src/jalview/ws/jws2/JabaWsServerQuery.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
   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 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  * The Jalview Authors are detailed in the 'AUTHORS' file.
  18  */
  19 /**
  20  *
  21  */
  22 package jalview.ws.jws2;
  23
  24 import jalview.bin.Cache;
  25 import jalview.ws.jws2.jabaws2.Jws2Instance;
  26 import jalview.ws.jws2.jabaws2.Jws2InstanceFactory;
  27
  28 import java.util.HashSet;
  29 import java.util.Set;
  30
  31 import compbio.data.msa.Category;
  32 import compbio.data.msa.JABAService;
  33 import compbio.ws.client.Jws2Client;
  34 import compbio.ws.client.Services;
  35
  36 /**
  37  * @author JimP
  38  *
  39  */
  40 public class JabaWsServerQuery implements Runnable
  41 {
  42
  43   Jws2Discoverer jws2Discoverer = null;
  44
  45   String jwsservers = null;
  46
  47   boolean quit = false, running = false;
  48
  49   /**
  50    * @return the running
  51    */
  52   public boolean isRunning()
  53   {
  54     return running;
  55   }
  56
  57   /**
  58    * @param quit
  59    *          the quit to set
  60    */
  61   public void setQuit(boolean quit)
  62   {
  63     this.quit = quit;
  64   }
  65
  66   public JabaWsServerQuery(Jws2Discoverer jws2Discoverer, String jwsservers)
  67   {
  68     this.jws2Discoverer = jws2Discoverer;
  69     this.jwsservers = jwsservers;
  70   }
  71
  72   Services[] JABAWS1SERVERS = new Services[]
  73   { Services.ClustalWS, Services.MuscleWS, Services.MafftWS,
  74       Services.ProbconsWS, Services.TcoffeeWS };
  75
  76   Services[] JABAWS2SERVERS = new Services[]
  77   { Services.ClustalWS, Services.MuscleWS, Services.MafftWS,
  78       Services.ProbconsWS, Services.TcoffeeWS, Services.AAConWS,
  79       Services.DisemblWS, Services.GlobPlotWS, Services.IUPredWS,
  80       Services.JronnWS, Services.RNAalifoldWS };
  81
  82   /*
  83    * (non-Javadoc)
  84    *
  85    * @see java.lang.Runnable#run()
  86    */
  87   @Override
  88   public void run()
  89   {
  90     running = true;
  91     try
  92     {
  93       if (Jws2Client.validURL(jwsservers))
  94       {
  95         compbio.data.msa.RegistryWS registry = null;
  96         Set svccategories = null;
  97         boolean noservices = true;
  98         // look for services
  99         boolean jabasws2 = false;
 100         // If we are dealing with a JABAWS2 service, then just go and ask the
 101         // JABAWS 2 service registry
 102         Set<Services> srv_set = new HashSet<Services>();
 103
 104         Set<Category> categories = Category.getCategories();
 105         String svc_cat;
 106
 107         try
 108         {
 109           // JBPNote: why is RegistryWS in compbio.data.msa ?
 110           registry = Jws2Client.connectToRegistry(jwsservers);
 111           if (registry != null)
 112           {
 113             // System.err.println("Test Services Output\n"
 114             // + registry.testAllServices());
 115             // TODO: enumerate services and test those that haven't been tested
 116             // in the last n-days/hours/etc.
 117
 118             jabasws2 = true;
 119             srv_set = registry.getSupportedServices();
 120
 121             // dan test
 122             System.out.println("registry.getSupportedServices: " + srv_set.toString());
 123
 124             svccategories = registry.getServiceCategories();
 125
 126             // dan test
 127 //            System.out.println("registry.getServiceCategories: " + svccategories.toString());
 128
 129           }
 130         } catch (Exception ex)
 131         {
 132           System.err.println("Exception whilst trying to get at registry:");
 133           ex.printStackTrace();
 134           // if that failed, then we are probably working with a JABAWS1 server.
 135           // in that case, look for each service endpoint
 136           System.err.println("JWS2 Discoverer: " + jwsservers
 137                   + " is a JABAWS1 server. Using hardwired list.");
 138           for (Services srv : JABAWS1SERVERS)
 139           {
 140             srv_set.add(srv);
 141           }
 142         }
 143         for (Category cat : categories)
 144         {
 145           for (Services srv : cat.getServices())
 146           {
 147             if (quit)
 148             {
 149               running = false;
 150               return;
 151             }
 152             if (!srv_set.contains(srv))
 153             {
 154               continue;
 155             }
 156             JABAService service = null;
 157             try
 158             {
 159               service = Jws2Client.connect(jwsservers, srv);
 160             } catch (Exception e)
 161             {
 162               System.err.println("Jws2 Discoverer: Problem on "
 163                       + jwsservers + " with service " + srv + ":\n"
 164                       + e.getMessage());
 165               if (!(e instanceof javax.xml.ws.WebServiceException))
 166               {
 167                 e.printStackTrace();
 168               }
 169               // For moment, report service as a problem.
 170               jws2Discoverer.addInvalidServiceUrl(jwsservers);
 171             }
 172             ;
 173             if (service != null)
 174             {
 175               noservices = false;
 176               Jws2Instance svc = null;
 177               if (registry != null)
 178               {
 179
 180                 String description = registry.getServiceDescription(srv);
 181
 182                 svc = Jws2InstanceFactory.newJws2Instance(jwsservers, srv.toString(),
 183                         cat.name, description, service);
 184               }
 185               if (svc == null)
 186               {
 187                 svc = Jws2InstanceFactory.newJws2Instance(jwsservers, srv.toString(),
 188                         cat.name, "JABAWS 1 Alignment Service", service);
 189               }
 190               jws2Discoverer.addService(jwsservers, svc);
 191             }
 192
 193           }
 194         }
 195
 196         if (noservices)
 197         {
 198           jws2Discoverer.addUrlwithnoservices(jwsservers);
 199         }
 200       }
 201       else
 202       {
 203         jws2Discoverer.addInvalidServiceUrl(jwsservers);
 204         Cache.log.info("Ignoring invalid Jws2 service url " + jwsservers);
 205       }
 206     } catch (Exception e)
 207     {
 208       e.printStackTrace();
 209       Cache.log.warn("Exception when discovering Jws2 services.", e);
 210       jws2Discoverer.addInvalidServiceUrl(jwsservers);
 211     } catch (Error e)
 212     {
 213       Cache.log.error("Exception when discovering Jws2 services.", e);
 214       jws2Discoverer.addInvalidServiceUrl(jwsservers);
 215     }
 216     running = false;
 217   }
 218
 219 }