Diffusion Genome Privacy - SHCS App (ms_access_migration) Browse

SOAPMessageFormatter.java
19e88dbd7dbbms_access_migration

SOAPMessageFormatter.java
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			package ws;

			import java.io.ByteArrayOutputStream;
			import java.io.IOException;
			import java.io.ObjectOutputStream;
			import java.math.BigInteger;
			import java.security.SecureRandom;
			import java.util.ArrayList;
			import java.util.HashMap;
			import java.util.HashSet;
			import java.util.LinkedList;
			import java.util.logging.Level;
			import java.util.logging.Logger;

			import javax.xml.soap.MessageFactory;
			import javax.xml.soap.Name;
			import javax.xml.soap.SOAPBody;
			import javax.xml.soap.SOAPBodyElement;
			import javax.xml.soap.SOAPElement;
			import javax.xml.soap.SOAPEnvelope;
			import javax.xml.soap.SOAPException;
			import javax.xml.soap.SOAPMessage;
			import javax.xml.soap.SOAPPart;
			import javax.xml.transform.OutputKeys;
			import javax.xml.transform.Source;
			import javax.xml.transform.Transformer;
			import javax.xml.transform.TransformerException;
			import javax.xml.transform.TransformerFactory;
			import javax.xml.transform.stream.StreamResult;

			import org.apache.commons.codec.binary.Base64;

			import crypto.elgamal.fragment.FragmentEncoded;
			import framework.Marker;
			import framework.MarkerEncrypted;
			import framework.reply.ReplyDecryption;
			import framework.reply.ReplyMaterial;

			public class SOAPMessageFormatter {

			private static final Logger LOGGER = Logger.getLogger(SOAPMessageFormatter.class.getName());

			private static final String NS_RQT_MATERIAL = "rqt_material";
			private static final String NS_RQT_DECRYPT = "rqt_decrypt";
			private static final String NS_AWR_MATERIAL = "awr_material";
			private static final String NS_AWR_DECRYPT = "awr_decrypt";

			private static final String NS_ID_PATIENT = "patient";

			private static final String NS_LIST_ID_MARKER = "marker_id_list";
			private static final String NS_LIST_ID_CF = "cf_id_list";

			private static final String NS_LIST_MARKER = "marker_list";
			private static final String NS_LIST_CF = "cf_list";
			private static final String NS_LIST_HLA = "hla_list";

			private static final String NS_ID_MARKER = "marker_id";
			private static final String NS_ID_CF = "cf_id";
			private static final String NS_ID_HLA = "hla_id";

			private static final String NS_MARKER = "marker";
			private static final String NS_CF = "cf";
			private static final String NS_HLA = "hla";

			private static final String NS_VAL_MARKER_1 = "marker_val_1";
			private static final String NS_VAL_MARKER_2 = "marker_val_2";
			private static final String NS_VAL_CF_1 = "cf_val_1";
			private static final String NS_VAL_CF_2 = "cf_val_2";
			private static final String NS_VAL_HLA_1 = "hla_val_1";
			private static final String NS_VAL_HLA_2 = "hla_val_2";

			private static final String NS_DECRYPT_TS = "decrypt_ts";
			private static final String NS_DECRYPT_VAL = "decrypt_val";



			/**
			* Create SOAP message for given material request.
			* The request will have to following format:
			* <pre>
			* {@code
			* <NS_RQT_MATERIAL>
			* <NS_ID_PATIENT>myPatientId</NS_ID_PATIENT>
			* <NS_LIST_ID_MARKER>
			* <NS_ID_MARKER>rs_xxxxxxxx</NS_ID_MARKER>
			* ...
			* <NS_ID_MARKER>rs_xxxxxxxx</NS_ID_MARKER>
			* </NS_LIST_ID_MARKER>
			* <NS_LIST_ID_CF>
			* <NS_ID_CF>xx</NS_ID_CF>
			* <NS_ID_CF>yy</NS_ID_CF>
			* </NS_LIST_ID_CF>
			* </NS_RQT_MATERIAL>
			* }
			* </pre>
			*
			* @param patientId patient ID
			* @param markers set of markers requested
			* @param cfs set of clinical factors requested
			* @return SOAP message
			* @throws SOAPException
			*/
			public static SOAPMessage createRequestMaterialMsg(int patientId, HashSet<Marker> markers, HashSet<Integer> cfs) throws SOAPException {
			MessageFactory msgFct = MessageFactory.newInstance();
			SOAPMessage msg = msgFct.createMessage();

