Examples with MolgenisDataException org.molgenis.data.MolgenisDataException used on opensource projects

Example 1 with MolgenisDataException

use of org.molgenis.data.MolgenisDataException in project molgenis by molgenis.

the class ExcelUtils method renameSheet.

public static void renameSheet(String newSheetname, File file, int index) {
    try (FileInputStream fis = new FileInputStream(file);
        Workbook workbook = WorkbookFactory.create(fis)) {
        workbook.setSheetName(index, newSheetname);
        workbook.write(new FileOutputStream(file));
    } catch (Exception e) {
        throw new MolgenisDataException(e);
    }
}

Example 2 with MolgenisDataException

use of org.molgenis.data.MolgenisDataException in project molgenis by molgenis.

the class ImportServiceFactory method getImportService.

public ImportService getImportService(String fileName) {
    final Map<String, ImportService> importServicesMappedToExtensions = Maps.newHashMap();
    for (ImportService importService : importServices) {
        for (String extension : importService.getSupportedFileExtensions()) {
            importServicesMappedToExtensions.put(extension.toLowerCase(), importService);
        }
    }
    String extension = FileExtensionUtils.findExtensionFromPossibilities(fileName, importServicesMappedToExtensions.keySet());
    final ImportService importService = importServicesMappedToExtensions.get(extension);
    if (importService == null)
        throw new MolgenisDataException("Can not import file. No suitable importer found");
    return importService;
}

Example 3 with MolgenisDataException

use of org.molgenis.data.MolgenisDataException in project molgenis by molgenis.

the class ImportServiceFactory method getImportService.

/**
 * Finds a suitable ImportService for a FileRepositoryCollection.
 * <p>
 * Import of mixed backend types in one FileRepositoryCollection isn't supported.
 *
 * @return ImportService
 * @throws MolgenisDataException if no suitable ImportService is found for the FileRepositoryCollection
 */
public ImportService getImportService(File file, RepositoryCollection source) {
    final Map<String, ImportService> importServicesMappedToExtensions = Maps.newHashMap();
    importServices.stream().filter(importService -> importService.canImport(file, source)).forEach(importService -> {
        for (String extension : importService.getSupportedFileExtensions()) {
            importServicesMappedToExtensions.put(extension.toLowerCase(), importService);
        }
    });
    String extension = FileExtensionUtils.findExtensionFromPossibilities(file.getName(), importServicesMappedToExtensions.keySet());
    final ImportService importService = importServicesMappedToExtensions.get(extension);
    if (importService == null)
        throw new MolgenisDataException("Can not import file. No suitable importer found");
    return importService;
}

Example 4 with MolgenisDataException

use of org.molgenis.data.MolgenisDataException in project molgenis by molgenis.

the class DynamicEntity method validateValueType.

