@gen-epix/ui-client-casedb 4.1.0 → 4.3.0

package/dist/_chunks/Upload.js.map

@@ -1 +1 @@
-{"version":3,"file":"Upload.js","names":[],"sources":["../../src/components/ui/Upload/UploadNavigation.tsx","../../src/components/ui/Upload/UploadSelectFile.tsx","../../src/components/ui/Upload/UploadMapColumns.tsx","../../src/components/ui/CompletCaseTypeLoader/withEpiCompleteCaseTypeLoader.tsx","../../src/components/ui/Upload/UploadEditColumnValuesDialog.tsx","../../src/components/ui/Upload/UploadCaseResultTable.tsx","../../src/components/ui/Upload/UploadPreviewNavigation.tsx","../../src/components/ui/Upload/UploadPreview.tsx","../../src/components/ui/Upload/UploadCreateCases.tsx","../../src/components/ui/Upload/UploadSelectSequenceFiles.tsx","../../src/components/ui/Upload/UploadMapSequences.tsx","../../src/components/ui/Upload/Upload.tsx"],"sourcesContent":["import type { ContainerOwnProps } from '@mui/material';\nimport {\n  Box,\n  Button,\n} from '@mui/material';\nimport { use } from 'react';\nimport { useTranslation } from 'react-i18next';\nimport { useStore } from 'zustand';\n\nimport { UploadStoreContext } from '../../../stores/uploadStore';\n\nexport type UploadNavigationProps = {\n  readonly backLabel?: string;\n  readonly containerProps?: ContainerOwnProps;\n  readonly onGoBackButtonClick?: () => void;\n  readonly onProceedButtonClick?: () => void;\n  readonly proceedDisabled?: boolean;\n  readonly proceedLabel?: string;\n};\n\nexport const UploadNavigation = ({\n  backLabel,\n  onGoBackButtonClick: onGoBack,\n  onProceedButtonClick: onProceedButtonClick,\n  proceedDisabled,\n  proceedLabel,\n}: UploadNavigationProps) => {\n  const { t } = useTranslation();\n  const store = use(UploadStoreContext);\n  const stepOrder = useStore(store, (state) => state.stepOrder);\n  const activeStep = useStore(store, (state) => state.activeStep);\n  const goBackFromFirstStepCallback = useStore(store, (state) => state.goBackFromFirstStepCallback);\n  const goBackFromFirstStepLabel = useStore(store, (state) => state.goBackFromFirstStepLabel);\n\n  const isFirstStep = activeStep === stepOrder[0];\n  const onClickGoBack = isFirstStep ? (goBackFromFirstStepCallback ?? onGoBack) : onGoBack;\n  const effectiveBackLabel = isFirstStep ? (goBackFromFirstStepLabel ?? backLabel) : backLabel;\n\n  return (\n    <Box\n      sx={{\n        borderTop: (theme) => `1px solid ${theme.palette.divider}`,\n        display: 'flex',\n        gap: 2,\n        justifyContent: 'flex-end',\n        marginTop: 1,\n        paddingTop: 1,\n      }}\n    >\n      {onClickGoBack && (\n        <Button\n          onClick={onClickGoBack}\n          variant={'outlined'}\n        >\n          {effectiveBackLabel ?? t`Go back`}\n        </Button>\n      )}\n      {onProceedButtonClick && (\n        <Button\n          color={'secondary'}\n          disabled={proceedDisabled}\n          onClick={onProceedButtonClick}\n          variant={'contained'}\n        >\n          {proceedLabel ?? t`Next`}\n        </Button>\n      )}\n    </Box>\n  );\n\n};\n","import {\n  use,\n  useCallback,\n  useEffect,\n  useId,\n  useMemo,\n} from 'react';\nimport { useTranslation } from 'react-i18next';\nimport { yupResolver } from '@hookform/resolvers/yup';\nimport type { Resolver } from 'react-hook-form';\nimport { useForm } from 'react-hook-form';\nimport {\n  mixed,\n  object,\n  string,\n} from 'yup';\nimport {\n  Alert,\n  AlertTitle,\n  Container,\n  Typography,\n} from '@mui/material';\nimport { useStore } from 'zustand';\nimport { CaseDbCaseApi } from '@gen-epix/api-casedb';\nimport { ResponseHandler } from '@gen-epix/ui-client-common/components/ui/ResponseHandler';\nimport { useItemQuery } from '@gen-epix/ui-client-common/hooks/useItemQuery';\nimport { useArray } from '@gen-epix/ui-core/hooks/useArray';\nimport { GenericForm } from '@gen-epix/ui-core-form/components/helpers/GenericForm';\nimport type { FormFieldDefinition } from '@gen-epix/ui-core-form/models/form';\nimport { FORM_FIELD_DEFINITION_TYPE } from '@gen-epix/ui-core-form/models/form';\n\nimport {\n  useCaseTypeOptionsQuery,\n  useCaseTypesQuery,\n} from '../../../dataHooks/useCaseTypesQuery';\nimport { useDataCollectionOptionsQuery } from '../../../dataHooks/useDataCollectionsQuery';\nimport { useColsQuery } from '../../../dataHooks/useColsQuery';\nimport { UploadUtil } from '../../../utils/UploadUtil';\nimport { UploadStoreContext } from '../../../stores/uploadStore';\nimport { CASEDB_QUERY_KEY } from '../../../constants/query';\n\nimport { UploadNavigation } from './UploadNavigation';\n\ntype FormFields = {\n  caseTypeId: string;\n  createdInDataCollectionId: string;\n  fileList: unknown;\n  sheet: string;\n};\n\nexport const UploadSelectFile = () => {\n  const { t } = useTranslation();\n  const caseTypesQuery = useCaseTypesQuery();\n  const caseTypeOptionsQuery = useCaseTypeOptionsQuery();\n  const dataCollectionOptionsQuery = useDataCollectionOptionsQuery();\n  const colsQuery = useColsQuery();\n  const formId = useId();\n\n  const store = use(UploadStoreContext);\n\n  const caseTypeId = useStore(store, (state) => state.caseTypeId);\n  const fileList = useStore(store, (state) => state.fileList);\n  const fileName = useStore(store, (state) => state.fileName);\n  const fileParsingError = useStore(store, (state) => state.fileParsingError);\n  const goToNextStep = useStore(store, (state) => state.goToNextStep);\n  const createdInDataCollectionOptions = useStore(store, (state) => state.createdInDataCollectionOptions);\n  const rawData = useStore(store, (state) => state.rawData);\n  const setCols = useStore(store, (state) => state.setCols);\n  const setCaseTypeId = useStore(store, (state) => state.setCaseTypeId);\n  const setCompleteCaseType = useStore(store, (state) => state.setCompleteCaseType);\n  const setCreatedInDataCollectionId = useStore(store, (state) => state.setCreatedInDataCollectionId);\n  const setFileList = useStore(store, (state) => state.setFileList);\n  const setSheet = useStore(store, (state) => state.setSheet);\n  const setDataCollectionOptions = useStore(store, (state) => state.setDataCollectionOptions);\n  const sheet = useStore(store, (state) => state.sheet);\n  const sheetOptions = useStore(store, (state) => state.sheetOptions);\n\n  const schema = useMemo(() => object<FormFields>().shape({\n    caseTypeId: string().uuid4().required(),\n    createdInDataCollectionId: string().uuid4().required(),\n    fileList: mixed().required(t`File is required`),\n    sheet: string().when('fileList', {\n      is: UploadUtil.isXlsxFile(fileName),\n      otherwise: (sheetSchema) => sheetSchema.notRequired(),\n      then: (sheetSchema) => sheetSchema.required(t`Sheet is required`),\n    }),\n  }), [fileName, t]);\n\n  const formMethods = useForm<FormFields>({\n    defaultValues: {\n      caseTypeId: null,\n      createdInDataCollectionId: null,\n      fileList: null,\n      sheet: null,\n    },\n    resolver: yupResolver(schema) as unknown as Resolver<FormFields>,\n    values: {\n      caseTypeId: store.getState().caseTypeId ?? null,\n      createdInDataCollectionId: store.getState().createdInDataCollectionId ?? null,\n      fileList: store.getState().fileList ?? null,\n      sheet: store.getState().sheet ?? null,\n    },\n  });\n  const { handleSubmit, setError, setValue } = formMethods;\n\n  useEffect(() => {\n    if (Array.isArray(colsQuery?.data)) {\n      setCols(colsQuery.data);\n    }\n  }, [colsQuery.data, setCols]);\n\n  useEffect(() => {\n    if (dataCollectionOptionsQuery?.options?.length) {\n      setDataCollectionOptions(dataCollectionOptionsQuery.options);\n    }\n  }, [dataCollectionOptionsQuery?.options, setDataCollectionOptions]);\n\n  const { data: completeCaseType, error: completeCaseTypeError, isLoading: isCompleteCaseTypeLoading } = useItemQuery({\n    baseQueryKey: CASEDB_QUERY_KEY.COMPLETE_CASE_TYPES,\n    itemId: caseTypeId,\n    useQueryOptions: {\n      enabled: !!caseTypeId,\n      queryFn: async ({ signal }) => {\n        return (await CaseDbCaseApi.getInstance().completeCaseTypesGetOne(caseTypeId, { signal })).data;\n      },\n    },\n  });\n\n  useEffect(() => {\n    if (completeCaseType) {\n      setCompleteCaseType(completeCaseType);\n    }\n  }, [completeCaseType, setCompleteCaseType]);\n\n  const onFileListChange = useCallback(async (value: FileList) => {\n    await setFileList(value);\n  }, [setFileList]);\n\n  const onSheetChange = useCallback(async (value: unknown) => {\n    await setSheet(value as string);\n  }, [setSheet]);\n\n  const onCaseTypeIdChange = useCallback((value: unknown) => {\n    setCaseTypeId(value as string);\n  }, [setCaseTypeId]);\n\n  const onCreatedInDataCollectionIdChange = useCallback((value: unknown) => {\n    setCreatedInDataCollectionId(value as string);\n  }, [setCreatedInDataCollectionId]);\n\n  const formFieldDefinitions = useMemo<FormFieldDefinition<FormFields>[]>(() => {\n    const fields: FormFieldDefinition<FormFields>[] = [\n      {\n        accept: '.csv,.tsv,.txt,.xlsx',\n        definition: FORM_FIELD_DEFINITION_TYPE.FILE,\n        label: t`File`,\n        name: 'fileList',\n        onChange: onFileListChange,\n      } as const satisfies FormFieldDefinition<FormFields>,\n    ];\n\n    if (UploadUtil.isXlsxFile(fileName)) {\n      fields.push({\n        definition: FORM_FIELD_DEFINITION_TYPE.SELECT,\n        label: t`Sheet`,\n        name: 'sheet',\n        onChange: onSheetChange,\n        options: sheetOptions,\n      } as const satisfies FormFieldDefinition<FormFields>);\n    }\n\n    fields.push(...[\n      {\n        definition: FORM_FIELD_DEFINITION_TYPE.AUTOCOMPLETE,\n        disabled: !fileList,\n        label: t`Case type`,\n        loading: caseTypeOptionsQuery.isLoading,\n        name: 'caseTypeId',\n        onChange: onCaseTypeIdChange,\n        options: caseTypeOptionsQuery.options,\n      } as const satisfies FormFieldDefinition<FormFields>,\n      {\n        definition: FORM_FIELD_DEFINITION_TYPE.SELECT,\n        disabled: !fileList || !caseTypeId,\n        label: t`Create in data collection`,\n        loading: dataCollectionOptionsQuery.isLoading || isCompleteCaseTypeLoading,\n        name: 'createdInDataCollectionId',\n        onChange: onCreatedInDataCollectionIdChange,\n        options: createdInDataCollectionOptions,\n      } as const satisfies FormFieldDefinition<FormFields>,\n    ] as const);\n\n    return fields;\n  }, [t, onFileListChange, fileName, caseTypeOptionsQuery.options, caseTypeOptionsQuery.isLoading, fileList, onCaseTypeIdChange, createdInDataCollectionOptions, dataCollectionOptionsQuery.isLoading, isCompleteCaseTypeLoading, caseTypeId, onCreatedInDataCollectionIdChange, sheetOptions, onSheetChange]);\n\n  useEffect(() => {\n    if (fileParsingError) {\n      setError('fileList', { message: fileParsingError, type: 'manual' });\n    } else {\n      setError('fileList', undefined);\n    }\n  }, [fileParsingError, setError, setValue]);\n\n  const onFormSubmit = useCallback(async () => {\n    await goToNextStep();\n  }, [goToNextStep]);\n\n  const loadables = useArray([\n    caseTypesQuery,\n    caseTypeOptionsQuery,\n    dataCollectionOptionsQuery,\n    colsQuery,\n  ]);\n\n  const onProceedButtonClick = useCallback(async () => {\n    await handleSubmit(onFormSubmit)();\n  }, [handleSubmit, onFormSubmit]);\n\n  const canUpload = useMemo(() => {\n    if (colsQuery.isLoading === false && colsQuery.data?.length === 0) {\n      return false;\n    }\n    if (caseTypeOptionsQuery.isLoading === false && caseTypeOptionsQuery.options?.length === 0) {\n      return false;\n    }\n    if (dataCollectionOptionsQuery.isLoading === false && dataCollectionOptionsQuery.options?.length === 0) {\n      return false;\n    }\n    return true;\n  }, [colsQuery.data?.length, colsQuery.isLoading, caseTypeOptionsQuery.isLoading, caseTypeOptionsQuery.options?.length, dataCollectionOptionsQuery.isLoading, dataCollectionOptionsQuery.options?.length]);\n\n  return (\n\n    <ResponseHandler\n      error={completeCaseTypeError}\n      inlineSpinner\n      loadables={loadables}\n    >\n      <Container maxWidth={'lg'}>\n        {!canUpload && (\n          <Alert\n            severity={'warning'}\n            sx={{ mb: 2 }}\n          >\n            {t('Upload is disabled because you have insufficient data access to proceed. Contact your organization administrator for assistance.')}\n          </Alert>\n        )}\n        {canUpload && (\n          <>\n            {rawData && rawData.length > 0 && (\n              <Alert\n                severity={'info'}\n                sx={{ mb: 2 }}\n              >\n                <AlertTitle>\n                  {t('{{fileName}} loaded successfully', { fileName })}\n                </AlertTitle>\n                {sheet && (\n                  <Typography>\n                    {t('Sheet name: {{sheet}}', { sheet: sheet || '' })}\n                  </Typography>\n                )}\n                <Typography>\n                  {t('Number of columns: {{columnCount}}', { columnCount: rawData[0].length })}\n                </Typography>\n                <Typography>\n                  {t('Number of data rows: {{rowCount}}', { rowCount: rawData.length - 1 })}\n                </Typography>\n              </Alert>\n            )}\n            <GenericForm<FormFields>\n              formFieldDefinitions={formFieldDefinitions}\n              formId={formId}\n              formMethods={formMethods}\n              onSubmit={handleSubmit(onFormSubmit)}\n              schema={schema}\n            />\n            <UploadNavigation\n              onProceedButtonClick={onProceedButtonClick}\n            />\n          </>\n        )}\n\n      </Container>\n    </ResponseHandler>\n  );\n};\n","import type { ReactElement } from 'react';\nimport {\n  use,\n  useCallback,\n  useEffect,\n  useId,\n  useMemo,\n} from 'react';\nimport { yupResolver } from '@hookform/resolvers/yup';\nimport {\n  useForm,\n  useWatch,\n} from 'react-hook-form';\nimport {\n  Alert,\n  AlertTitle,\n  Box,\n  Container,\n  Table,\n  TableBody,\n  TableCell,\n  TableHead,\n  TableRow,\n} from '@mui/material';\nimport { useTranslation } from 'react-i18next';\nimport uniq from 'lodash/uniq';\nimport { useStore } from 'zustand';\nimport difference from 'lodash/difference';\nimport { ConfigService } from '@gen-epix/ui-client-common/classes/services/ConfigService';\nimport { ResponseHandler } from '@gen-epix/ui-client-common/components/ui/ResponseHandler';\nimport { useIdentifierIssuerOwnOrganizationOptionsQuery } from '@gen-epix/ui-client-common/dataHooks/useIdentifierIssuerOwnOrganizationQuery';\nimport { useArray } from '@gen-epix/ui-core/hooks/useArray';\nimport { Select } from '@gen-epix/ui-core-form/components/fields/Select';\nimport { GenericForm } from '@gen-epix/ui-core-form/components/helpers/GenericForm';\nimport type { FormFieldDefinition } from '@gen-epix/ui-core-form/models/form';\n\nimport { useColMapQuery } from '../../../dataHooks/useColsQuery';\nimport type { UploadMappedColumnsFormFields } from '../../../models/upload';\nimport { UploadStoreContext } from '../../../stores/uploadStore';\nimport { UploadUtil } from '../../../utils/UploadUtil';\n\nimport { UploadNavigation } from './UploadNavigation';\n\n\nexport const UploadMapColumns = () => {\n  const { t } = useTranslation();\n  const colMap = useColMapQuery();\n  const identifierIssuerOptionsQuery = useIdentifierIssuerOwnOrganizationOptionsQuery();\n\n  const store = use(UploadStoreContext);\n  const completeCaseType = useStore(store, (state) => state.completeCaseType);\n  const rawData = useStore(store, (state) => state.rawData);\n  const fileName = useStore(store, (state) => state.fileName);\n  const goToNextStep = useStore(store, (state) => state.goToNextStep);\n  const goToPreviousStep = useStore(store, (state) => state.goToPreviousStep);\n  const setMappedColumns = useStore(store, (state) => state.setMappedColumns);\n\n  const loadables = useArray([\n    colMap,\n    identifierIssuerOptionsQuery,\n  ]);\n\n  const columnMappingFormId = useId();\n\n  const schema = useMemo(() => {\n    return UploadUtil.getColumnMappingSchema(rawData, completeCaseType);\n  }, [completeCaseType, rawData]);\n\n  const defaultValues: UploadMappedColumnsFormFields = useMemo(() => {\n    return UploadUtil.getDefaultColumnMappingFormValues(rawData[0], store.getState().mappedColumns, identifierIssuerOptionsQuery.options);\n  }, [rawData, store, identifierIssuerOptionsQuery.options]);\n\n  const formMethods = useForm<UploadMappedColumnsFormFields>({\n    defaultValues: { ...defaultValues },\n    resolver: yupResolver(schema),\n    values: { ...defaultValues },\n  });\n\n  const { clearErrors, control, handleSubmit } = formMethods;\n  const columnMappingFormValues = useWatch({ control });\n\n  const formFieldDefinitions = useMemo<FormFieldDefinition<UploadMappedColumnsFormFields>[]>(() => {\n    return UploadUtil.getColumnMappingFormFieldDefinitions(completeCaseType, rawData[0], fileName).map(def => ({\n      ...def,\n      onChange: () => clearErrors(),\n    }));\n  }, [completeCaseType, rawData, fileName, clearErrors]);\n\n  useEffect(() => {\n    const perform = async () => {\n      await setMappedColumns(UploadUtil.getMappedColumnsFromFormData(columnMappingFormValues, rawData, colMap.map, completeCaseType));\n    };\n    // eslint-disable-next-line @typescript-eslint/no-floating-promises\n    perform();\n  }, [setMappedColumns, columnMappingFormValues, rawData, colMap.map, completeCaseType]);\n\n  const unMappedColumns = useMemo(() => {\n    const knownIndicies = rawData[0].map((_col, index) => index);\n    const mappedIndicies = UploadUtil.getMappedColumnsFromFormData(columnMappingFormValues, rawData, colMap.map, completeCaseType).map(mappedColumn => mappedColumn.originalIndex);\n    return difference(knownIndicies, mappedIndicies).map(index => {\n      return {\n        originalIndex: index,\n        originalLabel: rawData[0][index],\n      };\n    });\n  }, [colMap.map, rawData, columnMappingFormValues, completeCaseType]);\n\n  const onFormSubmit = useCallback(async (data: UploadMappedColumnsFormFields) => {\n    await setMappedColumns(UploadUtil.getMappedColumnsFromFormData(data, rawData, colMap.map, completeCaseType));\n    await goToNextStep();\n  }, [rawData, colMap.map, goToNextStep, setMappedColumns, completeCaseType]);\n\n  const sampleIdColIds = useMemo(() => {\n    return UploadUtil.getSampleIdColIds(completeCaseType);\n  }, [completeCaseType]);\n\n  const renderField = useCallback((definition: FormFieldDefinition<UploadMappedColumnsFormFields>, element: ReactElement) => {\n    const columnIndexInRawData = parseInt(definition.name, 10);\n    const columnValues = uniq(rawData.slice(1).map((row) => row[columnIndexInRawData] ?? '')).filter(x => !!x);\n    const firstFiveValuesString = columnValues.slice(0, 5).join(', ').trim() || t('<no data>');\n\n    let elementWithIssuer = element;\n    const fieldValue = columnMappingFormValues[definition.name];\n    if (sampleIdColIds.includes(fieldValue)) {\n      elementWithIssuer = (\n        <>\n          <Box>\n            {element}\n          </Box>\n          <Box\n            sx={{\n              marginTop: 1,\n            }}\n          >\n            <Select\n              label={t('{{columnLabel}}: Identifier issuer', { columnLabel: definition.label })}\n              loading={identifierIssuerOptionsQuery.isLoading}\n              name={fieldValue}\n              options={identifierIssuerOptionsQuery.options}\n            />\n          </Box>\n        </>\n      );\n    }\n\n    return (\n      <TableRow key={definition.name}>\n        <TableCell>\n          {definition.label}\n        </TableCell>\n        <TableCell>\n          {elementWithIssuer}\n        </TableCell>\n        <TableCell>\n          {firstFiveValuesString}\n        </TableCell>\n      </TableRow>\n    );\n  }, [columnMappingFormValues, identifierIssuerOptionsQuery.isLoading, identifierIssuerOptionsQuery.options, rawData, sampleIdColIds, t]);\n\n  const wrapForm = useCallback((children: ReactElement) => {\n    return (\n      <Table\n        size={'small'}\n      >\n        <TableHead\n          sx={{\n            backgroundColor: (theme) => theme.palette.background.paper,\n            position: 'sticky',\n            top: 0,\n            zIndex: (theme) => theme.zIndex.appBar - 1,\n          }}\n        >\n          <TableRow>\n            <TableCell sx={{ width: '33%' }}>\n              {t`Source`}\n            </TableCell>\n            <TableCell sx={{ width: '33%' }}>\n              {ConfigService.getInstance().config.applicationName}\n            </TableCell>\n            <TableCell sx={{ width: '34%' }}>\n              {t`Data preview (first 5 unique values)`}\n            </TableCell>\n          </TableRow>\n        </TableHead>\n        <TableBody>\n          {children}\n        </TableBody>\n      </Table>\n    );\n  }, [t]);\n\n  const onProceedButtonClick = useCallback(async () => {\n    await handleSubmit(onFormSubmit)();\n  }, [handleSubmit, onFormSubmit]);\n\n  const onGoBackButtonClick = useCallback(() => {\n    goToPreviousStep();\n  }, [goToPreviousStep]);\n\n  return (\n    <ResponseHandler loadables={loadables}>\n      <Box\n        sx={{\n          display: 'grid',\n          gridTemplateRows: 'max-content auto max-content',\n          height: '100%',\n        }}\n      >\n        <Container\n          maxWidth={'lg'}\n          sx={{\n            marginBottom: 2,\n          }}\n        >\n          <Alert severity={unMappedColumns.length === 0 ? 'info' : 'warning'}>\n            <AlertTitle>\n              {unMappedColumns.length === 0 ?\n                t('All columns in {{fileName}} have been mapped to known columns in {{applicationName}}', { applicationName: ConfigService.getInstance().config.applicationName, fileName })\n                : t('{{numUnmappedColumns}} column(s) in {{fileName}} are not mapped', { fileName, numUnmappedColumns: unMappedColumns.length })}\n            </AlertTitle>\n            {unMappedColumns.map((unmappedColumn) => (\n              <Box key={unmappedColumn.originalIndex}>\n                {t('The column \"{{columnName}}\" (column {{columnIndex}}) has not been mapped.', { columnIndex: unmappedColumn.originalIndex + 1, columnName: unmappedColumn.originalLabel })}\n              </Box>\n            ))}\n            {unMappedColumns.length === 0 && t('You can proceed to the next step.')