webservices/compbio/ws/client/WSTester.java

   1 /* Copyright (c) 2009 Peter Troshin\r
   2  *  \r
   3  *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0     \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.util.Arrays;\r
  30 import java.util.List;\r
  31 \r
  32 import javax.xml.ws.WebServiceException;\r
  33 \r
  34 import org.apache.log4j.Logger;\r
  35 \r
  36 import compbio.data.msa.JABAService;\r
  37 import compbio.data.msa.Metadata;\r
  38 import compbio.data.msa.MsaWS;\r
  39 import compbio.data.msa.SequenceAnnotation;\r
  40 import compbio.data.sequence.Alignment;\r
  41 import compbio.data.sequence.FastaSequence;\r
  42 import compbio.data.sequence.ScoreManager;\r
  43 import compbio.data.sequence.SequenceUtil;\r
  44 import compbio.metadata.JobStatus;\r
  45 import compbio.metadata.JobSubmissionException;\r
  46 import compbio.metadata.Limit;\r
  47 import compbio.metadata.LimitsManager;\r
  48 import compbio.metadata.Option;\r
  49 import compbio.metadata.Preset;\r
  50 import compbio.metadata.PresetManager;\r
  51 import compbio.metadata.ResultNotAvailableException;\r
  52 import compbio.metadata.RunnerConfig;\r
  53 import compbio.metadata.UnsupportedRuntimeException;\r
  54 import compbio.metadata.WrongParameterException;\r
  55 \r
  56 /**\r
  57  * Class for testing web services\r
  58  * \r
  59  * @author pvtroshin\r
  60  * \r
  61  * @version 1.0 February 2010\r
  62  */\r
  63 public class WSTester {\r
  64 \r
  65         private static Logger log = Logger.getLogger(WSTester.class);\r
  66         /**\r
  67          * Sequences to be used as input for all WS\r
  68          */\r
  69         static final String fastaInput = ">Foo\n"\r
  70                         + "MTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV"\r
  71                         + "\n>Bar\n"\r
  72                         + "ASDAAPEHPGIALWLHALEDAGQAEAAAAYTRAHQLLPEEPYITAQLLNAVA";\r
  73 \r
  74         static final String fastaAlignment = ">Foo\r\n"\r
  75                         + "MTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV--------\r\n"\r
  76                         + ">Bar\r\n"\r
  77                         + "ASDAAPEH------------PGIALWLHALE-DAGQAEAAA---AYTRAHQLLPEEPYITAQLLNAVA\r\n"\r
  78                         + "";\r
  79 \r
  80         static final List<FastaSequence> seqs = loadSeqs();\r
  81 \r
  82         private static final String FAILED = "FAILED";\r
  83         private static final String OK = "OK";\r
  84 \r
  85         private static final String UNSUPPORTED = "UNSUPPORTED";\r
  86 \r
  87         /**\r
  88          * Converting input to a form accepted by WS\r
  89          * \r
  90          * @return List of FastaSequence records\r
  91          */\r
  92         static List<FastaSequence> loadSeqs() {\r
  93                 try {\r
  94                         return SequenceUtil.readFasta(new ByteArrayInputStream(fastaInput\r
  95                                         .getBytes()));\r
  96                 } catch (IOException ignored) {\r
  97                         // Should not happen as a source is not a external stream\r
  98                         ignored.printStackTrace();\r
  99                 }\r
 100                 return null;\r
 101         }\r
 102 \r
 103         /**\r
 104          * Converting input to a form accepted by WS\r
 105          * \r
 106          * @return List of FastaSequence records\r
 107          */\r
 108         static List<FastaSequence> loadAlignment() {\r
 109                 try {\r
 110                         return SequenceUtil.readFasta(new ByteArrayInputStream(\r
 111                                         fastaAlignment.getBytes()));\r
 112                 } catch (IOException ignored) {\r
 113                         // Should not happen as a source is not a external stream\r
 114                         ignored.printStackTrace();\r
 115                 }\r
 116                 return null;\r
 117         }\r
 118 \r
 119         private final PrintWriter writer;\r
 120 \r
 121         public WSTester(PrintWriter writer) {\r
 122                 this.writer = writer;\r
 123         }\r
 124 \r
 125         /**\r
 126          * Prints usage\r
 127          */\r
 128         void printUsage() {\r
 129                 writer.println("Usage: <Class or Jar file name> " + hostkey\r
 130                                 + pseparator + "host_and_context " + "<" + servicekey\r
 131                                 + pseparator + "serviceName>");\r
 132                 writer.println();\r
 133                 writer.println(hostkey\r
