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: " + srv_set.toString());
 125
 126             svccategories = registry.getServiceCategories();
 127
 128             // dan test
 129 //            System.out.println("registry.getServiceCategories: " + svccategories.toString());
 130
 131           }
 132         } catch (Exception ex)
 133         {
 134           System.err.println("Exception whilst trying to get at registry:");
 135           ex.printStackTrace();
 136           // if that failed, then we are probably working with a JABAWS1 server.
 137           // in that case, look for each service endpoint
 138           System.err.println("JWS2 Discoverer: " + jwsservers
 139                   + " is a JABAWS1 server. Using hardwired list.");
 140           for (Services srv : JABAWS1SERVERS)
 141           {
 142             srv_set.add(srv);
 143           }
 144         }
 145         for (Category cat : categories)
 146         {
 147           for (Services srv : cat.getServices())
 148           {
 149             if (quit)
 150             {
 151               running = false;
 152               return;
 153             }
 154             if (!srv_set.contains(srv))
 155             {
 156               continue;
 157             }
 158             JABAService service = null;
 159             try
 160             {
 161               service = Jws2Client.connect(jwsservers, srv);
 162             } catch (Exception e)
 163             {
 164               System.err.println("Jws2 Discoverer: Problem on "
 165                       + jwsservers + " with service " + srv + ":\n"
 166                       + e.getMessage());
 167               if (!(e instanceof javax.xml.ws.WebServiceException))
 168               {
 169                 e.printStackTrace();
 170               }
 171               // For moment, report service as a problem.
 172               jws2Discoverer.addInvalidServiceUrl(jwsservers);
 173             }
 174             ;
 175             if (service != null)
 176             {
 177               noservices = false;
 178               Jws2Instance svc = null;
 179               if (registry != null)
 180               {
 181
 182                 String description = registry.getServiceDescription(srv);
 183
 184                 svc = Jws2InstanceFactory.newJws2Instance(jwsservers, srv.toString(),
 185                         cat.name, description, service);
 186               }
 187               if (svc == null)
 188               {
 189                 svc = Jws2InstanceFactory.newJws2Instance(jwsservers, srv.toString(),
 190                         cat.name, "JABAWS 1 Alignment Service", service);
 191               }
 192               jws2Discoverer.addService(jwsservers, svc);
 193             }
 194
 195           }
 196         }
 197
 198         if (noservices)
 199         {
 200           jws2Discoverer.addUrlwithnoservices(jwsservers);
 201         }
 202       }
 203       else
 204       {
 205         jws2Discoverer.addInvalidServiceUrl(jwsservers);
 206         Cache.log.info("Ignoring invalid Jws2 service url " + jwsservers);
 207       }
 208     } catch (Exception e)
 209     {
 210       e.printStackTrace();
 211       Cache.log.warn("Exception when discovering Jws2 services.", e);
 212       jws2Discoverer.addInvalidServiceUrl(jwsservers);
 213     } catch (Error e)
 214     {
 215       Cache.log.error("Exception when discovering Jws2 services.", e);
 216       jws2Discoverer.addInvalidServiceUrl(jwsservers);
 217     }
 218     running = false;
 219   }
 220
 221 }