@gen-epix/ui 1.15.0 → 1.15.2

package/src/utils/EpiUploadUtil/EpiUploadUtil.ts

@@ -1,857 +0,0 @@
-import readXlsxFile, { readSheetNames } from 'read-excel-file/browser';
-import { parse } from 'csv/browser/esm/sync';
-import type {
-  ObjectSchema,
-  AnyObject,
-} from 'yup';
-import {
-  lazy,
-  object,
-  string,
-} from 'yup';
-import { t } from 'i18next';
-import difference from 'lodash/difference';
-import uniq from 'lodash/uniq';
-import { format } from 'date-fns';
-
-import type {
-  Col,
-  CaseType,
-  CompleteCaseType,
-  CaseUploadResult,
-  CaseForUpload,
-  ReadSetForUpload,
-  SeqForUpload,
-  CaseBatchUploadResult,
-} from '../../api';
-import {
-  CaseApi,
-  ColType,
-  UploadAction,
-  ReadsFileFormat,
-  SeqFileFormat,
-  EtlStatus,
-} from '../../api';
-import { CaseTypeUtil } from '../CaseTypeUtil';
-import { CaseUtil } from '../CaseUtil';
-import { DATE_FORMAT } from '../../data/date';
-import { QueryUtil } from '../QueryUtil';
-import { QUERY_KEY } from '../../models/query';
-import type {
-  AutoCompleteOption,
-  FormFieldDefinition,
-  OptionBase,
-} from '../../models/form';
-import { FORM_FIELD_DEFINITION_TYPE } from '../../models/form';
-import type {
-  EpiUploadMappedColumn,
-  EpiUploadMappedColumnsFormFields,
-  EpiUploadCompleteColStats,
-  CaseUploadResultWithGeneratedId,
-  EpiUploadSequenceMapping,
-  EpiUploadSequenceMappingForCaseId,
-} from '../../models/epi';
-import { FileUtil } from '../FileUtil';
-import { UploadError } from '../../classes/errors';
-import { ValidationUtil } from '../ValidationUtil';
-
-export class EpiUploadUtil {
-  public static readonly caseIdColumnAliases = ['_case_id', 'case id', 'case_id', 'caseid', 'case.id'];
-  public static readonly caseDateColumnAliases = ['_case_date', 'case date', 'case_date', 'casedate', 'case.date'];
-  public static readonly colAliases = ['_case_type', 'case type', 'case_type', 'casetype', 'case.type'];
-
-  public static isXlsxFile(fileName: string): boolean {
-    return fileName?.toLowerCase()?.endsWith('.xlsx');
-  }
-
-  public static isTextFile(fileName: string): boolean {
-    const lowerName = fileName?.toLowerCase();
-    return lowerName?.endsWith('.csv') || lowerName?.endsWith('.tsv') || lowerName?.endsWith('.txt');
-  }
-
-  public static async getSheetNameOptions(fileList: FileList): Promise<AutoCompleteOption<string>[]> {
-    const file = fileList[0];
-    const fileName = file.name.toLowerCase();
-
-    if (EpiUploadUtil.isXlsxFile(fileName)) {
-      return (await readSheetNames(file)).map(name => ({ label: name, value: name }));
-    }
-    return [];
-  }
-
-  public static async readRawData(fileList: FileList, sheet?: string): Promise<string[][]> {
-    const file = fileList[0];
-    const fileName = file.name.toLowerCase();
-    let result: string[][] = [];
-
-    if (EpiUploadUtil.isTextFile(fileName)) {
-      // Parse CSV file
-      let text = await file.text();
-      if (fileName.endsWith('.tsv')) {
-        // Convert TSV to CSV by replacing tabs with commas
-        text = text.replace(/\t/g, ',');
-      }
-      if (fileName.endsWith('.txt')) {
-        // Attempt to auto-detect delimiter (comma, tab, semicolon)
-        const lines = text.split(/\r?\n/).filter(line => line.trim() !== '');
-        if (lines.length > 0) {
-          const delimiters = [',', '\t', ';'];
-          let bestDelimiter = ',';
-          let maxFields = 0;
-          delimiters.forEach(delimiter => {
-            const fieldsCount = lines[0].split(delimiter).length;
-            if (fieldsCount > maxFields) {
-              maxFields = fieldsCount;
-              bestDelimiter = delimiter;
-            }
-          });
-          if (bestDelimiter !== ',') {
-            const regex = new RegExp(bestDelimiter.replace(/[-/\\^$*+?.()|[\]{}]/g, '\\$&'), 'g');
-            text = text.replace(regex, ',');
-          }
-        }
-      }
-      result = parse(text, {
-        columns: false, // Keep as array of arrays
-        skip_empty_lines: true,
-        trim: true,
-      });
-    } else if (EpiUploadUtil.isXlsxFile(fileName)) {
-      // Parse Excel file
-      const excelData = await readXlsxFile(file, {
-        sheet,
-        trim: true,
-      });
