Java Utils.serializeObject方法代码示例

import gov.nih.nci.cagrid.common.Utils; //导入方法依赖的package包/类
public gridextensions.Data microarraySetToStatml(edu.columbia.geworkbench.cagrid.microarray.MicroarraySet microarraySet) throws RemoteException {
	try {
		// get XML
		StringWriter microarraySw = new StringWriter();
		Utils.serializeObject(microarraySet, new QName("MicroarraySet"), microarraySw);

		GeWorkbenchParser gwParser = new GeWorkbenchParser();
		gwParser.parseMicroarray(microarraySw.toString());
		
		GenePatternParser gpParser = new GenePatternParser();
		gpParser.setMicroarrayData(gpParser.getMicroarrayData());
		
		return gpParser.convertToStatml();
	} catch (Exception e) {
		e.printStackTrace();
		throw new RemoteException(e.getMessage());
	}
}
 

import gov.nih.nci.cagrid.common.Utils; //导入方法依赖的package包/类
/**
 * @return TypeAttribute[] unless xmlOnly == true, 
 * then a serialized CQLAttributeResult
 */
public Object next() {
       if (currentIndex >= results.length - 1) {
           // works because on first call, currentIndex == -1
           throw new NoSuchElementException();
       }
	currentIndex++;
	CQLAttributeResult result = results[currentIndex];
       if (xmlOnly) {
           StringWriter writer = new StringWriter();
           try {
               Utils.serializeObject(result, CQL_ATTRIBUTE_RESULT_QNAME, writer);
           } catch (Exception ex) {
               throw new RuntimeException("Error serializing attribute results: " + ex.getMessage(), ex);
           }
           return writer.getBuffer().toString();
       }
       return result.getAttribute();
}
 

import gov.nih.nci.cagrid.common.Utils; //导入方法依赖的package包/类
public ExtensionType getAuthorizationExtensionData() throws Exception {
    ExtensionType extension = new ExtensionType();
    extension.setExtensionType(ExtensionsLoader.AUTHORIZATION_EXTENSION);
    extension.setName(getAuthorizationExtensionDescriptionType().getName());  
    MembershipExpression expression = getGridgrouperExpressionEditor().getMembershipExpression();
    
    MembershipExpressionValidator.validateMembeshipExpression(expression);
    
    StringWriter sw = new StringWriter();
    Utils.serializeObject(expression, MembershipExpression.getTypeDesc().getXmlType(), sw);
    Document doc = XMLUtilities.stringToDocument(sw.toString());
    Element el = (Element)doc.getRootElement().detach();
    MessageElement elem = AxisJdomUtils.fromElement(el);
    
    ExtensionTypeExtensionData data = new ExtensionTypeExtensionData();
    data.set_any(new MessageElement[] {elem});
    extension.setExtensionData(data);
    return extension;
}
 

import gov.nih.nci.cagrid.common.Utils; //导入方法依赖的package包/类
Message getRequestMessage(IntegrationHubDto hubDto) throws LVException {
    try {
        QName qName = new QName(hubDto.getQName(), hubDto.getQRequest());
        Object requestObj = hubDto.getRequestObj();
        Utils.serializeObject(requestObj, qName , new PrintWriter(hubDto.getMessageXml()));
        Message requestMessage = new Message();
        Metadata metadata = new Metadata();
        metadata.setExternalIdentifier(hubDto.getExternalIdentifier());
        metadata.setCredentials(hubDto.getCredential());
        metadata.setServiceType(hubDto.getServiceType());
        requestMessage.setMetadata(metadata);
        requestMessage.setRequest(new Request());
        MessagePayload messagePayload = new MessagePayload();
        URI uri = new URI();
        uri.setPath(hubDto.getQName());
        messagePayload.setXmlSchemaDefinition(uri);
        MessageElement messageElement = new MessageElement(qName, requestObj);
        messagePayload.set_any(new MessageElement[] {messageElement });
        requestMessage.getRequest().setBusinessMessagePayload(messagePayload);
        return requestMessage;
    } catch (Exception e) {
        throw new LVException(e);
    }
}
 

