', 'qc acceptance', 'calibrator'],\n    python_import: 'from mint_sdk.templates import CalibrationCurveTemplate, save_template',\n    python_example: 'CalibrationCurveTemplate.create([0.1, 1, 10, 100], analyte=\"Glucose\", unit=\"uM\")',\n    frontend_import: \"import { toCalibrationCurveDataFrame, toTemplateDataFrame } from '@morscherlab/mint-sdk/templates'\",\n    frontend_adapters: ['toTemplateDataFrame', 'toCalibrationCurveDataFrame', 'toCalibrationCurveRows', 'toCalibrationCurveColumns'],\n    components: ['DataFrame', 'FitPanel', 'ChartContainer'],\n    add_command: 'mint add data-template calibration-curve --page',\n  },\n  {\n    name: 'time-course',\n    template_id: 'time-course',\n    template_version: '1.0',\n    label: 'Time course',\n    category: 'bio-data',\n    purpose: 'Longitudinal time points, conditions, replicates, and scheduled samples.',\n    aliases: ['longitudinal', 'time series', 'sampling schedule', 'kinetics'],\n    python_import: 'from mint_sdk.templates import TimeCourseTemplate, save_template',\n    python_example: 'TimeCourseTemplate.create([0, 6, 24], unit=\"hour\", conditions=[\"Control\", \"Treatment\"], replicates=3)',\n    frontend_import: \"import { toTemplateDataFrame, toTimeCourseSteps } from '@morscherlab/mint-sdk/templates'\",\n    frontend_adapters: ['toTemplateDataFrame', 'toTimeCourseDataFrame', 'toTimeCourseRows', 'toTimeCourseSteps', 'toTimeCourseColumns'],\n    components: ['ExperimentTimeline', 'DataFrame', 'ScheduleCalendar'],\n    add_command: 'mint add data-template time-course --page',\n  },\n  {\n    name: 'protocol-steps',\n    template_id: 'protocol-steps',\n    template_version: '1.0',\n    label: 'Protocol steps',\n    category: 'bio-data',\n    purpose: 'Ordered experiment protocol steps, durations, statuses, and run-sheet parameters.',\n    aliases: ['protocol', 'run sheet', 'workflow', 'method steps', 'sop'],\n    python_import: 'from mint_sdk.templates import ProtocolStepsTemplate, save_template',\n    python_example: 'ProtocolStepsTemplate.create([\"Seed cells\", \"Add treatment\", \"Measure viability\"])',\n    frontend_import: \"import { toProtocolSteps, toTemplateDataFrame } from '@morscherlab/mint-sdk/templates'\",\n    frontend_adapters: ['toTemplateDataFrame', 'toProtocolSteps', 'toProtocolDataFrame'],\n    components: ['ExperimentTimeline', 'ProtocolStepEditor', 'DataFrame'],\n    add_command: 'mint add data-template protocol-steps --page',\n  },\n  {\n    name: 'assay-matrix',\n    template_id: 'assay-matrix',\n    template_version: '1.0',\n    label: 'Assay matrix',\n    category: 'bio-data',\n    purpose: 'Sample-by-feature measurement matrices for omics, plate-reader, and marker assays.',\n    aliases: ['omics matrix', 'measurement matrix', 'readout matrix', 'feature table'],\n    python_import: 'from mint_sdk.templates import AssayMatrixTemplate, save_template',\n    python_example: 'AssayMatrixTemplate.create(samples=[\"S001\", \"S002\"], features=[\"Lactate\", \"Glucose\"])',\n    frontend_import: \"import { toAssayMatrixSampleOptions, toTemplateDataFrame } from '@morscherlab/mint-sdk/templates'\",\n    frontend_adapters: ['toTemplateDataFrame', 'toAssayMatrixDataFrame', 'toAssayMatrixRows', 'toAssayMatrixColumns', 'toAssayMatrixSampleOptions'],\n    components: ['DataFrame', 'ChartContainer', 'SampleSelector'],\n    add_command: 'mint add data-template assay-matrix --page',\n  },\n  {\n    name: 'reagent-list',\n    template_id: 'reagent-list',\n    template_version: '1.0',\n    label: 'Reagent list',\n    category: 'bio-data',\n    purpose: 'Experiment reagents, catalog numbers, lots, storage, locations, and stock status.',\n    aliases: ['reagents', 'inventory', 'antibodies', 'primers', 'compound stocks'],\n    python_import: 'from mint_sdk.templates import ReagentListTemplate, save_template',\n    python_example: 'ReagentListTemplate.create([\"DMSO\", \"Compound A\", \"Anti-HA antibody\"])',\n    frontend_import: \"import { toReagentListItems, toTemplateDataFrame } from '@morscherlab/mint-sdk/templates'\",\n    frontend_adapters: ['toTemplateDataFrame', 'toReagentDataFrame', 'toReagentListItems'],\n    components: ['ReagentList', 'DataFrame', 'ReagentEditor'],\n    add_command: 'mint add data-template reagent-list --page',\n  },\n  {\n    name: 'flow-cytometry-panel',\n    template_id: 'flow-cytometry-panel',\n    template_version: '1.0',\n    label: 'Flow cytometry panel',\n    category: 'bio-data',\n    purpose: 'Flow-cytometry markers, fluorophores, detectors, compensation controls, and panel metadata.',\n    aliases: ['flow panel', 'facs panel', 'cytometry panel', 'antibody panel'],\n    python_import: 'from mint_sdk.templates import FlowCytometryPanelTemplate, save_template',\n    python_example: 'FlowCytometryPanelTemplate.create([\"CD3\", \"CD4\", \"CD8\"], instrument=\"BD LSRFortessa\")',\n    frontend_import: \"import { toFlowPanelDataFrame, toTemplateDataFrame } from '@morscherlab/mint-sdk/templates'\",\n    frontend_adapters: ['toTemplateDataFrame', 'toFlowPanelDataFrame', 'toFlowPanelRows', 'toFlowPanelColumns'],\n    components: ['DataFrame', 'ReagentList', 'SampleSelector'],\n    add_command: 'mint add data-template flow-cytometry-panel --page',\n  },\n  {\n    name: 'instrument-run',\n    template_id: 'instrument-run',\n    template_version: '1.0',\n    label: 'Instrument run',\n    category: 'bio-data',\n    purpose: 'Instrument sequence tables, sample queues, methods, QC, blanks, and acquisition status.',\n    aliases: ['run queue', 'sequence table', 'sample queue', 'lcms run', 'instrument sequence', 'batch run'],\n    python_import: 'from mint_sdk.templates import InstrumentRunTemplate, save_template',\n    python_example: 'InstrumentRunTemplate.create([\"S001\", \"S002\"], instrument=\"LC-MS\")',\n    frontend_import: \"import { toInstrumentRunDataFrame, toInstrumentRunScheduleEvents, toInstrumentRunSteps, toTemplateDataFrame } from '@morscherlab/mint-sdk/templates'\",\n    frontend_adapters: ['toTemplateDataFrame', 'toInstrumentRunDataFrame', 'toInstrumentRunRows', 'toInstrumentRunColumns', 'toInstrumentRunSteps', 'toInstrumentRunScheduleEvents'],\n    components: ['DataFrame', 'ExperimentTimeline', 'ScheduleCalendar', 'SampleSelector'],\n    add_command: 'mint add data-template instrument-run --page',\n  },\n  {\n    name: 'qpcr-plate',\n    template_id: 'qpcr-plate',\n    template_version: '1.0',\n    label: 'qPCR plate',\n    category: 'bio-data',\n    purpose: 'qPCR/ddPCR plate layouts, samples, targets, replicate reactions, controls, and Cq fields.',\n    aliases: ['qpcr', 'qPCR', 'ddpcr', 'rt-qpcr', 'gene expression', 'primer plate'],\n    python_import: 'from mint_sdk.templates import QpcrPlateTemplate, save_template',\n    python_example: 'QpcrPlateTemplate.create(samples=[\"Control\", \"Treatment\"], targets=[\"ACTB\", \"GAPDH\"], replicates=3)',\n    frontend_import: \"import { toQpcrDataFrame, toQpcrWellPlateWells, toTemplateDataFrame } from '@morscherlab/mint-sdk/templates'\",\n    frontend_adapters: ['toTemplateDataFrame', 'toQpcrDataFrame', 'toQpcrRows', 'toQpcrColumns', 'toQpcrWellPlateWells'],\n    components: ['DataFrame', 'WellPlate', 'SampleSelector'],\n    add_command: 'mint add data-template qpcr-plate --page',\n  },\n] as const satisfies readonly BioTemplateCatalogEntry[]\n\nexport function listBioTemplateCatalog(): readonly BioTemplateCatalogEntry[] {\n  return bioTemplateCatalog\n}\n\nexport function getBioTemplateInfo(name: string): BioTemplateCatalogEntry | undefined {\n  return bioTemplateCatalog.find(entry => {\n    const identifiers = [\n      entry.name,\n      entry.template_id,\n      entry.label,\n      ...entry.aliases,\n    ]\n    return templateIdentifierMatches(name, identifiers)\n  })\n}\n\nexport function searchBioTemplateCatalog(query: string): readonly BioTemplateCatalogEntry[] {\n  const normalized = query.trim().toLowerCase()\n  if (!normalized) return bioTemplateCatalog\n\n  return bioTemplateCatalog.filter(entry => templateSearchMatches(normalized, [\n    entry.name,\n    entry.template_id,\n    entry.label,\n    entry.purpose,\n    entry.python_import,\n    entry.python_example,\n    entry.frontend_import,\n    entry.add_command,\n    ...entry.aliases,\n    ...entry.frontend_adapters,\n    ...entry.components,\n  ]))\n}\n","import { bioTemplateCatalog } from './catalog'\nimport type { TemplateId, TemplatePackId } from './types'\n\nimport { templateIdentifierMatches, templateSearchMatches } from './lookup'\n\nexport interface BioTemplatePackEntry {\n  name: TemplatePackId\n  label: string\n  category: 'bio-template-pack'\n  purpose: string\n  templates: readonly TemplateId[]\n  aliases: readonly string[]\n  frontend_adapters: readonly string[]\n  components: readonly string[]\n  add_command: string\n  docs_command: string\n}\n\ninterface BioTemplatePackDefinition {\n  name: TemplatePackId\n  label: string\n  purpose: string\n  templates: readonly TemplateId[]\n  aliases: readonly string[]\n}\n\nconst templateInfoById = new Map(\n  bioTemplateCatalog.map(entry => [entry.template_id, entry]),\n)\n\nfunction collectTemplateField(\n  templateIds: readonly TemplateId[],\n  field: 'frontend_adapters' | 'components',\n): readonly string[] {\n  const values: string[] = []\n  for (const templateId of templateIds) {\n    const entry = templateInfoById.get(templateId)\n    if (!entry) {\n      throw new Error(`Unknown bio template in pack catalog: ${templateId}`)\n    }\n    for (const value of entry[field]) {\n      if (!values.includes(value)) {\n        values.push(value)\n      }\n    }\n  }\n  return values\n}\n\nfunction createPack(definition: BioTemplatePackDefinition): BioTemplatePackEntry {\n  return {\n    ...definition,\n    category: 'bio-template-pack',\n    frontend_adapters: collectTemplateField(definition.templates, 'frontend_adapters'),\n    components: collectTemplateField(definition.templates, 'components'),\n    add_command: `mint add data-template-pack ${definition.name} --page`,\n    docs_command: `mint docs template-pack ${definition.name}`,\n  }\n}\n\nconst bioTemplatePackDefinitions = [\n  {\n    name: 'cell-culture-screen',\n    label: 'Cell culture screen',\n    purpose: 'Plate layout, sample metadata, sample prep, reagents, protocol, dose-response, and flow-panel setup.',\n    templates: [\n      'sample-sheet',\n      'sample-prep',\n      'plate-map',\n      'reagent-list',\n      'protocol-steps',\n      'dose-response',\n      'flow-cytometry-panel',\n    ],\n    aliases: ['cell culture', 'screen', 'drug screen', 'plate screen'],\n  },\n  {\n    name: 'omics-assay',\n    label: 'Omics assay',\n    purpose: 'Sample metadata, sample prep, reagents, protocol, instrument run queue, calibration curve, and measurement matrix.',\n    templates: [\n      'sample-sheet',\n      'sample-prep',\n      'reagent-list',\n      'protocol-steps',\n      'instrument-run',\n      'calibration-curve',\n      'assay-matrix',\n    ],\n    aliases: [\n      'omics',\n      'metabolomics',\n      'metabolism',\n      'metabolite profiling',\n      'proteomics',\n      'assay matrix',\n      'lcms',\n      'standard curve',\n    ],\n  },\n  {\n    name: 'longitudinal-study',\n    label: 'Longitudinal study',\n    purpose: 'Sample metadata, time-course schedule, protocol, and measurement matrix.',\n    templates: [\n      'sample-sheet',\n      'time-course',\n      'protocol-steps',\n      'assay-matrix',\n    ],\n    aliases: ['time series', 'time-course study', 'kinetics', 'longitudinal'],\n  },\n  {\n    name: 'molecular-assay',\n    label: 'Molecular assay',\n    purpose: 'Sample metadata, sample prep, reagents, protocol, instrument run queue, calibration curve, and qPCR/ddPCR plate setup.',\n    templates: [\n      'sample-sheet',\n      'sample-prep',\n      'reagent-list',\n      'protocol-steps',\n      'instrument-run',\n      'calibration-curve',\n      'qpcr-plate',\n    ],\n    aliases: ['molecular', 'qpcr', 'qPCR', 'gene expression', 'rt-qpcr', 'ddpcr'],\n  },\n] as const satisfies readonly BioTemplatePackDefinition[]\n\nexport const bioTemplatePacks = bioTemplatePackDefinitions.map(createPack) as readonly BioTemplatePackEntry[]\n\nexport function listBioTemplatePacks(): readonly BioTemplatePackEntry[] {\n  return bioTemplatePacks\n}\n\nexport function getBioTemplatePackInfo(name: string): BioTemplatePackEntry | undefined {\n  return bioTemplatePacks.find(entry => {\n    const identifiers = [\n      entry.name,\n      entry.label,\n      ...entry.aliases,\n    ]\n    return templateIdentifierMatches(name, identifiers)\n  })\n}\n\nexport function searchBioTemplatePacks(query: string): readonly BioTemplatePackEntry[] {\n  const normalized = query.trim().toLowerCase()\n  if (!normalized) return bioTemplatePacks\n\n  return bioTemplatePacks.filter(entry => templateSearchMatches(normalized, [\n    entry.name,\n    entry.label,\n    entry.purpose,\n    entry.add_command,\n    entry.docs_command,\n    ...entry.templates,\n    ...entry.aliases,\n    ...entry.frontend_adapters,\n    ...entry.components,\n  ]))\n}\n","import type { TemplateId, TemplatePresetId } from './types'\n\nimport { templateIdentifierMatches, templateSearchMatches } from './lookup'\n\nexport interface BioTemplatePresetEntry {\n  name: TemplatePresetId\n  label: string\n  category: 'bio-template-preset'\n  purpose: string\n  templates: readonly TemplateId[]\n  aliases: readonly string[]\n  python_import: string\n  python_example: string\n  frontend_import: string\n  frontend_adapters: readonly string[]\n  components: readonly string[]\n}\n\nexport const bioTemplatePresets = [\n  {\n    name: 'wellplate-screen',\n    label: 'Well-plate screen',\n    category: 'bio-template-preset',\n    purpose: 'Plate map, sample sheet, and dose-response payloads for plate-based screening assays.',\n    templates: ['plate-map', 'sample-sheet', 'dose-response'],\n    aliases: [\n      'wellplate',\n      'well-plate screen',\n      'drug screen',\n      'plate screen',\n      'dose response plate',\n      'dose design',\n      'dose planner',\n    ],\n    python_import: 'from mint_sdk.templates import create_wellplate_screen_collection, save_template_collection',\n    python_example: 'create_wellplate_screen_collection(samples=[\"Control\", \"Treatment\"], compounds={\"Drug A\": [10, 1, 0.1]}, unit=\"uM\")',\n    frontend_import: \"import { createWellPlateScreenCollection, toPlateMapEditorState, toTemplateDataFrame } from '@morscherlab/mint-sdk/templates'\",\n    frontend_adapters: ['toPlateMapEditorState', 'toTemplateDataFrame', 'toDoseConditions'],\n    components: ['PlateMapEditor', 'WellPlate', 'DataFrame', 'DoseCalculator'],\n  },\n  {\n    name: 'qpcr-expression',\n    label: 'qPCR expression',\n    category: 'bio-template-preset',\n    purpose: 'Sample metadata and qPCR/ddPCR plate layout for target-expression assays.',\n    templates: ['sample-sheet', 'qpcr-plate'],\n    aliases: ['qpcr', 'qPCR', 'rt-qpcr', 'ddpcr', 'gene expression', 'primer plate'],\n    python_import: 'from mint_sdk.templates import create_qpcr_expression_collection, save_template_collection',\n    python_example: 'create_qpcr_expression_collection(samples=[\"Control\", \"Treatment\"], targets=[\"ACTB\", \"GAPDH\"], replicates=3)',\n    frontend_import: \"import { createQpcrExpressionCollection, toQpcrWellPlateWells, toTemplateDataFrame } from '@morscherlab/mint-sdk/templates'\",\n    frontend_adapters: ['toTemplateDataFrame', 'toQpcrDataFrame', 'toQpcrWellPlateWells'],\n    components: ['DataFrame', 'WellPlate', 'SampleSelector'],\n  },\n  {\n    name: 'lcms-batch',\n    label: 'LC-MS batch',\n    category: 'bio-template-preset',\n    purpose: 'Sample metadata, instrument queue, and assay matrix payloads for omics acquisition batches.',\n    templates: ['sample-sheet', 'instrument-run', 'assay-matrix'],\n    aliases: [\n      'lcms',\n      'lc-ms',\n      'mass spec batch',\n      'omics batch',\n      'metabolomics',\n      'metabolism',\n      'metabolite profiling',\n      'run queue',\n      'sequence table',\n    ],\n    python_import: 'from mint_sdk.templates import create_lcms_batch_collection, save_template_collection',\n    python_example: 'create_lcms_batch_collection(samples=[\"S001\", \"S002\"], features=[\"Glucose\", \"Lactate\"], instrument=\"LC-MS\")',\n    frontend_import: \"import { createLcmsBatchCollection, toAssayMatrixSampleOptions, toInstrumentRunDataFrame, toInstrumentRunScheduleEvents, toInstrumentRunSteps, toTemplateDataFrame } from '@morscherlab/mint-sdk/templates'\",\n    frontend_adapters: ['toTemplateDataFrame', 'toInstrumentRunDataFrame', 'toInstrumentRunSteps', 'toInstrumentRunScheduleEvents', 'toAssayMatrixDataFrame', 'toAssayMatrixSampleOptions'],\n    components: ['DataFrame', 'ExperimentTimeline', 'ScheduleCalendar', 'ChartContainer', 'SampleSelector'],\n  },\n  {\n    name: 'targeted-metabolomics',\n    label: 'Targeted metabolomics',\n    category: 'bio-template-preset',\n    purpose: 'Sample metadata, extraction prep, internal standards, LC/GC-MS sequence, calibration curve, and metabolite readout matrix for quantitative metabolomics.',\n    templates: ['sample-sheet', 'sample-prep', 'reagent-list', 'instrument-run', 'calibration-curve', 'assay-matrix'],\n    aliases: [\n      'targeted metabolomics',\n      'quantitative metabolomics',\n      'lc-ms metabolomics',\n      'gc-ms metabolomics',\n      'targeted lcms',\n      'metabolite quantitation',\n      'mass spec quantitation',\n      'internal standards',\n      'peak area ratio',\n    ],\n    python_import: 'from mint_sdk.templates import create_targeted_metabolomics_collection, save_template_collection',\n    python_example: 'create_targeted_metabolomics_collection(samples=[\"S001\", \"S002\"], metabolites=[\"Glucose\", \"Lactate\"], internal_standards=[\"13C Glucose\"], instrument=\"LC-MS\")',\n    frontend_import: \"import { createTargetedMetabolomicsCollection, toInstrumentRunDataFrame, toCalibrationCurveDataFrame, toAssayMatrixDataFrame, toTemplateDataFrame } from '@morscherlab/mint-sdk/templates'\",\n    frontend_adapters: ['toTemplateDataFrame', 'toSamplePrepDataFrame', 'toReagentDataFrame', 'toInstrumentRunDataFrame', 'toInstrumentRunSteps', 'toInstrumentRunScheduleEvents', 'toCalibrationCurveDataFrame', 'toAssayMatrixDataFrame', 'toAssayMatrixSampleOptions'],\n    components: ['DataFrame', 'ReagentList', 'ExperimentTimeline', 'ScheduleCalendar', 'FitPanel', 'ChartContainer', 'SampleSelector'],\n  },\n  {\n    name: 'elisa-assay',\n    label: 'ELISA assay',\n    category: 'bio-template-preset',\n    purpose: 'Plate layout, sample metadata, standard curve, and readout matrix for ELISA and plate-reader assays.',\n    templates: ['plate-map', 'sample-sheet', 'calibration-curve', 'assay-matrix'],\n    aliases: ['elisa', 'plate reader assay', 'standard curve plate', 'absorbance assay', 'immunoassay'],\n    python_import: 'from mint_sdk.templates import create_elisa_assay_collection, save_template_collection',\n    python_example: 'create_elisa_assay_collection(samples=[\"Control\", \"Treatment\"], analyte=\"IL-6\", standard_concentrations=[1000, 100, 10, 1], unit=\"pg/mL\")',\n    frontend_import: \"import { createElisaAssayCollection, toPlateMapEditorState, toTemplateDataFrame } from '@morscherlab/mint-sdk/templates'\",\n    frontend_adapters: ['toPlateMapEditorState', 'toTemplateDataFrame', 'toCalibrationCurveDataFrame'],\n    components: ['PlateMapEditor', 'WellPlate', 'DataFrame', 'FitPanel', 'ChartContainer'],\n  },\n  {\n    name: 'flow-cytometry-assay',\n    label: 'Flow cytometry assay',\n    category: 'bio-template-preset',\n    purpose: 'Sample metadata, antibody marker panel, compensation controls, and readout matrix for flow-cytometry assays.',\n    templates: ['sample-sheet', 'flow-cytometry-panel', 'assay-matrix'],\n    aliases: [\n      'flow cytometry',\n      'facs',\n      'facs panel',\n      'flow panel',\n      'immune phenotyping',\n      'immunophenotyping',\n    ],\n    python_import: 'from mint_sdk.templates import create_flow_cytometry_assay_collection, save_template_collection',\n    python_example: 'create_flow_cytometry_assay_collection(samples=[\"Control\", \"Treatment\"], markers=[\"CD3\", \"CD4\", \"CD8\"], instrument=\"BD LSRFortessa\")',\n    frontend_import: \"import { createFlowCytometryAssayCollection, toFlowPanelDataFrame, toTemplateDataFrame } from '@morscherlab/mint-sdk/templates'\",\n    frontend_adapters: ['toTemplateDataFrame', 'toFlowPanelDataFrame', 'toAssayMatrixDataFrame'],\n    components: ['DataFrame', 'SampleSelector', 'ChartContainer'],\n  },\n  {\n    name: 'western-blot-assay',\n    label: 'Western blot assay',\n    category: 'bio-template-preset',\n    purpose: 'Sample metadata, antibody/reagent list, protocol steps, and normalized protein readout matrix for Western blot assays.',\n    templates: ['sample-sheet', 'reagent-list', 'protocol-steps', 'assay-matrix'],\n    aliases: ['western blot', 'western-blot', 'immunoblot', 'protein blot', 'protein expression'],\n    python_import: 'from mint_sdk.templates import create_western_blot_assay_collection, save_template_collection',\n    python_example: 'create_western_blot_assay_collection(samples=[\"Control\", \"Treatment\"], targets=[\"pERK\", \"ERK\"], loading_control=\"ACTB\")',\n    frontend_import: \"import { createWesternBlotAssayCollection, toReagentDataFrame, toProtocolDataFrame, toTemplateDataFrame } from '@morscherlab/mint-sdk/templates'\",\n    frontend_adapters: ['toTemplateDataFrame', 'toReagentDataFrame', 'toProtocolDataFrame'],\n    components: ['DataFrame', 'ReagentList', 'ExperimentTimeline', 'SampleSelector'],\n  },\n] as const satisfies readonly BioTemplatePresetEntry[]\n\nexport function listBioTemplatePresets(): readonly BioTemplatePresetEntry[] {\n  return bioTemplatePresets\n}\n\nexport function getBioTemplatePresetInfo(name: string): BioTemplatePresetEntry | undefined {\n  return bioTemplatePresets.find(entry => {\n    const identifiers = [\n      entry.name,\n      entry.label,\n      ...entry.aliases,\n    ]\n    return templateIdentifierMatches(name, identifiers)\n  })\n}\n\nexport function searchBioTemplatePresets(query: string): readonly BioTemplatePresetEntry[] {\n  const normalized = query.trim().toLowerCase()\n  if (!normalized) return bioTemplatePresets\n\n  return bioTemplatePresets.filter(entry => templateSearchMatches(normalized, [\n    entry.name,\n    entry.label,\n    entry.purpose,\n    entry.python_import,\n    entry.python_example,\n    entry.frontend_import,\n    ...entry.templates,\n    ...entry.aliases,\n    ...entry.frontend_adapters,\n    ...entry.components,\n  ]))\n}\n","import { extractTemplateCollection } from './templateEnvelopes'\nimport { getBioTemplateInfo } from './catalog'\nimport { getBioTemplatePackInfo } from './packs'\nimport { getBioTemplatePresetInfo } from './presets'\nimport type {\n  BioTemplateEnvelope,\n  TemplateCollectionEnvelope,\n  TemplateId,\n  TemplatePackId,\n  TemplatePresetId,\n} from './types'\n\ntype BioTemplateComponentTarget =\n  | TemplateId\n  | TemplatePackId\n  | TemplatePresetId\n  | string\n  | BioTemplateEnvelope<unknown>\n  | TemplateCollectionEnvelope\n\nexport function resolveComponentTemplateIds(target: BioTemplateComponentTarget): TemplateId[] {\n  if (typeof target === 'string') {\n    const preset = getBioTemplatePresetInfo(target)\n    if (preset) return [...preset.templates]\n    const pack = getBioTemplatePackInfo(target)\n    if (pack) return [...pack.templates]\n    const template = getBioTemplateInfo(target)\n    return template ? [template.template_id] : []\n  }\n\n  if (isTemplateEnvelope(target)) {\n    const template = getBioTemplateInfo(target.template_id)\n    return template ? [template.template_id] : []\n  }\n\n  const presetName = collectionPresetName(target)\n  if (presetName) {\n    const preset = getBioTemplatePresetInfo(presetName)\n    if (preset) return [...preset.templates]\n  }\n\n  const packName = collectionPackName(target)\n  if (packName) {\n    const pack = getBioTemplatePackInfo(packName)\n    if (pack) return [...pack.templates]\n  }\n\n  return Object.keys(extractTemplateCollection(target))\n    .map(templateId => getBioTemplateInfo(templateId)?.template_id)\n    .filter((templateId): templateId is TemplateId => templateId !== undefined)\n}\n\nexport function isTemplateEnvelope(value: unknown): value is BioTemplateEnvelope<unknown> {\n  return isRecord(value) && typeof value.template_id === 'string' && 'data' in value\n}\n\nfunction collectionPresetName(value: unknown): string | undefined {\n  if (!isRecord(value) || !isRecord(value.metadata)) return undefined\n  return typeof value.metadata.preset === 'string' ? value.metadata.preset : undefined\n}\n\nfunction collectionPackName(value: unknown): string | undefined {\n  if (!isRecord(value) || !isRecord(value.metadata)) return undefined\n  return typeof value.metadata.pack === 'string' ? value.metadata.pack : undefined\n}\n\nfunction isRecord(value: unknown): value is Record<string, unknown> {\n  return typeof value === 'object' && value !