}\n          </Alert>\n        </Container>\n        <Box\n          sx={{\n            overflowY: 'auto',\n            position: 'relative',\n          }}\n        >\n          <Box\n            sx={{\n              bottom: 0,\n              left: 0,\n              position: 'absolute',\n              right: 0,\n              top: 0,\n            }}\n          >\n            <Container>\n              <GenericForm<UploadMappedColumnsFormFields>\n                formFieldDefinitions={formFieldDefinitions}\n                formId={columnMappingFormId}\n                formMethods={formMethods}\n                onSubmit={handleSubmit(onFormSubmit)}\n                renderField={renderField}\n                schema={schema}\n                wrapForm={wrapForm}\n              />\n            </Container>\n          </Box>\n        </Box>\n        <Box>\n          <UploadNavigation\n            onGoBackButtonClick={onGoBackButtonClick}\n            onProceedButtonClick={onProceedButtonClick}\n          />\n        </Box>\n      </Box>\n    </ResponseHandler>\n  );\n};\n","import {\n  useCallback,\n  useState,\n} from 'react';\nimport type { ComponentType } from 'react';\n\nimport type { CompletCaseTypeLoaderProps } from './CompletCaseTypeLoader';\nimport { CompletCaseTypeLoader } from './CompletCaseTypeLoader';\n\nexport type WithEpiCompleteCaseTypeLoaderProps = CompletCaseTypeLoaderProps;\n\nexport const withEpiCompleteCaseTypeLoader = <P extends WithEpiCompleteCaseTypeLoaderProps>(WrappedComponent: ComponentType<P>): ComponentType<P> => {\n  return (props: WithEpiCompleteCaseTypeLoaderProps) => {\n    const [isCompleteCaseTypeLoaded, setIsCompleteCaseTypeLoaded] = useState<boolean>(false);\n\n    const onCompleteCaseTypeLoaded = useCallback(() => {\n      setIsCompleteCaseTypeLoaded(true);\n    }, []);\n\n    return (\n      <CompletCaseTypeLoader\n        caseTypeId={props.caseTypeId}\n        onCompleteCaseTypeLoaded={onCompleteCaseTypeLoaded}\n      >\n        {isCompleteCaseTypeLoaded && (\n          <WrappedComponent\n            {...props as P}\n          />\n        )}\n      </CompletCaseTypeLoader>\n    );\n  };\n};\n","import { useTranslation } from 'react-i18next';\nimport type {\n  CaseDbCase,\n  CaseDbCompleteCaseType,\n} from '@gen-epix/api-casedb';\nimport type { DialogAction } from '@gen-epix/ui-core-components/components/Dialog';\nimport type {\n  WithDialogRefMethods,\n  WithDialogRenderProps,\n} from '@gen-epix/ui-core-components/hoc/withDialog';\nimport { withDialog } from '@gen-epix/ui-core-components/hoc/withDialog';\nimport { TestIdUtil } from '@gen-epix/ui-core/utils/TestIdUtil';\nimport type { ReactElement } from 'react';\nimport {\n  useCallback,\n  useEffect,\n  useId,\n  useMemo,\n} from 'react';\nimport { yupResolver } from '@hookform/resolvers/yup';\nimport { useForm } from 'react-hook-form';\nimport {\n  Alert,\n  AlertTitle,\n  Box,\n} from '@mui/material';\nimport { GenericForm } from '@gen-epix/ui-core-form/components/helpers/GenericForm';\nimport { FormUtil } from '@gen-epix/ui-core-form/utils/FormUtil';\n\nimport { CaseTypeFormUtil } from '../../../utils/CaseTypeFormUtil';\n\n\nexport interface UploadEditColumnValuesDialogOpenProps {\n  colId: string;\n  completeCaseType: CaseDbCompleteCaseType;\n  shouldShowRightsWarning?: boolean;\n}\n\nexport interface UploadEditColumnValuesDialogProps extends WithDialogRenderProps<UploadEditColumnValuesDialogOpenProps> {\n  onSubmit: (content: CaseDbCase['content']) => void;\n}\n\nexport type UploadEditColumnValuesDialogRefMethods = WithDialogRefMethods<UploadEditColumnValuesDialogProps, UploadEditColumnValuesDialogOpenProps>;\n\n\nexport const UploadEditColumnValuesDialog = withDialog<UploadEditColumnValuesDialogProps, UploadEditColumnValuesDialogOpenProps>((\n  {\n    onActionsChange,\n    onClose,\n    onSubmit,\n    onTitleChange,\n    openProps,\n  }: UploadEditColumnValuesDialogProps,\n): ReactElement => {\n  const { t } = useTranslation();\n  const formId = useId();\n\n  const col = useMemo(() => {\n    return openProps.completeCaseType.cols[openProps.colId];\n  }, [openProps.completeCaseType.cols, openProps.colId]);\n\n  useEffect(() => {\n    onTitleChange(t('Edit values for {{colLabel}} (for selected rows)', { colLabel: col.label }));\n  }, [onTitleChange, col.label, t]);\n\n  const schema = useMemo(() => CaseTypeFormUtil.createYupSchema({\n    completeCaseType: openProps.completeCaseType,\n    includedColIds: [openProps.colId],\n  }), [openProps.completeCaseType, openProps.colId]);\n\n  const formMethods = useForm<CaseDbCase['content']>({\n    resolver: yupResolver(schema),\n  });\n  const { handleSubmit } = formMethods;\n\n  const { fieldDefinitions } = useMemo(() => {\n    return CaseTypeFormUtil.createFormDefinitions({\n      completeCaseType: openProps.completeCaseType,\n      includedColIds: [openProps.colId],\n    });\n  }, [openProps.completeCaseType, openProps.colId]);\n\n  const onFormSubmit = useCallback((content: CaseDbCase['content']) => {\n    onSubmit(FormUtil.createStringValuesFromFormValues(fieldDefinitions, content));\n    onClose();\n  }, [fieldDefinitions, onClose, onSubmit]);\n\n  useEffect(() => {\n    const actions: DialogAction[] = [\n      {\n        ...TestIdUtil.createAttributes('UploadEditColumnValuesDialog-submitButton'),\n        color: 'primary',\n        form: formId,\n        label: t`Save and revalidate`,\n        type: 'submit',\n        variant: 'contained',\n      },\n    ];\n    onActionsChange(actions);\n  }, [formId, onActionsChange, t]);\n\n  return (\n    <Box>\n      {openProps.shouldShowRightsWarning && (\n        <Box sx={{ marginBottom: 2 }}>\n          <Alert severity={'warning'}>\n            <AlertTitle>\n              {t`You do not have the necessary rights to edit all rows in this column.`}\n            </AlertTitle>\n            {t`Only the cases that you have write access to for this column will be updated. Please review the changes carefully before submitting.`}\n          </Alert>\n        </Box>\n      )}\n      <GenericForm<CaseDbCase['content']>\n        formFieldDefinitions={fieldDefinitions}\n        formId={formId}\n        formMethods={formMethods}\n        onSubmit={handleSubmit(onFormSubmit)}\n        schema={schema}\n      />\n    </Box>\n  );\n}, {\n  defaultTitle: '',\n  fullWidth: true,\n  maxWidth: 'md',\n  testId: 'UploadEditColumnValuesDialog',\n});\n","import type { ReactElement } from 'react';\nimport {\n  useCallback,\n  useMemo,\n  useRef,\n} from 'react';\nimport EditIcon from '@mui/icons-material/Edit';\nimport type { StoreApi } from 'zustand';\nimport {\n  Box,\n  ListItemIcon,\n  ListItemText,\n  MenuItem,\n  Tooltip,\n  useTheme,\n} from '@mui/material';\nimport ErrorOutlinedIcon from '@mui/icons-material/ErrorOutlined';\nimport AddIcon from '@mui/icons-material/Add';\nimport { useTranslation } from 'react-i18next';\nimport type {\n  CaseDbCase,\n  CaseDbCaseDataIssue,\n  CaseDbCaseUploadResult,\n  CaseDbCol,\n  CaseDbCompleteCaseType,\n} from '@gen-epix/api-casedb';\nimport { CaseDbDataIssueType } from '@gen-epix/api-casedb';\nimport type {\n  TableColumn,\n  TableColumnParams,\n  TableRowAndColumnParams,\n  TableRowParams,\n} from '@gen-epix/ui-client-common/models/table';\nimport type { TableStore } from '@gen-epix/ui-client-common/stores/tableStore';\nimport {\n  Table,\n  TableMenu,\n} from '@gen-epix/ui-client-common/components/ui/Table';\nimport { TABLE_COLUMN_FROZEN } from '@gen-epix/ui-client-common/models/table';\nimport { TableUtil } from '@gen-epix/ui-client-common/utils/TableUtil';\nimport { useInitializeTableStore } from '@gen-epix/ui-client-common/hooks/useInitializeTableStore';\n\nimport { CaseUtil } from '../../../utils/CaseUtil';\nimport type { CaseContentFormDialogRefMethods } from '../CaseContentFormDialog';\nimport { CaseContentFormDialog } from '../CaseContentFormDialog';\n\nimport type { UploadEditColumnValuesDialogRefMethods } from './UploadEditColumnValuesDialog';\nimport { UploadEditColumnValuesDialog } from './UploadEditColumnValuesDialog';\n\n\nexport type UploadCaseResultTableProps = {\n  readonly caseRightsColMap?: { [colId: string]: string[] };\n  readonly caseUploadResults?: CaseDbCaseUploadResult[];\n  readonly completeCaseType: CaseDbCompleteCaseType;\n  readonly getOriginalCellValue: (col: CaseDbCol, cellParams: TableRowAndColumnParams<CaseDbCaseUploadResult, null>, issue: CaseDbCaseDataIssue) => string;\n  readonly onCaseContentEditSubmit: (caseId: string, content: CaseDbCase['content']) => void;\n  readonly onColContentEditSubmit: (contentPerCaseId: { [caseId: string]: CaseDbCase['content'] }) => void;\n  readonly tableStore: StoreApi<TableStore<CaseDbCaseUploadResult>>;\n};\n\nexport const UploadCaseResultTable = ({ caseRightsColMap, caseUploadResults, completeCaseType, getOriginalCellValue, onCaseContentEditSubmit, onColContentEditSubmit, tableStore }: UploadCaseResultTableProps) => {\n  const theme = useTheme();\n  const { t } = useTranslation();\n  const caseFormDialogRef = useRef<CaseContentFormDialogRefMethods>(null);\n  const uploadEditColumnValuesDialogRef = useRef<UploadEditColumnValuesDialogRefMethods>(null);\n\n  const dataRulePriority: CaseDbDataIssueType[] = useMemo(() => [\n    CaseDbDataIssueType.UNAUTHORIZED,\n    CaseDbDataIssueType.INVALID,\n    CaseDbDataIssueType.CONFLICT,\n    CaseDbDataIssueType.MISSING,\n    CaseDbDataIssueType.DERIVED,\n    CaseDbDataIssueType.TRANSFORMED,\n  ], []);\n\n  const errorIssueTypes: CaseDbDataIssueType[] = useMemo(() => [\n    CaseDbDataIssueType.UNAUTHORIZED,\n    CaseDbDataIssueType.INVALID,\n  ], []);\n\n  const warningIssueTypes: CaseDbDataIssueType[] = useMemo(() => [\n    CaseDbDataIssueType.MISSING,\n    CaseDbDataIssueType.CONFLICT,\n  ], []);\n\n  const onTableCustomHeaderIconClick = useCallback((params: TableColumnParams<CaseDbCaseUploadResult, null>) => {\n    uploadEditColumnValuesDialogRef.current?.open({\n      colId: params.column.id,\n      completeCaseType,\n      shouldShowRightsWarning: caseRightsColMap?.[params.column.id]?.length !== caseUploadResults?.length,\n    });\n  }, [completeCaseType, caseRightsColMap, caseUploadResults]);\n\n  const onCaseContentFormDialogSubmit = useCallback((caseId: string, content: CaseDbCase['content']) => {\n    onCaseContentEditSubmit(caseId, content);\n  }, [onCaseContentEditSubmit]);\n\n  const onEpiUploadEditColumnValuesDialogSubmit = useCallback((content: CaseDbCase['content']) => {\n    const contentPerCaseId: { [caseId: string]: CaseDbCase['content'] } = {};\n    Object.keys(content).forEach((colId) => {\n      const caseIds = caseRightsColMap?.[colId] ?? [];\n      caseIds.forEach((caseId) => {\n        contentPerCaseId[caseId] = {\n          ...(contentPerCaseId[caseId] ?? {}),\n          [colId]: content[colId],\n        };\n      });\n    });\n    onColContentEditSubmit(contentPerCaseId);\n  }, [onColContentEditSubmit, caseRightsColMap]);\n\n  const getIssueTooltipMessages = useCallback((issues: CaseDbCaseDataIssue[]) => {\n    const messages: { key: string; message: string }[] = [];\n    issues.forEach((issue) => {\n      const columnLabel = completeCaseType.cols[issue.col_id].label;\n      const message = `${columnLabel}: ${issue.message}`;\n      messages.push({\n        key: `${issue.col_id}-${issue.data_issue_type}-${issue.code}`,\n        message,\n      });\n    });\n    return messages;\n  }, [completeCaseType.cols]);\n\n  const getIssueTooltipContent = useCallback((issues: CaseDbCaseDataIssue[]) => {\n    const messages = getIssueTooltipMessages(issues);\n    return (\n      <>\n        {messages.map(({ key, message }, index) => (\n          <Box\n            key={key}\n            sx={{ marginTop: index > 0 ? 1 : 0 }}\n          >\n            {message}\n          </Box>\n        ))}\n      </>\n    );\n  }, [getIssueTooltipMessages]);\n\n  const getIssueTooltipLabel = useCallback((issues: CaseDbCaseDataIssue[]) => {\n    const messages = getIssueTooltipMessages(issues);\n    return messages.map(m => m.message).join(', ');\n  }, [getIssueTooltipMessages]);\n\n  const getFilteredIssueTypes = useCallback((id: string, issues: CaseDbCaseDataIssue[], value: string) => {\n    return issues.filter((issue) => {\n      if (issue.col_id !== id) {\n        return false;\n      }\n      if (issue.data_issue_type === CaseDbDataIssueType.TRANSFORMED && issue.original_value === value) {\n        return false;\n      }\n      return true;\n    }).sort((a, b) => dataRulePriority.indexOf(a.data_issue_type) - dataRulePriority.indexOf(b.data_issue_type));\n  }, [dataRulePriority]);\n\n  const renderHasIssueHeader = useCallback(() => {\n    return (\n      <Tooltip\n        aria-hidden={false}\n        arrow\n        title={t('Indicates if there are any issues with the case')}\n      >\n        <ErrorOutlinedIcon\n          fontSize={'small'}\n        />\n      </Tooltip>\n    );\n  }, [t]);\n\n  const renderHasIssueCell = useCallback(({ row }: TableRowParams<CaseDbCaseUploadResult>) => {\n    const errorIssues = row.data_issues.filter(i => i.data_issue_type === CaseDbDataIssueType.INVALID || i.data_issue_type === CaseDbDataIssueType.UNAUTHORIZED);\n    if (errorIssues.length > 0) {\n      return (\n        <Tooltip\n          aria-hidden={false}\n          aria-label={getIssueTooltipLabel(errorIssues)}\n          arrow\n          title={getIssueTooltipContent(errorIssues)}\n        >\n          <ErrorOutlinedIcon\n            fontSize={'small'}\n            sx={{\n              color: theme.palette.error.main,\n              marginTop: '5px',\n            }}\n          />\n        </Tooltip>\n      );\n    }\n  }, [getIssueTooltipContent, getIssueTooltipLabel, theme.palette.error.main]);\n\n  const renderIsNewHeader = useCallback(() => {\n    return (\n      <Tooltip\n        aria-hidden={false}\n        arrow\n        title={t('Indicates if case is new (will be created)')}\n      >\n        <AddIcon\n          fontSize={'small'}\n        />\n      </Tooltip>\n    );\n  }, [t]);\n\n  const renderIsNewCell = useCallback(({ row }: TableRowParams<CaseDbCaseUploadResult>) => {\n    return row.id ? null : (\n      <AddIcon\n        aria-hidden={false}\n        aria-label={t`This case does not have an ID and will be created`}\n        fontSize={'small'}\n        sx={{\n          marginTop: '5px',\n          position: 'absolute',\n        }}\n      />\n    );\n  }, [t]);\n\n  const renderCell = useCallback(({ id, row }: TableRowParams<CaseDbCaseUploadResult>) => {\n    const rowValue = CaseUtil.getRowValue(row.validated_content, completeCaseType.cols[id], completeCaseType);\n    const value = rowValue.long;\n    const issues = getFilteredIssueTypes(id, row.data_issues, value);\n\n    if (issues.length === 0) {\n      return (\n        <>\n          {value}\n        </>\n      );\n    }\n\n    let iconColor: string = theme.palette.info.main;\n    if (errorIssueTypes.includes(issues[0].data_issue_type)) {\n      iconColor = theme.palette.error.main;\n    } else if (warningIssueTypes.includes(issues[0].data_issue_type)) {\n      iconColor = theme.palette.warning.main;\n    }\n\n    const originalValue = issues.find(x => x.original_value)?.original_value || '';\n    const shouldShowOriginalValue = originalValue && value && originalValue !== value;\n\n    const content = (\n      <>\n        {shouldShowOriginalValue && (\n          <>\n            <s>\n              {originalValue}\n            </s>\n            {'\\u00A0'}\n          </>\n        )}\n        {value && (\n          <>\n            {value}\n          </>\n        )}\n      </>\n    );\n\n\n    return (\n      <Box\n        sx={{\n          alignItems: 'center',\n          display: 'flex',\n        }}\n      >\n        <Box\n          sx={{\n            height: theme.spacing(2),\n            marginRight: theme.spacing(1),\n            minHeight: theme.spacing(2),\n            minWidth: theme.spacing(2),\n            position: 'relative',\n            width: theme.spacing(2),\n          }}\n        >\n          <Tooltip\n            arrow\n            title={getIssueTooltipContent(issues)}\n          >\n            <ErrorOutlinedIcon\n              fontSize={'small'}\n              sx={{\n                color: iconColor,\n                marginTop: '-2px',\n                position: 'absolute',\n              }}\n            />\n          </Tooltip>\n        </Box>\n        <Box\n          sx={{\n            overflow: 'hidden',\n            textOverflow: 'ellipsis',\n            whiteSpace: 'nowrap',\n          }}\n        >\n          {content}\n        </Box>\n      </Box>\n    );\n  }, [completeCaseType, errorIssueTypes, getFilteredIssueTypes, getIssueTooltipContent, theme, warningIssueTypes]);\n\n  const tableColumns = useMemo<TableColumn<CaseDbCaseUploadResult>[]>(() => {\n    const tableCols: TableColumn<CaseDbCaseUploadResult>[] = [];\n    if (!caseUploadResults?.length) {\n      return tableCols;\n    }\n    tableCols.push(TableUtil.createReadableIndexColumn());\n    tableCols.push(TableUtil.createSelectableColumn());\n    tableCols.push({\n      disableEllipsis: true,\n      frozen: TABLE_COLUMN_FROZEN.LEFT,\n      headerName: '',\n      hideInFilter: true,\n      id: 'gen-epix-ui-issue',\n      isInitiallyVisible: true,\n      renderCell: renderHasIssueCell,\n      renderHeader: renderHasIssueHeader,\n      resizable: false,\n      type: 'text',\n      valueGetter: () => '',\n      widthPx: 38,\n    });\n    tableCols.push({\n      disableEllipsis: true,\n      frozen: TABLE_COLUMN_FROZEN.LEFT,\n      headerName: '',\n      hideInFilter: true,\n      id: 'gen-epix-ui-id',\n      isInitiallyVisible: true,\n      renderCell: renderIsNewCell,\n      renderHeader: renderIsNewHeader,\n      resizable: false,\n      type: 'text',\n      valueGetter: () => '',\n      widthPx: 38,\n    });\n\n    const uniqueColIds: Set<string> = new Set();\n    caseUploadResults.forEach((validatedCase) => {\n      Object.keys(validatedCase.validated_content || {}).forEach((colId) => uniqueColIds.add(colId));\n      validatedCase.data_issues.forEach((issue) => uniqueColIds.add(issue.col_id));\n    });\n\n    // eslint-disable-next-line react-hooks/refs\n    completeCaseType.ordered_col_ids.forEach((colId) => {\n      if (!uniqueColIds.has(colId)) {\n        return;\n      }\n      const col = completeCaseType.cols[colId];\n\n      const issuesForCol = caseUploadResults.flatMap(vc => vc.data_issues.filter((i) => i.col_id === col.id));\n      const isInitiallyVisible = issuesForCol.length === 0 || issuesForCol.some(i => i.data_issue_type !== CaseDbDataIssueType.DERIVED);\n\n      const shouldShowCustomHeaderIcon = caseRightsColMap[col.id]?.length;\n\n      if (col) {\n        tableCols.push({\n          cellTitleGetter: (params) => {\n            const issue = params.row.data_issues.find((i) => i.col_id === col.id);\n            if (!issue && getOriginalCellValue) {\n              const originalValue = getOriginalCellValue(col, params, issue) ?? '';\n              return t('{{value}} (original value: \"{{originalValue}}\")', {\n                originalValue,\n                value: CaseUtil.getRowValue(params.row.validated_content, col, completeCaseType).short,\n              });\n            }\n            return '';\n          },\n          customHeaderIcon: shouldShowCustomHeaderIcon ? {\n            iconElement: (<EditIcon fontSize={'inherit'} />),\n            label: t('Edit values for {{colLabel}} (for selected rows)', { colLabel: col.label }),\n            onClick: onTableCustomHeaderIconClick,\n          } : undefined,\n          headerName: col.code,\n          hideInFilter: true,\n          id: col.id,\n          isInitiallyVisible,\n          renderCell,\n          type: 'text',\n          valueGetter: (params) => CaseUtil.getRowValue(params.row.validated_content, col, completeCaseType).short,\n          widthPx: 250,\n        } satisfies TableColumn<CaseDbCaseUploadResult>);\n      }\n    });\n\n    if (caseUploadResults.some(vc => vc.id)) {\n      tableCols.push({\n        headerName: t('case_id'),\n        hideInFilter: true,\n        id: 'case_id',\n        isInitiallyVisible: true,\n        type: 'text',\n        valueGetter: (params) => params.row.id || '',\n        widthPx: 250,\n      } satisfies TableColumn<CaseDbCaseUploadResult>);\n    }\n\n    tableCols.push(TableUtil.createActionsColumn({\n      getActions: (params: TableRowParams<CaseDbCaseUploadResult>) => {\n        const actions: ReactElement[] = [];\n        actions.push(\n          <MenuItem\n            key={'editCase'}\n            // eslint-disable-next-line @eslint-react/kit/jsx-no-bind\n            onClick={() => {\n              caseFormDialogRef.current?.open({\n                caseContent: params.row.validated_content,\n                caseId: params.row.id,\n                completeCaseType,\n                enabledColIds: completeCaseType.ordered_col_ids,\n                formId: `edit-case-form`,\n              });\n            }}\n          >\n            <ListItemIcon>\n              <EditIcon />\n            </ListItemIcon>\n            <ListItemText>\n              {t`Edit`}\n            </ListItemText>\n          </MenuItem>,\n        );\n        return actions;\n      },\n      t,\n    }));\n    return tableCols;\n  }, [caseUploadResults, renderHasIssueCell, renderHasIssueHeader, renderIsNewCell, renderIsNewHeader, completeCaseType, t, caseRightsColMap, onTableCustomHeaderIconClick, renderCell, getOriginalCellValue]);\n\n  useInitializeTableStore<CaseDbCaseUploadResult>({ columns: tableColumns, createFiltersFromColumns: true, rows: caseUploadResults, store: tableStore });\n\n  return (\n    <>\n      <Box>\n        <TableMenu\n          ContainerProps={{\n            sx: {\n              display: 'inline-block',\n              float: 'right',\n            },\n          }}\n        />\n      </Box>\n      <Table\n        font={theme['gen-epix-ui-client-casedb'].lineList.font}\n      />\n      <CaseContentFormDialog\n        onSubmit={onCaseContentFormDialogSubmit}\n        ref={caseFormDialogRef}\n      />\n      <UploadEditColumnValuesDialog\n        onSubmit={onEpiUploadEditColumnValuesDialogSubmit}\n        ref={uploadEditColumnValuesDialogRef}\n      />\n    </>\n  );\n};\n","import { useTranslation } from 'react-i18next';\nimport { useStore } from 'zustand';\nimport { use } from 'react';\nimport { useTableStoreContext } from '@gen-epix/ui-client-common/stores/tableStore';\nimport type { CaseDbCaseUploadResult } from '@gen-epix/api-casedb';\n\nimport { UploadStoreContext } from '../../../stores/uploadStore';\n\nimport { UploadNavigation } from './UploadNavigation';\n\nexport type UploadPreviewNavigationProps = {\n  readonly onGoBackButtonClick: () => void;\n  readonly onProceedButtonClick: () => void;\n};\n\nexport const UploadPreviewNavigation = ({ onGoBackButtonClick, onProceedButtonClick }: UploadPreviewNavigationProps) => {\n  const { t } = useTranslation();\n  const tableStore = useTableStoreContext<CaseDbCaseUploadResult>();\n  const uploadStore = use(UploadStoreContext);\n\n  const completeCaseType = useStore(uploadStore, (state) => state.completeCaseType);\n  const selectedIds = useStore(tableStore, (state) => state.selectedIds);\n\n  const proceedDisabled = !selectedIds.length || selectedIds.length > completeCaseType.props.create_max_n_cases;\n\n  return (\n    <UploadNavigation\n      onGoBackButtonClick={onGoBackButtonClick}\n      onProceedButtonClick={onProceedButtonClick}\n      proceedDisabled={proceedDisabled}\n      proceedLabel={selectedIds.length ? t('Proceed with {{count}} selected cases', { count: selectedIds.length }) : t('Proceed')}\n    />\n  );\n};\n","import {\n  use,\n  useCallback,\n  useEffect,\n  useMemo,\n  useRef,\n  useState,\n} from 'react';\nimport { useStore } from 'zustand';\nimport {\n  Alert,\n  AlertTitle,\n  Box,\n} from '@mui/material';\nimport { useTranslation } from 'react-i18next';\nimport { useShallow } from 'zustand/shallow';\nimport type {\n  CaseDbCase,\n  CaseDbCaseDataIssue,\n  CaseDbCaseUploadResult,\n  CaseDbCol,\n  CaseDbUploadCasesCommand,\n} from '@gen-epix/api-casedb';\nimport {\n  CaseDbCaseApi,\n  CaseDbDataIssueType,\n  CaseDbEtlStatus,\n  CaseDbUploadAction,\n} from '@gen-epix/api-casedb';\nimport type { ConfirmationRefMethods } from '@gen-epix/ui-core-components/components/Confirmation';\nimport type { TableRowAndColumnParams } from '@gen-epix/ui-client-common/models/table';\nimport { BackdropSpinner } from '@gen-epix/ui-core-components/components/BackdropSpinner';\nimport { Confirmation } from '@gen-epix/ui-core-components/components/Confirmation';\nimport {\n  createTableStore,\n  TableStoreContextProvider,\n} from '@gen-epix/ui-client-common/stores/tableStore';\nimport { QueryClientService } from '@gen-epix/ui-client-common/classes/services/QueryClientService';\nimport { ResponseHandler } from '@gen-epix/ui-client-common/components/ui/ResponseHandler';\nimport { useQueryMemo } from '@gen-epix/ui-client-common/hooks/useQueryMemo';\nimport { ObjectUtil } from '@gen-epix/ui-core/utils/ObjectUtil';\nimport { useArray } from '@gen-epix/ui-core/hooks/useArray';\n\nimport { UploadStoreContext } from '../../../stores/uploadStore';\nimport { withEpiCompleteCaseTypeLoader } from '../CompletCaseTypeLoader/withEpiCompleteCaseTypeLoader';\nimport { CaseUtil } from '../../../utils/CaseUtil';\n\nimport { UploadCaseResultTable } from './UploadCaseResultTable';\nimport { UploadPreviewNavigation } from './UploadPreviewNavigation';\n\nexport type UploadPreviewProps = {\n  readonly caseTypeId: string;\n};\n\nexport const UploadPreview = withEpiCompleteCaseTypeLoader<UploadPreviewProps>(({ caseTypeId }) => {\n  const { t } = useTranslation();\n\n  const store = use(UploadStoreContext);\n  const goToNextStep = useStore(store, (state) => state.goToNextStep);\n  const goToPreviousStep = useStore(store, (state) => state.goToPreviousStep);\n  const completeCaseType = useStore(store, (state) => state.completeCaseType);\n  const casesForVerificationFromSourceData = useStore(store, (state) => state.casesForVerificationFromSourceData);\n  const createdInDataCollectionId = useStore(store, (state) => state.createdInDataCollectionId);\n  const validateCasesQueryKey = useStore(store, (state) => state.validateCasesQueryKey);\n  const caseRightsColMap = useStore(store, (state) => state.caseRightsColMap);\n  const [exceedsMaxNumCases, setExceedsMaxNumCases] = useState(false);\n  const [isRevalidatingCases, setIsRevalidatingCases] = useState(false);\n  const [revalidationError, setRevalidationError] = useState<Error | null>(null);\n  const selectedIdsRef = useRef<string[]>([]);\n  const continueWithoutFixingConfirmationRef = useRef<ConfirmationRefMethods>(null);\n  const continueWithoutSelectingAllCasesRef = useRef<ConfirmationRefMethods>(null);\n\n  const getOriginalCellValue = useCallback((col: CaseDbCol, params: TableRowAndColumnParams<CaseDbCaseUploadResult, null>, _issue: CaseDbCaseDataIssue): string => {\n    return casesForVerificationFromSourceData[params.rowIndex]?.case?.content[col.id] ?? '';\n  }, [casesForVerificationFromSourceData]);\n\n  const caseUploadValidationResultQuery = useQueryMemo({\n    enabled: casesForVerificationFromSourceData.length > 0,\n    gcTime: Infinity,\n    queryFn: async ({ signal }) => {\n      const response = (await CaseDbCaseApi.getInstance().uploadCases(ObjectUtil.deepNullifyEmptyStrings<CaseDbUploadCasesCommand>({\n        case_batch: {\n          cases: casesForVerificationFromSourceData,\n        },\n        case_type_id: caseTypeId,\n        default_created_in_data_collection_id: createdInDataCollectionId ?? undefined,\n        on_exists: CaseDbUploadAction.UPDATE,\n        verify_only: true,\n      }), { signal })).data;\n      return response;\n    },\n    queryKey: validateCasesQueryKey,\n    select: (data) => data.cases.map((caseUploadResult, index) => ({\n      ...caseUploadResult,\n      id: casesForVerificationFromSourceData[index].id,\n    })),\n    staleTime: Infinity,\n  });\n\n\n  const loadables = useArray([\n    caseUploadValidationResultQuery,\n  ]);\n\n  const tableStore = useMemo(() => createTableStore<CaseDbCaseUploadResult>({\n    idSelectorCallback: (row) => row.id,\n  }), []);\n  const setSelectedIds = useStore(tableStore, useShallow((state) => state.setSelectedIds));\n\n  const revalidateCases = useCallback(async (casesToValidate: Array<{ content: CaseDbCase['content']; row: CaseDbCaseUploadResult }>) => {\n    setIsRevalidatingCases(true);\n    try {\n      const batchValidationResult = (await CaseDbCaseApi.getInstance().uploadCases(ObjectUtil.deepNullifyEmptyStrings<CaseDbUploadCasesCommand>({\n        case_batch: {\n          cases: casesToValidate.map(({ content, row }, index) => {\n            const caseFromSourceData = casesForVerificationFromSourceData.find(c => c.id === row.id);\n            return {\n              case: {\n                case_type_id: completeCaseType.id,\n                content: Object.fromEntries(\n                  Object.entries(content).map(([colId]) => {\n                    const col = completeCaseType.cols[colId];\n                    if (!col) {\n                      return [colId, content[colId]];\n                    }\n                    const rowValue = CaseUtil.getRowValue(content, col, completeCaseType);\n                    return [colId, rowValue.isMissing ? '' : rowValue.long];\n                  }),\n                ),\n                created_in_data_collection_id: caseFromSourceData?.case?.created_in_data_collection_id ?? createdInDataCollectionId,\n                id: row.id ?? casesForVerificationFromSourceData[index].id,\n              },\n            };\n          }),\n        },\n        case_type_id: caseTypeId,\n        default_created_in_data_collection_id: createdInDataCollectionId ?? undefined,\n        on_exists: CaseDbUploadAction.UPDATE,\n        verify_only: true,\n      }))).data;\n\n      const resultById = new Map(\n        casesToValidate.map(({ row }, index) => [row.id, batchValidationResult.cases[index]]),\n      );\n\n      QueryClientService.getInstance().queryClient.setQueryData(validateCasesQueryKey, {\n        cases: caseUploadValidationResultQuery.data.map(row => {\n          const newResult = resultById.get(row.id);\n          if (newResult) {\n            return { ...newResult, id: row.id };\n          }\n          return row;\n        }),\n      });\n\n      const newlyFailedIds: string[] = [];\n      casesToValidate.forEach(({ row }, index) => {\n        const newResult = batchValidationResult.cases[index];\n        if (newResult.status !