jalviewX
File JabaWsServerQuery.java
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Classes
| Class | Line # | Actions | ||||
|---|---|---|---|---|---|---|
| JabaWsServerQuery | 45 | 71 | 22 | 33 |
Contributing tests
This file is covered by 23 tests.
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| 1 | /* | |
| 2 | * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) | |
| 3 | * Copyright (C) $$Year-Rel$$ 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.io.IOException; | |
| 31 | import java.net.MalformedURLException; | |
| 32 | import java.net.URL; | |
| 33 | import java.util.HashSet; | |
| 34 | import java.util.Set; | |
| 35 | ||
| 36 | import compbio.data.msa.Category; | |
| 37 | import compbio.data.msa.JABAService; | |
| 38 | import compbio.ws.client.Jws2Client; | |
| 39 | import compbio.ws.client.Services; | |
| 40 | ||
| 41 | /** | |
| 42 | * @author JimP | |
| 43 | * | |
| 44 | */ | |
| 45 | public class JabaWsServerQuery implements Runnable | |
| 46 | { | |
| 47 | ||
| 48 | Jws2Discoverer jws2Discoverer = null; | |
| 49 | ||
| 50 | String jwsserver = null; | |
| 51 | ||
| 52 | boolean quit = false, running = false; | |
| 53 | ||
| 54 | /** | |
| 55 | * @return the running | |
| 56 | */ | |
| 57 | 119 |  public boolean isRunning() |
| 58 | { | |
| 59 | 119 | return running; |
| 60 | } | |
| 61 | ||
| 62 | /** | |
| 63 | * @param quit | |
| 64 | * the quit to set | |
| 65 | */ | |
| 66 | 3 | public void setQuit(boolean quit) |
| 67 | { | |
| 68 | 3 | this.quit = quit; |
| 69 | } | |
| 70 | ||
| 71 | 11 | public JabaWsServerQuery(Jws2Discoverer jws2Discoverer, String server) |
| 72 | { | |
| 73 | 11 | this.jws2Discoverer = jws2Discoverer; |
| 74 | 11 | this.jwsserver = server; |
| 75 | } | |
| 76 | ||
| 77 | Services[] JABAWS1SERVERS = new Services[] { Services.ClustalWS, | |
| 78 | Services.MuscleWS, Services.MafftWS, Services.ProbconsWS, | |
| 79 | Services.TcoffeeWS }; | |
| 80 | ||
| 81 | Services[] JABAWS2SERVERS = new Services[] { Services.ClustalWS, | |
| 82 | Services.MuscleWS, Services.MafftWS, Services.ProbconsWS, | |
| 83 | Services.TcoffeeWS, Services.AAConWS, Services.DisemblWS, | |
| 84 | Services.GlobPlotWS, Services.IUPredWS, Services.JronnWS, | |
| 85 | Services.RNAalifoldWS }; | |
| 86 | ||
| 87 | /* | |
| 88 | * (non-Javadoc) | |
| 89 | * | |
| 90 | * @see java.lang.Runnable#run() | |
| 91 | */ | |
| 92 | 11 | @Override |
| 93 | public void run() | |
| 94 | { | |
| 95 | 11 | running = true; |
| 96 | 11 | try |
| 97 | { | |
| 98 | // TODO this test doesn't seem to attempt a connection - should it? | |
| 99 | // would save a lot of failed tries with UnknownHostException | |
| 100 | 11 | if (isValidUrl(jwsserver)) |
| 101 | { | |
| 102 | 11 | compbio.data.msa.RegistryWS registry = null; |
| 103 | 11 | Set svccategories = null; |
| 104 | 11 | boolean noservices = true; |
| 105 | // look for services | |
| 106 | 11 | boolean jabasws2 = false; |
| 107 | // If we are dealing with a JABAWS2 service, then just go and ask the | |
| 108 | // JABAWS 2 service registry | |
| 109 | 11 | Set<Services> srv_set = new HashSet<Services>(); |
| 110 | ||
| 111 | 11 | Set<Category> categories = Category.getCategories(); |
| 112 | 11 | String svc_cat; |
| 113 | ||
| 114 | 11 | try |
| 115 | { | |
| 116 | // JBPNote: why is RegistryWS in compbio.data.msa ? | |
| 117 | 11 | registry = Jws2Client.connectToRegistry(jwsserver); |
| 118 | 11 | if (registry != null) |
| 119 | { | |
| 120 | // System.err.println("Test Services Output\n" | |
| 121 | // + registry.testAllServices()); | |
| 122 | // TODO: enumerate services and test those that haven't been tested | |
| 123 | // in the last n-days/hours/etc. | |
| 124 | ||
| 125 | 11 | jabasws2 = true; |
| 126 | 11 | srv_set = registry.getSupportedServices(); |
| 127 | ||
| 128 | // dan test | |
| 129 | 11 | System.out.println( |
| 130 | "registry.getSupportedServices: " + srv_set.toString()); | |
| 131 | ||
| 132 | 11 | svccategories = registry.getServiceCategories(); |
| 133 | ||
| 134 | // dan test | |
| 135 | // System.out.println("registry.getServiceCategories: " + | |
