/**
* Save the model into the file
*
* @param root the root of the model to save
* @param file the file to save
* @throws JAXBException on error
*/
public void save(Model root, File file) throws JAXBException {
try {
final StringWriter strw = new StringWriter();
marshaller.marshal(unmerge(root), strw);
/*
* Customize the file to be handled by the xml2modelica tool
*/
final StringBuffer buffer = strw.getBuffer();
final String newline = System.getProperty("line.separator");
Pattern pat = Pattern.compile("(/\\w*>)(<[\\w/])");
Matcher m = pat.matcher(buffer);
while (m.find()) {
final int index = m.end(1);
buffer.insert(index, newline);
m.reset();
}
buffer.append(newline);
new FileOutputStream(file).write(strw.toString().getBytes());
} catch (FactoryConfigurationError e) {
Logger.getLogger(Modelica.class.getName()).severe(e.toString());
} catch (IOException e) {
Logger.getLogger(Modelica.class.getName()).severe(e.toString());
}
}
/**
* Function to convert pm request to OMElement
*
* @param requestVdo String request to send to pm web service
* @return An OMElement containing the pm web service request
*/
public static OMElement getPmPayLoad(String requestVdo) throws Exception {
OMElement method = null;
try {
StringReader strReader = new StringReader(requestVdo);
XMLInputFactory xif = XMLInputFactory.newInstance();
XMLStreamReader reader = xif.createXMLStreamReader(strReader);
StAXOMBuilder builder = new StAXOMBuilder(reader);
method = builder.getDocumentElement();
/*
OMFactory fac = OMAbstractFactory.getOMFactory();
OMNamespace omNs = fac.createOMNamespace("http://www.i2b2.org/xsd/hive/msg",
"i2b2");
method = fac.createOMElement("request", omNs);
StringReader strReader = new StringReader(requestVdo);
XMLInputFactory xif = XMLInputFactory.newInstance();
XMLStreamReader reader = xif.createXMLStreamReader(strReader);
StAXOMBuilder builder = new StAXOMBuilder(reader);
//method = builder.getDocumentElement();
OMElement lineItem = builder.getDocumentElement();
method.addChild(lineItem);
*/
} catch (FactoryConfigurationError e) {
// TODO Auto-generated catch block
e.printStackTrace();
log.error(e.getMessage());
throw new Exception(e);
}
return method;
}
public static void main(String[] args) {
// File file = new File("c:/Experiment/h2-2_MS_1_004.img.bz2");
File file = new File("c:/Experiment/baa5d5/high.mtz");
String serverLocation = "http://localhost:8161/fileserver/";
String filename = "";
String entryType = "ENTRY_CREATE";
String ID = "c:/Experiment/5d5.mtz";
URL url = null;
// Generate checksum for the file here
byte[] fileContents;
try {
fileContents = FileUtil.getBytesFromFile(file);
filename = "5d5.mtz";
// FileUtil.getFileName("c:/Experiment/h2-2_MS_1_002.bz2");
url = new URL(serverLocation + filename);
MD5ChecksumProcessor c = new MD5ChecksumProcessor();
String checksum = c.generateChecksum(file);
String domain = "crystallography";
ADQueueWriterImpl qu = new ADQueueWriterImpl();
// upload a file to a webserver
FileServerClient client = new FileServerClient(url);
// boolean uploaded = client.upload(fileContents);
// If upload is true send a blob message with this file url
// if (uploaded=true){
// qu.sendBlobMessage(url,ID,domain,checksum,entryType,"12/10/2010 12:22:22");
try {
qu.sendByteArrayMessage(
fileContents, ID, checksum, domain, "baa5d5", entryType, "12/10/2010 12:22:22");
} catch (XMLStreamException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
// }
// qu.sendMessage(fileContents, ID, entryType, "");
// qu.sendBlobMessage("c:/Experiment/hello123.xml", "123.xml");
qu.disconnect();
} catch (JMSException e) {
// TODO Auto-generated catch block
e.printStackTrace();
// } catch (XMLStreamException e) {
// TODO Auto-generated catch block
// e.printStackTrace();
} catch (FactoryConfigurationError e) {
// TODO Auto-generated catch block
e.printStackTrace();
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
} catch (ChecksumProcessorException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
private void parseCoordElements(final File pom) {
Reader reader = null;
XMLStreamReader xml = null;
try {
reader = new FileReader(pom);
xml = XMLInputFactory.newFactory().createXMLStreamReader(reader);
final Stack<String> path = new Stack<String>();
while (xml.hasNext()) {
final int evt = xml.next();
switch (evt) {
case START_ELEMENT:
{
path.push(xml.getLocalName());
if (captureValue(path, xml)) {
// seems like xml.getElementText() traverses the END_ELEMENT event...
