+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ */
package jalview.ws.jws2;
+import java.awt.Color;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.beans.PropertyChangeEvent;
import java.beans.PropertyChangeListener;
+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 javax.swing.JMenu;
import javax.swing.JMenuItem;
+import javax.swing.event.MenuEvent;
+import javax.swing.event.MenuListener;
import org.apache.log4j.Level;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentView;
import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.gui.JalviewChangeSupport;
import jalview.ws.WSMenuEntryProviderI;
+import jalview.ws.params.ParamDatastoreI;
import compbio.data.msa.MsaWS;
import compbio.metadata.Option;
import compbio.metadata.Preset;
import compbio.metadata.PresetManager;
import compbio.metadata.RunnerConfig;
-import compbio.ws.client.Jws2Base;
-import compbio.ws.client.Jws2Base.Services;
+import compbio.ws.client.Jws2Client;
+import compbio.ws.client.Services;
/**
* discoverer for jws2 services. Follows the lightweight service discoverer
changeSupport.removePropertyChangeListener(listener);
}
- boolean running = false;
+ boolean running = false, aborted = false;
+
+ /**
+ * @param aborted
+ * the aborted to set
+ */
+ public void setAborted(boolean aborted)
+ {
+ this.aborted = aborted;
+ }
Thread oldthread = null;
- @Override
public void run()
{
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();
try
{
Class foo = getClass().getClassLoader().loadClass(
- "compbio.ws.client.Jws2Base");
+ "compbio.ws.client.Jws2Client");
} catch (ClassNotFoundException e)
{
System.err
{
services.removeAllElements();
}
- for (String jwsservers : getServiceUrls())
+ 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 (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);
- }
+ 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)
{
}
System.out.println("Discovered service: " + jwsservers + " "
+ srv.toString());
- services.add(new Jws2Instance(jwsservers, srv.toString(), service2));
+ Jws2Instance service = new Jws2Instance(jwsservers, srv.toString(),
+ service2);
+
+ services.add(service);
+ // retrieve the presets and parameter set and cache now
+ service.getParamStore().getPresets();
+ service.hasParameters();
}
public class Jws2Instance
PresetManager presets = null;
+ public JabaParamStore paramStore = null;
+
/**
* non thread safe - gets the presets for this service (blocks whilst it
* calls the service to get the preset set)
public String getHost()
{
return hosturl;
-/* try
- {
- URL serviceurl = new URL(hosturl);
- if (serviceurl.getPort()!=80)
- {
- return serviceurl.getHost()+":"+serviceurl.getPort();
- }
- return serviceurl.getHost();
- } catch (Exception e)
- {
- System.err.println("Failed to parse service URL '" + hosturl
- + "' as a valid URL!");
- }
- return null; */
+ /*
+ * try { URL serviceurl = new URL(hosturl); if (serviceurl.getPort()!=80)
+ * { return serviceurl.getHost()+":"+serviceurl.getPort(); } return
+ * serviceurl.getHost(); } catch (Exception e) {
+ * System.err.println("Failed to parse service URL '" + hosturl +
+ * "' as a valid URL!"); } return null;
+ */
}
+
/**
* @return short description of what the service will do
*/
- public String getActionText() {
- return "Align with "
- + serviceType;
+ public String getActionText()
+ {
+ return "Align with " + serviceType;
}
/**
- * non-thread safe - blocks whilst accessing service to get complete set of available options and parameters
+ * non-thread safe - blocks whilst accessing service to get complete set of
+ * available options and parameters
+ *
* @return
*/
public RunnerConfig getRunnerConfig()
{
return service.getRunnerOptions();
}
+
+ @Override
+ protected void finalize() throws Throwable
+ {
+ if (service != null)
+ {
+ try
+ {
+ Closeable svc = (Closeable) service;
+ service = null;
+ svc.close();
+ } catch (Exception e)
+ {
+ }
+ ;
+ }
+ super.finalize();
+ }
+
+ public ParamDatastoreI getParamStore()
+ {
+ if (paramStore == null)
+ {
+ try
+ {
+ paramStore = new JabaParamStore(this,
+ (Desktop.instance != null ? Desktop
+ .getUserParameterStore() : null));
+ } catch (Exception ex)
+ {
+ }
+
+ }
+ return paramStore;
+ }
+
+ public String getUri()
+ {
+ // this is only valid for Jaba 1.0 - this formula might have to change!
