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

package/dist/templates/templateControlSchemas.d.ts

@@ -0,0 +1,400 @@
+export declare const templateControlSchemas: {
+    'plate-map': {
+        plateName: {
+            label: string;
+            default: string;
+            section: string;
+            sectionLabel: string;
+            sectionSubtitle: string;
+            view: string;
+            sidebar: {
+                icon: string[];
+                iconColor: string;
+                iconBg: string;
+            };
+        };
+        plateFormat: {
+            label: string;
+            default: number;
+            options: readonly [6, 12, 24, 48, 96, 384];
+            section: string;
+            view: string;
+        };
+        sampleNames: {
+            type: "tags";
+            label: string;
+            default: string[];
+            section: string;
+            sectionLabel: string;
+            sectionSubtitle: string;
+            view: string;
+            sidebar: {
+                icon: string[];
+                iconColor: string;
+                iconBg: string;
+            };
+        };
+    };
+    'sample-sheet': {
+        sampleCount: {
+            type: "number";
+            label: string;
+            default: number;
+            min: number;
+            max: number;
+            section: string;
+            sectionLabel: string;
+            sectionSubtitle: string;
+            view: string;
+            sidebar: {
+                icon: string[];
+                iconColor: string;
+                iconBg: string;
+            };
+        };
+        includeGroups: {
+            label: string;
+            default: boolean;
+            section: string;
+            view: string;
+        };
+        includeBatch: {
+            label: string;
+            default: boolean;
+            section: string;
+            sectionLabel: string;
+            view: string;
+            sidebar: {
+                icon: string[];
+                iconColor: string;
+                iconBg: string;
+            };
+        };
+    };
+    'sample-prep': {
+        prepType: {
+            label: string;
+            default: string;
+            options: string[];
+            section: string;
+            sectionLabel: string;
+            sectionSubtitle: string;
+            view: string;
+            sidebar: {
+                icon: string[];
+                iconColor: string;
+                iconBg: string;
+            };
+        };
+        volumeUnit: {
+            label: string;
+            default: string;
+            options: string[];
+            section: string;
+            view: string;
+        };
+        outputVolume: {
+            type: "number";
+            label: string;
+            default: number;
+            min: number;
+            section: string;
+            view: string;
+        };
+    };
+    'dose-response': {
+        unit: {
+            label: string;
+            default: string;
+            options: readonly ["nM", "uM", "mM", "ug/mL", "mg/mL"];
+            section: string;
+            sectionLabel: string;
+            sectionSubtitle: string;
+            view: string;
+            sidebar: {
+                icon: string[];
+                iconColor: string;
+                iconBg: string;
+            };
+        };
+        replicates: {
+            type: "number";
+            label: string;
+            default: number;
+            min: number;
+            max: number;
+            section: string;
+            view: string;
+        };
+        includePlateLayout: {
+            label: string;
+            default: boolean;
+            section: string;
+            sectionLabel: string;
+            sectionSubtitle: string;
+            view: string;
+            sidebar: {
+                icon: string[];
+                iconColor: string;
+                iconBg: string;
+                defaultOpen: false;
+            };
+        };
+    };
+    'calibration-curve': {
+        analyte: {
+            label: string;
+            default: string;
+            section: string;
+            sectionLabel: string;
+            sectionSubtitle: string;
+            view: string;
+            sidebar: {
+                icon: string[];
+                iconColor: string;
+                iconBg: string;
+            };
+        };
+        model: {
+            label: string;
+            default: string;
+            options: string[];
+            section: string;
+            sectionLabel: string;
+            view: string;
+            sidebar: {
+                icon: string[];
+                iconColor: string;
+                iconBg: string;
+            };
+        };
+        minRSquared: {
+            type: "number";
+            label: string;
+            default: number;
+            min: number;
+            max: number;
+            props: {
+                step: number;
+            };
+            section: string;
+            view: string;
+        };
+    };
+    'time-course': {
+        timeUnit: {
+            label: string;
+            default: string;
+            options: string[];
+            section: string;
+            sectionLabel: string;
+            sectionSubtitle: string;
+            view: string;
+            sidebar: {
+                icon: string[];
+                iconColor: string;
