webservices/compbio/ws/client/WSTester.java

   1 /* Copyright (c) 2011 Peter Troshin\r
   2  *  \r
   3  *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0     \r
   4  * \r
   5  *  This library is free software; you can redistribute it and/or modify it under the terms of the\r
   6  *  Apache License version 2 as published by the Apache Software Foundation\r
   7  * \r
   8  *  This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
   9  *  even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
  10  *  License for more details.\r
  11  * \r
  12  *  A copy of the license is in apache_license.txt. It is also available here:\r
  13  * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
  14  * \r
  15  * Any republication or derived work distributed in source code form\r
  16  * must include this copyright and license notice.\r
  17  */\r
  18 \r
  19 package compbio.ws.client;\r
  20 \r
  21 import static compbio.ws.client.Constraints.hostkey;\r
  22 import static compbio.ws.client.Constraints.pseparator;\r
  23 import static compbio.ws.client.Constraints.servicekey;\r
  24 \r
  25 import java.io.ByteArrayInputStream;\r
  26 import java.io.Closeable;\r
  27 import java.io.IOException;\r
  28 import java.io.PrintWriter;\r
  29 import java.net.ConnectException;\r
  30 import java.util.Arrays;\r
  31 import java.util.List;\r
  32 \r
  33 import javax.xml.ws.WebServiceException;\r
  34 \r
  35 import compbio.data.msa.JABAService;\r
  36 import compbio.data.msa.Metadata;\r
  37 import compbio.data.msa.MsaWS;\r
  38 import compbio.data.msa.SequenceAnnotation;\r
  39 import compbio.data.sequence.Alignment;\r
  40 import compbio.data.sequence.FastaSequence;\r
  41 import compbio.data.sequence.ScoreManager;\r
  42 import compbio.data.sequence.SequenceUtil;\r
  43 import compbio.metadata.JobStatus;\r
  44 import compbio.metadata.Limit;\r
  45 import compbio.metadata.LimitsManager;\r
  46 import compbio.metadata.Option;\r
  47 import compbio.metadata.Preset;\r
  48 import compbio.metadata.PresetManager;\r
  49 import compbio.metadata.RunnerConfig;\r
  50 import compbio.metadata.UnsupportedRuntimeException;\r
  51 import compbio.util.FileUtil;\r
  52 import compbio.util.Util;\r
  53 \r
  54 /**\r
  55  * Class for testing web services\r
  56  * \r
  57  * @author pvtroshin\r
  58  * \r
  59  * @version 1.0 February 2010\r
  60  */\r
  61 public class WSTester {\r
  62 \r
  63         /**\r
  64          * Sequences to be used as input for all WS\r
  65          */\r
  66         public static final String fastaInput = ">Foo\n"\r
  67                         + "MTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV"\r
  68                         + "\n>Bar\n"\r
  69                         + "ASDAAPEHPGIALWLHALEDAGQAEAAAAYTRAHQLLPEEPYITAQLLNAVA\n";\r
  70 \r
  71         public static final String fastaAlignment = ">Foo\n"\r
  72                         + "MTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV--------\n"\r
  73                         + ">Bar\n"\r
  74                         + "ASDAAPEH------------PGIALWLHALE-DAGQAEAAA---AYTRAHQLLPEEPYITAQLLNAVA\n"\r
  75                         + "";\r
  76 \r
  77         \r
  78         \r
  79         static final List<FastaSequence> seqs = loadSeqs();\r
  80 \r
  81         private static final String FAILED = "FAILED";\r
  82         private static final String OK = "OK";\r
  83 \r
  84         private static final String UNSUPPORTED = "UNSUPPORTED";\r
  85 \r
  86         /**\r
  87          * Converting input to a form accepted by WS\r
  88          * \r
  89          * @return List of FastaSequence records\r
  90          */\r
  91         private static List<FastaSequence> loadSeqs() {\r
  92                 try {\r
  93                         return SequenceUtil.readFasta(new ByteArrayInputStream(fastaInput\r
  94                                         .getBytes()));\r
  95                 } catch (IOException ignored) {\r
  96                         // Should not happen as a source is not a external stream\r
  97                         ignored.printStackTrace();\r
  98                 }\r
  99                 return null;\r
 100         }\r
 101 \r
 102         /**\r
 103          * Converting input to a form accepted by WS\r
 104          * \r
 105          * @return List of FastaSequence records\r
 106          */\r
 107         private static List<FastaSequence> loadAlignment() {\r
 108                 try {\r
 109                         return SequenceUtil.readFasta(new ByteArrayInputStream(\r
 110                                         fastaAlignment.getBytes()));\r
 111                 } catch (IOException ignored) {\r
 112                         // Should not happen as a source is not a external stream\r
 113                         ignored.printStackTrace();\r
 114                 }\r
 115                 return null;\r
 116         }\r
 117 \r
 118         private final PrintWriter writer;\r
 119         private final String hostname;\r
 120 \r
 121         /**\r
 122          * Construct an instance of JABAWS tester\r
 123          * \r
 124          * @param hostname\r
 125          *            - fully qualified host and context name of JABAWS e.g.\r
 126          *            http://nanna.cluster.lifesci.dundee.ac.uk:8080/jaba\r
 127          * @param writer\r
 128          *            a PrintWriter instance to writer test log to.\r
 129          */\r
 130         public WSTester(String hostname, PrintWriter writer) {\r
