1 package jalview.ws.jws2;
4 import java.awt.event.ActionEvent;
5 import java.awt.event.ActionListener;
6 import java.beans.PropertyChangeEvent;
7 import java.beans.PropertyChangeListener;
8 import java.io.Closeable;
9 import java.net.ConnectException;
11 import java.util.HashSet;
12 import java.util.Hashtable;
13 import java.util.StringTokenizer;
14 import java.util.Vector;
16 import javax.swing.JMenu;
17 import javax.swing.JMenuItem;
18 import javax.swing.event.MenuEvent;
19 import javax.swing.event.MenuListener;
21 import org.apache.log4j.Level;
23 import jalview.bin.Cache;
24 import jalview.datamodel.AlignmentView;
25 import jalview.gui.AlignFrame;
26 import jalview.gui.Desktop;
27 import jalview.ws.WSMenuEntryProviderI;
28 import jalview.ws.params.ParamDatastoreI;
29 import compbio.data.msa.MsaWS;
30 import compbio.metadata.Option;
31 import compbio.metadata.Preset;
32 import compbio.metadata.PresetManager;
33 import compbio.metadata.RunnerConfig;
34 import compbio.ws.client.Jws2Client;
35 import compbio.ws.client.Services;
38 * discoverer for jws2 services. Follows the lightweight service discoverer
39 * pattern (archetyped by EnfinEnvision2OneWay)
44 public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
46 private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(
50 * change listeners are notified of "services" property changes
53 * to be added that consumes new services Hashtable object.
55 public void addPropertyChangeListener(
56 java.beans.PropertyChangeListener listener)
58 changeSupport.addPropertyChangeListener(listener);
67 public void removePropertyChangeListener(
68 java.beans.PropertyChangeListener listener)
70 changeSupport.removePropertyChangeListener(listener);
73 boolean running = false;
75 Thread oldthread = null;
79 if (running && oldthread != null && oldthread.isAlive())
84 oldthread = Thread.currentThread();
87 Class foo = getClass().getClassLoader().loadClass(
88 "compbio.ws.client.Jws2Client");
89 } catch (ClassNotFoundException e)
92 .println("Not enabling Jalview Webservices version 2: client jar is not available."
93 + "\nPlease check that your webstart JNLP file is up to date!");
99 services.removeAllElements();
101 for (String jwsservers : getServiceUrls())
105 if (Jws2Client.validURL(jwsservers))
108 for (Services srv : Services.values())
110 MsaWS service = null;
113 service = Jws2Client.connect(jwsservers, srv);
114 } catch (Exception e)
116 System.err.println("Jws2 Discoverer: Problem on "
117 + jwsservers + " with service " + srv + ":\n"
119 if (!(e instanceof javax.xml.ws.WebServiceException))
127 addService(jwsservers, srv, service);
134 Cache.log.info("Ignoring invalid Jws2 service url " + jwsservers);
136 } catch (Exception e)
139 Cache.log.warn("Exception when discovering Jws2 services.", e);
142 Cache.log.error("Exception when discovering Jws2 services.", e);
147 changeSupport.firePropertyChange("services", new Vector(), services);
151 * record this service endpoint so we can use it
157 private void addService(String jwsservers, Services srv, MsaWS service2)
159 if (services == null)
161 services = new Vector<Jws2Instance>();
163 System.out.println("Discovered service: " + jwsservers + " "
165 Jws2Instance service = new Jws2Instance(jwsservers, srv.toString(), service2);
167 services.add(service);
168 service.getParamStore();
171 public class Jws2Instance
173 public String hosturl;
175 public String serviceType;
177 public MsaWS service;
179 public Jws2Instance(String hosturl, String serviceType, MsaWS service)
182 this.hosturl = hosturl;
183 this.serviceType = serviceType;
184 this.service = service;
187 PresetManager presets = null;
189 public JabaParamStore paramStore = null;
192 * non thread safe - gets the presets for this service (blocks whilst it
193 * calls the service to get the preset set)
195 * @return service presets or null if exceptions were raised.