== null\n}\n","interface CloneableComponentBinding {\n  adapters: readonly string[]\n  props: readonly string[]\n}\n\ninterface NamedComponentBinding {\n  template_id: string\n  component: string\n}\n\ninterface ComponentImportStatement {\n  statement: string\n}\n\nexport function cloneBindingMap<TName extends string, TBinding extends CloneableComponentBinding>(\n  bindings: Record<TName, readonly TBinding[]>\n): Record<TName, TBinding[]> {\n  const result = {} as Record<TName, TBinding[]>\n  for (const name of Object.keys(bindings) as TName[]) {\n    result[name] = cloneBindings(bindings[name])\n  }\n  return result\n}\n\nexport function cloneBindings<TBinding extends CloneableComponentBinding>(\n  bindings: readonly TBinding[]\n): TBinding[] {\n  return bindings.map(cloneBinding)\n}\n\nexport function cloneBinding<TBinding extends CloneableComponentBinding>(binding: TBinding): TBinding {\n  return {\n    ...binding,\n    adapters: [...binding.adapters],\n    props: [...binding.props],\n  }\n}\n\nexport function uniquePropsName(\n  binding: NamedComponentBinding,\n  usedNames: Map<string, number>\n): string {\n  const base = toCamelIdentifier(`${binding.template_id} ${binding.component} props`)\n  const count = usedNames.get(base) ?? 0\n  usedNames.set(base, count + 1)\n  return count === 0 ? base : `${base}${count + 1}`\n}\n\nfunction toCamelIdentifier(value: string): string {\n  const words = value\n    .replace(/([a-z0-9])([A-Z])/g, '$1 $2')\n    .split(/[^A-Za-z0-9]+/)\n    .filter(Boolean)\n\n  if (words.length === 0) return 'componentProps'\n\n  return words\n    .map((word, index) => {\n      const lower = word.toLowerCase()\n      return index === 0 ? lower : lower.charAt(0).toUpperCase() + lower.slice(1)\n    })\n    .join('')\n}\n\nexport function toVueSfc(\n  imports: readonly ComponentImportStatement[],\n  setupLines: readonly string[],\n  template: string,\n  includeTargetTypeImport: boolean\n): string {\n  const importLines = [\n    ...imports.map(item => item.statement),\n    \"import { toBioTemplateComponentProps } from '@morscherlab/mint-sdk/templates'\",\n    ...(includeTargetTypeImport\n      ? [\"import type { BioTemplateEnvelope, TemplateCollectionEnvelope } from '@morscherlab/mint-sdk/templates'\"]\n      : []),\n  ]\n  const templateLines = template\n    ? template.split('\\n').map(line => `  ${line}`).join('\\n')\n    : ''\n\n  return [\n    '<script setup lang=\"ts\">',\n    ...importLines,\n    '',\n    ...setupLines,\n    '</script>',\n    '',\n    '<template>',\n    templateLines,\n    '</template>',\n  ].join('\\n')\n}\n","import type { TemplateId } from './types'\n\ninterface ComponentBinding {\n  id: string\n  template_id: TemplateId\n  component: string\n  adapters: readonly string[]\n  props: readonly string[]\n  description: string\n  importPath: '@morscherlab/mint-sdk'\n}\n\nexport const templateComponentBindings = {\n  'plate-map': [\n    binding('plate-map', 'PlateMapEditor', ['toPlateMapEditorState'], ['modelValue', 'format', 'samples'], 'Edit plate layouts from plate-map template data.'),\n    binding('plate-map', 'WellPlate', ['toWellPlateWells'], ['format', 'wells', 'sampleColors', 'legendItems'], 'Render the active plate as a well grid.'),\n  ],\n  'sample-sheet': [\n    binding('sample-sheet', 'DataFrame', ['toTemplateDataFrame'], ['data', 'columns', 'rowKey'], 'Render sample metadata as a sortable table.'),\n    binding('sample-sheet', 'SampleSelector', ['toSampleOptions'], ['samples', 'modelValue'], 'Select samples from sample-sheet records.'),\n  ],\n  'sample-prep': [\n    binding('sample-prep', 'DataFrame', ['toTemplateDataFrame'], ['data', 'columns', 'rowKey'], 'Render preparation steps as a table.'),\n  ],\n  'dose-response': [\n    binding('dose-response', 'DoseCalculator', ['toDoseConditions'], ['mode', 'targetWells'], 'Configure serial dilution and apply concentrations to wells.'),\n    binding('dose-response', 'WellPlate', ['toDoseLayoutState'], ['format', 'wells', 'sampleColors', 'legendItems'], 'Render the optional dose-response plate layout.'),\n  ],\n  'calibration-curve': [\n    binding('calibration-curve', 'DataFrame', ['toTemplateDataFrame'], ['data', 'columns', 'rowKey'], 'Render standards, QC, blanks, and response values.'),\n  ],\n  'time-course': [\n    binding('time-course', 'ExperimentTimeline', ['toTimeCourseSteps'], ['modelValue', 'orientation'], 'Render time points as an ordered timeline.'),\n    binding('time-course', 'DataFrame', ['toTemplateDataFrame'], ['data', 'columns', 'rowKey'], 'Render longitudinal samples as a table.'),\n  ],\n  'protocol-steps': [\n    binding('protocol-steps', 'ExperimentTimeline', ['toProtocolSteps'], ['modelValue', 'orientation', 'editable'], 'Render protocol steps as an editable timeline.'),\n    binding('protocol-steps', 'DataFrame', ['toTemplateDataFrame'], ['data', 'columns', 'rowKey'], 'Render protocol steps as a table.'),\n  ],\n  'assay-matrix': [\n    binding('assay-matrix', 'DataFrame', ['toTemplateDataFrame'], ['data', 'columns', 'rowKey'], 'Render sample-by-feature measurements.'),\n    binding('assay-matrix', 'SampleSelector', ['toAssayMatrixSampleOptions'], ['samples', 'modelValue'], 'Select samples from assay-matrix records.'),\n  ],\n  'reagent-list': [\n    binding('reagent-list', 'ReagentList', ['toReagentListItems'], ['modelValue'], 'Render reagents with lot, storage, and stock metadata.'),\n    binding('reagent-list', 'DataFrame', ['toTemplateDataFrame'], ['data', 'columns', 'rowKey'], 'Render reagents as a table.'),\n  ],\n  'flow-cytometry-panel': [\n    binding('flow-cytometry-panel', 'DataFrame', ['toTemplateDataFrame'], ['data', 'columns', 'rowKey'], 'Render markers, fluorophores, detectors, and controls.'),\n  ],\n  'instrument-run': [\n    binding('instrument-run', 'DataFrame', ['toTemplateDataFrame'], ['data', 'columns', 'rowKey'], 'Render acquisition queues, methods, QC, and run status.'),\n    binding(\n      'instrument-run',\n      'ScheduleCalendar',\n      ['toInstrumentRunScheduleEvents'],\n      ['modelValue', 'events', 'view', 'readonly', 'showNavigation', 'showViewToggle'],\n      'Render acquisition queues as a scheduled run calendar.',\n    ),\n    binding(\n      'instrument-run',\n      'ExperimentTimeline',\n      ['toInstrumentRunSteps'],\n      ['modelValue', 'orientation', 'showDuration', 'editable'],\n      'Render acquisition queues as an ordered run timeline.',\n    ),\n  ],\n  'qpcr-plate': [\n    binding('qpcr-plate', 'WellPlate', ['toQpcrWellPlateWells'], ['format', 'wells', 'sampleColors', 'legendItems'], 'Render qPCR reactions on a well plate.'),\n    binding('qpcr-plate', 'DataFrame', ['toTemplateDataFrame'], ['data', 'columns', 'rowKey'], 'Render qPCR reactions, targets, controls, and Cq values.'),\n  ],\n} satisfies Record<TemplateId, readonly ComponentBinding[]>\n\nfunction binding(\n  templateId: TemplateId,\n  component: string,\n  adapters: readonly string[],\n  props: readonly string[],\n  description: string\n): ComponentBinding {\n  return {\n    id: `${templateId}:${component}`,\n    template_id: templateId,\n    component,\n    adapters,\n    props,\n    description,\n    importPath: '@morscherlab/mint-sdk',\n  }\n}\n","import type { WellPlateFormat } from '../types'\n\nconst PLATE_DIMENSIONS: Record<number, readonly [number, number]> = {\n  6: [2, 3],\n  12: [3, 4],\n  24: [4, 6],\n  48: [6, 8],\n  54: [6, 9],\n  96: [8, 12],\n  384: [16, 24],\n}\n\nexport function wellIdsForFormat(format: number): string[] {\n  const dimensions = PLATE_DIMENSIONS[format]\n  if (!dimensions) {\n    throw new Error(`Unsupported plate format '${format}'.`)\n  }\n  const [rows, cols] = dimensions\n  return Array.from({ length: rows }, (_, row) =>\n    Array.from({ length: cols }, (_col, col) => `${rowLabel(row)}${col + 1}`)\n  ).flat()\n}\n\nexport function assertWellInFormat(wellId: string, format: number): void {\n  const dimensions = PLATE_DIMENSIONS[format]\n  if (!dimensions) {\n    throw new Error(`Unsupported plate format '${format}'.`)\n  }\n  const match = /^([A-Z]+)([1-9][0-9]*)$/.exec(wellId.toUpperCase())\n  if (!match) {\n    throw new Error(`Invalid well id '${wellId}'.`)\n  }\n  const row = rowIndex(match[1])\n  const col = Number(match[2]) - 1\n  const [rows, cols] = dimensions\n  if (row < 0 || col < 0 || row >= rows || col >= cols) {\n    throw new Error(`Well '${wellId}' is outside a ${format}-well plate.`)\n  }\n}\n\nexport function readPlateFormat(value: unknown, fallback: WellPlateFormat): WellPlateFormat {\n  const parsed = typeof value === 'number'\n    ? value\n    : typeof value === 'string'\n      ? Number(value)\n      : Number.NaN\n  return parsed in PLATE_DIMENSIONS ? (parsed as WellPlateFormat) : fallback\n}\n\nfunction rowLabel(index: number): string {\n  let label = ''\n  let current = index\n  while (true) {\n    label = String.fromCharCode(65 + (current % 26)) + label\n    current = Math.floor(current / 26) - 1\n    if (current < 0) return label\n  }\n}\n\nfunction rowIndex(label: string): number {\n  return [...label].reduce((value, char) => value * 26 + char.charCodeAt(0) - 64, 0) - 1\n}\n","import type {\n  AssayMatrixTemplateData,\n  CalibrationCurveTemplateData,\n  DoseResponseTemplateData,\n  FlowCytometryPanelTemplateData,\n  InstrumentRunTemplateData,\n  PlateMapTemplateData,\n  ProtocolStepsTemplateData,\n  QpcrPlateTemplateData,\n  ReagentListTemplateData,\n  SamplePrepTemplateData,\n  SampleSheetTemplateData,\n  TimeCourseTemplateData,\n} from './types'\nimport { assertWellInFormat } from './plateGeometry'\n\nexport function validatePlateMapData(data: PlateMapTemplateData): void {\n  if (!Array.isArray(data.plates) || data.plates.length === 0) {\n    throw new Error('Plate-map template requires at least one plate.')\n  }\n  const sampleIds = new Set(data.samples.map(sample => sample.id))\n  if (sampleIds.size !== data.samples.length) {\n    throw new Error('Plate-map sample ids must be unique.')\n  }\n  for (const plate of data.plates) {\n    for (const [wellId, well] of Object.entries(plate.wells)) {\n      if (well.id !== wellId) {\n        throw new Error(`Well key '${wellId}' does not match well id '${well.id}'.`)\n      }\n      if (well.sampleType && !sampleIds.has(well.sampleType)) {\n        throw new Error(`Well '${well.id}' references unknown sample '${well.sampleType}'.`)\n      }\n    }\n  }\n}\n\nexport function validateSampleSheetData(data: SampleSheetTemplateData): void {\n  if (!Array.isArray(data.samples) || data.samples.length === 0) {\n    throw new Error('Sample-sheet template requires at least one sample.')\n  }\n  const sampleIds = new Set(data.samples.map(sample => sample.sampleId))\n  if (sampleIds.size !== data.samples.length) {\n    throw new Error('Sample-sheet sample ids must be unique.')\n  }\n  for (const group of data.groups) {\n    for (const sampleId of group.samples) {\n      if (!sampleIds.has(sampleId)) {\n        throw new Error(`Group '${group.name}' references unknown sample '${sampleId}'.`)\n      }\n    }\n  }\n}\n\nexport function validateSamplePrepData(data: SamplePrepTemplateData): void {\n  if (!data.protocolName) {\n    throw new Error('Sample-prep template requires protocolName.')\n  }\n  if (!Array.isArray(data.steps) || data.steps.length === 0) {\n    throw new Error('Sample-prep template requires at least one step.')\n  }\n  const stepIds = new Set(data.steps.map(step => step.id))\n  if (stepIds.size !== data.steps.length) {\n    throw new Error('Sample-prep step ids must be unique.')\n  }\n  const orders = new Set(data.steps.map(step => step.order))\n  if (orders.size !== data.steps.length) {\n    throw new Error('Sample-prep step orders must be unique.')\n  }\n  for (const step of data.steps) {\n    if (!step.id || !step.name) {\n      throw new Error('Sample-prep steps require id and name.')\n    }\n    if (step.order < 0) {\n      throw new Error(`Sample-prep step '${step.id}' has a negative order.`)\n    }\n    if (!step.volumeUnit) {\n      throw new Error(`Sample-prep step '${step.id}' requires volumeUnit.`)\n    }\n    if (step.inputVolume !== undefined && step.inputVolume < 0) {\n      throw new Error(`Sample-prep step '${step.id}' has a negative input volume.`)\n    }\n    if (step.outputVolume !== undefined && step.outputVolume < 0) {\n      throw new Error(`Sample-prep step '${step.id}' has a negative output volume.`)\n    }\n    if (step.durationMin !== undefined && step.durationMin < 0) {\n      throw new Error(`Sample-prep step '${step.id}' has a negative duration.`)\n    }\n    if (!step.sourceSampleId && !step.destinationSampleId && !step.reagentId) {\n      throw new Error(`Sample-prep step '${step.id}' requires a source, destination, or reagent.`)\n    }\n  }\n}\n\nexport function validateDoseResponseData(data: DoseResponseTemplateData): void {\n  if (!Array.isArray(data.compounds) || data.compounds.length === 0) {\n    throw new Error('Dose-response template requires at least one compound.')\n  }\n  if (!data.unit) {\n    throw new Error('Dose-response template requires a unit.')\n  }\n  if (data.replicates < 1) {\n    throw new Error('Dose-response replicates must be at least 1.')\n  }\n  for (const compound of data.compounds) {\n    if (compound.concentrations.length === 0) {\n      throw new Error(`Compound '${compound.name}' requires at least one concentration.`)\n    }\n    if (compound.concentrations.some(value => value < 0)) {\n      throw new Error(`Compound '${compound.name}' has a negative concentration.`)\n    }\n  }\n}\n\nexport function validateCalibrationCurveData(data: CalibrationCurveTemplateData): void {\n  if (!data.analyte) {\n    throw new Error('Calibration-curve template requires an analyte.')\n  }\n  if (!data.xUnit) {\n    throw new Error('Calibration-curve template requires xUnit.')\n  }\n  if (!data.responseUnit) {\n    throw new Error('Calibration-curve template requires responseUnit.')\n  }\n  if (!Array.isArray(data.points) || data.points.length === 0) {\n    throw new Error('Calibration-curve template requires at least one point.')\n  }\n  if (data.acceptance.minRSquared < 0 || data.acceptance.minRSquared > 1) {\n    throw new Error('Calibration-curve minRSquared must be between 0 and 1.')\n  }\n  if (data.acceptance.standardTolerancePercent < 0 || data.acceptance.qcTolerancePercent < 0) {\n    throw new Error('Calibration-curve tolerances cannot be negative.')\n  }\n\n  const pointIds = new Set(data.points.map(point => point.id))\n  if (pointIds.size !== data.points.length) {\n    throw new Error('Calibration-curve point ids must be unique.')\n  }\n  const orders = new Set(data.points.map(point => point.order))\n  if (orders.size !== data.points.length) {\n    throw new Error('Calibration-curve point orders must be unique.')\n  }\n\n  let standards = 0\n  for (const point of data.points) {\n    if (!point.id || !point.level) {\n      throw new Error('Calibration-curve points require id and level.')\n    }\n    if (!point.unit) {\n      throw new Error(`Calibration-curve point '${point.id}' requires unit.`)\n    }\n    if (point.order < 0) {\n      throw new Error(`Calibration-curve point '${point.id}' has a negative order.`)\n    }\n    if (point.concentration < 0) {\n      throw new Error(`Calibration-curve point '${point.id}' has a negative concentration.`)\n    }\n    if ((point.role === 'standard' || point.role === 'qc') && point.concentration <= 0) {\n      throw new Error(`Calibration-curve point '${point.id}' requires positive concentration.`)\n    }\n    if (point.replicate < 1) {\n      throw new Error(`Calibration-curve point '${point.id}' replicate must be at least 1.`)\n    }\n    if (point.role === 'standard' && point.include) {\n      standards += 1\n    }\n  }\n\n  if (standards < 2) {\n    throw new Error('Calibration-curve template requires at least two included standards.')\n  }\n  if (data.acceptance.requireBlank && !data.points.some(point => point.role === 'blank')) {\n    throw new Error('Calibration-curve template requires a blank point when requireBlank is true.')\n  }\n}\n\nexport function validateTimeCourseData(data: TimeCourseTemplateData): void {\n  if (!Array.isArray(data.timepoints) || data.timepoints.length === 0) {\n    throw new Error('Time-course template requires at least one time point.')\n  }\n  if (!Array.isArray(data.conditions) || data.conditions.length === 0) {\n    throw new Error('Time-course template requires at least one condition.')\n  }\n  const timepointIds = new Set(data.timepoints.map(timepoint => timepoint.id))\n  if (timepointIds.size !== data.timepoints.length) {\n    throw new Error('Time-course time point ids must be unique.')\n  }\n  const conditionIds = new Set(data.conditions.map(condition => condition.id))\n  if (conditionIds.size !== data.conditions.length) {\n    throw new Error('Time-course condition ids must be unique.')\n  }\n  const sampleIds = new Set(data.samples.map(sample => sample.sampleId))\n  if (sampleIds.size !== data.samples.length) {\n    throw new Error('Time-course sample ids must be unique.')\n  }\n  for (const sample of data.samples) {\n    if (!timepointIds.has(sample.timepointId)) {\n      throw new Error(`Sample '${sample.sampleId}' references unknown time point.`)\n    }\n    if (!conditionIds.has(sample.conditionId)) {\n      throw new Error(`Sample '${sample.sampleId}' references unknown condition.`)\n    }\n  }\n}\n\nexport function validateProtocolStepsData(data: ProtocolStepsTemplateData): void {\n  if (!Array.isArray(data.steps) || data.steps.length === 0) {\n    throw new Error('Protocol-steps template requires at least one step.')\n  }\n  const stepIds = new Set(data.steps.map(step => step.id))\n  if (stepIds.size !== data.steps.length) {\n    throw new Error('Protocol-steps ids must be unique.')\n  }\n  const orders = new Set(data.steps.map(step => step.order))\n  if (orders.size !== data.steps.length) {\n    throw new Error('Protocol-steps orders must be unique.')\n  }\n  for (const step of data.steps) {\n    if (!step.id) {\n      throw new Error('Protocol step id is required.')\n    }\n    if (!step.name) {\n      throw new Error(`Protocol step '${step.id}' requires a name.`)\n    }\n    if (step.duration !== undefined && step.duration < 0) {\n      throw new Error(`Protocol step '${step.id}' has a negative duration.`)\n    }\n    if (step.order < 0) {\n      throw new Error(`Protocol step '${step.id}' has a negative order.`)\n    }\n  }\n}\n\nexport function validateAssayMatrixData(data: AssayMatrixTemplateData): void {\n  if (!Array.isArray(data.samples) || data.samples.length === 0) {\n    throw new Error('Assay-matrix template requires at least one sample.')\n  }\n  if (!Array.isArray(data.features) || data.features.length === 0) {\n    throw new Error('Assay-matrix template requires at least one feature.')\n  }\n  const sampleIds = new Set(data.samples.map(sample => sample.sampleId))\n  if (sampleIds.size !== data.samples.length) {\n    throw new Error('Assay-matrix sample ids must be unique.')\n  }\n  const featureIds = new Set(data.features.map(feature => feature.id))\n  if (featureIds.size !== data.features.length) {\n    throw new Error('Assay-matrix feature ids must be unique.')\n  }\n  const measurementIds = new Set<string>()\n  for (const measurement of data.measurements) {\n    const key = `${measurement.sampleId}:${measurement.featureId}`\n    if (measurementIds.has(key)) {\n      throw new Error(`Duplicate assay measurement for '${key}'.`)\n    }\n    measurementIds.add(key)\n    if (!sampleIds.has(measurement.sampleId)) {\n      throw new Error(`Measurement references unknown sample '${measurement.sampleId}'.`)\n    }\n    if (!featureIds.has(measurement.featureId)) {\n      throw new Error(`Measurement references unknown feature '${measurement.featureId}'.`)\n    }\n  }\n}\n\nexport function validateReagentListData(data: ReagentListTemplateData): void {\n  if (!Array.isArray(data.reagents) || data.reagents.length === 0) {\n    throw new Error('Reagent-list template requires at least one reagent.')\n  }\n  const reagentIds = new Set(data.reagents.map(reagent => reagent.id))\n  if (reagentIds.size !== data.reagents.length) {\n    throw new Error('Reagent-list reagent ids must be unique.')\n  }\n  for (const reagent of data.reagents) {\n    if (!reagent.id) {\n      throw new Error('Reagent-list reagent id is required.')\n    }\n    if (!reagent.name) {\n      throw new Error(`Reagent '${reagent.id}' requires a name.`)\n    }\n    if (reagent.stockLevel !== undefined && reagent.stockLevel < 0) {\n      throw new Error(`Reagent '${reagent.id}' has a negative stock level.`)\n    }\n  }\n}\n\nexport function validateFlowCytometryPanelData(data: FlowCytometryPanelTemplateData): void {\n  if (!Array.isArray(data.markers) || data.markers.length === 0) {\n    throw new Error('Flow-cytometry panel template requires at least one marker.')\n  }\n  const markerIds = new Set(data.markers.map(marker => marker.id))\n  if (markerIds.size !== data.markers.length) {\n    throw new Error('Flow-cytometry panel marker ids must be unique.')\n  }\n  const controlIds = new Set(data.controls.map(control => control.id))\n  if (controlIds.size !== data.controls.length) {\n    throw new Error('Flow-cytometry panel control ids must be unique.')\n  }\n  for (const marker of data.markers) {\n    if (!marker.id) {\n      throw new Error('Flow-cytometry panel marker id is required.')\n    }\n    if (!marker.marker) {\n      throw new Error(`Flow-cytometry panel marker '${marker.id}' requires a marker name.`)\n    }\n  }\n  for (const control of data.controls) {\n    if (!control.id) {\n      throw new Error('Flow-cytometry panel control id is required.')\n    }\n    if (!control.name) {\n      throw new Error(`Flow-cytometry panel control '${control.id}' requires a name.`)\n    }\n    if (control.markerId && !markerIds.has(control.markerId)) {\n      throw new Error(`Flow-cytometry panel control '${control.id}' references unknown marker '${control.markerId}'.`)\n    }\n  }\n}\n\nexport function validateInstrumentRunData(data: InstrumentRunTemplateData): void {\n  if (!Array.isArray(data.methods) || data.methods.length === 0) {\n    throw new Error('Instrument-run template requires at least one method.')\n  }\n  if (!Array.isArray(data.items) || data.items.length === 0) {\n    throw new Error('Instrument-run template requires at least one run item.')\n  }\n  const methodIds = new Set(data.methods.map(method => method.id))\n  if (methodIds.size !== data.methods.length) {\n    throw new Error('Instrument-run method ids must be unique.')\n  }\n  for (const method of data.methods) {\n    if (!method.id || !method.name) {\n      throw new Error('Instrument-run methods require id and name.')\n    }\n  }\n  const itemIds = new Set(data.items.map(item => item.id))\n  if (itemIds.size !== data.items.length) {\n    throw new Error('Instrument-run item ids must be unique.')\n  }\n  const orders = new Set(data.items.map(item => item.order))\n  if (orders.size !== data.items.length) {\n    throw new Error('Instrument-run item orders must be unique.')\n  }\n  for (const item of data.items) {\n    if (!item.id) {\n      throw new Error('Instrument-run items require id.')\n    }\n    if (!methodIds.has(item.methodId)) {\n      throw new Error(`Instrument-run item '${item.id}' references unknown method '${item.methodId}'.`)\n    }\n    if (item.kind === 'sample' && !item.sampleId) {\n      throw new Error(`Instrument-run sample item '${item.id}' requires sampleId.`)\n    }\n    if (item.order < 0) {\n      throw new Error(`Instrument-run item '${item.id}' has a negative order.`)\n    }\n    if (item.injectionVolume !== undefined && item.injectionVolume < 0) {\n      throw new Error(`Instrument-run item '${item.id}' has a negative injection volume.`)\n    }\n    if (item.expectedDurationMin !== undefined && item.expectedDurationMin < 0) {\n      throw new Error(`Instrument-run item '${item.id}' has a negative expected duration.`)\n    }\n  }\n}\n\nexport function validateQpcrPlateData(data: QpcrPlateTemplateData): void {\n  if (!Array.isArray(data.samples) || data.samples.length === 0) {\n    throw new Error('qPCR plate template requires at least one sample.')\n  }\n  if (!Array.isArray(data.targets) || data.targets.length === 0) {\n    throw new Error('qPCR plate template requires at least one target.')\n  }\n  if (!Array.isArray(data.reactions) || data.reactions.length === 0) {\n    throw new Error('qPCR plate template requires at least one reaction.')\n  }\n  const sampleIds = new Set(data.samples.map(sample => sample.sampleId))\n  if (sampleIds.size !== data.samples.length) {\n    throw new Error('qPCR plate sample ids must be unique.')\n  }\n  const targetIds = new Set(data.targets.map(target => target.id))\n  if (targetIds.size !== data.targets.length) {\n    throw new Error('qPCR plate target ids must be unique.')\n  }\n  const reactionIds = new Set(data.reactions.map(reaction => reaction.id))\n  if (reactionIds.size !== data.reactions.length) {\n    throw new Error('qPCR plate reaction ids must be unique.')\n  }\n  const wellIds = new Set(data.reactions.map(reaction => reaction.wellId))\n  if (wellIds.size !== data.reactions.length) {\n    throw new Error('qPCR plate reaction wells must be unique.')\n  }\n  for (const reaction of data.reactions) {\n    assertWellInFormat(reaction.wellId, data.format)\n    if (!reaction.id) {\n      throw new Error('qPCR reaction id is required.')