/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * 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.
+ * 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/>.
+ * 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.
*/
/**
*
import jalview.bin.Cache;
import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.jws2.jabaws2.Jws2InstanceFactory;
+import java.io.IOException;
+import java.net.MalformedURLException;
+import java.net.URL;
import java.util.HashSet;
import java.util.Set;
Jws2Discoverer jws2Discoverer = null;
- String jwsservers = null;
+ String jwsserver = null;
boolean quit = false, running = false;
this.quit = quit;
}
- public JabaWsServerQuery(Jws2Discoverer jws2Discoverer, String jwsservers)
+ public JabaWsServerQuery(Jws2Discoverer jws2Discoverer, String server)
{
this.jws2Discoverer = jws2Discoverer;
- this.jwsservers = jwsservers;
+ this.jwsserver = server;
}
- Services[] JABAWS1SERVERS = new Services[]
- { Services.ClustalWS, Services.MuscleWS, Services.MafftWS,
- Services.ProbconsWS, Services.TcoffeeWS };
+ 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[] 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)
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))
{
compbio.data.msa.RegistryWS registry = null;
Set svccategories = null;
try
{
// JBPNote: why is RegistryWS in compbio.data.msa ?
- registry = Jws2Client.connectToRegistry(jwsservers);
+ registry = Jws2Client.connectToRegistry(jwsserver);
if (registry != null)
{
// System.err.println("Test Services Output\n"
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());
+
}
} catch (Exception ex)
{
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
+ System.err.println("JWS2 Discoverer: " + jwsserver
+ " is a JABAWS1 server. Using hardwired list.");
for (Services srv : JABAWS1SERVERS)
{
srv_set.add(srv);
}
}
+
for (Category cat : categories)
{
for (Services srv : cat.getServices())
JABAService service = null;
try
{
- service = Jws2Client.connect(jwsservers, srv);
+ service = Jws2Client.connect(jwsserver, srv);
} catch (Exception e)
{
- System.err.println("Jws2 Discoverer: Problem on "
- + jwsservers + " with service " + srv + ":\n"
- + e.getMessage());
+ 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(jwsservers);
+ jws2Discoverer.addInvalidServiceUrl(jwsserver);
}
;
- if (service != null)
+ if (service != null
+ && !Jws2InstanceFactory.ignoreService(srv.toString()))
{
noservices = false;
Jws2Instance svc = null;
String description = registry.getServiceDescription(srv);
- svc = new Jws2Instance(jwsservers, srv.toString(),
- cat.name, description, service);
+ svc = Jws2InstanceFactory.newJws2Instance(jwsserver,
+ srv.toString(), cat.name, description, service);
}
if (svc == null)
{
- svc = new Jws2Instance(jwsservers, srv.toString(),
- cat.name, "JABAWS 1 Alignment Service", service);
+ svc = Jws2InstanceFactory.newJws2Instance(jwsserver,
+ srv.toString(), cat.name,
+ "JABAWS 1 Alignment Service", service);
}
- jws2Discoverer.addService(jwsservers, svc);
+ 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);
+ Cache.warn("Ignoring invalid Jws2 service url " + jwsserver);
}
} catch (Exception e)
{
e.printStackTrace();
- Cache.log.warn("Exception when discovering Jws2 services.", e);
- jws2Discoverer.addInvalidServiceUrl(jwsservers);
+ Cache.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);
+ Cache.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;
+ }
+ }
+ return result;
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff