/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*/
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 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.RNAalifoldWS };
+ 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"
+ // jalview.bin.Console.errPrintln("Test Services Output\n"
// + registry.testAllServices());
// TODO: enumerate services and test those that haven't been tested
// in the last n-days/hours/etc.
srv_set = registry.getSupportedServices();
// dan test
- System.out.println("registry.getSupportedServices: "
- + srv_set.toString());
+ jalview.bin.Console.outPrintln(
+ "registry.getSupportedServices: " + srv_set.toString());
svccategories = registry.getServiceCategories();
// dan test
- // System.out.println("registry.getServiceCategories: " +
+ // jalview.bin.Console.outPrintln("registry.getServiceCategories: "
+ // +
// svccategories.toString());
}
} catch (Exception ex)
{
- System.err.println("Exception whilst trying to get at registry:");
+ jalview.bin.Console.errPrintln(
+ "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
+ jalview.bin.Console.errPrintln("JWS2 Discoverer: " + jwsserver
+ " is a JABAWS1 server. Using hardwired list.");
for (Services srv : JABAWS1SERVERS)
{
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"
+ jalview.bin.Console.errPrintln("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 = Jws2InstanceFactory.newJws2Instance(jwsservers,
+ svc = Jws2InstanceFactory.newJws2Instance(jwsserver,
srv.toString(), cat.name, description, service);
}
if (svc == null)
{
- svc = Jws2InstanceFactory.newJws2Instance(jwsservers,
+ 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);
+ 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)
+ {
+ jalview.bin.Console.errPrintln("Invalid server URL: " + server);
+ result = false;
+ } catch (IOException e)
+ {
+ jalview.bin.Console.errPrintln("Error connecting to server: "
+ + server + ": " + e.toString());
+ result = false;
+ }
+ }
+ return result;
+ }
+
}