@morscherlab/mint-sdk 1.0.0-rc.4 → 1.0.0-rc.6

package/dist/templates/controlSchemaTypes.d.ts

@@ -1,4 +1,4 @@
-import { ControlDefinition } from '../composables/useControlSchema';
+import { ControlDefinition } from '../composables/controlSchemaTypes';
 import { BioTemplateEnvelope, TemplateCollectionEnvelope, TemplateId, TemplatePackId, TemplatePresetId } from './types';
 export type BioTemplateControlSchema = Record<string, ControlDefinition>;
 export type BioTemplateControlTarget = TemplateId | TemplatePackId | TemplatePresetId | string | BioTemplateEnvelope<unknown> | TemplateCollectionEnvelope;

package/dist/templates/index.js

@@ -1,2 +1,2 @@
-import { $ as toTimeCourseRows, $t as listBioTemplatePacks, A as createSamplePrepTemplate, At as toCalibrationCurveRows, B as toBioTemplateComponentProps, Bt as validatePlateMapData, C as createFlowCytometryPanelTemplate, Ct as toInstrumentRunScheduleEvents, D as createTimeCourseTemplate, Dt as toFlowPanelRows, E as createProtocolStepsTemplate, Et as toFlowPanelDataFrame, F as getBioTemplateComponentProps, Ft as validateAssayMatrixData, G as toTemplateDataFrame, Gt as validateSampleSheetData, H as toBioTemplateComponentPropsById, Ht as validateQpcrPlateData, I as listBioTemplateComponentBindings, It as validateCalibrationCurveData, J as toDoseLayoutState, Jt as getBioTemplatePresetInfo, K as toWellMapArray, Kt as validateTimeCourseData, L as toBioTemplateComponentBindings, Lt as validateDoseResponseData, M as createPlateMapTemplate, Mt as toAssayMatrixDataFrame, N as bioTemplatePresetControlValuesToOptions, Nt as toAssayMatrixRows, O as createCalibrationCurveTemplate, Ot as toCalibrationCurveColumns, P as getBioTemplateComponentBindings, Pt as toAssayMatrixSampleOptions, Q as toTimeCourseDataFrame, Qt as getBioTemplatePackInfo, R as toBioTemplateComponentBindingsById, Rt as validateFlowCytometryPanelData, S as createInstrumentRunTemplate, St as toInstrumentRunRows, T as createAssayMatrixTemplate, Tt as toFlowPanelColumns, U as toBioTemplateComponentSnippets, Ut as validateReagentListData, V as toBioTemplateComponentPropsByComponent, Vt as validateProtocolStepsData, W as toBioTemplateComponentUsage, Wt as validateSamplePrepData, X as toWellPlateWells, Xt as searchBioTemplatePresets, Y as toPlateMapEditorState, Yt as listBioTemplatePresets, Z as toTimeCourseColumns, Zt as bioTemplatePacks, _ as createElisaAssayCollection, _t as toProtocolDataFrame, a as getBioTemplateControlDefaults, an as TEMPLATE_COLLECTION_KEY, at as toSamplePrepColumns, b as createQpcrExpressionCollection, bt as toInstrumentRunColumns, c as listBioTemplatePresetControlSchemas, cn as createTemplateEnvelope, ct as toReagentColumns, d as createBioTemplatePresetCollectionFromControls, dn as extractTemplateCollection, dt as toReagentRows, en as searchBioTemplatePacks, et as toTimeCourseSteps, f as createWellPlateScreenCollection, fn as getTemplateData, ft as toQpcrColumns, g as createFlowCytometryAssayCollection, gt as toProtocolColumns, h as createWesternBlotAssayCollection, ht as toQpcrWellPlateWells, i as createBioTemplateControlToolkit, in as searchBioTemplateCatalog, it as toSampleRows, j as createSampleSheetTemplate, jt as toAssayMatrixColumns, k as createDoseResponseTemplate, kt as toCalibrationCurveDataFrame, l as requireBioTemplateControlSchema, ln as ensureTemplateEnvelope, lt as toReagentDataFrame, m as createDefaultBioTemplate, mt as toQpcrRows, n as bioTemplateControlsToSectionFormSchemas, nn as getBioTemplateInfo, nt as toSampleDataFrame, o as getBioTemplateControlSchema, on as assertTemplateEnvelope, ot as toSamplePrepDataFrame, p as createBioTemplatePackCollection, pt as toQpcrDataFrame, q as toDoseConditions, qt as bioTemplatePresets, r as bioTemplateControlsToSidebarPanels, rn as listBioTemplateCatalog, rt as toSampleOptions, s as listBioTemplateControlSchemas, sn as createTemplateCollection, st as toSamplePrepRows, t as bioTemplateControlsToFormSchema, tn as bioTemplateCatalog, tt as toSampleColumns, u as createBioTemplatePresetCollection, un as ensureTemplateFromCollection, ut as toReagentListItems, v as createTargetedMetabolomicsCollection, vt as toProtocolRows, w as createReagentListTemplate, wt as toInstrumentRunSteps, x as createQpcrPlateTemplate, xt as toInstrumentRunDataFrame, y as createLcmsBatchCollection, yt as toProtocolSteps, z as toBioTemplateComponentImports, zt as validateInstrumentRunData } from "../templates-bUAWMn5L.js";
