Java Code Examples for org.springframework.util.Assert

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Example 1
Project: NGB-master   File: ProjectManager.java   View source code 7 votes vote down vote up
private boolean checkNewProject(Project helpProject) {
    Project existingProject = projectDao.loadProject(helpProject.getName());

    boolean newProject = false;
    if (helpProject.getId() == null) {
        helpProject.setCreatedBy(AuthUtils.getCurrentUserId());
        helpProject.setCreatedDate(new Date());

        // for new project ensure that there is no project with this name
        Assert.isNull(existingProject, MessageHelper.getMessage(MessagesConstants.ERROR_PROJECT_NAME_EXISTS,
                                                                helpProject.getName()));
        newProject = true;
    } else {
        // for updated one - ensure that if there is a project with that name,
        // its ID is equal to this project's id
        Assert.isTrue(existingProject == null || existingProject.getId().equals(helpProject.getId()),
                      MessageHelper.getMessage(MessagesConstants.ERROR_PROJECT_NAME_EXISTS, helpProject.getName()));
    }
    return newProject;
}
 
Example 2
Project: lams   File: TagUtils.java   View source code 6 votes vote down vote up
/**
 * Determine whether the supplied {@link Tag} has any ancestor tag
 * of the supplied type.
 * @param tag the tag whose ancestors are to be checked
 * @param ancestorTagClass the ancestor {@link Class} being searched for
 * @return {@code true} if the supplied {@link Tag} has any ancestor tag
 * of the supplied type
 * @throws IllegalArgumentException if either of the supplied arguments is {@code null};
 * or if the supplied {@code ancestorTagClass} is not type-assignable to
 * the {@link Tag} class
 */
public static boolean hasAncestorOfType(Tag tag, Class<?> ancestorTagClass) {
	Assert.notNull(tag, "Tag cannot be null");
	Assert.notNull(ancestorTagClass, "Ancestor tag class cannot be null");
	if (!Tag.class.isAssignableFrom(ancestorTagClass)) {
		throw new IllegalArgumentException(
				"Class '" + ancestorTagClass.getName() + "' is not a valid Tag type");
	}
	Tag ancestor = tag.getParent();
	while (ancestor != null) {
		if (ancestorTagClass.isAssignableFrom(ancestor.getClass())) {
			return true;
		}
		ancestor = ancestor.getParent();
	}
	return false;
}
 
Example 3
Project: esup-ecandidat   File: CommissionController.java   View source code 6 votes vote down vote up
/**
 * Ouvre une fenêtre d'édition de commission.
 *
 * @param commission
 */
public void editCommission(final Commission commission, final Boolean isAdmin) {
	Assert.notNull(commission, applicationContext.getMessage("assert.notNull", null, UI.getCurrent().getLocale()));

	/* Verrou */
	if (!lockController.getLockOrNotify(commission, null)) {
		return;
	}
	if (commission.getI18nCommentRetourComm() == null) {
		commission.setI18nCommentRetourComm(
				new I18n(i18nController.getTypeTraduction(NomenclatureUtils.TYP_TRAD_COMM_COMMENT_RETOUR)));
	}
	CtrCandCommissionWindow window = new CtrCandCommissionWindow(commission, isAdmin);
	window.addCloseListener(e -> lockController.releaseLock(commission));
	UI.getCurrent().addWindow(window);
}
 
Example 4
Project: lams   File: HibernateTemplate.java   View source code 6 votes vote down vote up
@Override
public List<?> findByCriteria(final DetachedCriteria criteria, final int firstResult, final int maxResults)
		throws DataAccessException {

	Assert.notNull(criteria, "DetachedCriteria must not be null");
	return executeWithNativeSession(new HibernateCallback<List<?>>() {
		@Override
		@SuppressWarnings("unchecked")
		public List<?> doInHibernate(Session session) throws HibernateException {
			Criteria executableCriteria = criteria.getExecutableCriteria(session);
			prepareCriteria(executableCriteria);
			if (firstResult >= 0) {
				executableCriteria.setFirstResult(firstResult);
			}
			if (maxResults > 0) {
				executableCriteria.setMaxResults(maxResults);
			}
			return executableCriteria.list();
		}
	});
}
 
Example 5
Project: dswork   File: HibernateDao.java   View source code 6 votes vote down vote up
/**
 * 创建Query对象
 * @param hql HQL语句
 * @param values 可变条件
 * @return Query
 */
protected Query createQuery(final String hql, final Object... values)
{
	Assert.hasText(hql);
	Query query = (Query)getHibernateTemplate().execute(new HibernateCallback()
	{
		public Query doInHibernate(Session session) throws HibernateException//, SQLException
		{
			return session.createQuery(hql);
		}
	});
	for(int i = 0; i < values.length; i++)
	{
		query.setParameter(i, values[i]);
	}
	return query;
}
 