== CaseDbEtlStatus.SKIPPED && newResult.status !== CaseDbEtlStatus.SUCCESS && newResult.status !== CaseDbEtlStatus.UPDATED) {\n          if (!selectedIdsRef.current.includes(row.id)) {\n            selectedIdsRef.current.push(row.id);\n            newlyFailedIds.push(row.id);\n          }\n        }\n      });\n\n      if (newlyFailedIds.length > 0) {\n        const currentSelectedIds = tableStore.getState().selectedIds;\n        const idsToAdd = newlyFailedIds.filter(id => !currentSelectedIds.includes(id));\n        if (idsToAdd.length > 0) {\n          setSelectedIds([...currentSelectedIds, ...idsToAdd]);\n        }\n      }\n    } catch (error) {\n      setRevalidationError(error as Error);\n    } finally {\n      setIsRevalidatingCases(false);\n    }\n\n  }, [caseTypeId, caseUploadValidationResultQuery.data, casesForVerificationFromSourceData, completeCaseType, createdInDataCollectionId, setSelectedIds, tableStore, validateCasesQueryKey]);\n\n  const onColContentEditSubmit = useCallback(async (contentPerCaseId: { [caseId: string]: CaseDbCase['content'] }) => {\n    const selectedIds = tableStore.getState().selectedIds;\n    await revalidateCases(\n      caseUploadValidationResultQuery.data\n        .filter(row => selectedIds.includes(row.id))\n        .map(row => ({\n          content: { ...row.validated_content, ...contentPerCaseId[row.id] },\n          row,\n        })),\n    );\n  }, [caseUploadValidationResultQuery.data, revalidateCases, tableStore]);\n\n  const onCaseContentEditSubmit = useCallback(async (caseId: string, content: CaseDbCase['content']) => {\n    const originalCaseUploadResult = caseUploadValidationResultQuery.data.find(r => r.id === caseId);\n    await revalidateCases([{ content, row: originalCaseUploadResult }]);\n  }, [caseUploadValidationResultQuery.data, revalidateCases]);\n\n  useEffect(() => {\n    const unsubscribe = tableStore.subscribe((state, prevState) => {\n      if (state.selectedIds === prevState.selectedIds) {\n        return;\n      }\n      selectedIdsRef.current = state.selectedIds;\n      const newExceedsMaxNumCases = state.selectedIds.length > completeCaseType.props.create_max_n_cases;\n      setExceedsMaxNumCases(newExceedsMaxNumCases);\n    });\n\n    return () => {\n      unsubscribe();\n    };\n  }, [completeCaseType.props.create_max_n_cases, tableStore]);\n\n  useEffect(() => {\n    const newSelectedIds = (caseUploadValidationResultQuery.data ?? []).filter(validatedCase => {\n      return !validatedCase.data_issues.some(issue => issue.data_issue_type === CaseDbDataIssueType.INVALID || issue.data_issue_type === CaseDbDataIssueType.UNAUTHORIZED);\n    }).map(vc => vc.id);\n    setSelectedIds(newSelectedIds);\n  }, [caseUploadValidationResultQuery.data, setSelectedIds]);\n\n\n  const onProceedWithoutFixingIssues = useCallback(async () => {\n    const selectedIds = tableStore.getState().selectedIds;\n    const validCases = caseUploadValidationResultQuery.data.filter(row => selectedIds.includes(row.id) && !row.data_issues.some(issue => issue.data_issue_type === CaseDbDataIssueType.INVALID));\n    store.setState((state) => ({\n      ...state,\n      selectedIdsForUpload: validCases.map(c => c.id),\n      validatedCases: caseUploadValidationResultQuery.data,\n    }));\n    await goToNextStep();\n  }, [caseUploadValidationResultQuery.data, goToNextStep, store, tableStore]);\n\n  const onProceed = useCallback(async () => {\n    store.setState((state) => ({\n      ...state,\n      selectedIdsForUpload: selectedIdsRef.current,\n      validatedCases: caseUploadValidationResultQuery.data,\n    }));\n\n    await goToNextStep();\n  }, [goToNextStep, caseUploadValidationResultQuery.data, store]);\n\n  const onProceedButtonClick = useCallback(async () => {\n    if (caseUploadValidationResultQuery.data.some(row => tableStore.getState().selectedIds.includes(row.id) && (row.data_issues.some(issue => issue.data_issue_type === CaseDbDataIssueType.INVALID) || row.status === CaseDbEtlStatus.FAILED))) {\n      continueWithoutFixingConfirmationRef.current?.open();\n      return;\n    }\n\n    if (caseUploadValidationResultQuery.data.some(row => !tableStore.getState().selectedIds.includes(row.id) && !row.data_issues.some(issue => issue.data_issue_type === CaseDbDataIssueType.INVALID))) {\n      continueWithoutSelectingAllCasesRef.current?.open();\n      return;\n    }\n\n    await onProceed();\n  }, [caseUploadValidationResultQuery.data, onProceed, tableStore]);\n\n  const onGoBackButtonClick = useCallback(() => {\n    goToPreviousStep();\n  }, [goToPreviousStep]);\n\n  return (\n    <Box\n      sx={{\n        display: 'grid',\n        gridTemplateRows: `${exceedsMaxNumCases ? 'max-content' : ''} max-content auto max-content`,\n        height: '100%',\n        position: 'relative',\n        width: '100%',\n      }}\n    >\n      <TableStoreContextProvider store={tableStore}>\n        <ResponseHandler\n          error={revalidationError}\n          inlineSpinner\n          loadables={loadables}\n          loadingMessage={t('Validating cases')}\n          takingLongerTimeoutMs={10000}\n        >\n          {exceedsMaxNumCases && (\n            <Box\n              sx={{\n                marginY: 2,\n              }}\n            >\n              <Alert severity={'error'}>\n                <AlertTitle>\n                  {t('You have exceeded the maximum number of {{maxCases}} cases for this case type. Please reduce the number of selected cases before proceeding.', {\n                    maxCases: completeCaseType.props.create_max_n_cases,\n                  })}\n                </AlertTitle>\n              </Alert>\n            </Box>\n          )}\n          <UploadCaseResultTable\n            caseRightsColMap={caseRightsColMap}\n            caseUploadResults={caseUploadValidationResultQuery.data || []}\n            completeCaseType={completeCaseType}\n            getOriginalCellValue={getOriginalCellValue}\n            onCaseContentEditSubmit={onCaseContentEditSubmit}\n            onColContentEditSubmit={onColContentEditSubmit}\n            tableStore={tableStore}\n          />\n          <UploadPreviewNavigation\n            onGoBackButtonClick={onGoBackButtonClick}\n            onProceedButtonClick={onProceedButtonClick}\n          />\n        </ResponseHandler>\n      </TableStoreContextProvider>\n      <BackdropSpinner\n        label={t('Revalidating cases')}\n        open={isRevalidatingCases}\n      />\n      <Confirmation\n        body={t`Some of the selected cases contain issues. If you proceed, these cases will be excluded. Are you sure you want to proceed without them?`}\n        cancelLabel={t`Cancel`}\n        confirmLabel={t`Proceed`}\n        onConfirm={onProceedWithoutFixingIssues}\n        ref={continueWithoutFixingConfirmationRef}\n        title={t`Issues found with selected cases`}\n      />\n      <Confirmation\n        body={t`Not all cases are selected. Do you want to proceed without them?`}\n        cancelLabel={t`Cancel`}\n        confirmLabel={t`Proceed`}\n        onConfirm={onProceed}\n        ref={continueWithoutSelectingAllCasesRef}\n        title={t`Not all cases are selected.`}\n      />\n    </Box>\n  );\n});\n","import { useTranslation } from 'react-i18next';\nimport type { ReactNode } from 'react';\nimport {\n  use,\n  useCallback,\n  useEffect,\n  useMemo,\n  useState,\n} from 'react';\nimport {\n  Alert,\n  AlertTitle,\n  Box,\n  Button,\n  Container,\n} from '@mui/material';\nimport { useStore } from 'zustand';\nimport { GenericErrorMessage } from '@gen-epix/ui-client-common/components/ui/GenericErrorMessage';\nimport { InactivityService } from '@gen-epix/ui-client-common/classes/services/InactivityService';\nimport { LinearProgressWithLabel } from '@gen-epix/ui-core-components/components/LinearProgressWithLabel';\nimport { RouterService } from '@gen-epix/ui-client-common/classes/services/RouterService';\n\nimport { CaseTypeUtil } from '../../../utils/CaseTypeUtil';\nimport { UploadError } from '../../../classes/errors';\nimport { UploadStoreContext } from '../../../stores/uploadStore';\nimport { UploadUtil } from '../../../utils/UploadUtil';\n\nimport { UploadNavigation } from './UploadNavigation';\n\n\nexport const UploadCreateCases = () => {\n  const { t } = useTranslation();\n\n  const store = use(UploadStoreContext);\n  const reset = useStore(store, (state) => state.reset);\n  const goToPreviousStep = useStore(store, (state) => state.goToPreviousStep);\n  const sequenceMapping = useStore(store, (state) => state.sequenceMapping);\n  const sequenceFilesDataTransfer = useStore(store, (state) => state.sequenceFilesDataTransfer);\n  const validatedCases = useStore(store, (state) => state.validatedCases);\n  const selectedIdsForUpload = useStore(store, (state) => state.selectedIdsForUpload);\n  const casesForVerificationFromSourceData = useStore(store, (state) => state.casesForVerificationFromSourceData);\n  const uploadCompleteButtonCallback = useStore(store, (state) => state.uploadCompleteButtonCallback);\n  const uploadCompleteButtonLabel = useStore(store, (state) => state.uploadCompleteButtonLabel);\n  const onUploadComplete = useStore(store, (state) => state.onUploadComplete);\n\n  const completeCaseType = useStore(store, (state) => state.completeCaseType);\n  const [progress, setProgress] = useState(0);\n  const [progressMessage, setProgressMessage] = useState('');\n\n  const [isUploadStarted, setIsUploadStarted] = useState(false);\n  const [isUploadCompleted, setIsUploadCompleted] = useState(false);\n  const [error, setError] = useState<unknown>(undefined);\n\n  const sequenceFileStats = useMemo(() => {\n    return UploadUtil.getSequenceMappingStats(sequenceMapping, sequenceFilesDataTransfer);\n  }, [sequenceFilesDataTransfer, sequenceMapping]);\n\n  const selectedValidatedCases = useMemo(() => {\n    return validatedCases.filter(vc => selectedIdsForUpload.includes(vc.id));\n  }, [validatedCases, selectedIdsForUpload]);\n\n  useEffect(() => {\n    const abortController = new AbortController();\n    const { signal } = abortController;\n\n    const abort = () => {\n      abortController.abort();\n      InactivityService.getInstance().resume();\n    };\n\n    if (!isUploadStarted) {\n      return abort;\n    }\n    InactivityService.getInstance().pause();\n\n    const perform = async () => {\n      const result = await UploadUtil.createCasesAndUploadFiles({\n        assemblyProtocolId: store.getState().assemblyProtocolId,\n        casesForVerificationFromSourceData,\n        completeCaseType: store.getState().completeCaseType,\n        createdInDataCollectionId: store.getState().createdInDataCollectionId,\n        mappedColumns: store.getState().mappedColumns,\n        onComplete: () => {\n          setIsUploadCompleted(true);\n        },\n        onError: (e: Error) => {\n          setError(e);\n        },\n        onProgress: (percentage: number, message: string) => {\n          setProgress(percentage);\n          setProgressMessage(message);\n        },\n        sampleIdColId: store.getState().sampleIdColId,\n        selectedValidatedCases,\n        sequenceFilesDataTransfer,\n        sequenceMapping,\n        sequencingProtocolId: store.getState().sequencingProtocolId,\n        signal,\n      });\n      if (onUploadComplete) {\n        await onUploadComplete(result);\n      }\n    };\n\n    perform().catch((e) => {\n      if (!signal.aborted) {\n        setError(e);\n      }\n    });\n\n\n    return abort;\n  }, [isUploadStarted, sequenceFilesDataTransfer, sequenceMapping, store, t, selectedValidatedCases, casesForVerificationFromSourceData, onUploadComplete]);\n\n\n  const onStartOverButtonClick = useCallback(async () => {\n    await reset();\n  }, [reset]);\n\n  const onStartUploadButtonClick = useCallback(() => {\n    setIsUploadStarted(true);\n  }, []);\n\n  const onGoBackButtonClick = useCallback(() => {\n    goToPreviousStep();\n  }, [goToPreviousStep]);\n\n  const onGotoCasesButtonClick = useCallback(async () => {\n    const link = CaseTypeUtil.createCaseTypeLink(completeCaseType);\n    await RouterService.getInstance().router.navigate(link);\n  }, [completeCaseType]);\n\n  let content: ReactNode;\n\n  if (error) {\n    content = (\n      <Box>\n        {error instanceof UploadError && (\n          <Alert severity={'error'}>\n            <AlertTitle>\n              {t('Failed to create cases during upload.')}\n            </AlertTitle>\n            {t('An error occurred while creating cases. Please try again or contact support if the issue persists. Cases may have been partially created. No files were uploaded.')}\n          </Alert>\n        )}\n        <GenericErrorMessage error={error} />\n      </Box>\n    );\n  } else if (isUploadCompleted) {\n    content = (\n      <Box>\n        <Box>\n          <Alert severity={'success'}>\n            <AlertTitle>\n              {t('Upload completed.')}\n            </AlertTitle>\n          </Alert>\n        </Box>\n        <Box\n          sx={{\n            display: 'flex',\n            gap: 2,\n            justifyContent: 'flex-end',\n            marginBottom: 1,\n            marginTop: 2,\n          }}\n        >\n          {uploadCompleteButtonCallback && uploadCompleteButtonLabel ? (\n            <Button\n              // eslint-disable-next-line @eslint-react/kit/jsx-handler-names\n              onClick={uploadCompleteButtonCallback}\n              variant={'contained'}\n            >\n              {uploadCompleteButtonLabel}\n            </Button>\n          ) : (\n            <>\n              <Button\n                onClick={onStartOverButtonClick}\n                variant={'outlined'}\n              >\n                {t('Upload more cases')}\n              </Button>\n              <Button\n                onClick={onGotoCasesButtonClick}\n                variant={'contained'}\n              >\n                {t('View uploaded cases')}\n              </Button>\n            </>\n          )}\n        </Box>\n      </Box>\n    );\n  } else if (isUploadStarted) {\n    content = (\n      <Box>\n        <Box\n          sx={{\n            marginBottom: 4,\n          }}\n        >\n          <Alert severity={'info'}>\n            <AlertTitle>\n              {t('Uploading cases and files.')}\n            </AlertTitle>\n            {t('Please wait while the cases and associated files are being uploaded. This may take a while depending on the number and size of the files being uploaded.')}\n          </Alert>\n        </Box>\n        <Box\n          sx={{\n            marginBottom: 2,\n            marginTop: 4,\n          }}\n        >\n          <LinearProgressWithLabel value={progress} />\n        </Box>\n        <Box\n          sx={{\n            fontWeight: 700,\n          }}\n        >\n          {progressMessage}\n        </Box>\n      </Box>\n    );\n  } else {\n    content = (\n      <Box>\n        <Box>\n          <Box\n            sx={{\n              marginY: 2,\n            }}\n          >\n            <Alert severity={'info'}>\n              <AlertTitle>\n                {t('{{numCases}} cases are ready to be uploaded.', { numCases: selectedValidatedCases.length })}\n              </AlertTitle>\n            </Alert>\n          </Box>\n          {sequenceFileStats.mappedSequenceFiles.length > 0 && (\n            <Box\n              sx={{\n                marginY: 2,\n              }}\n            >\n              <Alert severity={'info'}>\n                <AlertTitle>\n                  {t('{{numSequenceFiles}} genome files are ready to be uploaded.', { numSequenceFiles: sequenceFileStats.mappedSequenceFiles.length })}\n                </AlertTitle>\n              </Alert>\n            </Box>\n          )}\n          {sequenceFileStats.mappedReadsFiles.length > 0 && (\n            <Box\n              sx={{\n                marginY: 2,\n              }}\n            >\n              <Alert severity={'info'}>\n                <AlertTitle>\n                  {t('{{numReadsFiles}} reads files are ready to be uploaded.', { numReadsFiles: sequenceFileStats.mappedReadsFiles.length })}\n                </AlertTitle>\n              </Alert>\n            </Box>\n          )}\n          {validatedCases.length - selectedValidatedCases.length > 0 && (\n            <Box\n              sx={{\n                marginY: 2,\n              }}\n            >\n              <Alert severity={'warning'}>\n                <AlertTitle>\n                  {t('{{numCases}} cases were not selected and will not be uploaded.', { numCases: validatedCases.length - selectedValidatedCases.length })}\n                </AlertTitle>\n              </Alert>\n            </Box>\n          )}\n          {sequenceFileStats.unmappedSequenceFiles.length > 0 && (\n            <Box\n              sx={{\n                marginY: 2,\n              }}\n            >\n              <Alert severity={'warning'}>\n                <AlertTitle>\n                  {t('{{unmappedSequenceFiles}} unmapped genome files will not be uploaded.', { unmappedSequenceFiles: sequenceFileStats.unmappedSequenceFiles.length })}\n                </AlertTitle>\n              </Alert>\n            </Box>\n          )}\n          {sequenceFileStats.unmappedReadsFiles.length > 0 && (\n            <Box\n              sx={{\n                marginY: 2,\n              }}\n            >\n              <Alert severity={'warning'}>\n                <AlertTitle>\n                  {t('{{unmappedReadsFiles}} unmapped reads files will not be uploaded.', { unmappedReadsFiles: sequenceFileStats.unmappedReadsFiles.length })}\n                </AlertTitle>\n              </Alert>\n            </Box>\n          )}\n        </Box>\n        <UploadNavigation\n          onGoBackButtonClick={onGoBackButtonClick}\n          onProceedButtonClick={onStartUploadButtonClick}\n          proceedLabel={'Start upload'}\n        />\n      </Box>\n    );\n  }\n\n  return (\n    <Container\n      maxWidth={'xl'}\n      sx={{\n        height: '100%',\n      }}\n    >\n      {content}\n    </Container>\n  );\n};\n","import {\n  Alert,\n  AlertTitle,\n  Box,\n  useTheme,\n} from '@mui/material';\nimport type { ReactElement } from 'react';\nimport {\n  use,\n  useCallback,\n  useEffect,\n  useId,\n  useMemo,\n  useState,\n} from 'react';\nimport { useTranslation } from 'react-i18next';\nimport { useStore } from 'zustand';\nimport {\n  object,\n  string,\n} from 'yup';\nimport { yupResolver } from '@hookform/resolvers/yup';\nimport type { Resolver } from 'react-hook-form';\nimport { useForm } from 'react-hook-form';\nimport { ResponseHandler } from '@gen-epix/ui-client-common/components/ui/ResponseHandler';\nimport { useArray } from '@gen-epix/ui-core/hooks/useArray';\nimport { GenericForm } from '@gen-epix/ui-core-form/components/helpers/GenericForm';\nimport type {\n  FormFieldDefinition,\n  SelectOption,\n} from '@gen-epix/ui-core-form/models/form';\nimport { FORM_FIELD_DEFINITION_TYPE } from '@gen-epix/ui-core-form/models/form';\nimport { MultiFileUploader } from '@gen-epix/ui-core-components/components/MultiFileUploader';\n\nimport { UploadUtil } from '../../../utils/UploadUtil';\nimport { UploadStoreContext } from '../../../stores/uploadStore';\nimport { useSequencingProtocolOptionsQuery } from '../../../dataHooks/useSequencingProtocolsQuery';\nimport { useAssemblyProtocolOptionsQuery } from '../../../dataHooks/useAssemblyProtocolsQuery';\n\nimport { UploadNavigation } from './UploadNavigation';\n\n\ntype FormFields = {\n  assemblyProtocolId: string;\n  sampleIdColId: string;\n  sequencingProtocolId: string;\n};\n\nconst getSelectedFiles = (dataTransfer?: DataTransfer) => {\n  return Array.from(dataTransfer?.files ?? []);\n};\n\nconst createSchema = ({\n  hasGenomeFiles,\n  hasReadsFiles,\n  hasSelectedFiles,\n}: {\n  hasGenomeFiles: boolean;\n  hasReadsFiles: boolean;\n  hasSelectedFiles: boolean;\n}) => {\n  return object<FormFields>().shape({\n    assemblyProtocolId: hasGenomeFiles ? string().uuid4().required() : string().nullable().notRequired(),\n    sampleIdColId: hasSelectedFiles ? string().uuid4().required() : string().nullable().notRequired(),\n    sequencingProtocolId: hasReadsFiles ? string().uuid4().required() : string().nullable().notRequired(),\n  });\n};\n\nexport const UploadSelectSequenceFiles = () => {\n  const { t } = useTranslation();\n  const theme = useTheme();\n\n  const store = use(UploadStoreContext);\n  const completeCaseType = useStore(store, (state) => state.completeCaseType);\n  const mappedColumns = useStore(store, (state) => state.mappedColumns);\n  const validatedCases = useStore(store, (state) => state.validatedCases);\n  const goToNextStep = useStore(store, (state) => state.goToNextStep);\n  const goToPreviousStep = useStore(store, (state) => state.goToPreviousStep);\n  const setSequenceFilesDataTransfer = useStore(store, (state) => state.setSequenceFilesDataTransfer);\n  const sampleIdColId = useStore(store, (state) => state.sampleIdColId);\n  const initialDataTransfer = useStore(store, (state) => state.sequenceFilesDataTransfer);\n  const [currentDataTransfer, setCurrentDataTransfer] = useState(initialDataTransfer);\n\n  const formId = useId();\n\n  const sequencingProtocolOptionsQuery = useSequencingProtocolOptionsQuery();\n  const assemblyProtocolOptionsQuery = useAssemblyProtocolOptionsQuery();\n\n  const loadables = useArray([\n    sequencingProtocolOptionsQuery,\n    assemblyProtocolOptionsQuery,\n  ]);\n\n  const sampleIdColIdOptions = useMemo<SelectOption<string>[]>(() => {\n    return mappedColumns.filter(mc => mc.isSampleIdColumn).map(mc => ({\n      label: mc.col.label,\n      value: mc.col.id,\n    } satisfies SelectOption<string>));\n  }, [mappedColumns]);\n\n  const selectedFiles = useMemo(() => {\n    return getSelectedFiles(currentDataTransfer);\n  }, [currentDataTransfer]);\n\n  const hasSelectedFiles = selectedFiles.length > 0;\n  const hasGenomeFiles = useMemo(() => {\n    return selectedFiles.some(file => UploadUtil.isGenomeFile(file.name));\n  }, [selectedFiles]);\n  const hasReadsFiles = useMemo(() => {\n    return selectedFiles.some(file => UploadUtil.isReadsFile(file.name));\n  }, [selectedFiles]);\n\n  const schema = useMemo(() => {\n    return createSchema({\n      hasGenomeFiles,\n      hasReadsFiles,\n      hasSelectedFiles,\n    });\n  }, [hasGenomeFiles, hasReadsFiles, hasSelectedFiles]);\n\n  const defaultFormValues = useMemo<FormFields>(() => {\n    return {\n      assemblyProtocolId: store.getState().assemblyProtocolId ?? null,\n      sampleIdColId: store.getState().sampleIdColId ?? null,\n      sequencingProtocolId: store.getState().sequencingProtocolId ?? null,\n    };\n  }, [store]);\n\n  const formMethods = useForm<FormFields>({\n    defaultValues: defaultFormValues,\n    resolver: yupResolver(schema) as unknown as Resolver<FormFields>,\n    values: defaultFormValues,\n  });\n  const { handleSubmit, setValue } = formMethods;\n\n  useEffect(() => {\n    if (sequencingProtocolOptionsQuery.isLoading || assemblyProtocolOptionsQuery.isLoading) {\n      return;\n    }\n    if (!store.getState().sequencingProtocolId) {\n      setValue('sequencingProtocolId', sequencingProtocolOptionsQuery.options[0]?.value || null);\n      store.setState({ sequencingProtocolId: sequencingProtocolOptionsQuery.options[0]?.value || null });\n    }\n    if (!store.getState().assemblyProtocolId) {\n      setValue('assemblyProtocolId', assemblyProtocolOptionsQuery.options[0]?.value || null);\n      store.setState({ assemblyProtocolId: assemblyProtocolOptionsQuery.options[0]?.value || null });\n    }\n    if (!store.getState().sampleIdColId) {\n      setValue('sampleIdColId', sampleIdColIdOptions[0]?.value || null);\n      store.setState({ sampleIdColId: sampleIdColIdOptions[0]?.value || null });\n    }\n  }, [assemblyProtocolOptionsQuery.isLoading, assemblyProtocolOptionsQuery.options, sequencingProtocolOptionsQuery.isLoading, sequencingProtocolOptionsQuery.options, setValue, store, sampleIdColIdOptions]);\n\n  const onSequencingProtocolChange = useCallback((value: string) => {\n    store.setState({ sequencingProtocolId: value });\n  }, [store]);\n\n  const onAssemblyProtocolChange = useCallback((value: string) => {\n    store.setState({ assemblyProtocolId: value });\n  }, [store]);\n\n  const onSampleIdColIdChange = useCallback((value: string) => {\n    store.setState({ sampleIdColId: value });\n  }, [store]);\n\n  const formFieldDefinitions = useMemo<FormFieldDefinition<FormFields>[]>(() => {\n    return [\n      {\n        definition: FORM_FIELD_DEFINITION_TYPE.SELECT,\n        label: t`Genome files: assembly protocol`,\n        loading: assemblyProtocolOptionsQuery.isLoading,\n        name: 'assemblyProtocolId',\n        onChange: onAssemblyProtocolChange,\n        options: assemblyProtocolOptionsQuery.options,\n      } as const satisfies FormFieldDefinition<FormFields>,\n      {\n        definition: FORM_FIELD_DEFINITION_TYPE.SELECT,\n        label: t`Reads files: sequencing protocol`,\n        loading: sequencingProtocolOptionsQuery.isLoading,\n        name: 'sequencingProtocolId',\n        onChange: onSequencingProtocolChange,\n        options: sequencingProtocolOptionsQuery.options,\n      } as const satisfies FormFieldDefinition<FormFields>,\n      {\n        definition: FORM_FIELD_DEFINITION_TYPE.SELECT,\n        label: t`Sample ID column`,\n        name: 'sampleIdColId',\n        onChange: onSampleIdColIdChange,\n        options: sampleIdColIdOptions,\n      } as const satisfies FormFieldDefinition<FormFields>,\n    ];\n  }, [assemblyProtocolOptionsQuery.isLoading, assemblyProtocolOptionsQuery.options, onAssemblyProtocolChange, onSampleIdColIdChange, onSequencingProtocolChange, sampleIdColIdOptions, sequencingProtocolOptionsQuery.isLoading, sequencingProtocolOptionsQuery.options, t]);\n\n\n  const hasWritableSampleIdColumn = useMemo(() => {\n    return mappedColumns.some(mappedColumn => {\n      return mappedColumn.isSampleIdColumn && mappedColumn.sampleIdentifierIssuerId;\n    });\n  }, [mappedColumns]);\n\n  const hasRowContentForSampleIdColId = useMemo(() => {\n    if (!sampleIdColId) {\n      return false;\n    }\n    return validatedCases.some(vc => {\n      return vc.validated_content[sampleIdColId]?.trim().length > 0;\n    });\n  }, [sampleIdColId, validatedCases]);\n\n  const completeCaseTypeColStats = useMemo(() => {\n    return UploadUtil.getCompleteCaseTypeColStats(completeCaseType);\n  }, [completeCaseType]);\n\n  const canUploadSequences = useMemo(() => {\n    return completeCaseTypeColStats.sequenceColumns.length > 0;\n  }, [completeCaseTypeColStats]);\n\n  const canUploadReads = useMemo(() => {\n    return completeCaseTypeColStats.readsColumns.length > 0;\n  }, [completeCaseTypeColStats]);\n\n  const canUpload = useMemo(() => {\n    return hasWritableSampleIdColumn && hasRowContentForSampleIdColId && (canUploadSequences || canUploadReads);\n  }, [hasWritableSampleIdColumn, hasRowContentForSampleIdColId, canUploadSequences, canUploadReads]);\n\n  const accept = useMemo(() => {\n    let acc = '';\n    if (canUploadSequences) {\n      acc += '.fa,.fasta,.fa.gz,.fasta.gz,';\n    }\n    if (canUploadReads) {\n      acc += '.fq,.fastq,.fq.gz,.fastq.gz,';\n    }\n    return acc;\n  }, [canUploadReads, canUploadSequences]);\n\n  const onProceedButtonClick = useCallback(async () => {\n    setSequenceFilesDataTransfer(canUpload ? currentDataTransfer : new DataTransfer());\n    await handleSubmit(async () => {\n      await goToNextStep();\n    })();\n  }, [canUpload, currentDataTransfer, goToNextStep, handleSubmit, setSequenceFilesDataTransfer]);\n\n  const onGoBackButtonClick = useCallback(() => {\n    goToPreviousStep();\n  }, [goToPreviousStep]);\n\n  const onDataTransferChange = useCallback((dt: DataTransfer) => {\n    setCurrentDataTransfer(dt);\n    setSequenceFilesDataTransfer(dt);\n  }, [setSequenceFilesDataTransfer]);\n\n  const wrapForm = useCallback((children: ReactElement) => {\n    return (\n      <Box\n        sx={{\n          display: 'grid',\n          gap: theme.spacing(1),\n          gridTemplateColumns: '1fr 1fr 1fr',\n        }}\n      >\n        {children}\n      </Box>\n    );\n  }, [theme]);\n\n  const cantUploadMessage = useMemo<{ message: string; title: string }>(() => {\n    if (!hasWritableSampleIdColumn) {\n      return {\n        message: t`No columns have been mapped as writable sample ID column with selected identifier issuer provider.`,\n        title: t('Uploading of files is disabled.'),\n      };\n    }\n    if (!hasRowContentForSampleIdColId) {\n      return {\n        message: t`No rows have a sample ID filled for the selected sample ID column.`,\n        title: t('Uploading of files is disabled.'),\n      };\n    }\n    if (!canUploadReads) {\n      return {\n        message: t`The selected case type does not support uploading read files.`,\n        title: t('Uploading of read files is disabled.'),\n      };\n    }\n    if (!canUploadSequences) {\n      return {\n        message: t`The selected case type does not support uploading sequence files.`,\n        title: t('Uploading of sequence files is disabled.'),\n      };\n    }\n    return null;\n  }, [canUploadReads, canUploadSequences, hasRowContentForSampleIdColId, hasWritableSampleIdColumn, t]);\n\n  const onSubmit = useCallback(() => {\n    // noop, as we handle form submission manually in onProceedButtonClick\n  }, []);\n\n  return (\n    <ResponseHandler\n      loadables={loadables}\n    >\n      <Box\n        sx={{\n          display: 'grid',\n          gridTemplateRows: `${canUpload ? '' : 'max-content '}max-content auto max-content`,\n          height: '100%',\n          position: 'relative',\n        }}\n      >\n        {!canUpload && (\n          <Box\n            sx={{\n              marginBottom: 2,\n            }}\n          >\n            <Alert severity={'error'}>\n              <AlertTitle>\n                {cantUploadMessage.title}\n              </AlertTitle>\n              {cantUploadMessage.message}\n            </Alert>\n          </Box>\n        )}\n        <Box\n          sx={{\n            borderBottom: `1px solid ${theme.palette.divider}`,\n          }}\n        >\n          <Box\n            sx={{\n              maxWidth: theme.spacing(128),\n            }}\n          >\n            <GenericForm<FormFields>\n              formFieldDefinitions={formFieldDefinitions}\n              formId={formId}\n              formMethods={formMethods}\n              onSubmit={onSubmit}\n              schema={schema}\n              wrapForm={wrapForm}\n            />\n          </Box>\n          {!canUploadSequences && (\n            <Box\n              sx={{\n                marginY: 1,\n              }}\n            >\n              <Alert severity={'info'}>\n                <AlertTitle>\n                  {t('Uploading of sequences has been disabled.')}\n                </AlertTitle>\n                <Box>\n                  {t('Uploading of sequences is not supported for the selected case type.')}\n                </Box>\n              </Alert>\n            </Box>\n          )}\n          {!canUploadReads && (\n            <Box\n              sx={{\n                marginY: 1,\n              }}\n            >\n              <Alert severity={'info'}>\n                <AlertTitle>\n                  {t('Uploading of read files has been disabled.')}\n                </AlertTitle>\n                <Box>\n                  {t('Uploading of read files is not supported for the selected case type.')}\n                </Box>\n              </Alert>\n            </Box>\n          )}\n        </Box>\n        <Box\n          sx={{\n            position: 'relative',\n          }}\n        >\n\n          <Box\n            sx={{\n              bottom: 0,\n              height: '100%',\n              left: 0,\n              position: 'absolute',\n              right: 0,\n              top: 0,\n            }}\n          >\n            {canUpload && (\n              <MultiFileUploader\n                accept={accept}\n                initialDataTransfer={initialDataTransfer}\n                numFilesAllowed={Infinity}\n                onDataTransferChange={onDataTransferChange}\n              />\n            )}\n          </Box>\n        </Box>\n        <UploadNavigation\n          onGoBackButtonClick={onGoBackButtonClick}\n          onProceedButtonClick={onProceedButtonClick}\n          proceedLabel={!canUpload ? t`Proceed` : undefined}\n        />\n      </Box>\n    </ResponseHandler>\n  );\n};\n","import {\n  Alert,\n  AlertTitle,\n  Autocomplete,\n  Box,\n  TextField,\n  useTheme,\n} from '@mui/material';\nimport {\n  use,\n  useCallback,\n  useEffect,\n  useId,\n  useMemo,\n  useRef,\n} from 'react';\nimport { useTranslation } from 'react-i18next';\nimport { useStore } from 'zustand';\nimport { useShallow } from 'zustand/react/shallow';\nimport type {\n  CaseDbCaseUploadResult,\n  CaseDbCol,\n} from '@gen-epix/api-casedb';\nimport type {\n  TableColumn,\n  TableRowParams,\n} from '@gen-epix/ui-client-common/models/table';\nimport {\n  createTableStore,\n  TableStoreContextProvider,\n} from '@gen-epix/ui-client-common/stores/tableStore';\nimport { Table } from '@gen-epix/ui-client-common/components/ui/Table';\nimport { TableUtil } from '@gen-epix/ui-client-common/utils/TableUtil';\nimport { useInitializeTableStore } from '@gen-epix/ui-client-common/hooks/useInitializeTableStore';\n\nimport { CaseUtil } from '../../../utils/CaseUtil';\nimport { UploadStoreContext } from '../../../stores/uploadStore';\nimport { UploadUtil } from '../../../utils/UploadUtil';\n\nimport { UploadNavigation } from './UploadNavigation';\n\nexport const UploadMapSequences = () => {\n  const { t } = useTranslation();\n  const theme = useTheme();\n\n  const store = use(UploadStoreContext);\n  const goToNextStep = useStore(store, (state) => state.goToNextStep);\n  const goToPreviousStep = useStore(store, (state) => state.goToPreviousStep);\n  const completeCaseType = useStore(store, (state) => state.completeCaseType);\n  const sampleIdColId = useStore(store, (state) => state.sampleIdColId);\n  const sequenceFilesDataTransfer = useStore(store, (state) => state.sequenceFilesDataTransfer);\n  const selectedValidatedCases = useStore(store, useShallow((state) => {\n    const selectedIdsForUpload = state.selectedIdsForUpload;\n    return state.validatedCases.filter(vc => selectedIdsForUpload.includes(vc.id));\n  }));\n  const setSequenceMapping = useStore(store, (state) => state.setSequenceMapping);\n\n  const completeCaseTypeColStats = useMemo(() => {\n    return UploadUtil.getCompleteCaseTypeColStats(completeCaseType);\n  }, [completeCaseType]);\n\n  const alertTitleId = useId();\n  const alertContentId = useId();\n\n  const uploadSequenceMappingRef = useRef(store.getState().sequenceMapping);\n\n  const onProceedButtonClick = useCallback(async () => {\n    setSequenceMapping(uploadSequenceMappingRef.current);\n    await goToNextStep();\n  }, [setSequenceMapping, goToNextStep]);\n\n  const onGoBackButtonClick = useCallback(() => {\n    goToPreviousStep();\n  }, [goToPreviousStep]);\n\n  const updateAlert = useCallback(() => {\n    // Note: This is done via DOM manipulation to prevent excessive re-renders of the entire table\n\n    const alertTitleElement = document.getElementById(alertTitleId);\n    const alertContentElement = document.getElementById(alertContentId);\n    if (!alertTitleElement || !alertContentElement) {\n      return;\n    }\n    const {\n      mappedFiles,\n      numberOfFilesToMap,\n      unmappedFileNames,\n    } = UploadUtil.getSequenceMappingStats(uploadSequenceMappingRef.current, sequenceFilesDataTransfer);\n\n    alertTitleElement.innerHTML = numberOfFilesToMap === mappedFiles.length ? t('All {{numberOfFilesToMap}} files are mapped', { numberOfFilesToMap }) : t('{{mappedFilesLength}} of {{numberOfFilesToMap}} files mapped', { mappedFilesLength: mappedFiles.length, numberOfFilesToMap });\n    alertContentElement.innerHTML = numberOfFilesToMap === mappedFiles.length ? '' : t('Unmapped files: {{unmappedFileNames}}', { unmappedFileNames: unmappedFileNames.join(', ') });\n  }, [alertContentId, alertTitleId, sequenceFilesDataTransfer, t]);\n\n  useEffect(() => {\n    updateAlert();\n  }, [updateAlert]);\n\n  const tableStore = useMemo(() => createTableStore<CaseDbCaseUploadResult>({\n    idSelectorCallback: (row) => row.id,\n  }), []);\n\n  const caseHasColumnContent = useCallback((rows: CaseDbCaseUploadResult[], col: CaseDbCol): boolean => {\n    return rows.some((row) => {\n      const value = CaseUtil.getRowValue(row.validated_content, col, completeCaseType);\n      return value && !value?.isMissing;\n    });\n  }, [completeCaseType]);\n\n  const sequenceDropDownOptions = useMemo(() => {\n    return Array.from(sequenceFilesDataTransfer.files).map((file) => file.name).filter(name => name.endsWith('.fasta') || name.endsWith('.fa') || name.endsWith('.fa.gz') || name.endsWith('.fasta.gz'));\n  }, [sequenceFilesDataTransfer.files]);\n\n  const readsDropDownOptions = useMemo(() => {\n    return Array.from(sequenceFilesDataTransfer.files).map((file) => file.name).filter(name => name.endsWith('.fastq') || name.endsWith('.fq') || name.endsWith('.fq.gz') || name.endsWith('.fastaq.gz'));\n  }, [sequenceFilesDataTransfer.files]);\n\n  const createDropDown = useCallback((kwArgs: { dropDownOptions: string[]; dropDownValue: string; label: string; onChange: (newValue: string) => void }) => {\n    const { dropDownOptions, dropDownValue, label, onChange } = kwArgs;\n\n    return (\n      <Autocomplete\n        freeSolo\n        fullWidth\n        // eslint-disable-next-line @eslint-react/kit/jsx-no-bind\n        onChange={(_, newValue) => {\n          onChange(newValue);\n          setSequenceMapping(uploadSequenceMappingRef.current);\n          updateAlert();\n        }}\n        options={dropDownOptions}\n        // eslint-disable-next-line @eslint-react/kit/jsx-no-bind\n        renderInput={(params) => (\n          <TextField\n            {...params}\n            label={label}\n            size={'small'}\n          />\n        )}\n        sx={{\n          lineHeight: 'initial',\n        }}\n        value={dropDownValue}\n      />\n    );\n  }, [setSequenceMapping, updateAlert]);\n\n  const renderSequenceCell = useCallback((tableRowParams: TableRowParams<CaseDbCaseUploadResult>) => {\n    const col = completeCaseType.cols[tableRowParams.id];\n\n    const id = tableRowParams.row.id;\n    const dropDownValue = uploadSequenceMappingRef.current?.[tableRowParams.row.id]?.sequenceFileNames[col.id] || '';\n    const onChange = (newValue: string) => {\n      if (!newValue) {\n        delete uploadSequenceMappingRef.current?.[id]?.sequenceFileNames[col.id];\n      } else {\n        uploadSequenceMappingRef.current[id].sequenceFileNames[col.id] = newValue;\n      }\n    };\n\n    return (\n      <Box\n        sx={{\n          alignItems: 'center',\n          display: 'flex',\n          flexDirection: 'column',\n          height: '100%',\n          justifyContent: 'center',\n        }}\n      >\n        {createDropDown({\n          dropDownOptions: sequenceDropDownOptions,\n          dropDownValue,\n          label: col.label,\n          onChange,\n        })}\n      </Box>\n    );\n  }, [completeCaseType, createDropDown, sequenceDropDownOptions]);\n\n\n  const renderReadsCell = useCallback((tableRowParams: TableRowParams<CaseDbCaseUploadResult>) => {\n    const col = completeCaseType.cols[tableRowParams.id];\n    const isSequenceColumn = completeCaseTypeColStats.sequenceColumns.includes(col);\n\n    const id = tableRowParams.row.id;\n    const dropDownValueFwd = uploadSequenceMappingRef.current?.[id]?.readsFileNames?.[col.id]?.fwd || '';\n    const dropDownValueRev = uploadSequenceMappingRef.current?.[id]?.readsFileNames?.[col.id]?.rev || '';\n    const onChangeFwd = (newValue: string) => {\n      if (!newValue) {\n\n        delete uploadSequenceMappingRef.current?.[id]?.readsFileNames?.[col.id]?.fwd;\n      } else {\n        uploadSequenceMappingRef.current[id].readsFileNames[col.id].fwd = newValue;\n      }\n    };\n    const onChangeRev = (newValue: string) => {\n      if (!newValue) {\n\n        delete uploadSequenceMappingRef.current?.[id]?.readsFileNames?.[col.id]?.rev;\n      } else {\n        uploadSequenceMappingRef.current[id].readsFileNames[col.id].rev = newValue;\n      }\n    };\n\n    return (\n      <Box\n        sx={{\n          alignItems: 'center',\n          display: 'flex',\n          flexDirection: 'row',\n          gap: 1,\n          height: '100%',\n          justifyContent: 'center',\n        }}\n      >\n        {createDropDown({\n          dropDownOptions: isSequenceColumn ? sequenceDropDownOptions : readsDropDownOptions,\n          dropDownValue: dropDownValueFwd,\n          label: `${col.label} FWD`,\n          onChange: onChangeFwd,\n        })}\n        {createDropDown({\n          dropDownOptions: isSequenceColumn ? sequenceDropDownOptions : readsDropDownOptions,\n          dropDownValue: dropDownValueRev,\n          label: `${col.label} REV`,\n          onChange: onChangeRev,\n        })}\n      </Box>\n    );\n  }, [completeCaseType, completeCaseTypeColStats.sequenceColumns, createDropDown, sequenceDropDownOptions, readsDropDownOptions]);\n\n\n  const tableColumns = useMemo<TableColumn<CaseDbCaseUploadResult>[]>(() => {\n    const tableCols: TableColumn<CaseDbCaseUploadResult>[] = [];\n    tableCols.push(\n      TableUtil.createReadableIndexColumn(),\n    );\n\n    const columnsUsedForMapping = [\n      ...completeCaseTypeColStats.sampleIdColumns,\n      ...completeCaseTypeColStats.sequenceColumns,\n      ...completeCaseTypeColStats.readsColumns,\n    ];\n\n    const sampleIdCol = completeCaseTypeColStats.sampleIdColumns.find(x => x.id === sampleIdColId);\n    if (sampleIdCol && caseHasColumnContent(selectedValidatedCases, sampleIdCol)) {\n      tableCols.push({\n        headerName: sampleIdCol.label,\n        hideInFilter: true,\n        id: sampleIdCol.id,\n        isInitiallyVisible: true,\n        type: 'text',\n        valueGetter: (params) => CaseUtil.getRowValue(params.row.validated_content, sampleIdCol, completeCaseType).short,\n        widthPx: 300,\n      });\n    }\n\n    // eslint-disable-next-line react-hooks/refs\n    completeCaseTypeColStats.sequenceColumns.forEach((col) => {\n      tableCols.push({\n        cellTitleGetter: () => null,\n        headerName: col.label,\n        hideInFilter: true,\n        id: col.id,\n        isInitiallyVisible: true,\n        renderCell: renderSequenceCell,\n        type: 'text',\n        valueGetter: (params) => CaseUtil.getRowValue(params.row.validated_content, col, completeCaseType).short,\n        widthPx: 400,\n      });\n    });\n\n    // eslint-disable-next-line react-hooks/refs\n    completeCaseTypeColStats.readsColumns.forEach((col) => {\n      tableCols.push({\n        cellTitleGetter: () => null,\n        headerName: col.label,\n        hideInFilter: true,\n        id: col.id,\n        isInitiallyVisible: true,\n        renderCell: renderReadsCell,\n        type: 'text',\n        valueGetter: (params) => CaseUtil.getRowValue(params.row.validated_content, col, completeCaseType).short,\n        widthPx: 800,\n      });\n    });\n\n    const uniqueColIds: Set<string> = new Set();\n    selectedValidatedCases.forEach((vc) => {\n      Object.keys(vc.validated_content || {}).forEach((colId) => uniqueColIds.add(colId));\n    });\n\n    const colIdsToIgnore = [...completeCaseTypeColStats.sequenceColumns.map(x => x.id), ...completeCaseTypeColStats.readsColumns.map(x => x.id), sampleIdCol?.id];\n\n    completeCaseType.ordered_col_ids.forEach((colId) => {\n      if (colIdsToIgnore.includes(colId) || !uniqueColIds.has(colId) || columnsUsedForMapping.find(c => c.id === colId)) {\n        return;\n      }\n\n      const col = completeCaseType.cols[colId];\n      if (col) {\n        tableCols.push({\n          headerName: col.code,\n          hideInFilter: true,\n          id: col.id,\n          isInitiallyVisible: true,\n          type: 'text',\n          valueGetter: (params) => CaseUtil.getRowValue(params.row.validated_content, col, completeCaseType).short,\n          widthPx: 250,\n        } satisfies TableColumn<CaseDbCaseUploadResult>);\n      }\n    });\n\n    return tableCols;\n  }, [caseHasColumnContent, completeCaseType, completeCaseTypeColStats.readsColumns, completeCaseTypeColStats.sampleIdColumns, completeCaseTypeColStats.sequenceColumns, renderReadsCell, renderSequenceCell, sampleIdColId, selectedValidatedCases]);\n\n  useInitializeTableStore<CaseDbCaseUploadResult>({ columns: tableColumns, createFiltersFromColumns: true, rows: selectedValidatedCases, store: tableStore });\n\n  return (\n    <Box\n      sx={{\n        display: 'grid',\n        gridTemplateRows: 'max-content auto max-content',\n        height: '100%',\n      }}\n    >\n      <Box sx={{ paddingBottom: 1 }}>\n        <Alert severity={'info'}>\n          <AlertTitle id={alertTitleId} />\n          <Box id={alertContentId} />\n        </Alert>\n      </Box>\n      <TableStoreContextProvider store={tableStore}>\n        <Table\n          font={theme['gen-epix-ui-client-casedb'].lineList.font}\n          rowHeight={7}\n        />\n        <UploadNavigation\n          onGoBackButtonClick={onGoBackButtonClick}\n          onProceedButtonClick={onProceedButtonClick}\n        />\n      </TableStoreContextProvider>\n    </Box>\n  );\n};\n","import Box from '@mui/material/Box';\nimport { useTranslation } from 'react-i18next';\nimport {\n  use,\n  useMemo,\n} from 'react';\nimport {\n  Container,\n  useTheme,\n} from '@mui/material';\nimport { useStore } from 'zustand';\nimport { Stepper } from '@gen-epix/ui-core-components/components/Stepper';\nimport type { Step } from '@gen-epix/ui-core-components/components/Stepper';\n\nimport { UploadStoreContext } from '../../../stores/uploadStore';\nimport { UPLOAD_STEP } from '../../../models/upload';\n\nimport { UploadSelectFile } from './UploadSelectFile';\nimport { UploadMapColumns } from './UploadMapColumns';\nimport { UploadPreview } from './UploadPreview';\nimport { UploadCreateCases } from './UploadCreateCases';\nimport { UploadSelectSequenceFiles } from './UploadSelectSequenceFiles';\nimport { UploadMapSequences } from './UploadMapSequences';\n\nexport const Upload = () => {\n  const { t } = useTranslation();\n  const theme = useTheme();\n\n  const store = use(UploadStoreContext);\n  const completeCaseType = useStore(store, (state) => state.completeCaseType);\n  const activeStep = useStore(store, (state) => state.activeStep);\n  const stepOrder = useStore(store, (state) => state.stepOrder);\n\n  const stepLabels = useMemo<Record<UPLOAD_STEP, string>>(() => {\n    return {\n      [UPLOAD_STEP.CREATE_CASES]: t`Submit`,\n      [UPLOAD_STEP.MAP_COLUMNS]: t`Map columns`,\n      [UPLOAD_STEP.MAP_SEQUENCES]: t`Map sequences`,\n      [UPLOAD_STEP.PREVIEW]: t`Preview`,\n      [UPLOAD_STEP.SELECT_FILE]: t`Select file`,\n      [UPLOAD_STEP.SELECT_SEQUENCE_FILES]: t`Select sequence files`,\n    };\n  }, [t]);\n\n  const optionalSteps = useMemo<UPLOAD_STEP[]>(() => {\n    return [\n      UPLOAD_STEP.SELECT_SEQUENCE_FILES,\n      UPLOAD_STEP.MAP_SEQUENCES,\n    ];\n  }, []);\n\n  const steps = useMemo<Step[]>(() => {\n    return stepOrder.map((step) => ({\n      key: String(step),\n      label: stepLabels[step],\n      optional: optionalSteps.includes(step),\n    }));\n  }, [optionalSteps, stepLabels, stepOrder]);\n\n  return (\n    <Box\n      sx={{\n        display: 'grid',\n        gridTemplateRows: 'max-content auto',\n        height: '100%',\n        position: 'relative',\n        width: '100%',\n      }}\n    >\n      <Container>\n        <Stepper\n          activeStep={String(activeStep)}\n          steps={steps}\n          sx={{\n            marginY: 2,\n      