1 /*******************************************************************************
2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
3 * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
5 * This file is part of Jalview.
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.
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.
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 *******************************************************************************/
21 package jalview.ws.jws2;
23 import jalview.bin.Cache;
24 import jalview.ws.jws2.jabaws2.Jws2Instance;
26 import java.util.HashSet;
29 import compbio.data.msa.Category;
30 import compbio.data.msa.JABAService;
31 import compbio.ws.client.Jws2Client;
32 import compbio.ws.client.Services;
38 public class JabaWsServerQuery implements Runnable
41 Jws2Discoverer jws2Discoverer = null;
43 String jwsservers = null;
45 boolean quit = false, running = false;
50 public boolean isRunning()
59 public void setQuit(boolean quit)
64 public JabaWsServerQuery(Jws2Discoverer jws2Discoverer, String jwsservers)
66 this.jws2Discoverer = jws2Discoverer;
67 this.jwsservers = jwsservers;
73 * @see java.lang.Runnable#run()
81 if (Jws2Client.validURL(jwsservers))
83 compbio.data.msa.RegistryWS registry = null;
84 Set svccategories = null;
85 boolean noservices = true;
87 boolean jabasws2 = false;
88 // If we are dealing with a JABAWS2 service, then just go and ask the
89 // JABAWS 2 service registry
90 Set<Services> srv_set = new HashSet<Services>();
92 Set<Category> categories = Category.getCategories();
97 // JBPNote: why is RegistryWS in compbio.data.msa ?
98 registry = Jws2Client.connectToRegistry(jwsservers);
101 // System.err.println("Test Services Output\n"
102 // + registry.testAllServices());
103 // TODO: enumerate services and test those that haven't been tested
104 // in the last n-days/hours/etc.
107 srv_set = registry.getSupportedServices();
108 svccategories = registry.getServiceCategories();
111 } catch (Exception ex)
113 System.err.println("Exception whilst trying to get at registry:");
114 ex.printStackTrace();
115 // if that failed, then we are probably working with a JABAWS1 server.
116 // in that case, look for each service endpoint
117 System.err.println("JWS2 Discoverer: " + jwsservers
118 + " is a JABAWS1 server. Using hardwired list.");
119 for (Services srv : new Services[]
120 { Services.ClustalWS, Services.MuscleWS, Services.MafftWS,
121 Services.ProbconsWS, Services.TcoffeeWS })
126 for (Category cat : categories)
128 for (Services srv : cat.getServices())
135 if (!srv_set.contains(srv))
139 JABAService service = null;
142 service = Jws2Client.connect(jwsservers, srv);
143 } catch (Exception e)
145 System.err.println("Jws2 Discoverer: Problem on "
146 + jwsservers + " with service " + srv + ":\n"
148 if (!(e instanceof javax.xml.ws.WebServiceException))
152 // For moment, report service as a problem.
153 jws2Discoverer.addInvalidServiceUrl(jwsservers);
159 Jws2Instance svc = null;
160 if (registry != null)
163 String description = registry.getServiceDescription(srv);
165 svc = new Jws2Instance(jwsservers, srv.toString(),
166 cat.name, description, service);
170 svc = new Jws2Instance(jwsservers, srv.toString(), cat.name,
171 "JABAWS 1 Alignment Service", service);
173 jws2Discoverer.addService(jwsservers, svc);
181 jws2Discoverer.addUrlwithnoservices(jwsservers);
186 jws2Discoverer.addInvalidServiceUrl(jwsservers);
187 Cache.log.info("Ignoring invalid Jws2 service url " + jwsservers);
189 } catch (Exception e)
192 Cache.log.warn("Exception when discovering Jws2 services.", e);
193 jws2Discoverer.addInvalidServiceUrl(jwsservers);
196 Cache.log.error("Exception when discovering Jws2 services.", e);
197 jws2Discoverer.addInvalidServiceUrl(jwsservers);