/*
- * 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
+ * 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.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.beans.PropertyChangeListener;
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;
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
{
validServiceUrls.removeAllElements();
}
- ArrayList<String> svctypes=new ArrayList<String>();
+ 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)
+ if (svctypes.size() == 0)
{
- // TODO: remove this ugly hack to get Canonical JABA service ordering for all possible services
- for (Services sv:squery.JABAWS2SERVERS)
+ // TODO: remove this ugly hack to get Canonical JABA service ordering
+ // for all possible services
+ for (Services sv : squery.JABAWS2SERVERS)
{
- svctypes.add(sv.toString());
+ if (!ignoredServices.contains(sv.toString()))
+ {
+ svctypes.add(sv.toString());
+ }
}
}
boolean finished = true;
do
{
- finished=true;
+ finished = true;
try
{
Thread.sleep(100);
;
for (JabaWsServerQuery squery : qrys)
{
- finished = finished && !squery.isRunning();
+ if (squery.isRunning()){
+ finished=false;
+ }
}
if (aborted)
{
{
// 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)
+
+ if (services != null && services.size() > 0)
{
- Jws2Instance[] svcs=new Jws2Instance[services.size()];
- int[] spos=new int[services.size()];
- int ipos=0;
+ Jws2Instance[] svcs = new Jws2Instance[services.size()];
+ int[] spos = new int[services.size()];
+ int ipos = 0;
Vector svcUrls = getServiceUrls();
- for (Jws2Instance svc:services)
+ for (Jws2Instance svc : services)
{
- svcs[ipos]=svc;
- spos[ipos++]=1000*svcUrls.indexOf(svc.getHost()) + 1+svctypes.indexOf(svc.serviceType);
+ 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);
+ services = new Vector<Jws2Instance>();
+ for (Jws2Instance svc : svcs)
+ {
+ if (!ignoredServices.contains(svc.serviceType))
+ {
+ services.add(svc);
+ }
}
}
}
}
System.out.println("Discovered service: " + jwsservers + " "
+ service.toString());
-// Jws2Instance service = 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();
+ ParamDatastoreI pds = service.getParamStore();
+ if (pds != null)
+ {
+ pds.getPresets();
+ }
service.hasParameters();
- if (validServiceUrls==null)
+ if (validServiceUrls == null)
{
- validServiceUrls=new Vector();
+ validServiceUrls = new Vector();
}
validServiceUrls.add(jwsservers);
}
* holds list of services.
*/
protected Vector<Jws2Instance> services;
+
/**
- * attach all available web services to the appropriate submenu in the given JMenu
+ * attach all available web services to the appropriate submenu in the given
+ * JMenu
*/
public void attachWSMenuEntry(JMenu wsmenu, final AlignFrame alignFrame)
{
populateWSMenuEntry(wsmenu, alignFrame, null);
}
- private void populateWSMenuEntry(JMenu jws2al, final AlignFrame alignFrame, String typeFilter)
+ private boolean isRecalculable(String action)
+ {
+ return (action != null && action.equalsIgnoreCase("conservation"));
+ }
+
+ private void populateWSMenuEntry(JMenu jws2al,
+ final AlignFrame alignFrame, String typeFilter)
{
if (running || services == null || services.size() == 0)
{
* for moment we keep them separate.