+                iconBg: string;
+            };
+        };
+        replicates: {
+            type: "number";
+            label: string;
+            default: number;
+            min: number;
+            max: number;
+            section: string;
+            sectionLabel: string;
+            view: string;
+            sidebar: {
+                icon: string[];
+                iconColor: string;
+                iconBg: string;
+            };
+        };
+    };
+    'protocol-steps': {
+        defaultDuration: {
+            type: "number";
+            label: string;
+            default: number;
+            min: number;
+            section: string;
+            sectionLabel: string;
+            sectionSubtitle: string;
+            view: string;
+            sidebar: {
+                icon: string[];
+                iconColor: string;
+                iconBg: string;
+            };
+            props: {
+                suffix: string;
+            };
+        };
+        editable: {
+            label: string;
+            default: boolean;
+            section: string;
+            view: string;
+        };
+    };
+    'assay-matrix': {
+        featureType: {
+            label: string;
+            default: string;
+            options: string[];
+            section: string;
+            sectionLabel: string;
+            sectionSubtitle: string;
+            view: string;
+            sidebar: {
+                icon: string[];
+                iconColor: string;
+                iconBg: string;
+            };
+        };
+        normalizeValues: {
+            label: string;
+            default: boolean;
+            section: string;
+            sectionLabel: string;
+            view: string;
+            sidebar: {
+                icon: string[];
+                iconColor: string;
+                iconBg: string;
+                defaultOpen: false;
+            };
+        };
+    };
+    'reagent-list': {
+        reagentKind: {
+            label: string;
+            default: string;
+            options: string[];
+            section: string;
+            sectionLabel: string;
+            sectionSubtitle: string;
+            view: string;
+            sidebar: {
+                icon: string[];
+                iconColor: string;
+                iconBg: string;
+            };
+        };
+        trackStock: {
+            label: string;
+            default: boolean;
+            section: string;
+            view: string;
+        };
+    };
+    'flow-cytometry-panel': {
+        markers: {
+            type: "tags";
+            label: string;
+            default: string[];
+            section: string;
+            sectionLabel: string;
+            sectionSubtitle: string;
+            view: string;
+            sidebar: {
+                icon: string[];
+                iconColor: string;
+                iconBg: string;
+            };
+        };
+        instrument: {
+            label: string;
+            default: string;
+            section: string;
+            sectionLabel: string;
+            sectionSubtitle: string;
+            view: string;
+            sidebar: {
+                icon: string[];
+                iconColor: string;
+                iconBg: string;
+            };
+        };
+        includeDefaultControls: {
+            label: string;
+            default: boolean;
+            section: string;
+            view: string;
+        };
+    };
+    'instrument-run': {
+        instrument: {
+            label: string;
+            default: string;
+            options: string[];
+            section: string;
+            sectionLabel: string;
+            sectionSubtitle: string;
+            view: string;
+            sidebar: {
+                icon: string[];
+                iconColor: string;
+                iconBg: string;
+            };
+        };
+        method: {
+            label: string;
+            default: string;
+            section: string;
+            view: string;
+        };
+        includeQc: {
+            label: string;
+            default: boolean;
+            section: string;
+            sectionLabel: string;
+            view: string;
+            sidebar: {
+                icon: string[];
+                iconColor: string;
+                iconBg: string;
+                defaultOpen: false;
+            };
+        };
+    };
+    'qpcr-plate': {
+        chemistry: {
+            label: string;
+            default: string;
+            options: string[];
+            section: string;
+            sectionLabel: string;
+            sectionSubtitle: string;
+            view: string;
+            sidebar: {
+                icon: string[];
+                iconColor: string;
+                iconBg: string;
+            };
+        };
+        replicates: {
+            type: "number";
+            label: string;
+            default: number;
+            min: number;
+            max: number;
+            section: string;
+            view: string;
+        };
+        includeNoTemplateControls: {
+            label: string;
+            default: boolean;
+            section: string;
+            sectionLabel: string;
+            view: string;
+            sidebar: {
+                icon: string[];
+                iconColor: string;
+                iconBg: string;
+                defaultOpen: false;
+            };
+        };
+    };
+};