+import { $ as toTimeCourseRows, $t as listBioTemplatePacks, A as createSamplePrepTemplate, At as toCalibrationCurveRows, B as toBioTemplateComponentProps, Bt as validatePlateMapData, C as createFlowCytometryPanelTemplate, Ct as toInstrumentRunScheduleEvents, D as createTimeCourseTemplate, Dt as toFlowPanelRows, E as createProtocolStepsTemplate, Et as toFlowPanelDataFrame, F as getBioTemplateComponentProps, Ft as validateAssayMatrixData, G as toTemplateDataFrame, Gt as validateSampleSheetData, H as toBioTemplateComponentPropsById, Ht as validateQpcrPlateData, I as listBioTemplateComponentBindings, It as validateCalibrationCurveData, J as toDoseLayoutState, Jt as getBioTemplatePresetInfo, K as toWellMapArray, Kt as validateTimeCourseData, L as toBioTemplateComponentBindings, Lt as validateDoseResponseData, M as createPlateMapTemplate, Mt as toAssayMatrixDataFrame, N as bioTemplatePresetControlValuesToOptions, Nt as toAssayMatrixRows, O as createCalibrationCurveTemplate, Ot as toCalibrationCurveColumns, P as getBioTemplateComponentBindings, Pt as toAssayMatrixSampleOptions, Q as toTimeCourseDataFrame, Qt as getBioTemplatePackInfo, R as toBioTemplateComponentBindingsById, Rt as validateFlowCytometryPanelData, S as createInstrumentRunTemplate, St as toInstrumentRunRows, T as createAssayMatrixTemplate, Tt as toFlowPanelColumns, U as toBioTemplateComponentSnippets, Ut as validateReagentListData, V as toBioTemplateComponentPropsByComponent, Vt as validateProtocolStepsData, W as toBioTemplateComponentUsage, Wt as validateSamplePrepData, X as toWellPlateWells, Xt as searchBioTemplatePresets, Y as toPlateMapEditorState, Yt as listBioTemplatePresets, Z as toTimeCourseColumns, Zt as bioTemplatePacks, _ as createElisaAssayCollection, _t as toProtocolDataFrame, a as getBioTemplateControlDefaults, an as TEMPLATE_COLLECTION_KEY, at as toSamplePrepColumns, b as createQpcrExpressionCollection, bt as toInstrumentRunColumns, c as listBioTemplatePresetControlSchemas, cn as createTemplateEnvelope, ct as toReagentColumns, d as createBioTemplatePresetCollectionFromControls, dn as extractTemplateCollection, dt as toReagentRows, en as searchBioTemplatePacks, et as toTimeCourseSteps, f as createWellPlateScreenCollection, fn as getTemplateData, ft as toQpcrColumns, g as createFlowCytometryAssayCollection, gt as toProtocolColumns, h as createWesternBlotAssayCollection, ht as toQpcrWellPlateWells, i as createBioTemplateControlToolkit, in as searchBioTemplateCatalog, it as toSampleRows, j as createSampleSheetTemplate, jt as toAssayMatrixColumns, k as createDoseResponseTemplate, kt as toCalibrationCurveDataFrame, l as requireBioTemplateControlSchema, ln as ensureTemplateEnvelope, lt as toReagentDataFrame, m as createDefaultBioTemplate, mt as toQpcrRows, n as bioTemplateControlsToSectionFormSchemas, nn as getBioTemplateInfo, nt as toSampleDataFrame, o as getBioTemplateControlSchema, on as assertTemplateEnvelope, ot as toSamplePrepDataFrame, p as createBioTemplatePackCollection, pt as toQpcrDataFrame, q as toDoseConditions, qt as bioTemplatePresets, r as bioTemplateControlsToSidebarPanels, rn as listBioTemplateCatalog, rt as toSampleOptions, s as listBioTemplateControlSchemas, sn as createTemplateCollection, st as toSamplePrepRows, t as bioTemplateControlsToFormSchema, tn as bioTemplateCatalog, tt as toSampleColumns, u as createBioTemplatePresetCollection, un as ensureTemplateFromCollection, ut as toReagentListItems, v as createTargetedMetabolomicsCollection, vt as toProtocolRows, w as createReagentListTemplate, wt as toInstrumentRunSteps, x as createQpcrPlateTemplate, xt as toInstrumentRunDataFrame, y as createLcmsBatchCollection, yt as toProtocolSteps, z as toBioTemplateComponentImports, zt as validateInstrumentRunData } from "../templates-DSbHJC4v.js";
 export { TEMPLATE_COLLECTION_KEY, assertTemplateEnvelope, bioTemplateCatalog, bioTemplateControlsToFormSchema, bioTemplateControlsToSectionFormSchemas, bioTemplateControlsToSidebarPanels, bioTemplatePacks, bioTemplatePresetControlValuesToOptions, bioTemplatePresets, createAssayMatrixTemplate, createBioTemplateControlToolkit, createBioTemplatePackCollection, createBioTemplatePresetCollection, createBioTemplatePresetCollectionFromControls, createCalibrationCurveTemplate, createDefaultBioTemplate, createDoseResponseTemplate, createElisaAssayCollection, createFlowCytometryAssayCollection, createFlowCytometryPanelTemplate, createInstrumentRunTemplate, createLcmsBatchCollection, createPlateMapTemplate, createProtocolStepsTemplate, createQpcrExpressionCollection, createQpcrPlateTemplate, createReagentListTemplate, createSamplePrepTemplate, createSampleSheetTemplate, createTargetedMetabolomicsCollection, createTemplateCollection, createTemplateEnvelope, createTimeCourseTemplate, createWellPlateScreenCollection, createWesternBlotAssayCollection, ensureTemplateEnvelope, ensureTemplateFromCollection, extractTemplateCollection, getBioTemplateComponentBindings, getBioTemplateComponentProps, getBioTemplateControlDefaults, getBioTemplateControlSchema, getBioTemplateInfo, getBioTemplatePackInfo, getBioTemplatePresetInfo, getTemplateData, listBioTemplateCatalog, listBioTemplateComponentBindings, listBioTemplateControlSchemas, listBioTemplatePacks, listBioTemplatePresetControlSchemas, listBioTemplatePresets, requireBioTemplateControlSchema, searchBioTemplateCatalog, searchBioTemplatePacks, searchBioTemplatePresets, toAssayMatrixColumns, toAssayMatrixDataFrame, toAssayMatrixRows, toAssayMatrixSampleOptions, toBioTemplateComponentBindings, toBioTemplateComponentBindingsById, toBioTemplateComponentImports, toBioTemplateComponentProps, toBioTemplateComponentPropsByComponent, toBioTemplateComponentPropsById, toBioTemplateComponentSnippets, toBioTemplateComponentUsage, toCalibrationCurveColumns, toCalibrationCurveDataFrame, toCalibrationCurveRows, toDoseConditions, toDoseLayoutState, toFlowPanelColumns, toFlowPanelDataFrame, toFlowPanelRows, toInstrumentRunColumns, toInstrumentRunDataFrame, toInstrumentRunRows, toInstrumentRunScheduleEvents, toInstrumentRunSteps, toPlateMapEditorState, toProtocolColumns, toProtocolDataFrame, toProtocolRows, toProtocolSteps, toQpcrColumns, toQpcrDataFrame, toQpcrRows, toQpcrWellPlateWells, toReagentColumns, toReagentDataFrame, toReagentListItems, toReagentRows, toSampleColumns, toSampleDataFrame, toSampleOptions, toSamplePrepColumns, toSamplePrepDataFrame, toSamplePrepRows, toSampleRows, toTemplateDataFrame, toTimeCourseColumns, toTimeCourseDataFrame, toTimeCourseRows, toTimeCourseSteps, toWellMapArray, toWellPlateWells, validateAssayMatrixData, validateCalibrationCurveData, validateDoseResponseData, validateFlowCytometryPanelData, validateInstrumentRunData, validatePlateMapData, validateProtocolStepsData, validateQpcrPlateData, validateReagentListData, validateSamplePrepData, validateSampleSheetData, validateTimeCourseData };

package/dist/templates/templateAdapterTypes.d.ts

@@ -0,0 +1,48 @@
+import { DataFrameColumn, PlateCondition, PlateMapEditorState, ProtocolStep, Reagent, ScheduleEvent, SelectOption, Well } from '../types';
+export type PlateMapEditorAdapterResult = PlateMapEditorState;
+export type WellMapAdapterResult = Record<string, Well>;
+export type SampleRowsAdapterResult = Array<Record<string, unknown>>;
+export type SampleColumnsAdapterResult = DataFrameColumn<Record<string, unknown>>[];
+export interface DataFrameAdapterResult {
+    data: Array<Record<string, unknown>>;
+    columns: DataFrameColumn<Record<string, unknown>>[];
+    rowKey?: string;
+}
+export type SampleDataFrameAdapterResult = DataFrameAdapterResult;
+export type SampleOptionsAdapterResult = SelectOption<string>[];
+export type SamplePrepRowsAdapterResult = Array<Record<string, unknown>>;
+export type SamplePrepColumnsAdapterResult = DataFrameColumn<Record<string, unknown>>[];
+export type SamplePrepDataFrameAdapterResult = DataFrameAdapterResult;
+export type DoseConditionsAdapterResult = PlateCondition[];
+export type CalibrationCurveRowsAdapterResult = Array<Record<string, unknown>>;
+export type CalibrationCurveColumnsAdapterResult = DataFrameColumn<Record<string, unknown>>[];
+export type CalibrationCurveDataFrameAdapterResult = DataFrameAdapterResult;
+export type TimeCourseRowsAdapterResult = Array<Record<string, unknown>>;
+export type TimeCourseColumnsAdapterResult = DataFrameColumn<Record<string, unknown>>[];
+export type TimeCourseDataFrameAdapterResult = DataFrameAdapterResult;
+export type TimeCourseStepsAdapterResult = ProtocolStep[];
+export type ProtocolStepsAdapterResult = ProtocolStep[];
+export type ProtocolRowsAdapterResult = Array<Record<string, unknown>>;
+export type ProtocolColumnsAdapterResult = DataFrameColumn<Record<string, unknown>>[];
+export type ProtocolDataFrameAdapterResult = DataFrameAdapterResult;
+export type AssayMatrixRowsAdapterResult = Array<Record<string, unknown>>;
+export type AssayMatrixColumnsAdapterResult = DataFrameColumn<Record<string, unknown>>[];
+export type AssayMatrixDataFrameAdapterResult = DataFrameAdapterResult;
+export type AssayMatrixSampleOptionsAdapterResult = SelectOption<string>[];
+export type ReagentListItemsAdapterResult = Reagent[];
+export type ReagentRowsAdapterResult = Array<Record<string, unknown>>;
