+/*
+ * 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 <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.gui.JvSwingUtils;
import jalview.ws.WSMenuEntryProviderI;
+import jalview.ws.jws2.Jws2Discoverer.Jws2Instance;
+import jalview.ws.params.ParamDatastoreI;
import compbio.data.msa.MsaWS;
-import compbio.ws.client.Jws2Base;
-import compbio.ws.client.Jws2Base.Services;
+import compbio.metadata.Option;
+import compbio.metadata.Preset;
+import compbio.metadata.PresetManager;
+import compbio.metadata.RunnerConfig;
+import compbio.ws.client.Jws2Client;
+import compbio.ws.client.Services;
/**
* discoverer for jws2 services. Follows the lightweight service discoverer
*/
public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
{
- compbio.data.msa.MsaWS service;
- boolean running=false;
- @Override
+ private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(
+ this);
+
+ /**
+ * change listeners are notified of "services" property changes
+ *
+ * @param listener
+ * to be added that consumes new services Hashtable object.
+ */
+ public void addPropertyChangeListener(
+ java.beans.PropertyChangeListener listener)
+ {
+ changeSupport.addPropertyChangeListener(listener);
+ }
+
+ /**
+ *
+ *
+ * @param listener
+ * to be removed
+ */
+ public void removePropertyChangeListener(
+ java.beans.PropertyChangeListener listener)
+ {
+ changeSupport.removePropertyChangeListener(listener);
+ }
+
+ 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;
+
public void run()
{
- if (running)
+ if (running && oldthread != null && oldthread.isAlive())
{
- return;
- }
- running=true;
-// Cache.initLogger();
-// Cache.log.setLevel(Level.DEBUG);
- // TODO: Document and PACK JWS2
- String jwsservers = Cache.getDefault("JWS2HOSTURLS",
- "http://webservices.compbio.dundee.ac.uk:8084/jws2");
- try
- {
- if (Jws2Base.validURL(jwsservers))
+ if (!aborted)
+ {
+ return;
+ }
+ while (running)
{
- // look for services
- for (Services srv : Jws2Base.Services.values())
+ try
+ {
+ Cache.log
+ .debug("Waiting around for old discovery thread to finish.");
+ // wait around until old discoverer dies
+ Thread.sleep(100);
+ } catch (Exception e)
{
- MsaWS service = null;
- try
- {
- service = Jws2Base.connect(jwsservers, srv);
- } catch (Exception e)
- {
- }
- ;
- if (service != null)
- {
- addService(jwsservers, srv, service);
- }
}
+ }
+ Cache.log.debug("Old discovery thread has finished.");
+ }
+ running = true;
+ oldthread = Thread.currentThread();
+ try
+ {
+ Class foo = getClass().getClassLoader().loadClass(
+ "compbio.ws.client.Jws2Client");
+ } catch (ClassNotFoundException e)
+ {
+ System.err
+ .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();
+ }
+ 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
+ {
+ Thread.sleep(100);
+ } catch (Exception e)
+ {
}
- else
+ ;
+ for (JabaWsServerQuery squery : qrys)
{
- Cache.log.info("Ignoring invalid Jws2 service url " + jwsservers);
+ finished |= !squery.isRunning();
}
- } catch (Exception e)
- {
- Cache.log.warn("Exception when discovering Jws2 services.", e);
- } catch (Error e)
+ 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;
+ if (!aborted)
{
- Cache.log.error("Exception when discovering Jws2 services.", e);
+ changeSupport.firePropertyChange("services", new Vector(), services);
}
- running=false;
-
}
/**
* @param srv
* @param service2
*/
- private void addService(String jwsservers, Services srv, MsaWS service2)
+ synchronized void addService(String jwsservers, Services srv,
+ MsaWS service2)
{
- Cache.log.info("Discovered service: " + jwsservers + " "
- + srv.toString());
- if (services==null) {
+ if (services == null)
+ {
services = new Vector<Jws2Instance>();
}
- services.add(new Jws2Instance(jwsservers, "Align with "
- + srv.toString(), service2));
+ System.out.println("Discovered service: " + jwsservers + " "
+ + srv.toString());
+ 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
{
- String hosturl;
+ public String hosturl;
- String serviceType;
+ public String serviceType;
- MsaWS service;
+ public MsaWS service;
public Jws2Instance(String hosturl, String serviceType, MsaWS service)
{
this.service = service;
}
+ 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)
+ *
+ * @return service presets or null if exceptions were raised.
+ */
+ public PresetManager getPresets()
+ {
+ if (presets == null)
+ {
+ try
+ {
+ presets = service.getPresets();
+ } catch (Exception ex)
+ {
+ System.err
+ .println("Exception when retrieving presets for service "
+ + serviceType + " at " + hosturl);
+ }
+ }
+ return presets;
+ }
+
+ 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;
+ */
+ }
+
+ /**
+ * @return short description of what the service will do
+ */
+ public String getActionText()
+ {
+ return "Align with " + serviceType;
+ }
+
+ /**
+ * 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;
+ }
};
/**
* holds list of services.
*/
- Vector<Jws2Instance> services;
+ protected Vector<Jws2Instance> services;
- @Override
public void attachWSMenuEntry(JMenu wsmenu, final AlignFrame alignFrame)
{
- if (running || services==null || services.size() == 0)
+ // dynamically regenerate service list.
