X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fws%2Fjws2%2FJws2Discoverer.java;h=ed808f6e03a5022f501c5e9879beec63994a1bc8;hb=26e4caf025740afea870ed6ceb5894bc56316ba6;hp=2b809b52110bc2f945498879e851b28335a9fa1e;hpb=2526950b59bcd97094ff8aed26f397ab4d7987b2;p=jalview.git
diff --git a/src/jalview/ws/jws2/Jws2Discoverer.java b/src/jalview/ws/jws2/Jws2Discoverer.java
index 2b809b5..ed808f6 100644
--- a/src/jalview/ws/jws2/Jws2Discoverer.java
+++ b/src/jalview/ws/jws2/Jws2Discoverer.java
@@ -1,32 +1,60 @@
+/*
+ * 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.
+ *
+ * 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 .
+ */
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.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;
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
@@ -64,82 +92,114 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
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;
- @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
- .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 qrys = new ArrayList();
+ 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);
+ }
}
/**
@@ -149,7 +209,8 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
* @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)
{
@@ -157,7 +218,13 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
}
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
@@ -178,6 +245,8 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
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)
@@ -204,37 +273,94 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
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;
+ }
};
/**
@@ -242,99 +368,169 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
*/
protected Vector 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)
+ public void attachWSMenuEntry(JMenu wsmenu, final AlignFrame alignFrame)
{
- JMenu submenuinstance = null;
- for (int i=0,iSize=menu.getMenuComponentCount(); i> hosts = new Hashtable>();
+ String[] sorton;
+ for (Jws2Instance service : services)
{
- atpoint = jws2al;
- String host = service.getHost();
- String type = service.serviceType;
- if (byhost)
+ ArrayList 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());
}
- 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;
+ }
+ jalview.util.QuickSort.sort(sortbytype, orderedsvcs);
+ for (final Jws2Instance service : orderedsvcs)
+ {
+ 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 = 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() : ""));
+ }
+ 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); } });
- */
- }
- 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 "
- + 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
@@ -397,7 +593,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
public static Vector getServiceUrls()
{
String surls = Cache.getDefault(JWS2HOSTURLS,
- "http://www.compbio.dundee.ac.uk/jaws2");
+ "http://www.compbio.dundee.ac.uk/jabaws");
Vector urls = new Vector();
try
{
@@ -445,7 +641,164 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
public Vector getServices()
{
- return (services==null) ? new Vector(): new Vector(services);
+ return (services == null) ? new Vector()
+ : new Vector(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)
+ {
+ 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 invalidServiceUrls = null, urlsWithoutServices = null;
+
+ /**
+ * @return the invalidServiceUrls
+ */
+ public Vector getInvalidServiceUrls()
+ {
+ return invalidServiceUrls;
+ }
+
+ /**
+ * @return the urlsWithoutServices
+ */
+ public Vector 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();
+ }
+
+ 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();
+ }
+ 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;
}
}