-      result = excelData.map(row => row.map(cell => {
-        if (cell instanceof Date) {
-          return format(cell, DATE_FORMAT.DATE);
-        }
-        return cell?.toString() ?? undefined;
-      }));
-    } else {
-      throw new Error('Unsupported file format. Please select a CSV or Excel file.');
-    }
-    if (result.length < 2 || result[0].length < 2) {
-      throw new Error('The selected file does not contain enough data. Please ensure it has at least a header row and one data row.');
-    }
-    return result;
-  }
-
-  public static getSampleIdColIds(completeCaseType: CompleteCaseType): string[] {
-    const colsIds: string[] = [];
-    Object.values(Object.keys(completeCaseType.cols)).forEach(colId => {
-      const col = completeCaseType.cols[colId];
-      const refCol = completeCaseType.ref_cols[col.ref_col_id];
-      if (refCol?.col_type === ColType.ID_SAMPLE) {
-        colsIds.push(col.id);
-      }
-    });
-    return colsIds;
-  }
-
-
-  public static matchColumnLabel(columnLabel: string, col: Col): boolean {
-    if (!columnLabel || typeof columnLabel !== 'string') {
-      return false;
-    }
-    const labelLowerCase = columnLabel.toLocaleLowerCase();
-    return labelLowerCase === col.label.toLocaleLowerCase() || labelLowerCase === col.code.toLowerCase() || labelLowerCase === col.id.toLocaleLowerCase();
-  }
-
-  public static getCaseTypeFromColumnLabels(cols: Col[], columnLabels: string[]): CaseType {
-    const bestMatch = {
-      caseType: null as CaseType,
-      matchCount: 0,
-    };
-
-    // Group columns by case type ID to count matches per case type
-    const caseTypeMatches = new Map<string, { caseType: CaseType; matchCount: number }>();
-
-    cols.forEach(col => {
-      const matchCount = columnLabels.filter(label =>
-        this.matchColumnLabel(label, col)).length;
-
-      if (matchCount > 0) {
-        const caseTypeId = col.case_type_id;
-        const existing = caseTypeMatches.get(caseTypeId);
-
-        if (existing) {
-          existing.matchCount += matchCount;
-        } else {
-          // Note: We don't have access to the full CaseType object here,
-          // so we create a minimal one with the ID. In a real implementation,
-          // you might need to pass the complete case type data or modify the method signature.
-          caseTypeMatches.set(caseTypeId, {
-            caseType: { id: caseTypeId } as CaseType,
-            matchCount,
-          });
-        }
-      }
-    });
-
-    // Find the case type with the highest match count
-    caseTypeMatches.forEach(match => {
-      if (match.matchCount > bestMatch.matchCount) {
-        bestMatch.caseType = match.caseType;
-        bestMatch.matchCount = match.matchCount;
-      }
-    });
-
-    return bestMatch.caseType;
-  }
-
-  public static isCaseIdColumn(label: string): boolean {
-    return this.caseIdColumnAliases.includes(label.toLocaleLowerCase());
-  }
-
-  public static isCol(label: string): boolean {
-    return this.colAliases.includes(label.toLocaleLowerCase());
-  }
-
-  public static isCaseDateColumn(label: string): boolean {
-    return this.caseDateColumnAliases.includes(label.toLocaleLowerCase());
-  }
-
-  public static getInitialMappedColumns(completeCaseType: CompleteCaseType, rawData: string[][]): EpiUploadMappedColumn[] {
-    if (rawData.length === 0) {
-      return [];
-    }
-    const writableColIds = CaseTypeUtil.getWritableColIds(completeCaseType);
-    const filteredCols = CaseTypeUtil.getWritableImportExportColIds(completeCaseType).map(id => completeCaseType.cols[id]);
-    const sampleIdColIds = EpiUploadUtil.getSampleIdColIds(completeCaseType);
-    const mappedColumns = rawData[0].map((label, index) => {
-      const isCaseIdColumn = EpiUploadUtil.isCaseIdColumn(label);
-      const isCol = EpiUploadUtil.isCol(label);
-
-      let col: Col = null;
-      let isSampleIdColumn = false;
-
-      if (!isCaseIdColumn && !isCol) {
-        col = filteredCols.find(c => EpiUploadUtil.matchColumnLabel(label, c)) || null;
-        if (col && !writableColIds.includes(col.id)) {
-          col = null;
-        }
-        isSampleIdColumn = col ? sampleIdColIds.includes(col.id) : false;
-      }
-
