package jalview.ws.jws2; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.beans.PropertyChangeEvent; import java.beans.PropertyChangeListener; import java.net.ConnectException; import java.util.HashSet; import java.util.StringTokenizer; import java.util.Vector; import javax.swing.JMenu; import javax.swing.JMenuItem; import org.apache.log4j.Level; import jalview.bin.Cache; import jalview.datamodel.AlignmentView; import jalview.gui.AlignFrame; import jalview.ws.WSMenuEntryProviderI; import compbio.data.msa.MsaWS; import compbio.metadata.Preset; import compbio.metadata.PresetManager; import compbio.ws.client.Jws2Base; import compbio.ws.client.Jws2Base.Services; /** * discoverer for jws2 services. Follows the lightweight service discoverer * pattern (archetyped by EnfinEnvision2OneWay) * * @author JimP * */ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI { private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport( this); /** * change listeners are notified of "services" property changes * * @param listener * to be added that consumes new services Hashtable object. */ public void addPropertyChangeListener( java.beans.PropertyChangeListener listener) { changeSupport.addPropertyChangeListener(listener); } /** * * * @param listener * to be removed */ public void removePropertyChangeListener( java.beans.PropertyChangeListener listener) { changeSupport.removePropertyChangeListener(listener); } boolean running = false; Thread oldthread=null; @Override public void run() { if (running && oldthread!=null && oldthread.isAlive()) { return; } running = true; oldthread = Thread.currentThread(); try { Class foo = getClass().getClassLoader().loadClass( "compbio.ws.client.Jws2Base"); } catch (ClassNotFoundException e) { System.err .println("Not enabling Jalview Webservices version 2: client jar is not available." + "\nPlease check that your webstart JNLP file is up to date!"); running = false; return; } if (services != null) { services.removeAllElements(); } for (String jwsservers : getServiceUrls()) { try { if (Jws2Base.validURL(jwsservers)) { // look for services for (Services srv : Jws2Base.Services.values()) { MsaWS service = null; try { service = Jws2Base.connect(jwsservers, srv); } catch (Exception e) { System.err.println("Jws2 Discoverer: Problem on " + jwsservers + " with service " + srv + ":\n" + e.getMessage()); if (!(e instanceof javax.xml.ws.WebServiceException)) { e.printStackTrace(); } } ; if (service != null) { addService(jwsservers, srv, service); } } } else { Cache.log.info("Ignoring invalid Jws2 service url " + jwsservers); } } catch (Exception e) { e.printStackTrace(); Cache.log.warn("Exception when discovering Jws2 services.", e); } catch (Error e) { Cache.log.error("Exception when discovering Jws2 services.", e); } } oldthread = null; running = false; changeSupport.firePropertyChange("services", new Vector(), services); } /** * record this service endpoint so we can use it * * @param jwsservers * @param srv * @param service2 */ private void addService(String jwsservers, Services srv, MsaWS service2) { if (services == null) { services = new Vector(); } System.out.println("Discovered service: " + jwsservers + " " + srv.toString()); services.add(new Jws2Instance(jwsservers, "Align with " + srv.toString(), service2)); } public class Jws2Instance { String hosturl; String serviceType; MsaWS service; public Jws2Instance(String hosturl, String serviceType, MsaWS service) { super(); this.hosturl = hosturl; this.serviceType = serviceType; this.service = service; } PresetManager presets = null; /** * non thread safe - gets the presets for this service (blocks whilst it * calls the service to get the preset set) * * @return service presets or null if exceptions were raised. */ public PresetManager getPresets() { if (presets == null) { try { presets = service.getPresets(); } catch (Exception ex) { System.err .println("Exception when retrieving presets for service " + serviceType + " at " + hosturl); } } return presets; } }; /** * holds list of services. */ Vector services; @Override public void attachWSMenuEntry(JMenu wsmenu, final AlignFrame alignFrame) { if (running || services == null || services.size() == 0) { return; } /** * eventually, JWS2 services will appear under the same align/etc submenus. * for moment we keep them separate. */ JMenu jws2 = new JMenu("JWS2 Alignment"); MsaWSClient msacl = new MsaWSClient(); for (final Jws2Instance service : services) { msacl.attachWSMenuEntry(jws2, service, alignFrame); /* * JMenuItem sitem = new JMenuItem(service.serviceType); * sitem.setToolTipText("Hosted at " + service.hosturl); * sitem.addActionListener(new ActionListener() { * * @Override public void actionPerformed(ActionEvent e) { AlignmentView * msa = alignFrame.gatherSequencesForAlignment(); MsaWSClient client = * new MsaWSClient(service, "JWS2 Alignment of " + alignFrame.getTitle(), * msa, false, true, alignFrame.getViewport().getAlignment().getDataset(), * alignFrame); } }); */ } if (services.size() > 0) { wsmenu.add(jws2); } } public static void main(String[] args) { Thread runner = new Thread(getDiscoverer()); getDiscoverer().addPropertyChangeListener(new PropertyChangeListener() { @Override public void propertyChange(PropertyChangeEvent evt) { System.out.println("Changesupport: There are now " + getDiscoverer().services.size() + " services"); } }); runner.start(); while (runner.isAlive()) { try { Thread.sleep(50); } catch (InterruptedException e) { } ; } } private static Jws2Discoverer discoverer; public static Jws2Discoverer getDiscoverer() { if (discoverer == null) { discoverer = new Jws2Discoverer(); } return discoverer; } public boolean hasServices() { // TODO Auto-generated method stub return !running && services != null && services.size() > 0; } public boolean isRunning() { return running; } /** * the jalview .properties entry for JWS2 URLS */ final static String JWS2HOSTURLS = "JWS2HOSTURLS"; public static void setServiceUrls(Vector urls) { if (urls != null) { StringBuffer urlbuffer = new StringBuffer(); String sep = ""; for (String url : urls) { urlbuffer.append(sep); urlbuffer.append(url); sep = ","; } Cache.setProperty(JWS2HOSTURLS, urlbuffer.toString()); } else { Cache.removeProperty(JWS2HOSTURLS); } } public static Vector getServiceUrls() { String surls = Cache.getDefault(JWS2HOSTURLS, "http://webservices.compbio.dundee.ac.uk:8084/jws2"); Vector urls = new Vector(); try { StringTokenizer st = new StringTokenizer(surls, ","); while (st.hasMoreElements()) { String url = null; try { java.net.URL u = new java.net.URL(url = st.nextToken()); if (!urls.contains(url)) { urls.add(url); } else { jalview.bin.Cache.log.info("Ignoring duplicate url in " + JWS2HOSTURLS + " list"); } } catch (Exception ex) { jalview.bin.Cache.log .warn("Problem whilst trying to make a URL from '" + ((url != null) ? url : "") + "'"); jalview.bin.Cache.log .warn("This was probably due to a malformed comma separated list" + " in the " + JWS2HOSTURLS + " entry of $(HOME)/.jalview_properties)"); jalview.bin.Cache.log.debug("Exception was ", ex); } } } catch (Exception ex) { jalview.bin.Cache.log.warn( "Error parsing comma separated list of urls in " + JWS2HOSTURLS + " preference.", ex); } if (urls.size() >= 0) { return urls; } return null; } }