Example 6
Project: Spring-Security-Third-Edition   File: JpaMutableAclService.java   View source code 6 votes vote down vote up
/**
 * This implementation will simply delete all ACEs in the database and recreate them on each invocation of
 * this method. A more comprehensive implementation might use dirty state checking, or more likely use ORM
 * capabilities for create, update and delete operations of {@link MutableAcl}.
 */
@Override
public MutableAcl updateAcl(MutableAcl acl) throws NotFoundException {
    Assert.notNull(acl.getId(), "Object Identity doesn't provide an identifier");

    // Delete this ACL's ACEs in the acl_entry table
    aclDao.deleteEntries(retrieveObjectIdentityPrimaryKey(acl.getObjectIdentity()));

    // Create this ACL's ACEs in the acl_entry table
    createEntries(acl);

    // Change the mutable columns in acl_object_identity
    updateObjectIdentity(acl);

    // Clear the cache, including children
    clearCacheIncludingChildren(acl.getObjectIdentity());

    // Retrieve the ACL via superclass (ensures cache registration, proper retrieval etc)
    return (MutableAcl) readAclById(acl.getObjectIdentity());
}
 
Example 7
Project: lams   File: ClassPathBeanDefinitionScanner.java   View source code 6 votes vote down vote up
/**
 * Perform a scan within the specified base packages,
 * returning the registered bean definitions.
 * <p>This method does <i>not</i> register an annotation config processor
 * but rather leaves this up to the caller.
 * @param basePackages the packages to check for annotated classes
 * @return set of beans registered if any for tooling registration purposes (never {@code null})
 */
protected Set<BeanDefinitionHolder> doScan(String... basePackages) {
	Assert.notEmpty(basePackages, "At least one base package must be specified");
	Set<BeanDefinitionHolder> beanDefinitions = new LinkedHashSet<BeanDefinitionHolder>();
	for (String basePackage : basePackages) {
		Set<BeanDefinition> candidates = findCandidateComponents(basePackage);
		for (BeanDefinition candidate : candidates) {
			ScopeMetadata scopeMetadata = this.scopeMetadataResolver.resolveScopeMetadata(candidate);
			candidate.setScope(scopeMetadata.getScopeName());
			String beanName = this.beanNameGenerator.generateBeanName(candidate, this.registry);
			if (candidate instanceof AbstractBeanDefinition) {
				postProcessBeanDefinition((AbstractBeanDefinition) candidate, beanName);
			}
			if (candidate instanceof AnnotatedBeanDefinition) {
				AnnotationConfigUtils.processCommonDefinitionAnnotations((AnnotatedBeanDefinition) candidate);
			}
			if (checkCandidate(beanName, candidate)) {
				BeanDefinitionHolder definitionHolder = new BeanDefinitionHolder(candidate, beanName);
				definitionHolder = AnnotationConfigUtils.applyScopedProxyMode(scopeMetadata, definitionHolder, this.registry);
				beanDefinitions.add(definitionHolder);
				registerBeanDefinition(definitionHolder, this.registry);
			}
		}
	}
	return beanDefinitions;
}
 
Example 8
Project: lams   File: SessionFactoryUtils.java   View source code 6 votes vote down vote up
/**
 * Process all Hibernate Sessions that have been registered for deferred close
 * for the given SessionFactory.
 * @param sessionFactory the Hibernate SessionFactory to process deferred close for
 * @see #initDeferredClose
 * @see #releaseSession
 */
public static void processDeferredClose(SessionFactory sessionFactory) {
	Assert.notNull(sessionFactory, "No SessionFactory specified");
	Map<SessionFactory, Set<Session>> holderMap = deferredCloseHolder.get();
	if (holderMap == null || !holderMap.containsKey(sessionFactory)) {
		throw new IllegalStateException("Deferred close not active for SessionFactory [" + sessionFactory + "]");
	}
	logger.debug("Processing deferred close of Hibernate Sessions");
	Set<Session> sessions = holderMap.remove(sessionFactory);
	for (Session session : sessions) {
		closeSession(session);
	}
	if (holderMap.isEmpty()) {
		deferredCloseHolder.remove();
	}
}
 
Example 9
Project: lams   File: AbstractJdbcCall.java   View source code 6 votes vote down vote up
/**
 * Add a declared parameter to the list of parameters for the call.
 * Only parameters declared as {@code SqlParameter} and {@code SqlInOutParameter}
 * will be used to provide input values. This is different from the {@code StoredProcedure} class
 * which for backwards compatibility reasons allows input values to be provided for parameters declared
 * as {@code SqlOutParameter}.
 * @param parameter the {@link SqlParameter} to add
 */
public void addDeclaredParameter(SqlParameter parameter) {
	Assert.notNull(parameter, "The supplied parameter must not be null");
	if (!StringUtils.hasText(parameter.getName())) {
		throw new InvalidDataAccessApiUsageException(
				"You must specify a parameter name when declaring parameters for \"" + getProcedureName() + "\"");
	}
	this.declaredParameters.add(parameter);
	if (logger.isDebugEnabled()) {
		logger.debug("Added declared parameter for [" + getProcedureName() + "]: " + parameter.getName());
	}
}
 
