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MessagesUtil.java
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Fri, Oct 11, 02:00

MessagesUtil.java
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package ch.epfl.lca1.medco.i2b2;
import java.io.StringReader;
import java.io.StringWriter;
import javax.xml.bind.JAXBElement;
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.parsers.ParserConfigurationException;
import javax.xml.stream.XMLInputFactory;
import javax.xml.stream.XMLStreamException;
import javax.xml.stream.XMLStreamReader;
import edu.harvard.i2b2.crc.datavo.i2b2message.*;
import ch.epfl.lca1.medco.util.Logger;
import ch.epfl.lca1.medco.util.MedCoUtil;
import edu.harvard.i2b2.common.util.jaxb.JAXBUnWrapHelper;
import org.apache.axiom.om.OMElement;
import org.apache.axiom.om.impl.builder.StAXOMBuilder;
import ch.epfl.lca1.medco.util.exceptions.I2B2XMLException;
import edu.harvard.i2b2.common.util.jaxb.JAXBUtil;
import edu.harvard.i2b2.common.util.jaxb.JAXBUtilException;
import org.javatuples.Pair;
import org.javatuples.Triplet;
import org.w3c.dom.Document;
/**
* JAXB utils
*
* @author misbach
*
*/
public class MessagesUtil extends JAXBUtil {
// method OMElement -> JAXB (provide class or not)
// invese
// enough?
private static JAXBUnWrapHelper unwrapHelper = new JAXBUnWrapHelper();
private static MedCoUtil medCoUtil = MedCoUtil.getInstance();
public MessagesUtil(String[] packageName) {
super(packageName);
}
public static JAXBUnWrapHelper getUnwrapHelper() {
return unwrapHelper;
}
/**
* Build OM element from an i2b2 request message.
*
* @param reqMessage the i2b2 request message
* @return OM element wrapping the i2b2 request message
*
* @throws I2B2XMLException if there is an error while generating the element
*/
public OMElement buildOMElement(RequestMessageType reqMessage) throws I2B2XMLException {
// init objects
StringWriter strWriter = new StringWriter();
XMLInputFactory xif = XMLInputFactory.newInstance();
edu.harvard.i2b2.crc.datavo.i2b2message.ObjectFactory hiveObjectFactory =
new edu.harvard.i2b2.crc.datavo.i2b2message.ObjectFactory();
// generate element
try {
this.marshaller(hiveObjectFactory.createRequest(reqMessage), strWriter);
StringReader strReader = new StringReader(strWriter.toString());
XMLStreamReader reader = xif.createXMLStreamReader(strReader);
StAXOMBuilder builder = new StAXOMBuilder(reader);
OMElement request = builder.getDocumentElement();
return request;
} catch (JAXBUtilException | XMLStreamException e) {
throw Logger.error(new I2B2XMLException("Error while generating OM element. ", e));
}
}
@SuppressWarnings("unchecked")
public <RESP> RESP getBodyFromRespMessage(ResponseMessageType respMessage, Class<RESP> bodyType) throws I2B2XMLException {
Logger.debug("Extracting body (: " + bodyType.getName() + "), resp: " + respMessage);
RESP body;
try {
body = (RESP) unwrapHelper.getObjectByClass(
respMessage.getMessageBody().getAny(), bodyType);
} catch (JAXBUtilException e) {
throw Logger.error(new I2B2XMLException("Could not extract body.", e));
}
return body;
}
/**
* Construct a new I2B2 request message, reusing the information of another such a message.