/**
 * Validate is value is of the type defined by the attribute data type.
 *
 * @param attrName attribute name
 * @param value    value (must be of the type defined by the attribute data type.)
 */
protected void validateValueType(String attrName, Object value) {
    if (value == null) {
        return;
    }
    Attribute attr = entityType.getAttribute(attrName);
    if (attr == null) {
        throw new UnknownAttributeException(entityType, attrName);
    }
    AttributeType dataType = attr.getDataType();
    switch(dataType) {
        case BOOL:
            if (!(value instanceof Boolean)) {
                throw new MolgenisDataException(format("Value [%s] is of type [%s] instead of [%s] for attribute: [%s]", value.toString(), value.getClass().getSimpleName(), Boolean.class.getSimpleName(), attrName));
            }
            break;
        case CATEGORICAL:
        // expected type is FileMeta. validation is not possible because molgenis-data does not depend on molgenis-file
        case FILE:
        case XREF:
            if (!(value instanceof Entity)) {
                throw new MolgenisDataException(format("Value [%s] is of type [%s] instead of [%s] for attribute: [%s]", value.toString(), value.getClass().getSimpleName(), Entity.class.getSimpleName(), attrName));
            }
            break;
        case CATEGORICAL_MREF:
        case MREF:
        case ONE_TO_MANY:
            if (!(value instanceof Iterable)) {
                throw new MolgenisDataException(format("Value [%s] is of type [%s] instead of [%s] for attribute: [%s]", value.toString(), value.getClass().getSimpleName(), Iterable.class.getSimpleName(), attrName));
            }
            break;
        case COMPOUND:
            throw new IllegalArgumentException(format("Unexpected data type [%s] for attribute: [%s]", dataType.toString(), attrName));
        case DATE:
            if (!(value instanceof LocalDate)) {
                throw new MolgenisDataException(format("Value [%s] is of type [%s] instead of [%s] for attribute: [%s]", value.toString(), value.getClass().getSimpleName(), LocalDate.class.getSimpleName(), attrName));
            }
            break;
        case DATE_TIME:
            if (!(value instanceof Instant)) {
                throw new MolgenisDataException(format("Value [%s] is of type [%s] instead of [%s] for attribute: [%s]", value.toString(), value.getClass().getSimpleName(), Instant.class.getSimpleName(), attrName));
            }
            break;
        case DECIMAL:
            if (!(value instanceof Double)) {
                throw new MolgenisDataException(format("Value [%s] is of type [%s] instead of [%s] for attribute: [%s]", value.toString(), value.getClass().getSimpleName(), Double.class.getSimpleName(), attrName));
            }
            if (((Double) value).isNaN()) {
                throw new MolgenisDataException(format("Value [%s] for type [%s] is not allowed for attribute: [%s]", value.toString(), Double.class.getSimpleName(), attrName));
            }
            break;
        case EMAIL:
        case ENUM:
        case HTML:
        case HYPERLINK:
        case SCRIPT:
        case STRING:
        case TEXT:
            if (!(value instanceof String)) {
                throw new MolgenisDataException(format("Value [%s] is of type [%s] instead of [%s] for attribute: [%s]", value.toString(), value.getClass().getSimpleName(), String.class.getSimpleName(), attrName));
            }
            break;
        case INT:
            if (!(value instanceof Integer)) {
                throw new MolgenisDataException(format("Value [%s] is of type [%s] instead of [%s] for attribute: [%s]", value.toString(), value.getClass().getSimpleName(), Integer.class.getSimpleName(), attrName));
            }
            break;
        case LONG:
            if (!(value instanceof Long)) {
                throw new MolgenisDataException(format("Value [%s] is of type [%s] instead of [%s] for attribute: [%s]", value.toString(), value.getClass().getSimpleName(), Long.class.getSimpleName(), attrName));
            }
            break;
        default:
            throw new UnexpectedEnumException(dataType);
    }
}

Example 5 with MolgenisDataException

use of org.molgenis.data.MolgenisDataException in project molgenis by molgenis.

the class NegotiatorController method validateNegotiatorExport.

@PostMapping("/validate")
@ResponseBody
public ExportValidationResponse validateNegotiatorExport(@RequestBody NegotiatorRequest request) {
    boolean isValidRequest = true;
    String message = "";
    List<String> enabledCollectionsLabels;
    List<String> disabledCollectionLabels;
    NegotiatorEntityConfig entityConfig = getNegotiatorEntityConfig(request.getEntityId());
    if (null != entityConfig) {
        LOG.info("Validating negotiator request\n\n{}", request);
        List<Entity> collectionEntities = getCollectionEntities(request);
        List<Entity> disabledCollections = getDisabledCollections(collectionEntities, entityConfig);
        Function<Entity, String> getLabel = entity -> entity.getLabelValue().toString();
        disabledCollectionLabels = disabledCollections.stream().map(getLabel).collect(toList());
        enabledCollectionsLabels = collectionEntities.stream().filter(e -> !disabledCollections.contains(e)).map(getLabel).collect(toList());
        if (!disabledCollections.isEmpty()) {
            message = messageSource.getMessage("dataexplorer_directory_disabled", new Object[] { disabledCollections.size(), collectionEntities.size() }, getLocale());
        }
        if (collectionEntities.isEmpty() || (collectionEntities.size() == disabledCollections.size())) {
            isValidRequest = false;
            message = messageSource.getMessage("dataexplorer_directory_no_rows", new Object[] {}, getLocale());
        }
    } else {
        throw new MolgenisDataException(messageSource.getMessage("dataexplorer_directory_no_config", new Object[] {}, getLocale()));
    }
    return ExportValidationResponse.create(isValidRequest, message, enabledCollectionsLabels, disabledCollectionLabels);
}