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+{"version":3,"file":"Upload.js","names":[],"sources":["../../src/components/ui/Upload/UploadNavigation.tsx","../../src/components/ui/Upload/UploadSelectFile.tsx","../../src/components/ui/Upload/UploadMapColumns.tsx","../../src/components/ui/CompletCaseTypeLoader/withEpiCompleteCaseTypeLoader.tsx","../../src/components/ui/Upload/UploadEditColumnValuesDialog.tsx","../../src/components/ui/Upload/UploadCaseResultTable.tsx","../../src/components/ui/Upload/UploadPreviewNavigation.tsx","../../src/components/ui/Upload/UploadPreview.tsx","../../src/components/ui/Upload/UploadCreateCases.tsx","../../src/components/ui/Upload/UploadSelectSequenceFiles.tsx","../../src/components/ui/Upload/UploadMapSequences.tsx","../../src/components/ui/Upload/Upload.tsx"],"sourcesContent":["import type { ContainerOwnProps } from '@mui/material';\nimport {\n  Box,\n  Button,\n} from '@mui/material';\nimport { use } from 'react';\nimport { useTranslation } from 'react-i18next';\nimport { useStore } from 'zustand';\n\nimport { UploadStoreContext } from '../../../stores/uploadStore';\n\nexport type UploadNavigationProps = {\n  readonly backLabel?: string;\n  readonly containerProps?: ContainerOwnProps;\n  readonly onGoBackButtonClick?: () => void;\n  readonly onProceedButtonClick?: () => void;\n  readonly proceedDisabled?: boolean;\n  readonly proceedLabel?: string;\n};\n\nexport const UploadNavigation = ({\n  backLabel,\n  onGoBackButtonClick: onGoBack,\n  onProceedButtonClick: onProceedButtonClick,\n  proceedDisabled,\n  proceedLabel,\n}: UploadNavigationProps) => {\n  const { t } = useTranslation();\n  const store = use(UploadStoreContext);\n  const stepOrder = useStore(store, (state) => state.stepOrder);\n  const activeStep = useStore(store, (state) => state.activeStep);\n  const goBackFromFirstStepCallback = useStore(store, (state) => state.goBackFromFirstStepCallback);\n  const goBackFromFirstStepLabel = useStore(store, (state) => state.goBackFromFirstStepLabel);\n\n  const isFirstStep = activeStep === stepOrder[0];\n  const onClickGoBack = isFirstStep ? (goBackFromFirstStepCallback ?? onGoBack) : onGoBack;\n  const effectiveBackLabel = isFirstStep ? (goBackFromFirstStepLabel ?? backLabel) : backLabel;\n\n  return (\n    <Box\n      sx={{\n        borderTop: (theme) => `1px solid ${theme.palette.divider}`,\n        display: 'flex',\n        gap: 2,\n        justifyContent: 'flex-end',\n        marginTop: 1,\n        paddingTop: 1,\n      }}\n    >\n      {onClickGoBack && (\n        <Button\n          onClick={onClickGoBack}\n          variant={'outlined'}\n        >\n          {effectiveBackLabel ?? t`Go back`}\n        </Button>\n      )}\n      {onProceedButtonClick && (\n        <Button\n          color={'secondary'}\n          disabled={proceedDisabled}\n          onClick={onProceedButtonClick}\n          variant={'contained'}\n        >\n          {proceedLabel ?? t`Next`}\n        </Button>\n      )}\n    </Box>\n  );\n\n};\n","import {\n  use,\n  useCallback,\n  useEffect,\n  useId,\n  useMemo,\n} from 'react';\nimport { useTranslation } from 'react-i18next';\nimport { yupResolver } from '@hookform/resolvers/yup';\nimport type { Resolver } from 'react-hook-form';\nimport { useForm } from 'react-hook-form';\nimport {\n  mixed,\n  object,\n  string,\n} from 'yup';\nimport {\n  Alert,\n  AlertTitle,\n  Container,\n  Typography,\n} from '@mui/material';\nimport { useStore } from 'zustand';\nimport { CaseDbCaseApi } from '@gen-epix/api-casedb';\nimport { ResponseHandler } from '@gen-epix/ui-client-common/components/ui/ResponseHandler';\nimport { useItemQuery } from '@gen-epix/ui-client-common/hooks/useItemQuery';\nimport { useArray } from '@gen-epix/ui-core/hooks/useArray';\nimport { GenericForm } from '@gen-epix/ui-core-form/components/helpers/GenericForm';\nimport type { FormFieldDefinition } from '@gen-epix/ui-core-form/models/form';\nimport { FORM_FIELD_DEFINITION_TYPE } from '@gen-epix/ui-core-form/models/form';\n\nimport {\n  useCaseTypeOptionsQuery,\n  useCaseTypesQuery,\n} from '../../../dataHooks/useCaseTypesQuery';\nimport { useDataCollectionOptionsQuery } from '../../../dataHooks/useDataCollectionsQuery';\nimport { useColsQuery } from '../../../dataHooks/useColsQuery';\nimport { UploadUtil } from '../../../utils/UploadUtil';\nimport { UploadStoreContext } from '../../../stores/uploadStore';\nimport { CASEDB_QUERY_KEY } from '../../../constants/query';\n\nimport { UploadNavigation } from './UploadNavigation';\n\ntype FormFields = {\n  caseTypeId: string;\n  createdInDataCollectionId: string;\n  fileList: unknown;\n  sheet: string;\n};\n\nexport const UploadSelectFile = () => {\n  const { t } = useTranslation();\n  const caseTypesQuery = useCaseTypesQuery();\n  const caseTypeOptionsQuery = useCaseTypeOptionsQuery();\n  const dataCollectionOptionsQuery = useDataCollectionOptionsQuery();\n  const colsQuery = useColsQuery();\n  const formId = useId();\n\n  const store = use(UploadStoreContext);\n\n  const caseTypeId = useStore(store, (state) => state.caseTypeId);\n  const fileList = useStore(store, (state) => state.fileList);\n  const fileName = useStore(store, (state) => state.fileName);\n  const fileParsingError = useStore(store, (state) => state.fileParsingError);\n  const goToNextStep = useStore(store, (state) => state.goToNextStep);\n  const createdInDataCollectionOptions = useStore(store, (state) => state.createdInDataCollectionOptions);\n  const rawData = useStore(store, (state) => state.rawData);\n  const setCols = useStore(store, (state) => state.setCols);\n  const setCaseTypeId = useStore(store, (state) => state.setCaseTypeId);\n  const setCompleteCaseType = useStore(store, (state) => state.setCompleteCaseType);\n  const setCreatedInDataCollectionId = useStore(store, (state) => state.setCreatedInDataCollectionId);\n  const setFileList = useStore(store, (state) => state.setFileList);\n  const setSheet = useStore(store, (state) => state.setSheet);\n  const setDataCollectionOptions = useStore(store, (state) => state.setDataCollectionOptions);\n  const sheet = useStore(store, (state) => state.sheet);\n  const sheetOptions = useStore(store, (state) => state.sheetOptions);\n\n  const schema = useMemo(() => object<FormFields>().shape({\n    caseTypeId: string().uuid4().required(),\n    createdInDataCollectionId: string().uuid4().required(),\n    fileList: mixed().required(t`File is required`),\n    sheet: string().when('fileList', {\n      is: UploadUtil.isXlsxFile(fileName),\n      otherwise: (sheetSchema) => sheetSchema.notRequired(),\n      then: (sheetSchema) => sheetSchema.required(t`Sheet is required`),\n    }),\n  }), [fileName, t]);\n\n  const formMethods = useForm<FormFields>({\n    defaultValues: {\n      caseTypeId: null,\n      createdInDataCollectionId: null,\n      fileList: null,\n      sheet: null,\n    },\n    resolver: yupResolver(schema) as unknown as Resolver<FormFields>,\n    values: {\n      caseTypeId: store.getState().caseTypeId ?? null,\n      createdInDataCollectionId: store.getState().createdInDataCollectionId ?? null,\n      fileList: store.getState().fileList ?? null,\n      sheet: store.getState().sheet ?? null,\n    },\n  });\n  const { handleSubmit, setError, setValue } = formMethods;\n\n  useEffect(() => {\n    if (Array.isArray(colsQuery?.data)) {\n      setCols(colsQuery.data);\n    }\n  }, [colsQuery.data, setCols]);\n\n  useEffect(() => {\n    if (dataCollectionOptionsQuery?.options?.length) {\n      setDataCollectionOptions(dataCollectionOptionsQuery.options);\n    }\n  }, [dataCollectionOptionsQuery?.options, setDataCollectionOptions]);\n\n  const { data: completeCaseType, error: completeCaseTypeError, isLoading: isCompleteCaseTypeLoading } = useItemQuery({\n    baseQueryKey: CASEDB_QUERY_KEY.COMPLETE_CASE_TYPES,\n    itemId: caseTypeId,\n    useQueryOptions: {\n      enabled: !!caseTypeId,\n      queryFn: async ({ signal }) => {\n        return (await CaseDbCaseApi.getInstance().completeCaseTypesGetOne(caseTypeId, { signal })).data;\n      },\n    },\n  });\n\n  useEffect(() => {\n    if (completeCaseType) {\n      setCompleteCaseType(completeCaseType);\n    }\n  }, [completeCaseType, setCompleteCaseType]);\n\n  const onFileListChange = useCallback(async (value: FileList) => {\n    await setFileList(value);\n  }, [setFileList]);\n\n  const onSheetChange = useCallback(async (value: unknown) => {\n    await setSheet(value as string);\n  }, [setSheet]);\n\n  const onCaseTypeIdChange = useCallback((value: unknown) => {\n    setCaseTypeId(value as string);\n  }, [setCaseTypeId]);\n\n  const onCreatedInDataCollectionIdChange = useCallback((value: unknown) => {\n    setCreatedInDataCollectionId(value as string);\n  }, [setCreatedInDataCollectionId]);\n\n  const formFieldDefinitions = useMemo<FormFieldDefinition<FormFields>[]>(() => {\n    const fields: FormFieldDefinition<FormFields>[] = [\n      {\n        accept: '.csv,.tsv,.txt,.xlsx',\n        definition: FORM_FIELD_DEFINITION_TYPE.FILE,\n        label: t`File`,\n        name: 'fileList',\n        onChange: onFileListChange,\n      } as const satisfies FormFieldDefinition<FormFields>,\n    ];\n\n    if (UploadUtil.isXlsxFile(fileName)) {\n      fields.push({\n        definition: FORM_FIELD_DEFINITION_TYPE.SELECT,\n        label: t`Sheet`,\n        name: 'sheet',\n        onChange: onSheetChange,\n        options: sheetOptions,\n      } as const satisfies FormFieldDefinition<FormFields>);\n    }\n\n    fields.push(...[\n      {\n        definition: FORM_FIELD_DEFINITION_TYPE.AUTOCOMPLETE,\n        disabled: !fileList,\n        label: t`Case type`,\n        loading: caseTypeOptionsQuery.isLoading,\n        name: 'caseTypeId',\n        onChange: onCaseTypeIdChange,\n        options: caseTypeOptionsQuery.options,\n      } as const satisfies FormFieldDefinition<FormFields>,\n      {\n        definition: FORM_FIELD_DEFINITION_TYPE.SELECT,\n        disabled: !fileList || !caseTypeId,\n        label: t`Create in data collection`,\n        loading: dataCollectionOptionsQuery.isLoading || isCompleteCaseTypeLoading,\n        name: 'createdInDataCollectionId',\n        onChange: onCreatedInDataCollectionIdChange,\n        options: createdInDataCollectionOptions,\n      } as const satisfies FormFieldDefinition<FormFields>,\n    ] as const);\n\n    return fields;\n  }, [t, onFileListChange, fileName, caseTypeOptionsQuery.options, caseTypeOptionsQuery.isLoading, fileList, onCaseTypeIdChange, createdInDataCollectionOptions, dataCollectionOptionsQuery.isLoading, isCompleteCaseTypeLoading, caseTypeId, onCreatedInDataCollectionIdChange, sheetOptions, onSheetChange]);\n\n  useEffect(() => {\n    if (fileParsingError) {\n      setError('fileList', { message: fileParsingError, type: 'manual' });\n    } else {\n      setError('fileList', undefined);\n    }\n  }, [fileParsingError, setError, setValue]);\n\n  const onFormSubmit = useCallback(async () => {\n    await goToNextStep();\n  }, [goToNextStep]);\n\n  const loadables = useArray([\n    caseTypesQuery,\n    caseTypeOptionsQuery,\n    dataCollectionOptionsQuery,\n    colsQuery,\n  ]);\n\n  const onProceedButtonClick = useCallback(async () => {\n    await handleSubmit(onFormSubmit)();\n  }, [handleSubmit, onFormSubmit]);\n\n  const canUpload = useMemo(() => {\n    if (colsQuery.isLoading === false && colsQuery.data?.length === 0) {\n      return false;\n    }\n    if (caseTypeOptionsQuery.isLoading === false && caseTypeOptionsQuery.options?.length === 0) {\n      return false;\n    }\n    if (dataCollectionOptionsQuery.isLoading === false && dataCollectionOptionsQuery.options?.length === 0) {\n      return false;\n    }\n    return true;\n  }, [colsQuery.data?.length, colsQuery.isLoading, caseTypeOptionsQuery.isLoading, caseTypeOptionsQuery.options?.length, dataCollectionOptionsQuery.isLoading, dataCollectionOptionsQuery.options?.length]);\n\n  return (\n\n    <ResponseHandler\n      error={completeCaseTypeError}\n      inlineSpinner\n      loadables={loadables}\n    >\n      <Container maxWidth={'lg'}>\n        {!canUpload && (\n          <Alert\n            severity={'warning'}\n            sx={{ mb: 2 }}\n          >\n            {t('Upload is disabled because you have insufficient data access to proceed. Contact your organization administrator for assistance.')}\n          </Alert>\n        )}\n        {canUpload && (\n          <>\n            {rawData && rawData.length > 0 && (\n              <Alert\n                severity={'info'}\n                sx={{ mb: 2 }}\n              >\n                <AlertTitle>\n                  {t('{{fileName}} loaded successfully', { fileName })}\n                </AlertTitle>\n                {sheet && (\n                  <Typography>\n                    {t('Sheet name: {{sheet}}', { sheet: sheet || '' })}\n                  </Typography>\n                )}\n                <Typography>\n                  {t('Number of columns: {{columnCount}}', { columnCount: rawData[0].length })}\n                </Typography>\n                <Typography>\n                  {t('Number of data rows: {{rowCount}}', { rowCount: rawData.length - 1 })}\n                </Typography>\n              </Alert>\n            )}\n            <GenericForm<FormFields>\n              formFieldDefinitions={formFieldDefinitions}\n              formId={formId}\n              formMethods={formMethods}\n              onSubmit={handleSubmit(onFormSubmit)}\n              schema={schema}\n            />\n            <UploadNavigation\n              onProceedButtonClick={onProceedButtonClick}\n            />\n          </>\n        )}\n\n      </Container>\n    </ResponseHandler>\n  );\n};\n","import type { ReactElement } from 'react';\nimport {\n  use,\n  useCallback,\n  useEffect,\n  useId,\n  useMemo,\n} from 'react';\nimport { yupResolver } from '@hookform/resolvers/yup';\nimport {\n  useForm,\n  useWatch,\n} from 'react-hook-form';\nimport {\n  Alert,\n  AlertTitle,\n  Box,\n  Container,\n  Table,\n  TableBody,\n  TableCell,\n  TableHead,\n  TableRow,\n} from '@mui/material';\nimport { useTranslation } from 'react-i18next';\nimport uniq from 'lodash/uniq';\nimport { useStore } from 'zustand';\nimport difference from 'lodash/difference';\nimport { ConfigService } from '@gen-epix/ui-client-common/classes/services/ConfigService';\nimport { ResponseHandler } from '@gen-epix/ui-client-common/components/ui/ResponseHandler';\nimport { useIdentifierIssuerOwnOrganizationOptionsQuery } from '@gen-epix/ui-client-common/dataHooks/useIdentifierIssuerOwnOrganizationQuery';\nimport { useArray } from '@gen-epix/ui-core/hooks/useArray';\nimport { Select } from '@gen-epix/ui-core-form/components/fields/Select';\nimport { GenericForm } from '@gen-epix/ui-core-form/components/helpers/GenericForm';\nimport type { FormFieldDefinition } from '@gen-epix/ui-core-form/models/form';\n\nimport { useColMapQuery } from '../../../dataHooks/useColsQuery';\nimport type { UploadMappedColumnsFormFields } from '../../../models/upload';\nimport { UploadStoreContext } from '../../../stores/uploadStore';\nimport { UploadUtil } from '../../../utils/UploadUtil';\n\nimport { UploadNavigation } from './UploadNavigation';\n\n\nexport const UploadMapColumns = () => {\n  const { t } = useTranslation();\n  const colMap = useColMapQuery();\n  const identifierIssuerOptionsQuery = useIdentifierIssuerOwnOrganizationOptionsQuery();\n\n  const store = use(UploadStoreContext);\n  const completeCaseType = useStore(store, (state) => state.completeCaseType);\n  const rawData = useStore(store, (state) => state.rawData);\n  const fileName = useStore(store, (state) => state.fileName);\n  const goToNextStep = useStore(store, (state) => state.goToNextStep);\n  const goToPreviousStep = useStore(store, (state) => state.goToPreviousStep);\n  const setMappedColumns = useStore(store, (state) => state.setMappedColumns);\n\n  const loadables = useArray([\n    colMap,\n    identifierIssuerOptionsQuery,\n  ]);\n\n  const columnMappingFormId = useId();\n\n  const schema = useMemo(() => {\n    return UploadUtil.getColumnMappingSchema(rawData, completeCaseType);\n  }, [completeCaseType, rawData]);\n\n  const defaultValues: UploadMappedColumnsFormFields = useMemo(() => {\n    return UploadUtil.getDefaultColumnMappingFormValues(rawData[0], store.getState().mappedColumns, identifierIssuerOptionsQuery.options);\n  }, [rawData, store, identifierIssuerOptionsQuery.options]);\n\n  const formMethods = useForm<UploadMappedColumnsFormFields>({\n    defaultValues: { ...defaultValues },\n    resolver: yupResolver(schema),\n    values: { ...defaultValues },\n  });\n\n  const { clearErrors, control, handleSubmit } = formMethods;\n  const columnMappingFormValues = useWatch({ control });\n\n  const formFieldDefinitions = useMemo<FormFieldDefinition<UploadMappedColumnsFormFields>[]>(() => {\n    return UploadUtil.getColumnMappingFormFieldDefinitions(completeCaseType, rawData[0], fileName).map(def => ({\n      ...def,\n      onChange: () => clearErrors(),\n    }));\n  }, [completeCaseType, rawData, fileName, clearErrors]);\n\n  useEffect(() => {\n    const perform = async () => {\n      await setMappedColumns(UploadUtil.getMappedColumnsFromFormData(columnMappingFormValues, rawData, colMap.map, completeCaseType));\n    };\n    // eslint-disable-next-line @typescript-eslint/no-floating-promises\n    perform();\n  }, [setMappedColumns, columnMappingFormValues, rawData, colMap.map, completeCaseType]);\n\n  const unMappedColumns = useMemo(() => {\n    const knownIndicies = rawData[0].map((_col, index) => index);\n    const mappedIndicies = UploadUtil.getMappedColumnsFromFormData(columnMappingFormValues, rawData, colMap.map, completeCaseType).map(mappedColumn => mappedColumn.originalIndex);\n    return difference(knownIndicies, mappedIndicies).map(index => {\n      return {\n        originalIndex: index,\n        originalLabel: rawData[0][index],\n      };\n    });\n  }, [colMap.map, rawData, columnMappingFormValues, completeCaseType]);\n\n  const onFormSubmit = useCallback(async (data: UploadMappedColumnsFormFields) => {\n    await setMappedColumns(UploadUtil.getMappedColumnsFromFormData(data, rawData, colMap.map, completeCaseType));\n    await goToNextStep();\n  }, [rawData, colMap.map, goToNextStep, setMappedColumns, completeCaseType]);\n\n  const sampleIdColIds = useMemo(() => {\n    return UploadUtil.getSampleIdColIds(completeCaseType);\n  }, [completeCaseType]);\n\n  const renderField = useCallback((definition: FormFieldDefinition<UploadMappedColumnsFormFields>, element: ReactElement) => {\n    const columnIndexInRawData = parseInt(definition.name, 10);\n    const columnValues = uniq(rawData.slice(1).map((row) => row[columnIndexInRawData] ?? '')).filter(x => !!x);\n    const firstFiveValuesString = columnValues.slice(0, 5).join(', ').trim() || t('<no data>');\n\n    let elementWithIssuer = element;\n    const fieldValue = columnMappingFormValues[definition.name];\n    if (sampleIdColIds.includes(fieldValue)) {\n      elementWithIssuer = (\n        <>\n          <Box>\n            {element}\n          </Box>\n          <Box\n            sx={{\n              marginTop: 1,\n            }}\n          >\n            <Select\n              label={t('{{columnLabel}}: Identifier issuer', { columnLabel: definition.label })}\n              loading={identifierIssuerOptionsQuery.isLoading}\n              name={fieldValue}\n              options={identifierIssuerOptionsQuery.options}\n            />\n          </Box>\n        </>\n      );\n    }\n\n    return (\n      <TableRow key={definition.name}>\n        <TableCell>\n          {definition.label}\n        </TableCell>\n        <TableCell>\n          {elementWithIssuer}\n        </TableCell>\n        <TableCell>\n          {firstFiveValuesString}\n        </TableCell>\n      </TableRow>\n    );\n  }, [columnMappingFormValues, identifierIssuerOptionsQuery.isLoading, identifierIssuerOptionsQuery.options, rawData, sampleIdColIds, t]);\n\n  const wrapForm = useCallback((children: ReactElement) => {\n    return (\n      <Table\n        size={'small'}\n      >\n        <TableHead\n          sx={{\n            backgroundColor: (theme) => theme.palette.background.paper,\n            position: 'sticky',\n            top: 0,\n            zIndex: (theme) => theme.zIndex.appBar - 1,\n          }}\n        >\n          <TableRow>\n            <TableCell sx={{ width: '33%' }}>\n              {t`Source`}\n            </TableCell>\n            <TableCell sx={{ width: '33%' }}>\n              {ConfigService.getInstance().config.applicationName}\n            </TableCell>\n            <TableCell sx={{ width: '34%' }}>\n              {t`Data preview (first 5 unique values)`}\n            </TableCell>\n          </TableRow>\n        </TableHead>\n        <TableBody>\n          {children}\n        </TableBody>\n      </Table>\n    );\n  }, [t]);\n\n  const onProceedButtonClick = useCallback(async () => {\n    await handleSubmit(onFormSubmit)();\n  }, [handleSubmit, onFormSubmit]);\n\n  const onGoBackButtonClick = useCallback(() => {\n    goToPreviousStep();\n  }, [goToPreviousStep]);\n\n  return (\n    <ResponseHandler loadables={loadables}>\n      <Box\n        sx={{\n          display: 'grid',\n          gridTemplateRows: 'max-content auto max-content',\n          height: '100%',\n        }}\n      >\n        <Container\n          maxWidth={'lg'}\n          sx={{\n            marginBottom: 2,\n          }}\n        >\n          <Alert severity={unMappedColumns.length === 0 ? 'info' : 'warning'}>\n            <AlertTitle>\n              {unMappedColumns.length === 0 ?\n                t('All columns in {{fileName}} have been mapped to known columns in {{applicationName}}', { applicationName: ConfigService.getInstance().config.applicationName, fileName })\n                : t('{{numUnmappedColumns}} column(s) in {{fileName}} are not mapped', { fileName, numUnmappedColumns: unMappedColumns.length })}\n            </AlertTitle>\n            {unMappedColumns.map((unmappedColumn) => (\n              <Box key={unmappedColumn.originalIndex}>\n                {t('The column \"{{columnName}}\" (column {{columnIndex}}) has not been mapped.', { columnIndex: unmappedColumn.originalIndex + 1, columnName: unmappedColumn.originalLabel })}\n              </Box>\n            ))}\n            {unMappedColumns.length === 0 && t('You can proceed to the next step.')