/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
import java.io.Closeable;
import java.net.ConnectException;
import java.net.URL;
+import java.util.ArrayList;
import java.util.HashSet;
import java.util.Hashtable;
+import java.util.List;
import java.util.StringTokenizer;
import java.util.Vector;
import jalview.datamodel.AlignmentView;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
+import jalview.gui.JalviewChangeSupport;
+import jalview.gui.JvSwingUtils;
import jalview.ws.WSMenuEntryProviderI;
+import jalview.ws.jws2.Jws2Discoverer.Jws2Instance;
import jalview.ws.params.ParamDatastoreI;
import compbio.data.msa.MsaWS;
import compbio.metadata.Option;
changeSupport.removePropertyChangeListener(listener);
}
- boolean running = false;
+ boolean running = false, aborted = false;
+
+ /**
+ * @return the aborted
+ */
+ public boolean isAborted()
+ {
+ return aborted;
+ }
+
+ /**
+ * @param aborted
+ * the aborted to set
+ */
+ public void setAborted(boolean aborted)
+ {
+ this.aborted = aborted;
+ }
Thread oldthread = null;
{
if (running && oldthread != null && oldthread.isAlive())
{
- return;
+ if (!aborted)
+ {
+ return;
+ }
+ while (running)
+ {
+ try
+ {
+ Cache.log
+ .debug("Waiting around for old discovery thread to finish.");
+ // wait around until old discoverer dies
+ Thread.sleep(100);
+ } catch (Exception e)
+ {
+ }
+ }
+ Cache.log.debug("Old discovery thread has finished.");
}
running = true;
oldthread = Thread.currentThread();
} catch (ClassNotFoundException e)
{
System.err
- .println("Not enabling Jalview Webservices version 2: client jar is not available."
+ .println("Not enabling JABA Webservices : client jar is not available."
+ "\nPlease check that your webstart JNLP file is up to date!");
running = false;
return;
}
+ // reinitialise records of good and bad service URLs
if (services != null)
{
services.removeAllElements();
}
- for (String jwsservers : getServiceUrls())
+ if (urlsWithoutServices != null)
+ {
+ urlsWithoutServices.removeAllElements();
+ }
+ if (invalidServiceUrls != null)
+ {
+ invalidServiceUrls.removeAllElements();
+ }
+
+ List<JabaWsServerQuery> qrys = new ArrayList<JabaWsServerQuery>();
+ for (final String jwsservers : getServiceUrls())
+ {
+ JabaWsServerQuery squery = new JabaWsServerQuery(this, jwsservers);
+ qrys.add(squery);
+ new Thread(squery).start();
+ }
+ boolean finished = false;
+ do
{
try
{
- if (Jws2Client.validURL(jwsservers))
- {
- // look for services
- for (Services srv : Services.values())
- {
- MsaWS service = null;
- try
- {
- service = Jws2Client.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);
- }
+ Thread.sleep(100);
} catch (Exception e)
{
- e.printStackTrace();
- Cache.log.warn("Exception when discovering Jws2 services.", e);
- } catch (Error e)
+ }
+ ;
+ for (JabaWsServerQuery squery : qrys)
{
- Cache.log.error("Exception when discovering Jws2 services.", e);
+ finished |= !squery.isRunning();
}
- }
+ if (aborted)
+ {
+ Cache.log.debug("Aborting " + qrys.size()
+ + " JABAWS discovery threads.");
+ for (JabaWsServerQuery squery : qrys)
+ {
+ squery.setQuit(true);
+ }
+ }
+ } while (!aborted && !finished);
oldthread = null;
running = false;
- changeSupport.firePropertyChange("services", new Vector(), services);
+ if (!aborted)
+ {
+ changeSupport.firePropertyChange("services", new Vector(), services);
+ }
}
/**
* @param srv
* @param service2
*/
- private void addService(String jwsservers, Services srv, MsaWS service2)
+ synchronized void addService(String jwsservers, Services srv,
+ MsaWS service2)
{
if (services == null)
{
{
// this is only valid for Jaba 1.0 - this formula might have to change!
return hosturl
- + (hosturl.lastIndexOf("/") == (hosturl.length() - 1) ? "/"
- : "") + serviceType;
+ + (hosturl.lastIndexOf("/") == (hosturl.length() - 1) ? ""
+ : "/") + serviceType;
}
private boolean hasParams = false, lookedForParams = false;
*/
protected Vector<Jws2Instance> services;
- /**
- * find or add a submenu with the given title in the given menu
- *
- * @param menu
- * @param submenu
- * @return the new or existing submenu
- */
- private JMenu findOrCreateMenu(JMenu menu, String submenu)
- {
- JMenu submenuinstance = null;
- for (int i = 0, iSize = menu.getMenuComponentCount(); i < iSize; i++)
- {
- if (menu.getMenuComponent(i) instanceof JMenu
- && ((JMenu) menu.getMenuComponent(i)).getText().equals(
- submenu))
- {
- submenuinstance = (JMenu) menu.getMenuComponent(i);
- }
- }
- if (submenuinstance == null)
- {
- submenuinstance = new JMenu(submenu);
- menu.add(submenuinstance);
- }
- return submenuinstance;
-
- }
-
public void attachWSMenuEntry(JMenu wsmenu, final AlignFrame alignFrame)
{
// dynamically regenerate service list.