* TODO: hardcoded parameters (timeout, facility name, message header tag)
* TODO: unit test
*
* @param origReqMessage the original request message from which take the security info and the project id
* @return a new I2B2 request message, with security and project same as the provided request message
*
* @throws I2B2XMLException if the message is not correct
*
*/
public RequestMessageType newReqMessageFromReqMessage(RequestMessageType origReqMessage) {
SecurityType security = origReqMessage.getMessageHeader().getSecurity();
String projectId = origReqMessage.getMessageHeader().getProjectId();
return newReqMessageFromSecurity(security, projectId);
}
public RequestMessageType newReqMessageFromSecurity(SecurityType security, String projectId) {
return newReqMessage(security.getDomain(), projectId, security.getUsername(), security.getPassword().isIsToken(),
security.getPassword().getTokenMsTimeout(), security.getPassword().getValue());
}
public RequestMessageType newReqMessage(String domainId, String projectId, String username,
boolean passwordIsToken, int tokenTimeoutMs, String passwordValue) {
SecurityType security = new SecurityType();
security.setDomain(domainId);
security.setUsername(username);
PasswordType password = new PasswordType();
password.setIsToken(passwordIsToken);
password.setTokenMsTimeout(tokenTimeoutMs);
password.setValue(passwordValue);
security.setPassword(password);
// setup message header
MessageHeaderType messageHeader = null;//TODO (MessageHeaderType) medCoUtil.getSpringBeanFactory().getBean("message_header");
messageHeader.setSecurity(security);
messageHeader.setProjectId(projectId);
messageHeader.setReceivingApplication(messageHeader.getSendingApplication());
FacilityType facility = new FacilityType();
facility.setFacilityName("sample");
messageHeader.setSendingFacility(facility);
messageHeader.setReceivingFacility(facility);
// setup message body
//GetUserConfigurationType userConfig = new GetUserConfigurationType();
//userConfig.getProject().add(projectId);
//edu.harvard.i2b2.crc.datavo.pm.ObjectFactory of = new edu.harvard.i2b2.crc.datavo.pm.ObjectFactory();
BodyType body = new BodyType();
//body.getAny().add(of.createGetUserConfiguration(userConfig));
// setup request header
RequestHeaderType requestHeader = new RequestHeaderType();
requestHeader.setResultWaittimeMs(180000); //TODO: hardcoded value
// pack in request message
RequestMessageType requestMessage = new RequestMessageType();
requestMessage.setMessageBody(body);
requestMessage.setMessageHeader(messageHeader);
requestMessage.setRequestHeader(requestHeader);
Logger.debug("Correctly created new i2b2 request message" + requestMessage);
return requestMessage;
}
public RequestMessageType parseRequestMessage(String reqMsgString) throws I2B2XMLException {
try {
JAXBElement reqJaxb = unMashallFromString(reqMsgString);
RequestMessageType r = (RequestMessageType) reqJaxb.getValue();
return r;
} catch (JAXBUtilException e) {
throw Logger.error(new I2B2XMLException("Request not parsable.", e));
}
}
/**
* Converts a JAXB Element to a W3C Document.
*
* @param el the JAXB Element
* @return the corresponding W3C Document.
*
* @throws I2B2XMLException if the translation fails.
*/
public Document documentFromJAXBElement(JAXBElement el) throws I2B2XMLException {
try {
Document document = DocumentBuilderFactory.newInstance().newDocumentBuilder().newDocument();
marshaller(el, document);
return document;
} catch (JAXBUtilException | ParserConfigurationException e) {
throw Logger.error(new I2B2XMLException("Could not translate jaxbelement -> document", e));
}
}
public I2b2Status parseStatus(ResponseMessageType resp) throws I2B2XMLException {
try {
I2b2Status status = I2b2Status.valueOf(resp.getResponseHeader().getResultStatus().getStatus().getType());
status.setStatusMessage(resp.getResponseHeader().getResultStatus().getStatus().getValue());
return status;
} catch (IllegalArgumentException e) {
throw Logger.error(new I2B2XMLException("Status not parsable.", e));
}
}
public I2b2Status parseStatus(OMElement omElement) throws I2B2XMLException {
try {
JAXBElement responseJaxb = unMashallFromString(omElement.toString());
ResponseMessageType r = (ResponseMessageType) responseJaxb.getValue();
return parseStatus(r);
} catch (JAXBUtilException e) {
throw Logger.error(new I2B2XMLException("Status not parsable.", e));
}
}
public Pair<I2b2Status, BodyType> parseI2b2Response(String response) throws I2B2XMLException {
try {
JAXBElement responseJaxb = unMashallFromString(response);
ResponseMessageType resp = (ResponseMessageType) responseJaxb.getValue();
return new Pair<>(parseStatus(resp), resp.getMessageBody());
} catch (JAXBUtilException e) {
throw Logger.error(new I2B2XMLException("unmashalling exception", e));
}
}
public RequestMessageType parseI2b2Request(String req) throws I2B2XMLException {
try {
JAXBElement responseJaxb = unMashallFromString(req);
return (RequestMessageType) responseJaxb.getValue();
} catch (JAXBUtilException e) {
throw Logger.error(new I2B2XMLException("unmashalling exception", e));
}
}
}

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