			// remove header
			msg.getSOAPHeader().detachNode();

			SOAPPart soapPart = msg.getSOAPPart();
			SOAPEnvelope soapEnv = soapPart.getEnvelope();
			SOAPBody soapBody = soapEnv.getBody();

			Name rqtMatName = soapEnv.createName(NS_RQT_MATERIAL);
			Name patientName = soapEnv.createName(NS_ID_PATIENT);
			Name markerIdListName = soapEnv.createName(NS_LIST_ID_MARKER);
			Name markerIdName = soapEnv.createName(NS_ID_MARKER);
			Name cfIdListName = soapEnv.createName(NS_LIST_ID_CF);
			Name cfIdName = soapEnv.createName(NS_ID_CF);

			// create markers and CFs lists
			// -----------------------------------------------
			// <NS_RQT_MATERIAL>
			// <NS_ID_PATIENT>myPatientId</NS_ID_PATIENT>
			//
			// <NS_LIST_ID_MARKER>
			// ...
			// </NS_LIST_ID_MARKER>
			//
			// <NS_LIST_ID_CF>
			// ...
			// </NS_LIST_ID_CF>
			// </NS_RQT_MATERIAL>
			SOAPBodyElement rqtMatElem = soapBody.addBodyElement(rqtMatName);
			SOAPElement patientElem = rqtMatElem.addChildElement(patientName);
			SOAPElement markerIdListElem = rqtMatElem.addChildElement(markerIdListName);
			SOAPElement cfIdListElem = rqtMatElem.addChildElement(cfIdListName);

			// insert patient id value
			patientElem.addTextNode(Integer.valueOf(patientId).toString());

			// insert all markers
			// -----------------------------------------------
			// <NS_LIST_ID_MARKER>
			// <NS_ID_MARKER>rs_xxxxxxxx</NS_ID_MARKER>
			// ...
			// <NS_ID_MARKER>rs_xxxxxxxx</NS_ID_MARKER>
			// </NS_LIST_ID_MARKER>
			for (Marker marker : markers) {
			SOAPElement markerElem = markerIdListElem.addChildElement(markerIdName);
			markerElem.addTextNode(marker.getId());
			}

			// insert all clinical factors
			// -----------------------------------------------
			for (Integer cf : cfs) {
			SOAPElement cfElem = cfIdListElem.addChildElement(cfIdName);
			cfElem.addTextNode(cf.toString());
			}

			// save changes
			msg.saveChanges();

			return msg;
			}

			/**
			* Create SOAP message for given decryption request.
			* It will have to following format:
			*
			* <pre>
			* {@code
			* <NS_RQT_DECRYPT>
			* <NS_ID_PATIENT>myPatientId</NS_ID_PATIENT>
			* <NS_RQT_DECRYPT_TS>123456789</NS_RQT_DECRYPT_TS>
			* <NS_RQT_DECRYPT_VAL>ASDF7894fasdu==</NS_RQT_DECRYPT_VAL>
			* </NS_RQT_DECRYPT>
			* }
			* </pre>
			*
			* @param patientId patient ID
			* @param timestamp request timestamp
			* @param request Request serialized.
			* @return SOAP message
			* @throws SOAPException
			*/
			public static SOAPMessage createRequestDecryptMsg(int patientId, long timestamp, byte[] request) throws SOAPException {
			MessageFactory msgFct = MessageFactory.newInstance();
			SOAPMessage msg = msgFct.createMessage();

			// remove header
			msg.getSOAPHeader().detachNode();

			SOAPPart soapPart = msg.getSOAPPart();
			SOAPEnvelope soapEnv = soapPart.getEnvelope();
			SOAPBody soapBody = soapEnv.getBody();

			Name rqtDecryptName = soapEnv.createName(NS_RQT_DECRYPT);

			Name patientName = soapEnv.createName(NS_ID_PATIENT);
			Name rqtTimestamp = soapEnv.createName(NS_DECRYPT_TS);
			Name rqtRqtVal = soapEnv.createName(NS_DECRYPT_VAL);

			// create request
			// -----------------------------------------------
			// <NS_RQT_DECRYPT>
			// <NS_ID_PATIENT>myPatientId</NS_ID_PATIENT>
			//
			// <NS_DECRYPT_TS>123456789</NS_DECRYPT_TS>
			//
			// <NS_DECRYPT_VAL>ASDF7894fasdu==</NS_DECRYPT_VAL>
			// </NS_RQT_DECRYPT>
			SOAPBodyElement rqtDecryptElem = soapBody.addBodyElement(rqtDecryptName);