Example 10
Project: spring-data-generator   File: AbstractTemplateProvider.java   View source code 6 votes vote down vote up
public AbstractTemplateProvider(CustomResourceLoader customResourceLoader) {
    Assert.notNull(customResourceLoader, "CustomResourceLoader must not be null!");
    this.postfix = customResourceLoader.getPostfix();
    this.debug = true;
    this.excludeClasses = new Class[]{};
    this.overwrite = customResourceLoader.isOverwrite();
}
 
Example 11
Project: NGB-master   File: ReferenceGenomeManager.java   View source code 6 votes vote down vote up
/**
 * Saves metadata information about a reference genome that should become available in the
 * system.
 *
 * @param reference {@code Reference} represents a reference genome metadata that should be
 *                  stored in the system.
 * @return {@code Reference} is the same with the passed one to this call, but after succeeded
 * call it provides access to ID values
 * @throws IllegalArgumentException will be thrown if reference ID isn't specified or reference
 *                                  doesn't provide information about related chromosomes
 */
@Transactional(propagation = Propagation.REQUIRED)
public Reference register(final Reference reference) {
    Assert.isTrue(CollectionUtils.isNotEmpty(reference.getChromosomes()),
            getMessage("error.reference.aborted.saving.chromosomes"));
    Assert.notNull(reference.getId(), getMessage(MessageCode.UNKNOWN_REFERENCE_ID));
    biologicalDataItemDao.createBiologicalDataItem(reference.getIndex());
    if (reference.getCreatedDate() == null) {
        reference.setCreatedDate(new Date());
    }
    reference.setCreatedBy(AuthUtils.getCurrentUserId());
    if (reference.getType() == null) {
        reference.setType(BiologicalDataItemResourceType.FILE);
    }
    if (reference.getBioDataItemId() == null) {
        final Long referenceId = reference.getId();
        biologicalDataItemDao.createBiologicalDataItem(reference);
        referenceGenomeDao.createReferenceGenome(reference, referenceId);
    } else {
        referenceGenomeDao.createReferenceGenome(reference);
    }
    referenceGenomeDao.saveChromosomes(reference.getId(), reference.getChromosomes());
    return reference;
}
 
Example 12
Project: lams   File: BeanFactoryUtils.java   View source code 6 votes vote down vote up
/**
 * Get all bean names for the given type, including those defined in ancestor
 * factories. Will return unique names in case of overridden bean definitions.
 * <p>Does consider objects created by FactoryBeans if the "allowEagerInit"
 * flag is set, which means that FactoryBeans will get initialized. If the
 * object created by the FactoryBean doesn't match, the raw FactoryBean itself
 * will be matched against the type. If "allowEagerInit" is not set,
 * only raw FactoryBeans will be checked (which doesn't require initialization
 * of each FactoryBean).
 * @param lbf the bean factory
 * @param includeNonSingletons whether to include prototype or scoped beans too
 * or just singletons (also applies to FactoryBeans)
 * @param allowEagerInit whether to initialize <i>lazy-init singletons</i> and
 * <i>objects created by FactoryBeans</i> (or by factory methods with a
 * "factory-bean" reference) for the type check. Note that FactoryBeans need to be
 * eagerly initialized to determine their type: So be aware that passing in "true"
 * for this flag will initialize FactoryBeans and "factory-bean" references.
 * @param type the type that beans must match
 * @return the array of matching bean names, or an empty array if none
 */
public static String[] beanNamesForTypeIncludingAncestors(
		ListableBeanFactory lbf, Class<?> type, boolean includeNonSingletons, boolean allowEagerInit) {

	Assert.notNull(lbf, "ListableBeanFactory must not be null");
	String[] result = lbf.getBeanNamesForType(type, includeNonSingletons, allowEagerInit);
	if (lbf instanceof HierarchicalBeanFactory) {
		HierarchicalBeanFactory hbf = (HierarchicalBeanFactory) lbf;
		if (hbf.getParentBeanFactory() instanceof ListableBeanFactory) {
			String[] parentResult = beanNamesForTypeIncludingAncestors(
					(ListableBeanFactory) hbf.getParentBeanFactory(), type, includeNonSingletons, allowEagerInit);
			List<String> resultList = new ArrayList<String>();
			resultList.addAll(Arrays.asList(result));
			for (String beanName : parentResult) {
				if (!resultList.contains(beanName) && !hbf.containsLocalBean(beanName)) {
					resultList.add(beanName);
				}
			}
			result = StringUtils.toStringArray(resultList);
		}
	}
	return result;
}
 
Example 13
Project: otter-G   File: MainstemMonitor.java   View source code 6 votes vote down vote up
/**
 * 更新mainStem的同步状态数据
 */
public void single(MainStemEventData data) {
    Assert.notNull(data);
    Long nid = ArbitrateConfigUtils.getCurrentNid();
    if (!check()) {
        return;
    }

    data.setNid(nid);// 设置当前的nid
    String path = StagePathUtils.getMainStem(data.getPipelineId());
    byte[] bytes = JsonUtils.marshalToByte(data);// 初始化的数据对象
    try {
        zookeeper.writeData(path, bytes);
    } catch (ZkException e) {
        throw new ArbitrateException("mainStem_single", data.toString(), e);
    }
    activeData = data;
}
 
