/*
* 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 .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
/**
*
*/
package jalview.ws.jws2;
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;
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 jwsserver = null;
boolean quit = false, running = false;
/**
* @return the running
*/
public boolean isRunning()
{
return running;
}
/**
* @param quit
* the quit to set
*/
public void setQuit(boolean quit)
{
this.quit = quit;
}
public JabaWsServerQuery(Jws2Discoverer jws2Discoverer, String server)
{
this.jws2Discoverer = jws2Discoverer;
this.jwsserver = server;
}
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
{
// 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;
boolean noservices = true;
// look for services
boolean jabasws2 = false;
// If we are dealing with a JABAWS2 service, then just go and ask the
// JABAWS 2 service registry
Set srv_set = new HashSet();
Set categories = Category.getCategories();
String svc_cat;
try
{
// JBPNote: why is RegistryWS in compbio.data.msa ?
registry = Jws2Client.connectToRegistry(jwsserver);
if (registry != null)
{
// 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.
jabasws2 = true;
srv_set = registry.getSupportedServices();
// dan test
jalview.bin.Console.outPrintln(
"registry.getSupportedServices: " + srv_set.toString());
svccategories = registry.getServiceCategories();
// dan test
// jalview.bin.Console.outPrintln("registry.getServiceCategories: " +
// svccategories.toString());
}
} catch (Exception ex)
{
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
jalview.bin.Console.errPrintln("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())
{
if (quit)
{
running = false;
return;
}
if (!srv_set.contains(srv))
{
continue;
}
JABAService service = null;
try
{
service = Jws2Client.connect(jwsserver, srv);
} catch (Exception e)
{
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(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(jwsserver);
}
}
else
{
jws2Discoverer.addInvalidServiceUrl(jwsserver);
Console.warn("Ignoring invalid Jws2 service url " + jwsserver);
}
} catch (Exception e)
{
e.printStackTrace();
Console.warn("Exception when discovering Jws2 services.", e);
jws2Discoverer.addInvalidServiceUrl(jwsserver);
} catch (Error e)
{
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;
}
}