\n    }\n    if (!reaction.targetId || !targetIds.has(reaction.targetId)) {\n      throw new Error(`qPCR reaction '${reaction.id}' references unknown target '${reaction.targetId}'.`)\n    }\n    if (reaction.sampleId && !sampleIds.has(reaction.sampleId)) {\n      throw new Error(`qPCR reaction '${reaction.id}' references unknown sample '${reaction.sampleId}'.`)\n    }\n    if (reaction.controlKind === 'sample' && !reaction.sampleId) {\n      throw new Error(`qPCR sample reaction '${reaction.id}' requires sampleId.`)\n    }\n    if (reaction.replicate < 1) {\n      throw new Error(`qPCR reaction '${reaction.id}' replicate must be at least 1.`)\n    }\n    if (reaction.cq !== undefined && reaction.cq !== null && reaction.cq < 0) {\n      throw new Error(`qPCR reaction '${reaction.id}' has a negative Cq.`)\n    }\n    if (reaction.quantity !== undefined && reaction.quantity !== null && reaction.quantity < 0) {\n      throw new Error(`qPCR reaction '${reaction.id}' has a negative quantity.`)\n    }\n  }\n}\n","import type { SelectOption } from '../types'\nimport { getTemplateData } from './templateEnvelopes'\nimport { validateAssayMatrixData } from './templateValidators'\nimport type {\n  AssayMatrixColumnsAdapterResult,\n  AssayMatrixDataFrameAdapterResult,\n  AssayMatrixRowsAdapterResult,\n  AssayMatrixSampleOptionsAdapterResult,\n  AssayMatrixTemplate,\n  AssayMatrixTemplateData,\n} from './types'\n\nexport function toAssayMatrixRows(\n  template: AssayMatrixTemplate | AssayMatrixTemplateData\n): AssayMatrixRowsAdapterResult {\n  const data = getTemplateData(template, 'assay-matrix')\n  validateAssayMatrixData(data)\n  const measurements = new Map(\n    data.measurements.map(measurement => [\n      `${measurement.sampleId}:${measurement.featureId}`,\n      measurement.value ?? null,\n    ])\n  )\n\n  return data.samples.map(sample => {\n    const row: Record<string, unknown> = {\n      sampleId: sample.sampleId,\n      name: sample.name,\n      group: sample.group,\n      ...(sample.metadata ?? {}),\n    }\n    for (const feature of data.features) {\n      row[feature.id] = measurements.get(`${sample.sampleId}:${feature.id}`) ?? null\n    }\n    return row\n  })\n}\n\nexport function toAssayMatrixColumns(\n  template: AssayMatrixTemplate | AssayMatrixTemplateData\n): AssayMatrixColumnsAdapterResult {\n  const data = getTemplateData(template, 'assay-matrix')\n  validateAssayMatrixData(data)\n  return [\n    { key: 'sampleId', label: 'Sample ID', sortable: true },\n    { key: 'name', label: 'Name', sortable: true },\n    { key: 'group', label: 'Group', sortable: true },\n    ...data.features.map(feature => ({\n      key: feature.id,\n      label: feature.unit ? `${feature.name} (${feature.unit})` : feature.name,\n      sortable: true,\n      align: 'right' as const,\n    })),\n  ]\n}\n\nexport function toAssayMatrixDataFrame(\n  template: AssayMatrixTemplate | AssayMatrixTemplateData\n): AssayMatrixDataFrameAdapterResult {\n  return {\n    data: toAssayMatrixRows(template),\n    columns: toAssayMatrixColumns(template),\n    rowKey: 'sampleId',\n  }\n}\n\n/** Convert an assay-matrix template into SampleSelector options derived from assay samples. */\nexport function toAssayMatrixSampleOptions(\n  template: AssayMatrixTemplate | AssayMatrixTemplateData\n): AssayMatrixSampleOptionsAdapterResult {\n  const data = getTemplateData(template, 'assay-matrix')\n  validateAssayMatrixData(data)\n  return data.samples.map((sample): SelectOption<string> => ({\n    value: sample.sampleId,\n    label: sample.name ?? sample.sampleId,\n    description: sample.group,\n  }))\n}\n","import { getTemplateData } from './templateEnvelopes'\nimport { validateCalibrationCurveData } from './templateValidators'\nimport type {\n  CalibrationCurveColumnsAdapterResult,\n  CalibrationCurveDataFrameAdapterResult,\n  CalibrationCurveRowsAdapterResult,\n  CalibrationCurveTemplate,\n  CalibrationCurveTemplateData,\n} from './types'\n\nexport function toCalibrationCurveRows(\n  template: CalibrationCurveTemplate | CalibrationCurveTemplateData\n): CalibrationCurveRowsAdapterResult {\n  const data = getTemplateData(template, 'calibration-curve')\n  validateCalibrationCurveData(data)\n  return [...data.points]\n    .sort((a, b) => a.order - b.order)\n    .map(point => ({\n      id: point.id,\n      order: point.order,\n      role: point.role,\n      level: point.level,\n      concentration: point.concentration,\n      unit: point.unit,\n      expectedResponse: point.expectedResponse,\n      response: point.response,\n      replicate: point.replicate,\n      include: point.include,\n      status: point.status,\n      analyte: data.analyte,\n      model: data.model,\n      ...(point.metadata ?? {}),\n    }))\n}\n\nexport function toCalibrationCurveColumns(): CalibrationCurveColumnsAdapterResult {\n  return [\n    { key: 'order', label: 'Order', sortable: true, align: 'right' },\n    { key: 'role', label: 'Role', sortable: true },\n    { key: 'level', label: 'Level', sortable: true },\n    { key: 'concentration', label: 'Concentration', sortable: true, align: 'right' },\n    { key: 'unit', label: 'Unit', sortable: true },\n    { key: 'expectedResponse', label: 'Expected', sortable: true, align: 'right' },\n    { key: 'response', label: 'Response', sortable: true, align: 'right' },\n    { key: 'replicate', label: 'Replicate', sortable: true, align: 'right' },\n    { key: 'include', label: 'Include', sortable: true },\n    { key: 'status', label: 'Status', sortable: true },\n  ]\n}\n\nexport function toCalibrationCurveDataFrame(\n  template: CalibrationCurveTemplate | CalibrationCurveTemplateData\n): CalibrationCurveDataFrameAdapterResult {\n  return {\n    data: toCalibrationCurveRows(template),\n    columns: toCalibrationCurveColumns(),\n    rowKey: 'id',\n  }\n}\n","import { getTemplateData } from './templateEnvelopes'\nimport { validateFlowCytometryPanelData } from './templateValidators'\nimport type {\n  FlowCytometryPanelTemplate,\n  FlowCytometryPanelTemplateData,\n  FlowPanelColumnsAdapterResult,\n  FlowPanelDataFrameAdapterResult,\n  FlowPanelRowsAdapterResult,\n} from './types'\n\nexport function toFlowPanelRows(\n  template: FlowCytometryPanelTemplate | FlowCytometryPanelTemplateData\n): FlowPanelRowsAdapterResult {\n  const data = getTemplateData(template, 'flow-cytometry-panel')\n  validateFlowCytometryPanelData(data)\n  return data.markers.map(marker => {\n    const markerControls = data.controls\n      .filter(control => control.markerId === marker.id)\n      .map(control => control.name)\n      .join(', ')\n    return {\n      id: marker.id,\n      marker: marker.marker,\n      fluorophore: marker.fluorophore,\n      detector: marker.detector,\n      clone: marker.clone,\n      reagentId: marker.reagentId,\n      purpose: marker.purpose,\n      compensationRequired: marker.compensationRequired,\n      controls: markerControls,\n      instrument: data.instrument,\n      ...(marker.metadata ?? {}),\n    }\n  })\n}\n\nexport function toFlowPanelColumns(): FlowPanelColumnsAdapterResult {\n  return [\n    { key: 'marker', label: 'Marker', sortable: true },\n    { key: 'fluorophore', label: 'Fluorophore', sortable: true },\n    { key: 'detector', label: 'Detector', sortable: true },\n    { key: 'clone', label: 'Clone', sortable: true },\n    { key: 'purpose', label: 'Purpose', sortable: true },\n    { key: 'compensationRequired', label: 'Compensation', sortable: true },\n    { key: 'controls', label: 'Controls' },\n    { key: 'instrument', label: 'Instrument', sortable: true },\n  ]\n}\n\nexport function toFlowPanelDataFrame(\n  template: FlowCytometryPanelTemplate | FlowCytometryPanelTemplateData\n): FlowPanelDataFrameAdapterResult {\n  return {\n    data: toFlowPanelRows(template),\n    columns: toFlowPanelColumns(),\n    rowKey: 'id',\n  }\n}\n","import type {\n  ProtocolStepStatus,\n  ProtocolStepType,\n  ScheduleEventStatus,\n} from '../types'\nimport type {\n  InstrumentRunItem,\n  InstrumentRunItemKind,\n  InstrumentRunStatus,\n} from './types'\n\nexport function instrumentRunStepType(kind: InstrumentRunItemKind): ProtocolStepType {\n  switch (kind) {\n    case 'wash':\n      return 'wash'\n    case 'blank':\n    case 'qc':\n    case 'standard':\n    case 'calibration':\n    case 'sample':\n      return 'measurement'\n    default:\n      return 'custom'\n  }\n}\n\nexport function instrumentRunStepStatus(status: InstrumentRunStatus): ProtocolStepStatus {\n  switch (status) {\n    case 'running':\n      return 'in_progress'\n    case 'completed':\n      return 'completed'\n    case 'failed':\n      return 'failed'\n    case 'skipped':\n      return 'skipped'\n    case 'planned':\n    case 'queued':\n    default:\n      return 'pending'\n  }\n}\n\nexport function instrumentRunScheduleStatus(status: InstrumentRunStatus): ScheduleEventStatus {\n  switch (status) {\n    case 'running':\n      return 'in-progress'\n    case 'completed':\n      return 'confirmed'\n    case 'failed':\n    case 'skipped':\n      return 'cancelled'\n    case 'planned':\n    case 'queued':\n    default:\n      return 'pending'\n  }\n}\n\nexport function instrumentRunScheduleColor(kind: InstrumentRunItem['kind']): string {\n  switch (kind) {\n    case 'blank':\n      return '#64748b'\n    case 'qc':\n      return '#8b5cf6'\n    case 'standard':\n    case 'calibration':\n      return '#f59e0b'\n    case 'wash':\n      return '#06b6d4'\n    case 'sample':\n      return '#2563eb'\n    default:\n      return '#475569'\n  }\n}\n\nexport function dateFromMetadata(\n  metadata: Record<string, unknown> | undefined,\n  keys: readonly string[]\n): Date | undefined {\n  if (!metadata) return undefined\n  for (const key of keys) {\n    const value = metadata[key]\n    if (!(typeof value === 'string' || value instanceof Date)) continue\n    const date = new Date(value)\n    if (!Number.isNaN(date.getTime())) return date\n  }\n  return undefined\n}\n\nexport function addMinutes(date: Date, minutes: number): Date {\n  return new Date(date.getTime() + minutes * 60_000)\n}\n","import type {\n  ProtocolStep,\n  ScheduleEvent,\n} from '../types'\nimport { getTemplateData } from './templateEnvelopes'\nimport { validateInstrumentRunData } from './templateValidators'\nimport type {\n  InstrumentRunColumnsAdapterResult,\n  InstrumentRunDataFrameAdapterResult,\n  InstrumentRunRowsAdapterResult,\n  InstrumentRunScheduleEventsAdapterResult,\n  InstrumentRunStepsAdapterResult,\n  InstrumentRunTemplate,\n  InstrumentRunTemplateData,\n} from './types'\nimport {\n  addMinutes,\n  dateFromMetadata,\n  instrumentRunScheduleColor,\n  instrumentRunScheduleStatus,\n  instrumentRunStepStatus,\n  instrumentRunStepType,\n} from './instrumentRunAdapterHelpers'\n\nexport function toInstrumentRunRows(\n  template: InstrumentRunTemplate | InstrumentRunTemplateData\n): InstrumentRunRowsAdapterResult {\n  const data = getTemplateData(template, 'instrument-run')\n  validateInstrumentRunData(data)\n  const methods = new Map(data.methods.map(method => [method.id, method]))\n  return [...data.items]\n    .sort((a, b) => a.order - b.order)\n    .map(item => {\n      const method = methods.get(item.methodId)\n      return {\n        id: item.id,\n        order: item.order,\n        kind: item.kind,\n        sampleId: item.sampleId,\n        name: item.name ?? item.sampleId ?? item.kind,\n        method: method?.name ?? item.methodId,\n        vial: item.vial,\n        plateId: item.plateId,\n        wellId: item.wellId,\n        injectionVolume: item.injectionVolume,\n        expectedDurationMin: item.expectedDurationMin,\n        status: item.status,\n        instrument: data.instrument ?? method?.instrument,\n        ...(item.metadata ?? {}),\n      }\n    })\n}\n\nexport function toInstrumentRunColumns(): InstrumentRunColumnsAdapterResult {\n  return [\n    { key: 'order', label: 'Order', sortable: true, align: 'right' },\n    { key: 'kind', label: 'Kind', sortable: true },\n    { key: 'sampleId', label: 'Sample ID', sortable: true },\n    { key: 'name', label: 'Name', sortable: true },\n    { key: 'method', label: 'Method', sortable: true },\n    { key: 'vial', label: 'Vial', sortable: true },\n    { key: 'wellId', label: 'Well', sortable: true },\n    { key: 'injectionVolume', label: 'Injection', sortable: true, align: 'right' },\n    { key: 'expectedDurationMin', label: 'Duration', sortable: true, align: 'right' },\n    { key: 'status', label: 'Status', sortable: true },\n    { key: 'instrument', label: 'Instrument', sortable: true },\n  ]\n}\n\nexport function toInstrumentRunDataFrame(\n  template: InstrumentRunTemplate | InstrumentRunTemplateData\n): InstrumentRunDataFrameAdapterResult {\n  return {\n    data: toInstrumentRunRows(template),\n    columns: toInstrumentRunColumns(),\n    rowKey: 'id',\n  }\n}\n\n/** Convert an instrument-run template into ExperimentTimeline protocol steps for acquisition queue previews. */\nexport function toInstrumentRunSteps(\n  template: InstrumentRunTemplate | InstrumentRunTemplateData\n): InstrumentRunStepsAdapterResult {\n  const data = getTemplateData(template, 'instrument-run')\n  validateInstrumentRunData(data)\n  const methods = new Map(data.methods.map(method => [method.id, method]))\n  return [...data.items]\n    .sort((a, b) => a.order - b.order)\n    .map((item): ProtocolStep => {\n      const method = methods.get(item.methodId)\n      const name = item.name ?? item.sampleId ?? item.kind\n      return {\n        id: item.id,\n        type: instrumentRunStepType(item.kind),\n        name,\n        description: [\n          item.kind,\n          method?.name,\n          item.vial ? `Vial ${item.vial}` : undefined,\n          item.wellId ? `Well ${item.wellId}` : undefined,\n        ]\n          .filter(Boolean)\n          .join(' / '),\n        duration: item.expectedDurationMin,\n        status: instrumentRunStepStatus(item.status),\n        parameters: {\n          kind: item.kind,\n          sampleId: item.sampleId,\n          methodId: item.methodId,\n          method: method?.name,\n          vial: item.vial,\n          plateId: item.plateId,\n          wellId: item.wellId,\n          injectionVolume: item.injectionVolume,\n          instrument: data.instrument ?? method?.instrument,\n        },\n        order: item.order,\n      }\n    })\n}\n\n/** Convert an instrument-run template into readonly ScheduleCalendar events ordered by run queue timing. */\nexport function toInstrumentRunScheduleEvents(\n  template: InstrumentRunTemplate | InstrumentRunTemplateData\n): InstrumentRunScheduleEventsAdapterResult {\n  const data = getTemplateData(template, 'instrument-run')\n  validateInstrumentRunData(data)\n  const methods = new Map(data.methods.map(method => [method.id, method]))\n  let cursor = dateFromMetadata(data.metadata, ['scheduledStart', 'runStart', 'start', 'startedAt'])\n    ?? new Date('2024-01-01T08:00:00.000Z')\n\n  return [...data.items]\n    .sort((a, b) => a.order - b.order)\n    .map((item): ScheduleEvent => {\n      const method = methods.get(item.methodId)\n      const start = dateFromMetadata(item.metadata, ['scheduledStart', 'start', 'startedAt']) ?? cursor\n      const end = dateFromMetadata(item.metadata, ['scheduledEnd', 'end', 'completedAt'])\n        ?? addMinutes(start, Math.max(item.expectedDurationMin ?? 10, 1))\n      cursor = end\n\n      return {\n        id: item.id,\n        title: item.name ?? item.sampleId ?? item.kind,\n        start: start.toISOString(),\n        end: end.toISOString(),\n        color: instrumentRunScheduleColor(item.kind),\n        status: instrumentRunScheduleStatus(item.status),\n        draggable: false,\n        resizable: false,\n        metadata: {\n          kind: item.kind,\n          sampleId: item.sampleId,\n          methodId: item.methodId,\n          method: method?.name,\n          vial: item.vial,\n          plateId: item.plateId,\n          wellId: item.wellId,\n          injectionVolume: item.injectionVolume,\n          instrument: data.instrument ?? method?.instrument,\n        },\n      }\n    })\n}\n","import { getTemplateData } from './templateEnvelopes'\nimport { validateProtocolStepsData } from './templateValidators'\nimport type {\n  ProtocolColumnsAdapterResult,\n  ProtocolDataFrameAdapterResult,\n  ProtocolRowsAdapterResult,\n  ProtocolStepsAdapterResult,\n  ProtocolStepsTemplate,\n  ProtocolStepsTemplateData,\n} from './types'\n\nexport function toProtocolSteps(\n  template: ProtocolStepsTemplate | ProtocolStepsTemplateData\n): ProtocolStepsAdapterResult {\n  const data = getTemplateData(template, 'protocol-steps')\n  validateProtocolStepsData(data)\n  return [...data.steps]\n    .sort((a, b) => a.order - b.order)\n    .map(step => ({\n      id: step.id,\n      type: step.type,\n      name: step.name,\n      description: step.description,\n      duration: step.duration,\n      status: step.status,\n      parameters: step.parameters,\n      order: step.order,\n    }))\n}\n\nexport function toProtocolRows(\n  template: ProtocolStepsTemplate | ProtocolStepsTemplateData\n): ProtocolRowsAdapterResult {\n  const data = getTemplateData(template, 'protocol-steps')\n  validateProtocolStepsData(data)\n  return [...data.steps]\n    .sort((a, b) => a.order - b.order)\n    .map(step => ({\n      id: step.id,\n      order: step.order,\n      type: step.type,\n      name: step.name,\n      description: step.description,\n      duration: step.duration,\n      status: step.status,\n      ...(step.metadata ?? {}),\n    }))\n}\n\nexport function toProtocolColumns(): ProtocolColumnsAdapterResult {\n  return [\n    { key: 'order', label: 'Order', sortable: true, align: 'right' },\n    { key: 'name', label: 'Name', sortable: true },\n    { key: 'type', label: 'Type', sortable: true },\n    { key: 'duration', label: 'Duration', sortable: true, align: 'right' },\n    { key: 'status', label: 'Status', sortable: true },\n    { key: 'description', label: 'Description', sortable: true },\n  ]\n}\n\nexport function toProtocolDataFrame(\n  template: ProtocolStepsTemplate | ProtocolStepsTemplateData\n): ProtocolDataFrameAdapterResult {\n  return {\n    data: toProtocolRows(template),\n    columns: toProtocolColumns(),\n    rowKey: 'id',\n  }\n}\n","import type { Well } from '../types'\nimport { getTemplateData } from './templateEnvelopes'\nimport { validateQpcrPlateData } from './templateValidators'\nimport type {\n  QpcrColumnsAdapterResult,\n  QpcrDataFrameAdapterResult,\n  QpcrPlateTemplate,\n  QpcrPlateTemplateData,\n  QpcrRowsAdapterResult,\n  QpcrWellMapAdapterResult,\n} from './types'\n\nexport function toQpcrRows(\n  template: QpcrPlateTemplate | QpcrPlateTemplateData\n): QpcrRowsAdapterResult {\n  const data = getTemplateData(template, 'qpcr-plate')\n  validateQpcrPlateData(data)\n  const samples = new Map(data.samples.map(sample => [sample.sampleId, sample]))\n  const targets = new Map(data.targets.map(target => [target.id, target]))\n\n  return data.reactions.map(reaction => {\n    const sample = reaction.sampleId ? samples.get(reaction.sampleId) : undefined\n    const target = targets.get(reaction.targetId)\n    return {\n      id: reaction.id,\n      wellId: reaction.wellId,\n      sampleId: reaction.sampleId,\n      sample: sample?.name ?? reaction.sampleId ?? reaction.controlKind,\n      group: sample?.group,\n      targetId: reaction.targetId,\n      target: target?.name ?? reaction.targetId,\n      replicate: reaction.replicate,\n      controlKind: reaction.controlKind,\n      cq: reaction.cq ?? null,\n      quantity: reaction.quantity ?? null,\n      flags: reaction.flags.join(', '),\n      instrument: data.instrument,\n      chemistry: data.chemistry,\n      ...(reaction.metadata ?? {}),\n    }\n  })\n}\n\nexport function toQpcrColumns(): QpcrColumnsAdapterResult {\n  return [\n    { key: 'wellId', label: 'Well', sortable: true },\n    { key: 'sample', label: 'Sample', sortable: true },\n    { key: 'group', label: 'Group', sortable: true },\n    { key: 'target', label: 'Target', sortable: true },\n    { key: 'replicate', label: 'Replicate', sortable: true, align: 'right' },\n    { key: 'controlKind', label: 'Control', sortable: true },\n    { key: 'cq', label: 'Cq', sortable: true, align: 'right' },\n    { key: 'quantity', label: 'Quantity', sortable: true, align: 'right' },\n    { key: 'flags', label: 'Flags' },\n  ]\n}\n\nexport function toQpcrDataFrame(\n  template: QpcrPlateTemplate | QpcrPlateTemplateData\n): QpcrDataFrameAdapterResult {\n  return {\n    data: toQpcrRows(template),\n    columns: toQpcrColumns(),\n    rowKey: 'id',\n  }\n}\n\nexport function toQpcrWellPlateWells(\n  template: QpcrPlateTemplate | QpcrPlateTemplateData\n): QpcrWellMapAdapterResult {\n  const data = getTemplateData(template, 'qpcr-plate')\n  validateQpcrPlateData(data)\n  return Object.fromEntries(data.reactions.map(reaction => {\n    const [row, col] = wellPositionFromId(reaction.wellId)\n    return [\n      reaction.wellId,\n      {\n        id: reaction.wellId,\n        row,\n        col,\n        state: 'filled' as const,\n        sampleType: reaction.sampleId ?? reaction.controlKind,\n        value: reaction.cq ?? undefined,\n        metadata: {\n          reactionId: reaction.id,\n          sampleId: reaction.sampleId,\n          targetId: reaction.targetId,\n          replicate: reaction.replicate,\n          controlKind: reaction.controlKind,\n        },\n      } satisfies Well,\n    ]\n  }))\n}\n\nfunction wellPositionFromId(wellId: string): [number, number] {\n  const match = /^([A-Z]+)([1-9][0-9]*)$/.exec(wellId.toUpperCase())\n  if (!match) {\n    throw new Error(`Invalid well id '${wellId}'.`)\n  }\n  const row = [...match[1]].reduce((value, char) => value * 26 + char.charCodeAt(0) - 64, 0) - 1\n  const col = Number(match[2]) - 1\n  return [row, col]\n}\n","import { getTemplateData } from './templateEnvelopes'\nimport { validateReagentListData } from './templateValidators'\nimport type {\n  ReagentColumnsAdapterResult,\n  ReagentDataFrameAdapterResult,\n  ReagentListItemsAdapterResult,\n  ReagentListTemplate,\n  ReagentListTemplateData,\n  ReagentRowsAdapterResult,\n} from './types'\n\nexport function toReagentListItems(\n  template: ReagentListTemplate | ReagentListTemplateData\n): ReagentListItemsAdapterResult {\n  const data = getTemplateData(template, 'reagent-list')\n  validateReagentListData(data)\n  return data.reagents.map(reagent => ({\n    id: reagent.id,\n    name: reagent.name,\n    catalogNumber: reagent.catalogNumber,\n    lotNumber: reagent.lotNumber,\n    expiryDate: reagent.expiryDate,\n    storageCondition: reagent.storageCondition,\n    location: reagent.location,\n    stockLevel: reagent.stockLevel,\n    stockUnit: reagent.stockUnit,\n    supplier: reagent.supplier,\n    url: reagent.url,\n  }))\n}\n\nexport function toReagentRows(\n  template: ReagentListTemplate | ReagentListTemplateData\n): ReagentRowsAdapterResult {\n  const data = getTemplateData(template, 'reagent-list')\n  validateReagentListData(data)\n  return data.reagents.map(reagent => ({\n    id: reagent.id,\n    name: reagent.name,\n    kind: reagent.kind,\n    catalogNumber: reagent.catalogNumber,\n    lotNumber: reagent.lotNumber,\n    expiryDate: reagent.expiryDate,\n    storageCondition: reagent.storageCondition,\n    location: reagent.location,\n    stockLevel: reagent.stockLevel,\n    stockUnit: reagent.stockUnit,\n    supplier: reagent.supplier,\n    concentration: reagent.concentration,\n    ...(reagent.metadata ?? {}),\n  }))\n}\n\nexport function toReagentColumns(): ReagentColumnsAdapterResult {\n  return [\n    { key: 'name', label: 'Name', sortable: true },\n    { key: 'kind', label: 'Kind', sortable: true },\n    { key: 'catalogNumber', label: 'Catalog', sortable: true },\n    { key: 'lotNumber', label: 'Lot', sortable: true },\n    { key: 'expiryDate', label: 'Expiry', sortable: true },\n    { key: 'storageCondition', label: 'Storage', sortable: true },\n    { key: 'location', label: 'Location', sortable: true },\n    { key: 'stockLevel', label: 'Stock', sortable: true, align: 'right' },\n    { key: 'stockUnit', label: 'Unit', sortable: true },\n    { key: 'supplier', label: 'Supplier', sortable: true },\n  ]\n}\n\nexport function toReagentDataFrame(\n  template: ReagentListTemplate | ReagentListTemplateData\n): ReagentDataFrameAdapterResult {\n  return {\n    data: toReagentRows(template),\n    columns: toReagentColumns(),\n    rowKey: 'id',\n  }\n}\n","import { getTemplateData } from './templateEnvelopes'\nimport { validateSamplePrepData } from './templateValidators'\nimport type {\n  SamplePrepColumnsAdapterResult,\n  SamplePrepDataFrameAdapterResult,\n  SamplePrepRowsAdapterResult,\n  SamplePrepTemplate,\n  SamplePrepTemplateData,\n} from './types'\n\nexport function toSamplePrepRows(\n  template: SamplePrepTemplate | SamplePrepTemplateData\n): SamplePrepRowsAdapterResult {\n  const data = getTemplateData(template, 'sample-prep')\n  validateSamplePrepData(data)\n  return [...data.steps]\n    .sort((a, b) => a.order - b.order)\n    .map(step => ({\n      id: step.id,\n      order: step.order,\n      type: step.type,\n      name: step.name,\n      sourceSampleId: step.sourceSampleId,\n      sourceWellId: step.sourceWellId,\n      destinationSampleId: step.destinationSampleId,\n      destinationWellId: step.destinationWellId,\n      reagentId: step.reagentId,\n      inputVolume: step.inputVolume,\n      outputVolume: step.outputVolume,\n      volumeUnit: step.volumeUnit,\n      durationMin: step.durationMin,\n      status: step.status,\n      protocolName: data.protocolName,\n      ...