-      return {
-        originalIndex: index,
-        originalLabel: label,
-        col,
-        isCaseIdColumn,
-        isCol,
-        isSampleIdColumn,
-        sampleIdentifierIssuerId: null as string,
-      } satisfies EpiUploadMappedColumn;
-    });
-
-    return mappedColumns.filter(mc => {
-      return mc.isCaseIdColumn || mc.col;
-    });
-  }
-
-  public static getMappedColumnsFromFormData(data: EpiUploadMappedColumnsFormFields, rawData: string[][], colMap: Map<string, Col>, completeCaseType: CompleteCaseType): EpiUploadMappedColumn[] {
-    const mappedColumns: EpiUploadMappedColumn[] = [];
-    const sampleIdColIds = EpiUploadUtil.getSampleIdColIds(completeCaseType);
-    Object.entries(data).forEach(([originalIndexString, formValue]) => {
-      if (!formValue) {
-        return;
-      }
-      const originalIndex = parseInt(originalIndexString, 10);
-      const isCaseIdColumn = formValue === 'case_id';
-      let col: Col = null;
-      if (!isCaseIdColumn) {
-        col = colMap.get(formValue) || null;
-      }
-      let sampleIdentifierIssuerId: string = null;
-      const isSampleIdColumn = col ? sampleIdColIds.includes(col.id) : false;
-      if (isSampleIdColumn) {
-        sampleIdentifierIssuerId = data[formValue] || null;
-      }
-      mappedColumns.push({
-        isCaseIdColumn,
-        isSampleIdColumn,
-        col,
-        originalIndex,
-        originalLabel: rawData[0][originalIndex] || '',
-        sampleIdentifierIssuerId,
-      } satisfies EpiUploadMappedColumn);
-    });
-    return mappedColumns;
-  }
-
-  public static areMappedColumnsEqual(a: EpiUploadMappedColumn[], b: EpiUploadMappedColumn[]): boolean {
-    if (a.length !== b.length) {
-      return false;
-    }
-
-    return a.every((itemA, index) => {
-      const itemB = b[index];
-      const stringifiedA = `${itemA.originalIndex}-${itemA.originalLabel}`;
-      const stringifiedB = `${itemB.originalIndex}-${itemB.originalLabel}`;
-      return stringifiedA === stringifiedB;
-    });
-  }
-
-  // eslint-disable-next-line @typescript-eslint/no-empty-object-type
-  public static getColumnMappingSchema(rawData: string[][], completeCaseType: CompleteCaseType): ObjectSchema<{}, AnyObject, {}, ''> {
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
-    const fields: { [key: string]: any } = {};
-    const fieldNames: string[] = rawData[0].map((_, index) => index.toString());
-    const sampleIdColIds = EpiUploadUtil.getSampleIdColIds(completeCaseType);
-
-    sampleIdColIds.forEach((colId) => {
-      fields[colId] = lazy(() => string().nullable().when(fieldNames, (otherFieldValues, schema) => {
-        return schema.test('needs-identifier-issuer', t('An identifier issuer must be selected.'), (fieldValue) => {
-          const allFieldValues = [...otherFieldValues as string[], fieldValue];
-          if (allFieldValues.includes(colId)) {
-            return !!fieldValue;
-          }
-          return true;
-        });
-      }));
-    });
-
-    fieldNames.forEach((fieldName, fieldIndex) => {
-      const otherFieldNames = fieldNames.filter(name => name !== fieldName);
-      fields[fieldName] = lazy(() => string().nullable().when(otherFieldNames, (otherFieldValues, schema) => {
-        return schema
-          .test('unique', t('This column has already been mapped to another field.'), (fieldValue) => {
-            return !fieldValue || !otherFieldValues.includes(fieldValue);
-          })
-          .test('valid-case-id-values', t('The column mapped to the case id field must contain valid UUID\'s.'), (fieldValue) => {
-            if (fieldValue !== 'case_id') {
-              return true;
-            }
-            const values = rawData.slice(1).map(row => row[fieldIndex]);
-            return values.every(value => ValidationUtil.validate('UUID4', value));
-          });
-      }));
-    });
-
-    return object().shape(fields);
-  }
-
-  public static getColumnMappingFormFieldDefinitions(completeCaseType: CompleteCaseType, rawDataHeaders: string[], _fileName: string): FormFieldDefinition<EpiUploadMappedColumnsFormFields>[] {
-    const fields: FormFieldDefinition<EpiUploadMappedColumnsFormFields>[] = [];
-    const options: AutoCompleteOption<string>[] = [];
