}
}
- // TODO: move into separate menu builder class.
- if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
- {
- Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
- if (jws2servs != null)
- {
- if (jws2servs.hasServices())
- {
- jws2servs.attachWSMenuEntry(msawsmenu, me);
- }
- }
- }
+
// Add all submenus in the order they should appear on the web services menu
wsmenu.add(msawsmenu);
wsmenu.add(secstrmenu);
+ wsmenu.add(new JMenu("Disorder"));
wsmenu.add(analymenu);
+
// No search services yet
// wsmenu.add(seqsrchmenu);
{
webService.add(me.webServiceNoServices);
}
+ // TODO: move into separate menu builder class.
+ if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
+ {
+ Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
+ if (jws2servs != null)
+ {
+ if (jws2servs.hasServices())
+ {
+ jws2servs.attachWSMenuEntry(webService, me);
+ }
+ }
+ }
+
build_urlServiceMenu(me.webService);
build_fetchdbmenu(webService);
} catch (Exception e)
package jalview.ws.jws2;
import jalview.bin.Cache;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
-import compbio.data.msa.MsaWS;
+import java.util.HashSet;
+import java.util.Set;
+
+import compbio.data.msa.Category;
+import compbio.data.msa.JABAService;
import compbio.ws.client.Jws2Client;
import compbio.ws.client.Services;
/**
* @author JimP
- *
+ *
*/
public class JabaWsServerQuery implements Runnable
{
- Jws2Discoverer jws2Discoverer=null;
- String jwsservers=null;
- boolean quit=false,
- running=false;
+ Jws2Discoverer jws2Discoverer = null;
+
+ String jwsservers = null;
+
+ boolean quit = false, running = false;
+
/**
* @return the running
*/
- public boolean isRunning()
+ public boolean isRunning()
{
return running;
}
/**
- * @param quit the quit to set
+ * @param quit
+ * the quit to set
*/
public void setQuit(boolean quit)
{
public JabaWsServerQuery(Jws2Discoverer jws2Discoverer, String jwsservers)
{
this.jws2Discoverer = jws2Discoverer;
- this.jwsservers=jwsservers;
+ this.jwsservers = jwsservers;
}
- /* (non-Javadoc)
+ /*
+ * (non-Javadoc)
+ *
* @see java.lang.Runnable#run()
*/
@Override
public void run()
{
- running=true;
- try
+ running = true;
+ try
{
if (Jws2Client.validURL(jwsservers))
{
- boolean noservices=true;
+ compbio.data.msa.RegistryWS registry = null;
+ Set svccategories = null;
+ boolean noservices = true;
// look for services
- for (Services srv : Services.values())
+ boolean jabasws2 = false;
+ // If we are dealing with a JABAWS2 service, then just go and ask the
+ // JABAWS 2 service registry
+ Set<Services> srv_set = new HashSet<Services>();
+
+ Set<Category> categories = Category.getCategories();
+ String svc_cat;
+
+ try
{
- if (quit)
+ // JBPNote: why is RegistryWS in compbio.data.msa ?
+ registry = Jws2Client.connectToRegistry(jwsservers);
+ if (registry != null)
{
- running=false;
- return;
+ // System.err.println("Test Services Output\n"
+ // + registry.testAllServices());
+ // TODO: enumerate services and test those that haven't been tested
+ // in the last n-days/hours/etc.
+
+ jabasws2 = true;
+ srv_set = registry.getSupportedServices();
+ svccategories = registry.getServiceCategories();
+
}
- MsaWS service = null;
- try
+ } catch (Exception ex)
+ {
+ System.err.println("Exception whilst trying to get at registry:");
+ ex.printStackTrace();
+ // if that failed, then we are probably working with a JABAWS1 server.
+ // in that case, look for each service endpoint
+ System.err.println("JWS2 Discoverer: " + jwsservers
+ + " is a JABAWS1 server. Using hardwired list.");
+ for (Services srv : new Services[]
+ { Services.ClustalWS, Services.MuscleWS, Services.MafftWS,
+ Services.ProbconsWS, Services.TcoffeeWS })
{
- service = Jws2Client.connect(jwsservers, srv);
- } catch (Exception e)
+ srv_set.add(srv);
+ }
+ }
+ for (Category cat : categories)
+ {
+ for (Services srv : cat.getServices())
{
- System.err.println("Jws2 Discoverer: Problem on "
- + jwsservers + " with service " + srv + ":\n"
- + e.getMessage());
- if (!(e instanceof javax.xml.ws.WebServiceException))
+ if (quit)
{
- e.printStackTrace();
+ running = false;
+ return;
}
- // For moment, report service as a problem.
- jws2Discoverer.addInvalidServiceUrl(jwsservers);
- }
- ;
- if (service != null)
- {
- noservices=false;
- jws2Discoverer.addService(jwsservers, srv, service);
+ if (!srv_set.contains(srv))
+ {
+ continue;
+ }
+ JABAService service = null;
+ try
+ {
+ service = Jws2Client.connect(jwsservers, srv);
+ } catch (Exception e)
+ {
+ System.err.println("Jws2 Discoverer: Problem on "
+ + jwsservers + " with service " + srv + ":\n"
+ + e.getMessage());
+ if (!(e instanceof javax.xml.ws.WebServiceException))
+ {
+ e.printStackTrace();
+ }
+ // For moment, report service as a problem.
+ jws2Discoverer.addInvalidServiceUrl(jwsservers);
+ }
+ ;
+ if (service != null)
+ {
+ noservices = false;
+ Jws2Instance svc = null;
+ if (registry != null)
+ {
+
+ String description = registry.getServiceDescription(srv);
+
+ svc = new Jws2Instance(jwsservers, srv.toString(),
+ cat.name, description, service);
+ }
+ if (svc == null)
+ {
+ svc = new Jws2Instance(jwsservers, srv.toString(), cat.name,
+ "JABAWS 1 Alignment Service", service);
+ }
+ jws2Discoverer.addService(jwsservers, svc);
+ }
+
}
}
+
if (noservices)
{
jws2Discoverer.addUrlwithnoservices(jwsservers);
Cache.log.error("Exception when discovering Jws2 services.", e);
jws2Discoverer.addInvalidServiceUrl(jwsservers);
}
- running=false;
+ running = false;
}
}
* @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
* holds list of services.
*/
protected Vector<Jws2Instance> services;
-
+ /**
+ * 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.
- 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);
-
+ 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)
{
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)
{
// hostLabels.addElement(host + (bytype ?
// service.serviceType+service.getActionText() : ""));
}
- msacl.attachWSMenuEntry(atpoint, service, alignFrame);
+
+ service.attachWSMenuEntry(atpoint, alignFrame);
/*
* JMenuItem sitem = new JMenuItem(service.serviceType);
* sitem.setToolTipText("Hosted at " + service.hosturl);
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()
{
}
}
+ 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 null;
}
-
}
git://source.jalview.org / jalview.git / commitdiff