 131                 if (Util.isEmpty(hostname)) {\r
 132                         throw new NullPointerException("Hostname must be provided!");\r
 133                 }\r
 134                 this.hostname = hostname;\r
 135                 this.writer = writer;\r
 136         }\r
 137 \r
 138         /**\r
 139          * Prints usage\r
 140          */\r
 141         static void printUsage() {\r
 142                 System.out.println("Usage: <Class or Jar file name> " + hostkey\r
 143                                 + pseparator + "host_and_context " + "<" + servicekey\r
 144                                 + pseparator + "serviceName>");\r
 145                 System.out.println();\r
 146                 System.out\r
 147                                 .println(hostkey\r
 148                                                 + pseparator\r
 149                                                 + "<host_and_context> - a full URL to the JABAWS web server including context path e.g. http://10.31.1.159:8080/ws");\r
 150                 System.out\r
 151                                 .println(servicekey\r
 152                                                 + pseparator\r
 153                                                 + "<ServiceName> - optional if unspecified all services are tested otherwise one of "\r
 154                                                 + Arrays.toString(Services.values()));\r
 155                 System.out.println();\r
 156 \r
 157         }\r
 158 \r
 159         /**\r
 160          * Calls alignment with preset\r
 161          * \r
 162          * @param <T>\r
 163          * @param msaws\r
 164          * @param presets\r
 165          *            list of the Preset\r
 166          * @throws UnsupportedRuntimeException\r
 167          */\r
 168         private <T> boolean presetAlign(MsaWS<T> msaws, List<Preset<T>> presets)\r
 169                         throws UnsupportedRuntimeException {\r
 170                 boolean succeed = false;\r
 171                 for (Preset<T> preset : presets) {\r
 172                         writer.print("Aligning with preset '" + preset.getName() + "'... ");\r
 173                         Alignment al = null;\r
 174                         try {\r
 175                                 String taskId = msaws.presetAlign(seqs, preset);\r
 176                                 al = msaws.getResult(taskId);\r
 177                                 if (al != null) {\r
 178                                         writer.println(OK);\r
 179                                 }\r
 180                                 succeed = true;\r
 181                         } catch (Exception e) {\r
 182                                 if (e instanceof UnsupportedRuntimeException) {\r
 183                                         // If executable is not supported than none of the presets\r
 184                                         // are\r
 185                                         // going to work\r
 186                                         throw (UnsupportedRuntimeException) e;\r
 187                                 } else {\r
 188                                         reportException(e);\r
 189                                 }\r
 190                                 continue;\r
 191                         }\r
 192                 }\r
 193                 return succeed;\r
 194         }\r
 195 \r
 196         private <T> boolean testMsaWS(MsaWS<T> msaws) throws Exception {\r
 197                 assert msaws != null;\r
 198 \r
 199                 boolean succeed = testDefaultAlignment(msaws);\r
 200                 // If exception above is thrown than the tests below is not run\r
 201 \r
 202                 PresetManager<T> pmanager = msaws.getPresets();\r
 203                 if (pmanager != null && pmanager.getPresets().size() > 0) {\r
 204                         writer.println("Testing alignment with presets:");\r
 205                         List<Preset<T>> plist = pmanager.getPresets();\r
 206                         succeed = !succeed ? presetAlign(msaws, plist) : succeed;\r
 207                 }\r
 208                 testMetadata(msaws);\r
 209                 return succeed;\r
 210         }\r
 211         \r
 212         /**\r
 213          * Call most of web services functions and check the output\r
 214          * \r
 215          * @param <T>\r
 216          *            web service type\r
 217          * @param msaws\r
 218          * @throws UnsupportedRuntimeException\r
 219          *             is thrown if the connection to a web service was made, but\r
 220          *             the web service is not functional. e.g. when native\r
 221          *             executable does not exists for a server platform\r
 222          */\r
 223         @SuppressWarnings("unchecked")\r
 224         private <T> boolean checkService(JABAService wservice, Services service) {\r
 225                 try {\r
 226                         if (wservice == null) {\r
 227                                 throw new NullPointerException(\r
 228                                                 "JABAService instance must be provided!");\r
 229                         }\r
 230 \r
 231                         if (wservice instanceof MsaWS) {\r
 232                                 return testMsaWS((MsaWS<T>) wservice);\r
 233                         } else if (wservice instanceof SequenceAnnotation) {\r
