Java tutorial
/* Copyright (c) 2013, Washington University in St.Louis All rights reserved. Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. */ package edu.wustl.xipHost.application; import java.awt.Dimension; import java.awt.Toolkit; import java.io.File; import java.io.IOException; import java.net.MalformedURLException; import java.net.URISyntaxException; import java.net.URL; import java.util.ArrayList; import java.util.Collection; import java.util.HashMap; import java.util.Iterator; import java.util.List; import java.util.Map; import java.util.UUID; import java.util.concurrent.ExecutorService; import java.util.concurrent.Executors; import org.apache.commons.collections.MultiMap; import org.apache.commons.collections.map.MultiValueMap; import org.apache.log4j.Logger; import org.dcm4che2.data.Tag; import org.nema.dicom.wg23.ObjectDescriptor; import org.nema.dicom.wg23.ObjectLocator; import org.nema.dicom.wg23.Rectangle; import org.nema.dicom.wg23.Series; import org.nema.dicom.wg23.State; import org.nema.dicom.wg23.Study; import org.nema.dicom.wg23.Uuid; import edu.wustl.xipHost.avt2ext.ADRetrieveTarget; import edu.wustl.xipHost.avt2ext.AVTQuery; import edu.wustl.xipHost.avt2ext.AVTRetrieve2; import edu.wustl.xipHost.avt2ext.AVTRetrieve2Event; import edu.wustl.xipHost.avt2ext.AVTRetrieve2Listener; import edu.wustl.xipHost.avt2ext.AVTUtil; import edu.wustl.xipHost.iterator.IterationTarget; import edu.wustl.xipHost.iterator.IteratorElementEvent; import edu.wustl.xipHost.iterator.IteratorEvent; import edu.wustl.xipHost.iterator.NotificationRunner; import edu.wustl.xipHost.iterator.TargetElement; import edu.wustl.xipHost.iterator.TargetIteratorListener; import edu.wustl.xipHost.iterator.TargetIteratorRunner; import edu.wustl.xipHost.caGrid.GridLocation; import edu.wustl.xipHost.caGrid.GridQuery; import edu.wustl.xipHost.caGrid.GridLocation.Type; import edu.wustl.xipHost.dataAccess.DataAccessListener; import edu.wustl.xipHost.dataAccess.Query; import edu.wustl.xipHost.dataAccess.QueryEvent; import edu.wustl.xipHost.dataAccess.QueryTarget; import edu.wustl.xipHost.dataAccess.RetrieveEvent; import edu.wustl.xipHost.dataModel.Patient; import edu.wustl.xipHost.dataModel.SearchResult; import edu.wustl.xipHost.hostControl.Util; import edu.wustl.xipHost.wg23.ClientToApplication; import edu.wustl.xipHost.wg23.StateExecutor; import edu.wustl.xipHost.wg23.WG23DataModel; import edu.wustl.xipHost.worklist.WorklistEntry; public class Application implements TargetIteratorListener, AVTRetrieve2Listener, DataAccessListener { final static Logger logger = Logger.getLogger(Application.class); UUID id; String name; File exePath; String vendor; String version; File iconFile; String type; boolean requiresGUI; String wg23DataModelType; int concurrentInstances; IterationTarget iterationTarget; int numStateNotificationThreads = 2; ExecutorService exeService = Executors.newFixedThreadPool(numStateNotificationThreads); AVTUtil util = new AVTUtil(); public Application() { } public UUID getId() { return id; } public void setId(UUID id) { this.id = id; } public String getName() { return name; } public void setName(String name) { this.name = name; } public File getExePath() { return exePath; } public void setExePath(File exePath) { this.exePath = exePath; } public String getVendor() { return vendor; } public void setVendor(String vendor) { this.vendor = vendor; } public String getVersion() { return version; } public void setVersion(String version) { this.version = version; } public File getIconFile() { return iconFile; } public void setIconFile(File iconFile) { this.iconFile = iconFile; } public String getType() { return type; } public void setType(String type) { this.type = type; } public boolean isRequiresGUI() { return requiresGUI; } public void setRequiresGUI(boolean requiresGUI) { this.requiresGUI = requiresGUI; } public String getWg23DataModelType() { return wg23DataModelType; } public void setWg23DataModelType(String wg23DataModelType) { this.wg23DataModelType = wg23DataModelType; } public int getConcurrentInstances() { return concurrentInstances; } public void setConcurrentInstances(int concurrentInstances) { this.concurrentInstances = concurrentInstances; } public IterationTarget getIterationTarget() { return iterationTarget; } public void setIterationTarget(IterationTarget target) { iterationTarget = target; } File appTmpDir; public void setApplicationTmpDir(File tmpDir) { appTmpDir = tmpDir; } public File getApplicationTmpDir() { return appTmpDir; } File appOutputDir; public void setApplicationOutputDir(File outDir) { try { appOutputDir = Util.create("xipOUT_" + getName() + "_", "", outDir); } catch (IOException e) { logger.error(e, e); } } public File getApplicationOutputDir() { return appOutputDir; } public Rectangle getApplicationPreferredSize() { Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize(); Rectangle rect = new Rectangle(); logger.debug("Screen width: " + new Double(screenSize.getWidth()).intValue()); logger.debug("Screen height: " + new Double(screenSize.getHeight()).intValue()); rect.setWidth(new Double(screenSize.getWidth()).intValue()); rect.setHeight(new Double(screenSize.getHeight()).intValue()); return rect; } URL hostServiceURL; URL appServiceURL; public URL getApplicationServiceURL() { return appServiceURL; } public void launch(URL hostServiceURL, URL appServiceURL) { this.hostServiceURL = hostServiceURL; this.appServiceURL = appServiceURL; if (logger.isDebugEnabled()) { logger.info("Launching: " + getName()); logger.debug("Host service URL: " + this.hostServiceURL.toExternalForm().toString()); logger.debug("Hosted application service URL: " + this.appServiceURL.toExternalForm().toString()); logger.debug("Exe path: " + this.getExePath().getAbsolutePath()); } try { if (getExePath().toURI().toURL().toExternalForm().endsWith(".exe") || getExePath().toURI().toURL().toExternalForm().endsWith(".bat")) { try { Runtime.getRuntime() .exec("cmd /c start /min " + getExePath().toURI().toURL().toExternalForm() + " " + "--hostURL" + " " + hostServiceURL.toURI().toURL().toExternalForm() + " " + "--applicationURL" + " " + appServiceURL.toURI().toURL().toExternalForm()); } catch (IOException e) { logger.error(e, e); } catch (URISyntaxException e) { logger.error(e, e); } } } catch (MalformedURLException e) { logger.error(e, e); } } State priorState = null; State state = null; boolean firstLaunch = true; int numberOfSentNotifications = 0; MultiMap wg23DataModelItems = new MultiValueMap(); Thread threadNotification; @SuppressWarnings("unchecked") public void setState(State state) { priorState = this.state; this.state = state; logger.debug("\"" + getName() + "\"" + " state changed to: " + this.state); if (state.equals(State.IDLE)) { if (firstLaunch) { startClientToApplication(); firstLaunch = false; StateExecutor stateExecutor = new StateExecutor(this); stateExecutor.setState(State.INPROGRESS); exeService.execute(stateExecutor); } else { synchronized (this) { if (iter != null) { boolean doInprogress = true; synchronized (targetElements) { if (numberOfSentNotifications == targetElements.size()) { doInprogress = false; } } if (doInprogress == false) { StateExecutor stateExecutor = new StateExecutor(this); stateExecutor.setState(State.EXIT); exeService.execute(stateExecutor); } else { StateExecutor stateExecutor = new StateExecutor(this); stateExecutor.setState(State.INPROGRESS); exeService.execute(stateExecutor); } } else { StateExecutor stateExecutor = new StateExecutor(this); stateExecutor.setState(State.INPROGRESS); exeService.execute(stateExecutor); } } } } else if (state.equals(State.INPROGRESS)) { synchronized (targetElements) { while (targetElements.size() == 0 || targetElements.size() <= numberOfSentNotifications) { try { targetElements.wait(); } catch (InterruptedException e) { logger.error(e, e); } } TargetElement element = targetElements.get(numberOfSentNotifications); WG23DataModel wg23data = util.getWG23DataModel(element); //Extract