			SOAPElement patientElem = rqtDecryptElem.addChildElement(patientName);
			patientElem.addTextNode(Integer.valueOf(patientId).toString());

			SOAPElement tsElem = rqtDecryptElem.addChildElement(rqtTimestamp);
			tsElem.addTextNode(Long.valueOf(timestamp).toString());

			SOAPElement valElem = rqtDecryptElem.addChildElement(rqtRqtVal);
			String requestBase64 = Base64.encodeBase64String(request);
			valElem.addTextNode(requestBase64);

			// save changes
			msg.saveChanges();

			return msg;
			}

			public static SOAPMessage createReplyMaterialMsg(int patientId,
			HashMap<MarkerEncrypted, FragmentEncoded> markers,
			HashMap<Integer, FragmentEncoded> cfs,
			ArrayList<LinkedList<byte[]>> hlas) throws SOAPException, IOException {

			MessageFactory msgFct = MessageFactory.newInstance();
			SOAPMessage msg = msgFct.createMessage();

			// remove header
			msg.getSOAPHeader().detachNode();

			SOAPPart soapPart = msg.getSOAPPart();
			SOAPEnvelope soapEnv = soapPart.getEnvelope();
			SOAPBody soapBody = soapEnv.getBody();

			Name awrMatName = soapEnv.createName(NS_AWR_MATERIAL);
			Name patientName = soapEnv.createName(NS_ID_PATIENT);
			Name markerListName = soapEnv.createName(NS_LIST_MARKER);
			Name cfListName = soapEnv.createName(NS_LIST_CF);
			Name hlaListName = soapEnv.createName(NS_LIST_HLA);

			Name markerName = soapEnv.createName(NS_MARKER);
			Name markerIdName = soapEnv.createName(NS_ID_MARKER);
			Name markerVal1Name = soapEnv.createName(NS_VAL_MARKER_1);
			Name markerVal2Name = soapEnv.createName(NS_VAL_MARKER_2);

			Name cfName = soapEnv.createName(NS_CF);
			Name cfIdName = soapEnv.createName(NS_ID_CF);
			Name cfVal1Name = soapEnv.createName(NS_VAL_CF_1);
			Name cfVal2Name = soapEnv.createName(NS_VAL_CF_2);


			// create reply
			// -----------------------------------------------
			// <NS_AWR_MATERIAL>
			// <NS_ID_PATIENT>myPatientId</NS_ID_PATIENT>
			// <NS_LIST_MARKER>
			// ...
			// </NS_LIST_MARKER>
			// <NS_LIST_CF>
			// ...
			// </NS_LIST_CF>
			// <NS_HLA_LIST>
			// ...
			// </NS_HLA_LIST>
			// </NS_AWR_MATERIAL>
			SOAPBodyElement awrMatElem = soapBody.addBodyElement(awrMatName);

			SOAPElement patientElem = awrMatElem.addChildElement(patientName);
			SOAPElement markersElem = awrMatElem.addChildElement(markerListName);
			SOAPElement cfsElem = awrMatElem.addChildElement(cfListName);
			SOAPElement hlasElem = awrMatElem.addChildElement(hlaListName);

			patientElem.addTextNode(Integer.valueOf(patientId).toString());

			// insert all markers
			// -----------------------------------------------
			// <NS_LIST_MARKER>
			// <NS_MARKER>
			// <NS_ID_MARKER>rs_xxxx</NS_ID_MARKER>
			// <NS_VAL_MARKER>asdhBasdfY==</NS_VAL_MARKER>
			// </NS_MARKER>
			// ...
			// </NS_LIST_MARKER>
			for (MarkerEncrypted markerEnc : markers.keySet()) {
			SOAPElement markerElem = markersElem.addChildElement(markerName);
			SOAPElement markerIdElem = markerElem.addChildElement(markerIdName);
			SOAPElement markerVal1Elem = markerElem.addChildElement(markerVal1Name);
			SOAPElement markerVal2Elem = markerElem.addChildElement(markerVal2Name);

			FragmentEncoded frag = markers.get(markerEnc);
			markerIdElem.addTextNode(markerEnc.getMarker());
			markerVal1Elem.addTextNode(Base64.encodeBase64String(frag.getEncodedR()));
			markerVal2Elem.addTextNode(Base64.encodeBase64String(frag.getEncodedS()));
			}