+export type ReagentColumnsAdapterResult = DataFrameColumn<Record<string, unknown>>[];
+export type ReagentDataFrameAdapterResult = DataFrameAdapterResult;
+export type FlowPanelRowsAdapterResult = Array<Record<string, unknown>>;
+export type FlowPanelColumnsAdapterResult = DataFrameColumn<Record<string, unknown>>[];
+export type FlowPanelDataFrameAdapterResult = DataFrameAdapterResult;
+export type InstrumentRunRowsAdapterResult = Array<Record<string, unknown>>;
+export type InstrumentRunColumnsAdapterResult = DataFrameColumn<Record<string, unknown>>[];
+export type InstrumentRunDataFrameAdapterResult = DataFrameAdapterResult;
+export type InstrumentRunStepsAdapterResult = ProtocolStep[];
+export type InstrumentRunScheduleEventsAdapterResult = ScheduleEvent[];
+export type QpcrRowsAdapterResult = Array<Record<string, unknown>>;
+export type QpcrColumnsAdapterResult = DataFrameColumn<Record<string, unknown>>[];
+export type QpcrDataFrameAdapterResult = DataFrameAdapterResult;
+export type QpcrWellMapAdapterResult = Record<string, Well>;
+export type TemplateDataFrameAdapterResult = DataFrameAdapterResult;

package/dist/templates/templateCreateOptions.d.ts

@@ -0,0 +1,165 @@
+import { WellPlateFormat } from '../types';
+import { AssayFeature, AssaySample, CalibrationAcceptanceInput, CalibrationModel, CalibrationPointInput, CompoundDoseSeries, ControlDefinition, FlowPanelControl, FlowPanelMarker, InstrumentMethodInput, InstrumentRunItemInput, PlateMapTemplate, PlateMapTemplateData, ProtocolStepRecord, ReagentTemplateInput, SampleColumn, SampleGroupDefinition, SamplePrepStepInput, SamplePrepStepType, SampleRecord, TemplateSample, TimeCourseCondition, TimePoint, TimeUnit } from './types';
+import { QpcrChemistry, QpcrSample, QpcrTarget } from './templateQpcrTypes';
+export interface CreateBioTemplatePackCollectionOptions {
+    metadata?: Record<string, unknown>;
+}
+export interface CreatePlateMapTemplateOptions {
+    name?: string;
+    id?: string;
+    format?: WellPlateFormat;
+    samples?: Array<string | TemplateSample>;
+    metadata?: Record<string, unknown>;
+}
+export interface CreateSampleSheetTemplateOptions {
+    samples: SampleRecord[];
+    columns?: SampleColumn[];
+    groups?: SampleGroupDefinition[];
+    metadata?: Record<string, unknown>;
+}
+export interface CreateSamplePrepTemplateOptions {
+    samples: Array<string | SamplePrepStepInput>;
+    prepType?: SamplePrepStepType;
+    protocolName?: string;
+    volumeUnit?: string;
+    inputVolume?: number;
+    outputVolume?: number;
+    metadata?: Record<string, unknown>;
+}
+export interface CreateDoseResponseTemplateOptions {
+    compounds: Record<string, number[]> | CompoundDoseSeries[];
+    unit: string;
+    replicates?: number;
+    controls?: ControlDefinition[];
+    layout?: PlateMapTemplate | PlateMapTemplateData;
+    metadata?: Record<string, unknown>;
+}
+export interface CreateCalibrationCurveTemplateOptions {
+    concentrations: Array<number | CalibrationPointInput>;
+    analyte?: string;
+    unit?: string;
+    responseUnit?: string;
+    model?: CalibrationModel;
+    includeBlank?: boolean;
+    includeQc?: boolean;
+    acceptance?: CalibrationAcceptanceInput;
+    metadata?: Record<string, unknown>;
+}
+export interface CreateTimeCourseTemplateOptions {
+    timepoints: Array<number | TimePoint>;
+    unit: TimeUnit;
+    conditions: Array<string | TimeCourseCondition>;
+    replicates?: number;
+    metadata?: Record<string, unknown>;
+}
+export interface CreateAssayMatrixTemplateOptions {
+    samples: Array<string | AssaySample>;
+    features: Array<string | AssayFeature>;
+    values?: Record<string, Record<string, number | null | undefined>>;
+    metadata?: Record<string, unknown>;
+}
+export interface CreateProtocolStepsTemplateOptions {
+    steps: Array<string | (Partial<ProtocolStepRecord> & {
+        name: string;
+    })>;
+    metadata?: Record<string, unknown>;
+}
+export interface CreateReagentListTemplateOptions {
+    reagents: Array<string | ReagentTemplateInput>;
+    metadata?: Record<string, unknown>;
+}
+export interface CreateFlowCytometryPanelTemplateOptions {
+    markers: Array<string | (Partial<FlowPanelMarker> & {
+        marker: string;
+    })>;
+    controls?: Array<string | (Partial<FlowPanelControl> & {
+        name: string;
+    })>;
+    instrument?: string;
+    includeDefaultControls?: boolean;
+    metadata?: Record<string, unknown>;
+}
+export interface CreateInstrumentRunTemplateOptions {