-
-    options.push({
-      label: 'Case ID',
-      value: 'case_id',
-    });
-
-    const allowedColIds = CaseTypeUtil.getWritableImportExportColIds(completeCaseType);
-    completeCaseType.ordered_col_ids.filter(x => allowedColIds.includes(x)).forEach((colId) => {
-      const col = completeCaseType.cols[colId];
-
-      options.push({
-        label: col.label,
-        value: col.id,
-      });
-    });
-
-    rawDataHeaders.forEach((header, index) => {
-      fields.push({
-        definition: FORM_FIELD_DEFINITION_TYPE.SELECT,
-        name: index.toString(),
-        label: header,
-        options,
-      });
-    });
-
-    return fields;
-  }
-
-  public static getDefaultColumnMappingFormValues(rawDataHeaders: string[], mappedColumns: EpiUploadMappedColumn[], identifierIssuerOptions: OptionBase<string>[]): EpiUploadMappedColumnsFormFields {
-    const defaultFormValues: EpiUploadMappedColumnsFormFields = Object.fromEntries(Object.keys(rawDataHeaders).map<[string, null]>(x => [x.toString(), null]));
-    const caseIdColumn = mappedColumns.find(mappedColumn => mappedColumn.isCaseIdColumn);
-
-    if (caseIdColumn) {
-      defaultFormValues[caseIdColumn.originalIndex.toString()] = 'case_id';
-    }
-
-    mappedColumns.forEach((mappedColumn) => {
-      if (mappedColumn.col) {
-        defaultFormValues[mappedColumn.originalIndex.toString()] = mappedColumn.col.id;
-        if (mappedColumn.isSampleIdColumn) {
-          defaultFormValues[mappedColumn.col.id] = mappedColumn.sampleIdentifierIssuerId || identifierIssuerOptions.length === 1 ? identifierIssuerOptions[0].value : null;
-        }
-      }
-    });
-    return defaultFormValues;
-  }
-
-  public static isGenomeFile(fileName: string): boolean {
-    const lowerName = fileName.toLowerCase();
-    return lowerName.endsWith('.fa') ||
-      lowerName.endsWith('.fasta') ||
-      lowerName.endsWith('.fa.gz') ||
-      lowerName.endsWith('.fasta.gz');
-  }
-
-  public static isReadsFile(fileName: string): boolean {
-    const lowerName = fileName.toLowerCase();
-    return lowerName.endsWith('.fq') ||
-      lowerName.endsWith('.fastq') ||
-      lowerName.endsWith('.fq.gz') ||
-      lowerName.endsWith('.fastq.gz');
-  }
-
-  public static isSupportedGeneticFile(fileName: string): boolean {
-    return EpiUploadUtil.isGenomeFile(fileName) || EpiUploadUtil.isReadsFile(fileName);
-  }
-
-  public static hasSequenceColumnMapped(mappedColumns: EpiUploadMappedColumn[], completeCaseTypeColStats: EpiUploadCompleteColStats): boolean {
-    return mappedColumns.some((mappedColumn) => {
-      return completeCaseTypeColStats.sequenceColumns.some(seqCol => mappedColumn.col?.id === seqCol.id);
-    });
-  }
-
-  public static hasReadsColumnMapped(mappedColumns: EpiUploadMappedColumn[], completeCaseTypeColStats: EpiUploadCompleteColStats): boolean {
-    return mappedColumns.some((mappedColumn) => {
-      return completeCaseTypeColStats.readsColumns.some(readCol => mappedColumn.col?.id === readCol.id);
-    });
-  }
-
-
-  public static getCompleteCaseTypeColStats(completeCaseType: CompleteCaseType): EpiUploadCompleteColStats {
-    const sampleIdColumns = CaseTypeUtil.getColsByType(completeCaseType, [ColType.ID_SAMPLE]);
-    const sequenceColumns = CaseTypeUtil.getColsByType(completeCaseType, [ColType.GENETIC_SEQUENCE]);
-    const readsColumns = CaseTypeUtil.getColsByType(completeCaseType, [ColType.GENETIC_READS]);
-    const writableColumns = Object.values(completeCaseType.cols).filter(col => CaseTypeUtil.getWritableColIds(completeCaseType).includes(col.id));
-
-    return { sampleIdColumns, sequenceColumns, readsColumns, writableColumns };
-  }
-
-  private static idToRegex(id: string): RegExp {
-    // Create regex that matches the id somewhere in a string
-    return new RegExp(id.replace(/[-/\\^$*+?.()|[\]{}]/g, '\\$&'));
-  }
-
-  public static getEpiUploadSequenceMapping(completeCaseType: CompleteCaseType, validatedCases: CaseUploadResultWithGeneratedId[], sequenceFilesDataTransfer: DataTransfer): EpiUploadSequenceMapping {
-    if (!sequenceFilesDataTransfer || sequenceFilesDataTransfer.files.length === 0) {
-      return {};
-    }
-