Example 14
Project: springboot-shiro-cas-mybatis   File: DefaultHandlerResult.java   View source code 6 votes vote down vote up
/**
 * Instantiates a new handler result.
 *
 * @param source the source
 * @param metaData the meta data
 * @param p the p
 * @param warnings the warnings
 */
public DefaultHandlerResult(
        final AuthenticationHandler source,
        final CredentialMetaData metaData,
        final Principal p,
        final List<MessageDescriptor> warnings) {
    Assert.notNull(source, "Source cannot be null.");
    Assert.notNull(metaData, "Credential metadata cannot be null.");
    this.handlerName = source.getName();
    if (!StringUtils.hasText(this.handlerName)) {
        this.handlerName = source.getClass().getSimpleName();
    }
    this.credentialMetaData = metaData;
    this.principal = p;
    this.warnings = warnings;
}
 
Example 15
Project: gemini.blueprint   File: BootstrappingDependenciesEvent.java   View source code 6 votes vote down vote up
/**
 * Constructs a new <code>BootstrappingDependencyEvent</code> instance.
 * 
 * @param source
 */
public BootstrappingDependenciesEvent(ApplicationContext source, Bundle bundle,
		Collection<OsgiServiceDependencyEvent> nestedEvents, Filter filter, long timeLeft) {
	super(source, bundle);
	Assert.notNull(nestedEvents);
	this.dependencyEvents = nestedEvents;
	this.dependenciesFilter = filter;
	this.timeLeft = timeLeft;

	List<String> depFilters = new ArrayList<String>(dependencyEvents.size());

	for (OsgiServiceDependencyEvent dependency : nestedEvents) {
		depFilters.add(dependency.getServiceDependency().getServiceFilter().toString());
	}

	dependencyFilters = Collections.unmodifiableCollection(depFilters);
}
 
Example 16
Project: spring-i18n-support   File: MessageManagementServiceImpl.java   View source code 6 votes vote down vote up
/**
 * {@inheritDoc}
 *
 * @see MessageManagementService#putMessage(java.lang.String, java.util.Locale,
 * java.lang.String)
 */
@Override
public void putMessage(String codeId,
                       Locale locale,
                       String message,
                       String type) throws I18nException {
	Assert.hasLength(codeId);
	Assert.notNull(locale);
	LocaleUtils.toLocale(locale.toString()); // this validates the locale
	Assert.hasLength(message);
	MessageResource persisted = this.messageSourceDao.findTopByCodeAndLang(codeId, locale.toString());
	if (persisted != null) {
		//update case
		persisted.message(message).type(type);
	} else {
		//insert case
		persisted = new MessageResource()
				.code(codeId)
				.lang(locale.toString())
				.message(message)
				.type(type);
		persisted.id((type == null ? "" : type) + codeId + locale.toString());
	}
	this.messageSourceDao.save(persisted);
}
 
Example 17
Project: NGB-master   File: FeatureIndexDao.java   View source code 6 votes vote down vote up
private String getGroupByField(List<VcfFile> files, String groupBy) throws IOException {
    IndexSortField sortField = IndexSortField.getByName(groupBy);
    if (sortField == null) {
        VcfFilterInfo info = vcfManager.getFiltersInfo(
            files.stream().map(BaseEntity::getId).collect(Collectors.toList()));

        InfoItem infoItem = info.getInfoItemMap().get(groupBy);
        Assert.notNull(infoItem, "Unknown sort field: " + groupBy);

        if (infoItem.getType() == VCFHeaderLineType.Integer || infoItem.getType() == VCFHeaderLineType.Float) {
            return FeatureIndexFields.getGroupName(infoItem.getName().toLowerCase());
        } else {
            return infoItem.getName().toLowerCase();
        }
    } else {
        if (sortField.getType() == SortField.Type.INT || sortField.getType() == SortField.Type.FLOAT) {
            return sortField.getField().getGroupName();
        } else {
            return sortField.getField().fieldName;
        }
    }
}
 
Example 18
Project: lams   File: EhCacheCacheManager.java   View source code 6 votes vote down vote up
@Override
protected Collection<Cache> loadCaches() {
	net.sf.ehcache.CacheManager cacheManager = getCacheManager();
	Assert.notNull(cacheManager, "A backing EhCache CacheManager is required");
	Status status = cacheManager.getStatus();
	Assert.isTrue(Status.STATUS_ALIVE.equals(status),
			"An 'alive' EhCache CacheManager is required - current cache is " + status.toString());

	String[] names = cacheManager.getCacheNames();
	Collection<Cache> caches = new LinkedHashSet<Cache>(names.length);
	for (String name : names) {
		caches.add(new EhCacheCache(cacheManager.getEhcache(name)));
	}
	return caches;
}
 