197 public PresetManager getPresets()
203 presets = service.getPresets();
204 } catch (Exception ex)
207 .println("Exception when retrieving presets for service "
208 + serviceType + " at " + hosturl);
214 public String getHost()
218 * try { URL serviceurl = new URL(hosturl); if (serviceurl.getPort()!=80)
219 * { return serviceurl.getHost()+":"+serviceurl.getPort(); } return
220 * serviceurl.getHost(); } catch (Exception e) {
221 * System.err.println("Failed to parse service URL '" + hosturl +
222 * "' as a valid URL!"); } return null;
227 * @return short description of what the service will do
229 public String getActionText()
231 return "Align with " + serviceType;
235 * non-thread safe - blocks whilst accessing service to get complete set of
236 * available options and parameters
240 public RunnerConfig getRunnerConfig()
242 return service.getRunnerOptions();
246 protected void finalize() throws Throwable
252 Closeable svc = (Closeable) service;
255 } catch (Exception e)
263 public ParamDatastoreI getParamStore()
265 if (paramStore == null)
269 paramStore = new JabaParamStore(this,
270 (Desktop.instance != null ? Desktop
271 .getUserParameterStore() : null));
272 } catch (Exception ex)
280 public String getUri()
282 // this is only valid for Jaba 1.0 - this formula might have to change!
283 return hosturl+(hosturl.lastIndexOf("/")==(hosturl.length()-1) ? "/" : "") +serviceType;
285 private boolean hasParams=false,lookedForParams=false;
286 public boolean hasParameters()
288 if (!lookedForParams)
290 lookedForParams=true;
293 hasParams = (getRunnerConfig().getArguments().size() > 0);
294 } catch (Exception e)
304 * holds list of services.
306 protected Vector<Jws2Instance> services;
309 * find or add a submenu with the given title in the given menu
313 * @return the new or existing submenu
315 private JMenu findOrCreateMenu(JMenu menu, String submenu)
317 JMenu submenuinstance = null;
318 for (int i = 0, iSize = menu.getMenuComponentCount(); i < iSize; i++)
320 if (menu.getMenuComponent(i) instanceof JMenu
321 && ((JMenu) menu.getMenuComponent(i)).getText().equals(
324 submenuinstance = (JMenu) menu.getMenuComponent(i);
327 if (submenuinstance == null)
329 submenuinstance = new JMenu(submenu);
330 menu.add(submenuinstance);
332 return submenuinstance;
336 public void attachWSMenuEntry(JMenu wsmenu, final AlignFrame alignFrame)
338 // dynamically regenerate service list.
339 final JMenu jws2al = new JMenu("JABAWS Alignment");
340 jws2al.addMenuListener(new MenuListener()
342 // TODO: future: add menu listener to parent menu - so submenus are
343 // populated *before* they are selected.
345 public void menuSelected(MenuEvent e)
347 populateWSMenuEntry(jws2al, alignFrame);
351 public void menuDeselected(MenuEvent e)
353 // TODO Auto-generated method stub
358 public void menuCanceled(MenuEvent e)
360 // TODO Auto-generated method stub
369 private void populateWSMenuEntry(JMenu jws2al, final AlignFrame alignFrame)
371 if (running || services == null || services.size() == 0)
375 boolean byhost = Cache.getDefault("WSMENU_BYHOST", true), bytype = Cache
376 .getDefault("WSMENU_BYTYPE", true);
378 * eventually, JWS2 services will appear under the same align/etc submenus.
379 * for moment we keep them separate.