import gov.nih.nci.cagrid.common.Utils; //导入方法依赖的package包/类
private SubscriptionListener createSubscriptionListener(
    final FederatedQueryResultsRetrievalClient resultsClient, final InfoHolder info) {
    SubscriptionListener listener = new SubscriptionListener() {
        public void subscriptionValueChanged(ResourcePropertyValueChangeNotificationType notification) {
            try {
                String newMetadataDocument = AnyHelper.toSingleString(notification.getNewValue().get_any());
                FederatedQueryExecutionStatus status = Utils.deserializeObject(
                    new StringReader(newMetadataDocument), FederatedQueryExecutionStatus.class);
                StringWriter writer = new StringWriter();
                Utils.serializeObject(status, FederatedQueryResultsConstants.FEDERATEDQUERYEXECUTIONSTATUS, writer);
                LOG.debug("GOT NOTIFICATION:");
                LOG.debug(writer.getBuffer().toString());
                if ((info.success == null || !info.success.booleanValue()) && ProcessingStatus.Complete.equals(status.getCurrentStatus())) {
                    enumerateAndVerify(resultsClient);
                    LOG.debug("SETTING SUCCESS STATUS TO TRUE");
                    info.success = Boolean.TRUE;
                }
            } catch (Exception ex) {
                ex.printStackTrace();
                info.success = Boolean.FALSE;
                info.exception = ex;
            }
        }
    };
    return listener;
}
 

import gov.nih.nci.cagrid.common.Utils; //导入方法依赖的package包/类
private SubscriptionListener createSubscriptionListener(
    final FederatedQueryResultsClient resultsClient, final InfoHolder info) {
    SubscriptionListener listener = new SubscriptionListener() {
        public void subscriptionValueChanged(ResourcePropertyValueChangeNotificationType notification) {
            try {
                String newMetadataDocument = AnyHelper.toSingleString(notification.getNewValue().get_any());
                FederatedQueryExecutionStatus status = (FederatedQueryExecutionStatus) Utils.deserializeObject(
                    new StringReader(newMetadataDocument), FederatedQueryExecutionStatus.class);
                StringWriter writer = new StringWriter();
                Utils.serializeObject(status, FederatedQueryResultsConstants.FEDERATEDQUERYEXECUTIONSTATUS, writer);
                LOG.debug("GOT NOTIFICATION:");
                LOG.debug(writer.getBuffer().toString());
                if ((info.success == null || !info.success.booleanValue()) && ProcessingStatus.Complete.equals(status.getCurrentStatus())) {
                    enumerateAndVerify(resultsClient);
                    LOG.debug("SETTING SUCCESS STATUS TO TRUE");
                    info.success = Boolean.TRUE;
                }
            } catch (Exception ex) {
                ex.printStackTrace();
                info.success = Boolean.FALSE;
                info.exception = ex;
            }
        }
    };
    return listener;
}
 

import gov.nih.nci.cagrid.common.Utils; //导入方法依赖的package包/类
/**
 * Validates a CQL result set's contents against the restricted result set schema
 * 
 * @param resultSet
 * @throws SchemaValidationException
 */
public void validateCQLResultSet(CQLQueryResults resultSet) throws SchemaValidationException {
	// make sure we are ready to go
	initializeRestrictedXSD();

	if (resultSet == null) {
		LOG.debug("Null results passed, ignoring.");
		return;
	}

	StringWriter writer = new StringWriter();
	try {
		Utils.serializeObject(resultSet, CqlSchemaConstants.CQL_RESULT_COLLECTION_QNAME, writer);
	} catch (Exception e) {
		LOG.error(e);
		throw new SchemaValidationException("Problem serializing result set", e);
	}

	String xmlContents = writer.getBuffer().toString();
	if (LOG.isDebugEnabled()) {
		LOG.debug("RESULTS:\n" + xmlContents);
	}
	this.validator.validate(xmlContents);
}
 

import gov.nih.nci.cagrid.common.Utils; //导入方法依赖的package包/类
private void saveCurrentFile() {
    try {
        ValidationDescription description = createValidationDescription();
        
        FileWriter writer = new FileWriter(currentDeploymentDescriptionFile);
        Utils.serializeObject(description, GridDeploymentValidationLoader.VALIDATION_DESCRIPTION_QNAME, writer);
        writer.flush();
        writer.close();
    } catch (Exception ex) {
        ex.printStackTrace();
        String[] message = {
            "An error occured saving the deployment description:",
            ex.getMessage()
        };
        JOptionPane.showMessageDialog(this, message, "Error", JOptionPane.ERROR_MESSAGE);
    }
}
 

import gov.nih.nci.cagrid.common.Utils; //导入方法依赖的package包/类
@Override
public ExtensionType getAuthorizationExtensionData() throws Exception {
    CSMAuthorizationDescription desc = getCsmAuthorizationPanel().getAuthorization();
    