			// insert all clinical factors
			for (Integer cf : cfs.keySet()) {
			SOAPElement cfElem = cfsElem.addChildElement(cfName);
			SOAPElement cfIdElem = cfElem.addChildElement(cfIdName);
			SOAPElement cfVal1Elem = cfElem.addChildElement(cfVal1Name);
			SOAPElement cfVal2Elem = cfElem.addChildElement(cfVal2Name);

			FragmentEncoded frag = cfs.get(cf);
			cfIdElem.addTextNode(cf.toString());
			cfVal1Elem.addTextNode(Base64.encodeBase64String(frag.getEncodedR()));
			cfVal2Elem.addTextNode(Base64.encodeBase64String(frag.getEncodedS()));
			}

			insertHLA(hlasElem, soapEnv, "A", hlas.get(0), hlas.get(1));
			insertHLA(hlasElem, soapEnv, "B", hlas.get(2), hlas.get(3));
			insertHLA(hlasElem, soapEnv, "C", hlas.get(4), hlas.get(5));

			// save changes
			msg.saveChanges();

			return msg;
			}

			private static void insertHLA(SOAPElement hlasElem,
			SOAPEnvelope soapEnv,
			String id,
			LinkedList<byte[]> encHlaFirst,
			LinkedList<byte[]> encHlaSecond) throws SOAPException, IOException {

			Name hlaName = soapEnv.createName(NS_HLA);
			Name hlaIdName = soapEnv.createName(NS_ID_HLA);
			Name hlaVal1Name = soapEnv.createName(NS_VAL_HLA_1);
			Name hlaVal2Name = soapEnv.createName(NS_VAL_HLA_2);

			SOAPElement hlaElem = hlasElem.addChildElement(hlaName);
			SOAPElement hlaIdElem = hlaElem.addChildElement(hlaIdName);
			SOAPElement hlaVal1Elem = hlaElem.addChildElement(hlaVal1Name);
			SOAPElement hlaVal2Elem = hlaElem.addChildElement(hlaVal2Name);

			hlaIdElem.addTextNode(id);
			byte[] first = serializeLinkedList(encHlaFirst);
			byte[] second = serializeLinkedList(encHlaSecond);
			hlaVal1Elem.addTextNode(Base64.encodeBase64String(first));
			hlaVal2Elem.addTextNode(Base64.encodeBase64String(second));
			}

			private static byte[] serializeLinkedList(LinkedList<byte[]> part) throws IOException {
			ByteArrayOutputStream baos = new ByteArrayOutputStream();
			ObjectOutputStream oos = new ObjectOutputStream(baos);

			oos.writeObject(part);
			return baos.toByteArray();
			}

			public static SOAPMessage createReplyDecryptMsg(int patientId, long timestamp, byte[] reply) throws SOAPException {
			MessageFactory msgFct = MessageFactory.newInstance();
			SOAPMessage msg = msgFct.createMessage();

			// remove header
			msg.getSOAPHeader().detachNode();

			SOAPPart soapPart = msg.getSOAPPart();
			SOAPEnvelope soapEnv = soapPart.getEnvelope();
			SOAPBody soapBody = soapEnv.getBody();

			Name awrDecryptName = soapEnv.createName(NS_AWR_DECRYPT);

			Name patientName = soapEnv.createName(NS_ID_PATIENT);
			Name awrTimestamp = soapEnv.createName(NS_DECRYPT_TS);
			Name awrRqtVal = soapEnv.createName(NS_DECRYPT_VAL);

			// create reply
			// -----------------------------------------------
			// <NS_AWR_DECRYPT>
			// <NS_ID_PATIENT>myPatientId</NS_ID_PATIENT>
			//
			// <NS_DECRYPT_TS>123456789</NS_DECRYPT_TS>
			//
			// <NS_DECRYPT_VAL>ASDF7894fasdu==</NS_DECRYPT_VAL>
			// </NS_AWR_DECRYPT>
			SOAPBodyElement awrDecryptElem = soapBody.addBodyElement(awrDecryptName);

			SOAPElement patientElem = awrDecryptElem.addChildElement(patientName);
			patientElem.addTextNode(Integer.valueOf(patientId).toString());

			SOAPElement tsElem = awrDecryptElem.addChildElement(awrTimestamp);
			tsElem.addTextNode(Long.valueOf(timestamp).toString());

			SOAPElement valElem = awrDecryptElem.addChildElement(awrRqtVal);
			String requestBase64 = Base64.encodeBase64String(reply);
			valElem.addTextNode(requestBase64);