+    items: Array<string | InstrumentRunItemInput>;
+    method?: string | InstrumentMethodInput;
+    instrument?: string;
+    includeBlanks?: boolean;
+    includeQc?: boolean;
+    metadata?: Record<string, unknown>;
+}
+export interface CreateQpcrPlateTemplateOptions {
+    samples: Array<string | QpcrSample>;
+    targets: Array<string | QpcrTarget>;
+    format?: WellPlateFormat;
+    replicates?: number;
+    includeNoTemplateControls?: boolean;
+    instrument?: string;
+    chemistry?: QpcrChemistry;
+    metadata?: Record<string, unknown>;
+}
+export interface CreateWellPlateScreenCollectionOptions {
+    samples?: Array<string | SampleRecord>;
+    compounds?: Record<string, number[]> | CompoundDoseSeries[];
+    unit?: string;
+    replicates?: number;
+    plateName?: string;
+    plateFormat?: WellPlateFormat;
+    metadata?: Record<string, unknown>;
+}
+export interface CreateQpcrExpressionCollectionOptions {
+    samples?: Array<string | SampleRecord>;
+    targets?: Array<string | QpcrTarget>;
+    chemistry?: QpcrChemistry;
+    includeNoTemplateControls?: boolean;
+    format?: WellPlateFormat;
+    replicates?: number;
+    instrument?: string;
+    metadata?: Record<string, unknown>;
+}
+export interface CreateLcmsBatchCollectionOptions {
+    samples?: Array<string | SampleRecord>;
+    features?: Array<string | AssayFeature>;
+    instrument?: string;
+    method?: string | InstrumentMethodInput;
+    includeQc?: boolean;
+    metadata?: Record<string, unknown>;
+}
+export interface CreateTargetedMetabolomicsCollectionOptions {
+    samples?: Array<string | SampleRecord>;
+    metabolites?: Array<string | AssayFeature>;
+    internalStandards?: Array<string | ReagentTemplateInput>;
+    standardConcentrations?: number[];
+    concentrationUnit?: string;
+    responseUnit?: string;
+    calibrationAnalyte?: string;
+    instrument?: string;
+    method?: string | InstrumentMethodInput;
+    prepType?: SamplePrepStepType;
+    outputVolume?: number;
+    includeQc?: boolean;
+    metadata?: Record<string, unknown>;
+}
+export interface CreateElisaAssayCollectionOptions {
+    samples?: Array<string | SampleRecord>;
+    analyte?: string;
+    standardConcentrations?: number[];
+    unit?: string;
+    responseUnit?: string;
+    plateName?: string;
+    plateFormat?: WellPlateFormat;
+    metadata?: Record<string, unknown>;
+}
+export interface CreateFlowCytometryAssayCollectionOptions {
+    samples?: Array<string | SampleRecord>;
+    markers?: CreateFlowCytometryPanelTemplateOptions['markers'];
+    features?: Array<string | AssayFeature>;
+    instrument?: string;
+    includeDefaultControls?: boolean;
+    metadata?: Record<string, unknown>;
+}
+export interface CreateWesternBlotAssayCollectionOptions {
+    samples?: Array<string | SampleRecord>;
+    targets?: Array<string | AssayFeature>;
+    loadingControl?: string;
+    metadata?: Record<string, unknown>;
+}

package/dist/templates/templateQpcrTypes.d.ts

@@ -0,0 +1,42 @@
+import { WellPlateFormat } from '../types';
+import { BioTemplateEnvelope } from './types';
+export type QpcrChemistry = 'sybr' | 'taqman' | 'probe' | 'evagreen' | 'other';
+export type QpcrControlKind = 'sample' | 'no-template' | 'no-rt' | 'positive' | 'standard' | 'calibrator';
+export interface QpcrSample {
+    sampleId: string;
+    name?: string;
+    group?: string;
+    metadata?: Record<string, unknown>;
+}
+export interface QpcrTarget {
+    id: string;
+    name: string;
+    assayId?: string;
+    reporter?: string;
+    quencher?: string;
+    ampliconBp?: number;
+    metadata?: Record<string, unknown>;
+}
+export interface QpcrReaction {
+    id: string;
+    wellId: string;
+    sampleId?: string;
+    targetId: string;
+    replicate: number;
+    controlKind: QpcrControlKind;
+    cq?: number | null;
+    quantity?: number | null;
+    flags: string[];
+    metadata?: Record<string, unknown>;
+}
+export interface QpcrPlateTemplateData {
+    plateId: string;
+    format: WellPlateFormat;
+    samples: QpcrSample[];
+    targets: QpcrTarget[];
+    reactions: QpcrReaction[];
+    instrument?: string;
+    chemistry: QpcrChemistry;
+    metadata: Record<string, unknown>;
+}
+export type QpcrPlateTemplate = BioTemplateEnvelope<QpcrPlateTemplateData>;

package/dist/templates/types.d.ts

@@ -1,11 +1,9 @@
-import { DataFrameColumn, PlateCondition, PlateMap, PlateMapEditorState, ProtocolStep, Reagent, ScheduleEvent, SampleType, SelectOption, Well, WellPlateFormat } from '../types';
+import { PlateMap, ProtocolStep, Reagent, SampleType, Well } from '../types';