all ObjectDescriptors UUIDs and construct MultiValueMap containing UUID (key), ObjectDescriptor (value), ObjectLocator (value) List<ObjectDescriptor> objDescsTopLevel = wg23data.getAvailableData().getObjectDescriptors() .getObjectDescriptor(); for (ObjectDescriptor objDesc : objDescsTopLevel) { String uuid = objDesc.getUuid().getUuid(); wg23DataModelItems.put(uuid, objDesc); } List<org.nema.dicom.wg23.Patient> listPatients = wg23data.getAvailableData().getPatients() .getPatient(); for (org.nema.dicom.wg23.Patient patient : listPatients) { List<ObjectDescriptor> objDescsPatientLevel = patient.getObjectDescriptors() .getObjectDescriptor(); for (ObjectDescriptor objDesc : objDescsPatientLevel) { String uuid = objDesc.getUuid().getUuid(); wg23DataModelItems.put(uuid, objDesc); } List<Study> listStudies = patient.getStudies().getStudy(); for (Study study : listStudies) { List<ObjectDescriptor> objDescsStudyLevel = study.getObjectDescriptors() .getObjectDescriptor(); for (ObjectDescriptor objDesc : objDescsStudyLevel) { String uuid = objDesc.getUuid().getUuid(); wg23DataModelItems.put(uuid, objDesc); } List<Series> listSeries = study.getSeries().getSeries(); for (Series series : listSeries) { List<ObjectDescriptor> objDescsSeriesLevel = series.getObjectDescriptors() .getObjectDescriptor(); for (ObjectDescriptor objDesc : objDescsSeriesLevel) { String uuid = objDesc.getUuid().getUuid(); wg23DataModelItems.put(uuid, objDesc); } } } } Iterator<String> iterMultiValueMap = wg23DataModelItems.keySet().iterator(); ObjectLocator[] objLocators = wg23data.getObjectLocators(); while (iterMultiValueMap.hasNext()) { String uuid = iterMultiValueMap.next(); for (int i = 0; i < objLocators.length; i++) { ObjectLocator objLoc = objLocators[i]; String locUUID = objLoc.getUuid().getUuid(); if (locUUID.equalsIgnoreCase(uuid)) { wg23DataModelItems.put(uuid, objLoc); } } } NotificationRunner runner = new NotificationRunner(this); runner.setAvailableData(wg23data.getAvailableData()); threadNotification = new Thread(runner); threadNotification.start(); numberOfSentNotifications++; } } else if (state.equals(State.EXIT)) { //Reset application parameters for subsequent launch firstLaunch = true; retrievedTargetElements.clear(); targetElements.clear(); iter = null; numberOfSentNotifications = 0; retrievedTargetElements.clear(); } } public State getState() { return state; } public State getPriorState() { return priorState; } ClientToApplication clientToApplication; public void startClientToApplication() { clientToApplication = new ClientToApplication(appServiceURL); } public ClientToApplication getClientToApplication() { return clientToApplication; } Query query; public void setWorklistEntry(WorklistEntry entry) { String studyInstanceUID = entry.getStudyInstanceUID(); Map<Integer, Object> dicomCriteria = new HashMap<Integer, Object>(); Map<String, Object> aimCriteria = new HashMap<String, Object>(); String queryName = "AVT"; if (queryName.equalsIgnoreCase("AVT")) { dicomCriteria.put(Tag.StudyInstanceUID, studyInstanceUID); query = new AVTQuery(dicomCriteria, aimCriteria, QueryTarget.PATIENT, null, null); query.addDataAccessListener(this); Thread t = new Thread(query); t.start(); } else if (queryName.equalsIgnoreCase("Grid")) { System.setProperty("org.apache.commons.logging.Log", "org.apache.commons.logging.impl.NoOpLog"); //dicomCriteria.put(Tag.StudyInstanceUID, ""); dicomCriteria.put(Tag.StudyInstanceUID, "1.3.6.1.4.1.9328.50.1.9084"); //GridLocation location = new GridLocation("http://node05.cci.emory.edu:8081/wsrf/services/cagrid/DICOMDataService", // Type.DICOM, "DICOM", "DICOM Server Emory"); GridLocation location = new GridLocation( "http://imaging.nci.nih.gov/wsrf/services/cagrid/NCIACoreService", Type.DICOM, "NBIA-4.2", "NBIA Production Server at NCI"); query = new GridQuery(location); query.setQuery(dicomCriteria, aimCriteria, QueryTarget.PATIENT, null, null); query.addDataAccessListener(this); Thread t2 = new