-    const stats = EpiUploadUtil.getCompleteCaseTypeColStats(completeCaseType);
-    const result: EpiUploadSequenceMapping = {};
-
-    validatedCases.forEach((vc) => {
-      const caseSequenceMapping: EpiUploadSequenceMappingForCaseId = {
-        sequenceFileNames: {},
-        readsFileNames: {},
-      };
-
-      // modify by reference
-      result[vc.generatedId] = caseSequenceMapping;
-
-      if (stats.sequenceColumns.length !== 1 && stats.readsColumns.length !== 1) {
-        return;
-      }
-
-      const sampleIdColumnIds: string[] = [];
-      stats.sampleIdColumns.forEach((idCol) => {
-        const rowValue = CaseUtil.getRowValue(vc.validated_content, idCol, completeCaseType);
-        if (rowValue && !rowValue.isMissing) {
-          sampleIdColumnIds.push(rowValue.raw);
-        }
-      });
-      if (!sampleIdColumnIds.length) {
-        return;
-      }
-
-      stats.sequenceColumns.forEach((seqCol) => {
-        caseSequenceMapping.sequenceFileNames[seqCol.id] = '';
-      });
-      stats.readsColumns.forEach((readCol) => {
-        caseSequenceMapping.readsFileNames[readCol.id] = {
-          fwd: '',
-          rev: '',
-        };
-      });
-
-      const sequenceFiles: string[] = [];
-      const readsFiles: string[] = [];
-      Array.from(sequenceFilesDataTransfer.files).forEach((file) => {
-        const fileName = file.name;
-        const lowerName = fileName.toLowerCase();
-        const matchesId = sampleIdColumnIds.some((id) => lowerName.match(EpiUploadUtil.idToRegex(id.toLowerCase())));
-        if (matchesId) {
-          if (EpiUploadUtil.isGenomeFile(fileName)) {
-            sequenceFiles.push(fileName);
-          } else if (EpiUploadUtil.isReadsFile(fileName)) {
-            readsFiles.push(fileName);
-          }
-        }
-      });
-
-      if (stats.sequenceColumns.length === 1 && sequenceFiles.length === 1) {
-        caseSequenceMapping.sequenceFileNames[stats.sequenceColumns[0].id] = sequenceFiles[0];
-      }
-      if (stats.readsColumns.length === 1) {
-        if (readsFiles.length === 1) {
-          caseSequenceMapping.readsFileNames[stats.readsColumns[0].id].fwd = readsFiles[0];
-        }
-        if (readsFiles.length === 2) {
-          const sortedReadsFiles = readsFiles.sort((a, b) => a.localeCompare(b));
-          caseSequenceMapping.readsFileNames[stats.readsColumns[0].id].fwd = sortedReadsFiles[0];
-          caseSequenceMapping.readsFileNames[stats.readsColumns[0].id].rev = sortedReadsFiles[1];
-        }
-      }
-    });
-    return result;
-  }
-
-  public static getSequenceMappingStats(sequenceMapping: EpiUploadSequenceMapping, sequenceFilesDataTransfer: DataTransfer): {
-    numberOfFilesToMap: number;
-    mappedFiles: string[];
-    mappedSequenceFiles: string[];
-    mappedReadsFiles: string[];
-    unmappedFileNames: string[];
-    unmappedSequenceFiles: string[];
-    unmappedReadsFiles: string[];
-  } {
-    const sequenceFiles = Array.from(sequenceFilesDataTransfer.files).map(file => file.name).filter(fileName => EpiUploadUtil.isGenomeFile(fileName));
-    const readsFiles = Array.from(sequenceFilesDataTransfer.files).map(file => file.name).filter(fileName => EpiUploadUtil.isReadsFile(fileName));
-    const files = [...sequenceFiles, ...readsFiles];
-    const numberOfFilesToMap = files.length;
-
-    const mappedSequenceFiles = uniq(Object.values(sequenceMapping).flatMap(mapping => Object.values(mapping.sequenceFileNames)).filter(x => x));
-    const mappedReadsFiles = uniq(Object.values(sequenceMapping).flatMap(mapping => Object.values(mapping.readsFileNames).flatMap(reads => [reads.fwd, reads.rev])).filter(x => x));
-    const mappedFiles = [...mappedSequenceFiles, ...mappedReadsFiles];
-
-    const unmappedSequenceFiles = difference(sequenceFiles, mappedSequenceFiles);
-    const unmappedReadsFiles = difference(readsFiles, mappedReadsFiles);
-    const unmappedFileNames = difference(files, mappedFiles);
-
-    return {
-      numberOfFilesToMap,
-      mappedFiles,
-      mappedSequenceFiles,
-      mappedReadsFiles,
-      unmappedFileNames,
-      unmappedSequenceFiles,
-      unmappedReadsFiles,
-    };
-  }
-
-  public static async readFileAsBase64(file: File): Promise<string> {