*/
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 (!isRecalculable(service.action))
+ {
+ // add 'one shot' services to be displayed using the classic menu
+ // structure
+ enumerableServices.add(service);
+ }
+ else
+ {
+ if (!preferredHosts.containsKey(service.serviceType))
+ {
+ 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)
+ {
+ if (ph == null)
+ {
+ ph = new ArrayList<Jws2Instance>();
+ }
+ ph.add(service);
+ alternates.put(service.serviceType, ph);
+ }
+ }
+
+ }
+
+ // create GUI element for classic services
+ addEnumeratedServices(jws2al, alignFrame, enumerableServices);
+ // and the instantaneous services
+ for (final Jws2Instance service : preferredHosts.values())
+ {
+ atpoint = JvSwingUtils.findOrCreateMenu(jws2al, service.action);
+ JMenuItem hitm;
+ if (atpoint.getItemCount() > 1)
+ {
+ // previous service of this type already present
+ atpoint.addSeparator();
+ }
+ atpoint.add(hitm = new JMenuItem(service.getHost()));
+ 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"));
+
+ service.attachWSMenuEntry(atpoint, alignFrame);
+ if (alternates.containsKey(service.serviceType))
+ {
+ 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(); } });
+ */
+ }
+ }
+ }
+
+ /**
+ * add services using the Java 2.5/2.6/2.7 system which optionally creates
+ * submenus to index by host and service program type
+ */
+ private void addEnumeratedServices(final JMenu jws2al,
+ final AlignFrame alignFrame, List<Jws2Instance> enumerableServices)
+ {
+ 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 atpoint;
MsaWSClient msacl = new MsaWSClient();
- Vector hostLabels = new Vector();
- jws2al.removeAll();
- Hashtable<String,String> lasthostFor = new Hashtable<String,String>();
+ List<String> hostLabels = new ArrayList<String>();
+ 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)
+ ArrayList<String> hostlist = new ArrayList<String>();
+ for (Jws2Instance service : enumerableServices)
{
ArrayList<Jws2Instance> hostservices = hosts.get(service.getHost());
if (hostservices == null)
jalview.util.QuickSort.sort(sortbytype, orderedsvcs);
for (final Jws2Instance service : orderedsvcs)
{
- atpoint = JvSwingUtils.findOrCreateMenu(jws2al,service.action);
+ atpoint = JvSwingUtils.findOrCreateMenu(jws2al, service.action);
String type = service.serviceType;
if (byhost)
{
// contiguous
// group
JMenuItem hitm;
- atpoint.addSeparator();
- if (lasthostFor.get(service.action) == null || !lasthostFor.get(service.action).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"));
- lasthostFor.put(service.action,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() : ""));
}
-
+
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); }
- * });
- */
}
}
-
}
public static void main(String[] args)
{
- if (args.length>0)
+ if (args.length > 0)
{
testUrls = new Vector<String>();
- for (String url:args)
+ 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)
+ int i = 1;
+ for (Jws2Instance instance : getDiscoverer().services)
{
- System.out.println("Service "+i+++" "+instance.getClass()+"@"+instance.getHost()+": "+instance.getActionText());
+ System.out.println("Service " + i++ + " "
+ + instance.getClass() + "@"
+ + instance.getHost() + ": "
+ + instance.getActionText());
}
}
}
;
}
- try {
+ try
+ {
Thread.sleep(50);
- } catch (InterruptedException x) {}
+ } catch (InterruptedException x)
+ {
+ }
}
private static Jws2Discoverer discoverer;
}
}
- private static Vector<String> testUrls=null;
+ private static Vector<String> testUrls = null;
+
public static Vector<String> getServiceUrls()
{
- if (testUrls!=null)
+ if (testUrls != null)
{
// return test urls, if there are any, instead of touching cache
return testUrls;
return thr;
}
- Vector<String> invalidServiceUrls = null, urlsWithoutServices = null, validServiceUrls=null;
+ Vector<String> invalidServiceUrls = null, urlsWithoutServices = null,
+ validServiceUrls = null;
/**
* @return the invalidServiceUrls
public int getServerStatusFor(String url)
{
- if (validServiceUrls!=null && validServiceUrls.contains(url))
+ if (validServiceUrls != null && validServiceUrls.contains(url))
{
return 1;
}
- if (urlsWithoutServices!=null && urlsWithoutServices.contains(url))
- return 0;
- if (invalidServiceUrls!=null && invalidServiceUrls.contains(url))
+ 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