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

package/dist/templates/presetControlSchemas.d.ts

@@ -0,0 +1,534 @@
+export declare const presetControlSchemas: {
+    'wellplate-screen': {
+        sampleNames: {
+            default: string[];
+            type: "tags";
+            label: string;
+            section: string;
+            sectionLabel: string;
+            sectionSubtitle: string;
+            view: string;
+            sidebar: {
+                icon: string[];
+                iconColor: string;
+                iconBg: string;
+            };
+        };
+        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;
+            };
+        };
+        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;
+        };
+    };
+    'qpcr-expression': {
+        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;
+            };
+        };
+        sampleNames: {
+            type: "tags";
+            label: string;
+            default: string[];
+            section: string;
+            sectionLabel: string;
+            sectionSubtitle: string;
+            view: string;
+            sidebar: {
+                icon: string[];
+                iconColor: string;
+                iconBg: string;
+            };
+        };
+        targets: {
+            type: "tags";
+            label: string;
+            default: string[];
+            section: string;
+            sectionLabel: string;
+            view: string;
+            sidebar: {
+                icon: string[];
+                iconColor: string;
+                iconBg: string;
+            };
+        };
+    };
+    'lcms-batch': {
+        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;
+            };
+        };
+        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;
+            };
+        };
+        sampleNames: {
+            type: "tags";
+            label: string;
+            default: string[];
+            section: string;
+            sectionLabel: string;
+            sectionSubtitle: string;
+            view: string;
+            sidebar: {
+                icon: string[];
+                iconColor: string;
+                iconBg: string;
+            };
+        };
+        featureNames: {
+            type: "tags";
+            label: string;
+            default: string[];
+            section: string;
+            sectionLabel: string;
+            view: string;
+            sidebar: {
+                icon: string[];
+                iconColor: string;
+                iconBg: string;
+            };
+        };
+    };
+    'targeted-metabolomics': {
+        sampleNames: {
+            type: "tags";
+            label: string;
+            default: string[];
+            section: string;
+            sectionLabel: string;
+            sectionSubtitle: string;
+            view: string;
+            sidebar: {
+                icon: string[];
+                iconColor: string;
+                iconBg: string;
+            };
+        };
+        metaboliteNames: {
+            type: "tags";
+            label: string;
+            default: string[];
+            section: string;
+            sectionLabel: string;
+            sectionSubtitle: string;
+            view: string;
+            sidebar: {
+                icon: string[];
+                iconColor: string;
+                iconBg: string;
+            };
+        };
+        internalStandards: {
+            type: "tags";
+            label: string;
+            default: string[];
+            section: string;
+            sectionLabel: string;
+            sectionSubtitle: string;
+            view: string;
+            sidebar: {
+                icon: string[];
+                iconColor: string;
+                iconBg: string;
+            };
+        };
+        standardConcentrations: {
+            type: "tags";
+            label: string;
+            default: string[];
+            section: string;
+            view: string;
+        };
+        concentrationUnit: {
+            label: string;
+            default: string;
+            options: readonly ["nM", "uM", "mM", "ug/mL", "mg/mL"];
+            section: string;
+            view: string;
+        };
+        responseUnit: {
+            label: string;
+            default: string;
+            section: string;
+            sectionLabel: string;
+            view: string;
+            sidebar: {
+                icon: string[];
+                iconColor: string;
+                iconBg: string;
+            };
+        };
+        instrument: {
+            default: string;
+            label: string;
+            options: string[];
+            section: string;
+            sectionLabel: string;
+            sectionSubtitle: string;
+            view: string;
+            sidebar: {
+                icon: string[];
+                iconColor: string;
+                iconBg: string;
+            };
+        };
+        method: {
+            default: string;
+            label: string;
+            section: string;
