/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
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 jalview.ws.params.ParamDatastoreI;
+
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.HashMap;
import java.util.HashSet;
import java.util.Hashtable;
import java.util.List;
+import java.util.Map;
+import java.util.Set;
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.Jws2Client;
import compbio.ws.client.Services;
/**
public void run()
{
+
if (running && oldthread != null && oldthread.isAlive())
{
if (!aborted)
Cache.log.debug("Old discovery thread has finished.");
}
running = true;
+
+ // first set up exclusion list if needed
+ final Set<String> ignoredServices = new HashSet<String>();
+ for (String ignored:jalview.bin.Cache.getDefault("IGNORED_JABAWS_SERVICETYPES", Services.JpredWS.toString()).split("\\|"))
+ {
+ ignoredServices.add(ignored);
+ }
+
+
+ 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)
+ {
+ if (!ignoredServices.contains(sv.toString()))
+ {
+ 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();
+ if (squery.isRunning()){
+ finished=false;
+ }
}
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)
+ {
+ if (!ignoredServices.contains(svc.serviceType))
+ {
+ 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();
+ ParamDatastoreI pds = service.getParamStore();
+ if (pds != null)
+ {
+ pds.getPresets();
+ }
service.hasParameters();
+ if (validServiceUrls == null)
+ {
+ validServiceUrls = new Vector();
+ }
+ validServiceUrls.add(jwsservers);
}
- public class Jws2Instance
- {
- public String hosturl;
+ /**
+ * holds list of services.
+ */
+ protected Vector<Jws2Instance> services;
- public String serviceType;
+ /**
+ * attach all available web services to the appropriate submenu in the given
+ * JMenu
+ */
+ public void attachWSMenuEntry(JMenu wsmenu, final AlignFrame alignFrame)
+ {
+ // dynamically regenerate service list.
+ populateWSMenuEntry(wsmenu, alignFrame, null);
+ }
- public MsaWS service;
+ private boolean isRecalculable(String action)
+ {
+ return (action != null && action.equalsIgnoreCase("conservation"));
+ }
- public Jws2Instance(String hosturl, String serviceType, MsaWS service)
+ private void populateWSMenuEntry(JMenu jws2al,
+ final AlignFrame alignFrame, String typeFilter)
+ {
+ if (running || services == null || services.size() == 0)
{
- super();
- this.hosturl = hosturl;
- this.serviceType = serviceType;
- this.service = service;
+ return;
}
-
- PresetManager presets = null;
-
- public JabaParamStore paramStore = null;
-
+ boolean byhost = Cache.getDefault("WSMENU_BYHOST", false), bytype = Cache
+ .getDefault("WSMENU_BYTYPE", false);
/**
- * 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.
+ * eventually, JWS2 services will appear under the same align/etc submenus.
+ * for moment we keep them separate.
*/
- public PresetManager getPresets()
+ JMenu atpoint;
+ List<Jws2Instance> enumerableServices = new ArrayList<Jws2Instance>();
+ // jws2al.removeAll();
+ Map<String, Jws2Instance> preferredHosts = new HashMap<String, Jws2Instance>();
+ Map<String, List<Jws2Instance>> alternates = new HashMap<String, List<Jws2Instance>>();
+ for (Jws2Instance service : services.toArray(new Jws2Instance[0]))
{
- if (presets == null)
+ if (!isRecalculable(service.action))
{
- try