}\n          </Alert>\n        </Container>\n        <Box\n          sx={{\n            overflowY: 'auto',\n            position: 'relative',\n          }}\n        >\n          <Box\n            sx={{\n              bottom: 0,\n              left: 0,\n              position: 'absolute',\n              right: 0,\n              top: 0,\n            }}\n          >\n            <Container>\n              <GenericForm<UploadMappedColumnsFormFields>\n                formFieldDefinitions={formFieldDefinitions}\n                formId={columnMappingFormId}\n                formMethods={formMethods}\n                onSubmit={handleSubmit(onFormSubmit)}\n                renderField={renderField}\n                schema={schema}\n                wrapForm={wrapForm}\n              />\n            </Container>\n          </Box>\n        </Box>\n        <Box>\n          <UploadNavigation\n            onGoBackButtonClick={onGoBackButtonClick}\n            onProceedButtonClick={onProceedButtonClick}\n          />\n        </Box>\n      </Box>\n    </ResponseHandler>\n  );\n};\n","import {\n  useCallback,\n  useState,\n} from 'react';\nimport type { ComponentType } from 'react';\n\nimport type { CompletCaseTypeLoaderProps } from './CompletCaseTypeLoader';\nimport { CompletCaseTypeLoader } from './CompletCaseTypeLoader';\n\nexport type WithEpiCompleteCaseTypeLoaderProps = CompletCaseTypeLoaderProps;\n\nexport const withEpiCompleteCaseTypeLoader = <P extends WithEpiCompleteCaseTypeLoaderProps>(WrappedComponent: ComponentType<P>): ComponentType<P> => {\n  return (props: WithEpiCompleteCaseTypeLoaderProps) => {\n    const [isCompleteCaseTypeLoaded, setIsCompleteCaseTypeLoaded] = useState<boolean>(false);\n\n    const onCompleteCaseTypeLoaded = useCallback(() => {\n      setIsCompleteCaseTypeLoaded(true);\n    }, []);\n\n    return (\n      <CompletCaseTypeLoader\n        caseTypeId={props.caseTypeId}\n        onCompleteCaseTypeLoaded={onCompleteCaseTypeLoaded}\n      >\n        {isCompleteCaseTypeLoaded && (\n          <WrappedComponent\n            {...props as P}\n          />\n        )}\n      </CompletCaseTypeLoader>\n    );\n  };\n};\n","import { useTranslation } from 'react-i18next';\nimport type {\n  CaseDbCase,\n  CaseDbCompleteCaseType,\n} from '@gen-epix/api-casedb';\nimport type { DialogAction } from '@gen-epix/ui-core-components/components/Dialog';\nimport type {\n  WithDialogRefMethods,\n  WithDialogRenderProps,\n} from '@gen-epix/ui-core-components/hoc/withDialog';\nimport { withDialog } from '@gen-epix/ui-core-components/hoc/withDialog';\nimport { TestIdUtil } from '@gen-epix/ui-core/utils/TestIdUtil';\nimport type { ReactElement } from 'react';\nimport {\n  useCallback,\n  useEffect,\n  useId,\n  useMemo,\n} from 'react';\nimport { yupResolver } from '@hookform/resolvers/yup';\nimport { useForm } from 'react-hook-form';\nimport {\n  Alert,\n  AlertTitle,\n  Box,\n} from '@mui/material';\nimport { GenericForm } from '@gen-epix/ui-core-form/components/helpers/GenericForm';\nimport { FormUtil } from '@gen-epix/ui-core-form/utils/FormUtil';\n\nimport { CaseTypeFormUtil } from '../../../utils/CaseTypeFormUtil';\n\n\nexport interface UploadEditColumnValuesDialogOpenProps {\n  colId: string;\n  completeCaseType: CaseDbCompleteCaseType;\n  shouldShowRightsWarning?: boolean;\n}\n\nexport interface UploadEditColumnValuesDialogProps extends WithDialogRenderProps<UploadEditColumnValuesDialogOpenProps> {\n  onSubmit: (content: CaseDbCase['content']) => void;\n}\n\nexport type UploadEditColumnValuesDialogRefMethods = WithDialogRefMethods<UploadEditColumnValuesDialogProps, UploadEditColumnValuesDialogOpenProps>;\n\n\nexport const UploadEditColumnValuesDialog = withDialog<UploadEditColumnValuesDialogProps, UploadEditColumnValuesDialogOpenProps>((\n  {\n    onActionsChange,\n    onClose,\n    onSubmit,\n    onTitleChange,\n    openProps,\n  }: UploadEditColumnValuesDialogProps,\n): ReactElement => {\n  const { t } = useTranslation();\n  const formId = useId();\n\n  const col = useMemo(() => {\n    return openProps.completeCaseType.cols[openProps.colId];\n  }, [openProps.completeCaseType.cols, openProps.colId]);\n\n  useEffect(() => {\n    onTitleChange(t('Edit values for {{colLabel}} (for selected rows)', { colLabel: col.label }));\n  }, [onTitleChange, col.label, t]);\n\n  const schema = useMemo(() => CaseTypeFormUtil.createYupSchema({\n    completeCaseType: openProps.completeCaseType,\n    includedColIds: [openProps.colId],\n  }), [openProps.completeCaseType, openProps.colId]);\n\n  const formMethods = useForm<CaseDbCase['content']>({\n    resolver: yupResolver(schema),\n  });\n  const { handleSubmit } = formMethods;\n\n  const { fieldDefinitions } = useMemo(() => {\n    return CaseTypeFormUtil.createFormDefinitions({\n      completeCaseType: openProps.completeCaseType,\n      includedColIds: [openProps.colId],\n    });\n  }, [openProps.completeCaseType, openProps.colId]);\n\n  const onFormSubmit = useCallback((content: CaseDbCase['content']) => {\n    onSubmit(FormUtil.createStringValuesFromFormValues(fieldDefinitions, content));\n    onClose();\n  }, [fieldDefinitions, onClose, onSubmit]);\n\n  useEffect(() => {\n    const actions: DialogAction[] = [\n      {\n        ...TestIdUtil.createAttributes('UploadEditColumnValuesDialog-submitButton'),\n        color: 'primary',\n        form: formId,\n        label: t`Save and revalidate`,\n        type: 'submit',\n        variant: 'contained',\n      },\n    ];\n    onActionsChange(actions);\n  }, [formId, onActionsChange, t]);\n\n  return (\n    <Box>\n      {openProps.shouldShowRightsWarning && (\n        <Box sx={{ marginBottom: 2 }}>\n          <Alert severity={'warning'}>\n            <AlertTitle>\n              {t`You do not have the necessary rights to edit all rows in this column.`}\n            </AlertTitle>\n            {t`Only the cases that you have write access to for this column will be updated. Please review the changes carefully before submitting.`}\n          </Alert>\n        </Box>\n      )}\n      <GenericForm<CaseDbCase['content']>\n        formFieldDefinitions={fieldDefinitions}\n        formId={formId}\n        formMethods={formMethods}\n        onSubmit={handleSubmit(onFormSubmit)}\n        schema={schema}\n      />\n    </Box>\n  );\n}, {\n  defaultTitle: '',\n  fullWidth: true,\n  maxWidth: 'md',\n  testId: 'UploadEditColumnValuesDialog',\n});\n","import type { ReactElement } from 'react';\nimport {\n  useCallback,\n  useMemo,\n  useRef,\n} from 'react';\nimport EditIcon from '@mui/icons-material/Edit';\nimport type { StoreApi } from 'zustand';\nimport {\n  Box,\n  ListItemIcon,\n  ListItemText,\n  MenuItem,\n  Tooltip,\n  useTheme,\n} from '@mui/material';\nimport ErrorOutlinedIcon from '@mui/icons-material/ErrorOutlined';\nimport AddIcon from '@mui/icons-material/Add';\nimport { useTranslation } from 'react-i18next';\nimport type {\n  CaseDbCase,\n  CaseDbCaseDataIssue,\n  CaseDbCaseUploadResult,\n  CaseDbCol,\n  CaseDbCompleteCaseType,\n} from '@gen-epix/api-casedb';\nimport { CaseDbDataIssueType } from '@gen-epix/api-casedb';\nimport type {\n  TableColumn,\n  TableColumnParams,\n  TableRowAndColumnParams,\n  TableRowParams,\n} from '@gen-epix/ui-client-common/models/table';\nimport type { TableStore } from '@gen-epix/ui-client-common/stores/tableStore';\nimport {\n  Table,\n  TableMenu,\n} from '@gen-epix/ui-client-common/components/ui/Table';\nimport { TABLE_COLUMN_FROZEN } from '@gen-epix/ui-client-common/models/table';\nimport { TableUtil } from '@gen-epix/ui-client-common/utils/TableUtil';\nimport { useInitializeTableStore } from '@gen-epix/ui-client-common/hooks/useInitializeTableStore';\n\nimport { CaseUtil } from '../../../utils/CaseUtil';\nimport type { CaseContentFormDialogRefMethods } from '../CaseContentFormDialog';\nimport { CaseContentFormDialog } from '../CaseContentFormDialog';\n\nimport type { UploadEditColumnValuesDialogRefMethods } from './UploadEditColumnValuesDialog';\nimport { UploadEditColumnValuesDialog } from './UploadEditColumnValuesDialog';\n\n\nexport type UploadCaseResultTableProps = {\n  readonly caseRightsColMap?: { [colId: string]: string[] };\n  readonly caseUploadResults?: CaseDbCaseUploadResult[];\n  readonly completeCaseType: CaseDbCompleteCaseType;\n  readonly getOriginalCellValue: (col: CaseDbCol, cellParams: TableRowAndColumnParams<CaseDbCaseUploadResult, null>, issue: CaseDbCaseDataIssue) => string;\n  readonly onCaseContentEditSubmit: (caseId: string, content: CaseDbCase['content']) => void;\n  readonly onColContentEditSubmit: (contentPerCaseId: { [caseId: string]: CaseDbCase['content'] }) => void;\n  readonly tableStore: StoreApi<TableStore<CaseDbCaseUploadResult>>;\n};\n\nexport const UploadCaseResultTable = ({ caseRightsColMap, caseUploadResults, completeCaseType, getOriginalCellValue, onCaseContentEditSubmit, onColContentEditSubmit, tableStore }: UploadCaseResultTableProps) => {\n  const theme = useTheme();\n  const { t } = useTranslation();\n  const caseFormDialogRef = useRef<CaseContentFormDialogRefMethods>(null);\n  const uploadEditColumnValuesDialogRef = useRef<UploadEditColumnValuesDialogRefMethods>(null);\n\n  const dataRulePriority: CaseDbDataIssueType[] = useMemo(() => [\n    CaseDbDataIssueType.UNAUTHORIZED,\n    CaseDbDataIssueType.INVALID,\n    CaseDbDataIssueType.CONFLICT,\n    CaseDbDataIssueType.MISSING,\n    CaseDbDataIssueType.DERIVED,\n    CaseDbDataIssueType.TRANSFORMED,\n  ], []);\n\n  const errorIssueTypes: CaseDbDataIssueType[] = useMemo(() => [\n    CaseDbDataIssueType.UNAUTHORIZED,\n    CaseDbDataIssueType.INVALID,\n  ], []);\n\n  const warningIssueTypes: CaseDbDataIssueType[] = useMemo(() => [\n    CaseDbDataIssueType.MISSING,\n    CaseDbDataIssueType.CONFLICT,\n  ], []);\n\n  const onTableCustomHeaderIconClick = useCallback((params: TableColumnParams<CaseDbCaseUploadResult, null>) => {\n    uploadEditColumnValuesDialogRef.current?.open({\n      colId: params.column.id,\n      completeCaseType,\n      shouldShowRightsWarning: caseRightsColMap?.[params.column.id]?.length !== caseUploadResults?.length,\n    });\n  }, [completeCaseType, caseRightsColMap, caseUploadResults]);\n\n  const onCaseContentFormDialogSubmit = useCallback((caseId: string, content: CaseDbCase['content']) => {\n    onCaseContentEditSubmit(caseId, content);\n  }, [onCaseContentEditSubmit]);\n\n  const onEpiUploadEditColumnValuesDialogSubmit = useCallback((content: CaseDbCase['content']) => {\n    const contentPerCaseId: { [caseId: string]: CaseDbCase['content'] } = {};\n    Object.keys(content).forEach((colId) => {\n      const caseIds = caseRightsColMap?.[colId] ?? [];\n      caseIds.forEach((caseId) => {\n        contentPerCaseId[caseId] = {\n          ...(contentPerCaseId[caseId] ?? {}),\n          [colId]: content[colId],\n        };\n      });\n    });\n    onColContentEditSubmit(contentPerCaseId);\n  }, [onColContentEditSubmit, caseRightsColMap]);\n\n  const getIssueTooltipMessages = useCallback((issues: CaseDbCaseDataIssue[]) => {\n    const messages: { key: string; message: string }[] = [];\n    issues.forEach((issue) => {\n      const columnLabel = completeCaseType.cols[issue.col_id].label;\n      const message = `${columnLabel}: ${issue.message}`;\n      messages.push({\n        key: `${issue.col_id}-${issue.data_issue_type}-${issue.code}`,\n        message,\n      });\n    });\n    return messages;\n  }, [completeCaseType.cols]);\n\n  const getIssueTooltipContent = useCallback((issues: CaseDbCaseDataIssue[]) => {\n    const messages = getIssueTooltipMessages(issues);\n    return (\n      <>\n        {messages.map(({ key, message }, index) => (\n          <Box\n            key={key}\n            sx={{ marginTop: index > 0 ? 1 : 0 }}\n          >\n            {message}\n          </Box>\n        ))}\n      </>\n    );\n  }, [getIssueTooltipMessages]);\n\n  const getIssueTooltipLabel = useCallback((issues: CaseDbCaseDataIssue[]) => {\n    const messages = getIssueTooltipMessages(issues);\n    return messages.map(m => m.message).join(', ');\n  }, [getIssueTooltipMessages]);\n\n  const getFilteredIssueTypes = useCallback((id: string, issues: CaseDbCaseDataIssue[], value: string) => {\n    return issues.filter((issue) => {\n      if (issue.col_id !== id) {\n        return false;\n      }\n      if (issue.data_issue_type === CaseDbDataIssueType.TRANSFORMED && issue.original_value === value) {\n        return false;\n      }\n      return true;\n    }).sort((a, b) => dataRulePriority.indexOf(a.data_issue_type) - dataRulePriority.indexOf(b.data_issue_type));\n  }, [dataRulePriority]);\n\n  const renderHasIssueHeader = useCallback(() => {\n    return (\n      <Tooltip\n        aria-hidden={false}\n        arrow\n        title={t('Indicates if there are any issues with the case')}\n      >\n        <ErrorOutlinedIcon\n          fontSize={'small'}\n        />\n      </Tooltip>\n    );\n  }, [t]);\n\n  const renderHasIssueCell = useCallback(({ row }: TableRowParams<CaseDbCaseUploadResult>) => {\n    const errorIssues = row.data_issues.filter(i => i.data_issue_type === CaseDbDataIssueType.INVALID || i.data_issue_type === CaseDbDataIssueType.UNAUTHORIZED);\n    if (errorIssues.length > 0) {\n      return (\n        <Tooltip\n          aria-hidden={false}\n          aria-label={getIssueTooltipLabel(errorIssues)}\n          arrow\n          title={getIssueTooltipContent(errorIssues)}\n        >\n          <ErrorOutlinedIcon\n            fontSize={'small'}\n            sx={{\n              color: theme.palette.error.main,\n              marginTop: '5px',\n            }}\n          />\n        </Tooltip>\n      );\n    }\n  }, [getIssueTooltipContent, getIssueTooltipLabel, theme.palette.error.main]);\n\n  const renderIsNewHeader = useCallback(() => {\n    return (\n      <Tooltip\n        aria-hidden={false}\n        arrow\n        title={t('Indicates if case is new (will be created)')}\n      >\n        <AddIcon\n          fontSize={'small'}\n        />\n      </Tooltip>\n    );\n  }, [t]);\n\n  const renderIsNewCell = useCallback(({ row }: TableRowParams<CaseDbCaseUploadResult>) => {\n    return row.id ? null : (\n      <AddIcon\n        aria-hidden={false}\n        aria-label={t`This case does not have an ID and will be created`}\n        fontSize={'small'}\n        sx={{\n          marginTop: '5px',\n          position: 'absolute',\n        }}\n      />\n    );\n  }, [t]);\n\n  const renderCell = useCallback(({ id, row }: TableRowParams<CaseDbCaseUploadResult>) => {\n    const rowValue = CaseUtil.getRowValue(row.validated_content, completeCaseType.cols[id], completeCaseType);\n    const value = rowValue.long;\n    const issues = getFilteredIssueTypes(id, row.data_issues, value);\n\n    if (issues.length === 0) {\n      return (\n        <>\n          {value}\n        </>\n      );\n    }\n\n    let iconColor: string = theme.palette.info.main;\n    if (errorIssueTypes.includes(issues[0].data_issue_type)) {\n      iconColor = theme.palette.error.main;\n    } else if (warningIssueTypes.includes(issues[0].data_issue_type)) {\n      iconColor = theme.palette.warning.main;\n    }\n\n    const originalValue = issues.find(x => x.original_value)?.original_value || '';\n    const shouldShowOriginalValue = originalValue && value && originalValue !== value;\n\n    const content = (\n      <>\n        {shouldShowOriginalValue && (\n          <>\n            <s>\n              {originalValue}\n            </s>\n            {'\\u00A0'}\n          </>\n        )}\n        {value && (\n          <>\n            {value}\n          </>\n        )}\n      </>\n    );\n\n\n    return (\n      <Box\n        sx={{\n          alignItems: 'center',\n          display: 'flex',\n        }}\n      >\n        <Box\n          sx={{\n            height: theme.spacing(2),\n            marginRight: theme.spacing(1),\n            minHeight: theme.spacing(2),\n            minWidth: theme.spacing(2),\n            position: 'relative',\n            width: theme.spacing(2),\n          }}\n        >\n          <Tooltip\n            arrow\n            title={getIssueTooltipContent(issues)}\n          >\n            <ErrorOutlinedIcon\n              fontSize={'small'}\n              sx={{\n                color: iconColor,\n                marginTop: '-2px',\n                position: 'absolute',\n              }}\n            />\n          </Tooltip>\n        </Box>\n        <Box\n          sx={{\n            overflow: 'hidden',\n            textOverflow: 'ellipsis',\n            whiteSpace: 'nowrap',\n          }}\n        >\n          {content}\n        </Box>\n      </Box>\n    );\n  }, [completeCaseType, errorIssueTypes, getFilteredIssueTypes, getIssueTooltipContent, theme, warningIssueTypes]);\n\n  const tableColumns = useMemo<TableColumn<CaseDbCaseUploadResult>[]>(() => {\n    const tableCols: TableColumn<CaseDbCaseUploadResult>[] = [];\n    if (!caseUploadResults?.length) {\n      return tableCols;\n    }\n    tableCols.push(TableUtil.createReadableIndexColumn());\n    tableCols.push(TableUtil.createSelectableColumn());\n    tableCols.push({\n      disableEllipsis: true,\n      frozen: TABLE_COLUMN_FROZEN.LEFT,\n      headerName: '',\n      hideInFilter: true,\n      id: 'gen-epix-ui-issue',\n      isInitiallyVisible: true,\n      renderCell: renderHasIssueCell,\n      renderHeader: renderHasIssueHeader,\n      resizable: false,\n      type: 'text',\n      valueGetter: () => '',\n      widthPx: 38,\n    });\n    tableCols.push({\n      disableEllipsis: true,\n      frozen: TABLE_COLUMN_FROZEN.LEFT,\n      headerName: '',\n      hideInFilter: true,\n      id: 'gen-epix-ui-id',\n      isInitiallyVisible: true,\n      renderCell: renderIsNewCell,\n      renderHeader: renderIsNewHeader,\n      resizable: false,\n      type: 'text',\n      valueGetter: () => '',\n      widthPx: 38,\n    });\n\n    const uniqueColIds: Set<string> = new Set();\n    caseUploadResults.forEach((validatedCase) => {\n      Object.keys(validatedCase.validated_content || {}).forEach((colId) => uniqueColIds.add(colId));\n      validatedCase.data_issues.forEach((issue) => uniqueColIds.add(issue.col_id));\n    });\n\n    // eslint-disable-next-line react-hooks/refs\n    completeCaseType.ordered_col_ids.forEach((colId) => {\n      if (!uniqueColIds.has(colId)) {\n        return;\n      }\n      const col = completeCaseType.cols[colId];\n\n      const issuesForCol = caseUploadResults.flatMap(vc => vc.data_issues.filter((i) => i.col_id === col.id));\n      const isInitiallyVisible = issuesForCol.length === 0 || issuesForCol.some(i => i.data_issue_type !== CaseDbDataIssueType.DERIVED);\n\n      const shouldShowCustomHeaderIcon = caseRightsColMap[col.id]?.length;\n\n      if (col) {\n        tableCols.push({\n          cellTitleGetter: (params) => {\n            const issue = params.row.data_issues.find((i) => i.col_id === col.id);\n            if (!issue && getOriginalCellValue) {\n              const originalValue = getOriginalCellValue(col, params, issue) ?? '';\n              return t('{{value}} (original value: \"{{originalValue}}\")', {\n                originalValue,\n                value: CaseUtil.getRowValue(params.row.validated_content, col, completeCaseType).short,\n              });\n            }\n            return '';\n          },\n          customHeaderIcon: shouldShowCustomHeaderIcon ? {\n            iconElement: (<EditIcon fontSize={'inherit'} />),\n            label: t('Edit values for {{colLabel}} (for selected rows)', { colLabel: col.label }),\n            onClick: onTableCustomHeaderIconClick,\n          } : undefined,\n          headerName: col.code,\n          hideInFilter: true,\n          id: col.id,\n          isInitiallyVisible,\n          renderCell,\n          type: 'text',\n          valueGetter: (params) => CaseUtil.getRowValue(params.row.validated_content, col, completeCaseType).short,\n          widthPx: 250,\n        } satisfies TableColumn<CaseDbCaseUploadResult>);\n      }\n    });\n\n    if (caseUploadResults.some(vc => vc.id)) {\n      tableCols.push({\n        headerName: t('case_id'),\n        hideInFilter: true,\n        id: 'case_id',\n        isInitiallyVisible: true,\n        type: 'text',\n        valueGetter: (params) => params.row.id || '',\n        widthPx: 250,\n      } satisfies TableColumn<CaseDbCaseUploadResult>);\n    }\n\n    tableCols.push(TableUtil.createActionsColumn({\n      getActions: (params: TableRowParams<CaseDbCaseUploadResult>) => {\n        const actions: ReactElement[] = [];\n        actions.push(\n          <MenuItem\n            key={'editCase'}\n            // eslint-disable-next-line @eslint-react/kit/jsx-no-bind\n            onClick={() => {\n              caseFormDialogRef.current?.open({\n                caseContent: params.row.validated_content,\n                caseId: params.row.id,\n                completeCaseType,\n                enabledColIds: completeCaseType.ordered_col_ids,\n                formId: `edit-case-form`,\n              });\n            }}\n          >\n            <ListItemIcon>\n              <EditIcon />\n            </ListItemIcon>\n            <ListItemText>\n              {t`Edit`}\n            </ListItemText>\n          </MenuItem>,\n        );\n        return actions;\n      },\n      t,\n    }));\n    return tableCols;\n  }, [caseUploadResults, renderHasIssueCell, renderHasIssueHeader, renderIsNewCell, renderIsNewHeader, completeCaseType, t, caseRightsColMap, onTableCustomHeaderIconClick, renderCell, getOriginalCellValue]);\n\n  useInitializeTableStore<CaseDbCaseUploadResult>({ columns: tableColumns, createFiltersFromColumns: true, rows: caseUploadResults, store: tableStore });\n\n  return (\n    <>\n      <Box>\n        <TableMenu\n          ContainerProps={{\n            sx: {\n              display: 'inline-block',\n              float: 'right',\n            },\n          }}\n        />\n      </Box>\n      <Table\n        font={theme['gen-epix-ui-client-casedb'].lineList.font}\n      />\n      <CaseContentFormDialog\n        onSubmit={onCaseContentFormDialogSubmit}\n        ref={caseFormDialogRef}\n      />\n      <UploadEditColumnValuesDialog\n        onSubmit={onEpiUploadEditColumnValuesDialogSubmit}\n        ref={uploadEditColumnValuesDialogRef}\n      />\n    </>\n  );\n};\n","import { useTranslation } from 'react-i18next';\nimport { useStore } from 'zustand';\nimport { use } from 'react';\nimport { useTableStoreContext } from '@gen-epix/ui-client-common/stores/tableStore';\nimport type { CaseDbCaseUploadResult } from '@gen-epix/api-casedb';\n\nimport { UploadStoreContext } from '../../../stores/uploadStore';\n\nimport { UploadNavigation } from './UploadNavigation';\n\nexport type UploadPreviewNavigationProps = {\n  readonly onGoBackButtonClick: () => void;\n  readonly onProceedButtonClick: () => void;\n};\n\nexport const UploadPreviewNavigation = ({ onGoBackButtonClick, onProceedButtonClick }: UploadPreviewNavigationProps) => {\n  const { t } = useTranslation();\n  const tableStore = useTableStoreContext<CaseDbCaseUploadResult>();\n  const uploadStore = use(UploadStoreContext);\n\n  const completeCaseType = useStore(uploadStore, (state) => state.completeCaseType);\n  const selectedIds = useStore(tableStore, (state) => state.selectedIds);\n\n  const proceedDisabled = !selectedIds.length || selectedIds.length > completeCaseType.props.create_max_n_cases;\n\n  return (\n    <UploadNavigation\n      onGoBackButtonClick={onGoBackButtonClick}\n      onProceedButtonClick={onProceedButtonClick}\n      proceedDisabled={proceedDisabled}\n      proceedLabel={selectedIds.length ? t('Proceed with {{count}} selected cases', { count: selectedIds.length }) : t('Proceed')}\n    />\n  );\n};\n","import {\n  use,\n  useCallback,\n  useEffect,\n  useMemo,\n  useRef,\n  useState,\n} from 'react';\nimport { useStore } from 'zustand';\nimport {\n  Alert,\n  AlertTitle,\n  Box,\n} from '@mui/material';\nimport { useTranslation } from 'react-i18next';\nimport { useShallow } from 'zustand/shallow';\nimport type {\n  CaseDbCase,\n  CaseDbCaseDataIssue,\n  CaseDbCaseUploadResult,\n  CaseDbCol,\n  CaseDbUploadCasesCommand,\n} from '@gen-epix/api-casedb';\nimport {\n  CaseDbCaseApi,\n  CaseDbDataIssueType,\n  CaseDbEtlStatus,\n  CaseDbUploadAction,\n} from '@gen-epix/api-casedb';\nimport type { ConfirmationRefMethods } from '@gen-epix/ui-core-components/components/Confirmation';\nimport type { TableRowAndColumnParams } from '@gen-epix/ui-client-common/models/table';\nimport { BackdropSpinner } from '@gen-epix/ui-core-components/components/BackdropSpinner';\nimport { Confirmation } from '@gen-epix/ui-core-components/components/Confirmation';\nimport {\n  createTableStore,\n  TableStoreContextProvider,\n} from '@gen-epix/ui-client-common/stores/tableStore';\nimport { QueryClientService } from '@gen-epix/ui-client-common/classes/services/QueryClientService';\nimport { ResponseHandler } from '@gen-epix/ui-client-common/components/ui/ResponseHandler';\nimport { useQueryMemo } from '@gen-epix/ui-client-common/hooks/useQueryMemo';\nimport { ObjectUtil } from '@gen-epix/ui-core/utils/ObjectUtil';\nimport { useArray } from '@gen-epix/ui-core/hooks/useArray';\n\nimport { UploadStoreContext } from '../../../stores/uploadStore';\nimport { withEpiCompleteCaseTypeLoader } from '../CompletCaseTypeLoader/withEpiCompleteCaseTypeLoader';\nimport { CaseUtil } from '../../../utils/CaseUtil';\n\nimport { UploadCaseResultTable } from './UploadCaseResultTable';\nimport { UploadPreviewNavigation } from './UploadPreviewNavigation';\n\nexport type UploadPreviewProps = {\n  readonly caseTypeId: string;\n};\n\nexport const UploadPreview = withEpiCompleteCaseTypeLoader<UploadPreviewProps>(({ caseTypeId }) => {\n  const { t } = useTranslation();\n\n  const store = use(UploadStoreContext);\n  const goToNextStep = useStore(store, (state) => state.goToNextStep);\n  const goToPreviousStep = useStore(store, (state) => state.goToPreviousStep);\n  const completeCaseType = useStore(store, (state) => state.completeCaseType);\n  const casesForVerificationFromSourceData = useStore(store, (state) => state.casesForVerificationFromSourceData);\n  const createdInDataCollectionId = useStore(store, (state) => state.createdInDataCollectionId);\n  const validateCasesQueryKey = useStore(store, (state) => state.validateCasesQueryKey);\n  const caseRightsColMap = useStore(store, (state) => state.caseRightsColMap);\n  const [exceedsMaxNumCases, setExceedsMaxNumCases] = useState(false);\n  const [isRevalidatingCases, setIsRevalidatingCases] = useState(false);\n  const [revalidationError, setRevalidationError] = useState<Error | null>(null);\n  const selectedIdsRef = useRef<string[]>([]);\n  const continueWithoutFixingConfirmationRef = useRef<ConfirmationRefMethods>(null);\n  const continueWithoutSelectingAllCasesRef = useRef<ConfirmationRefMethods>(null);\n\n  const getOriginalCellValue = useCallback((col: CaseDbCol, params: TableRowAndColumnParams<CaseDbCaseUploadResult, null>, _issue: CaseDbCaseDataIssue): string => {\n    return casesForVerificationFromSourceData[params.rowIndex]?.case?.content[col.id] ?? '';\n  }, [casesForVerificationFromSourceData]);\n\n  const caseUploadValidationResultQuery = useQueryMemo({\n    enabled: casesForVerificationFromSourceData.length > 0,\n    gcTime: Infinity,\n    queryFn: async ({ signal }) => {\n      const response = (await CaseDbCaseApi.getInstance().uploadCases(ObjectUtil.deepNullifyEmptyStrings<CaseDbUploadCasesCommand>({\n        case_batch: {\n          cases: casesForVerificationFromSourceData,\n        },\n        case_type_id: caseTypeId,\n        default_created_in_data_collection_id: createdInDataCollectionId ?? undefined,\n        on_exists: CaseDbUploadAction.UPDATE,\n        verify_only: true,\n      }), { signal })).data;\n      return response;\n    },\n    queryKey: validateCasesQueryKey,\n    select: (data) => data.cases.map((caseUploadResult, index) => ({\n      ...caseUploadResult,\n      id: casesForVerificationFromSourceData[index].id,\n    })),\n    staleTime: Infinity,\n  });\n\n\n  const loadables = useArray([\n    caseUploadValidationResultQuery,\n  ]);\n\n  const tableStore = useMemo(() => createTableStore<CaseDbCaseUploadResult>({\n    idSelectorCallback: (row) => row.id,\n  }), []);\n  const setSelectedIds = useStore(tableStore, useShallow((state) => state.setSelectedIds));\n\n  const revalidateCases = useCallback(async (casesToValidate: Array<{ content: CaseDbCase['content']; row: CaseDbCaseUploadResult }>) => {\n    setIsRevalidatingCases(true);\n    try {\n      const batchValidationResult = (await CaseDbCaseApi.getInstance().uploadCases(ObjectUtil.deepNullifyEmptyStrings<CaseDbUploadCasesCommand>({\n        case_batch: {\n          cases: casesToValidate.map(({ content, row }, index) => {\n            const caseFromSourceData = casesForVerificationFromSourceData.find(c => c.id === row.id);\n            return {\n              case: {\n                case_type_id: completeCaseType.id,\n                content: Object.fromEntries(\n                  Object.entries(content).map(([colId]) => {\n                    const col = completeCaseType.cols[colId];\n                    if (!col) {\n                      return [colId, content[colId]];\n                    }\n                    const rowValue = CaseUtil.getRowValue(content, col, completeCaseType);\n                    return [colId, rowValue.isMissing ? '' : rowValue.long];\n                  }),\n                ),\n                created_in_data_collection_id: caseFromSourceData?.case?.created_in_data_collection_id ?? createdInDataCollectionId,\n                id: row.id ?? casesForVerificationFromSourceData[index].id,\n              },\n            };\n          }),\n        },\n        case_type_id: caseTypeId,\n        default_created_in_data_collection_id: createdInDataCollectionId ?? undefined,\n        on_exists: CaseDbUploadAction.UPDATE,\n        verify_only: true,\n      }))).data;\n\n      const resultById = new Map(\n        casesToValidate.map(({ row }, index) => [row.id, batchValidationResult.cases[index]]),\n      );\n\n      QueryClientService.getInstance().queryClient.setQueryData(validateCasesQueryKey, {\n        cases: caseUploadValidationResultQuery.data.map(row => {\n          const newResult = resultById.get(row.id);\n          if (newResult) {\n            return { ...newResult, id: row.id };\n          }\n          return row;\n        }),\n      });\n\n      const newlyFailedIds: string[] = [];\n      casesToValidate.forEach(({ row }, index) => {\n        const newResult = batchValidationResult.cases[index];\n        if (newResult.status !