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

Example 11 with MolgenisDataException

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

the class PackageWizardPage method handleRequest.

@Override
public String handleRequest(HttpServletRequest request, BindingResult result, Wizard wizard) {
    ImportWizardUtil.validateImportWizard(wizard);
    ImportWizard importWizard = (ImportWizard) wizard;
    String entityImportOption = importWizard.getEntityImportOption();
    if (entityImportOption != null) {
        try {
            // convert input to database action
            DatabaseAction entityDbAction = ImportWizardUtil.toDatabaseAction(entityImportOption);
            if (entityDbAction == null) {
                throw new IOException("unknown database action: " + entityImportOption);
            }
            RepositoryCollection repositoryCollection = fileRepositoryCollectionFactory.createFileRepositoryCollection(importWizard.getFile());
            ImportService importService = importServiceFactory.getImportService(importWizard.getFile(), repositoryCollection);
            // Do integration test only if there are no previous errors found
            if (!importWizard.getEntitiesImportable().containsValue(false)) {
                // The package name that is selected in the "package selection" page
                String selectedPackage = request.getParameter("selectedPackage");
                // The entities that can be imported
                Map<String, Boolean> entitiesImportable = importService.determineImportableEntities(metaDataService, repositoryCollection, selectedPackage);
                // The results of the attribute checks are stored in maps with the entityname as key, those need to be updated with the packagename
                updateFieldReports(importWizard, selectedPackage, entitiesImportable);
                // Set the entities that can be imported
                importWizard.setEntitiesImportable(entitiesImportable);
                // The entities that can not be imported. If even one entity can not be imported, everything fails
                List<String> entitiesNotImportable = entitiesImportable.entrySet().stream().filter(entity -> !entity.getValue()).map(Map.Entry::getKey).collect(toList());
                if (!entitiesNotImportable.isEmpty()) {
                    throw new MolgenisDataException("You are trying to upload entities that are not compatible with the already existing entities: " + entitiesNotImportable.toString());
                }
            }
        } catch (RuntimeException | IOException e) {
            ImportWizardUtil.handleException(e, importWizard, result, LOG, entityImportOption);
        }
    }
    return null;
}

Example 12 with MolgenisDataException

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

the class OptionsWizardPage method handleRequest.

@Override
public String handleRequest(HttpServletRequest request, BindingResult result, Wizard wizard) {
    ImportWizardUtil.validateImportWizard(wizard);
    ImportWizard importWizard = (ImportWizard) wizard;
    String entityImportOption = request.getParameter("entity_option");
    importWizard.setEntityImportOption(entityImportOption);
    if (importWizard.getMustChangeEntityName()) {
        String userGivenName = request.getParameter("name");
        if (StringUtils.isEmpty(userGivenName)) {
            result.addError(new ObjectError("wizard", "Please enter an entity name"));
            return null;
        }
        try {
            NameValidator.validateEntityName(userGivenName);
            if (dataService.hasRepository(userGivenName)) {
                result.addError(new ObjectError("wizard", "An entity with this name already exists."));
                return null;
            }
        } catch (MolgenisDataException e) {
            ImportWizardUtil.handleException(e, importWizard, result, LOG, entityImportOption);
            return null;
        }
        File tmpFile = importWizard.getFile();
        String fileName = tmpFile.getName();
        // FIXME: can this be done a bit cleaner?
        String extension = FileExtensionUtils.findExtensionFromPossibilities(fileName, fileRepositoryCollectionFactory.createFileRepositoryCollection(tmpFile).getFileNameExtensions());
        File file = new File(tmpFile.getParent(), userGivenName + "." + extension);
        if (!tmpFile.renameTo(file)) {
            LOG.error("Failed to rename '{}' to '{}'", tmpFile.getName(), file.getName());
        }
        importWizard.setFile(file);
    }
    try {
        return validateInput(importWizard.getFile(), importWizard, result);
    } catch (Exception e) {
        ImportWizardUtil.handleException(e, importWizard, result, LOG, entityImportOption);
    }
    return null;
}

Example 13 with MolgenisDataException

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

the class EntityTypeRepositorySecurityDecorator method isOperationPermitted.

@Override
public boolean isOperationPermitted(Object id, Action action) {
    AbstractPermission permission = getPermissionForOperation(action);
    boolean hasPermission = userPermissionEvaluator.hasPermission(new EntityTypeIdentity(id.toString()), permission);
    if (hasPermission && !permission.equals(EntityTypePermission.COUNT)) {
        boolean isSystem = systemEntityTypeRegistry.hasSystemEntityType(id.toString());
        if (isSystem && !currentUserIsSystem()) {
            throw new MolgenisDataException(format("No [%s] permission on EntityType [%s]", toMessagePermission(action), id));
        }
    }
    return hasPermission;
}

Example 14 with MolgenisDataException

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

the class RestService method convertMref.

private List<?> convertMref(Attribute attr, Object paramValue) {
    List<?> value;
    if (paramValue != null) {
        List<?> mrefParamValues;
        if (paramValue instanceof String) {
            mrefParamValues = asList(StringUtils.split((String) paramValue, ','));
        } else if (paramValue instanceof List<?>) {
            mrefParamValues = (List<?>) paramValue;
        } else {
            throw new MolgenisDataException(format("Attribute [%s] value is of type [%s] instead of [%s] or [%s]", attr.getName(), paramValue.getClass().getSimpleName(), String.class.getSimpleName(), List.class.getSimpleName()));
        }
        EntityType mrefEntity = attr.getRefEntity();
        Attribute mrefEntityIdAttr = mrefEntity.getIdAttribute();
        value = mrefParamValues.stream().map(mrefParamValue -> toEntityValue(mrefEntityIdAttr, mrefParamValue, null)).map(mrefIdValue -> entityManager.getReference(mrefEntity, mrefIdValue)).collect(toList());
    } else {
        value = emptyList();
    }
    return value;
}

Example 15 with MolgenisDataException

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

the class MultiAllelicResultFilterTest method filterResultsMergeMultilineMismatchPos.

@Test
public void filterResultsMergeMultilineMismatchPos() {
    MultiAllelicResultFilter filter = new MultiAllelicResultFilter(Collections.singletonList(attributeFactory.create().setName("annotation").setDataType(STRING)), true, vcfAttributes);
    try {
        filter.filterResults(Arrays.asList(entityMismatchPos, resultEntity10), entity10, false);
        Assert.fail("Should throw exception for mismatching positions");
    } catch (MolgenisDataException actual) {
        assertEquals(actual.getMessage(), "Mismatch in location! Location{chrom=1, pos=101} vs Location{chrom=1, pos=100}");
    }
}