-    return new Promise((resolve, reject) => {
-      const reader = new FileReader();
-      reader.onload = () => {
-        const result = reader.result as string;
-        const base64 = result.split(',')[1]; // Remove data:*/*;base64, prefix
-        resolve(base64);
-      };
-      reader.onerror = (_) => {
-        reject(Error('File read error'));
-      };
-      reader.readAsDataURL(file);
-    });
-  }
-
-  public static getCasesForVerification(kwArgs: { rawData: string[][]; mappedColumns: EpiUploadMappedColumn[]; caseTypeId: string; createdInDataCollectionId: string }): CaseForUpload[] {
-    const { rawData, mappedColumns, caseTypeId, createdInDataCollectionId } = kwArgs;
-    return rawData.slice(1).map((row) => {
-      const caseIdColumn = mappedColumns.find((mappedColumn) => mappedColumn.isCaseIdColumn)?.originalIndex;
-      const content: { [key: string]: string } = {};
-
-      mappedColumns.forEach((mappedColumn) => {
-        if (mappedColumn.col) {
-          content[mappedColumn.col.id] = row[mappedColumn.originalIndex];
-        }
-      });
-
-      const caseForCreateUpdate: CaseForUpload = {
-        id: caseIdColumn !== undefined ? row[caseIdColumn] : undefined,
-        case: {
-          content,
-          case_type_id: caseTypeId,
-          created_in_data_collection_id: createdInDataCollectionId,
-        },
-      };
-
-      return { ...caseForCreateUpdate, content };
-    });
-  }
-
-  public static async createCases(kwArgs: {
-    completeCaseType: CompleteCaseType;
-    assemblyProtocolId: string;
-    caseTypeId: string;
-    createdInDataCollectionId: string;
-    mappedColumns: EpiUploadMappedColumn[];
-    sampleIdColId: string;
-    sequenceMapping: EpiUploadSequenceMapping;
-    sequencingProtocolId: string;
-    signal: AbortSignal;
-    validatedCases: CaseUploadResult[];
-    validatedCasesWithGeneratedId: CaseUploadResultWithGeneratedId[];
-  }): Promise<CaseBatchUploadResult> {
-    const {
-      completeCaseType,
-      assemblyProtocolId,
-      caseTypeId,
-      createdInDataCollectionId,
-      mappedColumns,
-      sampleIdColId,
-      sequenceMapping,
-      sequencingProtocolId,
-      signal,
-      validatedCases,
-      validatedCasesWithGeneratedId,
-    } = kwArgs;
-    const { col: mappedSampleIdCol, sampleIdentifierIssuerId } = mappedColumns.find(mc => mc.col.id === sampleIdColId);
-
-    return (await CaseApi.instance.uploadCases({
-      case_type_id: caseTypeId,
-      created_in_data_collection_id: createdInDataCollectionId,
-      on_exists: UploadAction.UPDATE,
-      case_batch: {
-        cases: validatedCasesWithGeneratedId.map((vc, index) => {
-          const caseId = validatedCases[index].id ?? undefined;
-          const readSetsForUpload: ReadSetForUpload[] = [];
-          const seqsForUpload: SeqForUpload[] = [];
-          const externalSampleId = CaseUtil.getRowValue(
-            vc.validated_content,
-            mappedSampleIdCol,
-            completeCaseType,
-          )?.raw;
-
-          if (externalSampleId) {
-            if (sequenceMapping[vc.generatedId]?.sequenceFileNames) {
-              Object.entries(sequenceMapping[vc.generatedId].sequenceFileNames).forEach(([colId, fileName]) => {
-                if (fileName) {
-                  seqsForUpload.push({
-                    col_id: colId,
-                    case_id: caseId,
-                    other_sample_identifier: {
-                      external_id: externalSampleId,
-                      identifier_issuer_id: sampleIdentifierIssuerId,
-                    },
-                    assembly_protocol_id: assemblyProtocolId,
-                  } satisfies SeqForUpload);
-                }
-              });
-            }
-            if (sequenceMapping[vc.generatedId]?.readsFileNames) {
-              Object.entries(sequenceMapping[vc.generatedId].readsFileNames).forEach(([colId, fileNames]) => {
-                if (fileNames.fwd || fileNames.rev) {
-                  readSetsForUpload.push({
-                    col_id: colId,
-                    case_id: caseId,
-                    other_sample_identifier: {
-                      external_id: externalSampleId,
-                      identifier_issuer_id: sampleIdentifierIssuerId,