    ExtensionType extension = new ExtensionType();
    extension.setExtensionType(ExtensionsLoader.AUTHORIZATION_EXTENSION);
    extension.setName(getAuthorizationExtensionDescriptionType().getName());  
     
    StringWriter sw = new StringWriter();
    Utils.serializeObject(desc, desc.getTypeDesc().getXmlType(), sw);
    Document doc = XMLUtilities.stringToDocument(sw.toString());
    Element el = (Element)doc.getRootElement().detach();
    MessageElement elem = AxisJdomUtils.fromElement(el);
    
    ExtensionTypeExtensionData data = new ExtensionTypeExtensionData();
    data.set_any(new MessageElement[] {elem});
    extension.setExtensionData(data);
    return extension;
}
 

import gov.nih.nci.cagrid.common.Utils; //导入方法依赖的package包/类
private void writeAuditorsConfiguration(DataServiceAuditors auditors) throws Exception {
    if (CommonTools.servicePropertyExists(
        getServiceInfo().getServiceDescriptor(), 
        DataServiceConstants.DATA_SERVICE_AUDITORS_CONFIG_FILE_PROPERTY)) {
        try {
            // get the name of the auditor config file
            String filename = CommonTools.getServicePropertyValue(
                getServiceInfo().getServiceDescriptor(), 
                DataServiceConstants.DATA_SERVICE_AUDITORS_CONFIG_FILE_PROPERTY);
            File outFile = new File(getServiceInfo().getBaseDirectory().getAbsolutePath() 
                + File.separator + "etc" + File.separator + filename);
            FileWriter writer = new FileWriter(outFile);
            Utils.serializeObject(auditors, 
                DataServiceConstants.DATA_SERVICE_AUDITORS_QNAME, writer);
            writer.flush();
            writer.close();
        } catch (Exception ex) {
            ex.printStackTrace();
            throw new CodegenExtensionException(
                "Error writing auditor configuration: " + ex.getMessage(), ex);
        }
    }
}
 

import gov.nih.nci.cagrid.common.Utils; //导入方法依赖的package包/类
private void persistModelChanges() throws Throwable {
    // persist the changes made by the configuration steps
    File serviceModelFile = new File(getServiceInformation().getBaseDirectory(), IntroduceConstants.INTRODUCE_XML_FILE);
    LOG.debug("Persisting changes to service model (" + serviceModelFile.getAbsolutePath() + ")");
    FileWriter writer = new FileWriter(serviceModelFile);
    Utils.serializeObject(getServiceInformation().getServiceDescriptor(), IntroduceConstants.INTRODUCE_SKELETON_QNAME, writer);
    writer.flush();
    writer.close();
}
 

import gov.nih.nci.cagrid.common.Utils; //导入方法依赖的package包/类
public static CQLQuery checkDefaultPredicates(CQLQuery original) throws Exception {
    LOG.debug("Checking query for Attributes with no predicate defined");
    StringWriter originalWriter = new StringWriter();
    Utils.serializeObject(original, DataServiceConstants.CQL_QUERY_QNAME, originalWriter);
    Element root = XMLUtilities.stringToDocument(originalWriter.getBuffer().toString()).getRootElement();
    Filter attributeNoPredicateFilter = new Filter() {
        public boolean matches(Object o) {
            if (o instanceof Element) {
                Element e = (Element) o;
                if (e.getName().equals("Attribute") && e.getAttribute("predicate") == null) {
                    return true;
                }
            }
            return false;
        }
    };
    List<?> attributesWithNoPredicate = root.getContent(attributeNoPredicateFilter);
    Iterator<?> attribIter = attributesWithNoPredicate.iterator();
    while (attribIter.hasNext()) {
        LOG.debug("Adding default predicate to an attribute");
        Element elem = (Element) attribIter.next();
        elem.setAttribute("predicate", "EQUAL_TO");
    }
    String xml = XMLUtilities.elementToString(root);
    CQLQuery edited = Utils.deserializeObject(new StringReader(xml), CQLQuery.class);
    return edited;
}
 