 234                                 return testSequenceAnnotationWS(\r
 235                                                 (SequenceAnnotation<T>) wservice, service);\r
 236                         } else {\r
 237                                 throw new UnsupportedOperationException("The service: "\r
 238                                                 + wservice.getClass() + " is not supported! ");\r
 239                         }\r
 240                 } catch (Exception e) {\r
 241                         reportException(e);\r
 242                         return false;\r
 243                 }\r
 244         }\r
 245 \r
 246         private <T> boolean testSequenceAnnotationWS(\r
 247                         SequenceAnnotation<T> wservice, Services service) throws Exception {\r
 248                 writer.print("Calling analyse.........");\r
 249 \r
 250                 List<FastaSequence> input = loadSeqs();\r
 251                 if (service == Services.AAConWS || service == Services.RNAalifoldWS) {\r
 252                         input = loadAlignment();\r
 253                 }\r
 254                 boolean success = testDefaultAnalyse(input, wservice, null, null);\r
 255 \r
 256                 PresetManager<T> presetman = wservice.getPresets();\r
 257                 if (presetman != null) {\r
 258                         List<Preset<T>> presets = presetman.getPresets();\r
 259                         if (presets != null && !presets.isEmpty()) {\r
 260                                 Preset<T> preset = presets.get(0);\r
 261                                 writer.print("Calling analyse with Preset.........");\r
 262                                 success = testDefaultAnalyse(input, wservice, preset, null);\r
 263                         }\r
 264                 }\r
 265                 testMetadata(wservice);\r
 266                 return success;\r
 267         }\r
 268 \r
 269         private <T> boolean testDefaultAnalyse(List<FastaSequence> fastalist,\r
 270                         SequenceAnnotation<T> wsproxy, Preset<T> preset,\r
 271                         List<Option<T>> customOptions) throws Exception {\r
 272 \r
 273                 ScoreManager scores = null;\r
 274 \r
 275                 String jobId = null;\r
 276                 if (customOptions != null) {\r
 277                         jobId = wsproxy.customAnalize(fastalist, customOptions);\r
 278                 } else if (preset != null) {\r
 279                         jobId = wsproxy.presetAnalize(fastalist, preset);\r
 280                 } else {\r
 281                         jobId = wsproxy.analize(fastalist);\r
 282                 }\r
 283                 Thread.sleep(1000);\r
 284                 scores = wsproxy.getAnnotation(jobId);\r
 285                 if (scores != null) {\r
 286                         writer.println(OK);\r
 287                 }\r
 288 \r
 289                 return scores != null;\r
 290         }\r
 291 \r
 292         private void reportException(Exception e) {\r
 293                 writer.println(FAILED);\r
 294                 writer.println("Exception while waiting for results. "\r
 295                                 + "Exception details are below:");\r
 296                 writer.println(e.getLocalizedMessage());\r
 297                 e.printStackTrace(writer);\r
 298         }\r
 299 \r
 300         private <T> void testMetadata(Metadata<T> msaws)\r
 301                         throws UnsupportedRuntimeException {\r
 302 \r
 303                 writer.print("Querying presets...");\r
 304                 PresetManager<T> pmanager = msaws.getPresets();\r
 305                 if (pmanager != null && pmanager.getPresets().size() > 0) {\r
 306                         writer.println(OK);\r
 307                 } else {\r
 308                         writer.println(UNSUPPORTED);\r
 309                 }\r
 310 \r
 311                 writer.print("Querying Parameters...");\r
 312                 RunnerConfig<T> options = msaws.getRunnerOptions();\r
 313                 if (options != null && options.getArguments().size() > 0) {\r
 314                         writer.println(OK);\r
 315                 } else {\r
 316                         writer.println(UNSUPPORTED);\r
 317                 }\r
 318 \r
 319                 writer.print("Querying Limits...");\r
 320                 LimitsManager<T> limits = msaws.getLimits();\r
 321                 if (limits != null && limits.getLimits().size() > 0) {\r
 322                         writer.println(OK);\r
 323                         // writer.println("Limits details: \n" + limits.toString());\r
 324                 } else {\r
 325                         writer.println(UNSUPPORTED);\r
 326                 }\r
 327 \r
 328                 writer.print("Querying Local Engine Limits...");\r
 329                 Limit<T> localLimit = msaws\r
 330                                 .getLimit(PresetManager.LOCAL_ENGINE_LIMIT_PRESET);\r
 331                 if (localLimit != null) {\r
 332                         writer.println(OK);\r
 333                 } else {\r
 334                         writer.println(UNSUPPORTED);\r
 335                 }\r
 336         }\r
 337 \r
 338         /**\r
 339          * Align using default settings\r
 340          * \r
 341          * @param <T>\r
 342          * @param msaws\r
 343          * @throws UnsupportedRuntimeException\r
 344          */\r
