src/jalview/ws/jws2/JabaWsServerQuery.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 /**
  22  *
  23  */
  24 package jalview.ws.jws2;
  25
  26 import jalview.bin.Console;
  27 import jalview.ws.jws2.jabaws2.Jws2Instance;
  28 import jalview.ws.jws2.jabaws2.Jws2InstanceFactory;
  29
  30 import java.io.IOException;
  31 import java.net.MalformedURLException;
  32 import java.net.URL;
  33 import java.util.HashSet;
  34 import java.util.Set;
  35
  36 import compbio.data.msa.Category;
  37 import compbio.data.msa.JABAService;
  38 import compbio.ws.client.Jws2Client;
  39 import compbio.ws.client.Services;
  40
  41 /**
  42  * @author JimP
  43  *
  44  */
  45 public class JabaWsServerQuery implements Runnable
  46 {
  47
  48   Jws2Discoverer jws2Discoverer = null;
  49
  50   String jwsserver = null;
  51
  52   boolean quit = false, running = false;
  53
  54   /**
  55    * @return the running
  56    */
  57   public boolean isRunning()
  58   {
  59     return running;
  60   }
  61
  62   /**
  63    * @param quit
  64    *          the quit to set
  65    */
  66   public void setQuit(boolean quit)
  67   {
  68     this.quit = quit;
  69   }
  70
  71   public JabaWsServerQuery(Jws2Discoverer jws2Discoverer, String server)
  72   {
  73     this.jws2Discoverer = jws2Discoverer;
  74     this.jwsserver = server;
  75   }
  76
  77   Services[] JABAWS1SERVERS = new Services[] { Services.ClustalWS,
  78       Services.MuscleWS, Services.MafftWS, Services.ProbconsWS,
  79       Services.TcoffeeWS };
  80
  81   Services[] JABAWS2SERVERS = new Services[] { Services.ClustalWS,
  82       Services.MuscleWS, Services.MafftWS, Services.ProbconsWS,
  83       Services.TcoffeeWS, Services.AAConWS, Services.DisemblWS,
  84       Services.GlobPlotWS, Services.IUPredWS, Services.JronnWS,
  85       Services.RNAalifoldWS };
  86
  87   /*
  88    * (non-Javadoc)
  89    *
  90    * @see java.lang.Runnable#run()
  91    */
  92   @Override
  93   public void run()
  94   {
  95     running = true;
  96     try
  97     {
  98       // TODO this test doesn't seem to attempt a connection - should it?
  99       // would save a lot of failed tries with UnknownHostException
 100       if (isValidUrl(jwsserver))
 101       {
 102         compbio.data.msa.RegistryWS registry = null;
 103         Set svccategories = null;
 104         boolean noservices = true;
 105         // look for services
 106         boolean jabasws2 = false;
 107         // If we are dealing with a JABAWS2 service, then just go and ask the
 108         // JABAWS 2 service registry
 109         Set<Services> srv_set = new HashSet<Services>();
 110
 111         Set<Category> categories = Category.getCategories();
 112         String svc_cat;
 113
 114         try
 115         {
 116           // JBPNote: why is RegistryWS in compbio.data.msa ?
 117           registry = Jws2Client.connectToRegistry(jwsserver);
 118           if (registry != null)
 119           {
 120             // jalview.bin.Console.errPrintln("Test Services Output\n"
 121             // + registry.testAllServices());
 122             // TODO: enumerate services and test those that haven't been tested
 123             // in the last n-days/hours/etc.
 124
 125             jabasws2 = true;
 126             srv_set = registry.getSupportedServices();
 127
 128             // dan test
 129             jalview.bin.Console.outPrintln(
 130                     "registry.getSupportedServices: " + srv_set.toString());
 131
 132             svccategories = registry.getServiceCategories();
 133
 134             // dan test
 135             // jalview.bin.Console.outPrintln("registry.getServiceCategories: "
 136             // +
 137             // svccategories.toString());
 138
 139           }
 140         } catch (Exception ex)
 141         {
 142           jalview.bin.Console.errPrintln(
 143                   "Exception whilst trying to get at registry:");
 144           ex.printStackTrace();
 145           // if that failed, then we are probably working with a JABAWS1 server.