+ // add 'one shot' services to be displayed using the classic menu
+ // structure
+ enumerableServices.add(service);
+ }
+ else
+ {
+ if (!preferredHosts.containsKey(service.serviceType))
{
- presets = service.getPresets();
- } catch (Exception ex)
+ Jws2Instance preferredInstance = getPreferredServiceFor(
+ alignFrame, service.serviceType);
+ if (preferredInstance != null)
+ {
+ preferredHosts.put(service.serviceType, preferredInstance);
+ }
+ else
+ {
+ preferredHosts.put(service.serviceType, service);
+ }
+ }
+ List<Jws2Instance> ph = alternates.get(service.serviceType);
+ if (preferredHosts.get(service.serviceType) != service)
{
- System.err
- .println("Exception when retrieving presets for service "
- + serviceType + " at " + hosturl);
+ if (ph == null)
+ {
+ ph = new ArrayList<Jws2Instance>();
+ }
+ ph.add(service);
+ alternates.put(service.serviceType, ph);
}
}
- 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
+ // create GUI element for classic services
+ addEnumeratedServices(jws2al, alignFrame, enumerableServices);
+ // and the instantaneous services
+ for (final Jws2Instance service : preferredHosts.values())
{
- if (service != null)
+ atpoint = JvSwingUtils.findOrCreateMenu(jws2al, service.action);
+ JMenuItem hitm;
+ if (atpoint.getItemCount() > 1)
{
- try
- {
- Closeable svc = (Closeable) service;
- service = null;
- svc.close();
- } catch (Exception e)
- {
- }
- ;
+ // previous service of this type already present
+ atpoint.addSeparator();
}
- super.finalize();
- }
-
- public ParamDatastoreI getParamStore()
- {
- if (paramStore == null)
+ atpoint.add(hitm = new JMenuItem(service.getHost()));
+ hitm.setForeground(Color.blue);
+ hitm.addActionListener(new ActionListener()
{
- try
- {
- paramStore = new JabaParamStore(this,
- (Desktop.instance != null ? Desktop
- .getUserParameterStore() : null));
- } catch (Exception ex)
+
+ @Override
+ public void actionPerformed(ActionEvent e)
{
+ Desktop.showUrl(service.getHost());
}
+ });
+ hitm.setToolTipText(JvSwingUtils
+ .wrapTooltip("Opens the JABAWS server's homepage in web browser"));
- }
- 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)
+ service.attachWSMenuEntry(atpoint, alignFrame);
+ if (alternates.containsKey(service.serviceType))
{
- lookedForParams = true;
- try
- {
- hasParams = (getRunnerConfig().getArguments().size() > 0);
- } catch (Exception e)
+ atpoint.add(hitm = new JMenu("Switch server"));
+ hitm.setToolTipText(JvSwingUtils
+ .wrapTooltip("Choose a server for running this service"));
+ for (final Jws2Instance sv : alternates.get(service.serviceType))
{
+ JMenuItem itm;
+ hitm.add(itm = new JMenuItem(sv.getHost()));
+ itm.setForeground(Color.blue);
+ itm.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent arg0)
+ {
+ new Thread(new Runnable()
+ {
+ public void run()
+ {
+ setPreferredServiceFor(alignFrame, sv.serviceType,
+ sv.action, sv);
+ changeSupport.firePropertyChange("services",
+ new Vector(), services);
+ };
+ }).start();
+
+ }
+ });
}
+ /*
+ * hitm.addActionListener(new ActionListener() {
+ *
+ * @Override public void actionPerformed(ActionEvent arg0) { new
+ * Thread(new Runnable() {
+ *
+ * @Override public void run() { new SetPreferredServer(alignFrame,
+ * service.serviceType, service.action); } }).start(); } });
+ */
}
- return hasParams;
}
- };
+ }
/**
- * holds list of services.