 134                                 + pseparator\r
 135                                 + "<host_and_context> - a full URL to the JABAWS web server including context path e.g. http://10.31.1.159:8080/ws");\r
 136                 writer.println(servicekey\r
 137                                 + pseparator\r
 138                                 + "<ServiceName> - optional if unspecified all services are tested otherwise one of "\r
 139                                 + Arrays.toString(Services.values()));\r
 140                 writer.println();\r
 141 \r
 142         }\r
 143 \r
 144         /**\r
 145          * Calls alignment with preset\r
 146          * \r
 147          * @param <T>\r
 148          * @param msaws\r
 149          * @param presets\r
 150          *            list of the Preset\r
 151          * @throws UnsupportedRuntimeException\r
 152          */\r
 153         <T> boolean presetAlign(MsaWS<T> msaws, List<Preset<T>> presets)\r
 154                         throws UnsupportedRuntimeException {\r
 155                 boolean succeed = false;\r
 156                 for (Preset<T> preset : presets) {\r
 157                         writer.print("Aligning with preset '" + preset.getName() + "'... ");\r
 158                         Alignment al = null;\r
 159                         try {\r
 160                                 String taskId = msaws.presetAlign(seqs, preset);\r
 161                                 al = msaws.getResult(taskId);\r
 162                                 if (al != null) {\r
 163                                         writer.println(OK);\r
 164                                 }\r
 165                                 succeed = true;\r
 166                         } catch (UnsupportedRuntimeException e) {\r
 167                                 writer.println(FAILED);\r
 168                                 // If executable is not supported than none of the presets are\r
 169                                 // going to work\r
 170                                 throw new UnsupportedRuntimeException(e);\r
 171                         } catch (JobSubmissionException e) {\r
 172                                 // TODO custom message\r
 173                                 writer.println(FAILED);\r
 174                                 writer.println();\r
 175                                 writer.println(e.getLocalizedMessage());\r
 176                                 e.printStackTrace(writer);\r
 177                                 continue;\r
 178                         } catch (WrongParameterException e) {\r
 179                                 // TODO custom message\r
 180                                 writer.println(FAILED);\r
 181                                 writer.println();\r
 182                                 writer.println(e.getLocalizedMessage());\r
 183                                 e.printStackTrace(writer);\r
 184                                 continue;\r
 185                         } catch (ResultNotAvailableException e) {\r
 186                                 // TODO custom message\r
 187                                 writer.println(FAILED);\r
 188                                 writer.println();\r
 189                                 writer.println(e.getLocalizedMessage());\r
 190                                 e.printStackTrace(writer);\r
 191                                 continue;\r
 192                         }\r
 193                 }\r
 194                 return succeed;\r
 195         }\r
 196 \r
 197         private <T> boolean testMsaWS(MsaWS<T> msaws)\r
 198                         throws UnsupportedRuntimeException {\r
 199 \r
 200                 boolean succeed = testDefaultAlignment(msaws);\r
 201 \r
 202                 // If exception above is thrown than the tests below is not run\r
 203 \r
 204                 PresetManager<T> pmanager = msaws.getPresets();\r
 205                 if (pmanager != null && pmanager.getPresets().size() > 0) {\r
 206                         writer.println("Testing alignment with presets:");\r
 207                         List<Preset<T>> plist = pmanager.getPresets();\r
 208                         succeed = !succeed ? presetAlign(msaws, plist) : succeed;\r
 209                 }\r
 210                 testMetadata(msaws);\r
 211                 return succeed;\r
 212         }\r
 213         /**\r
 214          * Call most of web services functions and check the output\r
 215          * \r
 216          * @param <T>\r
 217          *            web service type\r
 218          * @param msaws\r