Example 19
Project: gemini.blueprint   File: DefaultFrameworkTemplate.java   View source code 6 votes vote down vote up
public DefaultFrameworkTemplate(Object target, Log log) {
	if (OsgiPlatformDetector.isR42()) {
		Assert.isInstanceOf(Framework.class, target);
		fwk = (Framework) target;
	} else {
		throw new IllegalStateException("Cannot use OSGi 4.2 Framework API in an OSGi 4.1 environment");
	}
	this.log = log;
}
 
Example 20
Project: NGB-master   File: ReferenceGenomeManager.java   View source code 6 votes vote down vote up
/**
 * Deletes a {@code Reference} instance from the server and database
 * @param reference an instnce to delete
 */
@Transactional(propagation = Propagation.REQUIRED)
public void unregister(final Reference reference) {
    Assert.notNull(reference, MessagesConstants.ERROR_INVALID_PARAM);
    Assert.notNull(reference.getId(), MessagesConstants.ERROR_INVALID_PARAM);

    if (reference.getType() != BiologicalDataItemResourceType.GA4GH) {
        List<Project> projectsWhereFileInUse = projectDao.loadProjectsByBioDataItemId(
                reference.getBioDataItemId());
        Assert.isTrue(projectsWhereFileInUse.isEmpty(), getMessage(MessagesConstants.ERROR_FILE_IN_USE,
                reference.getName(), reference.getId(), projectsWhereFileInUse.stream().map(BaseEntity::getName)
                        .collect(Collectors.joining(", "))));
        List<BaseEntity> fileList = loadAllFile(reference.getId());
        Assert.isTrue(fileList.isEmpty(), getMessage(MessagesConstants.ERROR_FILE_IN_LINK,
                reference.getName(), reference.getId(), fileList.stream().map(BaseEntity::getName)
                        .collect(Collectors.joining(", "))));
    }
    referenceGenomeDao.unregisterReferenceGenome(reference.getId());
    biologicalDataItemDao.deleteBiologicalDataItem(reference.getBioDataItemId());
}
 
Example 21
Project: spring-data-ebean   File: ParameterBinder.java   View source code 6 votes vote down vote up
/**
 * Binds the parameters to the given {@link Query}.
 *
 * @param query must not be {@literal null}.
 * @return
 */
public Object bind(Object query) {

    Assert.notNull(query, "Query must not be null!");

    int bindableParameterIndex = 0;
    int queryParameterPosition = 1;

    for (Parameter parameter : parameters) {

        if (canBindParameter(parameter)) {

            Object value = accessor.getBindableValue(bindableParameterIndex);
            bind(query, parameter, value, queryParameterPosition++);
            bindableParameterIndex++;
        }
    }

    return query;
}
 
Example 22
Project: sjk   File: AppServiceImpl.java   View source code 6 votes vote down vote up
@Override
public long getLatestCount(short catalog, Integer subCatalog, Long date, Integer noAds, Integer noVirus, Integer official) {
    Assert.isTrue(catalog > 0, "catalog negative!");
    if (subCatalog != null) {
        Assert.isTrue(subCatalog > -1, "date negative!");
    }
    if (date != null) {
        Assert.isTrue(date > -1, "date negative!");
    }
    Boolean bNoAds = null, bOfficial = null;
    if (noAds != null && noAds.intValue() == 1) {
        bNoAds = Boolean.TRUE;
    }
    if (official != null && official.intValue() == 1) {
        bOfficial = Boolean.TRUE;
    }
    Date startDate = null;
    Date endDate = null;
    if (date != null) {
        HighAndLowDate hld = new HighAndLowDate(date);
        startDate = hld.getLow();
        endDate = hld.getHigh();
    }
    return appMapper.getLatestCount(catalog, subCatalog, startDate, endDate, bNoAds, bOfficial);
}
 
Example 23
Project: NGB-master   File: BamManager.java   View source code 6 votes vote down vote up
/**
 * Loads a specific read form a BAM file, specified by ReadQuery object
 * @param query a {@link ReadQuery} object, that specifies a {@link Read} to load
 * @return a {@link Read} object
 * @throws IOException if somwthing goes wrong with the filesystem
 */
public Read loadRead(final ReadQuery query, String fileUrl, String indexUrl) throws IOException {
    Assert.notNull(query, MessagesConstants.ERROR_NULL_PARAM);
    Assert.isTrue(query.getId() != null ||
                  (StringUtils.isNotBlank(fileUrl) && StringUtils.isNotBlank(indexUrl)),
                  MessagesConstants.ERROR_NULL_PARAM);

    Assert.notNull(query.getChromosomeId(), MessagesConstants.ERROR_NULL_PARAM);
    Assert.notNull(query.getStartIndex(), MessagesConstants.ERROR_NULL_PARAM);
    Assert.notNull(query.getEndIndex(), MessagesConstants.ERROR_NULL_PARAM);
    Assert.notNull(query.getName(), MessagesConstants.ERROR_NULL_PARAM);

    final Chromosome chromosome = referenceGenomeManager.loadChromosome(query.getChromosomeId());
    BamFile bamFile;
    if (query.getId() != null) {
        bamFile= bamFileManager.loadBamFile(query.getId());
    } else {
        bamFile = bamHelper.makeUrlBamFile(fileUrl, indexUrl, chromosome.getReferenceId());
    }
    return getReadFromBamFile(query, chromosome, bamFile);
}
 