- final JMenu jws2al = new JMenu("JABAWS Alignment");
+ final JMenu jws2al = wsmenu; // new JMenu("JABAWS Alignment");
jws2al.addMenuListener(new MenuListener()
{
// TODO: future: add menu listener to parent menu - so submenus are
{
return;
}
- boolean byhost = Cache.getDefault("WSMENU_BYHOST", true), bytype = Cache
- .getDefault("WSMENU_BYTYPE", true);
+ boolean byhost = Cache.getDefault("WSMENU_BYHOST", false), bytype = Cache
+ .getDefault("WSMENU_BYTYPE", false);
/**
* eventually, JWS2 services will appear under the same align/etc submenus.
* for moment we keep them separate.
Vector hostLabels = new Vector();
jws2al.removeAll();
String lasthost = null;
- for (final Jws2Instance service : services)
+ Hashtable<String, ArrayList<Jws2Instance>> hosts = new Hashtable<String, ArrayList<Jws2Instance>>();
+ String[] sorton;
+ for (Jws2Instance service : services)
{
- atpoint = jws2al;
- String host = service.getHost();
- String type = service.serviceType;
- if (byhost)
+ ArrayList<Jws2Instance> hostservices = hosts.get(service.getHost());
+ if (hostservices == null)
{
- atpoint = findOrCreateMenu(atpoint, host);
- if (atpoint.getToolTipText() == null)
- {
- atpoint.setToolTipText("Services at " + host);
- }
+ hosts.put(service.getHost(),
+ hostservices = new ArrayList<Jws2Instance>());
}
- if (bytype)
+ hostservices.add(service);
+ }
+ sorton = hosts.keySet().toArray(new String[1]);
+ String hostlist[] = sorton.clone();
+ jalview.util.QuickSort.sort(sorton, hostlist);
+ for (String host : hostlist)
+ {
+ Jws2Instance orderedsvcs[] = hosts.get(host).toArray(
+ new Jws2Instance[1]);
+ String sortbytype[] = new String[orderedsvcs.length];
+ for (int i = 0; i < sortbytype.length; i++)
{
- atpoint = findOrCreateMenu(atpoint, type);
- if (atpoint.getToolTipText() == null)
- {
- atpoint.setToolTipText(service.getActionText());
- }
+ sortbytype[i] = orderedsvcs[i].serviceType;
}
- if (!byhost
- && !hostLabels.contains(host + service.serviceType
- + service.getActionText()))
- // !hostLabels.contains(host + (bytype ?
- // service.serviceType+service.getActionText() : "")))
+ jalview.util.QuickSort.sort(sortbytype, orderedsvcs);
+ for (final Jws2Instance service : orderedsvcs)
{
- // add a marker indicating where this service is hosted
- // relies on services from the same host being listed in a contiguous
- // group
- JMenuItem hitm;
- atpoint.addSeparator();
- if (lasthost == null || !lasthost.equals(host))
+ atpoint = jws2al;
+ String type = service.serviceType;
+ if (byhost)
+ {
+ atpoint = JvSwingUtils.findOrCreateMenu(atpoint, host);
+ if (atpoint.getToolTipText() == null)
+ {
+ atpoint.setToolTipText("Services at " + host);
+ }
+ }
+ if (bytype)
{
- atpoint.add(hitm = new JMenuItem(host));
- hitm.setForeground(Color.blue);
- lasthost = host;
+ atpoint = JvSwingUtils.findOrCreateMenu(atpoint, type);
+ if (atpoint.getToolTipText() == null)
+ {
+ atpoint.setToolTipText(service.getActionText());
+ }
+ }
+ if (!byhost
+ && !hostLabels.contains(host + service.serviceType
+ + service.getActionText()))
+ // !hostLabels.contains(host + (bytype ?
+ // service.serviceType+service.getActionText() : "")))
+ {
+ // add a marker indicating where this service is hosted
+ // relies on services from the same host being listed in a
+ // contiguous
+ // group
+ JMenuItem hitm;
+ atpoint.addSeparator();
+ if (lasthost == null || !lasthost.equals(host))
+ {
+ atpoint.add(hitm = new JMenuItem(host));
+ hitm.setForeground(Color.blue);
+ hitm.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ Desktop.showUrl(service.getHost());
+ }
+ });
+ hitm.setToolTipText(JvSwingUtils
+ .wrapTooltip("Opens the JABAWS server's homepage in web browser"));
+ lasthost = host;
+ }
+ hostLabels.addElement(host + service.serviceType
+ + service.getActionText());
+ // hostLabels.addElement(host + (bytype ?
