+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.bin.Console;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.jws2.jabaws2.Jws2InstanceFactory;
-import compbio.data.msa.MsaWS;
+import java.io.IOException;
+import java.net.MalformedURLException;
+import java.net.URL;
+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 jwsserver = 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)
{
this.quit = quit;
}
- public JabaWsServerQuery(Jws2Discoverer jws2Discoverer, String jwsservers)
+ public JabaWsServerQuery(Jws2Discoverer jws2Discoverer, String server)
{
this.jws2Discoverer = jws2Discoverer;
- this.jwsservers=jwsservers;
+ this.jwsserver = server;
}
- /* (non-Javadoc)
+ Services[] JABAWS1SERVERS = new Services[] { Services.ClustalWS,
+ Services.MuscleWS, Services.MafftWS, Services.ProbconsWS,
+ Services.TcoffeeWS };
+
+ Services[] JABAWS2SERVERS = new Services[] { Services.ClustalWS,
+ Services.MuscleWS, Services.MafftWS, Services.ProbconsWS,
+ Services.TcoffeeWS, Services.AAConWS, Services.DisemblWS,
+ Services.GlobPlotWS, Services.IUPredWS, Services.JronnWS,
+ Services.RNAalifoldWS };
+
+ /*
+ * (non-Javadoc)
+ *
* @see java.lang.Runnable#run()
*/
@Override
public void run()
{
- running=true;
- try
+ running = true;
+ try
{
- if (Jws2Client.validURL(jwsservers))
+ // TODO this test doesn't seem to attempt a connection - should it?
+ // would save a lot of failed tries with UnknownHostException
+ if (isValidUrl(jwsserver))
{
- 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(jwsserver);
+ 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();
+
+ // dan test
+ System.out.println(
+ "registry.getSupportedServices: " + srv_set.toString());
+
+ svccategories = registry.getServiceCategories();
+
+ // dan test
+ // System.out.println("registry.getServiceCategories: " +
+ // svccategories.toString());
+
}
- 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: " + jwsserver
+ + " is a JABAWS1 server. Using hardwired list.");
+ for (Services srv : JABAWS1SERVERS)
{
- 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(jwsserver, srv);
+ } catch (Exception e)
+ {
+ System.err.println("Jws2 Discoverer: Problem on " + jwsserver
+ + " with service " + srv + ":\n" + e.getMessage());
+ if (!(e instanceof javax.xml.ws.WebServiceException))
+ {
+ e.printStackTrace();
+ }
+ // For moment, report service as a problem.
+ jws2Discoverer.addInvalidServiceUrl(jwsserver);
+ }
+ ;
+ if (service != null
+ && !Jws2InstanceFactory.ignoreService(srv.toString()))
+ {
+ noservices = false;
+ Jws2Instance svc = null;
+ if (registry != null)
+ {
+
+ String description = registry.getServiceDescription(srv);
+
+ svc = Jws2InstanceFactory.newJws2Instance(jwsserver,
+ srv.toString(), cat.name, description, service);
+ }
+ if (svc == null)
+ {
+ svc = Jws2InstanceFactory.newJws2Instance(jwsserver,
+ srv.toString(), cat.name,
+ "JABAWS 1 Alignment Service", service);
+ }
+ jws2Discoverer.addService(jwsserver, svc);
+ }
+
}
}
+
if (noservices)
{
- jws2Discoverer.addUrlwithnoservices(jwsservers);
+ jws2Discoverer.addUrlwithnoservices(jwsserver);
}
}
else
{
- jws2Discoverer.addInvalidServiceUrl(jwsservers);
- Cache.log.info("Ignoring invalid Jws2 service url " + jwsservers);
+ jws2Discoverer.addInvalidServiceUrl(jwsserver);
+ Console.warn("Ignoring invalid Jws2 service url " + jwsserver);
}
} catch (Exception e)
{
e.printStackTrace();
- Cache.log.warn("Exception when discovering Jws2 services.", e);
- jws2Discoverer.addInvalidServiceUrl(jwsservers);
+ Console.warn("Exception when discovering Jws2 services.", e);
+ jws2Discoverer.addInvalidServiceUrl(jwsserver);
} catch (Error e)
{
- Cache.log.error("Exception when discovering Jws2 services.", e);
- jws2Discoverer.addInvalidServiceUrl(jwsservers);
+ Console.error("Exception when discovering Jws2 services.", e);
+ jws2Discoverer.addInvalidServiceUrl(jwsserver);
+ }
+ running = false;
+ }
+
+ /**
+ * Check if the URL is valid and responding.
+ *
+ * @return
+ */
+ private boolean isValidUrl(String server)
+ {
+ // return Jws2Client.validURL(jwsserver); // checks syntax only
+ boolean result = false;
+ if (server != null)
+ {
+ try
+ {
+ URL url = new URL(server);
+ url.openStream().close();
+ result = true;
+ } catch (MalformedURLException e)
+ {
+ System.err.println("Invalid server URL: " + server);
+ result = false;
+ } catch (IOException e)
+ {
+ System.err.println("Error connecting to server: " + server + ": "
+ + e.toString());
+ result = false;
+ }
}
- running=false;
+ return result;
}
}
git://source.jalview.org / jalview.git / blobdiff