+ return hosturl
+ + (hosturl.lastIndexOf("/") == (hosturl.length() - 1) ? "/"
+ : "") + serviceType;
+ }
+
+ private boolean hasParams = false, lookedForParams = false;
+
+ public boolean hasParameters()
+ {
+ if (!lookedForParams)
+ {
+ lookedForParams = true;
+ try
+ {
+ hasParams = (getRunnerConfig().getArguments().size() > 0);
+ } catch (Exception e)
+ {
+
+ }
+ }
+ return hasParams;
+ }
};
/**
/**
* 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++)
+ for (int i = 0, iSize = menu.getMenuComponentCount(); i < iSize; i++)
{
- if (menu.getMenuComponent(i) instanceof JMenu &&
- ((JMenu)menu.getMenuComponent(i)).getText().equals(submenu))
+ if (menu.getMenuComponent(i) instanceof JMenu
+ && ((JMenu) menu.getMenuComponent(i)).getText().equals(
+ submenu))
{
submenuinstance = (JMenu) menu.getMenuComponent(i);
}
}
- if (submenuinstance==null)
+ if (submenuinstance == null)
{
submenuinstance = new JMenu(submenu);
menu.add(submenuinstance);
}
return submenuinstance;
-
+
}
- @Override
+
public void attachWSMenuEntry(JMenu wsmenu, final AlignFrame alignFrame)
{
+ // dynamically regenerate service list.
+ final JMenu jws2al = new JMenu("JABAWS Alignment");
+ jws2al.addMenuListener(new MenuListener()
+ {
+ // TODO: future: add menu listener to parent menu - so submenus are
+ // populated *before* they are selected.
+ @Override
+ public void menuSelected(MenuEvent e)
+ {
+ populateWSMenuEntry(jws2al, alignFrame);
+ }
+
+ @Override
+ public void menuDeselected(MenuEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void menuCanceled(MenuEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ });
+ wsmenu.add(jws2al);
+
+ }
+
+ private void populateWSMenuEntry(JMenu jws2al, 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 atpoint, jws2al = new JMenu("JWS2 Alignment");
+ JMenu atpoint;
MsaWSClient msacl = new MsaWSClient();
+ Vector hostLabels = new Vector();
+ jws2al.removeAll();
+ String lasthost = null;
for (final Jws2Instance service : services)
{
atpoint = jws2al;
if (byhost)
{
atpoint = findOrCreateMenu(atpoint, host);
- if (atpoint.getToolTipText()==null) {
- atpoint.setToolTipText("Services at "+host);
+ if (atpoint.getToolTipText() == null)
+ {
+ atpoint.setToolTipText("Services at " + host);
}
}
if (bytype)
{
- atpoint = findOrCreateMenu(atpoint,type);
- if (atpoint.getToolTipText()==null) {
+ atpoint = 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);
+ lasthost = host;
+ }
+ 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);
* alignFrame); } });
*/
}
- if (services.size() > 0)
- {
- wsmenu.add(jws2al);
- }
-
}
public static void main(String[] args)
{
- Thread runner = new Thread(getDiscoverer());
- getDiscoverer().addPropertyChangeListener(new PropertyChangeListener()
+ Thread runner = getDiscoverer().startDiscoverer(new PropertyChangeListener()
{
- @Override
public void propertyChange(PropertyChangeEvent evt)
{
- System.out.println("Changesupport: There are now "
+ if (getDiscoverer().services!=null)
+ {System.out.println("Changesupport: There are now "
+ getDiscoverer().services.size() + " services");
+
+ }
}
});
- runner.start();
while (runner.isAlive())
{
try
public static Vector<String> getServiceUrls()
{
String surls = Cache.getDefault(JWS2HOSTURLS,
- "http://webservices.compbio.dundee.ac.uk:8084/jws2");
+ "http://www.compbio.dundee.ac.uk/jabaws");
Vector<String> urls = new Vector<String>();
try
{
public Vector<Jws2Instance> getServices()
{
- return (services==null) ? new Vector<Jws2Instance>(): new Vector<Jws2Instance>(services);
+ return (services == null) ? new Vector<Jws2Instance>()
+ : new Vector<Jws2Instance>(services);
+ }
+
+ /**
+ * test the given URL with the JabaWS test code
+ *
+ * @param foo
+ * @return
+ */
+ public static boolean testServiceUrl(URL foo)
+ {
+ try
+ {
+ compbio.ws.client.WSTester.main(new String[]
+ { "-h=" + foo.toString() });
+ } catch (Exception e)
+ {
+ return false;
+ } catch (OutOfMemoryError e)
+ {
+ return false;
+ } catch (Error e)
+ {
+ 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;
}
}
git://source.jalview.org / jalview.git / blobdiff