path.pop();
}
if (foundPreferredValues()) {
return;
}
break;
}
case END_ELEMENT:
{
path.pop();
break;
}
default:
{
}
}
}
} catch (final IOException e) {
logger.warn(
"Failed to peek at POM coordinate for: %s. Reason: %s\n"
+ "This POM will NOT be available as an ancestor to other models during effective-model building.",
e, pom, e.getMessage());
} catch (final XMLStreamException e) {
logger.warn(
"Failed to peek at POM coordinate for: %s. Reason: %s\n"
+ "This POM will NOT be available as an ancestor to other models during effective-model building.",
e, pom, e.getMessage());
} catch (final FactoryConfigurationError e) {
logger.warn(
"Failed to peek at POM coordinate for: %s. Reason: %s\n"
+ "This POM will NOT be available as an ancestor to other models during effective-model building.",
e, pom, e.getMessage());
} finally {
if (xml != null) {
try {
xml.close();
} catch (final XMLStreamException e) {
}
}
closeQuietly(reader);
}
}
public static String sendSOAP(
EndpointReference soapEPR, String requestString, String action, String operation)
throws Exception {
ServiceClient sender = PmServiceClient.getServiceClient();
OperationClient operationClient = sender.createClient(ServiceClient.ANON_OUT_IN_OP);
// creating message context
MessageContext outMsgCtx = new MessageContext();
// assigning message context's option object into instance variable
Options opts = outMsgCtx.getOptions();
// setting properties into option
log.debug(soapEPR);
opts.setTo(soapEPR);
opts.setAction(action);
opts.setTimeOutInMilliSeconds(180000);
log.debug(requestString);
SOAPEnvelope envelope = null;
try {
SOAPFactory fac = OMAbstractFactory.getSOAP11Factory();
envelope = fac.getDefaultEnvelope();
OMNamespace omNs =
fac.createOMNamespace(
"http://rpdr.partners.org/", //$NON-NLS-1$
"rpdr"); //$NON-NLS-1$
// creating the SOAP payload
OMElement method = fac.createOMElement(operation, omNs);
OMElement value = fac.createOMElement("RequestXmlString", omNs); // $NON-NLS-1$
value.setText(requestString);
method.addChild(value);
envelope.getBody().addChild(method);
} catch (FactoryConfigurationError e) {
log.error(e.getMessage());
throw new Exception(e);
}
outMsgCtx.setEnvelope(envelope);
operationClient.addMessageContext(outMsgCtx);
operationClient.execute(true);
MessageContext inMsgtCtx = operationClient.getMessageContext("In"); // $NON-NLS-1$
SOAPEnvelope responseEnv = inMsgtCtx.getEnvelope();
OMElement soapResponse = responseEnv.getBody().getFirstElement();
// System.out.println("Sresponse: "+ soapResponse.toString());
OMElement soapResult = soapResponse.getFirstElement();
// System.out.println("Sresult: "+ soapResult.toString());
String i2b2Response = soapResult.getText();
log.debug(i2b2Response);
return i2b2Response;
}
protected Message createBlobMessage(
URL fileURL,
String ID,
String checksum,
String domain,
String projectName,
String entryType,
String dateTime,
String experimentId,
ActiveMQSession session) {
BlobMessage message = null;
FileInputStream in = null;
String msgParam;
try {
msgParam =
createXMLParameter(ID, checksum, domain, projectName, entryType, dateTime, experimentId);
// in = new FileInputStream(fileLocation);
// message.setName(name);
// message = session.createBlobMessage(new File(fileLocation));
message = session.createBlobMessage(fileURL);
// message.setName(name);
message.setObjectProperty("msgParamXML", msgParam);
// message.setObjectProperty("checksum", checksum);
// message = session.createBlobMessage(in);
} catch (JMSException e) {
// TODO Auto-generated catch block
e.printStackTrace();
} catch (XMLStreamException e1) {
// TODO Auto-generated catch block
e1.printStackTrace();
} catch (FactoryConfigurationError e1) {
// TODO Auto-generated catch block
e1.printStackTrace();
}
return message;
}
/**
* Builds a SOAPEnvelope from DOM Document.
