@gen-epix/ui-client-casedb 4.0.0

package/dist/utils/UploadUtil/UploadUtil.d.ts

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+import { AnyObject, ObjectSchema } from 'yup';
+import { CaseDbCaseBatchUploadResult, CaseDbCaseForUpload, CaseDbCaseType, CaseDbCaseUploadResult, CaseDbCol, CaseDbCompleteCaseType } from '@gen-epix/api-casedb';
+import { AutoCompleteOption, FormFieldDefinition, OptionBase } from '@gen-epix/ui-form/models/form';
+import { UploadCompleteColStats, UploadMappedColumn, UploadMappedColumnsFormFields, UploadSequenceMapping } from '../../models/upload';
+export declare class UploadUtil {
+    static readonly caseDateColumnAliases: string[];
+    static readonly caseIdColumnAliases: string[];
+    static readonly colAliases: string[];
+    static areMappedColumnsEqual(a: UploadMappedColumn[], b: UploadMappedColumn[]): boolean;
+    static createCases(kwArgs: {
+        assemblyProtocolId: string;
+        casesForVerificationFromSourceData: CaseDbCaseForUpload[];
+        completeCaseType: CaseDbCompleteCaseType;
+        createdInDataCollectionId: string;
+        mappedColumns: UploadMappedColumn[];
+        sampleIdColId: string;
+        selectedValidatedCases: CaseDbCaseUploadResult[];
+        sequenceMapping: UploadSequenceMapping;
+        sequencingProtocolId: string;
+        signal: AbortSignal;
+    }): Promise<CaseDbCaseBatchUploadResult>;
+    static createCasesAndUploadFiles(kwArgs: {
+        assemblyProtocolId: string;
+        casesForVerificationFromSourceData: CaseDbCaseForUpload[];
+        completeCaseType: CaseDbCompleteCaseType;
+        createdInDataCollectionId: string;
+        mappedColumns: UploadMappedColumn[];
+        onComplete: () => void;
+        onError: (error: Error) => void;
+        onProgress: (progress: number, message: string) => void;
+        sampleIdColId: string;
+        selectedValidatedCases: CaseDbCaseUploadResult[];
+        sequenceFilesDataTransfer: DataTransfer;
+        sequenceMapping: UploadSequenceMapping;
+        sequencingProtocolId: string;
+        signal: AbortSignal;
+    }): Promise<CaseDbCaseBatchUploadResult>;
+    static getCasesForUpload(kwArgs: {
+        caseTypeId: string;
+        createdInDataCollectionId: string;
+        mappedColumns: UploadMappedColumn[];
+        rawData: string[][];
+    }): CaseDbCaseForUpload[];
+    static getCaseTypeFromColumnLabels(cols: CaseDbCol[], columnLabels: string[]): CaseDbCaseType;
+    static getColumnMappingFormFieldDefinitions(completeCaseType: CaseDbCompleteCaseType, rawDataHeaders: string[], _fileName: string): FormFieldDefinition<UploadMappedColumnsFormFields>[];
+    static getColumnMappingSchema(rawData: string[][], completeCaseType: CaseDbCompleteCaseType): ObjectSchema<{}, AnyObject, {}, ''>;
+    static getCompleteCaseTypeColStats(completeCaseType: CaseDbCompleteCaseType): UploadCompleteColStats;
+    static getDefaultColumnMappingFormValues(rawDataHeaders: string[], mappedColumns: UploadMappedColumn[], identifierIssuerOptions: OptionBase<string>[]): UploadMappedColumnsFormFields;
+    static getEpiUploadSequenceMapping(completeCaseType: CaseDbCompleteCaseType, validatedCases: CaseDbCaseUploadResult[], sequenceFilesDataTransfer: DataTransfer): UploadSequenceMapping;
+    static getInitialMappedColumns(completeCaseType: CaseDbCompleteCaseType, rawData: string[][]): UploadMappedColumn[];
+    static getMappedColumnsFromFormData(data: UploadMappedColumnsFormFields, rawData: string[][], colMap: Map<string, CaseDbCol>, completeCaseType: CaseDbCompleteCaseType): UploadMappedColumn[];
+    static getSampleIdColIds(completeCaseType: CaseDbCompleteCaseType): string[];
+    static getSequenceMappingStats(sequenceMapping: UploadSequenceMapping, sequenceFilesDataTransfer: DataTransfer): {
+        mappedFiles: string[];
+        mappedReadsFiles: string[];
+        mappedSequenceFiles: string[];
+        numberOfFilesToMap: number;
+        unmappedFileNames: string[];
+        unmappedReadsFiles: string[];
+        unmappedSequenceFiles: string[];
+    };
+    static getSheetNameOptions(fileList: FileList): Promise<AutoCompleteOption<string>[]>;
+    static hasReadsColumnMapped(mappedColumns: UploadMappedColumn[], completeCaseTypeColStats: UploadCompleteColStats): boolean;
+    static hasSequenceColumnMapped(mappedColumns: UploadMappedColumn[], completeCaseTypeColStats: UploadCompleteColStats): boolean;
+    static isCaseDateColumn(label: string): boolean;
+    static isCaseIdColumn(label: string): boolean;
+    static isCol(label: string): boolean;
+    static isGenomeFile(fileName: string): boolean;
+    static isReadsFile(fileName: string): boolean;
+    static isSupportedGeneticFile(fileName: string): boolean;
+    static isTextFile(fileName: string): boolean;
+    static isXlsxFile(fileName: string): boolean;
+    static matchColumnLabel(columnLabel: string, col: CaseDbCol): boolean;
+    static readFileAsBase64(file: File): Promise<string>;
+    static readRawData(fileList: FileList, sheet?: string): Promise<string[][]>;
+    static reportFileUploadProgress(kwArgs: {
+        endPercentage: number;
+        fileSize: number;
+        message: string;
+        onProgress: (progress: number, message: string) => void;
+        startPercentage: number;
+        totalFileSizeToUpload: number;
+        uploadedFileSize: number;
+    }): void;
+    static uploadFilesForCases(kwArgs: {
+        assemblyProtocolId: string;
+        caseBatchUploadResult: CaseDbCaseBatchUploadResult;
+        completeCaseType: CaseDbCompleteCaseType;
+        createdInDataCollectionId: string;
+        endPercentage: number;
+        mappedColumns: UploadMappedColumn[];
+        onComplete: () => void;
+        onError: (error: Error) => void;
+        onProgress: (progress: number, message: string) => void;
+        sampleIdColId: string;
+        selectedValidatedCases: CaseDbCaseUploadResult[];
+        sequenceFilesDataTransfer: DataTransfer;
+        sequenceMapping: UploadSequenceMapping;
+        sequencingProtocolId: string;
+        signal: AbortSignal;
+        startPercentage: number;
+    }): Promise<void>;
+    private static idToRegex;
+    private static mapExcelCellToString;
+    private static mapExcelSheetData;
+}

package/dist/utils/UploadUtil/index.d.ts

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+export * from './UploadUtil';

package/dist/utils/UploadUtil/index.js

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+import { t as e } from "../../_chunks/UploadUtil.js";
+export { e as UploadUtil };