-                    },
-                    sequencing_protocol_id: sequencingProtocolId,
-                  } satisfies ReadSetForUpload);
-                }
-              });
-            }
-          }
-
-          return {
-            case: {
-              id: caseId,
-              case_type_id: caseTypeId,
-              created_in_data_collection_id: createdInDataCollectionId,
-              content: vc.validated_content,
-            },
-            read_sets: readSetsForUpload,
-            seqs: seqsForUpload,
-          } satisfies CaseForUpload;
-        }),
-      },
-    }, { signal })).data;
-  }
-
-  public static reportFileUploadProgress(kwArgs: {
-    startPercentage: number;
-    endPercentage: number;
-    onProgress: (progress: number, message: string) => void;
-    totalFileSizeToUpload: number;
-    uploadedFileSize: number;
-    fileSize: number;
-    message: string;
-  }): void {
-    const {
-      startPercentage,
-      endPercentage,
-      onProgress,
-      totalFileSizeToUpload,
-      uploadedFileSize,
-      fileSize,
-      message,
-    } = kwArgs;
-
-    const percentageRange = endPercentage - startPercentage;
-    const percentageRangePerByte = percentageRange / totalFileSizeToUpload;
-    const overallProgress = startPercentage + (uploadedFileSize * percentageRangePerByte) + (fileSize * percentageRangePerByte);
-
-    onProgress(overallProgress, message);
-  }
-
-  public static async uploadFilesForCases(kwArgs: {
-    startPercentage: number;
-    endPercentage: number;
-    assemblyProtocolId: string;
-    caseTypeId: string;
-    completeCaseType: CompleteCaseType;
-    caseBatchUploadResult: CaseBatchUploadResult;
-    createdInDataCollectionId: string;
-    mappedColumns: EpiUploadMappedColumn[];
-    onComplete: () => void;
-    onError: (error: Error) => void;
-    onProgress: (progress: number, message: string) => void;
-    sampleIdColId: string;
-    sequenceFilesDataTransfer: DataTransfer;
-    sequenceMapping: EpiUploadSequenceMapping;
-    sequencingProtocolId: string;
-    signal: AbortSignal;
-    validatedCases: CaseUploadResult[];
-    validatedCasesWithGeneratedId: CaseUploadResultWithGeneratedId[];
-  }): Promise<void> {
-    const {
-      startPercentage,
-      endPercentage,
-      caseBatchUploadResult,
-      onProgress,
-      sequenceFilesDataTransfer,
-      sequenceMapping,
-      signal,
-    } = kwArgs;
-
-    const seqsToBeUploaded: Array<{ caseId: string; colId: string; fileName: string }> = [];
-    const readSetsToBeUploaded: Array<{ caseId: string; colId: string; fileName: string; is_fwd: boolean }> = [];
-    let totalFileSizeToUpload = 0;
-
-    for (const [index, caseUploadResult] of caseBatchUploadResult.cases.entries()) {
-      const { generatedId } = kwArgs.validatedCasesWithGeneratedId[index];
-      if (sequenceMapping[generatedId]) {
-        const caseId = caseUploadResult.id;
-        for (const [colId, fileName] of Object.entries(sequenceMapping[generatedId].sequenceFileNames)) {
-          if (fileName) {
-            const file = Array.from(sequenceFilesDataTransfer.files).find(f => f.name === fileName);
-            if (file) {
-              seqsToBeUploaded.push({ caseId, colId, fileName });
-              totalFileSizeToUpload = totalFileSizeToUpload + (file?.size || 0);
-            }
-          }
-        }
-        for (const [colId, fileNames] of Object.entries(sequenceMapping[generatedId].readsFileNames)) {
-          if (fileNames.fwd) {
-            const file = Array.from(sequenceFilesDataTransfer.files).find(f => f.name === fileNames.fwd);
-            if (file) {
-              readSetsToBeUploaded.push({ caseId, colId, fileName: fileNames.fwd, is_fwd: true });
-              totalFileSizeToUpload = totalFileSizeToUpload + (file?.size || 0);
-            }
-          }
-          if (fileNames.rev) {
-            const file = Array.from(sequenceFilesDataTransfer.files).find(f => f.name === fileNames.rev);
-            if (file) {
-              readSetsToBeUploaded.push({ caseId, colId, fileName: fileNames.rev, is_fwd: false });
-              totalFileSizeToUpload = totalFileSizeToUpload + (file?.size || 0);
-            }
