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SHRINECell.java
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Sat, Oct 5, 15:25

SHRINECell.java
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package ch.epfl.lca1.medco;
import ch.epfl.lca1.medco.i2b2.I2B2Cell;
import ch.epfl.lca1.medco.i2b2.crc.I2B2QueryRequest;
import ch.epfl.lca1.medco.i2b2.crc.I2B2QueryResponse;
import ch.epfl.lca1.medco.i2b2.pm.MedCoI2b2MessageHeader;
import ch.epfl.lca1.medco.util.Logger;
import ch.epfl.lca1.medco.util.exceptions.I2B2XMLException;
import edu.harvard.i2b2.common.exception.I2B2Exception;
import edu.harvard.i2b2.common.util.jaxb.JAXBUtilException;
import edu.harvard.i2b2.crc.datavo.i2b2message.RequestMessageType;
import edu.harvard.i2b2.crc.datavo.i2b2message.ResponseMessageType;
import org.apache.axiom.om.OMElement;
import org.apache.axiom.om.OMNode;
import org.apache.axiom.om.OMText;
import org.apache.axiom.om.impl.builder.StAXOMBuilder;
import org.apache.axiom.om.impl.llom.OMNodeImpl;
import org.w3c.dom.Document;
import javax.xml.bind.JAXBElement;
import javax.xml.namespace.QName;
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 java.io.StringReader;
import java.io.StringWriter;
// todo: harmonize error handling (i2b2status + exceptions)
public class SHRINECell extends I2B2Cell {
private static final String URL_PATH_SHRINE_REQ = "/request"; //URL--
public SHRINECell(String shrineCellUrl, MedCoI2b2MessageHeader auth) {
super(shrineCellUrl, auth);
}
/**
*
* @param shrineRequest
* @return
* @throws I2B2Exception
*/
public I2B2QueryResponse shrineQuery(I2B2QueryRequest shrineRequest) throws I2B2Exception {
// make query request (from query definition) with a patient set result output
I2B2QueryResponse parsedResp;
try {
// TODO: create custom service client that is used by all cells
Logger.info("New request to cell " + cellURL);
RequestMessageType newReqMessage = createRequestMessage(shrineRequest.getMessageBody());
OMElement reqMessageOM = buildOMElementShrineCustom(newReqMessage);
String answerMessage = CustomServiceClient.sendRESTCustomTimeout(cellURL + URL_PATH_SHRINE_REQ, reqMessageOM);
Logger.debug("Cell " + cellURL + " answered: " + answerMessage);
// extract response
JAXBElement responseJaxb = msgUtil.unMashallFromString(answerMessage);
ResponseMessageType resp = (ResponseMessageType) responseJaxb.getValue();
parsedResp = new I2B2QueryResponse(resp);
Logger.info("crc query request result: " + parsedResp.getI2b2Status());
} catch (Exception e) {
throw Logger.error(new I2B2Exception("Request failed.", e));
}
return parsedResp;
}
/**
* 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 buildOMElementShrineCustom(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 {
msgUtil.marshaller(hiveObjectFactory.createRequest(reqMessage), strWriter);
// insert shrine stuff
String orig = strWriter.toString();
String update1 =
orig.substring(0, orig.indexOf("</query_definition>")) +
"<use_shrine>1</use_shrine>\n" +
orig.substring(orig.indexOf("</query_definition>"));
String update2 =
update1.substring(0, update1.indexOf("</message_body>")) +
//"<shrine><queryTopicID>1</queryTopicID></shrine>\n" + todo: disabled to avoid topic match error
update1.substring(update1.indexOf("</message_body>"));
System.out.println("XXXXXXX");
System.out.println(update2);
StringReader strReader = new StringReader(update2);
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));
}
}
}

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