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.ws.jws2.jabaws2.Jws2Instance;
  28 import jalview.ws.jws2.jabaws2.Jws2InstanceFactory;
  29
  30 import java.util.HashSet;
  31 import java.util.Set;
  32
  33 import compbio.data.msa.Category;
  34 import compbio.data.msa.JABAService;
  35 import compbio.ws.client.Jws2Client;
  36 import compbio.ws.client.Services;
  37
  38 /**
  39  * @author JimP
  40  *
  41  */
  42 public class JabaWsServerQuery implements Runnable
  43 {
  44
  45   Jws2Discoverer jws2Discoverer = null;
  46
  47   String jwsservers = null;
  48
  49   boolean quit = false, running = false;
  50
  51   /**
  52    * @return the running
  53    */
  54   public boolean isRunning()
  55   {
  56     return running;
  57   }
  58
  59   /**
  60    * @param quit
  61    *          the quit to set
  62    */
  63   public void setQuit(boolean quit)
  64   {
  65     this.quit = quit;
  66   }
  67
  68   public JabaWsServerQuery(Jws2Discoverer jws2Discoverer, String jwsservers)
  69   {
  70     this.jws2Discoverer = jws2Discoverer;
  71     this.jwsservers = jwsservers;
  72   }
  73
  74   Services[] JABAWS1SERVERS = new Services[]
  75   { Services.ClustalWS, Services.MuscleWS, Services.MafftWS,
  76       Services.ProbconsWS, Services.TcoffeeWS };
  77
  78   Services[] JABAWS2SERVERS = new Services[]
  79   { Services.ClustalWS, Services.MuscleWS, Services.MafftWS,
  80       Services.ProbconsWS, Services.TcoffeeWS, Services.AAConWS,
  81       Services.DisemblWS, Services.GlobPlotWS, Services.IUPredWS,
  82       Services.JronnWS, Services.RNAalifoldWS };
  83
  84   /*
  85    * (non-Javadoc)
  86    *
  87    * @see java.lang.Runnable#run()
  88    */
  89   @Override
  90   public void run()
  91   {
  92     running = true;
  93     try
  94     {
  95       if (Jws2Client.validURL(jwsservers))
  96       {
  97         compbio.data.msa.RegistryWS registry = null;
  98         Set svccategories = null;
  99         boolean noservices = true;
 100         // look for services
 101         boolean jabasws2 = false;
 102         // If we are dealing with a JABAWS2 service, then just go and ask the
 103         // JABAWS 2 service registry
 104         Set<Services> srv_set = new HashSet<Services>();
 105
 106         Set<Category> categories = Category.getCategories();
 107         String svc_cat;
 108
 109         try
 110         {
 111           // JBPNote: why is RegistryWS in compbio.data.msa ?
 112           registry = Jws2Client.connectToRegistry(jwsservers);
 113           if (registry != null)
 114           {
 115             // System.err.println("Test Services Output\n"
 116             // + registry.testAllServices());
 117             // TODO: enumerate services and test those that haven't been tested
 118             // in the last n-days/hours/etc.
 119
 120             jabasws2 = true;
 121             srv_set = registry.getSupportedServices();
 122
 123             // dan test
 124             System.out.println("registry.getSupportedServices: "
 125                     + srv_set.toString());
 126
 127             svccategories = registry.getServiceCategories();
 128
 129             // dan test
 130             // System.out.println("registry.getServiceCategories: " +
 131             // svccategories.toString());
 132
 133           }
 134         } catch (Exception ex)
 135         {
 136           System.err.println("Exception whilst trying to get at registry:");
 137           ex.printStackTrace();
 138           // if that failed, then we are probably working with a JABAWS1 server.
 139           // in that case, look for each service endpoint
 140           System.err.println("JWS2 Discoverer: " + jwsservers
 141                   + " is a JABAWS1 server. Using hardwired list.");
 142           for (Services srv : JABAWS1SERVERS)
 143           {
 144             srv_set.add(srv);
 145           }
 146         }
 147
 148         for (Category cat : categories)
 149         {
 150           for (Services srv : cat.getServices())
 151           {
 152             if (quit)
 153             {
 154               running = false;
 155               return;
 156             }
 157             if (!srv_set.contains(srv))
 158             {
 159               continue;
 160             }
 161             JABAService service = null;
 162             try
 163             {
 164               service = Jws2Client.connect(jwsservers, srv);
 165             } catch (Exception e)
 166             {
 167               System.err.println("Jws2 Discoverer: Problem on "
 168                       + jwsservers + " with service " + srv + ":\n"
 169                       + e.getMessage());
 170               if (!(e instanceof javax.xml.ws.WebServiceException))
 171               {
 172                 e.printStackTrace();
 173               }
 174               // For moment, report service as a problem.
 175               jws2Discoverer.addInvalidServiceUrl(jwsservers);
 176             }
 177             ;
 178             if (service != null)
 179             {
 180               noservices = false;
 181               Jws2Instance svc = null;
 182               if (registry != null)
 183               {
 184
 185                 String description = registry.getServiceDescription(srv);
 186
 187                 svc = Jws2InstanceFactory.newJws2Instance(jwsservers,
 188                         srv.toString(), cat.name, description, service);
 189               }
 190               if (svc == null)
 191               {
 192                 svc = Jws2InstanceFactory.newJws2Instance(jwsservers,
 193                         srv.toString(), cat.name,
 194                         "JABAWS 1 Alignment Service", service);
 195               }
 196               jws2Discoverer.addService(jwsservers, svc);
 197             }
 198
 199           }
 200         }
 201
 202         if (noservices)
 203         {
 204           jws2Discoverer.addUrlwithnoservices(jwsservers);
 205         }
 206       }
 207       else
 208       {
 209         jws2Discoverer.addInvalidServiceUrl(jwsservers);
 210         Cache.log.info("Ignoring invalid Jws2 service url " + jwsservers);
 211       }
 212     } catch (Exception e)
 213     {
 214       e.printStackTrace();
 215       Cache.log.warn("Exception when discovering Jws2 services.", e);
 216       jws2Discoverer.addInvalidServiceUrl(jwsservers);
 217     } catch (Error e)
 218     {
 219       Cache.log.error("Exception when discovering Jws2 services.", e);
 220       jws2Discoverer.addInvalidServiceUrl(jwsservers);
 221     }
 222     running = false;
 223   }
 224
 225 }