/*******************************************************************************
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 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.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;
}
}
git://source.jalview.org / jalview.git / blobdiff