(step.metadata ?? {}),\n    }))\n}\n\nexport function toSamplePrepColumns(): SamplePrepColumnsAdapterResult {\n  return [\n    { key: 'order', label: 'Order', sortable: true, align: 'right' },\n    { key: 'type', label: 'Type', sortable: true },\n    { key: 'name', label: 'Step', sortable: true },\n    { key: 'sourceSampleId', label: 'Source', sortable: true },\n    { key: 'sourceWellId', label: 'Source well', sortable: true },\n    { key: 'destinationSampleId', label: 'Destination', sortable: true },\n    { key: 'destinationWellId', label: 'Destination well', sortable: true },\n    { key: 'reagentId', label: 'Reagent', sortable: true },\n    { key: 'inputVolume', label: 'Input', sortable: true, align: 'right' },\n    { key: 'outputVolume', label: 'Output', sortable: true, align: 'right' },\n    { key: 'volumeUnit', label: 'Unit', sortable: true },\n    { key: 'status', label: 'Status', sortable: true },\n  ]\n}\n\nexport function toSamplePrepDataFrame(\n  template: SamplePrepTemplate | SamplePrepTemplateData\n): SamplePrepDataFrameAdapterResult {\n  return {\n    data: toSamplePrepRows(template),\n    columns: toSamplePrepColumns(),\n    rowKey: 'id',\n  }\n}\n","import type {\n  DataFrameColumn,\n  SelectOption,\n} from '../types'\nimport { getTemplateData } from './templateEnvelopes'\nimport { validateSampleSheetData } from './templateValidators'\nimport type {\n  SampleColumnsAdapterResult,\n  SampleDataFrameAdapterResult,\n  SampleOptionsAdapterResult,\n  SampleRowsAdapterResult,\n  SampleSheetTemplate,\n  SampleSheetTemplateData,\n} from './types'\n\nexport function toSampleRows(\n  template: SampleSheetTemplate | SampleSheetTemplateData\n): SampleRowsAdapterResult {\n  const data = getTemplateData(template, 'sample-sheet')\n  validateSampleSheetData(data)\n  return data.samples.map(sample => ({\n    sampleId: sample.sampleId,\n    name: sample.name,\n    group: sample.group,\n    batch: sample.batch,\n    replicate: sample.replicate,\n    plateId: sample.plateId,\n    wellId: sample.wellId,\n    ...(sample.metadata ?? {}),\n  }))\n}\n\nexport function toSampleColumns(\n  template: SampleSheetTemplate | SampleSheetTemplateData\n): SampleColumnsAdapterResult {\n  const data = getTemplateData(template, 'sample-sheet')\n  validateSampleSheetData(data)\n  return data.columns.map((column): DataFrameColumn<Record<string, unknown>> => ({\n    key: sampleColumnKey(column.id),\n    label: column.label,\n    sortable: true,\n    align: column.type === 'number' || column.type === 'integer' ? 'right' : 'left',\n  }))\n}\n\nexport function toSampleDataFrame(\n  template: SampleSheetTemplate | SampleSheetTemplateData\n): SampleDataFrameAdapterResult {\n  return {\n    data: toSampleRows(template),\n    columns: toSampleColumns(template),\n    rowKey: 'sampleId',\n  }\n}\n\nexport function toSampleOptions(\n  template: SampleSheetTemplate | SampleSheetTemplateData\n): SampleOptionsAdapterResult {\n  const data = getTemplateData(template, 'sample-sheet')\n  validateSampleSheetData(data)\n  return data.samples.map((sample): SelectOption<string> => ({\n    value: sample.sampleId,\n    label: sample.name ?? sample.sampleId,\n    description: [sample.group, sample.batch].filter(Boolean).join(' / ') || undefined,\n  }))\n}\n\nfunction sampleColumnKey(columnId: string): string {\n  const aliases: Record<string, string> = {\n    sample_id: 'sampleId',\n    plate_id: 'plateId',\n    well_id: 'wellId',\n  }\n  return aliases[columnId] ?? columnId\n}\n","import { getTemplateData } from './templateEnvelopes'\nimport { validateTimeCourseData } from './templateValidators'\nimport type {\n  TimeCourseColumnsAdapterResult,\n  TimeCourseDataFrameAdapterResult,\n  TimeCourseRowsAdapterResult,\n  TimeCourseStepsAdapterResult,\n  TimeCourseTemplate,\n  TimeCourseTemplateData,\n} from './types'\n\nexport function toTimeCourseRows(\n  template: TimeCourseTemplate | TimeCourseTemplateData\n): TimeCourseRowsAdapterResult {\n  const data = getTemplateData(template, 'time-course')\n  validateTimeCourseData(data)\n  const timepoints = new Map(data.timepoints.map(timepoint => [timepoint.id, timepoint]))\n  const conditions = new Map(data.conditions.map(condition => [condition.id, condition]))\n\n  return data.samples.map(sample => {\n    const timepoint = timepoints.get(sample.timepointId)\n    const condition = conditions.get(sample.conditionId)\n    return {\n      sampleId: sample.sampleId,\n      condition: condition?.name ?? sample.conditionId,\n      timepoint: timepoint?.label ?? sample.timepointId,\n      value: timepoint?.value,\n      unit: timepoint?.unit,\n      replicate: sample.replicate,\n      ...(sample.metadata ?? {}),\n    }\n  })\n}\n\nexport function toTimeCourseColumns(): TimeCourseColumnsAdapterResult {\n  return [\n    { key: 'sampleId', label: 'Sample ID', sortable: true },\n    { key: 'condition', label: 'Condition', sortable: true },\n    { key: 'timepoint', label: 'Time Point', sortable: true },\n    { key: 'value', label: 'Value', sortable: true, align: 'right' },\n    { key: 'unit', label: 'Unit', sortable: true },\n    { key: 'replicate', label: 'Replicate', sortable: true, align: 'right' },\n  ]\n}\n\nexport function toTimeCourseDataFrame(\n  template: TimeCourseTemplate | TimeCourseTemplateData\n): TimeCourseDataFrameAdapterResult {\n  return {\n    data: toTimeCourseRows(template),\n    columns: toTimeCourseColumns(),\n    rowKey: 'sampleId',\n  }\n}\n\nexport function toTimeCourseSteps(\n  template: TimeCourseTemplate | TimeCourseTemplateData\n): TimeCourseStepsAdapterResult {\n  const data = getTemplateData(template, 'time-course')\n  validateTimeCourseData(data)\n  return data.timepoints.map((timepoint, index) => ({\n    id: timepoint.id,\n    type: 'measurement',\n    name: timepoint.label,\n    description: `${data.conditions.length} condition${data.conditions.length === 1 ? '' : 's'}`,\n    status: 'pending',\n    order: index,\n    parameters: {\n      value: timepoint.value,\n      unit: timepoint.unit,\n    },\n  }))\n}\n","import type {\n  PlateMapEditorState,\n} from '../types'\nimport { getTemplateData } from './templateEnvelopes'\nimport { validatePlateMapData } from './templateValidators'\nimport type {\n  PlateMapEditorAdapterResult,\n  PlateMapTemplate,\n  PlateMapTemplateData,\n  WellMapAdapterResult,\n} from './types'\n\nexport function toPlateMapEditorState(\n  template: PlateMapTemplate | PlateMapTemplateData\n): PlateMapEditorAdapterResult {\n  const data = getTemplateData(template, 'plate-map')\n  validatePlateMapData(data)\n  const activePlateId = data.activePlateId ?? data.plates[0].id\n  return {\n    plates: data.plates,\n    activePlateId,\n    samples: data.samples,\n    selectedWells: data.selectedWells ?? [],\n    activeSampleId: data.activeSampleId,\n  } satisfies PlateMapEditorState\n}\n\nexport function toWellPlateWells(\n  template: PlateMapTemplate | PlateMapTemplateData,\n  plateId?: string\n): WellMapAdapterResult {\n  const state = toPlateMapEditorState(template)\n  const plate = state.plates.find(candidate => candidate.id === (plateId ?? state.activePlateId))\n    ?? state.plates[0]\n  return plate.wells\n}\n","import type {\n  PlateCondition,\n  PlateMapEditorState,\n} from '../types'\nimport { toPlateMapEditorState } from './plateMapAdapters'\nimport { getTemplateData } from './templateEnvelopes'\nimport { validateDoseResponseData } from './templateValidators'\nimport type {\n  DoseConditionsAdapterResult,\n  DoseResponseTemplate,\n  DoseResponseTemplateData,\n} from './types'\n\nconst CONDITION_COLORS = [\n  '#3B82F6',\n  '#10B981',\n  '#EF4444',\n  '#F59E0B',\n  '#8B5CF6',\n  '#F97316',\n  '#06B6D4',\n  '#14B8A6',\n  '#6B7280',\n]\n\nexport function toDoseConditions(\n  template: DoseResponseTemplate | DoseResponseTemplateData\n): DoseConditionsAdapterResult {\n  const data = getTemplateData(template, 'dose-response')\n  validateDoseResponseData(data)\n  return data.compounds.map((compound, index): PlateCondition => ({\n    label: compound.name,\n    color: String(compound.metadata?.color ?? CONDITION_COLORS[index % CONDITION_COLORS.length]),\n    concentrations: compound.concentrations,\n    unit: data.unit,\n  }))\n}\n\nexport function toDoseLayoutState(\n  template: DoseResponseTemplate | DoseResponseTemplateData\n): PlateMapEditorState | undefined {\n  const data = getTemplateData(template, 'dose-response')\n  validateDoseResponseData(data)\n  return data.layout ? toPlateMapEditorState(data.layout) : undefined\n}\n","import type { Well } from '../types'\nimport type {\n  AssayMatrixTemplate,\n  BioTemplateEnvelope,\n  CalibrationCurveTemplate,\n  DataFrameTemplate,\n  FlowCytometryPanelTemplate,\n  InstrumentRunTemplate,\n  ProtocolStepsTemplate,\n  QpcrPlateTemplate,\n  ReagentListTemplate,\n  SamplePrepTemplate,\n  SampleSheetTemplate,\n  TimeCourseTemplate,\n  TemplateDataFrameAdapterResult,\n} from './types'\nimport { toAssayMatrixDataFrame } from './assayMatrixAdapters'\nimport { toCalibrationCurveDataFrame } from './calibrationCurveAdapters'\nimport { toFlowPanelDataFrame } from './flowPanelAdapters'\nimport { toInstrumentRunDataFrame } from './instrumentRunAdapters'\nimport { toProtocolDataFrame } from './protocolAdapters'\nimport { toQpcrDataFrame } from './qpcrAdapters'\nimport { toReagentDataFrame } from './reagentAdapters'\nimport { toSamplePrepDataFrame } from './samplePrepAdapters'\nimport { toSampleDataFrame } from './sampleSheetAdapters'\nimport { toTimeCourseDataFrame } from './timeCourseAdapters'\n\nexport {\n  toAssayMatrixColumns,\n  toAssayMatrixDataFrame,\n  toAssayMatrixRows,\n  toAssayMatrixSampleOptions,\n} from './assayMatrixAdapters'\n\nexport {\n  toCalibrationCurveColumns,\n  toCalibrationCurveDataFrame,\n  toCalibrationCurveRows,\n} from './calibrationCurveAdapters'\n\nexport {\n  toDoseConditions,\n  toDoseLayoutState,\n} from './doseResponseAdapters'\n\nexport {\n  toFlowPanelColumns,\n  toFlowPanelDataFrame,\n  toFlowPanelRows,\n} from './flowPanelAdapters'\n\nexport {\n  toInstrumentRunColumns,\n  toInstrumentRunDataFrame,\n  toInstrumentRunRows,\n  toInstrumentRunScheduleEvents,\n  toInstrumentRunSteps,\n} from './instrumentRunAdapters'\n\nexport {\n  toPlateMapEditorState,\n  toWellPlateWells,\n} from './plateMapAdapters'\n\nexport {\n  toProtocolColumns,\n  toProtocolDataFrame,\n  toProtocolRows,\n  toProtocolSteps,\n} from './protocolAdapters'\n\nexport {\n  toQpcrColumns,\n  toQpcrDataFrame,\n  toQpcrRows,\n  toQpcrWellPlateWells,\n} from './qpcrAdapters'\n\nexport {\n  toReagentColumns,\n  toReagentDataFrame,\n  toReagentListItems,\n  toReagentRows,\n} from './reagentAdapters'\n\nexport {\n  toSamplePrepColumns,\n  toSamplePrepDataFrame,\n  toSamplePrepRows,\n} from './samplePrepAdapters'\n\nexport {\n  toSampleColumns,\n  toSampleDataFrame,\n  toSampleOptions,\n  toSampleRows,\n} from './sampleSheetAdapters'\n\nexport {\n  toTimeCourseColumns,\n  toTimeCourseDataFrame,\n  toTimeCourseRows,\n  toTimeCourseSteps,\n} from './timeCourseAdapters'\n\nexport function toTemplateDataFrame(\n  template: DataFrameTemplate | BioTemplateEnvelope<unknown>\n): TemplateDataFrameAdapterResult {\n  switch (template.template_id) {\n    case 'sample-sheet':\n      return toSampleDataFrame(template as SampleSheetTemplate)\n    case 'sample-prep':\n      return toSamplePrepDataFrame(template as SamplePrepTemplate)\n    case 'calibration-curve':\n      return toCalibrationCurveDataFrame(template as CalibrationCurveTemplate)\n    case 'time-course':\n      return toTimeCourseDataFrame(template as TimeCourseTemplate)\n    case 'protocol-steps':\n      return toProtocolDataFrame(template as ProtocolStepsTemplate)\n    case 'assay-matrix':\n      return toAssayMatrixDataFrame(template as AssayMatrixTemplate)\n    case 'reagent-list':\n      return toReagentDataFrame(template as ReagentListTemplate)\n    case 'flow-cytometry-panel':\n      return toFlowPanelDataFrame(template as FlowCytometryPanelTemplate)\n    case 'instrument-run':\n      return toInstrumentRunDataFrame(template as InstrumentRunTemplate)\n    case 'qpcr-plate':\n      return toQpcrDataFrame(template as QpcrPlateTemplate)\n    default:\n      throw new Error(`Template '${String(template.template_id)}' does not expose a DataFrame adapter.`)\n  }\n}\n\nexport function toWellMapArray(wells: Record<string, Well>): Well[] {\n  return Object.values(wells)\n}\n","import type {\n  PlateMapEditorState,\n  WellLegendItem,\n} from '../types'\n\nexport function activePlateFromState(state: PlateMapEditorState) {\n  return state.plates.find(plate => plate.id === state.activePlateId) ?? state.plates[0]\n}\n\nexport function sampleColorsFromPlateState(state: PlateMapEditorState): Record<string, string> {\n  return Object.fromEntries(\n    state.samples\n      .filter(sample => sample.color)\n      .map(sample => [sample.id, sample.color as string])\n  )\n}\n\nexport function legendItemsFromPlateState(state: PlateMapEditorState): WellLegendItem[] {\n  return state.samples.map((sample, index) => ({\n    type: sample.id,\n    label: sample.name,\n    color: sample.color ?? colorForIndex(index),\n  }))\n}\n\nexport function colorForIndex(index: number): string {\n  const colors = ['#3B82F6', '#10B981', '#EF4444', '#F59E0B', '#8B5CF6', '#F97316', '#06B6D4', '#14B8A6']\n  return colors[index % colors.length]\n}\n","import { cloneBinding } from './componentBindingHelpers'\nimport { templateComponentBindings } from './componentBindingCatalog'\nimport type {\n  BioTemplateComponentPropsBinding,\n} from './componentBindings'\nimport type { TemplateId } from './types'\n\nexport function propsBinding(\n  templateId: TemplateId,\n  component: string,\n  propsObject: Record<string, unknown>\n): BioTemplateComponentPropsBinding {\n  const matched = templateComponentBindings[templateId].find(binding => binding.component === component)\n  if (!matched) {\n    throw new Error(`No component binding registered for '${templateId}' and '${component}'.`)\n  }\n  return {\n    ...cloneBinding(matched),\n    propsObject,\n  }\n}\n","import {\n  toDoseConditions,\n  toDoseLayoutState,\n} from './adapters'\nimport {\n  activePlateFromState,\n  sampleColorsFromPlateState,\n} from './componentPlateHelpers'\nimport { propsBinding } from './componentPropsFactory'\nimport type { BioTemplateComponentPropsBinding } from './componentBindings'\nimport type { DoseResponseTemplate } from './types'\n\nexport function doseResponseProps(template: DoseResponseTemplate): BioTemplateComponentPropsBinding[] {\n  const conditions = toDoseConditions(template)\n  const layout = toDoseLayoutState(template)\n  const targetWells = layout ? Object.keys(activePlateFromState(layout).wells) : []\n  const props = [\n    propsBinding('dose-response', 'DoseCalculator', {\n      mode: 'serial',\n      targetWells,\n      disabled: conditions.length === 0,\n    }),\n  ]\n\n  if (layout) {\n    const plate = activePlateFromState(layout)\n    props.push(propsBinding('dose-response', 'WellPlate', {\n      format: plate.format,\n      wells: plate.wells,\n      sampleColors: sampleColorsFromPlateState(layout),\n      legendItems: conditions.map(condition => ({\n        type: condition.label,\n        label: condition.label,\n        color: condition.color,\n      })),\n      showLegend: true,\n      showSampleTypeIndicator: true,\n    }))\n  }\n\n  return props\n}\n","import {\n  toAssayMatrixSampleOptions,\n  toInstrumentRunScheduleEvents,\n  toReagentListItems,\n  toSampleOptions,\n  toTemplateDataFrame,\n} from './adapters'\nimport { propsBinding } from './componentPropsFactory'\nimport type { BioTemplateComponentPropsBinding } from './componentBindings'\nimport type {\n  AssayMatrixTemplate,\n  DataFrameTemplate,\n  InstrumentRunTemplate,\n  ProtocolStepsTemplate,\n  ReagentListTemplate,\n  SampleSheetTemplate,\n  TemplateId,\n  TimeCourseTemplate,\n} from './types'\n\nexport function dataFrameProps(template: DataFrameTemplate): BioTemplateComponentPropsBinding {\n  const frame = toTemplateDataFrame(template)\n  return propsBinding(template.template_id as TemplateId, 'DataFrame', {\n    ...frame,\n    searchable: true,\n    sortable: true,\n    size: 'sm',\n  })\n}\n\nexport function sampleSelectorProps(template: SampleSheetTemplate): BioTemplateComponentPropsBinding {\n  const options = toSampleOptions(template)\n  return propsBinding('sample-sheet', 'SampleSelector', {\n    samples: options.map(option => option.label),\n    modelValue: [],\n  })\n}\n\nexport function assayMatrixSampleSelectorProps(template: AssayMatrixTemplate): BioTemplateComponentPropsBinding {\n  const options = toAssayMatrixSampleOptions(template)\n  return propsBinding('assay-matrix', 'SampleSelector', {\n    samples: options.map(option => option.label),\n    modelValue: [],\n  })\n}\n\nexport function timelineProps(\n  template: TimeCourseTemplate | ProtocolStepsTemplate | InstrumentRunTemplate,\n  steps: unknown[],\n  editable = false\n): BioTemplateComponentPropsBinding {\n  return propsBinding(template.template_id as TemplateId, 'ExperimentTimeline', {\n    modelValue: steps,\n    orientation: 'vertical',\n    editable,\n  })\n}\n\nexport function scheduleCalendarProps(template: InstrumentRunTemplate): BioTemplateComponentPropsBinding {\n  const events = toInstrumentRunScheduleEvents(template)\n  return propsBinding('instrument-run', 'ScheduleCalendar', {\n    modelValue: events[0]?.start,\n    events,\n    view: 'day',\n    readonly: true,\n    showNavigation: false,\n    showViewToggle: false,\n  })\n}\n\nexport function reagentListProps(template: ReagentListTemplate): BioTemplateComponentPropsBinding {\n  return propsBinding('reagent-list', 'ReagentList', {\n    modelValue: toReagentListItems(template),\n    searchable: true,\n    sortable: true,\n  })\n}\n","import {\n  toPlateMapEditorState,\n  toWellPlateWells,\n} from './adapters'\nimport {\n  activePlateFromState,\n  legendItemsFromPlateState,\n  sampleColorsFromPlateState,\n} from './componentPlateHelpers'\nimport { propsBinding } from './componentPropsFactory'\nimport type { BioTemplateComponentPropsBinding } from './componentBindings'\nimport type { PlateMapTemplate } from './types'\n\nexport function plateMapProps(template: PlateMapTemplate): BioTemplateComponentPropsBinding[] {\n  const state = toPlateMapEditorState(template)\n  const plate = activePlateFromState(state)\n  return [\n    propsBinding('plate-map', 'PlateMapEditor', {\n      modelValue: state,\n      format: plate.format,\n      samples: state.samples,\n    }),\n    propsBinding('plate-map', 'WellPlate', {\n      format: plate.format,\n      wells: toWellPlateWells(template),\n      sampleColors: sampleColorsFromPlateState(state),\n      legendItems: legendItemsFromPlateState(state),\n      showLegend: true,\n      showSampleTypeIndicator: true,\n    }),\n  ]\n}\n","import type { WellLegendItem } from '../types'\nimport { toQpcrWellPlateWells } from './adapters'\nimport { colorForIndex } from './componentPlateHelpers'\nimport { getTemplateData } from './templateEnvelopes'\nimport { dataFrameProps } from './componentGenericProps'\nimport { propsBinding } from './componentPropsFactory'\nimport type { BioTemplateComponentPropsBinding } from './componentBindings'\nimport type { QpcrPlateTemplate } from './types'\n\nexport function qpcrPlateProps(template: QpcrPlateTemplate): BioTemplateComponentPropsBinding[] {\n  const data = getTemplateData(template, 'qpcr-plate')\n  const frame = dataFrameProps(template)\n  return [\n    propsBinding('qpcr-plate', 'WellPlate', {\n      format: data.format,\n      wells: toQpcrWellPlateWells(template),\n      sampleColors: Object.fromEntries(data.samples.map((sample, index) => [sample.sampleId, colorForIndex(index)])),\n      legendItems: data.samples.map((sample, index): WellLegendItem => ({\n        type: sample.sampleId,\n        label: sample.name ?? sample.sampleId,\n        color: colorForIndex(index),\n      })),\n      showLegend: true,\n      showSampleTypeIndicator: true,\n    }),\n    frame,\n  ]\n}\n","import {\n  toInstrumentRunSteps,\n  toProtocolSteps,\n  toTimeCourseSteps,\n} from './adapters'\nimport { doseResponseProps } from './componentDoseResponseProps'\nimport {\n  assayMatrixSampleSelectorProps,\n  dataFrameProps,\n  reagentListProps,\n  sampleSelectorProps,\n  scheduleCalendarProps,\n  timelineProps,\n} from './componentGenericProps'\nimport { plateMapProps } from './componentPlateMapProps'\nimport { qpcrPlateProps } from './componentQpcrPlateProps'\nimport type { BioTemplateComponentPropsBinding } from './componentBindings'\nimport type {\n  AssayMatrixTemplate,\n  BioTemplateEnvelope,\n  DataFrameTemplate,\n  DoseResponseTemplate,\n  InstrumentRunTemplate,\n  PlateMapTemplate,\n  ProtocolStepsTemplate,\n  QpcrPlateTemplate,\n  ReagentListTemplate,\n  SampleSheetTemplate,\n  TimeCourseTemplate,\n} from './types'\n\nexport function propsForTemplate(template: BioTemplateEnvelope<unknown>): BioTemplateComponentPropsBinding[] {\n  switch (template.template_id) {\n    case 'plate-map':\n      return plateMapProps(template as PlateMapTemplate)\n    case 'sample-sheet':\n      return [\n        dataFrameProps(template as DataFrameTemplate),\n        sampleSelectorProps(template as SampleSheetTemplate),\n      ]\n    case 'sample-prep':\n    case 'calibration-curve':\n    case 'flow-cytometry-panel':\n      return [dataFrameProps(template as DataFrameTemplate)]\n    case 'assay-matrix':\n      return [\n        dataFrameProps(template as DataFrameTemplate),\n        assayMatrixSampleSelectorProps(template as AssayMatrixTemplate),\n      ]\n    case 'instrument-run':\n      return [\n        dataFrameProps(template as DataFrameTemplate),\n        scheduleCalendarProps(template as InstrumentRunTemplate),\n        timelineProps(template as InstrumentRunTemplate, toInstrumentRunSteps(template as InstrumentRunTemplate)),\n      ]\n    case 'dose-response':\n      return doseResponseProps(template as DoseResponseTemplate)\n    case 'time-course':\n      return [\n        timelineProps(template as TimeCourseTemplate, toTimeCourseSteps(template as TimeCourseTemplate)),\n        dataFrameProps(template as DataFrameTemplate),\n      ]\n    case 'protocol-steps':\n      return [\n        timelineProps(template as ProtocolStepsTemplate, toProtocolSteps(template as ProtocolStepsTemplate), true),\n        dataFrameProps(template as DataFrameTemplate),\n      ]\n    case 'reagent-list':\n      return [\n        reagentListProps(template as ReagentListTemplate),\n        dataFrameProps(template as DataFrameTemplate),\n      ]\n    case 'qpcr-plate':\n      return qpcrPlateProps(template as QpcrPlateTemplate)\n    default:\n      return []\n  }\n}\n","import { extractTemplateCollection } from './templateEnvelopes'\nimport {\n  isTemplateEnvelope,\n  resolveComponentTemplateIds,\n} from './componentTargetResolvers'\nimport {\n  cloneBinding,\n  cloneBindingMap,\n  cloneBindings,\n  toVueSfc,\n  uniquePropsName,\n} from './componentBindingHelpers'\nimport { templateComponentBindings } from './componentBindingCatalog'\nimport { propsForTemplate } from './componentTemplateProps'\nimport type {\n  BioTemplateEnvelope,\n  TemplateCollectionEnvelope,\n  TemplateId,\n  TemplatePackId,\n  TemplatePresetId,\n} from './types'\n\nexport type BioTemplateComponentTarget =\n  | TemplateId\n  | TemplatePackId\n  | TemplatePresetId\n  | string\n  | BioTemplateEnvelope<unknown>\n  | TemplateCollectionEnvelope\n\nexport interface BioTemplateComponentBinding {\n  id: string\n  template_id: TemplateId\n  component: string\n  adapters: readonly string[]\n  props: readonly string[]\n  description: string\n  importPath: '@morscherlab/mint-sdk'\n}\n\nexport interface BioTemplateComponentPropsBinding extends BioTemplateComponentBinding {\n  propsObject: Record<string, unknown>\n}\n\nexport interface BioTemplateResolvedComponentBinding extends Omit<BioTemplateComponentBinding, 'props'> {\n  /** Prop names advertised by the static template/component compatibility catalog. */\n  propNames: readonly string[]\n  /** Concrete props ready for direct `v-bind=\"componentBindingsById[id].props\"` use. */\n  props: Record<string, unknown>\n  /** Backward-compatible alias for callers that already consume componentProps entries. */\n  propsObject: Record<string, unknown>\n}\n\nexport type BioTemplateComponentBindingsById = Record<string, BioTemplateResolvedComponentBinding>\nexport type BioTemplateComponentPropsById = Record<string, Record<string, unknown>>\nexport type BioTemplateComponentPropsByComponent = Record<string, Record<string, unknown>[]>\n\nexport interface BioTemplateComponentPropsLookupOptions {\n  templateId?: TemplateId\n  id?: string\n}\n\nexport interface BioTemplateComponentImport {\n  importPath: BioTemplateComponentBinding['importPath']\n  components: string[]\n  statement: string\n}\n\nexport interface BioTemplateComponentSnippet extends BioTemplateComponentBinding {\n  propsName: string\n  propsExpression: string\n  template: string\n}\n\nexport interface BioTemplateComponentSnippetOptions {\n  propsVariable?: string\n}\n\nexport interface BioTemplateComponentUsageOptions extends BioTemplateComponentSnippetOptions {\n  targetExpression?: string\n  targetPropName?: string\n}\n\nexport interface BioTemplateComponentUsage {\n  imports: BioTemplateComponentImport[]\n  componentProps: BioTemplateComponentPropsBinding[]\n  snippets: BioTemplateComponentSnippet[]\n  propsDeclarations: string[]\n  scriptSetup: string\n  template: string\n  sfc: string\n}\n\nexport function listBioTemplateComponentBindings(): Record<TemplateId, BioTemplateComponentBinding[]> {\n  return cloneBindingMap(templateComponentBindings)\n}\n\nexport function getBioTemplateComponentBindings(\n  target: BioTemplateComponentTarget\n): BioTemplateComponentBinding[] {\n  const templateIds = resolveComponentTemplateIds(target)\n  return templateIds.flatMap(templateId => cloneBindings(templateComponentBindings[templateId]))\n}\n\nexport function toBioTemplateComponentProps(\n  target: BioTemplateEnvelope<unknown> | TemplateCollectionEnvelope\n): BioTemplateComponentPropsBinding[] {\n  if (isTemplateEnvelope(target)) {\n    return propsForTemplate(target)\n  }\n\n  const collection = extractTemplateCollection(target)\n  return Object.values(collection).flatMap(template => propsForTemplate(template))\n}\n\n/** Return resolved component bindings with concrete props for direct slot rendering. */\nexport function toBioTemplateComponentBindings(\n  target: BioTemplateEnvelope<unknown> | TemplateCollectionEnvelope,\n): BioTemplateResolvedComponentBinding[] {\n  return toBioTemplateComponentProps(target).map(toResolvedComponentBinding)\n}\n\n/** Return resolved component bindings keyed by stable template component id. */\nexport function toBioTemplateComponentBindingsById(\n  target: BioTemplateEnvelope<unknown> | TemplateCollectionEnvelope,\n): BioTemplateComponentBindingsById {\n  return Object.fromEntries(\n    toBioTemplateComponentBindings(target).map(binding => [binding.id, binding]),\n  )\n}\n\n/** Return component props keyed by stable binding id for direct `v-bind=\"componentPropsById[id]\"` use. */\nexport function toBioTemplateComponentPropsById(\n  target: BioTemplateEnvelope<unknown> | TemplateCollectionEnvelope,\n): BioTemplateComponentPropsById {\n  return Object.fromEntries(\n    toBioTemplateComponentProps(target).map(binding => [binding.id, binding.propsObject]),\n  )\n}\n\n/** Return component props grouped by SDK component name for direct WellPlate/DoseCalculator binding. */\nexport function toBioTemplateComponentPropsByComponent(\n  target: BioTemplateEnvelope<unknown> | TemplateCollectionEnvelope,\n): BioTemplateComponentPropsByComponent {\n  const grouped: BioTemplateComponentPropsByComponent = {}\n  for (const binding of toBioTemplateComponentProps(target)) {\n    const props = grouped[binding.component] ?? []\n    props.push(binding.propsObject)\n    grouped[binding.component] = props\n  }\n  return grouped\n}\n\n/** Return the first props object for an SDK component, optionally restricted by template id or binding id. */\nexport function getBioTemplateComponentProps(\n  target: BioTemplateEnvelope<unknown> | TemplateCollectionEnvelope,\n  component: string,\n  options: BioTemplateComponentPropsLookupOptions = {},\n): Record<string, unknown> | undefined {\n  return toBioTemplateComponentProps(target).find((binding) => {\n    if (binding.component !