Thread(query); t2.start(); } } Iterator<TargetElement> iter; @SuppressWarnings("unchecked") @Override public void fullIteratorAvailable(IteratorEvent e) { iter = (Iterator<TargetElement>) e.getSource(); logger.debug("Full TargetIterator available at time " + System.currentTimeMillis()); } List<TargetElement> targetElements = new ArrayList<TargetElement>(); @Override public void targetElementAvailable(IteratorElementEvent e) { synchronized (targetElements) { TargetElement element = (TargetElement) e.getSource(); logger.debug( "TargetElement available. ID: " + element.getId() + " at time " + System.currentTimeMillis()); targetElements.add(element); targetElements.notify(); } } public List<ObjectLocator> retrieveAndGetLocators(List<Uuid> listUUIDs) { //Start data retrieval related to the element ADRetrieveTarget retrieveTarget = ADRetrieveTarget.DICOM_AND_AIM; AVTRetrieve2 avtRetrieve = null; TargetElement element = null; try { synchronized (targetElements) { element = targetElements.get(numberOfSentNotifications - 1); avtRetrieve = new AVTRetrieve2(element, retrieveTarget); avtRetrieve.addAVTListener(this); } } catch (IOException e1) { logger.error(e1, e1); } Thread t = new Thread(avtRetrieve); t.start(); //Wait for actual data being retrieved before sending file pointers String retrievedElementID = element.getId(); synchronized (retrievedTargetElements) { while (!retrievedTargetElements.contains(retrievedElementID)) { try { retrievedTargetElements.wait(); } catch (InterruptedException e) { logger.error(e, e); } } } if (listUUIDs == null) { return new ArrayList<ObjectLocator>(); } else { ArrayList<ObjectLocator> listObjLocs = new ArrayList<ObjectLocator>(); for (Uuid uuid : listUUIDs) { String strUuid = uuid.getUuid(); Collection<?> objs = (Collection<?>) wg23DataModelItems.get(strUuid); Iterator<?> iterObjs = objs.iterator(); while (iterObjs.hasNext()) { Object object = iterObjs.next(); if (object instanceof ObjectLocator) { ObjectLocator objLoc = (ObjectLocator) object; listObjLocs.add(objLoc); logger.debug("Item location: " + strUuid + " " + objLoc.getUri()); } } } return listObjLocs; } } List<String> retrievedTargetElements = new ArrayList<String>(); @Override public void retriveCompleted(AVTRetrieve2Event e) { synchronized (retrievedTargetElements) { String elementID = (String) e.getSource(); retrievedTargetElements.add(elementID); retrievedTargetElements.notify(); logger.debug( "Data retrived for TargetElement: " + elementID + " at time: " + System.currentTimeMillis()); } } @Override public void queryResultsAvailable(QueryEvent e) { logger.debug("Query result available"); Query source = (Query) e.getSource(); if (source instanceof AVTQuery) { logger.debug("Source: " + AVTQuery.class.getName()); SearchResult selectedDataSearchResult = source.getSearchResult(); logger.debug("Found patients: "); for (Patient patient : selectedDataSearchResult.getPatients()) { logger.debug(patient.getPatientID() + " " + patient.getPatientName()); } //Start TargetIteratorRunner TargetIteratorRunner targetIter = new TargetIteratorRunner(selectedDataSearchResult, getIterationTarget(), query, getApplicationTmpDir(), this); try { Thread t = new Thread(targetIter); t.start(); } catch (Exception e1) { logger.error(e1, e1); } } else if (source instanceof GridQuery) { logger.debug("Source: " + GridQuery.class.getName()); SearchResult selectedDataSearchResult = source.getSearchResult(); logger.debug("Found patients: "); for (Patient patient : selectedDataSearchResult.getPatients()) { logger.debug(patient.getPatientID() + " " + patient.getPatientName()); } TargetIteratorRunner targetIter = new TargetIteratorRunner(selectedDataSearchResult, getIterationTarget(), query, getApplicationTmpDir(), this); try { Thread t = new Thread(targetIter); t.start(); } catch (Exception e1) { logger.error(e1, e1); } } else { logger.debug("Source: " + source.getClass().getName()); } } @Override public void retriveResultsAvailable(RetrieveEvent e) { // TODO Auto-generated method stub } }