2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
3 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
18 package jalview.ws.jws2;
20 import java.awt.Color;
21 import java.awt.event.ActionEvent;
22 import java.awt.event.ActionListener;
23 import java.beans.PropertyChangeEvent;
24 import java.beans.PropertyChangeListener;
25 import java.io.Closeable;
26 import java.net.ConnectException;
28 import java.util.ArrayList;
29 import java.util.HashSet;
30 import java.util.Hashtable;
31 import java.util.List;
32 import java.util.StringTokenizer;
33 import java.util.Vector;
35 import javax.swing.JMenu;
36 import javax.swing.JMenuItem;
37 import javax.swing.event.MenuEvent;
38 import javax.swing.event.MenuListener;
40 import org.apache.log4j.Level;
42 import jalview.bin.Cache;
43 import jalview.datamodel.AlignmentView;
44 import jalview.gui.AlignFrame;
45 import jalview.gui.Desktop;
46 import jalview.gui.JalviewChangeSupport;
47 import jalview.ws.WSMenuEntryProviderI;
48 import jalview.ws.params.ParamDatastoreI;
49 import compbio.data.msa.MsaWS;
50 import compbio.metadata.Option;
51 import compbio.metadata.Preset;
52 import compbio.metadata.PresetManager;
53 import compbio.metadata.RunnerConfig;
54 import compbio.ws.client.Jws2Client;
55 import compbio.ws.client.Services;
58 * discoverer for jws2 services. Follows the lightweight service discoverer
59 * pattern (archetyped by EnfinEnvision2OneWay)
64 public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
66 private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(
70 * change listeners are notified of "services" property changes
73 * to be added that consumes new services Hashtable object.
75 public void addPropertyChangeListener(
76 java.beans.PropertyChangeListener listener)
78 changeSupport.addPropertyChangeListener(listener);
87 public void removePropertyChangeListener(
88 java.beans.PropertyChangeListener listener)
90 changeSupport.removePropertyChangeListener(listener);
93 boolean running = false, aborted = false;
98 public boolean isAborted()
107 public void setAborted(boolean aborted)
109 this.aborted = aborted;
112 Thread oldthread = null;
116 if (running && oldthread != null && oldthread.isAlive())
127 .debug("Waiting around for old discovery thread to finish.");
128 // wait around until old discoverer dies
130 } catch (Exception e)
134 Cache.log.debug("Old discovery thread has finished.");
137 oldthread = Thread.currentThread();
140 Class foo = getClass().getClassLoader().loadClass(
141 "compbio.ws.client.Jws2Client");
142 } catch (ClassNotFoundException e)
145 .println("Not enabling JABA Webservices : client jar is not available."
146 + "\nPlease check that your webstart JNLP file is up to date!");
150 // reinitialise records of good and bad service URLs
151 if (services != null)
153 services.removeAllElements();
155 if (urlsWithoutServices != null)
157 urlsWithoutServices.removeAllElements();
159 if (invalidServiceUrls != null)
161 invalidServiceUrls.removeAllElements();
164 List<JabaWsServerQuery> qrys = new ArrayList<JabaWsServerQuery>();
165 for (final String jwsservers : getServiceUrls())
167 JabaWsServerQuery squery = new JabaWsServerQuery(this, jwsservers);
169 new Thread(squery).start();
171 boolean finished = false;
177 } catch (Exception e)
181 for (JabaWsServerQuery squery : qrys)
183 finished |= !squery.isRunning();
187 Cache.log.debug("Aborting " + qrys.size()
188 + " JABAWS discovery threads.");
189 for (JabaWsServerQuery squery : qrys)
191 squery.setQuit(true);
194 } while (!aborted && !finished);
199 changeSupport.firePropertyChange("services", new Vector(), services);
204 * record this service endpoint so we can use it
210 synchronized void addService(String jwsservers, Services srv,
213 if (services == null)
215 services = new Vector<Jws2Instance>();
217 System.out.println("Discovered service: " + jwsservers + " "
219 Jws2Instance service = new Jws2Instance(jwsservers, srv.toString(),
222 services.add(service);
223 // retrieve the presets and parameter set and cache now
224 service.getParamStore().getPresets();
225 service.hasParameters();
228 public class Jws2Instance
230 public String hosturl;
232 public String serviceType;
234 public MsaWS service;
236 public Jws2Instance(String hosturl, String serviceType, MsaWS service)
239 this.hosturl = hosturl;
240 this.serviceType = serviceType;
241 this.service = service;
244 PresetManager presets = null;
246 public JabaParamStore paramStore = null;
249 * non thread safe - gets the presets for this service (blocks whilst it
250 * calls the service to get the preset set)
252 * @return service presets or null if exceptions were raised.