import gov.nih.nci.cagrid.common.Utils; //导入方法依赖的package包/类
private SubscriptionListener createSubscriptionListener(
    final FederatedQueryResultsClient resultsClient, final InfoHolder info) {
    SubscriptionListener listener = new SubscriptionListener() {
        private boolean completeDetected = false;
        
        public void subscriptionValueChanged(ResourcePropertyValueChangeNotificationType notification) {
            try {
                String newMetadataDocument = AnyHelper.toSingleString(notification.getNewValue().get_any());
                FederatedQueryExecutionStatus status = Utils.deserializeObject(
                    new StringReader(newMetadataDocument), FederatedQueryExecutionStatus.class);
                StringWriter writer = new StringWriter();
                Utils.serializeObject(status, FederatedQueryResultsConstants.FEDERATEDQUERYEXECUTIONSTATUS, writer);
                if (LOG.isDebugEnabled())  {
                    LOG.debug("GOT NOTIFICATION:");
                    LOG.debug(writer.getBuffer().toString());
                }
                if (!completeDetected && ProcessingStatus.Complete.equals(status.getCurrentStatus())) {
                    completeDetected = true;
                    LOG.debug("EXECUTING TRANSFER AND VERIFY PROCESS");
                    transferAndVerify(resultsClient);
                    LOG.debug("SETTING SUCCESS STATUS TO TRUE");
                    info.success = Boolean.TRUE;
                }
            } catch (Exception ex) {
                ex.printStackTrace();
                info.success = Boolean.FALSE;
                info.exception = ex;
            }
        }
    };
    return listener;
}
 

import gov.nih.nci.cagrid.common.Utils; //导入方法依赖的package包/类
/**
 * Write the XML representation of the specified query results to the specified
 * writer, using the configuration specified by the WSDD configuration.
 * If either the results or writer are null, an IllegalArgumentException will be thrown.
 * 
 * @param results
 * @param writer
 * @param wsddStream
 * @throws Exception
 */
public static void serializeDCQLQueryResults(DCQLQueryResultsCollection results, Writer writer, InputStream wsddStream) throws Exception {
    if (results == null || writer == null) {
        throw new IllegalArgumentException("Null is not a valid argument");
    }
    if (wsddStream == null) {
        Utils.serializeObject(results, DCQLConstants.DCQL_RESULTS_QNAME, writer);
    } else {
        Utils.serializeObject(results, DCQLConstants.DCQL_RESULTS_QNAME, writer, wsddStream);
    }
}
 

import gov.nih.nci.cagrid.common.Utils; //导入方法依赖的package包/类
public CQLResult next() {
    CQLResult result = null;
    if (queryModifier == null) {
        // object result
        Object instance = cqlResultsIterator.next();
        try {
            // serialize the object so it can go into an AnyNode
            StringWriter xmlWriter = new StringWriter();
            if (wsddStream == null) {
                Utils.serializeObject(instance, targetQName, xmlWriter);
            } else {
                wsddStream.reset();
                Utils.serializeObject(instance, targetQName, xmlWriter, wsddStream);
            }
            AnyNode node = AnyNodeHelper.convertStringToAnyNode(xmlWriter.toString());
            result = new CQLObjectResult(node);
        } catch (Exception ex) {
            NoSuchElementException nse = new NoSuchElementException("Unable to convert object to AnyNode: " + ex.getMessage());
            nse.initCause(ex);
            throw nse;
        }
    } else {
        if (queryModifier.isCountOnly()) {
            String value = String.valueOf(cqlResultsIterator.next());
            result = new CQLAggregateResult(Aggregation.COUNT, "id", value);
        } else {
            // distinct or multiple attribute results
            String[] attributeNames = queryModifier.getDistinctAttribute() != null 
                ? new String[] {queryModifier.getDistinctAttribute()} : queryModifier.getAttributeNames();
            Object[] values = (Object[]) cqlResultsIterator.next();
            TargetAttribute[] tas = new TargetAttribute[attributeNames.length];
            for (int i = 0; i < attributeNames.length; i++) {
                tas[i] = new TargetAttribute(attributeNames[i], String.valueOf(values[i]));
            }
            result = new CQLAttributeResult(tas);
        }
    }
    return result;
}