*
* @param doc - The dom document that contains a SOAP message
* @param useDoom
* @return
* @throws WSSecurityException
*/
public static SOAPEnvelope getSOAPEnvelopeFromDOMDocument(Document doc, boolean useDoom)
throws WSSecurityException {
if (useDoom) {
try {
// Get processed headers
SOAPEnvelope env = (SOAPEnvelope) doc.getDocumentElement();
ArrayList processedHeaderQNames = new ArrayList();
SOAPHeader soapHeader = env.getHeader();
if (soapHeader != null) {
Iterator headerBlocs = soapHeader.getChildElements();
while (headerBlocs.hasNext()) {
OMElement element = (OMElement) headerBlocs.next();
SOAPHeaderBlock header = null;
if (element instanceof SOAPHeaderBlock) {
header = (SOAPHeaderBlock) element;
// If a header block is not an instance of SOAPHeaderBlock, it means that
// it is a header we have added in rampart eg. EncryptedHeader and should
// be converted to SOAPHeaderBlock for processing
} else {
header = soapHeader.addHeaderBlock(element.getLocalName(), element.getNamespace());
Iterator attrIter = element.getAllAttributes();
while (attrIter.hasNext()) {
OMAttribute attr = (OMAttribute) attrIter.next();
header.addAttribute(
attr.getLocalName(), attr.getAttributeValue(), attr.getNamespace());
}
Iterator nsIter = element.getAllDeclaredNamespaces();
while (nsIter.hasNext()) {
OMNamespace ns = (OMNamespace) nsIter.next();
header.declareNamespace(ns);
}
// retrieve all child nodes (including any text nodes)
// and re-attach to header block
Iterator children = element.getChildren();
while (children.hasNext()) {
OMNode child = (OMNode) children.next();
child.detach();
header.addChild(child);
}
element.detach();
soapHeader.build();
header.setProcessed();
}
if (header.isProcessed()) {
processedHeaderQNames.add(element.getQName());
}
}
}
XMLStreamReader reader = ((OMElement) doc.getDocumentElement()).getXMLStreamReader();
StAXSOAPModelBuilder stAXSOAPModelBuilder = new StAXSOAPModelBuilder(reader, null);
SOAPEnvelope envelope = stAXSOAPModelBuilder.getSOAPEnvelope();
// Set the processed flag of the processed headers
SOAPHeader header = envelope.getHeader();
for (Iterator iter = processedHeaderQNames.iterator(); iter.hasNext(); ) {
QName name = (QName) iter.next();
Iterator omKids = header.getChildrenWithName(name);
if (omKids.hasNext()) {
((SOAPHeaderBlock) omKids.next()).setProcessed();
}
}
envelope.build();
return envelope;
} catch (FactoryConfigurationError e) {
throw new WSSecurityException(e.getMessage());
}
} else {
try {
ByteArrayOutputStream os = new ByteArrayOutputStream();
XMLUtils.outputDOM(doc.getDocumentElement(), os, true);
ByteArrayInputStream bais = new ByteArrayInputStream(os.toByteArray());
StAXSOAPModelBuilder stAXSOAPModelBuilder =
new StAXSOAPModelBuilder(
XMLInputFactory.newInstance().createXMLStreamReader(bais), null);
return stAXSOAPModelBuilder.getSOAPEnvelope();
} catch (Exception e) {
throw new WSSecurityException(e.getMessage());
}
}
}