254 public PresetManager getPresets()
260 presets = service.getPresets();
261 } catch (Exception ex)
264 .println("Exception when retrieving presets for service "
265 + serviceType + " at " + hosturl);
271 public String getHost()
275 * try { URL serviceurl = new URL(hosturl); if (serviceurl.getPort()!=80)
276 * { return serviceurl.getHost()+":"+serviceurl.getPort(); } return
277 * serviceurl.getHost(); } catch (Exception e) {
278 * System.err.println("Failed to parse service URL '" + hosturl +
279 * "' as a valid URL!"); } return null;
284 * @return short description of what the service will do
286 public String getActionText()
288 return "Align with " + serviceType;
292 * non-thread safe - blocks whilst accessing service to get complete set of
293 * available options and parameters
297 public RunnerConfig getRunnerConfig()
299 return service.getRunnerOptions();
303 protected void finalize() throws Throwable
309 Closeable svc = (Closeable) service;
312 } catch (Exception e)
320 public ParamDatastoreI getParamStore()
322 if (paramStore == null)
326 paramStore = new JabaParamStore(this,
327 (Desktop.instance != null ? Desktop
328 .getUserParameterStore() : null));
329 } catch (Exception ex)
337 public String getUri()
339 // this is only valid for Jaba 1.0 - this formula might have to change!
341 + (hosturl.lastIndexOf("/") == (hosturl.length() - 1) ? "/"
345 private boolean hasParams = false, lookedForParams = false;
347 public boolean hasParameters()
349 if (!lookedForParams)
351 lookedForParams = true;
354 hasParams = (getRunnerConfig().getArguments().size() > 0);
355 } catch (Exception e)
365 * holds list of services.
367 protected Vector<Jws2Instance> services;
370 * find or add a submenu with the given title in the given menu
374 * @return the new or existing submenu
376 private JMenu findOrCreateMenu(JMenu menu, String submenu)
378 JMenu submenuinstance = null;
379 for (int i = 0, iSize = menu.getMenuComponentCount(); i < iSize; i++)
381 if (menu.getMenuComponent(i) instanceof JMenu
382 && ((JMenu) menu.getMenuComponent(i)).getText().equals(
385 submenuinstance = (JMenu) menu.getMenuComponent(i);
388 if (submenuinstance == null)
390 submenuinstance = new JMenu(submenu);
391 menu.add(submenuinstance);
393 return submenuinstance;
397 public void attachWSMenuEntry(JMenu wsmenu, final AlignFrame alignFrame)
399 // dynamically regenerate service list.
400 final JMenu jws2al = new JMenu("JABAWS Alignment");
401 jws2al.addMenuListener(new MenuListener()
403 // TODO: future: add menu listener to parent menu - so submenus are
404 // populated *before* they are selected.
406 public void menuSelected(MenuEvent e)
408 populateWSMenuEntry(jws2al, alignFrame);
412 public void menuDeselected(MenuEvent e)
414 // TODO Auto-generated method stub
419 public void menuCanceled(MenuEvent e)
421 // TODO Auto-generated method stub
430 private void populateWSMenuEntry(JMenu jws2al, final AlignFrame alignFrame)
432 if (running || services == null || services.size() == 0)
436 boolean byhost = Cache.getDefault("WSMENU_BYHOST", true), bytype = Cache
437 .getDefault("WSMENU_BYTYPE", true);
439 * eventually, JWS2 services will appear under the same align/etc submenus.
440 * for moment we keep them separate.
443 MsaWSClient msacl = new MsaWSClient();
444 Vector hostLabels = new Vector();
446 String lasthost = null;
447 for (final Jws2Instance service : services)
450 String host = service.getHost();
451 String type = service.serviceType;
454 atpoint = findOrCreateMenu(atpoint, host);
455 if (atpoint.getToolTipText() == null)
457 atpoint.setToolTipText("Services at " + host);
462 atpoint = findOrCreateMenu(atpoint, type);
463 if (atpoint.getToolTipText() == null)
465 atpoint.setToolTipText(service.getActionText());
469 && !hostLabels.contains(host + service.serviceType
470 + service.getActionText()))
471 // !hostLabels.contains(host + (bytype ?
472 // service.serviceType+service.getActionText() : "")))
474 // add a marker indicating where this service is hosted
475 // relies on services from the same host being listed in a contiguous
478 atpoint.addSeparator();
479 if (lasthost == null || !lasthost.equals(host))
481 atpoint.add(hitm = new JMenuItem(host));
482 hitm.setForeground(Color.blue);
485 hostLabels.addElement(host + service.serviceType
486 + service.getActionText());
487 // hostLabels.addElement(host + (bytype ?