== CaseDbEtlStatus.SKIPPED && newResult.status !== CaseDbEtlStatus.SUCCESS && newResult.status !== CaseDbEtlStatus.UPDATED) {\n          if (!selectedIdsRef.current.includes(row.id)) {\n            selectedIdsRef.current.push(row.id);\n            newlyFailedIds.push(row.id);\n          }\n        }\n      });\n\n      if (newlyFailedIds.length > 0) {\n        const currentSelectedIds = tableStore.getState().selectedIds;\n        const idsToAdd = newlyFailedIds.filter(id => !currentSelectedIds.includes(id));\n        if (idsToAdd.length > 0) {\n          setSelectedIds([...currentSelectedIds, ...idsToAdd]);\n        }\n      }\n    } catch (error) {\n      setRevalidationError(error as Error);\n    } finally {\n      setIsRevalidatingCases(false);\n    }\n\n  }, [caseTypeId, caseUploadValidationResultQuery.data, casesForVerificationFromSourceData, completeCaseType, createdInDataCollectionId, setSelectedIds, tableStore, validateCasesQueryKey]);\n\n  const onColContentEditSubmit = useCallback(async (contentPerCaseId: { [caseId: string]: CaseDbCase['content'] }) => {\n    const selectedIds = tableStore.getState().selectedIds;\n    await revalidateCases(\n      caseUploadValidationResultQuery.data\n        .filter(row => selectedIds.includes(row.id))\n        .map(row => ({\n          content: { ...row.validated_content, ...contentPerCaseId[row.id] },\n          row,\n        })),\n    );\n  }, [caseUploadValidationResultQuery.data, revalidateCases, tableStore]);\n\n  const onCaseContentEditSubmit = useCallback(async (caseId: string, content: CaseDbCase['content']) => {\n    const originalCaseUploadResult = caseUploadValidationResultQuery.data.find(r => r.id === caseId);\n    await revalidateCases([{ content, row: originalCaseUploadResult }]);\n  }, [caseUploadValidationResultQuery.data, revalidateCases]);\n\n  useEffect(() => {\n    const unsubscribe = tableStore.subscribe((state, prevState) => {\n      if (state.selectedIds === prevState.selectedIds) {\n        return;\n      }\n      selectedIdsRef.current = state.selectedIds;\n      const newExceedsMaxNumCases = state.selectedIds.length > completeCaseType.props.create_max_n_cases;\n      setExceedsMaxNumCases(newExceedsMaxNumCases);\n    });\n\n    return () => {\n      unsubscribe();\n    };\n  }, [completeCaseType.props.create_max_n_cases, tableStore]);\n\n  useEffect(() => {\n    const newSelectedIds = (caseUploadValidationResultQuery.data ?? []).filter(validatedCase => {\n      return !validatedCase.data_issues.some(issue => issue.data_issue_type === CaseDbDataIssueType.INVALID || issue.data_issue_type === CaseDbDataIssueType.UNAUTHORIZED);\n    }).map(vc => vc.id);\n    setSelectedIds(newSelectedIds);\n  }, [caseUploadValidationResultQuery.data, setSelectedIds]);\n\n\n  const onProceedWithoutFixingIssues = useCallback(async () => {\n    const selectedIds = tableStore.getState().selectedIds;\n    const validCases = caseUploadValidationResultQuery.data.filter(row => selectedIds.includes(row.id) && !row.data_issues.some(issue => issue.data_issue_type === CaseDbDataIssueType.INVALID));\n    store.setState((state) => ({\n      ...state,\n      selectedIdsForUpload: validCases.map(c => c.id),\n      validatedCases: caseUploadValidationResultQuery.data,\n    }));\n    await goToNextStep();\n  }, [caseUploadValidationResultQuery.data, goToNextStep, store, tableStore]);\n\n  const onProceed = useCallback(async () => {\n    store.setState((state) => ({\n      ...state,\n      selectedIdsForUpload: selectedIdsRef.current,\n      validatedCases: caseUploadValidationResultQuery.data,\n    }));\n\n    await goToNextStep();\n  }, [goToNextStep, caseUploadValidationResultQuery.data, store]);\n\n  const onProceedButtonClick = useCallback(async () => {\n    if (caseUploadValidationResultQuery.data.some(row => tableStore.getState().selectedIds.includes(row.id) && (row.data_issues.some(issue => issue.data_issue_type === CaseDbDataIssueType.INVALID) || row.status === CaseDbEtlStatus.FAILED))) {\n      continueWithoutFixingConfirmationRef.current?.open();\n      return;\n    }\n\n    if (caseUploadValidationResultQuery.data.some(row => !tableStore.getState().selectedIds.includes(row.id) && !row.data_issues.some(issue => issue.data_issue_type === CaseDbDataIssueType.INVALID))) {\n      continueWithoutSelectingAllCasesRef.current?.open();\n      return;\n    }\n\n    await onProceed();\n  }, [caseUploadValidationResultQuery.data, onProceed, tableStore]);\n\n  const onGoBackButtonClick = useCallback(() => {\n    goToPreviousStep();\n  }, [goToPreviousStep]);\n\n  return (\n    <Box\n      sx={{\n        display: 'grid',\n        gridTemplateRows: `${exceedsMaxNumCases ? 'max-content' : ''} max-content auto max-content`,\n        height: '100%',\n        position: 'relative',\n        width: '100%',\n      }}\n    >\n      <TableStoreContextProvider store={tableStore}>\n        <ResponseHandler\n          error={revalidationError}\n          inlineSpinner\n          loadables={loadables}\n          loadingMessage={t('Validating cases')}\n          takingLongerTimeoutMs={10000}\n        >\n          {exceedsMaxNumCases && (\n            <Box\n              sx={{\n                marginY: 2,\n              }}\n            >\n              <Alert severity={'error'}>\n                <AlertTitle>\n                  {t('You have exceeded the maximum number of {{maxCases}} cases for this case type. Please reduce the number of selected cases before proceeding.', {\n                    maxCases: completeCaseType.props.create_max_n_cases,\n                  })}\n                </AlertTitle>\n              </Alert>\n            </Box>\n          )}\n          <UploadCaseResultTable\n            caseRightsColMap={caseRightsColMap}\n            caseUploadResults={caseUploadValidationResultQuery.data || []}\n            completeCaseType={completeCaseType}\n            getOriginalCellValue={getOriginalCellValue}\n            onCaseContentEditSubmit={onCaseContentEditSubmit}\n            onColContentEditSubmit={onColContentEditSubmit}\n            tableStore={tableStore}\n          />\n          <UploadPreviewNavigation\n            onGoBackButtonClick={onGoBackButtonClick}\n            onProceedButtonClick={onProceedButtonClick}\n          />\n        </ResponseHandler>\n      </TableStoreContextProvider>\n      <BackdropSpinner\n        label={t('Revalidating cases')}\n        open={isRevalidatingCases}\n      />\n      <Confirmation\n        body={t`Some of the selected cases contain issues. If you proceed, these cases will be excluded. Are you sure you want to proceed without them?`}\n        cancelLabel={t`Cancel`}\n        confirmLabel={t`Proceed`}\n        onConfirm={onProceedWithoutFixingIssues}\n        ref={continueWithoutFixingConfirmationRef}\n        title={t`Issues found with selected cases`}\n      />\n      <Confirmation\n        body={t`Not all cases are selected. Do you want to proceed without them?`}\n        cancelLabel={t`Cancel`}\n        confirmLabel={t`Proceed`}\n        onConfirm={onProceed}\n        ref={continueWithoutSelectingAllCasesRef}\n        title={t`Not all cases are selected.`}\n      />\n    </Box>\n  );\n});\n","import { useTranslation } from 'react-i18next';\nimport type { ReactNode } from 'react';\nimport {\n  use,\n  useCallback,\n  useEffect,\n  useMemo,\n  useState,\n} from 'react';\nimport {\n  Alert,\n  AlertTitle,\n  Box,\n  Button,\n  Container,\n} from '@mui/material';\nimport { useStore } from 'zustand';\nimport { GenericErrorMessage } from '@gen-epix/ui-client-common/components/ui/GenericErrorMessage';\nimport { InactivityService } from '@gen-epix/ui-client-common/classes/services/InactivityService';\nimport { LinearProgressWithLabel } from '@gen-epix/ui-core-components/components/LinearProgressWithLabel';\nimport { RouterService } from '@gen-epix/ui-client-common/classes/services/RouterService';\n\nimport { CaseTypeUtil } from '../../../utils/CaseTypeUtil';\nimport { UploadError } from '../../../classes/errors';\nimport { UploadStoreContext } from '../../../stores/uploadStore';\nimport { UploadUtil } from '../../../utils/UploadUtil';\n\nimport { UploadNavigation } from './UploadNavigation';\n\n\nexport const UploadCreateCases = () => {\n  const { t } = useTranslation();\n\n  const store = use(UploadStoreContext);\n  const reset = useStore(store, (state) => state.reset);\n  const goToPreviousStep = useStore(store, (state) => state.goToPreviousStep);\n  const sequenceMapping = useStore(store, (state) => state.sequenceMapping);\n  const sequenceFilesDataTransfer = useStore(store, (state) => state.sequenceFilesDataTransfer);\n  const validatedCases = useStore(store, (state) => state.validatedCases);\n  const selectedIdsForUpload = useStore(store, (state) => state.selectedIdsForUpload);\n  const casesForVerificationFromSourceData = useStore(store, (state) => state.casesForVerificationFromSourceData);\n  const uploadCompleteButtonCallback = useStore(store, (state) => state.uploadCompleteButtonCallback);\n  const uploadCompleteButtonLabel = useStore(store, (state) => state.uploadCompleteButtonLabel);\n  const onUploadComplete = useStore(store, (state) => state.onUploadComplete);\n\n  const completeCaseType = useStore(store, (state) => state.completeCaseType);\n  const [progress, setProgress] = useState(0);\n  const [progressMessage, setProgressMessage] = useState('');\n\n  const [isUploadStarted, setIsUploadStarted] = useState(false);\n  const [isUploadCompleted, setIsUploadCompleted] = useState(false);\n  const [error, setError] = useState<unknown>(undefined);\n\n  const sequenceFileStats = useMemo(() => {\n    return UploadUtil.getSequenceMappingStats(sequenceMapping, sequenceFilesDataTransfer);\n  }, [sequenceFilesDataTransfer, sequenceMapping]);\n\n  const selectedValidatedCases = useMemo(() => {\n    return validatedCases.filter(vc => selectedIdsForUpload.includes(vc.id));\n  }, [validatedCases, selectedIdsForUpload]);\n\n  useEffect(() => {\n    const abortController = new AbortController();\n    const { signal } = abortController;\n\n    const abort = () => {\n      abortController.abort();\n      InactivityService.getInstance().resume();\n    };\n\n    if (!isUploadStarted) {\n      return abort;\n    }\n    InactivityService.getInstance().pause();\n\n    const perform = async () => {\n      const result = await UploadUtil.createCasesAndUploadFiles({\n        assemblyProtocolId: store.getState().assemblyProtocolId,\n        casesForVerificationFromSourceData,\n        completeCaseType: store.getState().completeCaseType,\n        createdInDataCollectionId: store.getState().createdInDataCollectionId,\n        mappedColumns: store.getState().mappedColumns,\n        onComplete: () => {\n          setIsUploadCompleted(true);\n        },\n        onError: (e: Error) => {\n          setError(e);\n        },\n        onProgress: (percentage: number, message: string) => {\n          setProgress(percentage);\n          setProgressMessage(message);\n        },\n        sampleIdColId: store.getState().sampleIdColId,\n        selectedValidatedCases,\n        sequenceFilesDataTransfer,\n        sequenceMapping,\n        sequencingProtocolId: store.getState().sequencingProtocolId,\n        signal,\n      });\n      if (onUploadComplete) {\n        await onUploadComplete(result);\n      }\n    };\n\n    perform().catch((e) => {\n      if (!signal.aborted) {\n        setError(e);\n      }\n    });\n\n\n    return abort;\n  }, [isUploadStarted, sequenceFilesDataTransfer, sequenceMapping, store, t, selectedValidatedCases, casesForVerificationFromSourceData, onUploadComplete]);\n\n\n  const onStartOverButtonClick = useCallback(async () => {\n    await reset();\n  }, [reset]);\n\n  const onStartUploadButtonClick = useCallback(() => {\n    setIsUploadStarted(true);\n  }, []);\n\n  const onGoBackButtonClick = useCallback(() => {\n    goToPreviousStep();\n  }, [goToPreviousStep]);\n\n  const onGotoCasesButtonClick = useCallback(async () => {\n    const link = CaseTypeUtil.createCaseTypeLink(completeCaseType);\n    await RouterService.getInstance().router.navigate(link);\n  }, [completeCaseType]);\n\n  let content: ReactNode;\n\n  if (error) {\n    content = (\n      <Box>\n        {error instanceof UploadError && (\n          <Alert severity={'error'}>\n            <AlertTitle>\n              {t('Failed to create cases during upload.')}\n            </AlertTitle>\n            {t('An error occurred while creating cases. Please try again or contact support if the issue persists. Cases may have been partially created. No files were uploaded.')}\n          </Alert>\n        )}\n        <GenericErrorMessage error={error} />\n      </Box>\n    );\n  } else if (isUploadCompleted) {\n    content = (\n      <Box>\n        <Box>\n          <Alert severity={'success'}>\n            <AlertTitle>\n              {t('Upload completed.')}\n            </AlertTitle>\n          </Alert>\n        </Box>\n        <Box\n          sx={{\n            display: 'flex',\n            gap: 2,\n            justifyContent: 'flex-end',\n            marginBottom: 1,\n            marginTop: 2,\n          }}\n        >\n          {uploadCompleteButtonCallback && uploadCompleteButtonLabel ? (\n            <Button\n              // eslint-disable-next-line @eslint-react/kit/jsx-handler-names\n              onClick={uploadCompleteButtonCallback}\n              variant={'contained'}\n            >\n              {uploadCompleteButtonLabel}\n            </Button>\n          ) : (\n            <>\n              <Button\n                onClick={onStartOverButtonClick}\n                variant={'outlined'}\n              >\n                {t('Upload more cases')}\n              </Button>\n              <Button\n                onClick={onGotoCasesButtonClick}\n                variant={'contained'}\n              >\n                {t('View uploaded cases')}\n              </Button>\n            </>\n          )}\n        </Box>\n      </Box>\n    );\n  } else if (isUploadStarted) {\n    content = (\n      <Box>\n        <Box\n          sx={{\n            marginBottom: 4,\n          }}\n        >\n          <Alert severity={'info'}>\n            <AlertTitle>\n              {t('Uploading cases and files.')}\n            </AlertTitle>\n            {t('Please wait while the cases and associated files are being uploaded. This may take a while depending on the number and size of the files being uploaded.')}\n          </Alert>\n        </Box>\n        <Box\n          sx={{\n            marginBottom: 2,\n            marginTop: 4,\n          }}\n        >\n          <LinearProgressWithLabel value={progress} />\n        </Box>\n        <Box\n          sx={{\n            fontWeight: 700,\n          }}\n        >\n          {progressMessage}\n        </Box>\n      </Box>\n    );\n  } else {\n    content = (\n      <Box>\n        <Box>\n          <Box\n            sx={{\n              marginY: 2,\n            }}\n          >\n            <Alert severity={'info'}>\n              <AlertTitle>\n                {t('{{numCases}} cases are ready to be uploaded.', { numCases: selectedValidatedCases.length })}\n              </AlertTitle>\n            </Alert>\n          </Box>\n          {sequenceFileStats.mappedSequenceFiles.length > 0 && (\n            <Box\n              sx={{\n                marginY: 2,\n              }}\n            >\n              <Alert severity={'info'}>\n                <AlertTitle>\n                  {t('{{numSequenceFiles}} genome files are ready to be uploaded.', { numSequenceFiles: sequenceFileStats.mappedSequenceFiles.length })}\n                </AlertTitle>\n              </Alert>\n            </Box>\n          )}\n          {sequenceFileStats.mappedReadsFiles.length > 0 && (\n            <Box\n              sx={{\n                marginY: 2,\n              }}\n            >\n              <Alert severity={'info'}>\n                <AlertTitle>\n                  {t('{{numReadsFiles}} reads files are ready to be uploaded.', { numReadsFiles: sequenceFileStats.mappedReadsFiles.length })}\n                </AlertTitle>\n              </Alert>\n            </Box>\n          )}\n          {validatedCases.length - selectedValidatedCases.length > 0 && (\n            <Box\n              sx={{\n                marginY: 2,\n              }}\n            >\n              <Alert severity={'warning'}>\n                <AlertTitle>\n                  {t('{{numCases}} cases were not selected and will not be uploaded.', { numCases: validatedCases.length - selectedValidatedCases.length })}\n                </AlertTitle>\n              </Alert>\n            </Box>\n          )}\n          {sequenceFileStats.unmappedSequenceFiles.length > 0 && (\n            <Box\n              sx={{\n                marginY: 2,\n              }}\n            >\n              <Alert severity={'warning'}>\n                <AlertTitle>\n                  {t('{{unmappedSequenceFiles}} unmapped genome files will not be uploaded.', { unmappedSequenceFiles: sequenceFileStats.unmappedSequenceFiles.length })}\n                </AlertTitle>\n              </Alert>\n            </Box>\n          )}\n          {sequenceFileStats.unmappedReadsFiles.length > 0 && (\n            <Box\n              sx={{\n                marginY: 2,\n              }}\n            >\n              <Alert severity={'warning'}>\n                <AlertTitle>\n                  {t('{{unmappedReadsFiles}} unmapped reads files will not be uploaded.', { unmappedReadsFiles: sequenceFileStats.unmappedReadsFiles.length })}\n                </AlertTitle>\n              </Alert>\n            </Box>\n          )}\n        </Box>\n        <UploadNavigation\n          onGoBackButtonClick={onGoBackButtonClick}\n          onProceedButtonClick={onStartUploadButtonClick}\n          proceedLabel={'Start upload'}\n        />\n      </Box>\n    );\n  }\n\n  return (\n    <Container\n      maxWidth={'xl'}\n      sx={{\n        height: '100%',\n      }}\n    >\n      {content}\n    </Container>\n  );\n};\n","import {\n  Alert,\n  AlertTitle,\n  Box,\n  useTheme,\n} from '@mui/material';\nimport type { ReactElement } from 'react';\nimport {\n  use,\n  useCallback,\n  useEffect,\n  useId,\n  useMemo,\n  useState,\n} from 'react';\nimport { useTranslation } from 'react-i18next';\nimport { useStore } from 'zustand';\nimport {\n  object,\n  string,\n} from 'yup';\nimport { yupResolver } from '@hookform/resolvers/yup';\nimport type { Resolver } from 'react-hook-form';\nimport { useForm } from 'react-hook-form';\nimport { ResponseHandler } from '@gen-epix/ui-client-common/components/ui/ResponseHandler';\nimport { useArray } from '@gen-epix/ui-core/hooks/useArray';\nimport { GenericForm } from '@gen-epix/ui-core-form/components/helpers/GenericForm';\nimport type {\n  FormFieldDefinition,\n  SelectOption,\n} from '@gen-epix/ui-core-form/models/form';\nimport { FORM_FIELD_DEFINITION_TYPE } from '@gen-epix/ui-core-form/models/form';\nimport { MultiFileUploader } from '@gen-epix/ui-core-components/components/MultiFileUploader';\n\nimport { UploadUtil } from '../../../utils/UploadUtil';\nimport { UploadStoreContext } from '../../../stores/uploadStore';\nimport { useSequencingProtocolOptionsQuery } from '../../../dataHooks/useSequencingProtocolsQuery';\nimport { useAssemblyProtocolOptionsQuery } from '../../../dataHooks/useAssemblyProtocolsQuery';\n\nimport { UploadNavigation } from './UploadNavigation';\n\n\ntype FormFields = {\n  assemblyProtocolId: string;\n  sampleIdColId: string;\n  sequencingProtocolId: string;\n};\n\nconst getSelectedFiles = (dataTransfer?: DataTransfer) => {\n  return Array.from(dataTransfer?.files ?? []);\n};\n\nconst createSchema = ({\n  hasGenomeFiles,\n  hasReadsFiles,\n  hasSelectedFiles,\n}: {\n  hasGenomeFiles: boolean;\n  hasReadsFiles: boolean;\n  hasSelectedFiles: boolean;\n}) => {\n  return object<FormFields>().shape({\n    assemblyProtocolId: hasGenomeFiles ? string().uuid4().required() : string().nullable().notRequired(),\n    sampleIdColId: hasSelectedFiles ? string().uuid4().required() : string().nullable().notRequired(),\n    sequencingProtocolId: hasReadsFiles ? string().uuid4().required() : string().nullable().notRequired(),\n  });\n};\n\nexport const UploadSelectSequenceFiles = () => {\n  const { t } = useTranslation();\n  const theme = useTheme();\n\n  const store = use(UploadStoreContext);\n  const completeCaseType = useStore(store, (state) => state.completeCaseType);\n  const mappedColumns = useStore(store, (state) => state.mappedColumns);\n  const validatedCases = useStore(store, (state) => state.validatedCases);\n  const goToNextStep = useStore(store, (state) => state.goToNextStep);\n  const goToPreviousStep = useStore(store, (state) => state.goToPreviousStep);\n  const setSequenceFilesDataTransfer = useStore(store, (state) => state.setSequenceFilesDataTransfer);\n  const sampleIdColId = useStore(store, (state) => state.sampleIdColId);\n  const initialDataTransfer = useStore(store, (state) => state.sequenceFilesDataTransfer);\n  const [currentDataTransfer, setCurrentDataTransfer] = useState(initialDataTransfer);\n\n  const formId = useId();\n\n  const sequencingProtocolOptionsQuery = useSequencingProtocolOptionsQuery();\n  const assemblyProtocolOptionsQuery = useAssemblyProtocolOptionsQuery();\n\n  const loadables = useArray([\n    sequencingProtocolOptionsQuery,\n    assemblyProtocolOptionsQuery,\n  ]);\n\n  const sampleIdColIdOptions = useMemo<SelectOption<string>[]>(() => {\n    return mappedColumns.filter(mc => mc.isSampleIdColumn).map(mc => ({\n      label: mc.col.label,\n      value: mc.col.id,\n    } satisfies SelectOption<string>));\n  }, [mappedColumns]);\n\n  const selectedFiles = useMemo(() => {\n    return getSelectedFiles(currentDataTransfer);\n  }, [currentDataTransfer]);\n\n  const hasSelectedFiles = selectedFiles.length > 0;\n  const hasGenomeFiles = useMemo(() => {\n    return selectedFiles.some(file => UploadUtil.isGenomeFile(file.name));\n  }, [selectedFiles]);\n  const hasReadsFiles = useMemo(() => {\n    return selectedFiles.some(file => UploadUtil.isReadsFile(file.name));\n  }, [selectedFiles]);\n\n  const schema = useMemo(() => {\n    return createSchema({\n      hasGenomeFiles,\n      hasReadsFiles,\n      hasSelectedFiles,\n    });\n  }, [hasGenomeFiles, hasReadsFiles, hasSelectedFiles]);\n\n  const defaultFormValues = useMemo<FormFields>(() => {\n    return {\n      assemblyProtocolId: store.getState().assemblyProtocolId ?? null,\n      sampleIdColId: store.getState().sampleIdColId ?? null,\n      sequencingProtocolId: store.getState().sequencingProtocolId ?? null,\n    };\n  }, [store]);\n\n  const formMethods = useForm<FormFields>({\n    defaultValues: defaultFormValues,\n    resolver: yupResolver(schema) as unknown as Resolver<FormFields>,\n    values: defaultFormValues,\n  });\n  const { handleSubmit, setValue } = formMethods;\n\n  useEffect(() => {\n    if (sequencingProtocolOptionsQuery.isLoading || assemblyProtocolOptionsQuery.isLoading) {\n      return;\n    }\n    if (!store.getState().sequencingProtocolId) {\n      setValue('sequencingProtocolId', sequencingProtocolOptionsQuery.options[0]?.value || null);\n      store.setState({ sequencingProtocolId: sequencingProtocolOptionsQuery.options[0]?.value || null });\n    }\n    if (!store.getState().assemblyProtocolId) {\n      setValue('assemblyProtocolId', assemblyProtocolOptionsQuery.options[0]?.value || null);\n      store.setState({ assemblyProtocolId: assemblyProtocolOptionsQuery.options[0]?.value || null });\n    }\n    if (!store.getState().sampleIdColId) {\n      setValue('sampleIdColId', sampleIdColIdOptions[0]?.value || null);\n      store.setState({ sampleIdColId: sampleIdColIdOptions[0]?.value || null });\n    }\n  }, [assemblyProtocolOptionsQuery.isLoading, assemblyProtocolOptionsQuery.options, sequencingProtocolOptionsQuery.isLoading, sequencingProtocolOptionsQuery.options, setValue, store, sampleIdColIdOptions]);\n\n  const onSequencingProtocolChange = useCallback((value: string) => {\n    store.setState({ sequencingProtocolId: value });\n  }, [store]);\n\n  const onAssemblyProtocolChange = useCallback((value: string) => {\n    store.setState({ assemblyProtocolId: value });\n  }, [store]);\n\n  const onSampleIdColIdChange = useCallback((value: string) => {\n    store.setState({ sampleIdColId: value });\n  }, [store]);\n\n  const formFieldDefinitions = useMemo<FormFieldDefinition<FormFields>[]>(() => {\n    return [\n      {\n        definition: FORM_FIELD_DEFINITION_TYPE.SELECT,\n        label: t`Genome files: assembly protocol`,\n        loading: assemblyProtocolOptionsQuery.isLoading,\n        name: 'assemblyProtocolId',\n        onChange: onAssemblyProtocolChange,\n        options: assemblyProtocolOptionsQuery.options,\n      } as const satisfies FormFieldDefinition<FormFields>,\n      {\n        definition: FORM_FIELD_DEFINITION_TYPE.SELECT,\n        label: t`Reads files: sequencing protocol`,\n        loading: sequencingProtocolOptionsQuery.isLoading,\n        name: 'sequencingProtocolId',\n        onChange: onSequencingProtocolChange,\n        options: sequencingProtocolOptionsQuery.options,\n      } as const satisfies FormFieldDefinition<FormFields>,\n      {\n        definition: FORM_FIELD_DEFINITION_TYPE.SELECT,\n        label: t`Sample ID column`,\n        name: 'sampleIdColId',\n        onChange: onSampleIdColIdChange,\n        options: sampleIdColIdOptions,\n      } as const satisfies FormFieldDefinition<FormFields>,\n    ];\n  }, [assemblyProtocolOptionsQuery.isLoading, assemblyProtocolOptionsQuery.options, onAssemblyProtocolChange, onSampleIdColIdChange, onSequencingProtocolChange, sampleIdColIdOptions, sequencingProtocolOptionsQuery.isLoading, sequencingProtocolOptionsQuery.options, t]);\n\n\n  const hasWritableSampleIdColumn = useMemo(() => {\n    return mappedColumns.some(mappedColumn => {\n      return mappedColumn.isSampleIdColumn && mappedColumn.sampleIdentifierIssuerId;\n    });\n  }, [mappedColumns]);\n\n  const hasRowContentForSampleIdColId = useMemo(() => {\n    if (!sampleIdColId) {\n      return false;\n    }\n    return validatedCases.some(vc => {\n      return vc.validated_content[sampleIdColId]?.trim().length > 0;\n    });\n  }, [sampleIdColId, validatedCases]);\n\n  const completeCaseTypeColStats = useMemo(() => {\n    return UploadUtil.getCompleteCaseTypeColStats(completeCaseType);\n  }, [completeCaseType]);\n\n  const canUploadSequences = useMemo(() => {\n    return completeCaseTypeColStats.sequenceColumns.length > 0;\n  }, [completeCaseTypeColStats]);\n\n  const canUploadReads = useMemo(() => {\n    return completeCaseTypeColStats.readsColumns.length > 0;\n  }, [completeCaseTypeColStats]);\n\n  const canUpload = useMemo(() => {\n    return hasWritableSampleIdColumn && hasRowContentForSampleIdColId && (canUploadSequences || canUploadReads);\n  }, [hasWritableSampleIdColumn, hasRowContentForSampleIdColId, canUploadSequences, canUploadReads]);\n\n  const accept = useMemo(() => {\n    let acc = '';\n    if (canUploadSequences) {\n      acc += '.fa,.fasta,.fa.gz,.fasta.gz,';\n    }\n    if (canUploadReads) {\n      acc += '.fq,.fastq,.fq.gz,.fastq.gz,';\n    }\n    return acc;\n  }, [canUploadReads, canUploadSequences]);\n\n  const onProceedButtonClick = useCallback(async () => {\n    setSequenceFilesDataTransfer(canUpload ? currentDataTransfer : new DataTransfer());\n    await handleSubmit(async () => {\n      await goToNextStep();\n    })();\n  }, [canUpload, currentDataTransfer, goToNextStep, handleSubmit, setSequenceFilesDataTransfer]);\n\n  const onGoBackButtonClick = useCallback(() => {\n    goToPreviousStep();\n  }, [goToPreviousStep]);\n\n  const onDataTransferChange = useCallback((dt: DataTransfer) => {\n    setCurrentDataTransfer(dt);\n    setSequenceFilesDataTransfer(dt);\n  }, [setSequenceFilesDataTransfer]);\n\n  const wrapForm = useCallback((children: ReactElement) => {\n    return (\n      <Box\n        sx={{\n          display: 'grid',\n          gap: theme.spacing(1),\n          gridTemplateColumns: '1fr 1fr 1fr',\n        }}\n      >\n        {children}\n      </Box>\n    );\n  }, [theme]);\n\n  const cantUploadMessage = useMemo<{ message: string; title: string }>(() => {\n    if (!hasWritableSampleIdColumn) {\n      return {\n        message: t`No columns have been mapped as writable sample ID column with selected identifier issuer provider.`,\n        title: t('Uploading of files is disabled.'),\n      };\n    }\n    if (!hasRowContentForSampleIdColId) {\n      return {\n        message: t`No rows have a sample ID filled for the selected sample ID column.`,\n        title: t('Uploading of files is disabled.'),\n      };\n    }\n    if (!canUploadReads) {\n      return {\n        message: t`The selected case type does not support uploading read files.`,\n        title: t('Uploading of read files is disabled.'),\n      };\n    }\n    if (!canUploadSequences) {\n      return {\n        message: t`The selected case type does not support uploading sequence files.`,\n        title: t('Uploading of sequence files is disabled.'),\n      };\n    }\n    return null;\n  }, [canUploadReads, canUploadSequences, hasRowContentForSampleIdColId, hasWritableSampleIdColumn, t]);\n\n  const onSubmit = useCallback(() => {\n    // noop, as we handle form submission manually in onProceedButtonClick\n  }, []);\n\n  return (\n    <ResponseHandler\n      loadables={loadables}\n    >\n      <Box\n        sx={{\n          display: 'grid',\n          gridTemplateRows: `${canUpload ? '' : 'max-content '}max-content auto max-content`,\n          height: '100%',\n          position: 'relative',\n        }}\n      >\n        {!canUpload && (\n          <Box\n            sx={{\n              marginBottom: 2,\n            }}\n          >\n            <Alert severity={'error'}>\n              <AlertTitle>\n                {cantUploadMessage.title}\n              </AlertTitle>\n              {cantUploadMessage.message}\n            </Alert>\n          </Box>\n        )}\n        <Box\n          sx={{\n            borderBottom: `1px solid ${theme.palette.divider}`,\n          }}\n        >\n          <Box\n            sx={{\n              maxWidth: theme.spacing(128),\n            }}\n          >\n            <GenericForm<FormFields>\n              formFieldDefinitions={formFieldDefinitions}\n              formId={formId}\n              formMethods={formMethods}\n              onSubmit={onSubmit}\n              schema={schema}\n              wrapForm={wrapForm}\n            />\n          </Box>\n          {!canUploadSequences && (\n            <Box\n              sx={{\n                marginY: 1,\n              }}\n            >\n              <Alert severity={'info'}>\n                <AlertTitle>\n                  {t('Uploading of sequences has been disabled.')}\n                </AlertTitle>\n                <Box>\n                  {t('Uploading of sequences is not supported for the selected case type.')}\n                </Box>\n              </Alert>\n            </Box>\n          )}\n          {!canUploadReads && (\n            <Box\n              sx={{\n                marginY: 1,\n              }}\n            >\n              <Alert severity={'info'}>\n                <AlertTitle>\n                  {t('Uploading of read files has been disabled.')}\n                </AlertTitle>\n                <Box>\n                  {t('Uploading of read files is not supported for the selected case type.')}\n                </Box>\n              </Alert>\n            </Box>\n          )}\n        </Box>\n        <Box\n          sx={{\n            position: 'relative',\n          }}\n        >\n\n          <Box\n            sx={{\n              bottom: 0,\n              height: '100%',\n              left: 0,\n              position: 'absolute',\n              right: 0,\n              top: 0,\n            }}\n          >\n            {canUpload && (\n              <MultiFileUploader\n                accept={accept}\n                initialDataTransfer={initialDataTransfer}\n                numFilesAllowed={Infinity}\n                onDataTransferChange={onDataTransferChange}\n              />\n            )}\n          </Box>\n        </Box>\n        <UploadNavigation\n          onGoBackButtonClick={onGoBackButtonClick}\n          onProceedButtonClick={onProceedButtonClick}\n          proceedLabel={!canUpload ? t`Proceed` : undefined}\n        />\n      </Box>\n    </ResponseHandler>\n  );\n};\n","import {\n  Alert,\n  AlertTitle,\n  Autocomplete,\n  Box,\n  TextField,\n  useTheme,\n} from '@mui/material';\nimport {\n  use,\n  useCallback,\n  useEffect,\n  useId,\n  useMemo,\n  useRef,\n} from 'react';\nimport { useTranslation } from 'react-i18next';\nimport { useStore } from 'zustand';\nimport { useShallow } from 'zustand/react/shallow';\nimport type {\n  CaseDbCaseUploadResult,\n  CaseDbCol,\n} from '@gen-epix/api-casedb';\nimport type {\n  TableColumn,\n  TableRowParams,\n} from '@gen-epix/ui-client-common/models/table';\nimport {\n  createTableStore,\n  TableStoreContextProvider,\n} from '@gen-epix/ui-client-common/stores/tableStore';\nimport { Table } from '@gen-epix/ui-client-common/components/ui/Table';\nimport { TableUtil } from '@gen-epix/ui-client-common/utils/TableUtil';\nimport { useInitializeTableStore } from '@gen-epix/ui-client-common/hooks/useInitializeTableStore';\n\nimport { CaseUtil } from '../../../utils/CaseUtil';\nimport { UploadStoreContext } from '../../../stores/uploadStore';\nimport { UploadUtil } from '../../../utils/UploadUtil';\n\nimport { UploadNavigation } from './UploadNavigation';\n\nexport const UploadMapSequences = () => {\n  const { t } = useTranslation();\n  const theme = useTheme();\n\n  const store = use(UploadStoreContext);\n  const goToNextStep = useStore(store, (state) => state.goToNextStep);\n  const goToPreviousStep = useStore(store, (state) => state.goToPreviousStep);\n  const completeCaseType = useStore(store, (state) => state.completeCaseType);\n  const sampleIdColId = useStore(store, (state) => state.sampleIdColId);\n  const sequenceFilesDataTransfer = useStore(store, (state) => state.sequenceFilesDataTransfer);\n  const selectedValidatedCases = useStore(store, useShallow((state) => {\n    const selectedIdsForUpload = state.selectedIdsForUpload;\n    return state.validatedCases.filter(vc => selectedIdsForUpload.includes(vc.id));\n  }));\n  const setSequenceMapping = useStore(store, (state) => state.setSequenceMapping);\n\n  const completeCaseTypeColStats = useMemo(() => {\n    return UploadUtil.getCompleteCaseTypeColStats(completeCaseType);\n  }, [completeCaseType]);\n\n  const alertTitleId = useId();\n  const alertContentId = useId();\n\n  const uploadSequenceMappingRef = useRef(store.getState().sequenceMapping);\n\n  const onProceedButtonClick = useCallback(async () => {\n    setSequenceMapping(uploadSequenceMappingRef.current);\n    await goToNextStep();\n  }, [setSequenceMapping, goToNextStep]);\n\n  const onGoBackButtonClick = useCallback(() => {\n    goToPreviousStep();\n  }, [goToPreviousStep]);\n\n  const updateAlert = useCallback(() => {\n    // Note: This is done via DOM manipulation to prevent excessive re-renders of the entire table\n\n    const alertTitleElement = document.getElementById(alertTitleId);\n    const alertContentElement = document.getElementById(alertContentId);\n    if (!alertTitleElement || !alertContentElement) {\n      return;\n    }\n    const {\n      mappedFiles,\n      numberOfFilesToMap,\n      unmappedFileNames,\n    } = UploadUtil.getSequenceMappingStats(uploadSequenceMappingRef.current, sequenceFilesDataTransfer);\n\n    alertTitleElement.innerHTML = numberOfFilesToMap === mappedFiles.length ? t('All {{numberOfFilesToMap}} files are mapped', { numberOfFilesToMap }) : t('{{mappedFilesLength}} of {{numberOfFilesToMap}} files mapped', { mappedFilesLength: mappedFiles.length, numberOfFilesToMap });\n    alertContentElement.innerHTML = numberOfFilesToMap === mappedFiles.length ? '' : t('Unmapped files: {{unmappedFileNames}}', { unmappedFileNames: unmappedFileNames.join(', ') });\n  }, [alertContentId, alertTitleId, sequenceFilesDataTransfer, t]);\n\n  useEffect(() => {\n    updateAlert();\n  }, [updateAlert]);\n\n  const tableStore = useMemo(() => createTableStore<CaseDbCaseUploadResult>({\n    idSelectorCallback: (row) => row.id,\n  }), []);\n\n  const caseHasColumnContent = useCallback((rows: CaseDbCaseUploadResult[], col: CaseDbCol): boolean => {\n    return rows.some((row) => {\n      const value = CaseUtil.getRowValue(row.validated_content, col, completeCaseType);\n      return value && !value?.isMissing;\n    });\n  }, [completeCaseType]);\n\n  const sequenceDropDownOptions = useMemo(() => {\n    return Array.from(sequenceFilesDataTransfer.files).map((file) => file.name).filter(name => name.endsWith('.fasta') || name.endsWith('.fa') || name.endsWith('.fa.gz') || name.endsWith('.fasta.gz'));\n  }, [sequenceFilesDataTransfer.files]);\n\n  const readsDropDownOptions = useMemo(() => {\n    return Array.from(sequenceFilesDataTransfer.files).map((file) => file.name).filter(name => name.endsWith('.fastq') || name.endsWith('.fq') || name.endsWith('.fq.gz') || name.endsWith('.fastaq.gz'));\n  }, [sequenceFilesDataTransfer.files]);\n\n  const createDropDown = useCallback((kwArgs: { dropDownOptions: string[]; dropDownValue: string; label: string; onChange: (newValue: string) => void }) => {\n    const { dropDownOptions, dropDownValue, label, onChange } = kwArgs;\n\n    return (\n      <Autocomplete\n        freeSolo\n        fullWidth\n        // eslint-disable-next-line @eslint-react/kit/jsx-no-bind\n        onChange={(_, newValue) => {\n          onChange(newValue);\n          setSequenceMapping(uploadSequenceMappingRef.current);\n          updateAlert();\n        }}\n        options={dropDownOptions}\n        // eslint-disable-next-line @eslint-react/kit/jsx-no-bind\n        renderInput={(params) => (\n          <TextField\n            {...params}\n            label={label}\n            size={'small'}\n          />\n        )}\n        sx={{\n          lineHeight: 'initial',\n        }}\n        value={dropDownValue}\n      />\n    );\n  }, [setSequenceMapping, updateAlert]);\n\n  const renderSequenceCell = useCallback((tableRowParams: TableRowParams<CaseDbCaseUploadResult>) => {\n    const col = completeCaseType.cols[tableRowParams.id];\n\n    const id = tableRowParams.row.id;\n    const dropDownValue = uploadSequenceMappingRef.current?.[tableRowParams.row.id]?.sequenceFileNames[col.id] || '';\n    const onChange = (newValue: string) => {\n      if (!newValue) {\n        delete uploadSequenceMappingRef.current?.[id]?.sequenceFileNames[col.id];\n      } else {\n        uploadSequenceMappingRef.current[id].sequenceFileNames[col.id] = newValue;\n      }\n    };\n\n    return (\n      <Box\n        sx={{\n          alignItems: 'center',\n          display: 'flex',\n          flexDirection: 'column',\n          height: '100%',\n          justifyContent: 'center',\n        }}\n      >\n        {createDropDown({\n          dropDownOptions: sequenceDropDownOptions,\n          dropDownValue,\n          label: col.label,\n          onChange,\n        })}\n      </Box>\n    );\n  }, [completeCaseType, createDropDown, sequenceDropDownOptions]);\n\n\n  const renderReadsCell = useCallback((tableRowParams: TableRowParams<CaseDbCaseUploadResult>) => {\n    const col = completeCaseType.cols[tableRowParams.id];\n    const isSequenceColumn = completeCaseTypeColStats.sequenceColumns.includes(col);\n\n    const id = tableRowParams.row.id;\n    const dropDownValueFwd = uploadSequenceMappingRef.current?.[id]?.readsFileNames?.[col.id]?.fwd || '';\n    const dropDownValueRev = uploadSequenceMappingRef.current?.[id]?.readsFileNames?.[col.id]?.rev || '';\n    const onChangeFwd = (newValue: string) => {\n      if (!newValue) {\n\n        delete uploadSequenceMappingRef.current?.[id]?.readsFileNames?.[col.id]?.fwd;\n      } else {\n        uploadSequenceMappingRef.current[id].readsFileNames[col.id].fwd = newValue;\n      }\n    };\n    const onChangeRev = (newValue: string) => {\n      if (!newValue) {\n\n        delete uploadSequenceMappingRef.current?.[id]?.readsFileNames?.[col.id]?.rev;\n      } else {\n        uploadSequenceMappingRef.current[id].readsFileNames[col.id].rev = newValue;\n      }\n    };\n\n    return (\n      <Box\n        sx={{\n          alignItems: 'center',\n          display: 'flex',\n          flexDirection: 'row',\n          gap: 1,\n          height: '100%',\n          justifyContent: 'center',\n        }}\n      >\n        {createDropDown({\n          dropDownOptions: isSequenceColumn ? sequenceDropDownOptions : readsDropDownOptions,\n          dropDownValue: dropDownValueFwd,\n          label: `${col.label} FWD`,\n          onChange: onChangeFwd,\n        })}\n        {createDropDown({\n          dropDownOptions: isSequenceColumn ? sequenceDropDownOptions : readsDropDownOptions,\n          dropDownValue: dropDownValueRev,\n          label: `${col.label} REV`,\n          onChange: onChangeRev,\n        })}\n      </Box>\n    );\n  }, [completeCaseType, completeCaseTypeColStats.sequenceColumns, createDropDown, sequenceDropDownOptions, readsDropDownOptions]);\n\n\n  const tableColumns = useMemo<TableColumn<CaseDbCaseUploadResult>[]>(() => {\n    const tableCols: TableColumn<CaseDbCaseUploadResult>[] = [];\n    tableCols.push(\n      TableUtil.createReadableIndexColumn(),\n    );\n\n    const columnsUsedForMapping = [\n      ...completeCaseTypeColStats.sampleIdColumns,\n      ...completeCaseTypeColStats.sequenceColumns,\n      ...completeCaseTypeColStats.readsColumns,\n    ];\n\n    const sampleIdCol = completeCaseTypeColStats.sampleIdColumns.find(x => x.id === sampleIdColId);\n    if (sampleIdCol && caseHasColumnContent(selectedValidatedCases, sampleIdCol)) {\n      tableCols.push({\n        headerName: sampleIdCol.label,\n        hideInFilter: true,\n        id: sampleIdCol.id,\n        isInitiallyVisible: true,\n        type: 'text',\n        valueGetter: (params) => CaseUtil.getRowValue(params.row.validated_content, sampleIdCol, completeCaseType).short,\n        widthPx: 300,\n      });\n    }\n\n    // eslint-disable-next-line react-hooks/refs\n    completeCaseTypeColStats.sequenceColumns.forEach((col) => {\n      tableCols.push({\n        cellTitleGetter: () => null,\n        headerName: col.label,\n        hideInFilter: true,\n        id: col.id,\n        isInitiallyVisible: true,\n        renderCell: renderSequenceCell,\n        type: 'text',\n        valueGetter: (params) => CaseUtil.getRowValue(params.row.validated_content, col, completeCaseType).short,\n        widthPx: 400,\n      });\n    });\n\n    // eslint-disable-next-line react-hooks/refs\n    completeCaseTypeColStats.readsColumns.forEach((col) => {\n      tableCols.push({\n        cellTitleGetter: () => null,\n        headerName: col.label,\n        hideInFilter: true,\n        id: col.id,\n        isInitiallyVisible: true,\n        renderCell: renderReadsCell,\n        type: 'text',\n        valueGetter: (params) => CaseUtil.getRowValue(params.row.validated_content, col, completeCaseType).short,\n        widthPx: 800,\n      });\n    });\n\n    const uniqueColIds: Set<string> = new Set();\n    selectedValidatedCases.forEach((vc) => {\n      Object.keys(vc.validated_content || {}).forEach((colId) => uniqueColIds.add(colId));\n    });\n\n    const colIdsToIgnore = [...completeCaseTypeColStats.sequenceColumns.map(x => x.id), ...completeCaseTypeColStats.readsColumns.map(x => x.id), sampleIdCol?.id];\n\n    completeCaseType.ordered_col_ids.forEach((colId) => {\n      if (colIdsToIgnore.includes(colId) || !uniqueColIds.has(colId) || columnsUsedForMapping.find(c => c.id === colId)) {\n        return;\n      }\n\n      const col = completeCaseType.cols[colId];\n      if (col) {\n        tableCols.push({\n          headerName: col.code,\n          hideInFilter: true,\n          id: col.id,\n          isInitiallyVisible: true,\n          type: 'text',\n          valueGetter: (params) => CaseUtil.getRowValue(params.row.validated_content, col, completeCaseType).short,\n          widthPx: 250,\n        } satisfies TableColumn<CaseDbCaseUploadResult>);\n      }\n    });\n\n    return tableCols;\n  }, [caseHasColumnContent, completeCaseType, completeCaseTypeColStats.readsColumns, completeCaseTypeColStats.sampleIdColumns, completeCaseTypeColStats.sequenceColumns, renderReadsCell, renderSequenceCell, sampleIdColId, selectedValidatedCases]);\n\n  useInitializeTableStore<CaseDbCaseUploadResult>({ columns: tableColumns, createFiltersFromColumns: true, rows: selectedValidatedCases, store: tableStore });\n\n  return (\n    <Box\n      sx={{\n        display: 'grid',\n        gridTemplateRows: 'max-content auto max-content',\n        height: '100%',\n      }}\n    >\n      <Box sx={{ paddingBottom: 1 }}>\n        <Alert severity={'info'}>\n          <AlertTitle id={alertTitleId} />\n          <Box id={alertContentId} />\n        </Alert>\n      </Box>\n      <TableStoreContextProvider store={tableStore}>\n        <Table\n          font={theme['gen-epix-ui-client-casedb'].lineList.font}\n          rowHeight={7}\n        />\n        <UploadNavigation\n          onGoBackButtonClick={onGoBackButtonClick}\n          onProceedButtonClick={onProceedButtonClick}\n        />\n      </TableStoreContextProvider>\n    </Box>\n  );\n};\n","import Box from '@mui/material/Box';\nimport { useTranslation } from 'react-i18next';\nimport {\n  use,\n  useMemo,\n} from 'react';\nimport {\n  Container,\n  useTheme,\n} from '@mui/material';\nimport { useStore } from 'zustand';\nimport { Stepper } from '@gen-epix/ui-core-components/components/Stepper';\nimport type { Step } from '@gen-epix/ui-core-components/components/Stepper';\n\nimport { UploadStoreContext } from '../../../stores/uploadStore';\nimport { UPLOAD_STEP } from '../../../models/upload';\n\nimport { UploadSelectFile } from './UploadSelectFile';\nimport { UploadMapColumns } from './UploadMapColumns';\nimport { UploadPreview } from './UploadPreview';\nimport { UploadCreateCases } from './UploadCreateCases';\nimport { UploadSelectSequenceFiles } from './UploadSelectSequenceFiles';\nimport { UploadMapSequences } from './UploadMapSequences';\n\nexport const Upload = () => {\n  const { t } = useTranslation();\n  const theme = useTheme();\n\n  const store = use(UploadStoreContext);\n  const completeCaseType = useStore(store, (state) => state.completeCaseType);\n  const activeStep = useStore(store, (state) => state.activeStep);\n  const stepOrder = useStore(store, (state) => state.stepOrder);\n\n  const stepLabels = useMemo<Record<UPLOAD_STEP, string>>(() => {\n    return {\n      [UPLOAD_STEP.CREATE_CASES]: t`Submit`,\n      [UPLOAD_STEP.MAP_COLUMNS]: t`Map columns`,\n      [UPLOAD_STEP.MAP_SEQUENCES]: t`Map sequences`,\n      [UPLOAD_STEP.PREVIEW]: t`Preview`,\n      [UPLOAD_STEP.SELECT_FILE]: t`Select file`,\n      [UPLOAD_STEP.SELECT_SEQUENCE_FILES]: t`Select sequence files`,\n    };\n  }, [t]);\n\n  const optionalSteps = useMemo<UPLOAD_STEP[]>(() => {\n    return [\n      UPLOAD_STEP.SELECT_SEQUENCE_FILES,\n      UPLOAD_STEP.MAP_SEQUENCES,\n    ];\n  }, []);\n\n  const steps = useMemo<Step[]>(() => {\n    return stepOrder.map((step) => ({\n      key: String(step),\n      label: stepLabels[step],\n      optional: optionalSteps.includes(step),\n    }));\n  }, [optionalSteps, stepLabels, stepOrder]);\n\n  return (\n    <Box\n      sx={{\n        display: 'grid',\n        gridTemplateRows: 'max-content auto',\n        height: '100%',\n        position: 'relative',\n        width: '100%',\n      }}\n    >\n      <Container>\n        <Stepper\n          activeStep={String(activeStep)}\n          steps={steps}\n          sx={{\n            marginY: 2,\n      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