+            view: string;
+        };
+        prepType: {
+            default: string;
+            label: string;
+            options: string[];
+            section: string;
+            sectionLabel: string;
+            sectionSubtitle: string;
+            view: string;
+            sidebar: {
+                icon: string[];
+                iconColor: string;
+                iconBg: string;
+            };
+        };
+        outputVolume: {
+            type: "number";
+            label: string;
+            default: number;
+            min: number;
+            section: string;
+            view: string;
+        };
+        includeQc: {
+            label: string;
+            default: boolean;
+            section: string;
+            sectionLabel: string;
+            view: string;
+            sidebar: {
+                icon: string[];
+                iconColor: string;
+                iconBg: string;
+                defaultOpen: false;
+            };
+        };
+    };
+    'elisa-assay': {
+        sampleNames: {
+            type: "tags";
+            label: string;
+            default: string[];
+            section: string;
+            sectionLabel: string;
+            sectionSubtitle: string;
+            view: string;
+            sidebar: {
+                icon: string[];
+                iconColor: string;
+                iconBg: string;
+            };
+        };
+        analyte: {
+            label: string;
+            default: string;
+            section: string;
+            sectionLabel: string;
+            sectionSubtitle: string;
+            view: string;
+            sidebar: {
+                icon: string[];
+                iconColor: string;
+                iconBg: string;
+            };
+        };
+        standardConcentrations: {
+            type: "tags";
+            label: string;
+            default: string[];
+            section: string;
+            view: string;
+        };
+        unit: {
+            label: string;
+            default: string;
+            options: string[];
+            section: string;
+            view: string;
+        };
+        responseUnit: {
+            label: string;
+            default: string;
+            section: string;
+            sectionLabel: string;
+            view: string;
+            sidebar: {
+                icon: string[];
+                iconColor: string;
+                iconBg: string;
+            };
+        };
+        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;
+        };
+    };
+    'flow-cytometry-assay': {
+        sampleNames: {
+            type: "tags";
+            label: string;
+            default: string[];
+            section: string;
+            sectionLabel: string;
+            sectionSubtitle: string;
+            view: string;
+            sidebar: {
+                icon: string[];
+                iconColor: string;
+                iconBg: string;
+            };
+        };
+        markers: {
+            default: string[];
+            type: "tags";
+            label: string;
+            section: string;
+            sectionLabel: string;
+            sectionSubtitle: string;
+            view: string;
+            sidebar: {
+                icon: string[];
+                iconColor: string;
+                iconBg: string;
+            };
+        };
+        featureNames: {
+            type: "tags";
+            label: string;
+            default: string[];
+            section: string;
+            sectionLabel: string;
+            sectionSubtitle: string;
+            view: string;
+            sidebar: {
+                icon: string[];
+                iconColor: string;
+                iconBg: string;
+            };
+        };
+        instrument: {
+            default: string;
+            label: 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;
+        };
+    };
+    'western-blot-assay': {
+        sampleNames: {
+            type: "tags";
+            label: string;
+            default: string[];
+            section: string;
+            sectionLabel: string;
+            sectionSubtitle: string;
+            view: string;
+            sidebar: {
+                icon: string[];
+                iconColor: string;
+                iconBg: string;
+            };
+        };
+        targets: {
+            type: "tags";
+            label: string;
+            default: string[];
+            section: string;
+            sectionLabel: string;
+            sectionSubtitle: string;
+            view: string;
+            sidebar: {
+                icon: string[];
+                iconColor: string;
+                iconBg: string;
+            };
+        };
+        loadingControl: {
+            label: string;
+            default: string;
+            section: string;
+            sectionLabel: string;
+            view: string;
+            sidebar: {
+                icon: string[];
+                iconColor: string;
+                iconBg: string;
+            };
+        };
+    };
+};