382 MsaWSClient msacl = new MsaWSClient();
383 Vector hostLabels = new Vector();
385 String lasthost=null;
386 for (final Jws2Instance service : services)
389 String host = service.getHost();
390 String type = service.serviceType;
393 atpoint = findOrCreateMenu(atpoint, host);
394 if (atpoint.getToolTipText() == null)
396 atpoint.setToolTipText("Services at " + host);
401 atpoint = findOrCreateMenu(atpoint, type);
402 if (atpoint.getToolTipText() == null)
404 atpoint.setToolTipText(service.getActionText());
407 if (!byhost && !hostLabels.contains(host + service.getActionText()))
409 // add a marker indicating where this service is hosted
410 // relies on services from the same host being listed in a contiguous
413 atpoint.addSeparator();
414 if (lasthost==null || !lasthost.equals(host))
416 atpoint.add(hitm = new JMenuItem(host));
417 hitm.setForeground(Color.blue);
419 hostLabels.addElement(lasthost=host);
421 msacl.attachWSMenuEntry(atpoint, service, alignFrame);
423 * JMenuItem sitem = new JMenuItem(service.serviceType);
424 * sitem.setToolTipText("Hosted at " + service.hosturl);
425 * sitem.addActionListener(new ActionListener() {
427 * @Override public void actionPerformed(ActionEvent e) { AlignmentView
428 * msa = alignFrame.gatherSequencesForAlignment(); MsaWSClient client =
429 * new MsaWSClient(service, "JWS2 Alignment of " + alignFrame.getTitle(),
430 * msa, false, true, alignFrame.getViewport().getAlignment().getDataset(),
436 public static void main(String[] args)
438 Thread runner = new Thread(getDiscoverer());
439 getDiscoverer().addPropertyChangeListener(new PropertyChangeListener()
442 public void propertyChange(PropertyChangeEvent evt)
444 System.out.println("Changesupport: There are now "
445 + getDiscoverer().services.size() + " services");
449 while (runner.isAlive())
454 } catch (InterruptedException e)
461 private static Jws2Discoverer discoverer;
463 public static Jws2Discoverer getDiscoverer()
465 if (discoverer == null)
467 discoverer = new Jws2Discoverer();
472 public boolean hasServices()
474 // TODO Auto-generated method stub
475 return !running && services != null && services.size() > 0;
478 public boolean isRunning()
484 * the jalview .properties entry for JWS2 URLS
486 final static String JWS2HOSTURLS = "JWS2HOSTURLS";
488 public static void setServiceUrls(Vector<String> urls)
492 StringBuffer urlbuffer = new StringBuffer();
494 for (String url : urls)
496 urlbuffer.append(sep);
497 urlbuffer.append(url);
500 Cache.setProperty(JWS2HOSTURLS, urlbuffer.toString());
504 Cache.removeProperty(JWS2HOSTURLS);
508 public static Vector<String> getServiceUrls()
510 String surls = Cache.getDefault(JWS2HOSTURLS,
511 "http://www.compbio.dundee.ac.uk/jabaws");
512 Vector<String> urls = new Vector<String>();
515 StringTokenizer st = new StringTokenizer(surls, ",");
516 while (st.hasMoreElements())
521 java.net.URL u = new java.net.URL(url = st.nextToken());
522 if (!urls.contains(url))
528 jalview.bin.Cache.log.info("Ignoring duplicate url in "
529 + JWS2HOSTURLS + " list");
531 } catch (Exception ex)
533 jalview.bin.Cache.log
534 .warn("Problem whilst trying to make a URL from '"
535 + ((url != null) ? url : "<null>") + "'");
536 jalview.bin.Cache.log
537 .warn("This was probably due to a malformed comma separated list"
540 + " entry of $(HOME)/.jalview_properties)");
541 jalview.bin.Cache.log.debug("Exception was ", ex);
544 } catch (Exception ex)
546 jalview.bin.Cache.log.warn(
547 "Error parsing comma separated list of urls in "
548 + JWS2HOSTURLS + " preference.", ex);
550 if (urls.size() >= 0)
557 public Vector<Jws2Instance> getServices()
559 return (services == null) ? new Vector<Jws2Instance>()
560 : new Vector<Jws2Instance>(services);
564 * test the given URL with the JabaWS test code
569 public static boolean testServiceUrl(URL foo)
573 compbio.ws.client.WSTester.main(new String[]
574 { "-h=" + foo.toString() });
575 } catch (Exception e)
578 } catch (OutOfMemoryError e)