Example 24
Project: NGB-master   File: ReferenceManager.java   View source code 6 votes vote down vote up
/**
 * Validates and parses the given to make sure that all mandatory properties,
 * describing genome data, are provided.
 * <p>
 * The default values will be assigned in cases when it is possible to do. E.g., to treat omitted
 * custom name for a genome it's possible to use an original name of corresponded file without
 * extension.
 *
 * @param path {@code File}     Path to fasta file
 * @param name {@code String}   Alternative name
 */
private String parse(final String path, final String name) {
    Assert.notNull(path, getMessage(MessageCode.RESOURCE_NOT_FOUND));
    // checks that an original file name is provided, because it is used as a name
    // for a genome if custom name isn't specified
    String fileName = StringUtils.trimToNull(FilenameUtils.getName(path));
    Assert.notNull(fileName, getMessage(MessageCode.MANDATORY_FILE_NAME));
    // checks that file is in one of supported formats
    boolean supported = false;
    final Collection<String> formats = FastaUtils.getFastaExtensions();
    for (final String ext : formats) {
        if (fileName.endsWith(ext)) {
            supported = true;
            fileName = Utils.removeFileExtension(fileName, ext);
            break;
        }
    }
    if (!supported) {
        throw new IllegalArgumentException(getMessage("error.reference.illegal.file.type",
                StringUtils.join(formats, ", ")));
    }
    // if no custom name is provided for a genome, then a file name without extension should be
    // used by default
    return StringUtils.defaultString(StringUtils.trimToNull(name), fileName);
}
 
Example 25
Project: keti   File: GraphGenericRepository.java   View source code 6 votes vote down vote up
/**
 * Returns the entity with attributes only on the requested vertex. No parent attributes are included.
 */
public E getEntity(final ZoneEntity zone, final String identifier) {
    try {
        GraphTraversal<Vertex, Vertex> traversal = this.graphTraversal.V().has(ZONE_ID_KEY, zone.getName())
                .has(getEntityIdKey(), identifier);
        if (!traversal.hasNext()) {
            return null;
        }
        Vertex vertex = traversal.next();
        E entity = vertexToEntity(vertex);

        // There should be only one entity with a given entity id.
        Assert.isTrue(!traversal.hasNext(),
                String.format("There are two entities with the same %s.", getEntityIdKey()));
        return entity;
    } finally {
        this.graphTraversal.tx().commit();
    }
}
 
Example 26
Project: amanda   File: AbstractSelfReferenceRepository.java   View source code 6 votes vote down vote up
@Transactional
@Override
@SuppressWarnings("unchecked")
public void delete(ID id) {

    Assert.notNull(id, "The given id must not be null!");

    // CriteriaBuilder builder = this.entityManager.getCriteriaBuilder();
    // CriteriaDelete<T> query = builder.createCriteriaDelete(domainClass);
    //
    // Root<T> root = query.from(domainClass);
    // this.entityManager.createQuery(query.where(
    //         builder.equal(root.get("id"), id)
    // )).executeUpdate();

    T entity = findOne(id);
    if (entity == null)
        throw new EmptyResultDataAccessException(
                String.format("No %s entity with id %s exists!", domainClass, id), 1);

    delete((SelfReference<T>) entity);

}
 
Example 27
Project: lams   File: CustomizableTraceInterceptor.java   View source code 5 votes vote down vote up
/**
 * Set the template used for method entry log messages.
 * This template can contain any of the following placeholders:
 * <ul>
 * <li>{@code $[targetClassName]}</li>
 * <li>{@code $[targetClassShortName]}</li>
 * <li>{@code $[argumentTypes]}</li>
 * <li>{@code $[arguments]}</li>
 * </ul>
 */
public void setEnterMessage(String enterMessage) throws IllegalArgumentException {
	Assert.hasText(enterMessage, "'enterMessage' must not be empty");
	checkForInvalidPlaceholders(enterMessage);
	Assert.doesNotContain(enterMessage, PLACEHOLDER_RETURN_VALUE,
			"enterMessage cannot contain placeholder [" + PLACEHOLDER_RETURN_VALUE + "]");
	Assert.doesNotContain(enterMessage, PLACEHOLDER_EXCEPTION,
			"enterMessage cannot contain placeholder [" + PLACEHOLDER_EXCEPTION + "]");
	Assert.doesNotContain(enterMessage, PLACEHOLDER_INVOCATION_TIME,
			"enterMessage cannot contain placeholder [" + PLACEHOLDER_INVOCATION_TIME + "]");
	this.enterMessage = enterMessage;
}
 
