Java tutorial
/* * Copyright (c) 2006-2012 Massachusetts General Hospital * All rights reserved. This program and the accompanying materials * are made available under the terms of the i2b2 Software License v2.1 * which accompanies this distribution. * * Contributors: * * Wensong Pan * */ package edu.harvard.i2b2.explorer.serviceClient; import java.io.File; import java.io.RandomAccessFile; import java.io.StringReader; import java.io.StringWriter; import java.util.ArrayList; import java.util.HashSet; import javax.swing.JOptionPane; import javax.xml.stream.XMLInputFactory; import javax.xml.stream.XMLStreamReader; import org.apache.axiom.om.OMAbstractFactory; import org.apache.axiom.om.OMElement; import org.apache.axiom.om.OMNamespace; import org.apache.axiom.om.impl.builder.StAXOMBuilder; import org.apache.axiom.soap.SOAPEnvelope; import org.apache.axiom.soap.SOAPFactory; import org.apache.axis2.AxisFault; import org.apache.axis2.Constants; import org.apache.axis2.addressing.EndpointReference; import org.apache.axis2.client.OperationClient; import org.apache.axis2.client.Options; import org.apache.axis2.client.ServiceClient; import org.apache.axis2.context.ConfigurationContext; import org.apache.axis2.context.ConfigurationContextFactory; import org.apache.axis2.context.MessageContext; import org.apache.axis2.transport.http.HTTPConstants; import org.apache.axis2.transport.http.HttpTransportProperties; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import org.jdom.input.SAXBuilder; import org.jdom.output.Format; import org.jdom.output.XMLOutputter; import edu.harvard.i2b2.common.datavo.pdo.PatientSet; import edu.harvard.i2b2.common.datavo.pdo.PatientType; import edu.harvard.i2b2.eclipse.UserInfoBean; import edu.harvard.i2b2.eclipse.plugins.explorer.utils.MessageUtil; import edu.harvard.i2b2.explorer.dataModel.PDOItem; import edu.harvard.i2b2.explorer.dataModel.PDORequestMessageModel; import edu.harvard.i2b2.explorer.dataModel.PDOResponseMessageModel; import edu.harvard.i2b2.explorer.dataModel.PDOValueModel; import edu.harvard.i2b2.explorer.dataModel.TimelineFactory; import edu.harvard.i2b2.explorer.dataModel.TimelineRow; import edu.harvard.i2b2.explorer.ui.MainComposite; public class PDOQueryClient { private static final Log log = LogFactory.getLog(PDOQueryClient.class); private static EndpointReference targetEPR; private static String getPDOServiceName() { return UserInfoBean.getInstance().getCellDataUrl("CRC") + "pdorequest"; } private static String getPDQServiceName() { return UserInfoBean.getInstance().getCellDataUrl("CRC") + "request"; } public static OMElement getQueryPayLoad(String str) throws Exception { StringReader strReader = new StringReader(str); XMLInputFactory xif = XMLInputFactory.newInstance(); XMLStreamReader reader = xif.createXMLStreamReader(strReader); StAXOMBuilder builder = new StAXOMBuilder(reader); OMElement lineItem = builder.getDocumentElement(); // log.debug("Line item string " + lineItem.toString()); return lineItem; } public static String sendPDQQueryRequestREST(String XMLstr) { try { MessageUtil.getInstance().setRequest("URL: " + getPDQServiceName() + "\n" + XMLstr); OMElement payload = getQueryPayLoad(XMLstr); Options options = new Options(); targetEPR = new EndpointReference(getPDQServiceName()); options.setTo(targetEPR); options.setTransportInProtocol(Constants.TRANSPORT_HTTP); options.setProperty(Constants.Configuration.ENABLE_REST, Constants.VALUE_TRUE); options.setProperty(HTTPConstants.SO_TIMEOUT, new Integer(600000)); options.setProperty(HTTPConstants.CONNECTION_TIMEOUT, new Integer(600000)); ServiceClient sender = new ServiceClient(); sender.setOptions(options); OMElement responseElement = sender.sendReceive(payload); MessageUtil.getInstance() .setResponse("URL: " + getPDQServiceName() + "\n" + responseElement.toString()); return responseElement.toString(); } catch (AxisFault axisFault) { axisFault.printStackTrace(); java.awt.EventQueue.invokeLater(new Runnable() { public void