/*
- * 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.
*
*/
package jalview.ws.jws2;
+import jalview.bin.Cache;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.gui.JvSwingUtils;
+import jalview.ws.WSMenuEntryProviderI;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+
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.Arrays;
import java.util.HashSet;
import java.util.Hashtable;
import java.util.List;
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.Jws2Client;
import compbio.ws.client.Services;
/**
Cache.log.debug("Old discovery thread has finished.");
}
running = true;
+ changeSupport.firePropertyChange("services", services, new Vector());
oldthread = Thread.currentThread();
try
{
{
invalidServiceUrls.removeAllElements();
}
+ if (validServiceUrls != null)
+ {
+ validServiceUrls.removeAllElements();
+ }
+ ArrayList<String> svctypes=new ArrayList<String>();
List<JabaWsServerQuery> qrys = new ArrayList<JabaWsServerQuery>();
for (final String jwsservers : getServiceUrls())
{
JabaWsServerQuery squery = new JabaWsServerQuery(this, jwsservers);
+ if (svctypes.size()==0)
+ {
+ // TODO: remove this ugly hack to get Canonical JABA service ordering for all possible services
+ for (Services sv:squery.JABAWS2SERVERS)
+ {
+ svctypes.add(sv.toString());
+ }
+
+ }
qrys.add(squery);
new Thread(squery).start();
}
- boolean finished = false;
+ boolean finished = true;
do
{
+ finished=true;
try
{
Thread.sleep(100);
;
for (JabaWsServerQuery squery : qrys)
{
- finished |= !squery.isRunning();
+ finished = finished && !squery.isRunning();
}
if (aborted)
{
}
}
} while (!aborted && !finished);
- oldthread = null;
- running = false;
if (!aborted)
{
- changeSupport.firePropertyChange("services", new Vector(), services);
+ // resort services according to order found in jabaws service list
+ // also ensure servics for each host are ordered in same way.
+
+ if (services!=null && services.size()>0)
+ {
+ Jws2Instance[] svcs=new Jws2Instance[services.size()];
+ int[] spos=new int[services.size()];
+ int ipos=0;
+ Vector svcUrls = getServiceUrls();
+ for (Jws2Instance svc:services)
+ {
+ svcs[ipos]=svc;
+ spos[ipos++]=1000*svcUrls.indexOf(svc.getHost()) + 1+svctypes.indexOf(svc.serviceType);
+ }
+ jalview.util.QuickSort.sort(spos, svcs);
+ services=new Vector<Jws2Instance>();
+ for (Jws2Instance svc:svcs) {
+ services.add(svc);
+ }
+ }
}
+ oldthread = null;
+ running = false;
+ changeSupport.firePropertyChange("services", new Vector(), services);
}
/**
* @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.getParamStore().getPresets();
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 (validServiceUrls==null)
{
- if (paramStore == null)
- {
- try
- {
- paramStore = new JabaParamStore(this,
- (Desktop.instance != null ? Desktop
- .getUserParameterStore() : null));
- } catch (Exception ex)
- {
- }
-
- }
- return paramStore;
+ validServiceUrls=new Vector();
}
-
- 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;
- }
- };
+ validServiceUrls.add(jwsservers);
+ }
/**
* 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.
MsaWSClient msacl = new MsaWSClient();
Vector hostLabels = new Vector();
jws2al.removeAll();
- String lasthost = null;
- for (final Jws2Instance service : services)
+ Hashtable<String,String> lasthostFor = new Hashtable<String,String>();
+ Hashtable<String, ArrayList<Jws2Instance>> hosts = new Hashtable<String, ArrayList<Jws2Instance>>();
+ ArrayList<String> hostlist=new ArrayList<String>();
+ 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>());
+ hostlist.add(service.getHost());
}
- if (bytype)
+ hostservices.add(service);
+ }
+ // now add hosts in order of the given array
+ 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.add(hitm = new JMenuItem(host));
- hitm.setForeground(Color.blue);
- lasthost = host;
+ atpoint = JvSwingUtils.findOrCreateMenu(atpoint, host);
+ if (atpoint.getToolTipText() == null)
+ {
+ atpoint.setToolTipText("Services at " + host);
+ }
}
- hostLabels.addElement(host + service.serviceType
- + service.getActionText());
- // hostLabels.addElement(host + (bytype ?
- // service.serviceType+service.getActionText() : ""));
+ 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 (lasthostFor.get(service.action) == null || !lasthostFor.get(service.action).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"));
+ lasthostFor.put(service.action,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)
{
+ if (args.length>0)
+ {
+ testUrls = new Vector<String>();
+ for (String url:args)
+ {
+ testUrls.add(url);
+ };
+ }
Thread runner = getDiscoverer().startDiscoverer(
new PropertyChangeListener()
{
{
System.out.println("Changesupport: There are now "
+ getDiscoverer().services.size() + " services");
+ int i=1;
+ for (Jws2Instance instance:getDiscoverer().services)
+ {
+ System.out.println("Service "+i+++" "+instance.getClass()+"@"+instance.getHost()+": "+instance.getActionText());
+ }
}
}
}
;
}
+ try {
+ Thread.sleep(50);
+ } catch (InterruptedException x) {}
}
private static Jws2Discoverer discoverer;
}
}
+ 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>();
return thr;
}
- Vector<String> invalidServiceUrls = null, urlsWithoutServices = null;
+ Vector<String> invalidServiceUrls = null, urlsWithoutServices = null, validServiceUrls=null;
/**
* @return the invalidServiceUrls
}
/**
- * add an 'empty' JABA server to the list. Only servers not already in the 'bad URL' list will be added to this list.
+ * 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
*/
return null;
}
+ public int getServerStatusFor(String url)
+ {
+ if (validServiceUrls!=null && validServiceUrls.contains(url))
+ {
+ return 1;
+ }
+ if (urlsWithoutServices!=null && urlsWithoutServices.contains(url))
+ return 0;
+ if (invalidServiceUrls!=null && invalidServiceUrls.contains(url))
+ {
+ return -1;
+ }
+ return -2;
+ }
+
+ /**
+ * pick the user's preferred service based on a set of URLs (jaba server locations) and service URIs (specifying version and service interface class)
+ *
+ * @param serviceURL
+ * @return null or best match for given uri/ls.
+ */
+ public Jws2Instance getPreferredServiceFor(String[] serviceURLs)
+ {
+ HashSet<String> urls=new HashSet<String>();
+ urls.addAll(Arrays.asList(serviceURLs));
+ Jws2Instance match=null;
+ for (Jws2Instance svc:services)
+ {
+ if (urls.contains(svc.getServiceTypeURI()))
+ {
+ if (match==null) {
+ // for moment we always pick service from server ordered first in user's preferences
+ match=svc;
+ }
+ if (urls.contains(svc.getUri()))
+ {
+ // stop and return - we've matched type URI and URI for service endpoint
+ return svc;
+ }
+ }
+ }
+ return match;
+ }
}
git://source.jalview.org / jalview.git / blobdiff