src/jalview/ws/jws2/JabaWsServerQuery.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
   3  * Copyright (C) 2014 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.Cache;
  27 import jalview.gui.Desktop;
  28 import jalview.ws.jws2.jabaws2.Jws2Instance;
  29 import jalview.ws.jws2.jabaws2.Jws2InstanceFactory;
  30
  31 import java.util.HashSet;
  32 import java.util.Set;
  33
  34 import javax.swing.JOptionPane;
  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 jwsservers = 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 jwsservers)
  72   {
  73     this.jws2Discoverer = jws2Discoverer;
  74     this.jwsservers = jwsservers;
  75   }
  76
  77   Services[] JABAWS1SERVERS = new Services[]
  78   { Services.ClustalWS, Services.MuscleWS, Services.MafftWS,
  79       Services.ProbconsWS, Services.TcoffeeWS };
  80
  81   Services[] JABAWS2SERVERS = new Services[]
  82   { Services.ClustalWS, Services.MuscleWS, Services.MafftWS,
  83       Services.ProbconsWS, Services.TcoffeeWS, Services.AAConWS,
  84       Services.DisemblWS, Services.GlobPlotWS, Services.IUPredWS,
  85       Services.JronnWS, 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       if (Jws2Client.validURL(jwsservers))
  99       {
 100         compbio.data.msa.RegistryWS registry = null;
 101         Set svccategories = null;
 102         boolean noservices = true;
 103         // look for services
 104         boolean jabasws2 = false;
 105         // If we are dealing with a JABAWS2 service, then just go and ask the
 106         // JABAWS 2 service registry
 107         Set<Services> srv_set = new HashSet<Services>();
 108
 109         Set<Category> categories = Category.getCategories();
 110         String svc_cat;
 111
 112         try
 113         {
 114           // JBPNote: why is RegistryWS in compbio.data.msa ?
 115           registry = Jws2Client.connectToRegistry(jwsservers);
 116           if (registry != null)
 117           {
 118             // System.err.println("Test Services Output\n"
 119             // + registry.testAllServices());
 120             // TODO: enumerate services and test those that haven't been tested
 121             // in the last n-days/hours/etc.
 122
 123             jabasws2 = true;
 124             srv_set = registry.getSupportedServices();
 125
 126             // dan test
 127             System.out.println("registry.getSupportedServices: "
 128                     + srv_set.toString());
 129
 130             svccategories = registry.getServiceCategories();
 131
 132             // dan test
 133             // System.out.println("registry.getServiceCategories: " +
 134             // svccategories.toString());
 135
 136           }
 137         } catch (javax.xml.ws.WebServiceException ex)
 138         {
 139           JOptionPane
 140                   .showInternalMessageDialog(
 141                           Desktop.desktop,
 142                           "Exception whilst trying to access the webservice registry:",
 143                           "Webservice glitch", JOptionPane.WARNING_MESSAGE);
 144           System.err.println("Exception whilst trying to get at registry:");
 145           ex.printStackTrace();
 146           // if that failed, then we are probably working with a JABAWS1 server.
 147           // in that case, look for each service endpoint
 148           System.err.println("JWS2 Discoverer: " + jwsservers
 149                   + " is a JABAWS1 server. Using hardwired list.");
 150           for (Services srv : JABAWS1SERVERS)
 151           {
 152             srv_set.add(srv);
 153           }
 154         }
 155  catch (Exception ex)
 156         {
 157           ex.printStackTrace();
 158         }
 159         for (Category cat : categories)
 160         {
 161           for (Services srv : cat.getServices())
 162           {
 163             if (quit)
 164             {
 165               running = false;
 166               return;
 167             }
 168             if (!srv_set.contains(srv))
 169             {
 170               continue;
 171             }
 172             JABAService service = null;
 173             try
 174             {
 175               service = Jws2Client.connect(jwsservers, srv);
 176             } catch (Exception e)
 177             {
 178               System.err.println("Jws2 Discoverer: Problem on "
 179                       + jwsservers + " with service " + srv + ":\n"
 180                       + e.getMessage());
 181               if (!(e instanceof javax.xml.ws.WebServiceException))
 182               {
 183                 e.printStackTrace();
 184               }
 185               // For moment, report service as a problem.
 186               jws2Discoverer.addInvalidServiceUrl(jwsservers);
 187             }
 188             ;
 189             if (service != null)
 190             {
 191               noservices = false;
 192               Jws2Instance svc = null;
 193               if (registry != null)
 194               {
 195
 196                 String description = registry.getServiceDescription(srv);
 197
 198                 svc = Jws2InstanceFactory.newJws2Instance(jwsservers,
 199                         srv.toString(), cat.name, description, service);
 200               }
 201               if (svc == null)
 202               {
 203                 svc = Jws2InstanceFactory.newJws2Instance(jwsservers,
 204                         srv.toString(), cat.name,
 205                         "JABAWS 1 Alignment Service", service);
 206               }
 207               jws2Discoverer.addService(jwsservers, svc);
 208             }
 209
 210           }
 211         }
 212
 213         if (noservices)
 214         {
 215           jws2Discoverer.addUrlwithnoservices(jwsservers);
 216         }
 217       }
 218       else
 219       {
 220         jws2Discoverer.addInvalidServiceUrl(jwsservers);
 221         Cache.log.info("Ignoring invalid Jws2 service url " + jwsservers);
 222       }
 223     } catch (Exception e)
 224     {
 225       e.printStackTrace();
 226       Cache.log.warn("Exception when discovering Jws2 services.", e);
 227       jws2Discoverer.addInvalidServiceUrl(jwsservers);
 228     } catch (Error e)
 229     {
 230       Cache.log.error("Exception when discovering Jws2 services.", e);
 231       jws2Discoverer.addInvalidServiceUrl(jwsservers);
 232     }
 233     running = false;
 234   }
 235
 236 }