Example 28
Project: gemini.blueprint   File: ConfigAdminPropertiesFactoryBean.java   View source code 5 votes vote down vote up
public void afterPropertiesSet() throws Exception {
	Assert.hasText(persistentId, "persistentId property is required");
	Assert.notNull(bundleContext, "bundleContext property is required");
	Assert.isTrue(initTimeout >= 0, "a positive initTimeout is required");

	if (!initLazy) {
		createProperties();
	}
}
 
Example 29
Project: keti   File: AbstractCacheHealthIndicator.java   View source code 5 votes vote down vote up
public AbstractCacheHealthIndicator(final RedisConnectionFactory redisConnectionFactory, final String cacheType,
        final boolean cachingEnabled) {
    Assert.notNull(redisConnectionFactory, "ConnectionFactory must not be null");
    this.redisConnectionFactory = redisConnectionFactory;
    this.cacheType = cacheType;
    this.cachingEnabled = cachingEnabled;
}
 
Example 30
Project: amanda   File: FileSystemStorageService.java   View source code 5 votes vote down vote up
@Override
public void delete(String[] paths) {
    Assert.notEmpty(paths, "Paths must not be empty");
    for (String path : paths) {
        LOGGER.info("delete path: " + rootLocation.resolve(path).toAbsolutePath());
        FileSystemUtils.deleteRecursively(rootLocation.resolve(path).toFile());
    }
}
 
Example 31
Project: NGB-master   File: ProjectManager.java   View source code 5 votes vote down vote up
private void checkReference(Reference reference, List<BiologicalDataItem> projectItems) {
    for (BiologicalDataItem item : projectItems) {
        if (FeatureFile.class.isAssignableFrom(item.getClass())) {
            FeatureFile file = (FeatureFile) item;
            Assert.isTrue(reference.getId().equals(file.getReferenceId()),
                    MessageHelper.getMessage(MessagesConstants.ERROR_PROJECT_NON_MATCHING_REFERENCE,
                            file.getName()));
        }
    }
}
 
Example 32
Project: spring-data-documentdb   File: SimpleDocumentDbRepository.java   View source code 5 votes vote down vote up
/**
 * find one entity per id with partitions
 *
 * @param id
 * @param partitionKeyValue
 * @return
 */
public T findOne(ID id, String partitionKeyValue) {
    Assert.notNull(id, "id must not be null");
    Assert.notNull(partitionKeyValue, "partitionKeyValue must not be null");

    return documentDbOperations.findById(
            entityInformation.getCollectionName(),
            id,
            entityInformation.getJavaType(),
            partitionKeyValue);
}
 
Example 33
Project: NGB-master   File: BlockCompressedDataInputStream.java   View source code 5 votes vote down vote up
/**
 * Reads a long value from stream
 * @return an unsigned byte value
 * @throws IOException if no value was read
 */
public final long readLong() throws IOException {
    final byte[] readBuffer = new byte[LONG_SIZE];
    final int countByte = read(readBuffer);
    Assert.isTrue(countByte == readBuffer.length);
    return (((long) readBuffer[OFFSET_0] << SHIFT56) +
            ((long) (readBuffer[OFFSET_1] & BYTE_MASK) << SHIFT48) +
            ((long) (readBuffer[OFFSET_2] & BYTE_MASK) << SHIFT40) +
            ((long) (readBuffer[OFFSET_3] & BYTE_MASK) << SHIFT32) +
            ((long) (readBuffer[OFFSET_4] & BYTE_MASK) << SHIFT24) +
            ((readBuffer[OFFSET_5] & BYTE_MASK) << TWO_BYTE_SIZE) +
            ((readBuffer[OFFSET_6] & BYTE_MASK) << BYTE_SIZE) +
            readBuffer[OFFSET_7]) & BYTE_MASK;
}
 
Example 34
Project: spring-cloud-samples   File: BaseRepositoryImpl.java   View source code 5 votes vote down vote up
@Override
public <X> List<X> find(String hql, Map<String, ?> params, Pageable pageable, Class<X> clazz) {
    Assert.hasText(hql, "hql can not been null or blank");
    Query query = entityManager.createQuery(hql);
    if (query != null) {
        query.unwrap(QueryImpl.class).setResultTransformer(Transformers.aliasToBean(clazz));
        query.setFirstResult(pageable.getOffset());
        query.setMaxResults(pageable.getPageSize());
        if (params != null) {
            params.entrySet().forEach(param -> query.setParameter(param.getKey(), param.getValue()));
        }
        return query.getResultList();
    }
    return Lists.newArrayList();
}
 
Example 35
Project: NGB-master   File: BiologicalDataItemDao.java   View source code 5 votes vote down vote up
/**
 * Persists a BiologicalDataItem instance into the database
 * @param item BiologicalDataItem to persist
 */
@Transactional(propagation = Propagation.MANDATORY)
public void createBiologicalDataItem(BiologicalDataItem item) {
    if (!item.getFormat().isIndex() ||
            (item.getFormat().isIndex() && !StringUtils.isEmpty(item.getName()))) {