== component) return false\n    if (options.id !== undefined && binding.id !== options.id) return false\n    if (options.templateId !== undefined && binding.template_id !== options.templateId) return false\n    return true\n  })?.propsObject\n}\n\nfunction toResolvedComponentBinding(\n  binding: BioTemplateComponentPropsBinding,\n): BioTemplateResolvedComponentBinding {\n  const { props: propNames, propsObject, ...rest } = binding\n  return {\n    ...rest,\n    propNames,\n    props: propsObject,\n    propsObject,\n  }\n}\n\nexport function toBioTemplateComponentImports(\n  target: BioTemplateComponentTarget\n): BioTemplateComponentImport[] {\n  const groups = new Map<BioTemplateComponentBinding['importPath'], string[]>()\n\n  for (const binding of getBioTemplateComponentBindings(target)) {\n    const components = groups.get(binding.importPath) ?? []\n    if (!components.includes(binding.component)) components.push(binding.component)\n    groups.set(binding.importPath, components)\n  }\n\n  return Array.from(groups.entries()).map(([importPath, components]) => ({\n    importPath,\n    components,\n    statement: `import { ${components.join(', ')} } from '${importPath}'`,\n  }))\n}\n\nexport function toBioTemplateComponentSnippets(\n  target: BioTemplateEnvelope<unknown> | TemplateCollectionEnvelope,\n  options: BioTemplateComponentSnippetOptions = {}\n): BioTemplateComponentSnippet[] {\n  const propsVariable = options.propsVariable ?? 'componentProps'\n  const usedNames = new Map<string, number>()\n\n  return toBioTemplateComponentProps(target).map((binding, index) => {\n    const propsName = uniquePropsName(binding, usedNames)\n    const propsExpression = `${propsVariable}[${index}].propsObject`\n    return {\n      ...cloneBinding(binding),\n      propsName,\n      propsExpression,\n      template: `<${binding.component} v-bind=\"${propsExpression}\" />`,\n    }\n  })\n}\n\nexport function toBioTemplateComponentUsage(\n  target: BioTemplateEnvelope<unknown> | TemplateCollectionEnvelope,\n  options: BioTemplateComponentUsageOptions = {}\n): BioTemplateComponentUsage {\n  const propsVariable = options.propsVariable ?? 'componentProps'\n  const usesGeneratedTargetProp = options.targetExpression === undefined\n  const targetPropName = options.targetPropName ?? 'templateCollection'\n  const targetExpression = options.targetExpression ?? `props.${targetPropName}`\n  const componentProps = toBioTemplateComponentProps(target)\n  const snippets = toBioTemplateComponentSnippets(target, { propsVariable }).map(snippet => ({\n    ...snippet,\n    propsExpression: snippet.propsName,\n    template: `<${snippet.component} v-bind=\"${snippet.propsName}\" />`,\n  }))\n  const propsDeclarations = snippets.map(\n    (snippet, index) => `const ${snippet.propsName} = ${propsVariable}[${index}].propsObject`\n  )\n  const setupLines = [\n    ...(usesGeneratedTargetProp\n      ? [`const props = defineProps<{ ${targetPropName}: BioTemplateEnvelope<unknown> | TemplateCollectionEnvelope }>()`]\n      : []),\n    `const ${propsVariable} = toBioTemplateComponentProps(${targetExpression})`,\n    ...propsDeclarations,\n  ]\n  const imports = toBioTemplateComponentImports(target)\n  const template = snippets.map(snippet => snippet.template).join('\\n')\n\n  return {\n    imports,\n    componentProps,\n    snippets,\n    propsDeclarations,\n    scriptSetup: setupLines.join('\\n'),\n    template,\n    sfc: toVueSfc(imports, setupLines, template, usesGeneratedTargetProp),\n  }\n}\n","import {\n  readBoolean,\n  readInteger,\n  readNumber,\n  readNumberList,\n  readOptionalString,\n  readString,\n  readStringList,\n} from './builderReadUtils'\nimport { readPlateFormat } from './plateGeometry'\nimport { getBioTemplatePresetInfo } from './presets'\nimport type {\n  CreateElisaAssayCollectionOptions,\n  CreateFlowCytometryAssayCollectionOptions,\n  CreateLcmsBatchCollectionOptions,\n  CreateQpcrExpressionCollectionOptions,\n  CreateQpcrPlateTemplateOptions,\n  CreateSamplePrepTemplateOptions,\n  CreateTargetedMetabolomicsCollectionOptions,\n  CreateWellPlateScreenCollectionOptions,\n  CreateWesternBlotAssayCollectionOptions,\n  TemplatePresetId,\n} from './types'\n\nexport type BioTemplateControlValues = Record<string, unknown>\n\nexport function bioTemplatePresetControlValuesToOptions(\n  name: 'wellplate-screen',\n  values: BioTemplateControlValues\n): CreateWellPlateScreenCollectionOptions\nexport function bioTemplatePresetControlValuesToOptions(\n  name: 'qpcr-expression',\n  values: BioTemplateControlValues\n): CreateQpcrExpressionCollectionOptions\nexport function bioTemplatePresetControlValuesToOptions(\n  name: 'lcms-batch',\n  values: BioTemplateControlValues\n): CreateLcmsBatchCollectionOptions\nexport function bioTemplatePresetControlValuesToOptions(\n  name: 'targeted-metabolomics',\n  values: BioTemplateControlValues\n): CreateTargetedMetabolomicsCollectionOptions\nexport function bioTemplatePresetControlValuesToOptions(\n  name: 'elisa-assay',\n  values: BioTemplateControlValues\n): CreateElisaAssayCollectionOptions\nexport function bioTemplatePresetControlValuesToOptions(\n  name: 'flow-cytometry-assay',\n  values: BioTemplateControlValues\n): CreateFlowCytometryAssayCollectionOptions\nexport function bioTemplatePresetControlValuesToOptions(\n  name: 'western-blot-assay',\n  values: BioTemplateControlValues\n): CreateWesternBlotAssayCollectionOptions\nexport function bioTemplatePresetControlValuesToOptions(\n  name: TemplatePresetId | string,\n  values: BioTemplateControlValues\n):\n  | CreateWellPlateScreenCollectionOptions\n  | CreateQpcrExpressionCollectionOptions\n  | CreateLcmsBatchCollectionOptions\n  | CreateTargetedMetabolomicsCollectionOptions\n  | CreateElisaAssayCollectionOptions\n  | CreateFlowCytometryAssayCollectionOptions\n  | CreateWesternBlotAssayCollectionOptions\nexport function bioTemplatePresetControlValuesToOptions(\n  name: TemplatePresetId | string,\n  values: BioTemplateControlValues\n):\n  | CreateWellPlateScreenCollectionOptions\n  | CreateQpcrExpressionCollectionOptions\n  | CreateLcmsBatchCollectionOptions\n  | CreateTargetedMetabolomicsCollectionOptions\n  | CreateElisaAssayCollectionOptions\n  | CreateFlowCytometryAssayCollectionOptions\n  | CreateWesternBlotAssayCollectionOptions {\n  const preset = getBioTemplatePresetInfo(name)\n  if (!preset) {\n    throw new Error(`Unknown template preset '${name}'.`)\n  }\n\n  if (preset.name === 'wellplate-screen') {\n    return {\n      samples: readStringList(values.sampleNames, ['Control', 'Treatment']),\n      plateName: readString(values.plateName, 'Screen plate'),\n      plateFormat: readPlateFormat(values.plateFormat, 96),\n      unit: readString(values.unit, 'uM'),\n      replicates: readInteger(values.replicates, 3),\n    }\n  }\n\n  if (preset.name === 'qpcr-expression') {\n    return {\n      samples: readStringList(values.sampleNames, ['Control', 'Treatment']),\n      targets: readStringList(values.targets, ['ACTB', 'GAPDH']),\n      chemistry: readString(values.chemistry, 'sybr') as CreateQpcrPlateTemplateOptions['chemistry'],\n      format: readPlateFormat(values.plateFormat, 96),\n      includeNoTemplateControls: readBoolean(values.includeNoTemplateControls, true),\n      replicates: readInteger(values.replicates, 3),\n      instrument: readOptionalString(values.instrument),\n    }\n  }\n\n  if (preset.name === 'lcms-batch') {\n    return {\n      samples: readStringList(values.sampleNames, ['S001', 'S002']),\n      features: readStringList(values.featureNames, ['Glucose', 'Lactate']),\n      instrument: readString(values.instrument, 'LC-MS'),\n      method: readString(values.method, 'Default method'),\n      includeQc: readBoolean(values.includeQc, true),\n    }\n  }\n\n  if (preset.name === 'targeted-metabolomics') {\n    return {\n      samples: readStringList(values.sampleNames, ['S001', 'S002']),\n      metabolites: readStringList(values.metaboliteNames, ['Glucose', 'Lactate', 'Pyruvate']),\n      internalStandards: readStringList(\n        values.internalStandards,\n        ['Stable isotope internal standard mix'],\n      ),\n      standardConcentrations: readNumberList(values.standardConcentrations, [0.1, 1, 10, 100]),\n      concentrationUnit: readString(values.concentrationUnit, 'uM'),\n      responseUnit: readString(values.responseUnit, 'peak area ratio'),\n      calibrationAnalyte: readOptionalString(values.calibrationAnalyte),\n      instrument: readString(values.instrument, 'LC-MS'),\n      method: readString(values.method, 'Targeted metabolomics'),\n      prepType: readString(values.prepType, 'extraction') as CreateSamplePrepTemplateOptions['prepType'],\n      outputVolume: readNumber(values.outputVolume, 50),\n      includeQc: readBoolean(values.includeQc, true),\n    }\n  }\n\n  if (preset.name === 'elisa-assay') {\n    return {\n      samples: readStringList(values.sampleNames, ['Control', 'Treatment']),\n      analyte: readString(values.analyte, 'Analyte'),\n      standardConcentrations: readNumberList(values.standardConcentrations, [1000, 100, 10, 1]),\n      unit: readString(values.unit, 'pg/mL'),\n      responseUnit: readString(values.responseUnit, 'OD450'),\n      plateName: readString(values.plateName, 'ELISA plate'),\n      plateFormat: readPlateFormat(values.plateFormat, 96),\n    }\n  }\n\n  if (preset.name === 'flow-cytometry-assay') {\n    return {\n      samples: readStringList(values.sampleNames, ['Control', 'Treatment']),\n      markers: readStringList(values.markers, ['CD3', 'CD4', 'CD8']),\n      features: readStringList(values.featureNames, ['CD3+ cells', 'CD4+ cells', 'CD8+ cells']),\n      instrument: readString(values.instrument, 'Flow cytometer'),\n      includeDefaultControls: readBoolean(values.includeDefaultControls, true),\n    }\n  }\n\n  if (preset.name === 'western-blot-assay') {\n    return {\n      samples: readStringList(values.sampleNames, ['Control', 'Treatment']),\n      targets: readStringList(values.targets, ['Target protein']),\n      loadingControl: readString(values.loadingControl, 'ACTB'),\n    }\n  }\n\n  throw new Error(`Unknown template preset '${name}'.`)\n}\n","export const DEFAULT_SAMPLE_COLORS = [\n  '#3B82F6',\n  '#10B981',\n  '#EF4444',\n  '#F59E0B',\n  '#8B5CF6',\n  '#F97316',\n  '#06B6D4',\n  '#14B8A6',\n  '#6B7280',\n]\n","export function sampleIdFromName(name: string, index: number): string {\n  return idFromName(name, `sample-${index + 1}`)\n}\n\nexport function compoundIdFromName(name: string, index: number): string {\n  return idFromName(name, `compound-${index + 1}`)\n}\n\nexport function idFromName(name: string, fallback: string): string {\n  const slug = name.toLowerCase().replace(/[^a-z0-9]+/g, '-').replace(/^-|-$/g, '')\n  return slug || fallback\n}\n\nexport function timepointId(value: number, unit: string, index: number): string {\n  const raw = Number.isInteger(value)\n    ? String(value)\n    : String(value).replace(/0+$/, '').replace(/\\.$/, '')\n  const token = raw.replace('.', 'p')\n  return token ? `t${token}-${unit}` : `timepoint-${index + 1}`\n}\n","import { DEFAULT_SAMPLE_COLORS } from './builderDefaults'\nimport { sampleIdFromName } from './builderIdUtils'\nimport { createTemplateEnvelope } from './templateEnvelopes'\nimport type {\n  CreatePlateMapTemplateOptions,\n  PlateMapTemplate,\n  TemplateSample,\n} from './types'\n\nexport function createPlateMapTemplate(\n  options: CreatePlateMapTemplateOptions = {}\n): PlateMapTemplate {\n  const {\n    id = 'plate-1',\n    name = 'Plate 1',\n    format = 96,\n    samples = [],\n    metadata = {},\n  } = options\n\n  const sampleDefinitions = samples.map((sample, index): TemplateSample => {\n    if (typeof sample !== 'string') return sample\n    return {\n      id: sampleIdFromName(sample, index),\n      name: sample,\n      color: DEFAULT_SAMPLE_COLORS[index % DEFAULT_SAMPLE_COLORS.length],\n    }\n  })\n\n  return createTemplateEnvelope('plate-map', {\n    plates: [\n      {\n        id,\n        name,\n        format,\n        wells: {},\n      },\n    ],\n    samples: sampleDefinitions,\n    activePlateId: id,\n    selectedWells: [],\n  }, metadata)\n}\n","import type {\n  SamplePrepStep,\n  SamplePrepStepInput,\n  SampleRecord,\n} from './types'\nimport {\n  idFromName,\n  sampleIdFromName,\n} from './builderIdUtils'\n\nexport function normalizeSampleRecord(sample: SampleRecord): SampleRecord {\n  return {\n    ...sample,\n    metadata: sample.metadata ?? {},\n  }\n}\n\nexport function presetSampleRecords(samples: Array<string | SampleRecord>): SampleRecord[] {\n  return samples.map((sample, index) => {\n    if (typeof sample !== 'string') return normalizeSampleRecord(sample)\n    return {\n      sampleId: sampleIdFromName(sample, index),\n      name: sample,\n      metadata: {},\n    }\n  })\n}\n\nexport function normalizeSamplePrepStep(\n  step: SamplePrepStepInput,\n  prepType: SamplePrepStep['type'],\n  volumeUnit: string,\n  order: number,\n  index: number\n): SamplePrepStep {\n  const type = step.type ?? prepType\n  const sourceSampleId = step.sourceSampleId\n  const name = step.name || `Prepare ${sourceSampleId ?? index + 1}`\n  return {\n    id: step.id || idFromName(name, `${type}-${index + 1}`),\n    order: step.order ?? order,\n    type,\n    name,\n    sourceSampleId,\n    sourcePlateId: step.sourcePlateId,\n    sourceWellId: step.sourceWellId,\n    destinationSampleId: step.destinationSampleId,\n    destinationPlateId: step.destinationPlateId,\n    destinationWellId: step.destinationWellId,\n    reagentId: step.reagentId,\n    inputVolume: step.inputVolume,\n    outputVolume: step.outputVolume,\n    volumeUnit: step.volumeUnit || volumeUnit,\n    durationMin: step.durationMin,\n    status: step.status ?? 'planned',\n    metadata: step.metadata ?? {},\n  }\n}\n","import { normalizeSampleRecord } from './sampleNormalizers'\nimport { createTemplateEnvelope } from './templateEnvelopes'\nimport { validateSampleSheetData } from './templateValidators'\nimport type {\n  CreateSampleSheetTemplateOptions,\n  SampleSheetTemplate,\n  SampleSheetTemplateData,\n} from './types'\n\nexport function createSampleSheetTemplate(\n  options: CreateSampleSheetTemplateOptions\n): SampleSheetTemplate {\n  const data: SampleSheetTemplateData = {\n    samples: options.samples.map(normalizeSampleRecord),\n    columns: options.columns ?? [\n      { id: 'sampleId', label: 'Sample ID', type: 'string', required: true, groupable: false },\n      { id: 'name', label: 'Name', type: 'string', required: false, groupable: false },\n    ],\n    groups: options.groups ?? [],\n  }\n  validateSampleSheetData(data)\n  return createTemplateEnvelope('sample-sheet', data, options.metadata ?? {})\n}\n","import { idFromName } from './builderIdUtils'\nimport { normalizeSamplePrepStep } from './sampleNormalizers'\nimport { createTemplateEnvelope } from './templateEnvelopes'\nimport { validateSamplePrepData } from './templateValidators'\nimport type {\n  CreateSamplePrepTemplateOptions,\n  SamplePrepStep,\n  SamplePrepTemplate,\n  SamplePrepTemplateData,\n} from './types'\n\nexport function createSamplePrepTemplate(\n  options: CreateSamplePrepTemplateOptions\n): SamplePrepTemplate {\n  const prepType = options.prepType ?? 'extraction'\n  const volumeUnit = options.volumeUnit ?? 'uL'\n  const steps: SamplePrepStep[] = []\n  let order = 1\n\n  for (const [index, sample] of options.samples.entries()) {\n    if (typeof sample !== 'string') {\n      const step = normalizeSamplePrepStep(sample, prepType, volumeUnit, order, index)\n      steps.push(step)\n      order = Math.max(order, step.order + 1)\n      continue\n    }\n    const sourceSampleId = idFromName(sample, `sample-${index + 1}`)\n    steps.push({\n      id: `${sourceSampleId}-prep`,\n      order,\n      type: prepType,\n      name: `Prepare ${sample}`,\n      sourceSampleId,\n      destinationSampleId: `${sourceSampleId}-prepared`,\n      inputVolume: options.inputVolume,\n      outputVolume: options.outputVolume,\n      volumeUnit,\n      status: 'planned',\n      metadata: {},\n    })\n    order += 1\n  }\n\n  const data: SamplePrepTemplateData = {\n    protocolName: options.protocolName ?? 'Sample preparation',\n    steps,\n    metadata: options.metadata ?? {},\n  }\n  validateSamplePrepData(data)\n  return createTemplateEnvelope('sample-prep', data, options.metadata ?? {})\n}\n","import type {\n  CalibrationAcceptance,\n  CalibrationPoint,\n  CalibrationPointInput,\n  CompoundDoseSeries,\n  ControlDefinition,\n} from './types'\nimport { idFromName } from './builderIdUtils'\n\nexport function normalizeCompound(compound: CompoundDoseSeries): CompoundDoseSeries {\n  return {\n    ...compound,\n    concentrations: [...compound.concentrations].sort((a, b) => b - a),\n    metadata: compound.metadata ?? {},\n  }\n}\n\nexport function normalizeCalibrationAcceptance(\n  acceptance?: Partial<CalibrationAcceptance>,\n  requireBlank = true\n): CalibrationAcceptance {\n  return {\n    minRSquared: acceptance?.minRSquared ?? 0.99,\n    standardTolerancePercent: acceptance?.standardTolerancePercent ?? 15,\n    qcTolerancePercent: acceptance?.qcTolerancePercent ?? 20,\n    requireBlank: acceptance?.requireBlank ?? requireBlank,\n    metadata: acceptance?.metadata ?? {},\n  }\n}\n\nexport function normalizeCalibrationPoint(\n  point: CalibrationPointInput,\n  unit: string,\n  order: number,\n  index: number\n): CalibrationPoint {\n  const role = point.role ?? 'standard'\n  const level = point.level || `${role.charAt(0).toUpperCase()}${role.slice(1)} ${index + 1}`\n  return {\n    id: point.id || idFromName(level, `${role}-${index + 1}`),\n    order: point.order ?? order,\n    role,\n    level,\n    concentration: point.concentration ?? 0,\n    unit: point.unit || unit,\n    expectedResponse: point.expectedResponse,\n    response: point.response,\n    replicate: point.replicate ?? 1,\n    include: point.include ?? true,\n    status: point.status ?? 'planned',\n    metadata: point.metadata ?? {},\n  }\n}\n\nexport function normalizeControl(control: ControlDefinition): ControlDefinition {\n  return {\n    ...control,\n    metadata: control.metadata ?? {},\n  }\n}\n","import { compoundIdFromName } from './builderIdUtils'\nimport {\n  normalizeCompound,\n  normalizeControl,\n} from './calibrationNormalizers'\nimport {\n  createTemplateEnvelope,\n  getTemplateData,\n} from './templateEnvelopes'\nimport { validateDoseResponseData } from './templateValidators'\nimport type {\n  CreateDoseResponseTemplateOptions,\n  DoseResponseTemplate,\n  DoseResponseTemplateData,\n  PlateMapTemplateData,\n} from './types'\n\nexport function createDoseResponseTemplate(\n  options: CreateDoseResponseTemplateOptions\n): DoseResponseTemplate {\n  const compounds = Array.isArray(options.compounds)\n    ? options.compounds.map(normalizeCompound)\n    : Object.entries(options.compounds).map(([name, concentrations], index) => normalizeCompound({\n      id: compoundIdFromName(name, index),\n      name,\n      concentrations,\n      metadata: {},\n    }))\n\n  const layout = options.layout\n    ? getTemplateData<PlateMapTemplateData>(options.layout)\n    : undefined\n\n  const data: DoseResponseTemplateData = {\n    compounds,\n    unit: options.unit,\n    replicates: options.replicates ?? 1,\n    controls: (options.controls ?? []).map(normalizeControl),\n    layout,\n    metadata: options.metadata ?? {},\n  }\n  validateDoseResponseData(data)\n  return createTemplateEnvelope('dose-response', data, options.metadata ?? {})\n}\n","import { idFromName } from './builderIdUtils'\nimport {\n  normalizeCalibrationAcceptance,\n  normalizeCalibrationPoint,\n} from './calibrationNormalizers'\nimport { createTemplateEnvelope } from './templateEnvelopes'\nimport { validateCalibrationCurveData } from './templateValidators'\nimport type {\n  CalibrationCurveTemplate,\n  CalibrationCurveTemplateData,\n  CalibrationPoint,\n  CreateCalibrationCurveTemplateOptions,\n} from './types'\n\nexport function createCalibrationCurveTemplate(\n  options: CreateCalibrationCurveTemplateOptions\n): CalibrationCurveTemplate {\n  const unit = options.unit ?? 'uM'\n  const points: CalibrationPoint[] = []\n  let order = 1\n\n  if (options.includeBlank !== false) {\n    points.push({\n      id: 'blank',\n      order,\n      role: 'blank',\n      level: 'Blank',\n      concentration: 0,\n      unit,\n      replicate: 1,\n      include: true,\n      status: 'planned',\n      metadata: {},\n    })\n    order += 1\n  }\n\n  const standardValues: number[] = []\n  for (const [index, concentration] of options.concentrations.entries()) {\n    if (typeof concentration !== 'number') {\n      const point = normalizeCalibrationPoint(concentration, unit, order, index)\n      points.push(point)\n      if (point.role === 'standard') standardValues.push(point.concentration)\n      order = Math.max(order, point.order + 1)\n      continue\n    }\n    standardValues.push(concentration)\n    points.push({\n      id: `std-${index + 1}`,\n      order,\n      role: 'standard',\n      level: `Standard ${index + 1}`,\n      concentration,\n      unit,\n      replicate: 1,\n      include: true,\n      status: 'planned',\n      metadata: {},\n    })\n    order += 1\n  }\n\n  if (options.includeQc !== false) {\n    const positiveValues = [...standardValues].filter(value => value > 0).sort((a, b) => a - b)\n    const qcValues = positiveValues.length === 0\n      ? []\n      : positiveValues[0] === positiveValues[positiveValues.length - 1]\n        ? [positiveValues[0]]\n        : [positiveValues[0], positiveValues[positiveValues.length - 1]]\n    for (const [index, concentration] of qcValues.entries()) {\n      const level = index === 0 ? 