+import { QpcrPlateTemplate } from './templateQpcrTypes';
 export type TemplateKind = 'experiment-design';
 export type TemplateId = 'plate-map' | 'sample-sheet' | 'sample-prep' | 'dose-response' | 'calibration-curve' | 'time-course' | 'protocol-steps' | 'assay-matrix' | 'reagent-list' | 'flow-cytometry-panel' | 'instrument-run' | 'qpcr-plate';
 export type TemplatePresetId = 'wellplate-screen' | 'qpcr-expression' | 'lcms-batch' | 'targeted-metabolomics' | 'elisa-assay' | 'flow-cytometry-assay' | 'western-blot-assay';
 export type TemplatePackId = 'cell-culture-screen' | 'omics-assay' | 'longitudinal-study' | 'molecular-assay';
-export interface CreateBioTemplatePackCollectionOptions {
-    metadata?: Record<string, unknown>;
-}
 export interface BioTemplateEnvelope<TData = Record<string, unknown>> {
     template_id: TemplateId | string;
     template_version: string;
@@ -300,250 +298,7 @@ export type InstrumentRunItemInput = Partial<InstrumentRunItem> & {
     name?: string;
     sampleId?: string;
 };
-export type QpcrChemistry = 'sybr' | 'taqman' | 'probe' | 'evagreen' | 'other';
-export type QpcrControlKind = 'sample' | 'no-template' | 'no-rt' | 'positive' | 'standard' | 'calibrator';
-export interface QpcrSample {
-    sampleId: string;
-    name?: string;
-    group?: string;
-    metadata?: Record<string, unknown>;
-}
-export interface QpcrTarget {
-    id: string;
-    name: string;
-    assayId?: string;
-    reporter?: string;
-    quencher?: string;
-    ampliconBp?: number;
-    metadata?: Record<string, unknown>;
-}
-export interface QpcrReaction {
-    id: string;
-    wellId: string;
-    sampleId?: string;
-    targetId: string;
-    replicate: number;
-    controlKind: QpcrControlKind;
-    cq?: number | null;
-    quantity?: number | null;
-    flags: string[];
-    metadata?: Record<string, unknown>;
-}
-export interface QpcrPlateTemplateData {
-    plateId: string;
-    format: WellPlateFormat;
-    samples: QpcrSample[];
-    targets: QpcrTarget[];
-    reactions: QpcrReaction[];
-    instrument?: string;
-    chemistry: QpcrChemistry;
-    metadata: Record<string, unknown>;
-}
-export type QpcrPlateTemplate = BioTemplateEnvelope<QpcrPlateTemplateData>;
 export type DataFrameTemplate = SampleSheetTemplate | SamplePrepTemplate | CalibrationCurveTemplate | TimeCourseTemplate | ProtocolStepsTemplate | AssayMatrixTemplate | ReagentListTemplate | FlowCytometryPanelTemplate | InstrumentRunTemplate | QpcrPlateTemplate;
-export interface CreatePlateMapTemplateOptions {
-    name?: string;
-    id?: string;
-    format?: WellPlateFormat;
-    samples?: Array<string | TemplateSample>;
-    metadata?: Record<string, unknown>;
-}
-export interface CreateSampleSheetTemplateOptions {
-    samples: SampleRecord[];
-    columns?: SampleColumn[];
-    groups?: SampleGroupDefinition[];
-    metadata?: Record<string, unknown>;
-}
-export interface CreateSamplePrepTemplateOptions {
-    samples: Array<string | SamplePrepStepInput>;
-    prepType?: SamplePrepStepType;
-    protocolName?: string;
-    volumeUnit?: string;
-    inputVolume?: number;
-    outputVolume?: number;
-    metadata?: Record<string, unknown>;
-}
-export interface CreateDoseResponseTemplateOptions {
-    compounds: Record<string, number[]> | CompoundDoseSeries[];
-    unit: string;
-    replicates?: number;
-    controls?: ControlDefinition[];
-    layout?: PlateMapTemplate | PlateMapTemplateData;
-    metadata?: Record<string, unknown>;
-}
-export interface CreateCalibrationCurveTemplateOptions {
-    concentrations: Array<number | CalibrationPointInput>;
-    analyte?: string;
-    unit?: string;
-    responseUnit?: string;
-    model?: CalibrationModel;
-    includeBlank?: boolean;
-    includeQc?: boolean;
-    acceptance?: CalibrationAcceptanceInput;
-    metadata?: Record<string, unknown>;
-}
-export interface CreateTimeCourseTemplateOptions {
-    timepoints: Array<number | TimePoint>;
-    unit: TimeUnit;
-    conditions: Array<string | TimeCourseCondition>;
-    replicates?: number;
-    metadata?: Record<string, unknown>;
-}
-export interface CreateAssayMatrixTemplateOptions {
-    samples: Array<string | AssaySample>;
-    features: Array<string | AssayFeature>;
-    values?: Record<string, Record<string, number | null | undefined>>;
-    metadata?: Record<string, unknown>;
-}
-export interface CreateProtocolStepsTemplateOptions {
-    steps: Array<string | (Partial<ProtocolStepRecord> & {
-        name: string;
-    })>;
-    metadata?: Record<string, unknown>;