+ // service.serviceType+service.getActionText() : ""));
}
- hostLabels.addElement(host + service.serviceType
- + service.getActionText());
- // hostLabels.addElement(host + (bytype ?
- // service.serviceType+service.getActionText() : ""));
+ msacl.attachWSMenuEntry(atpoint, 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); }
+ * });
+ */
}
- msacl.attachWSMenuEntry(atpoint, 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); } });
- */
}
+
}
public static void main(String[] args)
{
- Thread runner = new Thread(getDiscoverer());
- getDiscoverer().addPropertyChangeListener(new PropertyChangeListener()
- {
+ Thread runner = getDiscoverer().startDiscoverer(
+ new PropertyChangeListener()
+ {
- public void propertyChange(PropertyChangeEvent evt)
- {
- System.out.println("Changesupport: There are now "
- + getDiscoverer().services.size() + " services");
- }
- });
- runner.start();
+ public void propertyChange(PropertyChangeEvent evt)
+ {
+ if (getDiscoverer().services != null)
+ {
+ System.out.println("Changesupport: There are now "
+ + getDiscoverer().services.size() + " services");
+
+ }
+ }
+ });
while (runner.isAlive())
{
try
{ "-h=" + foo.toString() });
} catch (Exception e)
{
+ e.printStackTrace();
return false;
} catch (OutOfMemoryError e)
{
+ e.printStackTrace();
return false;
} catch (Error e)
{
+ e.printStackTrace();
return false;
}
+
return true;
}
+ /**
+ * Start a fresh discovery thread and notify the given object when we're
+ * finished. Any known existing threads will be killed before this one is
+ * started.
+ *
+ * @param changeSupport2
+ * @return new thread
+ */
+ public Thread startDiscoverer(PropertyChangeListener changeSupport2)
+ {
+ if (isRunning())
+ {
+ setAborted(true);
+ }
+ addPropertyChangeListener(changeSupport2);
+ Thread thr = new Thread(this);
+ thr.start();
+ return thr;
+ }
+
+ Vector<String> invalidServiceUrls = null, urlsWithoutServices = null;
+
+ /**
+ * @return the invalidServiceUrls
+ */
+ public Vector<String> getInvalidServiceUrls()
+ {
+ return invalidServiceUrls;
+ }
+
+ /**
+ * @return the urlsWithoutServices
+ */
+ public Vector<String> getUrlsWithoutServices()
+ {
+ return urlsWithoutServices;
+ }
+
+ /**
+ * add an 'empty' JABA server to the list. Only servers not already in the
+ * 'bad URL' list will be added to this list.
+ *
+ * @param jwsservers
+ */
+ public synchronized void addUrlwithnoservices(String jwsservers)
+ {
+ if (urlsWithoutServices == null)
+ {
+ urlsWithoutServices = new Vector<String>();
+ }
+
+ if ((invalidServiceUrls == null || !invalidServiceUrls
+ .contains(jwsservers))
+ && !urlsWithoutServices.contains(jwsservers))
+ {
+ urlsWithoutServices.add(jwsservers);
+ }
+ }
+
+ /**
+ * add a bad URL to the list
+ *
+ * @param jwsservers
+ */
+ public synchronized void addInvalidServiceUrl(String jwsservers)
+ {
+ if (invalidServiceUrls == null)
+ {
+ invalidServiceUrls = new Vector<String>();
+ }
+ if (!invalidServiceUrls.contains(jwsservers))
+ {
+ invalidServiceUrls.add(jwsservers);
+ }
+ }
+
+ /**
+ *
+ * @return a human readable report of any problems with the service URLs used
+ * for discovery
+ */
+ public String getErrorMessages()
+ {
+ if (!isRunning() && !isAborted())
+ {
+ StringBuffer ermsg = new StringBuffer();
+ boolean list = false;
+ if (getInvalidServiceUrls() != null
+ && getInvalidServiceUrls().size() > 0)
+ {
+ ermsg.append("URLs that could not be contacted: \n");
+ for (String svcurl : getInvalidServiceUrls())
+ {
+ if (list)
+ {
+ ermsg.append(", ");
+ }
+ list = true;
+ ermsg.append(svcurl);
+ }
+ ermsg.append("\n\n");
+ }
+ list = false;
+ if (getUrlsWithoutServices() != null
+ && getUrlsWithoutServices().size() > 0)
+ {
+ ermsg.append("URLs without any JABA Services : \n");
+ for (String svcurl : getUrlsWithoutServices())
+ {
+ if (list)
+ {
+ ermsg.append(", ");
+ }
+ list = true;
+ ermsg.append(svcurl);
+ }
+ ermsg.append("\n");
+ }
+ if (ermsg.length() > 1)
+ {
+ return ermsg.toString();
+ }
+
+ }
+ return null;
+ }
+
}