| 136 | // svccategories.toString()); | |
| 137 | ||
| 138 | } | |
| 139 | } catch (Exception ex) | |
| 140 | { | |
| 141 | 0 | System.err.println("Exception whilst trying to get at registry:"); |
| 142 | 0 | ex.printStackTrace(); |
| 143 | // if that failed, then we are probably working with a JABAWS1 server. | |
| 144 | // in that case, look for each service endpoint | |
| 145 | 0 | System.err.println("JWS2 Discoverer: " + jwsserver |
| 146 | + " is a JABAWS1 server. Using hardwired list."); | |
| 147 | 0 | for (Services srv : JABAWS1SERVERS) |
| 148 | { | |
| 149 | 0 | srv_set.add(srv); |
| 150 | } | |
| 151 | } | |
| 152 | ||
| 153 | 11 | for (Category cat : categories) |
| 154 | { | |
| 155 | 38 | for (Services srv : cat.getServices()) |
| 156 | { | |
| 157 | 134 | if (quit) |
| 158 | { | |
| 159 | 2 | running = false; |
| 160 | 2 | return; |
| 161 | } | |
| 162 | 132 | if (!srv_set.contains(srv)) |
| 163 | { | |
| 164 | 0 | continue; |
| 165 | } | |
| 166 | 132 | JABAService service = null; |
| 167 | 132 | try |
| 168 | { | |
| 169 | 132 | service = Jws2Client.connect(jwsserver, srv); |
| 170 | } catch (Exception e) | |
| 171 | { | |
| 172 | 0 | System.err.println("Jws2 Discoverer: Problem on " + jwsserver |
| 173 | + " with service " + srv + ":\n" + e.getMessage()); | |
| 174 | 0 | if (!(e instanceof javax.xml.ws.WebServiceException)) |
| 175 | { | |
| 176 | 0 | e.printStackTrace(); |
| 177 | } | |
| 178 | // For moment, report service as a problem. | |
| 179 | 0 | jws2Discoverer.addInvalidServiceUrl(jwsserver); |
| 180 | } | |
| 181 | 132 | ; |
| 182 | 132 | if (service != null |
| 183 | && !Jws2InstanceFactory.ignoreService(srv.toString())) | |
| 184 | { | |
| 185 | 132 | noservices = false; |
| 186 | 132 | Jws2Instance svc = null; |
| 187 | 132 | if (registry != null) |
| 188 | { | |
| 189 | ||
| 190 | 132 | String description = registry.getServiceDescription(srv); |
| 191 | ||
| 192 | 132 | svc = Jws2InstanceFactory.newJws2Instance(jwsserver, |
| 193 | srv.toString(), cat.name, description, service); | |
| 194 | } | |
| 195 | 132 | if (svc == null) |
| 196 | { | |
| 197 | 0 | svc = Jws2InstanceFactory.newJws2Instance(jwsserver, |
| 198 | srv.toString(), cat.name, | |
| 199 | "JABAWS 1 Alignment Service", service); | |
| 200 | } | |
| 201 | 132 | jws2Discoverer.addService(jwsserver, svc); |
| 202 | } | |
| 203 | ||
| 204 | } | |
| 205 | } | |
| 206 | ||
| 207 | 9 | if (noservices) |
| 208 | { | |
| 209 | 0 | jws2Discoverer.addUrlwithnoservices(jwsserver); |
| 210 | } | |
| 211 | } | |
| 212 | else | |
| 213 | { | |
| 214 | 0 | jws2Discoverer.addInvalidServiceUrl(jwsserver); |
| 215 | 0 | Cache.log.warn("Ignoring invalid Jws2 service url " + jwsserver); |
| 216 | } | |
| 217 | } catch (Exception e) | |
| 218 | { | |
| 219 | 0 | e.printStackTrace(); |
| 220 | 0 | Cache.log.warn("Exception when discovering Jws2 services.", e); |
| 221 | 0 | jws2Discoverer.addInvalidServiceUrl(jwsserver); |
| 222 | } catch (Error e) | |
| 223 | { | |
| 224 | 0 | Cache.log.error("Exception when discovering Jws2 services.", e); |
| 225 | 0 | jws2Discoverer.addInvalidServiceUrl(jwsserver); |
| 226 | } | |
| 227 | 9 | running = false; |
| 228 | } | |
| 229 | ||
| 230 | /** | |
| 231 | * Check if the URL is valid and responding. | |
| 232 | * | |
| 233 | * @return | |
| 234 | */ | |
| 235 | 11 | private boolean isValidUrl(String server) |
| 236 | { | |
| 237 | // return Jws2Client.validURL(jwsserver); // checks syntax only | |
| 238 | 11 | boolean result = false; |
| 239 | 11 | if (server != null) |
| 240 | { | |
| 241 | 11 | try |
| 242 | { | |
| 243 | 11 | URL url = new URL(server); |
| 244 | 11 | url.openStream().close(); |
| 245 | 11 | result = true; |
| 246 | } catch (MalformedURLException e) | |
| 247 | { | |
| 248 | 0 | System.err.println("Invalid server URL: " + server); |
| 249 | 0 | result = false; |
| 250 | } catch (IOException e) | |
| 251 | { | |
| 252 | 0 | System.err.println("Error connecting to server: " + server + ": " |
| 253 | + e.toString()); | |
| 254 | 0 | result = false; |
| 255 | } | |
| 256 | } | |
| 257 | 11 | return result; |
| 258 | } | |
| 259 | ||
| 260 | } |