 146           // in that case, look for each service endpoint
 147           jalview.bin.Console.errPrintln("JWS2 Discoverer: " + jwsserver
 148                   + " is a JABAWS1 server. Using hardwired list.");
 149           for (Services srv : JABAWS1SERVERS)
 150           {
 151             srv_set.add(srv);
 152           }
 153         }
 154
 155         for (Category cat : categories)
 156         {
 157           for (Services srv : cat.getServices())
 158           {
 159             if (quit)
 160             {
 161               running = false;
 162               return;
 163             }
 164             if (!srv_set.contains(srv))
 165             {
 166               continue;
 167             }
 168             JABAService service = null;
 169             try
 170             {
 171               service = Jws2Client.connect(jwsserver, srv);
 172             } catch (Exception e)
 173             {
 174               jalview.bin.Console.errPrintln("Jws2 Discoverer: Problem on "
 175                       + jwsserver + " with service " + srv + ":\n"
 176                       + e.getMessage());
 177               if (!(e instanceof javax.xml.ws.WebServiceException))
 178               {
 179                 e.printStackTrace();
 180               }
 181               // For moment, report service as a problem.
 182               jws2Discoverer.addInvalidServiceUrl(jwsserver);
 183             }
 184             ;
 185             if (service != null
 186                     && !Jws2InstanceFactory.ignoreService(srv.toString()))
 187             {
 188               noservices = false;
 189               Jws2Instance svc = null;
 190               if (registry != null)
 191               {
 192
 193                 String description = registry.getServiceDescription(srv);
 194
 195                 svc = Jws2InstanceFactory.newJws2Instance(jwsserver,
 196                         srv.toString(), cat.name, description, service);
 197               }
 198               if (svc == null)
 199               {
 200                 svc = Jws2InstanceFactory.newJws2Instance(jwsserver,
 201                         srv.toString(), cat.name,
 202                         "JABAWS 1 Alignment Service", service);
 203               }
 204               jws2Discoverer.addService(jwsserver, svc);
 205             }
 206
 207           }
 208         }
 209
 210         if (noservices)
 211         {
 212           jws2Discoverer.addUrlwithnoservices(jwsserver);
 213         }
 214       }
 215       else
 216       {
 217         jws2Discoverer.addInvalidServiceUrl(jwsserver);
 218         Console.warn("Ignoring invalid Jws2 service url " + jwsserver);
 219       }
 220     } catch (Exception e)
 221     {
 222       e.printStackTrace();
 223       Console.warn("Exception when discovering Jws2 services.", e);
 224       jws2Discoverer.addInvalidServiceUrl(jwsserver);
 225     } catch (Error e)
 226     {
 227       Console.error("Exception when discovering Jws2 services.", e);
 228       jws2Discoverer.addInvalidServiceUrl(jwsserver);
 229     }
 230     running = false;
 231   }
 232
 233   /**
 234    * Check if the URL is valid and responding.
 235    *
 236    * @return
 237    */
 238   private boolean isValidUrl(String server)
 239   {
 240     // return Jws2Client.validURL(jwsserver); // checks syntax only
 241     boolean result = false;
 242     if (server != null)
 243     {
 244       try
 245       {
 246         URL url = new URL(server);
 247         url.openStream().close();
 248         result = true;
 249       } catch (MalformedURLException e)
 250       {
 251         jalview.bin.Console.errPrintln("Invalid server URL: " + server);
 252         result = false;
 253       } catch (IOException e)
 254       {
 255         jalview.bin.Console.errPrintln("Error connecting to server: "
 256                 + server + ": " + e.toString());
 257         result = false;
 258       }
 259     }
 260     return result;
 261   }
 262
 263 }