run() { JOptionPane.showMessageDialog(null, "Trouble with connection to the remote server, " + "this is often a network error, please try again", "Network Error", JOptionPane.INFORMATION_MESSAGE); } }); return null; } catch (Exception e) { e.printStackTrace(); return null; } } public static String sendPDQQueryRequestSOAP(String XMLstr) { try { MessageUtil.getInstance().setRequest("URL: " + getPDQServiceName() + "\n" + XMLstr); HttpTransportProperties.Authenticator basicAuthentication = new HttpTransportProperties.Authenticator(); basicAuthentication.setUsername(UserInfoBean.getInstance().getUserName()); basicAuthentication.setPassword(UserInfoBean.getInstance().getUserPassword()); OMElement payload = getQueryPayLoad(XMLstr); Options options = new Options(); // options.setProperty(HTTPConstants.PROXY, proxyProperties); targetEPR = new EndpointReference(getPDQServiceName()); options.setTo(targetEPR); options.setProperty(org.apache.axis2.transport.http.HTTPConstants.AUTHENTICATE, basicAuthentication); options.setTimeOutInMilliSeconds(900000); options.setTransportInProtocol(Constants.TRANSPORT_HTTP); ConfigurationContext configContext = ConfigurationContextFactory.createConfigurationContextFromFileSystem(null, null); // Blocking invocation ServiceClient sender = new ServiceClient(configContext, null); sender.setOptions(options); OMElement responseElement = sender.sendReceive(payload); // log.debug("Client Side response " + responseElement.toString()); MessageUtil.getInstance() .setResponse("URL: " + getPDQServiceName() + "\n" + responseElement.toString()); return responseElement.toString(); } catch (AxisFault axisFault) { axisFault.printStackTrace(); if (axisFault.getMessage().indexOf("No route to host") >= 0) { java.awt.EventQueue.invokeLater(new Runnable() { public void run() { JOptionPane.showMessageDialog(null, "Unable to make a connection to the remote server,\n this is often a network error, please try again", "Network Error", JOptionPane.INFORMATION_MESSAGE); } }); } else if (axisFault.getMessage().indexOf("Read timed out") >= 0) { java.awt.EventQueue.invokeLater(new Runnable() { public void run() { JOptionPane.showMessageDialog(null, "Unable to obtain a response from the remote server, this is often a network error, please try again", "Network Error", JOptionPane.INFORMATION_MESSAGE); } }); } return null; } catch (Exception e) { e.printStackTrace(); return null; } } public static String sendPDOQueryRequestREST(String XMLstr) { try { SAXBuilder parser = new SAXBuilder(); String xmlContent = XMLstr; java.io.StringReader xmlStringReader = new java.io.StringReader(xmlContent); org.jdom.Document tableDoc = parser.build(xmlStringReader); XMLOutputter o = new XMLOutputter(); o.setFormat(Format.getPrettyFormat()); StringWriter str = new StringWriter(); o.output(tableDoc, str); //jMessageTextArea.setText(str.toString()); //text.setText(str.toString()); MessageUtil.getInstance().setRequest("URL: " + getPDOServiceName() + "\n" + str); OMElement payload = getQueryPayLoad(XMLstr); Options options = new Options(); targetEPR = new EndpointReference(getPDOServiceName()); options.setTo(targetEPR); options.setTransportInProtocol(Constants.TRANSPORT_HTTP); options.setProperty(Constants.Configuration.ENABLE_REST, Constants.VALUE_TRUE); options.setProperty(HTTPConstants.SO_TIMEOUT, new Integer(600000)); options.setProperty(HTTPConstants.CONNECTION_TIMEOUT, new Integer(600000)); ServiceClient sender = new ServiceClient(); sender.setOptions(options); OMElement responseElement = sender.sendReceive(payload); // log.debug("Client Side response " + responseElement.toString()); xmlStringReader = new java.io.StringReader(responseElement.toString()); tableDoc = parser.build(xmlStringReader); o = new XMLOutputter(); o.setFormat(Format.getPrettyFormat()); str = new StringWriter(); o.output(tableDoc, str); MessageUtil.getInstance().setResponse("URL: " + getPDOServiceName() + "\n" + str); //responseElement.toString()); return responseElement.toString(); } catch (AxisFault