 219          * @throws UnsupportedRuntimeException\r
 220          *             is thrown if the connection to a web service was made, but\r
 221          *             the web service is not functional. e.g. when native\r
 222          *             executable does not exists for a server platform\r
 223          */\r
 224         @SuppressWarnings("unchecked")\r
 225         public <T> boolean checkService(JABAService wservice) {\r
 226                 try {\r
 227                         if (wservice == null) {\r
 228                                 throw new NullPointerException(\r
 229                                                 "JABAService instance must be provided!");\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((SequenceAnnotation<T>) wservice);\r
 235                         } else {\r
 236                                 throw new UnsupportedOperationException("The service: "\r
 237                                                 + wservice.getClass() + " is not supported! ");\r
 238                         }\r
 239                 } catch (UnsupportedRuntimeException e) {\r
 240                         writer.println(e.getLocalizedMessage());\r
 241                         e.printStackTrace(writer);\r
 242                         return false;\r
 243                 }\r
 244         }\r
 245 \r
 246         private <T> boolean testSequenceAnnotationWS(SequenceAnnotation<T> wservice)\r
 247                         throws UnsupportedRuntimeException {\r
 248                 boolean success = testDefaultAnalyse(loadAlignment(), wservice, null,\r
 249                                 null);\r
 250                 PresetManager<T> presetman = wservice.getPresets();\r
 251                 if (presetman != null) {\r
 252                         List<Preset<T>> presets = presetman.getPresets();\r
 253                         if (presets != null && !presets.isEmpty()) {\r
 254                                 Preset<T> preset = presets.get(0);\r
 255                                 success = testDefaultAnalyse(loadAlignment(), wservice, preset,\r
 256                                                 null);\r
 257                         }\r
 258                 }\r
 259                 testMetadata(wservice);\r
 260                 return success;\r
 261         }\r
 262 \r
 263         <T> boolean testDefaultAnalyse(List<FastaSequence> fastalist,\r
 264                         SequenceAnnotation<T> wsproxy, Preset<T> preset,\r
 265                         List<Option<T>> customOptions) throws UnsupportedRuntimeException {\r
 266 \r
 267                 ScoreManager scores = null;\r
 268                 try {\r
 269                         String jobId = null;\r
 270                         if (customOptions != null) {\r
 271                                 jobId = wsproxy.customAnalize(fastalist, customOptions);\r
 272                         } else if (preset != null) {\r
 273                                 jobId = wsproxy.presetAnalize(fastalist, preset);\r
 274                         } else {\r
 275                                 jobId = wsproxy.analize(fastalist);\r
 276                         }\r
 277                         writer.println("\n\ncalling analise.........");\r
 278                         Thread.sleep(1000);\r
 279                         scores = wsproxy.getAnnotation(jobId);\r
 280 \r
 281                 } catch (JobSubmissionException e) {\r
 282                         writer.println("Exception while submitting job to a web server. "\r
 283                                         + "Exception details are below:");\r
 284                         e.printStackTrace(writer);\r
 285                 } catch (ResultNotAvailableException e) {\r
 286                         writer.println("Exception while waiting for results. "\r
 287                                         + "Exception details are below:");\r
 288                         e.printStackTrace(writer);\r
 289                 } catch (InterruptedException e) {\r
 290                         // ignore and propagate an interruption\r
 291                         Thread.currentThread().interrupt();\r
 292                         writer.println("Exception while waiting for results. "\r
 293                                         + "Exception details are below:");\r
 294                         e.printStackTrace(writer);\r
 295                 } catch (WrongParameterException e) {\r
 296                         writer.println("Exception while parsing the web method input parameters. "\r