+ final JMenu jws2al = wsmenu; // 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;
}
+ 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.
*/
- JMenu jws2 = new JMenu("JWS2 Alignment");
+ JMenu atpoint;
MsaWSClient msacl = new MsaWSClient();
- for (final Jws2Instance service : services)
+ Vector hostLabels = new Vector();
+ jws2al.removeAll();
+ String lasthost = null;
+ Hashtable<String, ArrayList<Jws2Instance>> hosts = new Hashtable<String, ArrayList<Jws2Instance>>();
+ String[] sorton;
+ for (Jws2Instance service : services)
{
- msacl.attachWSMenuEntry(jws2, service, alignFrame);
- /*JMenuItem sitem = new JMenuItem(service.serviceType);
- sitem.setToolTipText("Hosted at " + service.hosturl);
- sitem.addActionListener(new ActionListener()
+ ArrayList<Jws2Instance> hostservices = hosts.get(service.getHost());
+ if (hostservices == null)
{
-
- @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);
- }
- });*/
+ hosts.put(service.getHost(),
+ hostservices = new ArrayList<Jws2Instance>());
+ }
+ hostservices.add(service);
}
- if (services.size()>0)
+ sorton = hosts.keySet().toArray(new String[1]);
+ String hostlist[] = sorton.clone();
+ jalview.util.QuickSort.sort(sorton, hostlist);
+ for (String host : hostlist)
{
- wsmenu.add(jws2);
+ Jws2Instance orderedsvcs[] = hosts.get(host).toArray(
+ new Jws2Instance[1]);
+ String sortbytype[] = new String[orderedsvcs.length];
+ for (int i = 0; i < sortbytype.length; i++)
+ {
+ 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); }
+ * });
+ */
+ }
}
-
+
}
+
public static void main(String[] args)
{
- Thread runner = new Thread(getDiscoverer());
- runner.start();
+ Thread runner = getDiscoverer().startDiscoverer(
+ new PropertyChangeListener()
+ {
+
+ public void propertyChange(PropertyChangeEvent evt)
+ {
+ if (getDiscoverer().services != null)
+ {
+ System.out.println("Changesupport: There are now "
+ + getDiscoverer().services.size() + " services");
+
+ }
+ }
+ });
while (runner.isAlive())
{
try
;
}
}
+
private static Jws2Discoverer discoverer;
+
public static Jws2Discoverer getDiscoverer()
{
- if (discoverer==null)
+ if (discoverer == null)
{
discoverer = new Jws2Discoverer();
}
public boolean hasServices()
{
// TODO Auto-generated method stub
- return services!=null && services.size()>0;
+ return !running && services != null && services.size() > 0;
+ }
+
+ public boolean isRunning()
+ {
+ return running;
+ }
+
+ /**
+ * the jalview .properties entry for JWS2 URLS
+ */
+ final static String JWS2HOSTURLS = "JWS2HOSTURLS";
+
+ public static void setServiceUrls(Vector<String> urls)
+ {
+ if (urls != null)
+ {
+ StringBuffer urlbuffer = new StringBuffer();
+ String sep = "";
+ for (String url : urls)
+ {
+ urlbuffer.append(sep);
+ urlbuffer.append(url);
+ sep = ",";
+ }
+ Cache.setProperty(JWS2HOSTURLS, urlbuffer.toString());
+ }
+ else
+ {
+ Cache.removeProperty(JWS2HOSTURLS);
+ }
+ }
+
+ public static Vector<String> getServiceUrls()
+ {
+ String surls = Cache.getDefault(JWS2HOSTURLS,
+ "http://www.compbio.dundee.ac.uk/jabaws");
+ Vector<String> urls = new Vector<String>();
+ try
+ {
+ StringTokenizer st = new StringTokenizer(surls, ",");
+ while (st.hasMoreElements())
+ {
+ String url = null;
+ try
+ {
+ java.net.URL u = new java.net.URL(url = st.nextToken());
+ if (!urls.contains(url))
+ {
+ urls.add(url);
+ }
+ else
+ {
+ jalview.bin.Cache.log.info("Ignoring duplicate url in "
+ + JWS2HOSTURLS + " list");
+ }
+ } catch (Exception ex)
+ {
+ jalview.bin.Cache.log
+ .warn("Problem whilst trying to make a URL from '"
+ + ((url != null) ? url : "<null>") + "'");
+ jalview.bin.Cache.log
+ .warn("This was probably due to a malformed comma separated list"
+ + " in the "
+ + JWS2HOSTURLS
+ + " entry of $(HOME)/.jalview_properties)");
+ jalview.bin.Cache.log.debug("Exception was ", ex);
+ }
+ }
+ } catch (Exception ex)
+ {
+ jalview.bin.Cache.log.warn(
+ "Error parsing comma separated list of urls in "
+ + JWS2HOSTURLS + " preference.", ex);
+ }
+ if (urls.size() >= 0)
+ {
+ return urls;
+ }
+ return null;
+ }
+
+ public Vector<Jws2Instance> getServices()
+ {
+ 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)
+ {
+ 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;
}
-
+
}
git://source.jalview.org / jalview.git / blobdiff