src/jalview/ws/jws2/JabaWsServerQuery.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
   3  * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
   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 of the License, or (at your option) any later version.
  10  *
  11  * Jalview is distributed in the hope that it will be useful, but
  12  * WITHOUT ANY WARRANTY; without even the implied warranty
  13  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  14  * PURPOSE.  See the GNU General Public License for more details.
  15  *
  16  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  17  */
  18 /**
  19  *
  20  */
  21 package jalview.ws.jws2;
  22
  23 import jalview.bin.Cache;
  24 import jalview.ws.jws2.jabaws2.Jws2Instance;
  25 import jalview.ws.jws2.jabaws2.Jws2InstanceFactory;
  26
  27 import java.util.HashSet;
  28 import java.util.Set;
  29
  30 import compbio.data.msa.Category;
  31 import compbio.data.msa.JABAService;
  32 import compbio.ws.client.Jws2Client;
  33 import compbio.ws.client.Services;
  34
  35 /**
  36  * @author JimP
  37  *
  38  */
  39 public class JabaWsServerQuery implements Runnable
  40 {
  41
  42   Jws2Discoverer jws2Discoverer = null;
  43
  44   String jwsservers = null;
  45
  46   boolean quit = false, running = false;
  47
  48   /**
  49    * @return the running
  50    */
  51   public boolean isRunning()
  52   {
  53     return running;
  54   }
  55
  56   /**
  57    * @param quit
  58    *          the quit to set
  59    */
  60   public void setQuit(boolean quit)
  61   {
  62     this.quit = quit;
  63   }
  64
  65   public JabaWsServerQuery(Jws2Discoverer jws2Discoverer, String jwsservers)
  66   {
  67     this.jws2Discoverer = jws2Discoverer;
  68     this.jwsservers = jwsservers;
  69   }
  70
  71   Services[] JABAWS1SERVERS = new Services[]
  72   { Services.ClustalWS, Services.MuscleWS, Services.MafftWS,
  73       Services.ProbconsWS, Services.TcoffeeWS };
  74
  75   Services[] JABAWS2SERVERS = new Services[]
  76   { Services.ClustalWS, Services.MuscleWS, Services.MafftWS,
  77       Services.ProbconsWS, Services.TcoffeeWS, Services.AAConWS,
  78       Services.DisemblWS, Services.GlobPlotWS, Services.IUPredWS,
  79       Services.JronnWS, Services.RNAalifoldWS };
  80
  81   /*
  82    * (non-Javadoc)
  83    *
  84    * @see java.lang.Runnable#run()
  85    */
  86   @Override
  87   public void run()
  88   {
  89     running = true;
  90     try
  91     {
  92       if (Jws2Client.validURL(jwsservers))
  93       {
  94         compbio.data.msa.RegistryWS registry = null;
  95         Set svccategories = null;
  96         boolean noservices = true;
  97         // look for services
  98         boolean jabasws2 = false;
  99         // If we are dealing with a JABAWS2 service, then just go and ask the
 100         // JABAWS 2 service registry
 101         Set<Services> srv_set = new HashSet<Services>();
 102
 103         Set<Category> categories = Category.getCategories();
 104         String svc_cat;
 105
 106         try
 107         {
 108           // JBPNote: why is RegistryWS in compbio.data.msa ?
 109           registry = Jws2Client.connectToRegistry(jwsservers);
 110           if (registry != null)
 111           {
 112             // System.err.println("Test Services Output\n"
 113             // + registry.testAllServices());
 114             // TODO: enumerate services and test those that haven't been tested
 115             // in the last n-days/hours/etc.
 116
 117             jabasws2 = true;
 118             srv_set = registry.getSupportedServices();
 119
 120             // dan test
 121             System.out.println("registry.getSupportedServices: " + srv_set.toString());
 122
 123             svccategories = registry.getServiceCategories();
 124
 125             // dan test
 126 //            System.out.println("registry.getServiceCategories: " + svccategories.toString());
 127
 128           }
 129         } catch (Exception ex)
 130         {
 131           System.err.println("Exception whilst trying to get at registry:");
 132           ex.printStackTrace();
 133           // if that failed, then we are probably working with a JABAWS1 server.
 134           // in that case, look for each service endpoint
 135           System.err.println("JWS2 Discoverer: " + jwsservers
 136                   + " is a JABAWS1 server. Using hardwired list.");
 137           for (Services srv : JABAWS1SERVERS)
 138           {
 139             srv_set.add(srv);
 140           }
 141         }
 142         for (Category cat : categories)
 143         {
 144           for (Services srv : cat.getServices())
 145           {
 146             if (quit)
 147             {
 148               running = false;
 149               return;
 150             }
 151             if (!srv_set.contains(srv))
 152             {
 153               continue;
 154             }
 155             JABAService service = null;
 156             try
 157             {
 158               service = Jws2Client.connect(jwsservers, srv);
 159             } catch (Exception e)
 160             {
 161               System.err.println("Jws2 Discoverer: Problem on "
 162                       + jwsservers + " with service " + srv + ":\n"
 163                       + e.getMessage());
 164               if (!(e instanceof javax.xml.ws.WebServiceException))
 165               {
 166                 e.printStackTrace();
 167               }
 168               // For moment, report service as a problem.
 169               jws2Discoverer.addInvalidServiceUrl(jwsservers);
 170             }
 171             ;
 172             if (service != null)
 173             {
 174               noservices = false;
 175               Jws2Instance svc = null;
 176               if (registry != null)
 177               {
 178
 179                 String description = registry.getServiceDescription(srv);
 180
 181                 svc = Jws2InstanceFactory.newJws2Instance(jwsservers, srv.toString(),
 182                         cat.name, description, service);
 183               }
 184               if (svc == null)
 185               {
 186                 svc = Jws2InstanceFactory.newJws2Instance(jwsservers, srv.toString(),
 187                         cat.name, "JABAWS 1 Alignment Service", service);
 188               }
 189               jws2Discoverer.addService(jwsservers, svc);
 190             }
 191
 192           }
 193         }
 194
 195         if (noservices)
 196         {
 197           jws2Discoverer.addUrlwithnoservices(jwsservers);
 198         }
 199       }
 200       else
 201       {
 202         jws2Discoverer.addInvalidServiceUrl(jwsservers);
 203         Cache.log.info("Ignoring invalid Jws2 service url " + jwsservers);
 204       }
 205     } catch (Exception e)
 206     {
 207       e.printStackTrace();
 208       Cache.log.warn("Exception when discovering Jws2 services.", e);
 209       jws2Discoverer.addInvalidServiceUrl(jwsservers);
 210     } catch (Error e)
 211     {
 212       Cache.log.error("Exception when discovering Jws2 services.", e);
 213       jws2Discoverer.addInvalidServiceUrl(jwsservers);
 214     }
 215     running = false;
 216   }
 217
 218 }