'QC low' : 'QC high'\n      points.push({\n        id: idFromName(level, `qc-${index + 1}`),\n        order,\n        role: 'qc',\n        level,\n        concentration,\n        unit,\n        replicate: 1,\n        include: true,\n        status: 'planned',\n        metadata: {},\n      })\n      order += 1\n    }\n  }\n\n  const data: CalibrationCurveTemplateData = {\n    analyte: options.analyte ?? 'Analyte',\n    model: options.model ?? 'linear',\n    xUnit: unit,\n    responseUnit: options.responseUnit ?? 'response',\n    points,\n    acceptance: normalizeCalibrationAcceptance(options.acceptance, options.includeBlank !== false),\n    metadata: options.metadata ?? {},\n  }\n  validateCalibrationCurveData(data)\n  return createTemplateEnvelope('calibration-curve', data, options.metadata ?? {})\n}\n","import type {\n  ProtocolStepRecord,\n  TimeCourseCondition,\n  TimePoint,\n} from './types'\nimport { idFromName } from './builderIdUtils'\n\nexport function normalizeTimePoint(timepoint: TimePoint): TimePoint {\n  return {\n    ...timepoint,\n    metadata: timepoint.metadata ?? {},\n  }\n}\n\nexport function normalizeCondition(condition: TimeCourseCondition): TimeCourseCondition {\n  return {\n    ...condition,\n    metadata: condition.metadata ?? {},\n  }\n}\n\nexport function normalizeProtocolStep(\n  step: Partial<ProtocolStepRecord> & { name: string },\n  index: number\n): ProtocolStepRecord {\n  return {\n    id: step.id ?? idFromName(step.name, `step-${index + 1}`),\n    type: step.type ?? 'custom',\n    name: step.name,\n    description: step.description,\n    duration: step.duration,\n    status: step.status ?? 'pending',\n    parameters: step.parameters ?? {},\n    order: step.order ?? index,\n    metadata: step.metadata ?? {},\n  }\n}\n","import { DEFAULT_SAMPLE_COLORS } from './builderDefaults'\nimport {\n  idFromName,\n  timepointId,\n} from './builderIdUtils'\nimport {\n  normalizeCondition,\n  normalizeTimePoint,\n} from './protocolNormalizers'\nimport { createTemplateEnvelope } from './templateEnvelopes'\nimport { validateTimeCourseData } from './templateValidators'\nimport type {\n  CreateTimeCourseTemplateOptions,\n  TimeCourseCondition,\n  TimeCourseTemplate,\n  TimeCourseTemplateData,\n  TimePoint,\n} from './types'\n\nexport function createTimeCourseTemplate(\n  options: CreateTimeCourseTemplateOptions\n): TimeCourseTemplate {\n  const timepoints = options.timepoints.map((timepoint, index): TimePoint => {\n    if (typeof timepoint !== 'number') return normalizeTimePoint(timepoint)\n    return {\n      id: timepointId(timepoint, options.unit, index),\n      label: `${timepoint} ${options.unit}`,\n      value: timepoint,\n      unit: options.unit,\n      metadata: {},\n    }\n  }).sort((a, b) => a.value - b.value)\n\n  const conditions = options.conditions.map((condition, index): TimeCourseCondition => {\n    if (typeof condition !== 'string') return normalizeCondition(condition)\n    return {\n      id: idFromName(condition, `condition-${index + 1}`),\n      name: condition,\n      color: DEFAULT_SAMPLE_COLORS[index % DEFAULT_SAMPLE_COLORS.length],\n      metadata: {},\n    }\n  })\n\n  const samples = conditions.flatMap(condition =>\n    timepoints.flatMap(timepoint =>\n      Array.from({ length: options.replicates ?? 1 }, (_, index) => ({\n        sampleId: `${condition.id}-${timepoint.id}-r${index + 1}`,\n        conditionId: condition.id,\n        timepointId: timepoint.id,\n        replicate: index + 1,\n        metadata: {},\n      }))\n    )\n  )\n\n  const data: TimeCourseTemplateData = {\n    timepoints,\n    conditions,\n    samples,\n    metadata: options.metadata ?? {},\n  }\n  validateTimeCourseData(data)\n  return createTemplateEnvelope('time-course', data, options.metadata ?? {})\n}\n","import { idFromName } from './builderIdUtils'\nimport { normalizeProtocolStep } from './protocolNormalizers'\nimport { createTemplateEnvelope } from './templateEnvelopes'\nimport { validateProtocolStepsData } from './templateValidators'\nimport type {\n  CreateProtocolStepsTemplateOptions,\n  ProtocolStepRecord,\n  ProtocolStepsTemplate,\n  ProtocolStepsTemplateData,\n} from './types'\n\nexport function createProtocolStepsTemplate(\n  options: CreateProtocolStepsTemplateOptions\n): ProtocolStepsTemplate {\n  const steps = options.steps.map((step, index): ProtocolStepRecord => {\n    if (typeof step === 'string') {\n      return {\n        id: idFromName(step, `step-${index + 1}`),\n        type: 'custom',\n        name: step,\n        status: 'pending',\n        parameters: {},\n        order: index,\n        metadata: {},\n      }\n    }\n    return normalizeProtocolStep(step, index)\n  }).sort((a, b) => a.order - b.order)\n\n  const data: ProtocolStepsTemplateData = {\n    steps,\n    metadata: options.metadata ?? {},\n  }\n  validateProtocolStepsData(data)\n  return createTemplateEnvelope('protocol-steps', data, options.metadata ?? {})\n}\n","import type {\n  AssayFeature,\n  AssaySample,\n} from './types'\nimport { idFromName } from './builderIdUtils'\n\nexport function createAssaySampleLookup(samples: AssaySample[]): Map<string, string> {\n  const lookup = new Map<string, string>()\n  for (const sample of samples) {\n    addLookupAlias(lookup, sample.sampleId, sample.sampleId)\n    if (sample.name) {\n      addLookupAlias(lookup, sample.name, sample.sampleId)\n      addLookupAlias(lookup, idFromName(sample.name, sample.sampleId), sample.sampleId)\n    }\n  }\n  return lookup\n}\n\nexport function createAssayFeatureLookup(features: AssayFeature[]): Map<string, string> {\n  const lookup = new Map<string, string>()\n  for (const feature of features) {\n    addLookupAlias(lookup, feature.id, feature.id)\n    addLookupAlias(lookup, feature.name, feature.id)\n    addLookupAlias(lookup, idFromName(feature.name, feature.id), feature.id)\n  }\n  return lookup\n}\n\nfunction addLookupAlias(lookup: Map<string, string>, alias: string, value: string): void {\n  if (!lookup.has(alias)) {\n    lookup.set(alias, value)\n  }\n}\n","import type {\n  AssayFeature,\n  AssaySample,\n  ReagentRecord,\n  ReagentTemplateInput,\n} from './types'\n\nexport function normalizeAssaySample(sample: AssaySample): AssaySample {\n  return {\n    ...sample,\n    metadata: sample.metadata ?? {},\n  }\n}\n\nexport function normalizeAssayFeature(feature: AssayFeature): AssayFeature {\n  return {\n    ...feature,\n    metadata: feature.metadata ?? {},\n  }\n}\n\nexport function normalizeReagent(reagent: ReagentTemplateInput): ReagentRecord {\n  return {\n    ...reagent,\n    expiryDate: normalizeDateString(reagent.expiryDate),\n    kind: reagent.kind ?? 'reagent',\n    metadata: reagent.metadata ?? {},\n  }\n}\n\nfunction normalizeDateString(value: Date | string | null | undefined): string | undefined {\n  if (value === undefined || value === null) return undefined\n  return value instanceof Date ? value.toISOString() : value\n}\n","import {\n  createAssayFeatureLookup,\n  createAssaySampleLookup,\n} from './assayLookups'\nimport {\n  normalizeAssayFeature,\n  normalizeAssaySample,\n} from './assayNormalizers'\nimport { idFromName } from './builderIdUtils'\nimport { createTemplateEnvelope } from './templateEnvelopes'\nimport { validateAssayMatrixData } from './templateValidators'\nimport type {\n  AssayFeature,\n  AssayMatrixTemplate,\n  AssayMatrixTemplateData,\n  AssaySample,\n  CreateAssayMatrixTemplateOptions,\n} from './types'\n\nexport function createAssayMatrixTemplate(\n  options: CreateAssayMatrixTemplateOptions\n): AssayMatrixTemplate {\n  const samples = options.samples.map((sample, index): AssaySample => {\n    if (typeof sample !== 'string') return normalizeAssaySample(sample)\n    return {\n      sampleId: idFromName(sample, `sample-${index + 1}`),\n      name: sample,\n      metadata: {},\n    }\n  })\n  const features = options.features.map((feature, index): AssayFeature => {\n    if (typeof feature !== 'string') return normalizeAssayFeature(feature)\n    return {\n      id: idFromName(feature, `feature-${index + 1}`),\n      name: feature,\n      type: 'readout',\n      metadata: {},\n    }\n  })\n  const sampleLookup = createAssaySampleLookup(samples)\n  const featureLookup = createAssayFeatureLookup(features)\n  const measurements = Object.entries(options.values ?? {}).flatMap(([sampleId, featureValues]) =>\n    Object.entries(featureValues).map(([featureId, value]) => ({\n      sampleId: sampleLookup.get(sampleId) ?? sampleId,\n      featureId: featureLookup.get(featureId) ?? featureId,\n      value,\n      metadata: {},\n    }))\n  )\n\n  const data: AssayMatrixTemplateData = {\n    samples,\n    features,\n    measurements,\n    metadata: options.metadata ?? {},\n  }\n  validateAssayMatrixData(data)\n  return createTemplateEnvelope('assay-matrix', data, options.metadata ?? {})\n}\n","import { normalizeReagent } from './assayNormalizers'\nimport { idFromName } from './builderIdUtils'\nimport { createTemplateEnvelope } from './templateEnvelopes'\nimport { validateReagentListData } from './templateValidators'\nimport type {\n  CreateReagentListTemplateOptions,\n  ReagentListTemplate,\n  ReagentListTemplateData,\n  ReagentRecord,\n} from './types'\n\nexport function createReagentListTemplate(\n  options: CreateReagentListTemplateOptions\n): ReagentListTemplate {\n  const reagents = options.reagents.map((reagent, index): ReagentRecord => {\n    if (typeof reagent !== 'string') return normalizeReagent(reagent)\n    return {\n      id: idFromName(reagent, `reagent-${index + 1}`),\n      name: reagent,\n      kind: 'reagent',\n      metadata: {},\n    }\n  })\n  const data: ReagentListTemplateData = {\n    reagents,\n    metadata: options.metadata ?? {},\n  }\n  validateReagentListData(data)\n  return createTemplateEnvelope('reagent-list', data, options.metadata ?? {})\n}\n","import type {\n  FlowPanelControl,\n  FlowPanelMarker,\n} from './types'\nimport { idFromName } from './builderIdUtils'\n\nexport function normalizeFlowMarker(\n  marker: Partial<FlowPanelMarker> & { marker: string },\n  index: number\n): FlowPanelMarker {\n  return {\n    id: marker.id ?? idFromName(marker.marker, `marker-${index + 1}`),\n    marker: marker.marker,\n    fluorophore: marker.fluorophore ?? 'unassigned',\n    detector: marker.detector,\n    clone: marker.clone,\n    reagentId: marker.reagentId,\n    purpose: marker.purpose ?? 'phenotype',\n    compensationRequired: marker.compensationRequired ?? true,\n    metadata: marker.metadata ?? {},\n  }\n}\n\nexport function normalizeFlowControl(\n  control: Partial<FlowPanelControl> & { name: string },\n  index: number\n): FlowPanelControl {\n  return {\n    id: control.id ?? idFromName(control.name, `control-${index + 1}`),\n    name: control.name,\n    kind: control.kind ?? 'other',\n    markerId: control.markerId,\n    required: control.required ?? true,\n    metadata: control.metadata ?? {},\n  }\n}\n\nexport function defaultFlowControls(markers: FlowPanelMarker[]): FlowPanelControl[] {\n  return [\n    {\n      id: 'unstained',\n      name: 'Unstained',\n      kind: 'unstained',\n      required: true,\n      metadata: {},\n    },\n    ...markers\n      .filter(marker => marker.compensationRequired)\n      .map(marker => ({\n        id: `${marker.id}-single-stain`,\n        name: `${marker.marker} single stain`,\n        kind: 'single-stain' as const,\n        markerId: marker.id,\n        required: true,\n        metadata: {},\n      })),\n  ]\n}\n","import { idFromName } from './builderIdUtils'\nimport {\n  defaultFlowControls,\n  normalizeFlowControl,\n  normalizeFlowMarker,\n} from './flowNormalizers'\nimport { createTemplateEnvelope } from './templateEnvelopes'\nimport { validateFlowCytometryPanelData } from './templateValidators'\nimport type {\n  CreateFlowCytometryPanelTemplateOptions,\n  FlowCytometryPanelTemplate,\n  FlowCytometryPanelTemplateData,\n  FlowPanelControl,\n  FlowPanelMarker,\n} from './types'\n\nexport function createFlowCytometryPanelTemplate(\n  options: CreateFlowCytometryPanelTemplateOptions\n): FlowCytometryPanelTemplate {\n  const markers = options.markers.map((marker, index): FlowPanelMarker => {\n    if (typeof marker !== 'string') return normalizeFlowMarker(marker, index)\n    return {\n      id: idFromName(marker, `marker-${index + 1}`),\n      marker,\n      fluorophore: 'unassigned',\n      purpose: 'phenotype',\n      compensationRequired: true,\n      metadata: {},\n    }\n  })\n  const controls = options.controls === undefined\n    ? options.includeDefaultControls === false\n      ? []\n      : defaultFlowControls(markers)\n    : options.controls.map((control, index): FlowPanelControl => {\n        if (typeof control !== 'string') return normalizeFlowControl(control, index)\n        return {\n          id: idFromName(control, `control-${index + 1}`),\n          name: control,\n          kind: 'other',\n          required: true,\n          metadata: {},\n        }\n      })\n  const data: FlowCytometryPanelTemplateData = {\n    markers,\n    controls,\n    instrument: options.instrument,\n    metadata: options.metadata ?? {},\n  }\n  validateFlowCytometryPanelData(data)\n  return createTemplateEnvelope('flow-cytometry-panel', data, options.metadata ?? {})\n}\n","import type {\n  InstrumentMethod,\n  InstrumentRunItem,\n  QpcrSample,\n  QpcrTarget,\n} from './types'\nimport { idFromName } from './builderIdUtils'\n\nexport function normalizeInstrumentMethod(\n  method: Partial<InstrumentMethod> & { name?: string },\n  fallbackInstrument?: string\n): InstrumentMethod {\n  const name = method.name || method.id || 'Default method'\n  return {\n    id: method.id || idFromName(name, 'method-1'),\n    name,\n    instrument: method.instrument ?? fallbackInstrument,\n    acquisitionMode: method.acquisitionMode,\n    metadata: method.metadata ?? {},\n  }\n}\n\nexport function normalizeInstrumentRunItem(\n  item: Partial<InstrumentRunItem> & { name?: string; sampleId?: string },\n  defaultMethodId: string,\n  fallbackOrder: number,\n  index: number\n): InstrumentRunItem {\n  const kind = item.kind ?? 'sample'\n  const sampleId = item.sampleId || (kind === 'sample'\n    ? idFromName(item.name ?? `Sample ${index + 1}`, `sample-${index + 1}`)\n    : undefined)\n  const label = item.name ?? sampleId ?? kind\n  return {\n    id: item.id || idFromName(label, `${kind}-${index + 1}`),\n    order: item.order ?? fallbackOrder,\n    kind,\n    sampleId,\n    name: item.name,\n    methodId: item.methodId || defaultMethodId,\n    vial: item.vial,\n    plateId: item.plateId,\n    wellId: item.wellId,\n    injectionVolume: item.injectionVolume,\n    expectedDurationMin: item.expectedDurationMin,\n    status: item.status ?? 'planned',\n    metadata: item.metadata ?? {},\n  }\n}\n\nexport function normalizeQpcrSample(sample: QpcrSample): QpcrSample {\n  return {\n    ...sample,\n    metadata: sample.metadata ?? {},\n  }\n}\n\nexport function normalizeQpcrTarget(target: QpcrTarget): QpcrTarget {\n  return {\n    ...target,\n    metadata: target.metadata ?? {},\n  }\n}\n","import { idFromName } from './builderIdUtils'\nimport {\n  normalizeInstrumentMethod,\n  normalizeInstrumentRunItem,\n} from './runNormalizers'\nimport { createTemplateEnvelope } from './templateEnvelopes'\nimport { validateInstrumentRunData } from './templateValidators'\nimport type {\n  CreateInstrumentRunTemplateOptions,\n  InstrumentRunItem,\n  InstrumentRunTemplate,\n  InstrumentRunTemplateData,\n} from './types'\n\nexport function createInstrumentRunTemplate(\n  options: CreateInstrumentRunTemplateOptions\n): InstrumentRunTemplate {\n  const method = typeof options.method === 'string' || options.method === undefined\n    ? {\n        id: idFromName(options.method ?? 'Default method', 'method-1'),\n        name: options.method ?? 'Default method',\n        instrument: options.instrument,\n        metadata: {},\n      }\n    : normalizeInstrumentMethod(options.method, options.instrument)\n  const items: InstrumentRunItem[] = []\n  let order = 1\n\n  if (options.includeBlanks !== false) {\n    items.push({\n      id: 'blank-start',\n      order,\n      kind: 'blank',\n      name: 'Blank start',\n      methodId: method.id,\n      status: 'planned',\n      metadata: {},\n    })\n    order += 1\n  }\n\n  if (options.includeQc !== false) {\n    items.push({\n      id: 'qc-start',\n      order,\n      kind: 'qc',\n      name: 'QC start',\n      methodId: method.id,\n      status: 'planned',\n      metadata: {},\n    })\n    order += 1\n  }\n\n  for (const [index, item] of options.items.entries()) {\n    if (typeof item !== 'string') {\n      const normalized = normalizeInstrumentRunItem(item, method.id, order, index)\n      items.push(normalized)\n      order = Math.max(order, normalized.order + 1)\n      continue\n    }\n    const sampleId = idFromName(item, `sample-${index + 1}`)\n    items.push({\n      id: `${sampleId}-run`,\n      order,\n      kind: 'sample',\n      sampleId,\n      name: item,\n      methodId: method.id,\n      status: 'planned',\n      metadata: {},\n    })\n    order += 1\n  }\n\n  if (options.includeQc !== false) {\n    items.push({\n      id: 'qc-end',\n      order,\n      kind: 'qc',\n      name: 'QC end',\n      methodId: method.id,\n      status: 'planned',\n      metadata: {},\n    })\n  }\n\n  const data: InstrumentRunTemplateData = {\n    runId: 'run-1',\n    instrument: options.instrument,\n    methods: [method],\n    items,\n    metadata: options.metadata ?? {},\n  }\n  validateInstrumentRunData(data)\n  return createTemplateEnvelope('instrument-run', data, options.metadata ?? {})\n}\n","import { idFromName } from './builderIdUtils'\nimport { wellIdsForFormat } from './plateGeometry'\nimport {\n  normalizeQpcrSample,\n  normalizeQpcrTarget,\n} from './runNormalizers'\nimport { createTemplateEnvelope } from './templateEnvelopes'\nimport { validateQpcrPlateData } from './templateValidators'\nimport type {\n  CreateQpcrPlateTemplateOptions,\n  QpcrPlateTemplate,\n  QpcrPlateTemplateData,\n  QpcrReaction,\n  QpcrSample,\n  QpcrTarget,\n} from './types'\n\nexport function createQpcrPlateTemplate(\n  options: CreateQpcrPlateTemplateOptions\n): QpcrPlateTemplate {\n  const format = options.format ?? 96\n  const replicates = options.replicates ?? 3\n  if (replicates < 1) {\n    throw new Error('qPCR replicates must be at least 1.')\n  }\n\n  const samples = options.samples.map((sample, index): QpcrSample => {\n    if (typeof sample !== 'string') return normalizeQpcrSample(sample)\n    return {\n      sampleId: idFromName(sample, `sample-${index + 1}`),\n      name: sample,\n      metadata: {},\n    }\n  })\n  const targets = options.targets.map((target, index): QpcrTarget => {\n    if (typeof target !== 'string') return normalizeQpcrTarget(target)\n    return {\n      id: idFromName(target, `target-${index + 1}`),\n      name: target,\n      metadata: {},\n    }\n  })\n  const wells = wellIdsForFormat(format)\n  let wellIndex = 0\n  const reactions: QpcrReaction[] = []\n\n  for (const sample of samples) {\n    for (const target of targets) {\n      for (let replicate = 1; replicate <= replicates; replicate += 1) {\n        const wellId = wells[wellIndex]\n        if (!wellId) throw new Error(`qPCR plate format ${format} does not have enough wells.`)\n        reactions.push({\n          id: `${sample.sampleId}-${target.id}-r${replicate}`,\n          wellId,\n          sampleId: sample.sampleId,\n          targetId: target.id,\n          replicate,\n          controlKind: 'sample',\n          flags: [],\n          metadata: {},\n        })\n        wellIndex += 1\n      }\n    }\n  }\n\n  if (options.includeNoTemplateControls !== false) {\n    for (const target of targets) {\n      const wellId = wells[wellIndex]\n      if (!wellId) throw new Error(`qPCR plate format ${format} does not have enough wells.`)\n      reactions.push({\n        id: `ntc-${target.id}`,\n        wellId,\n        targetId: target.id,\n        replicate: 1,\n        controlKind: 'no-template',\n        flags: [],\n        metadata: {},\n      })\n      wellIndex += 1\n    }\n  }\n\n  const data: QpcrPlateTemplateData = {\n    plateId: 'qpcr-plate-1',\n    format,\n    samples,\n    targets,\n    reactions,\n    instrument: options.instrument,\n    chemistry: options.chemistry ?? 'sybr',\n    metadata: options.metadata ?? {},\n  }\n  validateQpcrPlateData(data)\n  return createTemplateEnvelope('qpcr-plate', data, options.metadata ?? {})\n}\n","import { createQpcrPlateTemplate } from './qpcrPlateBuilder'\nimport { createSampleSheetTemplate } from './sampleSheetBuilder'\nimport { presetSampleRecords } from './sampleNormalizers'\nimport { createTemplateCollection } from './templateEnvelopes'\nimport type {\n  CreateQpcrExpressionCollectionOptions,\n  TemplateCollectionEnvelope,\n} from './types'\n\nexport function createQpcrExpressionCollection(\n  options: CreateQpcrExpressionCollectionOptions = {}\n): TemplateCollectionEnvelope {\n  const sampleRecords = presetSampleRecords(options.samples ?? ['Control', 'Treatment'])\n  const sampleSheet = createSampleSheetTemplate({ samples: sampleRecords })\n  const qpcr = createQpcrPlateTemplate({\n    samples: sampleRecords.map(sample => ({\n      sampleId: sample.sampleId,\n      name: sample.name,\n      group: sample.group,\n      metadata: sample.metadata ?? {},\n    })),\n    targets: options.targets ?? ['ACTB', 'GAPDH'],\n    chemistry: options.chemistry,\n    format: options.format,\n    includeNoTemplateControls: options.includeNoTemplateControls,\n    replicates: options.replicates ?? 3,\n    instrument: options.instrument,\n  })\n  return createTemplateCollection(\n    [sampleSheet, qpcr],\n    { preset: 'qpcr-expression', ...(options.metadata ?? {}) }\n  )\n}\n","import { createAssayMatrixTemplate } from './assayMatrixBuilder'\nimport { createInstrumentRunTemplate } from './instrumentRunBuilder'\nimport { createSampleSheetTemplate } from './sampleSheetBuilder'\nimport { presetSampleRecords } from './sampleNormalizers'\nimport { createTemplateCollection } from './templateEnvelopes'\nimport type {\n  CreateLcmsBatchCollectionOptions,\n  TemplateCollectionEnvelope,\n} from './types'\n\nexport function createLcmsBatchCollection(\n  options: CreateLcmsBatchCollectionOptions = {}\n): TemplateCollectionEnvelope {\n  const sampleRecords = presetSampleRecords(options.samples ?? ['S001', 'S002'])\n  const sampleSheet = createSampleSheetTemplate({ samples: sampleRecords })\n  const instrumentRun = createInstrumentRunTemplate({\n    items: sampleRecords.map(sample => ({\n      sampleId: sample.sampleId,\n      name: sample.name ?? sample.sampleId,\n    })),\n    method: options.method ?? 'Default method',\n    instrument: options.instrument ?? 'LC-MS',\n    includeQc: options.includeQc,\n  })\n  const assayMatrix = createAssayMatrixTemplate({\n    samples: sampleRecords.map(sample => ({\n      sampleId: sample.sampleId,\n      name: sample.name,\n      group: sample.group,\n      metadata: sample.metadata ?? {},\n    })),\n    features: options.features ?? ['Glucose', 'Lactate'],\n  })\n  return createTemplateCollection(\n    [sampleSheet, instrumentRun, assayMatrix],\n    { preset: 'lcms-batch', ...(options.metadata ?? {}) }\n  )\n}\n","import type {\n  AssayFeature,\n  CalibrationPoint,\n  InstrumentRunItemInput,\n  ReagentTemplateInput,\n  SampleRecord,\n} from './types'\nimport {\n  normalizeAssayFeature,\n  normalizeReagent,\n} from './assayNormalizers'\nimport { idFromName } from './builderIdUtils'\n\nexport function normalizeMetaboliteFeatures(\n  metabolites: Array<string | AssayFeature>,\n  responseUnit: string,\n): AssayFeature[] {\n  return metabolites.map((metabolite, index) => {\n    if (typeof metabolite === 'string') {\n      return {\n        id: idFromName(metabolite, `metabolite-${index + 1}`),\n        name: metabolite,\n        type: 'metabolite',\n        unit: responseUnit,\n        metadata: { quantitation: 'targeted' },\n      }\n    }\n\n    const feature = normalizeAssayFeature(metabolite)\n    return {\n      ...feature,\n      type: feature.type ?? 'metabolite',\n      unit: feature.unit ?? responseUnit,\n      metadata: {\n        quantitation: 'targeted',\n        ...feature.metadata,\n      },\n    }\n  })\n}\n\nexport function normalizeInternalStandardReagents(\n  internalStandards: Array<string | ReagentTemplateInput>,\n): ReagentTemplateInput[] {\n  return internalStandards.map((standard, index) => {\n    if (typeof standard === 'string') {\n      return {\n        id: idFromName(standard, `internal-standard-${index + 1}`),\n        name: standard,\n        kind: 'compound',\n        metadata: { role: 'internal-standard' },\n      }\n    }\n\n    const reagent = normalizeReagent(standard)\n    return {\n      ...reagent,\n      kind: standard.kind ?? 'compound',\n      metadata: {\n        role: 'internal-standard',\n        ...reagent.metadata,\n      },\n    }\n  })\n}\n\nexport function targetedMetabolomicsRunItems(\n  samples: SampleRecord[],\n  calibrationPoints: CalibrationPoint[],\n  includeQc: boolean,\n): InstrumentRunItemInput[] {\n  const calibrationItems = calibrationPoints\n    .filter(point => point.role !