488 // service.serviceType+service.getActionText() : ""));
490 msacl.attachWSMenuEntry(atpoint, service, alignFrame);
492 * JMenuItem sitem = new JMenuItem(service.serviceType);
493 * sitem.setToolTipText("Hosted at " + service.hosturl);
494 * sitem.addActionListener(new ActionListener() {
496 * @Override public void actionPerformed(ActionEvent e) { AlignmentView
497 * msa = alignFrame.gatherSequencesForAlignment(); MsaWSClient client =
498 * new MsaWSClient(service, "JWS2 Alignment of " + alignFrame.getTitle(),
499 * msa, false, true, alignFrame.getViewport().getAlignment().getDataset(),
505 public static void main(String[] args)
507 Thread runner = getDiscoverer().startDiscoverer(
508 new PropertyChangeListener()
511 public void propertyChange(PropertyChangeEvent evt)
513 if (getDiscoverer().services!=null)
515 System.out.println("Changesupport: There are now "
516 + getDiscoverer().services.size() + " services");
521 while (runner.isAlive())
526 } catch (InterruptedException e)
533 private static Jws2Discoverer discoverer;
535 public static Jws2Discoverer getDiscoverer()
537 if (discoverer == null)
539 discoverer = new Jws2Discoverer();
544 public boolean hasServices()
546 // TODO Auto-generated method stub
547 return !running && services != null && services.size() > 0;
550 public boolean isRunning()
556 * the jalview .properties entry for JWS2 URLS
558 final static String JWS2HOSTURLS = "JWS2HOSTURLS";
560 public static void setServiceUrls(Vector<String> urls)
564 StringBuffer urlbuffer = new StringBuffer();
566 for (String url : urls)
568 urlbuffer.append(sep);
569 urlbuffer.append(url);
572 Cache.setProperty(JWS2HOSTURLS, urlbuffer.toString());
576 Cache.removeProperty(JWS2HOSTURLS);
580 public static Vector<String> getServiceUrls()
582 String surls = Cache.getDefault(JWS2HOSTURLS,
583 "http://www.compbio.dundee.ac.uk/jabaws");
584 Vector<String> urls = new Vector<String>();
587 StringTokenizer st = new StringTokenizer(surls, ",");
588 while (st.hasMoreElements())
593 java.net.URL u = new java.net.URL(url = st.nextToken());
594 if (!urls.contains(url))
600 jalview.bin.Cache.log.info("Ignoring duplicate url in "
601 + JWS2HOSTURLS + " list");
603 } catch (Exception ex)
605 jalview.bin.Cache.log
606 .warn("Problem whilst trying to make a URL from '"
607 + ((url != null) ? url : "<null>") + "'");
608 jalview.bin.Cache.log
609 .warn("This was probably due to a malformed comma separated list"
612 + " entry of $(HOME)/.jalview_properties)");
613 jalview.bin.Cache.log.debug("Exception was ", ex);
616 } catch (Exception ex)
618 jalview.bin.Cache.log.warn(
619 "Error parsing comma separated list of urls in "
620 + JWS2HOSTURLS + " preference.", ex);
622 if (urls.size() >= 0)
629 public Vector<Jws2Instance> getServices()
631 return (services == null) ? new Vector<Jws2Instance>()
632 : new Vector<Jws2Instance>(services);
636 * test the given URL with the JabaWS test code
641 public static boolean testServiceUrl(URL foo)
645 compbio.ws.client.WSTester.main(new String[]
646 { "-h=" + foo.toString() });
647 } catch (Exception e)
651 } catch (OutOfMemoryError e)
664 * Start a fresh discovery thread and notify the given object when we're
665 * finished. Any known existing threads will be killed before this one is
668 * @param changeSupport2
671 public Thread startDiscoverer(PropertyChangeListener changeSupport2)
677 addPropertyChangeListener(changeSupport2);
678 Thread thr = new Thread(this);
683 Vector<String> invalidServiceUrls = null, urlsWithoutServices = null;
686 * @return the invalidServiceUrls
688 public Vector<String> getInvalidServiceUrls()
690 return invalidServiceUrls;
694 * @return the urlsWithoutServices
696 public Vector<String> getUrlsWithoutServices()
698 return urlsWithoutServices;
702 * add an 'empty' JABA server to the list
706 public synchronized void addUrlwithnoservices(String jwsservers)
708 if (urlsWithoutServices == null)
710 urlsWithoutServices = new Vector<String>();
712 if (!urlsWithoutServices.contains(jwsservers))
714 urlsWithoutServices.add(jwsservers);
719 * add a bad URL to the list
723 public synchronized void addInvalidServiceUrl(String jwsservers)
725 if (invalidServiceUrls == null)
727 invalidServiceUrls = new Vector<String>();
729 if (!invalidServiceUrls.contains(jwsservers))
731 invalidServiceUrls.add(jwsservers);
737 * @return a human readable report of any problems with the service URLs used
740 public String getErrorMessages()
742 if (!isRunning() && !isAborted())
744 StringBuffer ermsg = new StringBuffer();
745 boolean list = false;
746 if (getInvalidServiceUrls() != null
747 && getInvalidServiceUrls().size() > 0)
749 ermsg.append("Invalid Service URLS: \n");
750 for (String svcurl : getInvalidServiceUrls())
757 ermsg.append(svcurl);
759 ermsg.append("\n\n");
762 if (getUrlsWithoutServices() != null
763 && getUrlsWithoutServices().size() > 0)
765 ermsg.append("URLs without any JABA Services : \n");
766 for (String svcurl : getUrlsWithoutServices())
773 ermsg.append(svcurl);
777 if (ermsg.length() > 1)
779 return ermsg.toString();