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/templateEnvelopes.d.ts

@@ -0,0 +1,9 @@
+import { BioTemplateEnvelope, TemplateCollection, TemplateCollectionEnvelope, TemplateId } from './types';
+export declare const TEMPLATE_COLLECTION_KEY = "templates";
+export declare function createTemplateEnvelope<TData>(templateId: TemplateId, data: TData, metadata?: Record<string, unknown>, templateVersion?: string): BioTemplateEnvelope<TData>;
+export declare function createTemplateCollection(templates: Array<BioTemplateEnvelope<unknown>>, metadata?: Record<string, unknown>): TemplateCollectionEnvelope;
+export declare function extractTemplateCollection(value: unknown): TemplateCollection;
+export declare function ensureTemplateFromCollection<TTemplate extends BioTemplateEnvelope<unknown>>(value: unknown, templateId: TemplateId | string): TTemplate;
+export declare function assertTemplateEnvelope<TData>(value: unknown, templateId: TemplateId | string): asserts value is BioTemplateEnvelope<TData>;
+export declare function ensureTemplateEnvelope<TTemplate extends BioTemplateEnvelope<unknown>>(value: unknown, templateId: TemplateId | string): TTemplate;
+export declare function getTemplateData<TData>(template: BioTemplateEnvelope<TData> | TData, templateId?: TemplateId | string): TData;

package/dist/templates/templatePackCollectionBuilder.d.ts

@@ -0,0 +1,2 @@
+import { CreateBioTemplatePackCollectionOptions, TemplateCollectionEnvelope, TemplatePackId } from './types';
+export declare function createBioTemplatePackCollection(name: TemplatePackId | string, options?: CreateBioTemplatePackCollectionOptions): TemplateCollectionEnvelope;

package/dist/templates/templatePresetCollectionBuilder.d.ts

@@ -0,0 +1,18 @@
+import { BioTemplateControlValues } from './builderPresetControls';
+import { CreateElisaAssayCollectionOptions, CreateFlowCytometryAssayCollectionOptions, CreateLcmsBatchCollectionOptions, CreateQpcrExpressionCollectionOptions, CreateTargetedMetabolomicsCollectionOptions, CreateWellPlateScreenCollectionOptions, CreateWesternBlotAssayCollectionOptions, TemplateCollectionEnvelope, TemplatePresetId } from './types';
+export declare function createBioTemplatePresetCollection(name: 'wellplate-screen', options?: CreateWellPlateScreenCollectionOptions): TemplateCollectionEnvelope;
+export declare function createBioTemplatePresetCollection(name: 'qpcr-expression', options?: CreateQpcrExpressionCollectionOptions): TemplateCollectionEnvelope;
+export declare function createBioTemplatePresetCollection(name: 'lcms-batch', options?: CreateLcmsBatchCollectionOptions): TemplateCollectionEnvelope;
+export declare function createBioTemplatePresetCollection(name: 'targeted-metabolomics', options?: CreateTargetedMetabolomicsCollectionOptions): TemplateCollectionEnvelope;
+export declare function createBioTemplatePresetCollection(name: 'elisa-assay', options?: CreateElisaAssayCollectionOptions): TemplateCollectionEnvelope;
+export declare function createBioTemplatePresetCollection(name: 'flow-cytometry-assay', options?: CreateFlowCytometryAssayCollectionOptions): TemplateCollectionEnvelope;
+export declare function createBioTemplatePresetCollection(name: 'western-blot-assay', options?: CreateWesternBlotAssayCollectionOptions): TemplateCollectionEnvelope;
+export declare function createBioTemplatePresetCollection(name: string, options?: CreateWellPlateScreenCollectionOptions | CreateQpcrExpressionCollectionOptions | CreateLcmsBatchCollectionOptions | CreateTargetedMetabolomicsCollectionOptions | CreateElisaAssayCollectionOptions | CreateFlowCytometryAssayCollectionOptions | CreateWesternBlotAssayCollectionOptions): TemplateCollectionEnvelope;
+export declare function createBioTemplatePresetCollectionFromControls(name: 'wellplate-screen', values: BioTemplateControlValues): TemplateCollectionEnvelope;
+export declare function createBioTemplatePresetCollectionFromControls(name: 'qpcr-expression', values: BioTemplateControlValues): TemplateCollectionEnvelope;
+export declare function createBioTemplatePresetCollectionFromControls(name: 'lcms-batch', values: BioTemplateControlValues): TemplateCollectionEnvelope;
+export declare function createBioTemplatePresetCollectionFromControls(name: 'targeted-metabolomics', values: BioTemplateControlValues): TemplateCollectionEnvelope;
+export declare function createBioTemplatePresetCollectionFromControls(name: 'elisa-assay', values: BioTemplateControlValues): TemplateCollectionEnvelope;
+export declare function createBioTemplatePresetCollectionFromControls(name: 'flow-cytometry-assay', values: BioTemplateControlValues): TemplateCollectionEnvelope;
+export declare function createBioTemplatePresetCollectionFromControls(name: 'western-blot-assay', values: BioTemplateControlValues): TemplateCollectionEnvelope;
+export declare function createBioTemplatePresetCollectionFromControls(name: TemplatePresetId | string, values: BioTemplateControlValues): TemplateCollectionEnvelope;