axisFault) { axisFault.printStackTrace(); java.awt.EventQueue.invokeLater(new Runnable() { public void run() { JOptionPane.showMessageDialog(null, "Trouble with connection to the remote server, " + "this is often a network error, please try again", "Network Error", JOptionPane.INFORMATION_MESSAGE); } }); return null; } catch (java.lang.OutOfMemoryError e) { e.printStackTrace(); return "memory error"; } catch (Exception e) { e.printStackTrace(); return null; } } public static String sendPDOQueryRequestSOAP(String XMLstr) { try { MessageUtil.getInstance().setRequest("URL: " + getPDOServiceName() + "\n" + XMLstr); ServiceClient sender = AxisServiceClient.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 targetEPR = new EndpointReference(UserInfoBean.getInstance().getCellDataUrl("IM")); log.debug(targetEPR); opts.setTo(targetEPR); opts.setAction("http://rpdr.partners.org/GetPatientDataObject"); opts.setTimeOutInMilliSeconds(180000); log.debug(XMLstr); SOAPEnvelope envelope = null; SOAPFactory fac = OMAbstractFactory.getSOAP11Factory(); envelope = fac.getDefaultEnvelope(); OMNamespace omNs = fac.createOMNamespace("http://rpdr.partners.org/", "rpdr"); // creating the SOAP payload OMElement method = fac.createOMElement("GetPatientDataObject", omNs); OMElement value = fac.createOMElement("RequestXmlString", omNs); value.setText(XMLstr); method.addChild(value); envelope.getBody().addChild(method); outMsgCtx.setEnvelope(envelope); operationClient.addMessageContext(outMsgCtx); operationClient.execute(true); MessageContext inMsgtCtx = operationClient.getMessageContext("In"); SOAPEnvelope responseEnv = inMsgtCtx.getEnvelope(); OMElement soapResponse = responseEnv.getBody().getFirstElement(); // log.debug("Sresponse: "+ soapResponse.toString()); OMElement soapResult = soapResponse.getFirstElement(); // log.debug("Sresult: "+ soapResult.toString()); String i2b2Response = soapResult.getText(); log.debug(i2b2Response); MessageUtil.getInstance().setResponse("URL: " + getPDOServiceName() + "\n" + i2b2Response); return i2b2Response; } catch (AxisFault axisFault) { axisFault.printStackTrace(); if (axisFault.getMessage().indexOf("No route to host") >= 0) { java.awt.EventQueue.invokeLater(new Runnable() { public void run() { JOptionPane.showMessageDialog(null, "Unable to make a connection to the remote server,\n this is often a network error, please try again", "Network Error", JOptionPane.INFORMATION_MESSAGE); } }); } else if (axisFault.getMessage().indexOf("Read timed out") >= 0) { java.awt.EventQueue.invokeLater(new Runnable() { public void run() { JOptionPane.showMessageDialog(null, "Unable to obtain a response from the remote server, this is often a network error, please try again", "Network Error", JOptionPane.INFORMATION_MESSAGE); } }); } return null; } catch (Exception e) { e.printStackTrace(); return null; } } public static String getlldString(ArrayList<TimelineRow> tlrows, String patientRefId, int minPatient, int maxPatient, boolean bDisplayAll, boolean writeFile, boolean displayDemographics, MainComposite explorer, String filter) { try { HashSet<String> conceptPaths = new HashSet<String>(); // HashSet<String> providerPaths = new HashSet<String>(); // HashSet<String> visitPaths = new HashSet<String>(); ArrayList<PDOItem> items = new ArrayList<PDOItem>(); for (int i = 0; i < tlrows.size(); i++) { for (int j = 0; j < tlrows.get(i).pdoItems.size(); j++) { PDOItem pdoItem = tlrows.get(i).pdoItems.get(j); String path = pdoItem.fullPath; if (conceptPaths.contains(path)) { //continue; } conceptPaths.add(path); // for(int k=0; k<pdoItem.valDisplayProperties.size(); k++) // { items.add(pdoItem); // } } } PDORequestMessageModel pdoFactory = new PDORequestMessageModel(); String pid = null; if (patientRefId.equalsIgnoreCase("All")) { pid = "-1"; } else { pid = patientRefId; } String xmlStr = pdoFactory.requestXmlMessage(items, pid, new Integer(minPatient), new Integer(maxPatient), false, filter); // explorer.lastRequestMessage(xmlStr); String result = null;// sendPDOQueryRequestREST(xmlStr); if (System.getProperty("webServiceMethod").equals("SOAP")) { result = PDOQueryClient.sendPDOQueryRequestSOAP(xmlStr); } else { result = PDOQueryClient.sendPDOQueryRequestREST(xmlStr); } if (result == null || result.equalsIgnoreCase("memory error")) { return result; } // explorer.lastResponseMessage(result); return new TimelineFactory().generateTimelineData(result, tlrows, writeFile, bDisplayAll, displayDemographics, explorer); } /* * catch(org.apache.axis2.AxisFault e) { e.printStackTrace(); * java.awt.EventQueue.invokeLater(new Runnable() { public void run() { * JOptionPane.showMessageDialog(null, * "Trouble with connection to the remote server, " + * "this is often a network error, please try again", "Network Error", * JOptionPane.INFORMATION_MESSAGE); } }); * * return null; } */ catch (Exception e) { e.printStackTrace(); return null; } } private static void testWriteTableFile(String result) { StringBuilder resultFile = new StringBuilder(); try { PDOResponseMessageModel pdoresponsefactory = new PDOResponseMessageModel(); PatientSet patientDimensionSet = pdoresponsefactory.getPatientSetFromResponseXML(result); if (patientDimensionSet != null) { log.debug("Total patient: " + patientDimensionSet.getPatient().size()); for (int i = 0; i < patientDimensionSet.getPatient().size(); i++) { PatientType patientType = patientDimensionSet.getPatient().get(i); log.debug("PatientNum: " + patientType.getPatientId()); // + ","+patientType.getRaceCd() // +","+patientType.getSexCd() // +","+patientType.getAgeInYearsNum() // +","+patientType.getVitalStatusCd()); resultFile.append(patientType.getPatientId()); // +","+patientType.getRaceCd() // +","+patientType.getSexCd() // +","+patientType.getAgeInYearsNum() // +","+patientType.getVitalStatusCd()+"\n"); } } /* * List<PatientDataType.ObservationFactSet> factSets = * pdoresponsefactory.getFactSetsFromResponseXML(result); * * for(int j=0; j<factSets.size(); j++) { * PatientDataType.ObservationFactSet observationFactSet = * factSets.get(j); * //pdoresponsefactory.getFactSetFromResponseXML(result); if * (observationFactSet != null) { * log.debug("Total fact: "+observationFactSet * .getObservationFact().size() * +" for "+observationFactSet.getPath() * +"-"+observationFactSet.getConceptName()); for(int i=0; * i<observationFactSet.getObservationFact().size(); i++) { * ObservationFactType obsFactType = * observationFactSet.getObservationFact().get(i); * log.debug("PatientNum: "+obsFactType.getPatientNum() * +" concept_cd: " + obsFactType.getConceptCd() +" start_date: " + * obsFactType.getStartDate().getYear() * +"_"+obsFactType.getStartDate().getMonth() * +"_"+obsFactType.getStartDate().getDay() * +"_"+obsFactType.getNvalNum() +"_"+obsFactType.getConceptCd() * +"_"+obsFactType.getPatientNum()); } } } */ String tableFile = "C:\\tableview\\data\\patienttable.txt"; File oDelete = new File(tableFile); if (oDelete != null) oDelete.delete(); RandomAccessFile f = new RandomAccessFile(tableFile, "rw"); TimelineFactory.append(f, "PatientNumber,Race,Sex,Age,Dead\n"); TimelineFactory.append(f, resultFile.toString()); f.close(); /* * log.debug("\nTesting lld:"); for(int i=0; * i<patientDimensionSet.getPatientDimension().size();i++) { * PatientDimensionType patientType = * patientDimensionSet.getPatientDimension().get(i); Integer pnum = * patientType.getPatientNum(); log.debug("PatientNum: " + * patientType.getPatientNum()); * * for(int j=0; j<factSets.size(); j++) { * PatientDataType.ObservationFactSet observationFactSet = * factSets.get(j); String path = observationFactSet.getPath(); * StringBuilder resultString = new StringBuilder(); int total = 0; * XMLGregorianCalendar curStartDate = null; for(int k=0; * k<observationFactSet.getObservationFact().size(); k++) { * ObservationFactType obsFactType = * observationFactSet.getObservationFact().get(k); * * if(pnum.intValue() == obsFactType.getPatientNum().intValue()) { * if((curStartDate != null) && * (obsFactType.getStartDate().compare(curStartDate) == * DatatypeConstants.EQUAL)) { continue; } * * resultString.append("PatientNum: "+obsFactType.getPatientNum() * //+" for "+path +" concept_cd: " + obsFactType.getConceptCd() * +" start_date: " + obsFactType.getStartDate().getYear() * +"_"+obsFactType.getStartDate().getMonth() * +"_"+obsFactType.getStartDate().getDay() * +"_"+obsFactType.getStartDate().getHour() * +":"+obsFactType.getStartDate().getMinute() * +"_"+obsFactType.getNvalNum() +"_"+obsFactType.getConceptCd() * +"_"+obsFactType.getPatientNum() * +"_"+obsFactType.getEndDate()+"\n"); total++; curStartDate = * obsFactType.getStartDate(); } } * * log.debug("-- "+path+" has "+total+" events"); * log.debug(resultString.toString()); } } */ } catch (Exception e) { e.printStackTrace(); } } public static void main(String[] args) throws Exception { PDORequestMessageModel pdoFactory = new PDORequestMessageModel(); String conceptPath = new String( "\\RPDR\\Labtests\\LAB\\(LLB16) Chemistry\\(LLB21) General Chemistries\\CA"); ArrayList<String> paths = new ArrayList<String>(); // paths.add(conceptPath); conceptPath = new String("\\RPDR\\Labtests\\LAB\\(LLB16) Chemistry\\(LLB21) General Chemistries\\GGT"); paths.add(conceptPath); // conceptPath = new // String("\\RPDR\\Labtests\\LAB\\(LLB16) Chemistry\\(LLB21) General Chemistries\\GGT"); // paths.add(conceptPath); ArrayList<String> ppaths = new ArrayList<String>(); conceptPath = new String("\\Providers\\BWH"); // ppaths.add(conceptPath); String xmlStr = pdoFactory.requestXmlMessage(null, "1545", new Integer(1), new Integer(20), false, ""); String result = sendPDOQueryRequestREST(xmlStr); // FileWriter fwr = new FileWriter("c:\\testdir\\response.txt"); // fwr.write(result); log.debug(result); PDOItem set = new PDOItem(); set.fullPath = "\\RPDR\\Labtests\\LAB\\(LLB16) Chemistry\\(LLB21) General Chemistries\\CA"; set.hasValueDisplayProperty = true; PDOValueModel valdp = new PDOValueModel(); valdp.left = 0.0; valdp.right = 8.4; valdp.color = "red"; valdp.height = "Very Low"; set.valDisplayProperties.add(valdp); valdp = new PDOValueModel(); valdp.left = 8.4; valdp.right = 8.9; valdp.color = "gold"; valdp.height = "Low"; set.valDisplayProperties.add(valdp); valdp = new PDOValueModel(); valdp.left = 8.9; valdp.right = 10.0; valdp.color = "green"; valdp.height = "Medium"; set.valDisplayProperties.add(valdp); valdp = new PDOValueModel(); valdp.left = 10.0; valdp.right = 10.6; valdp.color = "gold"; valdp.height = "Tall"; set.valDisplayProperties.add(valdp); valdp = new PDOValueModel(); valdp.left = 10.6; valdp.right = Integer.MAX_VALUE; valdp.color = "red"; valdp.height = "Very Tall"; set.valDisplayProperties.add(valdp); set.tableType = "fact"; TimelineRow row = new TimelineRow(); row.pdoItems.add(set); row.displayName = "Calcium (Group:CA)"; ArrayList<TimelineRow> rows = new ArrayList<TimelineRow>(); rows.add(row); set = new PDOItem(); set.fullPath = "\\RPDR\\Labtests\\LAB\\(LLB16) Chemistry\\(LLB21) General Chemistries\\GGT"; set.hasValueDisplayProperty = true; valdp = new PDOValueModel(); valdp.left = 0.0; valdp.right = 1.0; valdp.color = "red"; valdp.height = "Very Low"; set.valDisplayProperties.add(valdp); valdp = new PDOValueModel(); valdp.left = 1.0; valdp.right = 19.0; valdp.color = "gold"; valdp.height = "Low"; set.valDisplayProperties.add(valdp); valdp = new PDOValueModel(); valdp.left = 19.0; valdp.right = 34.0; valdp.color = "green"; valdp.height = "Medium"; set.valDisplayProperties.add(valdp); valdp = new PDOValueModel(); valdp.left = 34.0; valdp.right = 82.0; valdp.color = "gold"; valdp.height = "Tall"; set.valDisplayProperties.add(valdp); valdp = new PDOValueModel(); valdp.left = 82.0; valdp.right = Integer.MAX_VALUE; valdp.color = "red"; valdp.height = "Very Tall"; set.valDisplayProperties.add(valdp); set.tableType = "fact"; row = new TimelineRow(); row.pdoItems.add(set); row.displayName = "Gamma Glutamyltrans (Group:GGT)"; rows.add(row); // testWritelld(result, rows, true); testWriteTableFile(result); } }