-}
-export interface CreateReagentListTemplateOptions {
-    reagents: Array<string | ReagentTemplateInput>;
-    metadata?: Record<string, unknown>;
-}
-export interface CreateFlowCytometryPanelTemplateOptions {
-    markers: Array<string | (Partial<FlowPanelMarker> & {
-        marker: string;
-    })>;
-    controls?: Array<string | (Partial<FlowPanelControl> & {
-        name: string;
-    })>;
-    instrument?: string;
-    includeDefaultControls?: boolean;
-    metadata?: Record<string, unknown>;
-}
-export interface CreateInstrumentRunTemplateOptions {
-    items: Array<string | InstrumentRunItemInput>;
-    method?: string | InstrumentMethodInput;
-    instrument?: string;
-    includeBlanks?: boolean;
-    includeQc?: boolean;
-    metadata?: Record<string, unknown>;
-}
-export interface CreateQpcrPlateTemplateOptions {
-    samples: Array<string | QpcrSample>;
-    targets: Array<string | QpcrTarget>;
-    format?: WellPlateFormat;
-    replicates?: number;
-    includeNoTemplateControls?: boolean;
-    instrument?: string;
-    chemistry?: QpcrChemistry;
-    metadata?: Record<string, unknown>;
-}
-export interface CreateWellPlateScreenCollectionOptions {
-    samples?: Array<string | SampleRecord>;
-    compounds?: Record<string, number[]> | CompoundDoseSeries[];
-    unit?: string;
-    replicates?: number;
-    plateName?: string;
-    plateFormat?: WellPlateFormat;
-    metadata?: Record<string, unknown>;
-}
-export interface CreateQpcrExpressionCollectionOptions {
-    samples?: Array<string | SampleRecord>;
-    targets?: Array<string | QpcrTarget>;
-    chemistry?: QpcrChemistry;
-    includeNoTemplateControls?: boolean;
-    format?: WellPlateFormat;
-    replicates?: number;
-    instrument?: string;
-    metadata?: Record<string, unknown>;
-}
-export interface CreateLcmsBatchCollectionOptions {
-    samples?: Array<string | SampleRecord>;
-    features?: Array<string | AssayFeature>;
-    instrument?: string;
-    method?: string | InstrumentMethodInput;
-    includeQc?: boolean;
-    metadata?: Record<string, unknown>;
-}
-export interface CreateTargetedMetabolomicsCollectionOptions {
-    samples?: Array<string | SampleRecord>;
-    metabolites?: Array<string | AssayFeature>;
-    internalStandards?: Array<string | ReagentTemplateInput>;
-    standardConcentrations?: number[];
-    concentrationUnit?: string;
-    responseUnit?: string;
-    calibrationAnalyte?: string;
-    instrument?: string;
-    method?: string | InstrumentMethodInput;
-    prepType?: SamplePrepStepType;
-    outputVolume?: number;
-    includeQc?: boolean;
-    metadata?: Record<string, unknown>;
-}
-export interface CreateElisaAssayCollectionOptions {
-    samples?: Array<string | SampleRecord>;
-    analyte?: string;
-    standardConcentrations?: number[];
-    unit?: string;
-    responseUnit?: string;
-    plateName?: string;
-    plateFormat?: WellPlateFormat;
-    metadata?: Record<string, unknown>;
-}
-export interface CreateFlowCytometryAssayCollectionOptions {
-    samples?: Array<string | SampleRecord>;
-    markers?: CreateFlowCytometryPanelTemplateOptions['markers'];
-    features?: Array<string | AssayFeature>;
-    instrument?: string;
-    includeDefaultControls?: boolean;
-    metadata?: Record<string, unknown>;
-}
-export interface CreateWesternBlotAssayCollectionOptions {
-    samples?: Array<string | SampleRecord>;
-    targets?: Array<string | AssayFeature>;
-    loadingControl?: string;
-    metadata?: Record<string, unknown>;
-}
-export type PlateMapEditorAdapterResult = PlateMapEditorState;
-export type WellMapAdapterResult = Record<string, Well>;
-export type SampleRowsAdapterResult = Array<Record<string, unknown>>;
-export type SampleColumnsAdapterResult = DataFrameColumn<Record<string, unknown>>[];
-export interface DataFrameAdapterResult {
-    data: Array<Record<string, unknown>>;
-    columns: DataFrameColumn<Record<string, unknown>>[];
-    rowKey?: string;
-}
-export type SampleDataFrameAdapterResult = DataFrameAdapterResult;
-export type SampleOptionsAdapterResult = SelectOption<string>[];
-export type SamplePrepRowsAdapterResult = Array<Record<string, unknown>>;
-export type SamplePrepColumnsAdapterResult = DataFrameColumn<Record<string, unknown>>[];
-export type SamplePrepDataFrameAdapterResult = DataFrameAdapterResult;
-export type DoseConditionsAdapterResult = PlateCondition[];
-export type CalibrationCurveRowsAdapterResult = Array<Record<string, unknown>>;
-export type CalibrationCurveColumnsAdapterResult = DataFrameColumn<Record<string, unknown>>[];