package/dist/templates/protocolAdapters.d.ts

@@ -0,0 +1,5 @@
+import { ProtocolColumnsAdapterResult, ProtocolDataFrameAdapterResult, ProtocolRowsAdapterResult, ProtocolStepsAdapterResult, ProtocolStepsTemplate, ProtocolStepsTemplateData } from './types';
+export declare function toProtocolSteps(template: ProtocolStepsTemplate | ProtocolStepsTemplateData): ProtocolStepsAdapterResult;
+export declare function toProtocolRows(template: ProtocolStepsTemplate | ProtocolStepsTemplateData): ProtocolRowsAdapterResult;
+export declare function toProtocolColumns(): ProtocolColumnsAdapterResult;
+export declare function toProtocolDataFrame(template: ProtocolStepsTemplate | ProtocolStepsTemplateData): ProtocolDataFrameAdapterResult;

package/dist/templates/protocolNormalizers.d.ts

@@ -0,0 +1,6 @@
+import { ProtocolStepRecord, TimeCourseCondition, TimePoint } from './types';
+export declare function normalizeTimePoint(timepoint: TimePoint): TimePoint;
+export declare function normalizeCondition(condition: TimeCourseCondition): TimeCourseCondition;
+export declare function normalizeProtocolStep(step: Partial<ProtocolStepRecord> & {
+    name: string;
+}, index: number): ProtocolStepRecord;

package/dist/templates/protocolStepsBuilder.d.ts

@@ -0,0 +1,2 @@
+import { CreateProtocolStepsTemplateOptions, ProtocolStepsTemplate } from './types';
+export declare function createProtocolStepsTemplate(options: CreateProtocolStepsTemplateOptions): ProtocolStepsTemplate;

package/dist/templates/qpcrAdapters.d.ts

@@ -0,0 +1,5 @@
+import { QpcrColumnsAdapterResult, QpcrDataFrameAdapterResult, QpcrPlateTemplate, QpcrPlateTemplateData, QpcrRowsAdapterResult, QpcrWellMapAdapterResult } from './types';
+export declare function toQpcrRows(template: QpcrPlateTemplate | QpcrPlateTemplateData): QpcrRowsAdapterResult;
+export declare function toQpcrColumns(): QpcrColumnsAdapterResult;
+export declare function toQpcrDataFrame(template: QpcrPlateTemplate | QpcrPlateTemplateData): QpcrDataFrameAdapterResult;
+export declare function toQpcrWellPlateWells(template: QpcrPlateTemplate | QpcrPlateTemplateData): QpcrWellMapAdapterResult;

package/dist/templates/qpcrExpressionCollectionBuilder.d.ts

@@ -0,0 +1,2 @@
+import { CreateQpcrExpressionCollectionOptions, TemplateCollectionEnvelope } from './types';
+export declare function createQpcrExpressionCollection(options?: CreateQpcrExpressionCollectionOptions): TemplateCollectionEnvelope;

package/dist/templates/qpcrPlateBuilder.d.ts

@@ -0,0 +1,2 @@
+import { CreateQpcrPlateTemplateOptions, QpcrPlateTemplate } from './types';
+export declare function createQpcrPlateTemplate(options: CreateQpcrPlateTemplateOptions): QpcrPlateTemplate;

package/dist/templates/reagentAdapters.d.ts

@@ -0,0 +1,5 @@
+import { ReagentColumnsAdapterResult, ReagentDataFrameAdapterResult, ReagentListItemsAdapterResult, ReagentListTemplate, ReagentListTemplateData, ReagentRowsAdapterResult } from './types';
+export declare function toReagentListItems(template: ReagentListTemplate | ReagentListTemplateData): ReagentListItemsAdapterResult;
+export declare function toReagentRows(template: ReagentListTemplate | ReagentListTemplateData): ReagentRowsAdapterResult;
+export declare function toReagentColumns(): ReagentColumnsAdapterResult;
+export declare function toReagentDataFrame(template: ReagentListTemplate | ReagentListTemplateData): ReagentDataFrameAdapterResult;

package/dist/templates/reagentListBuilder.d.ts

@@ -0,0 +1,2 @@
+import { CreateReagentListTemplateOptions, ReagentListTemplate } from './types';
+export declare function createReagentListTemplate(options: CreateReagentListTemplateOptions): ReagentListTemplate;

package/dist/templates/runNormalizers.d.ts

@@ -0,0 +1,10 @@
+import { InstrumentMethod, InstrumentRunItem, QpcrSample, QpcrTarget } from './types';
+export declare function normalizeInstrumentMethod(method: Partial<InstrumentMethod> & {
+    name?: string;
+}, fallbackInstrument?: string): InstrumentMethod;
+export declare function normalizeInstrumentRunItem(item: Partial<InstrumentRunItem> & {
+    name?: string;
+    sampleId?: string;
+}, defaultMethodId: string, fallbackOrder: number, index: number): InstrumentRunItem;
+export declare function normalizeQpcrSample(sample: QpcrSample): QpcrSample;
+export declare function normalizeQpcrTarget(target: QpcrTarget): QpcrTarget;