        Assert.isTrue(!StringUtils.isEmpty(item.getName()),
                "File name is required for registration.");
        List<BiologicalDataItem> items = loadFilesByNameStrict(item.getName());
        Assert.isTrue(items.isEmpty(), MessageHelper
                .getMessage(MessagesConstants.ERROR_FILE_NAME_EXISTS, item.getName()));
        item.setId(daoHelper.createId(biologicalDataItemSequenceName));
    } else {
        item.setId(daoHelper.createId(biologicalDataItemSequenceName));
        item.setName("INDEX " + item.getId());
    }

    final MapSqlParameterSource params = new MapSqlParameterSource();

    params.addValue(BiologicalDataItemParameters.BIO_DATA_ITEM_ID.name(), item.getId());
    params.addValue(BiologicalDataItemParameters.NAME.name(), item.getName());
    params.addValue(BiologicalDataItemParameters.TYPE.name(), item.getType().getId());
    params.addValue(BiologicalDataItemParameters.PATH.name(), item.getPath());
    params.addValue(BiologicalDataItemParameters.FORMAT.name(), item.getFormat().getId());
    params.addValue(BiologicalDataItemParameters.CREATED_DATE.name(), item.getCreatedDate());
    params.addValue(BiologicalDataItemParameters.CREATED_BY.name(), item.getCreatedBy());
    params.addValue(BiologicalDataItemParameters.BUCKET_ID.name(), item.getBucketId());

    getNamedParameterJdbcTemplate().update(insertBiologicalDataItemQuery, params);
}
 
Example 36
Project: minlia-iot   File: AbstractAnnotationApiSerializer.java   View source code 5 votes vote down vote up
/**
 * 添加节点
 */
private void addElement(Element rootElement, String elementName, Object obj, boolean required) {
  if (obj == null && !required) {
    return;
  }
  Assert.notNull(obj, elementName);
  Class<?> clazz = obj.getClass();
  Element element = rootElement.addElement(elementName);
  if (clazz == Integer.class || clazz == Long.class) {
    element.setText(obj.toString());
  } else {
    element.addCDATA(obj.toString());
  }
}
 
Example 37
Project: spring-data-documentdb   File: DocumentDbTemplate.java   View source code 5 votes vote down vote up
public DocumentDbTemplate(DocumentDbFactory documentDbFactory,
                          MappingDocumentDbConverter mappingDocumentDbConverter,
                          String dbName) {
    Assert.notNull(documentDbFactory, "DocumentDbFactory must not be null!");
    Assert.notNull(mappingDocumentDbConverter, "MappingDocumentDbConverter must not be null!");

    this.databaseName = dbName;
    this.documentDbFactory = documentDbFactory;
    this.mappingDocumentDbConverter = mappingDocumentDbConverter;
    this.collectionCache = new ArrayList<>();
}
 
Example 38
Project: gemini.blueprint   File: OsgiServiceReferenceUtils.java   View source code 5 votes vote down vote up
/**
 * Returns references to <em>all</em> services matching the given class name and OSGi filter.
 * 
 * @param bundleContext OSGi bundle context
 * @param clazz fully qualified class name (can be <code>null</code>)
 * @param filter valid OSGi filter (can be <code>null</code>)
 * @return non-<code>null</code> array of references to matching services
 */
public static ServiceReference[] getServiceReferences(BundleContext bundleContext, String clazz, String filter) {
	Assert.notNull(bundleContext, "bundleContext should be not null");

	try {
		ServiceReference[] refs = bundleContext.getServiceReferences(clazz, filter);
		return (refs == null ? new ServiceReference[0] : refs);
	} catch (InvalidSyntaxException ise) {
		throw (RuntimeException) new IllegalArgumentException("invalid filter: " + ise.getFilter()).initCause(ise);
	}
}
 
Example 39
Project: spring-webflux-client   File: ExchangeFilterFunctions.java   View source code 5 votes vote down vote up
static ExchangeFilterFunction loggingFilter(Logger logger, LogLevel logLevel) {
    Assert.notNull(logger, "'logger' Can't be null");
    Assert.notNull(logLevel, "'logLevel' Can't be null");

    return (clientRequest, exchangeFunction) -> logClientRequest(
            clientRequest,
            exchangeFunction,
            logger,
            logLevel);
}
 
Example 40
Project: gemini.blueprint   File: RunnableTimedExecution.java   View source code 5 votes vote down vote up
public static boolean execute(Runnable task, long waitTime, TaskExecutor taskExecutor) {
	Assert.notNull(task);

	Counter counter = new Counter("counter for task: " + task);
	Runnable wrapper = new MonitoredRunnable(task, counter);

	boolean internallyManaged = false;

	if (taskExecutor == null) {
		taskExecutor = new SimpleTaskExecutor();
		internallyManaged = true;
	}

	counter.increment();

	taskExecutor.execute(wrapper);

	if (counter.waitForZero(waitTime)) {
		log.error(task + " did not finish in " + waitTime
				+ "ms; consider taking a snapshot and then shutdown the VM in case the thread still hangs");

		//log.error("Current Thread dump***\n" + ThreadDump.dumpThreads());

		if (internallyManaged) {
			try {
				((DisposableBean) taskExecutor).destroy();
			} catch (Exception e) {
				log.error("Exception thrown while destroying internally managed thread executor", e);
			}
		}
		return true;
	}

	return false;
}