== 'qc' || includeQc)\n    .filter(point => point.role === 'blank' || point.role === 'standard' || point.role === 'qc')\n    .map((point): InstrumentRunItemInput => ({\n      id: `${point.id}-run`,\n      kind: calibrationRunItemKind(point.role),\n      name: point.level,\n      metadata: {\n        concentration: point.concentration,\n        unit: point.unit,\n        role: point.role,\n      },\n    }))\n\n  const sampleItems = samples.map((sample): InstrumentRunItemInput => ({\n    sampleId: sample.sampleId,\n    name: sample.name ?? sample.sampleId,\n    kind: 'sample',\n  }))\n\n  return [...calibrationItems, ...sampleItems]\n}\n\nexport function firstFeatureName(features: AssayFeature[], fallback: string): string {\n  return features.find(feature => feature.name)?.name ?? fallback\n}\n\nfunction calibrationRunItemKind(role: CalibrationPoint['role']): 'blank' | 'standard' | 'qc' {\n  if (role === 'blank' || role === 'standard' || role === 'qc') return role\n  return 'standard'\n}\n","import { createAssayMatrixTemplate } from './assayMatrixBuilder'\nimport { createCalibrationCurveTemplate } from './calibrationCurveBuilder'\nimport { createInstrumentRunTemplate } from './instrumentRunBuilder'\nimport { createReagentListTemplate } from './reagentListBuilder'\nimport { createSamplePrepTemplate } from './samplePrepBuilder'\nimport { createSampleSheetTemplate } from './sampleSheetBuilder'\nimport { presetSampleRecords } from './sampleNormalizers'\nimport {\n  firstFeatureName,\n  normalizeInternalStandardReagents,\n  normalizeMetaboliteFeatures,\n  targetedMetabolomicsRunItems,\n} from './targetedMetabolomicsHelpers'\nimport { createTemplateCollection } from './templateEnvelopes'\nimport type {\n  CreateTargetedMetabolomicsCollectionOptions,\n  TemplateCollectionEnvelope,\n} from './types'\n\nexport function createTargetedMetabolomicsCollection(\n  options: CreateTargetedMetabolomicsCollectionOptions = {}\n): TemplateCollectionEnvelope {\n  const sampleRecords = presetSampleRecords(options.samples ?? ['S001', 'S002'])\n  const responseUnit = options.responseUnit ?? 'peak area ratio'\n  const concentrationUnit = options.concentrationUnit ?? 'uM'\n  const metaboliteFeatures = normalizeMetaboliteFeatures(\n    options.metabolites ?? ['Glucose', 'Lactate', 'Pyruvate'],\n    responseUnit,\n  )\n  const sampleSheet = createSampleSheetTemplate({ samples: sampleRecords })\n  const samplePrep = createSamplePrepTemplate({\n    samples: sampleRecords.map(sample => sample.sampleId),\n    prepType: options.prepType ?? 'extraction',\n    protocolName: 'Metabolomics sample preparation',\n    outputVolume: options.outputVolume ?? 50,\n    metadata: { assay: 'targeted-metabolomics' },\n  })\n  const reagents = createReagentListTemplate({\n    reagents: normalizeInternalStandardReagents(\n      options.internalStandards ?? ['Stable isotope internal standard mix'],\n    ),\n    metadata: { assay: 'targeted-metabolomics' },\n  })\n  const calibrationCurve = createCalibrationCurveTemplate({\n    concentrations: options.standardConcentrations ?? [0.1, 1, 10, 100],\n    analyte: options.calibrationAnalyte ?? firstFeatureName(metaboliteFeatures, 'Metabolite panel'),\n    unit: concentrationUnit,\n    responseUnit,\n    model: 'linear-weighted-1-x',\n    includeQc: options.includeQc,\n    metadata: { assay: 'targeted-metabolomics' },\n  })\n  const instrumentRun = createInstrumentRunTemplate({\n    items: targetedMetabolomicsRunItems(\n      sampleRecords,\n      calibrationCurve.data.points,\n      options.includeQc !== false,\n    ),\n    method: options.method ?? 'Targeted metabolomics',\n    instrument: options.instrument ?? 'LC-MS',\n    includeBlanks: false,\n    includeQc: false,\n    metadata: { assay: 'targeted-metabolomics' },\n  })\n  const assayMatrix = createAssayMatrixTemplate({\n    samples: sampleRecords.map(sample => ({\n      sampleId: sample.sampleId,\n      name: sample.name,\n      group: sample.group,\n      metadata: sample.metadata ?? {},\n    })),\n    features: metaboliteFeatures,\n    metadata: { assay: 'targeted-metabolomics', responseUnit },\n  })\n  return createTemplateCollection(\n    [sampleSheet, samplePrep, reagents, instrumentRun, calibrationCurve, assayMatrix],\n    { preset: 'targeted-metabolomics', ...(options.metadata ?? {}) }\n  )\n}\n","import { createAssayMatrixTemplate } from './assayMatrixBuilder'\nimport { DEFAULT_SAMPLE_COLORS } from './builderDefaults'\nimport { idFromName } from './builderIdUtils'\nimport { createCalibrationCurveTemplate } from './calibrationCurveBuilder'\nimport { createPlateMapTemplate } from './plateMapBuilder'\nimport { createSampleSheetTemplate } from './sampleSheetBuilder'\nimport { presetSampleRecords } from './sampleNormalizers'\nimport { createTemplateCollection } from './templateEnvelopes'\nimport type {\n  CreateElisaAssayCollectionOptions,\n  TemplateCollectionEnvelope,\n} from './types'\n\nexport function createElisaAssayCollection(\n  options: CreateElisaAssayCollectionOptions = {}\n): TemplateCollectionEnvelope {\n  const sampleRecords = presetSampleRecords(options.samples ?? ['Control', 'Treatment'])\n  const analyte = options.analyte ?? 'Analyte'\n  const responseUnit = options.responseUnit ?? 'OD450'\n  const plate = createPlateMapTemplate({\n    name: options.plateName ?? 'ELISA plate',\n    format: options.plateFormat ?? 96,\n    samples: [\n      { id: 'blank', name: 'Blank' },\n      { id: 'standard', name: 'Standards' },\n      { id: 'qc', name: 'QC' },\n      ...sampleRecords.map((sample, index) => ({\n        id: sample.sampleId,\n        name: sample.name ?? sample.sampleId,\n        color: DEFAULT_SAMPLE_COLORS[index % DEFAULT_SAMPLE_COLORS.length],\n      })),\n    ],\n  })\n  const sampleSheet = createSampleSheetTemplate({ samples: sampleRecords })\n  const calibrationCurve = createCalibrationCurveTemplate({\n    concentrations: options.standardConcentrations ?? [1000, 100, 10, 1],\n    analyte,\n    unit: options.unit ?? 'pg/mL',\n    responseUnit,\n    model: 'four-parameter-logistic',\n  })\n  const assayMatrix = createAssayMatrixTemplate({\n    samples: sampleRecords.map(sample => ({\n      sampleId: sample.sampleId,\n      name: sample.name,\n      group: sample.group,\n      metadata: sample.metadata ?? {},\n    })),\n    features: [{\n      id: idFromName(analyte, 'analyte'),\n      name: analyte,\n      type: 'protein',\n      unit: responseUnit,\n      metadata: {},\n    }],\n    metadata: { analyte, responseUnit },\n  })\n  return createTemplateCollection(\n    [plate, sampleSheet, calibrationCurve, assayMatrix],\n    { preset: 'elisa-assay', ...(options.metadata ?? {}) }\n  )\n}\n","import { createAssayMatrixTemplate } from './assayMatrixBuilder'\nimport { createFlowCytometryPanelTemplate } from './flowCytometryPanelBuilder'\nimport { createSampleSheetTemplate } from './sampleSheetBuilder'\nimport { presetSampleRecords } from './sampleNormalizers'\nimport { createTemplateCollection } from './templateEnvelopes'\nimport type {\n  CreateFlowCytometryAssayCollectionOptions,\n  TemplateCollectionEnvelope,\n} from './types'\n\nexport function createFlowCytometryAssayCollection(\n  options: CreateFlowCytometryAssayCollectionOptions = {}\n): TemplateCollectionEnvelope {\n  const sampleRecords = presetSampleRecords(options.samples ?? ['Control', 'Treatment'])\n  const markers = options.markers ?? ['CD3', 'CD4', 'CD8']\n  const sampleSheet = createSampleSheetTemplate({ samples: sampleRecords })\n  const flowPanel = createFlowCytometryPanelTemplate({\n    markers,\n    instrument: options.instrument ?? 'Flow cytometer',\n    includeDefaultControls: options.includeDefaultControls,\n  })\n  const assayMatrix = createAssayMatrixTemplate({\n    samples: sampleRecords.map(sample => ({\n      sampleId: sample.sampleId,\n      name: sample.name,\n      group: sample.group,\n      metadata: sample.metadata ?? {},\n    })),\n    features: options.features ?? flowPanel.data.markers.map(marker => ({\n      id: marker.id,\n      name: `${marker.marker}+ cells`,\n      type: 'cell',\n      unit: '%',\n      metadata: { marker: marker.marker, fluorophore: marker.fluorophore },\n    })),\n  })\n  return createTemplateCollection(\n    [sampleSheet, flowPanel, assayMatrix],\n    { preset: 'flow-cytometry-assay', ...(options.metadata ?? {}) }\n  )\n}\n","import { createAssayMatrixTemplate } from './assayMatrixBuilder'\nimport { idFromName } from './builderIdUtils'\nimport { createProtocolStepsTemplate } from './protocolStepsBuilder'\nimport { createReagentListTemplate } from './reagentListBuilder'\nimport { createSampleSheetTemplate } from './sampleSheetBuilder'\nimport { presetSampleRecords } from './sampleNormalizers'\nimport { createTemplateCollection } from './templateEnvelopes'\nimport type {\n  CreateWesternBlotAssayCollectionOptions,\n  TemplateCollectionEnvelope,\n} from './types'\n\nexport function createWesternBlotAssayCollection(\n  options: CreateWesternBlotAssayCollectionOptions = {}\n): TemplateCollectionEnvelope {\n  const sampleRecords = presetSampleRecords(options.samples ?? ['Control', 'Treatment'])\n  const loadingControl = options.loadingControl ?? 'ACTB'\n  const targetNames = (options.targets ?? ['Target protein']).map(target =>\n    typeof target === 'string' ? target : target.name ?? target.id\n  )\n  const featureNames = loadingControl && !targetNames.includes(loadingControl)\n    ? [...targetNames, loadingControl]\n    : targetNames\n  const sampleSheet = createSampleSheetTemplate({ samples: sampleRecords })\n  const reagentList = createReagentListTemplate({\n    reagents: [\n      { id: 'primary-antibody', name: 'Primary antibody', kind: 'antibody', storageCondition: '4C' },\n      { id: 'secondary-antibody', name: 'Secondary antibody', kind: 'antibody', storageCondition: '4C' },\n      { id: 'lysis-buffer', name: 'Lysis buffer', kind: 'buffer', storageCondition: '4C' },\n      { id: 'blocking-buffer', name: 'Blocking buffer', kind: 'buffer', storageCondition: '4C' },\n      { id: 'wash-buffer', name: 'TBST wash buffer', kind: 'buffer', storageCondition: 'RT' },\n      { id: 'substrate', name: 'Detection substrate', kind: 'reagent', storageCondition: '4C' },\n    ],\n    metadata: { assay: 'western-blot' },\n  })\n  const protocol = createProtocolStepsTemplate({\n    steps: [\n      { id: 'lyse-samples', type: 'addition', name: 'Lyse samples', duration: 30 },\n      { id: 'run-gel', type: 'custom', name: 'Run SDS-PAGE', duration: 90 },\n      { id: 'transfer', type: 'transfer', name: 'Transfer to membrane', duration: 60 },\n      { id: 'block', type: 'incubation', name: 'Block membrane', duration: 60 },\n      { id: 'primary-antibody', type: 'incubation', name: 'Primary antibody incubation', duration: 960 },\n      { id: 'secondary-antibody', type: 'incubation', name: 'Secondary antibody incubation', duration: 60 },\n      { id: 'detect', type: 'measurement', name: 'Detect and quantify bands', duration: 30 },\n    ],\n    metadata: { assay: 'western-blot' },\n  })\n  const assayMatrix = createAssayMatrixTemplate({\n    samples: sampleRecords.map(sample => ({\n      sampleId: sample.sampleId,\n      name: sample.name,\n      group: sample.group,\n      metadata: sample.metadata ?? {},\n    })),\n    features: featureNames.map((feature, index) => ({\n      id: idFromName(feature, `feature-${index + 1}`),\n      name: feature,\n      type: 'protein',\n      unit: 'relative intensity',\n      metadata: { loadingControl: feature === loadingControl },\n    })),\n    metadata: { assay: 'western-blot', loadingControl },\n  })\n  return createTemplateCollection(\n    [sampleSheet, reagentList, protocol, assayMatrix],\n    { preset: 'western-blot-assay', ...(options.metadata ?? {}) }\n  )\n}\n","import { getBioTemplateInfo } from './catalog'\nimport { createAssayMatrixTemplate } from './assayMatrixBuilder'\nimport { createCalibrationCurveTemplate } from './calibrationCurveBuilder'\nimport { createDoseResponseTemplate } from './doseResponseBuilder'\nimport { createFlowCytometryPanelTemplate } from './flowCytometryPanelBuilder'\nimport { createInstrumentRunTemplate } from './instrumentRunBuilder'\nimport { createPlateMapTemplate } from './plateMapBuilder'\nimport { createProtocolStepsTemplate } from './protocolStepsBuilder'\nimport { createQpcrPlateTemplate } from './qpcrPlateBuilder'\nimport { createReagentListTemplate } from './reagentListBuilder'\nimport { createSamplePrepTemplate } from './samplePrepBuilder'\nimport { createSampleSheetTemplate } from './sampleSheetBuilder'\nimport { createTimeCourseTemplate } from './timeCourseBuilder'\nimport type {\n  BioTemplateEnvelope,\n  TemplateId,\n} from './types'\n\nexport function createDefaultBioTemplate(templateId: TemplateId | string): BioTemplateEnvelope<unknown> {\n  const template = getBioTemplateInfo(templateId)\n  if (!template) {\n    throw new Error(`Unknown bio template '${templateId}'.`)\n  }\n\n  switch (template.template_id) {\n    case 'plate-map':\n      return createPlateMapTemplate({\n        name: 'Plate 1',\n        samples: ['Control', 'Treatment'],\n      })\n    case 'sample-sheet':\n      return createSampleSheetTemplate({\n        samples: [\n          { sampleId: 'S001', name: 'Control 1', group: 'Control' },\n          { sampleId: 'S002', name: 'Treatment 1', group: 'Treatment' },\n        ],\n      })\n    case 'sample-prep':\n      return createSamplePrepTemplate({\n        samples: ['S001', 'S002'],\n        prepType: 'extraction',\n        outputVolume: 50,\n      })\n    case 'dose-response':\n      return createDoseResponseTemplate({\n        compounds: {\n          'Compound A': [10, 1, 0.1],\n        },\n        unit: 'uM',\n        replicates: 3,\n      })\n    case 'calibration-curve':\n      return createCalibrationCurveTemplate({\n        concentrations: [0.1, 1, 10, 100],\n        analyte: 'Analyte',\n        unit: 'uM',\n      })\n    case 'time-course':\n      return createTimeCourseTemplate({\n        timepoints: [0, 6, 24],\n        unit: 'hour',\n        conditions: ['Control', 'Treatment'],\n        replicates: 3,\n      })\n    case 'protocol-steps':\n      return createProtocolStepsTemplate({\n        steps: [\n          {\n            id: 'seed-cells',\n            type: 'addition',\n            name: 'Seed cells',\n            description: 'Add cells to wells or culture vessels.',\n            duration: 15,\n          },\n          {\n            id: 'incubate-overnight',\n            type: 'incubation',\n            name: 'Incubate overnight',\n            duration: 960,\n            parameters: { temperature: '37 C', co2: '5%' },\n          },\n          {\n            id: 'measure-readout',\n            type: 'measurement',\n            name: 'Measure readout',\n            duration: 45,\n          },\n        ],\n      })\n    case 'assay-matrix':\n      return createAssayMatrixTemplate({\n        samples: ['S001', 'S002'],\n        features: ['Lactate', 'Glucose'],\n        values: {\n          s001: { lactate: 1.2, glucose: 5.4 },\n          s002: { lactate: 2.1, glucose: 4.8 },\n        },\n      })\n    case 'reagent-list':\n      return createReagentListTemplate({\n        reagents: ['DMSO', 'Compound A', 'Anti-HA antibody'],\n      })\n    case 'flow-cytometry-panel':\n      return createFlowCytometryPanelTemplate({\n        markers: ['CD3', 'CD4', 'CD8'],\n        instrument: 'BD LSRFortessa',\n      })\n    case 'instrument-run':\n      return createInstrumentRunTemplate({\n        items: ['S001', 'S002'],\n        instrument: 'LC-MS',\n        method: 'Default method',\n      })\n    case 'qpcr-plate':\n      return createQpcrPlateTemplate({\n        samples: ['Control', 'Treatment'],\n        targets: ['ACTB', 'GAPDH'],\n        replicates: 3,\n        instrument: 'QuantStudio',\n      })\n    default:\n      throw new Error(`Unknown bio template '${templateId}'.`)\n  }\n}\n","import { getBioTemplatePackInfo } from './packs'\nimport { createDefaultBioTemplate } from './defaultBioTemplateBuilder'\nimport { createTemplateCollection } from './templateEnvelopes'\nimport type {\n  CreateBioTemplatePackCollectionOptions,\n  TemplateCollectionEnvelope,\n  TemplatePackId,\n} from './types'\n\nexport function createBioTemplatePackCollection(\n  name: TemplatePackId | string,\n  options: CreateBioTemplatePackCollectionOptions = {},\n): TemplateCollectionEnvelope {\n  const pack = getBioTemplatePackInfo(name)\n  if (!pack) {\n    throw new Error(`Unknown template pack '${name}'.`)\n  }\n\n  return createTemplateCollection(\n    pack.templates.map(templateId => createDefaultBioTemplate(templateId)),\n    { pack: pack.name, ...(options.metadata ?? {}) },\n  )\n}\n","import { DEFAULT_SAMPLE_COLORS } from './builderDefaults'\nimport { createDoseResponseTemplate } from './doseResponseBuilder'\nimport { createPlateMapTemplate } from './plateMapBuilder'\nimport { createSampleSheetTemplate } from './sampleSheetBuilder'\nimport { presetSampleRecords } from './sampleNormalizers'\nimport { createTemplateCollection } from './templateEnvelopes'\nimport type {\n  CreateWellPlateScreenCollectionOptions,\n  TemplateCollectionEnvelope,\n} from './types'\n\nexport function createWellPlateScreenCollection(\n  options: CreateWellPlateScreenCollectionOptions = {}\n): TemplateCollectionEnvelope {\n  const sampleRecords = presetSampleRecords(options.samples ?? ['Control', 'Treatment'])\n  const plate = createPlateMapTemplate({\n    name: options.plateName ?? 'Screen plate',\n    format: options.plateFormat ?? 96,\n    samples: sampleRecords.map((sample, index) => ({\n      id: sample.sampleId,\n      name: sample.name ?? sample.sampleId,\n      color: DEFAULT_SAMPLE_COLORS[index % DEFAULT_SAMPLE_COLORS.length],\n    })),\n  })\n  const sampleSheet = createSampleSheetTemplate({ samples: sampleRecords })\n  const doseResponse = createDoseResponseTemplate({\n    compounds: options.compounds ?? { 'Compound A': [10, 1, 0.1] },\n    unit: options.unit ?? 'uM',\n    replicates: options.replicates ?? 3,\n    layout: plate,\n  })\n  return createTemplateCollection(\n    [plate, sampleSheet, doseResponse],\n    { preset: 'wellplate-screen', ...(options.metadata ?? {}) }\n  )\n}\n","import { bioTemplatePresetControlValuesToOptions } from './builderPresetControls'\nimport type { BioTemplateControlValues } from './builderPresetControls'\nimport { createElisaAssayCollection } from './elisaAssayCollectionBuilder'\nimport { createFlowCytometryAssayCollection } from './flowCytometryAssayCollectionBuilder'\nimport { createLcmsBatchCollection } from './lcmsBatchCollectionBuilder'\nimport { getBioTemplatePresetInfo } from './presets'\nimport { createQpcrExpressionCollection } from './qpcrExpressionCollectionBuilder'\nimport { createTargetedMetabolomicsCollection } from './targetedMetabolomicsCollectionBuilder'\nimport { createWellPlateScreenCollection } from './wellPlateScreenCollectionBuilder'\nimport { createWesternBlotAssayCollection } from './westernBlotAssayCollectionBuilder'\nimport type {\n  CreateElisaAssayCollectionOptions,\n  CreateFlowCytometryAssayCollectionOptions,\n  CreateLcmsBatchCollectionOptions,\n  CreateQpcrExpressionCollectionOptions,\n  CreateTargetedMetabolomicsCollectionOptions,\n  CreateWellPlateScreenCollectionOptions,\n  CreateWesternBlotAssayCollectionOptions,\n  TemplateCollectionEnvelope,\n  TemplatePresetId,\n} from './types'\n\nexport function createBioTemplatePresetCollection(\n  name: 'wellplate-screen',\n  options?: CreateWellPlateScreenCollectionOptions\n): TemplateCollectionEnvelope\nexport function createBioTemplatePresetCollection(\n  name: 'qpcr-expression',\n  options?: CreateQpcrExpressionCollectionOptions\n): TemplateCollectionEnvelope\nexport function createBioTemplatePresetCollection(\n  name: 'lcms-batch',\n  options?: CreateLcmsBatchCollectionOptions\n): TemplateCollectionEnvelope\nexport function createBioTemplatePresetCollection(\n  name: 'targeted-metabolomics',\n  options?: CreateTargetedMetabolomicsCollectionOptions\n): TemplateCollectionEnvelope\nexport function createBioTemplatePresetCollection(\n  name: 'elisa-assay',\n  options?: CreateElisaAssayCollectionOptions\n): TemplateCollectionEnvelope\nexport function createBioTemplatePresetCollection(\n  name: 'flow-cytometry-assay',\n  options?: CreateFlowCytometryAssayCollectionOptions\n): TemplateCollectionEnvelope\nexport function createBioTemplatePresetCollection(\n  name: 'western-blot-assay',\n  options?: CreateWesternBlotAssayCollectionOptions\n): TemplateCollectionEnvelope\nexport function createBioTemplatePresetCollection(\n  name: string,\n  options?:\n    | CreateWellPlateScreenCollectionOptions\n    | CreateQpcrExpressionCollectionOptions\n    | CreateLcmsBatchCollectionOptions\n    | CreateTargetedMetabolomicsCollectionOptions\n    | CreateElisaAssayCollectionOptions\n    | CreateFlowCytometryAssayCollectionOptions\n    | CreateWesternBlotAssayCollectionOptions\n): TemplateCollectionEnvelope\nexport function createBioTemplatePresetCollection(\n  name: TemplatePresetId | string,\n  options:\n    | CreateWellPlateScreenCollectionOptions\n    | CreateQpcrExpressionCollectionOptions\n    | CreateLcmsBatchCollectionOptions\n    | CreateTargetedMetabolomicsCollectionOptions\n    | CreateElisaAssayCollectionOptions\n    | CreateFlowCytometryAssayCollectionOptions\n    | CreateWesternBlotAssayCollectionOptions = {}\n): TemplateCollectionEnvelope {\n  const preset = getBioTemplatePresetInfo(name)\n  if (!preset) {\n    throw new Error(`Unknown template preset '${name}'.`)\n  }\n  if (preset.name === 'wellplate-screen') {\n    return createWellPlateScreenCollection(options as CreateWellPlateScreenCollectionOptions)\n  }\n  if (preset.name === 'qpcr-expression') {\n    return createQpcrExpressionCollection(options as CreateQpcrExpressionCollectionOptions)\n  }\n  if (preset.name === 'lcms-batch') {\n    return createLcmsBatchCollection(options as CreateLcmsBatchCollectionOptions)\n  }\n  if (preset.name === 'targeted-metabolomics') {\n    return createTargetedMetabolomicsCollection(options as CreateTargetedMetabolomicsCollectionOptions)\n  }\n  if (preset.name === 'elisa-assay') {\n    return createElisaAssayCollection(options as CreateElisaAssayCollectionOptions)\n  }\n  if (preset.name === 'flow-cytometry-assay') {\n    return createFlowCytometryAssayCollection(options as CreateFlowCytometryAssayCollectionOptions)\n  }\n  if (preset.name === 'western-blot-assay') {\n    return createWesternBlotAssayCollection(options as CreateWesternBlotAssayCollectionOptions)\n  }\n  throw new Error(`Unknown template preset '${name}'.`)\n}\n\nexport function createBioTemplatePresetCollectionFromControls(\n  name: 'wellplate-screen',\n  values: BioTemplateControlValues\n): TemplateCollectionEnvelope\nexport function createBioTemplatePresetCollectionFromControls(\n  name: 'qpcr-expression',\n  values: BioTemplateControlValues\n): TemplateCollectionEnvelope\nexport function createBioTemplatePresetCollectionFromControls(\n  name: 'lcms-batch',\n  values: BioTemplateControlValues\n): TemplateCollectionEnvelope\nexport function createBioTemplatePresetCollectionFromControls(\n  name: 'targeted-metabolomics',\n  values: BioTemplateControlValues\n): TemplateCollectionEnvelope\nexport function createBioTemplatePresetCollectionFromControls(\n  name: 'elisa-assay',\n  values: BioTemplateControlValues\n): TemplateCollectionEnvelope\nexport function createBioTemplatePresetCollectionFromControls(\n  name: 'flow-cytometry-assay',\n  values: BioTemplateControlValues\n): TemplateCollectionEnvelope\nexport function createBioTemplatePresetCollectionFromControls(\n  name: 'western-blot-assay',\n  values: BioTemplateControlValues\n): TemplateCollectionEnvelope\nexport function createBioTemplatePresetCollectionFromControls(\n  name: TemplatePresetId | string,\n  values: BioTemplateControlValues\n): TemplateCollectionEnvelope\nexport function createBioTemplatePresetCollectionFromControls(\n  name: TemplatePresetId | string,\n  values: BioTemplateControlValues\n): TemplateCollectionEnvelope {\n  const options = bioTemplatePresetControlValuesToOptions(name, values)\n  return createBioTemplatePresetCollection(name, options)\n}\n","import type {\n  BioTemplateControlSchema,\n} from './controlSchemaTypes'\n\nexport function cloneSchemaMap<TName extends string>(\n  schemas: Record<TName, BioTemplateControlSchema>\n): Record<TName, BioTemplateControlSchema> {\n  const result = {} as Record<TName, BioTemplateControlSchema>\n  for (const name of Object.keys(schemas) as TName[]) {\n    result[name] = cloneControlSchema(schemas[name])\n  }\n  return result\n}\n\nexport function cloneControlSchema(schema: BioTemplateControlSchema): BioTemplateControlSchema {\n  return Object.fromEntries(\n    Object.entries(schema).map(([name, definition]) => [name, cloneControlDefinition(definition)])\n  )\n}\n\nexport function cloneControlDefinition(\n  definition: BioTemplateControlSchema[string]\n): BioTemplateControlSchema[string] {\n  return {\n    ...definition,\n    options: definition.options ? [...definition.options] : undefined,\n    props: definition.props ? { ...definition.props } : undefined,\n    sidebar: typeof definition.sidebar === 'object' && definition.sidebar !