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/templateValidators.d.ts

@@ -0,0 +1,13 @@
+import { AssayMatrixTemplateData, CalibrationCurveTemplateData, DoseResponseTemplateData, FlowCytometryPanelTemplateData, InstrumentRunTemplateData, PlateMapTemplateData, ProtocolStepsTemplateData, QpcrPlateTemplateData, ReagentListTemplateData, SamplePrepTemplateData, SampleSheetTemplateData, TimeCourseTemplateData } from './types';
+export declare function validatePlateMapData(data: PlateMapTemplateData): void;
+export declare function validateSampleSheetData(data: SampleSheetTemplateData): void;
+export declare function validateSamplePrepData(data: SamplePrepTemplateData): void;
+export declare function validateDoseResponseData(data: DoseResponseTemplateData): void;
+export declare function validateCalibrationCurveData(data: CalibrationCurveTemplateData): void;
+export declare function validateTimeCourseData(data: TimeCourseTemplateData): void;
+export declare function validateProtocolStepsData(data: ProtocolStepsTemplateData): void;
+export declare function validateAssayMatrixData(data: AssayMatrixTemplateData): void;
+export declare function validateReagentListData(data: ReagentListTemplateData): void;
+export declare function validateFlowCytometryPanelData(data: FlowCytometryPanelTemplateData): void;
+export declare function validateInstrumentRunData(data: InstrumentRunTemplateData): void;
+export declare function validateQpcrPlateData(data: QpcrPlateTemplateData): void;

package/dist/templates/timeCourseAdapters.d.ts

@@ -0,0 +1,5 @@
+import { TimeCourseColumnsAdapterResult, TimeCourseDataFrameAdapterResult, TimeCourseRowsAdapterResult, TimeCourseStepsAdapterResult, TimeCourseTemplate, TimeCourseTemplateData } from './types';
+export declare function toTimeCourseRows(template: TimeCourseTemplate | TimeCourseTemplateData): TimeCourseRowsAdapterResult;
+export declare function toTimeCourseColumns(): TimeCourseColumnsAdapterResult;
+export declare function toTimeCourseDataFrame(template: TimeCourseTemplate | TimeCourseTemplateData): TimeCourseDataFrameAdapterResult;
+export declare function toTimeCourseSteps(template: TimeCourseTemplate | TimeCourseTemplateData): TimeCourseStepsAdapterResult;

package/dist/templates/timeCourseBuilder.d.ts

@@ -0,0 +1,2 @@
+import { CreateTimeCourseTemplateOptions, TimeCourseTemplate } from './types';
+export declare function createTimeCourseTemplate(options: CreateTimeCourseTemplateOptions): TimeCourseTemplate;