-export type CalibrationCurveDataFrameAdapterResult = DataFrameAdapterResult;
-export type TimeCourseRowsAdapterResult = Array<Record<string, unknown>>;
-export type TimeCourseColumnsAdapterResult = DataFrameColumn<Record<string, unknown>>[];
-export type TimeCourseDataFrameAdapterResult = DataFrameAdapterResult;
-export type TimeCourseStepsAdapterResult = ProtocolStep[];
-export type ProtocolStepsAdapterResult = ProtocolStep[];
-export type ProtocolRowsAdapterResult = Array<Record<string, unknown>>;
-export type ProtocolColumnsAdapterResult = DataFrameColumn<Record<string, unknown>>[];
-export type ProtocolDataFrameAdapterResult = DataFrameAdapterResult;
-export type AssayMatrixRowsAdapterResult = Array<Record<string, unknown>>;
-export type AssayMatrixColumnsAdapterResult = DataFrameColumn<Record<string, unknown>>[];
-export type AssayMatrixDataFrameAdapterResult = DataFrameAdapterResult;
-export type AssayMatrixSampleOptionsAdapterResult = SelectOption<string>[];
-export type ReagentListItemsAdapterResult = Reagent[];
-export type ReagentRowsAdapterResult = Array<Record<string, unknown>>;
-export type ReagentColumnsAdapterResult = DataFrameColumn<Record<string, unknown>>[];
-export type ReagentDataFrameAdapterResult = DataFrameAdapterResult;
-export type FlowPanelRowsAdapterResult = Array<Record<string, unknown>>;
-export type FlowPanelColumnsAdapterResult = DataFrameColumn<Record<string, unknown>>[];
-export type FlowPanelDataFrameAdapterResult = DataFrameAdapterResult;
-export type InstrumentRunRowsAdapterResult = Array<Record<string, unknown>>;
-export type InstrumentRunColumnsAdapterResult = DataFrameColumn<Record<string, unknown>>[];
-export type InstrumentRunDataFrameAdapterResult = DataFrameAdapterResult;
-export type InstrumentRunStepsAdapterResult = ProtocolStep[];
-export type InstrumentRunScheduleEventsAdapterResult = ScheduleEvent[];
-export type QpcrRowsAdapterResult = Array<Record<string, unknown>>;
-export type QpcrColumnsAdapterResult = DataFrameColumn<Record<string, unknown>>[];
-export type QpcrDataFrameAdapterResult = DataFrameAdapterResult;
-export type QpcrWellMapAdapterResult = Record<string, Well>;
-export type TemplateDataFrameAdapterResult = DataFrameAdapterResult;
+export type { QpcrChemistry, QpcrControlKind, QpcrPlateTemplate, QpcrPlateTemplateData, QpcrReaction, QpcrSample, QpcrTarget, } from './templateQpcrTypes';
+export type { CreateAssayMatrixTemplateOptions, CreateBioTemplatePackCollectionOptions, CreateCalibrationCurveTemplateOptions, CreateDoseResponseTemplateOptions, CreateElisaAssayCollectionOptions, CreateFlowCytometryAssayCollectionOptions, CreateFlowCytometryPanelTemplateOptions, CreateInstrumentRunTemplateOptions, CreateLcmsBatchCollectionOptions, CreatePlateMapTemplateOptions, CreateProtocolStepsTemplateOptions, CreateQpcrExpressionCollectionOptions, CreateQpcrPlateTemplateOptions, CreateReagentListTemplateOptions, CreateSamplePrepTemplateOptions, CreateSampleSheetTemplateOptions, CreateTargetedMetabolomicsCollectionOptions, CreateTimeCourseTemplateOptions, CreateWellPlateScreenCollectionOptions, CreateWesternBlotAssayCollectionOptions, } from './templateCreateOptions';
+export type { AssayMatrixColumnsAdapterResult, AssayMatrixDataFrameAdapterResult, AssayMatrixRowsAdapterResult, AssayMatrixSampleOptionsAdapterResult, CalibrationCurveColumnsAdapterResult, CalibrationCurveDataFrameAdapterResult, CalibrationCurveRowsAdapterResult, DataFrameAdapterResult, DoseConditionsAdapterResult, FlowPanelColumnsAdapterResult, FlowPanelDataFrameAdapterResult, FlowPanelRowsAdapterResult, InstrumentRunColumnsAdapterResult, InstrumentRunDataFrameAdapterResult, InstrumentRunRowsAdapterResult, InstrumentRunScheduleEventsAdapterResult, InstrumentRunStepsAdapterResult, PlateMapEditorAdapterResult, ProtocolColumnsAdapterResult, ProtocolDataFrameAdapterResult, ProtocolRowsAdapterResult, ProtocolStepsAdapterResult, QpcrColumnsAdapterResult, QpcrDataFrameAdapterResult, QpcrRowsAdapterResult, QpcrWellMapAdapterResult, ReagentColumnsAdapterResult, ReagentDataFrameAdapterResult, ReagentListItemsAdapterResult, ReagentRowsAdapterResult, SampleColumnsAdapterResult, SampleDataFrameAdapterResult, SampleOptionsAdapterResult, SamplePrepColumnsAdapterResult, SamplePrepDataFrameAdapterResult, SamplePrepRowsAdapterResult, SampleRowsAdapterResult, TemplateDataFrameAdapterResult, TimeCourseColumnsAdapterResult, TimeCourseDataFrameAdapterResult, TimeCourseRowsAdapterResult, TimeCourseStepsAdapterResult, WellMapAdapterResult, } from './templateAdapterTypes';