-          }
-        }
-      }
-    }
-
-    // upload in order of cases
-    let uploadedFileSize = 0;
-    for (const caseUploadResult of caseBatchUploadResult.cases) {
-      const caseSeqToBeUploaded = seqsToBeUploaded.find(s => s.caseId === caseUploadResult.id);
-      const caseReadSetsToBeUploaded = readSetsToBeUploaded.filter(rs => rs.caseId === caseUploadResult.id);
-
-      if (caseSeqToBeUploaded) {
-        const file = Array.from(sequenceFilesDataTransfer.files).find(f => f.name === caseSeqToBeUploaded.fileName);
-        if (file) {
-          const fileSize = file.size;
-          const base64Data = await EpiUploadUtil.readFileAsBase64(file);
-          await CaseApi.instance.createFileForSeq(caseSeqToBeUploaded.caseId, caseSeqToBeUploaded.colId, {
-            file_content: base64Data,
-            file_compression: FileUtil.getFileCompressionFromFileName(caseSeqToBeUploaded.fileName),
-            file_format: SeqFileFormat.FASTA,
-          }, { signal });
-          EpiUploadUtil.reportFileUploadProgress({
-            startPercentage,
-            endPercentage,
-            onProgress,
-            totalFileSizeToUpload,
-            uploadedFileSize,
-            fileSize,
-            message: t('Uploading sequence file "{{fileName}}" for case ID "{{caseId}}"...', { fileName: caseSeqToBeUploaded.fileName, caseId: caseSeqToBeUploaded.caseId }),
-          });
-          uploadedFileSize += fileSize;
-        }
-      }
-      for (const caseReadSetToBeUploaded of caseReadSetsToBeUploaded) {
-        const file = Array.from(sequenceFilesDataTransfer.files).find(f => f.name === caseReadSetToBeUploaded.fileName);
-        if (file) {
-          const fileSize = file.size;
-          const base64Data = await EpiUploadUtil.readFileAsBase64(file);
-          await CaseApi.instance.createFileForReadSet(caseReadSetToBeUploaded.caseId, caseReadSetToBeUploaded.colId, {
-            file_content: base64Data,
-            file_compression: FileUtil.getFileCompressionFromFileName(caseReadSetToBeUploaded.fileName),
-            file_format: ReadsFileFormat.FASTQ,
-            is_fwd: caseReadSetToBeUploaded.is_fwd,
-          }, { signal });
-          EpiUploadUtil.reportFileUploadProgress({
-            startPercentage,
-            endPercentage,
-            onProgress,
-            totalFileSizeToUpload,
-            uploadedFileSize,
-            fileSize,
-            message: t('Uploading read set file "{{fileName}}" for case ID "{{caseId}}"...', { fileName: caseReadSetToBeUploaded.fileName, caseId: caseReadSetToBeUploaded.caseId }),
-          });
-          uploadedFileSize += fileSize;
-        }
-      }
-    }
-  }
-
-  public static async createCasesAndUploadFiles(kwArgs: {
-    completeCaseType: CompleteCaseType;
-    assemblyProtocolId: string;
-    caseTypeId: string;
-    createdInDataCollectionId: string;
-    mappedColumns: EpiUploadMappedColumn[];
-    onComplete: () => void;
-    sampleIdColId: string;
-    onError: (error: Error) => void;
-    onProgress: (progress: number, message: string) => void;
-    sequenceFilesDataTransfer: DataTransfer;
-    sequenceMapping: EpiUploadSequenceMapping;
-    sequencingProtocolId: string;
-    signal: AbortSignal;
-    validatedCases: CaseUploadResult[];
-    validatedCasesWithGeneratedId: CaseUploadResultWithGeneratedId[];
-  }): Promise<void> {
-    const {
-      onComplete,
-      onError,
-      onProgress,
-    } = kwArgs;
-
-    try {
-      onProgress(0, t('Creating cases...'));
-      const caseBatchUploadResult = await EpiUploadUtil.createCases(kwArgs);
-
-      if (caseBatchUploadResult.status === EtlStatus.FAILED) {
-        throw new UploadError(t('Failed to create cases during upload.'), caseBatchUploadResult);
-      }
-
-      await EpiUploadUtil.uploadFilesForCases({ ...kwArgs, caseBatchUploadResult, startPercentage: 1, endPercentage: 99 });
-      onProgress(100, t('Upload complete.'));
-
-      await QueryUtil.invalidateQueryKeys(QueryUtil.getQueryKeyDependencies([QUERY_KEY.CASES], true));
-      onComplete();
-    } catch (error) {
-      onError(error instanceof Error ? error : new Error('Unknown error occurred during upload'));
-      throw error;
-    }
-  }
-}