 345         private <T> boolean testDefaultAlignment(MsaWS<T> msaws) throws Exception {\r
 346                 writer.print("Testing alignment with default parameters:");\r
 347                 Alignment al = null;\r
 348                 boolean succeed = false;\r
 349 \r
 350                 String taskId = msaws.align(seqs);\r
 351                 writer.print("\nQuerying job status...");\r
 352                 JobStatus status = msaws.getJobStatus(taskId);\r
 353                 while (status != JobStatus.FINISHED) {\r
 354                         Thread.sleep(1000);\r
 355                         status = msaws.getJobStatus(taskId);\r
 356                 }\r
 357                 writer.println(OK);\r
 358                 writer.print("Retrieving results...");\r
 359                 al = msaws.getResult(taskId);\r
 360                 succeed = true;\r
 361                 if (al != null) {\r
 362                         writer.println(OK);\r
 363                 }\r
 364                 return succeed;\r
 365         }\r
 366         \r
 367         \r
 368         /**\r
 369          * Test JWS2 web services\r
 370          * \r
 371          * @param <T>\r
 372          *            web service type\r
 373          * @param args\r
 374          *            -h=<Your web application server host name, port and JWS2\r
 375          *            context path>\r
 376          * \r
 377          *            -s=<ServiceName> which is optional. If service name is not\r
 378          *            provided then all known JWS2 web services are tested\r
 379          * @throws IOException\r
 380          */\r
 381         public static <T> void main(String[] args) throws IOException {\r
 382 \r
 383                 if (args == null || args.length < 1) {\r
 384                         WSTester.printUsage();\r
 385                         System.exit(0);\r
 386                 }\r
 387                 String host = CmdHelper.getHost(args);\r
 388                 String serviceName = CmdHelper.getServiceName(args);\r
 389                 if (!Jws2Client.validURL(host)) {\r
 390                         System.err\r
 391                                         .println("<host_and_context> parameter is not provided or is incorrect!");\r
 392                         System.exit(1);\r
 393                 }\r
 394                 WSTester tester = new WSTester(host, new PrintWriter(System.out, true));\r
 395 \r
 396                 if (serviceName != null) {\r
 397                         Services service = Services.getService(serviceName);\r
 398                         if (service == null) {\r
 399                                 tester.writer.println("Service '" + serviceName\r
 400                                                 + "' is not supported. Valid values are: "\r
 401                                                 + Arrays.toString(Services.values()));\r
 402                                 tester.writer.println();\r
 403                                 printUsage();\r
 404                                 System.exit(1);\r
 405                         }\r
 406                         tester.checkService(service);\r
 407                         System.exit(0);\r
 408                 }\r
 409 \r
 410                 tester.writer\r
 411                                 .println("<ServiceName> is not provided checking all known services...");\r
 412 \r
 413                 for (Services serv : Services.values()) {\r
 414                         tester.writer.println();\r
 415                         tester.checkService(serv);\r
 416                 }\r
 417 \r
 418         }\r
 419 \r
 420         /**\r
 421          * Test JABA web service\r
 422          * \r
 423          * @param service\r
 424          *            the service to test\r
 425          * @return true if the service works as expected, false otherwise\r
 426          * @throws WebServiceException\r
 427          * @throws ConnectException\r
 428          */\r
 429         public boolean checkService(Services service) throws ConnectException,\r
 430                         WebServiceException {\r
 431                 JABAService ws = Jws2Client.connect(hostname, service);\r
 432                 if (ws == null) {\r
 433                         writer.println("Cannot estabilish the connection to host "\r
 434                                         + hostname + " with service " + service.toString());\r
 435                         return false;\r
 436                 }\r
 437                 boolean succeed = false;\r
 438                 try {\r
 439                         writer.println("Checking service " + service.toString());\r
 440                         succeed = checkService(ws, service);\r
 441                 } finally {\r
 442                         FileUtil.closeSilently(((Closeable) ws));\r
 443                 }\r
 444                 reportResults(service, succeed);\r
 445                 return succeed;\r
 446         }\r
 447 \r
 448         private void reportResults(Services serv, boolean succeed) {\r
 449                 if (succeed) {\r
 450                         writer.println("Check is completed. The Service " + serv\r
 451                                         + " IS WORKING\n");\r
 452                 } else {\r
 453                         writer.println("Check is aborted. The Service " + serv\r
 454                                         + " HAS SOME PROBLEMS\n");\r
 455                 }\r
 456         }\r
 457 }\r