== null\n      ? { ...definition.sidebar }\n      : definition.sidebar,\n  }\n}\n","import {\n  getBioTemplateInfo,\n} from './catalog'\nimport {\n  cloneControlDefinition,\n} from './controlSchemaClone'\nimport type {\n  BioTemplateControlSchema,\n} from './controlSchemaTypes'\nimport type {\n  TemplateId,\n} from './types'\n\nexport function mergeTemplateControlSchemas(\n  templateIds: TemplateId[],\n  templateSchemas: Record<TemplateId, BioTemplateControlSchema>\n): BioTemplateControlSchema {\n  const merged: BioTemplateControlSchema = {}\n  for (const templateId of templateIds) {\n    const schema = templateSchemas[templateId]\n    const template = getBioTemplateInfo(templateId)\n    for (const [name, definition] of Object.entries(schema)) {\n      const key = `${camelize(templateId)}${capitalize(name)}`\n      merged[key] = {\n        ...cloneControlDefinition(definition),\n        section: definition.section ?? templateId,\n        sectionLabel: definition.sectionLabel ?? template?.label ?? templateId,\n      }\n    }\n  }\n  return merged\n}\n\nfunction camelize(value: string): string {\n  return value.replace(/-([a-z0-9])/g, (_, char: string) => char.toUpperCase())\n}\n\nfunction capitalize(value: string): string {\n  return value.charAt(0).toUpperCase() + value.slice(1)\n}\n","import {\n  getBioTemplateInfo,\n} from './catalog'\nimport {\n  getBioTemplatePackInfo,\n} from './packs'\nimport {\n  getBioTemplatePresetInfo,\n} from './presets'\nimport {\n  extractTemplateCollection,\n} from './templateEnvelopes'\nimport type {\n  BioTemplateEnvelope,\n  TemplateId,\n  TemplatePresetId,\n} from './types'\nimport type {\n  BioTemplateControlTarget,\n} from './controlSchemaTypes'\n\nexport type ControlSchemaResolvedTarget =\n  | { kind: 'template'; name: TemplateId }\n  | { kind: 'pack'; templates: TemplateId[] }\n  | { kind: 'preset'; name: TemplatePresetId }\n  | { kind: 'collection'; templates: TemplateId[] }\n\nexport function resolveControlSchemaTarget(\n  target: BioTemplateControlTarget\n): ControlSchemaResolvedTarget | undefined {\n  if (typeof target === 'string') {\n    const preset = getBioTemplatePresetInfo(target)\n    if (preset) return { kind: 'preset', name: preset.name }\n    const pack = getBioTemplatePackInfo(target)\n    if (pack) return { kind: 'pack', templates: [...pack.templates] }\n    const template = getBioTemplateInfo(target)\n    if (template) return { kind: 'template', name: template.template_id }\n    return undefined\n  }\n\n  if (isTemplateEnvelope(target)) {\n    const template = getBioTemplateInfo(target.template_id)\n    return template ? { kind: 'template', name: template.template_id } : undefined\n  }\n\n  const presetName = collectionPresetName(target)\n  if (presetName) {\n    const preset = getBioTemplatePresetInfo(presetName)\n    if (preset) return { kind: 'preset', name: preset.name }\n  }\n\n  const packName = collectionPackName(target)\n  if (packName) {\n    const pack = getBioTemplatePackInfo(packName)\n    if (pack) return { kind: 'pack', templates: [...pack.templates] }\n  }\n\n  const collection = extractTemplateCollection(target)\n  const templateIds = Object.keys(collection)\n    .map(id => getBioTemplateInfo(id)?.template_id)\n    .filter((id): id is TemplateId => id !== undefined)\n  return templateIds.length > 0 ? { kind: 'collection', templates: templateIds } : undefined\n}\n\nexport function describeControlTarget(target: BioTemplateControlTarget): string {\n  if (typeof target === 'string') return target\n  if (isTemplateEnvelope(target)) return target.template_id\n  return collectionPresetName(target) ?? collectionPackName(target) ?? 'template collection'\n}\n\nfunction isTemplateEnvelope(value: unknown): value is BioTemplateEnvelope<unknown> {\n  return isRecord(value) && typeof value.template_id === 'string' && 'data' in value\n}\n\nfunction collectionPresetName(value: unknown): string | undefined {\n  if (!isRecord(value) || !isRecord(value.metadata)) return undefined\n  return typeof value.metadata.preset === 'string' ? value.metadata.preset : undefined\n}\n\nfunction collectionPackName(value: unknown): string | undefined {\n  if (!isRecord(value) || !isRecord(value.metadata)) return undefined\n  return typeof value.metadata.pack === 'string' ? value.metadata.pack : undefined\n}\n\nfunction isRecord(value: unknown): value is Record<string, unknown> {\n  return typeof value === 'object' && value !== null\n}\n","export const ICONS = {\n  plate: ['M4 4h16v16H4z', 'M8 4v16', 'M12 4v16', 'M16 4v16', 'M4 8h16', 'M4 12h16', 'M4 16h16'],\n  samples: ['M16 21v-2a4 4 0 0 0-8 0v2', 'M12 11a4 4 0 1 0 0-8 4 4 0 0 0 0 8'],\n  dose: ['M10 2v8L4 20h16l-6-10V2', 'M8 2h8', 'M7 14h10'],\n  table: ['M3 5h18', 'M3 12h18', 'M3 19h18', 'M8 5v14', 'M16 5v14'],\n  run: ['M4 17l6-6 4 4 6-8', 'M4 21h16'],\n  settings: ['M12 8a4 4 0 1 0 0 8 4 4 0 0 0 0-8', 'M4 12h2', 'M18 12h2', 'M12 4v2', 'M12 18v2'],\n}\n\nexport const PLATE_FORMAT_OPTIONS = [6, 12, 24, 48, 96, 384] as const\nexport const CONCENTRATION_UNITS = ['nM', 'uM', 'mM', 'ug/mL', 'mg/mL'] as const\n","import {\n  CONCENTRATION_UNITS,\n  ICONS,\n  PLATE_FORMAT_OPTIONS,\n} from './controlSchemaConstants'\nimport type {\n  BioTemplateControlSchema,\n} from './controlSchemaTypes'\nimport type {\n  TemplateId,\n} from './types'\n\nexport const templateControlSchemas = {\n  'plate-map': {\n    plateName: {\n      label: 'Plate name',\n      default: 'Plate 1',\n      section: 'layout',\n      sectionLabel: 'Layout',\n      sectionSubtitle: 'Plate geometry',\n      view: 'design',\n      sidebar: { icon: ICONS.plate, iconColor: '#6366f1', iconBg: '#e0e7ff' },\n    },\n    plateFormat: {\n      label: 'Format',\n      default: 96,\n      options: PLATE_FORMAT_OPTIONS,\n      section: 'layout',\n      view: 'design',\n    },\n    sampleNames: {\n      type: 'tags',\n      label: 'Samples',\n      default: ['Control', 'Treatment'],\n      section: 'samples',\n      sectionLabel: 'Samples',\n      sectionSubtitle: 'Groups and legend',\n      view: 'design',\n      sidebar: { icon: ICONS.samples, iconColor: '#10b981', iconBg: '#d1fae5' },\n    },\n  },\n  'sample-sheet': {\n    sampleCount: {\n      type: 'number',\n      label: 'Sample count',\n      default: 2,\n      min: 1,\n      max: 10000,\n      section: 'samples',\n      sectionLabel: 'Samples',\n      sectionSubtitle: 'Metadata table',\n      view: 'design',\n      sidebar: { icon: ICONS.samples, iconColor: '#10b981', iconBg: '#d1fae5' },\n    },\n    includeGroups: {\n      label: 'Include groups',\n      default: true,\n      section: 'samples',\n      view: 'design',\n    },\n    includeBatch: {\n      label: 'Include batch',\n      default: false,\n      section: 'columns',\n      sectionLabel: 'Columns',\n      view: 'design',\n      sidebar: { icon: ICONS.table, iconColor: '#0ea5e9', iconBg: '#e0f2fe' },\n    },\n  },\n  'sample-prep': {\n    prepType: {\n      label: 'Prep type',\n      default: 'extraction',\n      options: ['extraction', 'dilution', 'normalization', 'transfer', 'quench', 'custom'],\n      section: 'protocol',\n      sectionLabel: 'Protocol',\n      sectionSubtitle: 'Prep workflow',\n      view: 'design',\n      sidebar: { icon: ICONS.run, iconColor: '#f97316', iconBg: '#ffedd5' },\n    },\n    volumeUnit: {\n      label: 'Volume unit',\n      default: 'uL',\n      options: ['uL', 'mL'],\n      section: 'protocol',\n      view: 'design',\n    },\n    outputVolume: {\n      type: 'number',\n      label: 'Output volume',\n      default: 50,\n      min: 0,\n      section: 'protocol',\n      view: 'design',\n    },\n  },\n  'dose-response': {\n    unit: {\n      label: 'Dose unit',\n      default: 'uM',\n      options: CONCENTRATION_UNITS,\n      section: 'dose',\n      sectionLabel: 'Dose Design',\n      sectionSubtitle: 'Concentration series',\n      view: 'design',\n      sidebar: { icon: ICONS.dose, iconColor: '#8b5cf6', iconBg: '#ede9fe' },\n    },\n    replicates: {\n      type: 'number',\n      label: 'Replicates',\n      default: 3,\n      min: 1,\n      max: 24,\n      section: 'dose',\n      view: 'design',\n    },\n    includePlateLayout: {\n      label: 'Create plate layout',\n      default: true,\n      section: 'layout',\n      sectionLabel: 'Layout',\n      sectionSubtitle: 'Well assignment',\n      view: 'design',\n      sidebar: { icon: ICONS.plate, iconColor: '#6366f1', iconBg: '#e0e7ff', defaultOpen: false },\n    },\n  },\n  'calibration-curve': {\n    analyte: {\n      label: 'Analyte',\n      default: 'Analyte',\n      section: 'standards',\n      sectionLabel: 'Standards',\n      sectionSubtitle: 'Curve setup',\n      view: 'analysis',\n      sidebar: { icon: ICONS.dose, iconColor: '#8b5cf6', iconBg: '#ede9fe' },\n    },\n    model: {\n      label: 'Model',\n      default: 'linear',\n      options: ['linear', 'linear-weighted-1-x', 'linear-weighted-1-x2', 'quadratic', 'four-parameter-logistic'],\n      section: 'fit',\n      sectionLabel: 'Fit',\n      view: 'analysis',\n      sidebar: { icon: ICONS.settings, iconColor: '#6366f1', iconBg: '#e0e7ff' },\n    },\n    minRSquared: {\n      type: 'number',\n      label: 'Minimum R squared',\n      default: 0.99,\n      min: 0,\n      max: 1,\n      props: { step: 0.001 },\n      section: 'fit',\n      view: 'analysis',\n    },\n  },\n  'time-course': {\n    timeUnit: {\n      label: 'Time unit',\n      default: 'hour',\n      options: ['second', 'minute', 'hour', 'day', 'week'],\n      section: 'schedule',\n      sectionLabel: 'Schedule',\n      sectionSubtitle: 'Sampling timeline',\n      view: 'design',\n      sidebar: { icon: ICONS.run, iconColor: '#0ea5e9', iconBg: '#e0f2fe' },\n    },\n    replicates: {\n      type: 'number',\n      label: 'Replicates',\n      default: 3,\n      min: 1,\n      max: 24,\n      section: 'samples',\n      sectionLabel: 'Samples',\n      view: 'design',\n      sidebar: { icon: ICONS.samples, iconColor: '#10b981', iconBg: '#d1fae5' },\n    },\n  },\n  'protocol-steps': {\n    defaultDuration: {\n      type: 'number',\n      label: 'Default duration',\n      default: 30,\n      min: 0,\n      section: 'protocol',\n      sectionLabel: 'Protocol',\n      sectionSubtitle: 'Step defaults',\n      view: 'design',\n      sidebar: { icon: ICONS.run, iconColor: '#f97316', iconBg: '#ffedd5' },\n      props: { suffix: 'min' },\n    },\n    editable: {\n      label: 'Editable timeline',\n      default: true,\n      section: 'protocol',\n      view: 'design',\n    },\n  },\n  'assay-matrix': {\n    featureType: {\n      label: 'Feature type',\n      default: 'metabolite',\n      options: ['metabolite', 'protein', 'gene', 'cell', 'compound', 'readout', 'other'],\n      section: 'features',\n      sectionLabel: 'Features',\n      sectionSubtitle: 'Measurement matrix',\n      view: 'analysis',\n      sidebar: { icon: ICONS.table, iconColor: '#0ea5e9', iconBg: '#e0f2fe' },\n    },\n    normalizeValues: {\n      label: 'Normalize values',\n      default: false,\n      section: 'analysis',\n      sectionLabel: 'Analysis',\n      view: 'analysis',\n      sidebar: { icon: ICONS.settings, iconColor: '#6366f1', iconBg: '#e0e7ff', defaultOpen: false },\n    },\n  },\n  'reagent-list': {\n    reagentKind: {\n      label: 'Reagent kind',\n      default: 'reagent',\n      options: ['compound', 'antibody', 'primer', 'enzyme', 'buffer', 'media', 'kit', 'reagent', 'other'],\n      section: 'inventory',\n      sectionLabel: 'Inventory',\n      sectionSubtitle: 'Reagent metadata',\n      view: 'design',\n      sidebar: { icon: ICONS.table, iconColor: '#10b981', iconBg: '#d1fae5' },\n    },\n    trackStock: {\n      label: 'Track stock level',\n      default: true,\n      section: 'inventory',\n      view: 'design',\n    },\n  },\n  'flow-cytometry-panel': {\n    markers: {\n      type: 'tags',\n      label: 'Markers',\n      default: ['CD3', 'CD4', 'CD8'],\n      section: 'panel',\n      sectionLabel: 'Panel',\n      sectionSubtitle: 'Markers and controls',\n      view: 'design',\n      sidebar: { icon: ICONS.table, iconColor: '#0ea5e9', iconBg: '#e0f2fe' },\n    },\n    instrument: {\n      label: 'Instrument',\n      default: 'Flow cytometer',\n      section: 'panel',\n      sectionLabel: 'Panel',\n      sectionSubtitle: 'Markers and controls',\n      view: 'design',\n      sidebar: { icon: ICONS.settings, iconColor: '#6366f1', iconBg: '#e0e7ff' },\n    },\n    includeDefaultControls: {\n      label: 'Default controls',\n      default: true,\n      section: 'panel',\n      view: 'design',\n    },\n  },\n  'instrument-run': {\n    instrument: {\n      label: 'Instrument',\n      default: 'LC-MS',\n      options: ['LC-MS', 'GC-MS', 'Orbitrap', 'Triple quadrupole', 'Plate reader', 'Other'],\n      section: 'acquisition',\n      sectionLabel: 'Acquisition',\n      sectionSubtitle: 'Run queue',\n      view: 'run',\n      sidebar: { icon: ICONS.run, iconColor: '#ef4444', iconBg: '#fee2e2' },\n    },\n    method: {\n      label: 'Method',\n      default: 'Default method',\n      section: 'acquisition',\n      view: 'run',\n    },\n    includeQc: {\n      label: 'Include QC',\n      default: true,\n      section: 'quality',\n      sectionLabel: 'Quality Control',\n      view: 'run',\n      sidebar: { icon: ICONS.settings, iconColor: '#6366f1', iconBg: '#e0e7ff', defaultOpen: false },\n    },\n  },\n  'qpcr-plate': {\n    chemistry: {\n      label: 'Chemistry',\n      default: 'sybr',\n      options: ['sybr', 'taqman', 'probe', 'evagreen', 'other'],\n      section: 'assay',\n      sectionLabel: 'Assay',\n      sectionSubtitle: 'qPCR setup',\n      view: 'design',\n      sidebar: { icon: ICONS.plate, iconColor: '#6366f1', iconBg: '#e0e7ff' },\n    },\n    replicates: {\n      type: 'number',\n      label: 'Replicates',\n      default: 3,\n      min: 1,\n      max: 12,\n      section: 'assay',\n      view: 'design',\n    },\n    includeNoTemplateControls: {\n      label: 'No-template controls',\n      default: true,\n      section: 'controls',\n      sectionLabel: 'Controls',\n      view: 'design',\n      sidebar: { icon: ICONS.settings, iconColor: '#8b5cf6', iconBg: '#ede9fe', defaultOpen: false },\n    },\n  },\n} satisfies Record<TemplateId, BioTemplateControlSchema>\n","import {\n  CONCENTRATION_UNITS,\n  ICONS,\n  PLATE_FORMAT_OPTIONS,\n} from './controlSchemaConstants'\nimport type {\n  BioTemplateControlSchema,\n} from './controlSchemaTypes'\nimport {\n  templateControlSchemas,\n} from './templateControlSchemas'\nimport type {\n  TemplatePresetId,\n} from './types'\n\nexport const presetControlSchemas = {\n  'wellplate-screen': {\n    ...templateControlSchemas['plate-map'],\n    ...templateControlSchemas['dose-response'],\n    sampleNames: {\n      ...templateControlSchemas['plate-map'].sampleNames,\n      default: ['Control', 'Treatment'],\n    },\n  },\n  'qpcr-expression': {\n    sampleNames: {\n      type: 'tags',\n      label: 'Samples',\n      default: ['Control', 'Treatment'],\n      section: 'samples',\n      sectionLabel: 'Samples',\n      sectionSubtitle: 'Expression groups',\n      view: 'design',\n      sidebar: { icon: ICONS.samples, iconColor: '#10b981', iconBg: '#d1fae5' },\n    },\n    targets: {\n      type: 'tags',\n      label: 'Targets',\n      default: ['ACTB', 'GAPDH'],\n      section: 'assay',\n      sectionLabel: 'Assay',\n      view: 'design',\n      sidebar: { icon: ICONS.plate, iconColor: '#6366f1', iconBg: '#e0e7ff' },\n    },\n    ...templateControlSchemas['qpcr-plate'],\n  },\n  'lcms-batch': {\n    sampleNames: {\n      type: 'tags',\n      label: 'Samples',\n      default: ['S001', 'S002'],\n      section: 'samples',\n      sectionLabel: 'Samples',\n      sectionSubtitle: 'Batch samples',\n      view: 'run',\n      sidebar: { icon: ICONS.samples, iconColor: '#10b981', iconBg: '#d1fae5' },\n    },\n    featureNames: {\n      type: 'tags',\n      label: 'Features',\n      default: ['Glucose', 'Lactate'],\n      section: 'features',\n      sectionLabel: 'Features',\n      view: 'analysis',\n      sidebar: { icon: ICONS.table, iconColor: '#0ea5e9', iconBg: '#e0f2fe' },\n    },\n    ...templateControlSchemas['instrument-run'],\n    ...templateControlSchemas['assay-matrix'],\n  },\n  'targeted-metabolomics': {\n    sampleNames: {\n      type: 'tags',\n      label: 'Samples',\n      default: ['S001', 'S002'],\n      section: 'samples',\n      sectionLabel: 'Samples',\n      sectionSubtitle: 'Unknowns and QC pool',\n      view: 'run',\n      sidebar: { icon: ICONS.samples, iconColor: '#10b981', iconBg: '#d1fae5' },\n    },\n    metaboliteNames: {\n      type: 'tags',\n      label: 'Metabolites',\n      default: ['Glucose', 'Lactate', 'Pyruvate'],\n      section: 'features',\n      sectionLabel: 'Metabolites',\n      sectionSubtitle: 'Quantitation panel',\n      view: 'analysis',\n      sidebar: { icon: ICONS.table, iconColor: '#0ea5e9', iconBg: '#e0f2fe' },\n    },\n    internalStandards: {\n      type: 'tags',\n      label: 'Internal standards',\n      default: ['Stable isotope internal standard mix'],\n      section: 'standards',\n      sectionLabel: 'Standards',\n      sectionSubtitle: 'Calibration and internal standards',\n      view: 'analysis',\n      sidebar: { icon: ICONS.dose, iconColor: '#8b5cf6', iconBg: '#ede9fe' },\n    },\n    standardConcentrations: {\n      type: 'tags',\n      label: 'Calibration levels',\n      default: ['0.1', '1', '10', '100'],\n      section: 'standards',\n      view: 'analysis',\n    },\n    concentrationUnit: {\n      label: 'Concentration unit',\n      default: 'uM',\n      options: CONCENTRATION_UNITS,\n      section: 'standards',\n      view: 'analysis',\n    },\n    responseUnit: {\n      label: 'Response unit',\n      default: 'peak area ratio',\n      section: 'readout',\n      sectionLabel: 'Readout',\n      view: 'analysis',\n      sidebar: { icon: ICONS.table, iconColor: '#0ea5e9', iconBg: '#e0f2fe' },\n    },\n    instrument: {\n      ...templateControlSchemas['instrument-run'].instrument,\n      default: 'LC-MS',\n    },\n    method: {\n      ...templateControlSchemas['instrument-run'].method,\n      default: 'Targeted metabolomics',\n    },\n    prepType: {\n      ...templateControlSchemas['sample-prep'].prepType,\n      default: 'extraction',\n    },\n    outputVolume: templateControlSchemas['sample-prep'].outputVolume,\n    includeQc: templateControlSchemas['instrument-run'].includeQc,\n  },\n  'elisa-assay': {\n    sampleNames: {\n      type: 'tags',\n      label: 'Samples',\n      default: ['Control', 'Treatment'],\n      section: 'samples',\n      sectionLabel: 'Samples',\n      sectionSubtitle: 'Unknowns and controls',\n      view: 'design',\n      sidebar: { icon: ICONS.samples, iconColor: '#10b981', iconBg: '#d1fae5' },\n    },\n    analyte: {\n      label: 'Analyte',\n      default: 'Analyte',\n      section: 'standards',\n      sectionLabel: 'Standards',\n      sectionSubtitle: 'Calibration setup',\n      view: 'analysis',\n      sidebar: { icon: ICONS.dose, iconColor: '#8b5cf6', iconBg: '#ede9fe' },\n    },\n    standardConcentrations: {\n      type: 'tags',\n      label: 'Standards',\n      default: ['1000', '100', '10', '1'],\n      section: 'standards',\n      view: 'analysis',\n    },\n    unit: {\n      label: 'Concentration unit',\n      default: 'pg/mL',\n      options: ['pg/mL', 'ng/mL', 'ug/mL', 'nM', 'uM'],\n      section: 'standards',\n      view: 'analysis',\n    },\n    responseUnit: {\n      label: 'Response unit',\n      default: 'OD450',\n      section: 'readout',\n      sectionLabel: 'Readout',\n      view: 'analysis',\n      sidebar: { icon: ICONS.table, iconColor: '#0ea5e9', iconBg: '#e0f2fe' },\n    },\n    plateName: {\n      label: 'Plate name',\n      default: 'ELISA plate',\n      section: 'layout',\n      sectionLabel: 'Layout',\n      sectionSubtitle: 'Plate geometry',\n      view: 'design',\n      sidebar: { icon: ICONS.plate, iconColor: '#6366f1', iconBg: '#e0e7ff' },\n    },\n    plateFormat: {\n      label: 'Format',\n      default: 96,\n      options: PLATE_FORMAT_OPTIONS,\n      section: 'layout',\n      view: 'design',\n    },\n  },\n  'flow-cytometry-assay': {\n    sampleNames: {\n      type: 'tags',\n      label: 'Samples',\n      default: ['Control', 'Treatment'],\n      section: 'samples',\n      sectionLabel: 'Samples',\n      sectionSubtitle: 'Assay groups',\n      view: 'design',\n      sidebar: { icon: ICONS.samples, iconColor: '#10b981', iconBg: '#d1fae5' },\n    },\n    markers: {\n      ...templateControlSchemas['flow-cytometry-panel'].markers,\n      default: ['CD3', 'CD4', 'CD8'],\n    },\n    featureNames: {\n      type: 'tags',\n      label: 'Readouts',\n      default: ['CD3+ cells', 'CD4+ cells', 'CD8+ cells'],\n      section: 'features',\n      sectionLabel: 'Readouts',\n      sectionSubtitle: 'Assay matrix columns',\n      view: 'analysis',\n      sidebar: { icon: ICONS.table, iconColor: '#0ea5e9', iconBg: '#e0f2fe' },\n    },\n    instrument: {\n      ...templateControlSchemas['flow-cytometry-panel'].instrument,\n      default: 'Flow cytometer',\n    },\n    includeDefaultControls: templateControlSchemas['flow-cytometry-panel'].includeDefaultControls,\n  },\n  'western-blot-assay': {\n    sampleNames: {\n      type: 'tags',\n      label: 'Samples',\n      default: ['Control', 'Treatment'],\n      section: 'samples',\n      sectionLabel: 'Samples',\n      sectionSubtitle: 'Blot lanes and groups',\n      view: 'design',\n      sidebar: { icon: ICONS.samples, iconColor: '#10b981', iconBg: '#d1fae5' },\n    },\n    targets: {\n      type: 'tags',\n      label: 'Targets',\n      default: ['Target protein'],\n      section: 'assay',\n      sectionLabel: 'Assay',\n      sectionSubtitle: 'Protein targets',\n      view: 'design',\n      sidebar: { icon: ICONS.table, iconColor: '#0ea5e9', iconBg: '#e0f2fe' },\n    },\n    loadingControl: {\n      label: 'Loading control',\n      default: 'ACTB',\n      section: 'normalization',\n      sectionLabel: 'Normalization',\n      view: 'analysis',\n      sidebar: { icon: ICONS.settings, iconColor: '#6366f1', iconBg: '#e0e7ff' },\n    },\n  },\n} satisfies Record<TemplatePresetId, BioTemplateControlSchema>\n","import {\n  controlsToFormSchema,\n  controlsToSectionFormSchemas,\n  controlsToSidebarPanels,\n  getControlDefaults,\n  useControlSchema,\n  type ControlSchemaOptions,\n  type UseControlSchemaReturn,\n} from '../composables/useControlSchema'\nimport {\n  cloneControlSchema,\n  cloneSchemaMap,\n} from './controlSchemaClone'\nimport {\n  mergeTemplateControlSchemas,\n} from './controlSchemaMerge'\nimport {\n  describeControlTarget,\n  resolveControlSchemaTarget,\n} from './controlSchemaTargets'\nimport {\n  presetControlSchemas,\n} from './presetControlSchemas'\nimport {\n  templateControlSchemas,\n} from './templateControlSchemas'\nimport type {\n  TemplateId,\n  TemplatePresetId,\n} from './types'\nimport type {\n  BioTemplateControlSchema,\n  BioTemplateControlTarget,\n} from './controlSchemaTypes'\n\nexport type {\n  BioTemplateControlSchema,\n  BioTemplateControlTarget,\n} from './controlSchemaTypes'\n\nexport function listBioTemplateControlSchemas(): Record<TemplateId, BioTemplateControlSchema> {\n  return cloneSchemaMap(templateControlSchemas)\n}\n\nexport function listBioTemplatePresetControlSchemas(): Record<TemplatePresetId, BioTemplateControlSchema> {\n  return cloneSchemaMap(presetControlSchemas)\n}\n\nexport function getBioTemplateControlSchema(\n  target: BioTemplateControlTarget\n): BioTemplateControlSchema | undefined {\n  const resolved = resolveControlSchemaTarget(target)\n  if (!resolved) return undefined\n\n  if (resolved.kind === 'template') {\n    return cloneControlSchema(templateControlSchemas[resolved.name])\n  }\n  if (resolved.kind === 'preset') {\n    return cloneControlSchema(presetControlSchemas[resolved.name])\n  }\n  return mergeTemplateControlSchemas(resolved.templates, templateControlSchemas)\n}\n\nexport function requireBioTemplateControlSchema(\n  target: BioTemplateControlTarget\n): BioTemplateControlSchema {\n  const schema = getBioTemplateControlSchema(target)\n  if (!schema) {\n    throw new Error(`No built-in control schema found for '${describeControlTarget(target)}'.`)\n  }\n  return schema\n}\n\nexport function createBioTemplateControlToolkit(\n  target: BioTemplateControlTarget,\n  options: ControlSchemaOptions = {}\n): UseControlSchemaReturn<BioTemplateControlSchema> {\n  return useControlSchema(requireBioTemplateControlSchema(target), options)\n}\n\nexport function bioTemplateControlsToFormSchema(\n  target: BioTemplateControlTarget,\n  options: ControlSchemaOptions = {}\n) {\n  return controlsToFormSchema(requireBioTemplateControlSchema(target), options)\n}\n\nexport function bioTemplateControlsToSidebarPanels(\n  target: BioTemplateControlTarget,\n  options: ControlSchemaOptions = {}\n) {\n  return controlsToSidebarPanels(requireBioTemplateControlSchema(target), options)\n}\n\nexport function bioTemplateControlsToSectionFormSchemas(\n  target: BioTemplateControlTarget,\n  options: ControlSchemaOptions = {}\n) {\n  return controlsToSectionFormSchemas(requireBioTemplateControlSchema(target), options)\n}\n\nexport function getBioTemplateControlDefaults(target: BioTemplateControlTarget) {\n  return 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