			// save changes
			msg.saveChanges();

			return msg;
			}

			@Deprecated
			public static ReplyDecryption parseDecryptRqtMsg(SOAPMessage msg) throws SOAPException {
			SOAPBody soapBody = msg.getSOAPBody();

			SOAPBodyElement replyDecryptElem = (SOAPBodyElement)soapBody.getFirstChild();

			replyDecryptElem.getElementName().getQualifiedName();// FIXME

			// TODO
			return null;
			}

			@Deprecated
			public static ReplyMaterial parseMaterialRqtMsg(SOAPMessage msg) {

			// TODO
			return null;
			}

			/**
			* Returns the XML representation of SOAP object
			* nicely formatted with indentation and new lines.
			*
			* @param msg SOAP message to be formatted
			* @return nicely formatted SOAP message
			* @throws SOAPException
			*/
			public static String printSOAPMessage(SOAPMessage msg) throws SOAPException {
			String s = "FAILED TO TRANSFORM SOAP TO STRING";

			TransformerFactory transformerFct = TransformerFactory.newInstance();
			try {
			Transformer transformer = transformerFct.newTransformer();

			transformer.setOutputProperty(OutputKeys.INDENT, "yes");
			transformer.setOutputProperty("{http://xml.apache.org/xslt}indent-amount", "2");

			Source sourceContent = msg.getSOAPPart().getContent();
			ByteArrayOutputStream baos = new ByteArrayOutputStream();
			StreamResult result = new StreamResult(baos);
			transformer.transform(sourceContent, result);

			s = baos.toString();
			} catch (TransformerException e) {
			LOGGER.log(Level.SEVERE, null, e);
			}
			return s;
			}

			public static void main(String[] args) throws SOAPException, IOException {
			int patientId = 30351;
			long ts = System.currentTimeMillis();
			Marker m1 = new Marker("rs222");
			Marker m2 = new Marker("rs333");
			Integer cf1 = new Integer("2");
			Integer cf2 = new Integer("3");

			SecureRandom rand = new SecureRandom();

			// material request
			System.out.println("MATERIAL REQUEST:");
			HashSet<Marker> markerIndices = new HashSet<>();
			markerIndices.add(m1);
			markerIndices.add(m2);
			HashSet<Integer> cfIndices = new HashSet<>();
			cfIndices.add(cf1);
			cfIndices.add(cf2);
			SOAPMessage msgMatRqt = createRequestMaterialMsg(patientId, markerIndices, cfIndices);
			System.out.println(printSOAPMessage(msgMatRqt));

			// decrypt request
			System.out.println("DECRYPT REQUEST:");
			SOAPMessage msgDecRqt = createRequestDecryptMsg(patientId, ts, rndByte());
			System.out.println(printSOAPMessage(msgDecRqt));

			// decrypt reply
			System.out.println("DECRYPT REPLY");
			SOAPMessage msgDecAwr = createReplyDecryptMsg(patientId, ts, rndByte());
			System.out.println(printSOAPMessage(msgDecAwr));

			// material reply
			System.out.println("MATERIAL ANSWER");
			HashMap<MarkerEncrypted, FragmentEncoded> markers = new HashMap<>();
			markers.put(new MarkerEncrypted("rs222"), new FragmentEncoded(rndByte(), rndByte()));
			markers.put(new MarkerEncrypted("rs333"), new FragmentEncoded(rndByte(), rndByte()));
			HashMap<Integer, FragmentEncoded> cfs = new HashMap<>();
			cfs.put(cf1, new FragmentEncoded(rndByte(), rndByte()));
			cfs.put(cf2, new FragmentEncoded(rndByte(), rndByte()));
			ArrayList<LinkedList<byte[]>> hlas = new ArrayList<>();
			for (int i = 0; i < 6; i++) {
			LinkedList<byte[]> hlaX_i = new LinkedList<>();
			hlaX_i.add(rndByte());
			hlas.add(hlaX_i);
			}
			SOAPMessage msgMatAwr = createReplyMaterialMsg(patientId, markers, cfs, hlas);
			System.out.println(printSOAPMessage(msgMatAwr));
			}

			private static byte[] rndByte() {
			SecureRandom rnd = new SecureRandom();
			return new BigInteger(133, rnd).toByteArray();
			}

			}

genopri-shcs/project/PPPCommons/src/ws/SOAPMessageFormatter.java19e88dbd7dbbms_access_migration

SOAPMessageFormatter.javaView Options

genopri-shcs/project/PPPCommons/src/ws/SOAPMessageFormatter.java
19e88dbd7dbbms_access_migration

SOAPMessageFormatter.java
View Options