+ * add services using the Java 2.5/2.6/2.7 system which optionally creates
+ * submenus to index by host and service program type
*/
- protected Vector<Jws2Instance> services;
-
- public void attachWSMenuEntry(JMenu wsmenu, final AlignFrame alignFrame)
+ private void addEnumeratedServices(final JMenu jws2al,
+ final AlignFrame alignFrame, List<Jws2Instance> enumerableServices)
{
- // 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);
/**
*/
JMenu atpoint;
MsaWSClient msacl = new MsaWSClient();
- Vector hostLabels = new Vector();
- jws2al.removeAll();
- String lasthost = null;
+ List<String> hostLabels = new ArrayList<String>();
+ Hashtable<String, String> lasthostFor = new Hashtable<String, String>();
Hashtable<String, ArrayList<Jws2Instance>> hosts = new Hashtable<String, ArrayList<Jws2Instance>>();
- String[] sorton;
- for (Jws2Instance service : services)
+ ArrayList<String> hostlist = new ArrayList<String>();
+ for (Jws2Instance service : enumerableServices)
{
ArrayList<Jws2Instance> hostservices = hosts.get(service.getHost());
if (hostservices == null)
{
hosts.put(service.getHost(),
hostservices = new ArrayList<Jws2Instance>());
+ hostlist.add(service.getHost());
}
hostservices.add(service);
}
- sorton = hosts.keySet().toArray(new String[1]);
- String hostlist[] = sorton.clone();
- jalview.util.QuickSort.sort(sorton, hostlist);
+ // now add hosts in order of the given array
for (String host : hostlist)
{
Jws2Instance orderedsvcs[] = hosts.get(host).toArray(
jalview.util.QuickSort.sort(sortbytype, orderedsvcs);
for (final Jws2Instance service : orderedsvcs)
{
- atpoint = jws2al;
+ atpoint = JvSwingUtils.findOrCreateMenu(jws2al, service.action);
String type = service.serviceType;
if (byhost)
{
// contiguous
// group
JMenuItem hitm;
- atpoint.addSeparator();
- if (lasthost == null || !lasthost.equals(host))
+ if (hostLabels.contains(host))
+ {
+ atpoint.addSeparator();
+ }
+ else
+ {
+ hostLabels.add(host);
+ }
+ if (lasthostFor.get(service.action) == null
+ || !lasthostFor.get(service.action).equals(host))
{
atpoint.add(hitm = new JMenuItem(host));
hitm.setForeground(Color.blue);
});
hitm.setToolTipText(JvSwingUtils
.wrapTooltip("Opens the JABAWS server's homepage in web browser"));
- lasthost = host;
+ lasthostFor.put(service.action, host);
}
- hostLabels.addElement(host + service.serviceType
+ hostLabels.add(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); }
- * });
- */
+
+ service.attachWSMenuEntry(atpoint, 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
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;
+ if (services != 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;
+ }
+
+ Map<String, Map<String, String>> preferredServiceMap = new HashMap<String, Map<String, String>>();;
+
+ /**
+ * get current preferred service of the given type, or global default
+ *
+ * @param af
+ * null or a specific alignFrame
+ * @param serviceType
+ * Jws2Instance.serviceType for service
+ * @return null if no service of this type is available, the preferred service
+ * for the serviceType and af if specified and if defined.
+ */
+ public Jws2Instance getPreferredServiceFor(AlignFrame af,
+ String serviceType)
+ {
+ String serviceurl = null;
+ synchronized (preferredServiceMap)
+ {
+ String afid = (af == null) ? "" : af.getViewport().getSequenceSetId();
+ Map<String, String> prefmap = preferredServiceMap.get(afid);
+ if (afid.length() > 0 && prefmap == null)
+ {
+ // recover global setting, if any
+ prefmap = preferredServiceMap.get("");
+ }
+ if (prefmap != null)
+ {
+ serviceurl = prefmap.get(serviceType);
+ }
+
+ }
+ Jws2Instance response = null;
+ for (Jws2Instance svc : services)
+ {
+ if (svc.serviceType.equals(serviceType))
+ {
+ if (serviceurl == null || serviceurl.equals(svc.getHost()))
+ {
+ response = svc;
+ break;
+ }
+ }
+ }
+ return response;
+ }
+
+ public void setPreferredServiceFor(AlignFrame af, String serviceType,
+ String serviceAction, Jws2Instance selectedServer)
+ {
+ String afid = (af == null) ? "" : af.getViewport().getSequenceSetId();
+ if (preferredServiceMap == null)
+ {
+ preferredServiceMap = new HashMap<String, Map<String, String>>();
+ }
+ Map<String, String> prefmap = preferredServiceMap.get(afid);
+ if (prefmap == null)
+ {
+ prefmap = new HashMap<String, String>();
+ preferredServiceMap.put(afid, prefmap);
+ }
+ prefmap.put(serviceType, selectedServer.getHost());
+ prefmap.put(serviceAction, selectedServer.getHost());
+ }
+
+ public void setPreferredServiceFor(String serviceType,
+ String serviceAction, Jws2Instance selectedServer)
+ {
+ setPreferredServiceFor(null, serviceType, serviceAction, selectedServer);
+ }
}
git://source.jalview.org / jalview.git / blobdiff