/*
- * 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, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
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 jalview.gui.AlignFrame;
import jalview.gui.Desktop;
import jalview.gui.JalviewChangeSupport;
+import jalview.gui.JvSwingUtils;
import jalview.ws.WSMenuEntryProviderI;
-import jalview.ws.params.ParamDatastoreI;
-import compbio.data.msa.MsaWS;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+import compbio.data.msa.JABAService;
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;
boolean running = false, aborted = false;
/**
+ * @return the aborted
+ */
+ public boolean isAborted()
+ {
+ return aborted;
+ }
+
+ /**
* @param aborted
* the aborted to set
*/
} 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();
}
+ if (urlsWithoutServices != null)
+ {
+ urlsWithoutServices.removeAllElements();
+ }
+ if (invalidServiceUrls != null)
+ {
+ invalidServiceUrls.removeAllElements();
+ }
+
List<JabaWsServerQuery> qrys = new ArrayList<JabaWsServerQuery>();
for (final String jwsservers : getServiceUrls())
{
* @param srv
* @param service2
*/
- synchronized void addService(String jwsservers, Services srv,
- MsaWS service2)
+ synchronized void addService(String jwsservers, Jws2Instance service)
{
if (services == null)
{
services = new Vector<Jws2Instance>();
}
System.out.println("Discovered service: " + jwsservers + " "
- + srv.toString());
- Jws2Instance service = new Jws2Instance(jwsservers, srv.toString(),
- service2);
+ + service.toString());
+// Jws2Instance service = new Jws2Instance(jwsservers, srv.toString(),
+// service2);
services.add(service);
// retrieve the presets and parameter set and cache now
service.hasParameters();
}
- public class Jws2Instance
- {
- public String hosturl;
-
- public String serviceType;
-
- public MsaWS service;
-
- public Jws2Instance(String hosturl, String serviceType, MsaWS service)
- {
- super();
- this.hosturl = hosturl;
- this.serviceType = serviceType;
- 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.
*/
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
+ * attach all available web services to the appropriate submenu in the given JMenu
*/
- 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");
- 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);
-
+ populateWSMenuEntry(wsmenu, alignFrame, null);
}
- private void populateWSMenuEntry(JMenu jws2al, final AlignFrame alignFrame)
+ private void populateWSMenuEntry(JMenu jws2al, final AlignFrame alignFrame, String typeFilter)
{
if (running || services == null || services.size() == 0)
{
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 = JvSwingUtils.findOrCreateMenu(jws2al,service.action);
+ 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());
+ }
}
- hostLabels.addElement(host + service.serviceType
- + service.getActionText());
- // hostLabels.addElement(host + (bytype ?
- // service.serviceType+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() : ""));
+ }
+
+ service.attachWSMenuEntry(atpoint, 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 = getDiscoverer().startDiscoverer(new PropertyChangeListener()
+ if (args.length>0)
{
-
- public void propertyChange(PropertyChangeEvent evt)
+ testUrls = new Vector<String>();
+ for (String url:args)
{
- if (getDiscoverer().services!=null)
- {System.out.println("Changesupport: There are now "
- + getDiscoverer().services.size() + " services");
-
- }
- }
- });
+ testUrls.add(url);
+ };
+ }
+ 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 Vector<String> testUrls=null;
public static Vector<String> getServiceUrls()
{
+ if (testUrls!=null)
+ {
+ // return test urls, if there are any, instead of touching cache
+ return testUrls;
+ }
String surls = Cache.getDefault(JWS2HOSTURLS,
"http://www.compbio.dundee.ac.uk/jabaws");
Vector<String> urls = new Vector<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.
+ * 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
*/
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;
+ }
}