package/dist/templates/sampleNormalizers.d.ts

@@ -0,0 +1,4 @@
+import { SamplePrepStep, SamplePrepStepInput, SampleRecord } from './types';
+export declare function normalizeSampleRecord(sample: SampleRecord): SampleRecord;
+export declare function presetSampleRecords(samples: Array<string | SampleRecord>): SampleRecord[];
+export declare function normalizeSamplePrepStep(step: SamplePrepStepInput, prepType: SamplePrepStep['type'], volumeUnit: string, order: number, index: number): SamplePrepStep;

package/dist/templates/samplePrepAdapters.d.ts

@@ -0,0 +1,4 @@
+import { SamplePrepColumnsAdapterResult, SamplePrepDataFrameAdapterResult, SamplePrepRowsAdapterResult, SamplePrepTemplate, SamplePrepTemplateData } from './types';
+export declare function toSamplePrepRows(template: SamplePrepTemplate | SamplePrepTemplateData): SamplePrepRowsAdapterResult;
+export declare function toSamplePrepColumns(): SamplePrepColumnsAdapterResult;
+export declare function toSamplePrepDataFrame(template: SamplePrepTemplate | SamplePrepTemplateData): SamplePrepDataFrameAdapterResult;

package/dist/templates/samplePrepBuilder.d.ts

@@ -0,0 +1,2 @@
+import { CreateSamplePrepTemplateOptions, SamplePrepTemplate } from './types';
+export declare function createSamplePrepTemplate(options: CreateSamplePrepTemplateOptions): SamplePrepTemplate;

package/dist/templates/sampleSheetAdapters.d.ts

@@ -0,0 +1,5 @@
+import { SampleColumnsAdapterResult, SampleDataFrameAdapterResult, SampleOptionsAdapterResult, SampleRowsAdapterResult, SampleSheetTemplate, SampleSheetTemplateData } from './types';
+export declare function toSampleRows(template: SampleSheetTemplate | SampleSheetTemplateData): SampleRowsAdapterResult;
+export declare function toSampleColumns(template: SampleSheetTemplate | SampleSheetTemplateData): SampleColumnsAdapterResult;
+export declare function toSampleDataFrame(template: SampleSheetTemplate | SampleSheetTemplateData): SampleDataFrameAdapterResult;
+export declare function toSampleOptions(template: SampleSheetTemplate | SampleSheetTemplateData): SampleOptionsAdapterResult;

package/dist/templates/sampleSheetBuilder.d.ts

@@ -0,0 +1,2 @@
+import { CreateSampleSheetTemplateOptions, SampleSheetTemplate } from './types';
+export declare function createSampleSheetTemplate(options: CreateSampleSheetTemplateOptions): SampleSheetTemplate;

package/dist/templates/targetedMetabolomicsCollectionBuilder.d.ts

@@ -0,0 +1,2 @@
+import { CreateTargetedMetabolomicsCollectionOptions, TemplateCollectionEnvelope } from './types';
+export declare function createTargetedMetabolomicsCollection(options?: CreateTargetedMetabolomicsCollectionOptions): TemplateCollectionEnvelope;

package/dist/templates/targetedMetabolomicsHelpers.d.ts

@@ -0,0 +1,5 @@
+import { AssayFeature, CalibrationPoint, InstrumentRunItemInput, ReagentTemplateInput, SampleRecord } from './types';
+export declare function normalizeMetaboliteFeatures(metabolites: Array<string | AssayFeature>, responseUnit: string): AssayFeature[];
+export declare function normalizeInternalStandardReagents(internalStandards: Array<string | ReagentTemplateInput>): ReagentTemplateInput[];
+export declare function targetedMetabolomicsRunItems(samples: SampleRecord[], calibrationPoints: CalibrationPoint[], includeQc: boolean): InstrumentRunItemInput[];
+export declare function firstFeatureName(features: AssayFeature[], fallback: string): string;

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;