 297                                         + "Exception details are below:");\r
 298                         e.printStackTrace(writer);\r
 299                 }\r
 300                 return scores != null;\r
 301         }\r
 302 \r
 303         private <T> void testMetadata(Metadata<T> msaws)\r
 304                         throws UnsupportedRuntimeException {\r
 305 \r
 306                 writer.print("Querying presets...");\r
 307                 PresetManager<T> pmanager = msaws.getPresets();\r
 308                 if (pmanager != null && pmanager.getPresets().size() > 0) {\r
 309                         writer.println(OK);\r
 310                 } else {\r
 311                         writer.println(UNSUPPORTED);\r
 312                 }\r
 313 \r
 314                 writer.print("Querying Parameters...");\r
 315                 RunnerConfig<T> options = msaws.getRunnerOptions();\r
 316                 if (options != null && options.getArguments().size() > 0) {\r
 317                         writer.println(OK);\r
 318                 } else {\r
 319                         writer.println(UNSUPPORTED);\r
 320                 }\r
 321 \r
 322                 writer.print("Querying Limits...");\r
 323                 LimitsManager<T> limits = msaws.getLimits();\r
 324                 if (limits != null && limits.getLimits().size() > 0) {\r
 325                         writer.println(OK);\r
 326                 } else {\r
 327                         writer.println(UNSUPPORTED);\r
 328                 }\r
 329 \r
 330                 writer.print("Querying Local Engine Limits...");\r
 331                 Limit<T> localLimit = msaws\r
 332                                 .getLimit(PresetManager.LOCAL_ENGINE_LIMIT_PRESET);\r
 333                 if (localLimit != null) {\r
 334                         writer.println(OK);\r
 335                 } else {\r
 336                         writer.println(UNSUPPORTED);\r
 337                 }\r
 338         }\r
 339 \r
 340         /**\r
 341          * Align using default settings\r
 342          * \r
 343          * @param <T>\r
 344          * @param msaws\r
 345          * @throws UnsupportedRuntimeException\r
 346          */\r
 347         public <T> boolean testDefaultAlignment(MsaWS<T> msaws)\r
 348                         throws UnsupportedRuntimeException {\r
 349                 writer.print("Testing alignment with default parameters:");\r
 350                 Alignment al = null;\r
 351                 boolean succeed = false;\r
 352                 try {\r
 353                         String taskId = msaws.align(seqs);\r
 354                         writer.print("\nQuerying job status...");\r
 355                         JobStatus status = msaws.getJobStatus(taskId);\r
 356                         while (status != JobStatus.FINISHED) {\r
 357                                 Thread.sleep(1000);\r
 358                                 status = msaws.getJobStatus(taskId);\r
 359                         }\r
 360                         writer.println(OK);\r
 361                         writer.print("Retrieving results...");\r
 362                         al = msaws.getResult(taskId);\r
 363                         succeed = true;\r
 364                 } catch (ResultNotAvailableException e) {\r
 365                         writer.println(FAILED);\r
 366                         writer.println(e.getLocalizedMessage());\r
 367                         e.printStackTrace(writer);\r
 368                 } catch (JobSubmissionException e) {\r
 369                         writer.println(FAILED);\r
 370                         writer.println();\r
 371                         writer.println(e.getLocalizedMessage());\r
 372                         e.printStackTrace(writer);\r
 373                 } catch (InterruptedException e) {\r
 374                         writer.println(FAILED);\r
 375                         writer.println();\r
 376                         writer.println(e.getLocalizedMessage());\r
 377                         e.printStackTrace(writer);\r
 378                 }\r
 379                 if (al != null) {\r
 380                         writer.println(OK);\r
 381                 }\r
 382                 return succeed;\r
 383         }\r
 384 \r
 385         /**\r
 386          * Connect to a WS using the host and the service name\r
 387          * \r
 388          * @param <T>\r
 389          * @param host\r
 390          * @param service\r
 391          * @return\r
 392          */\r
 393         <T> JABAService connect(String host, Services service) {\r
 394                 JABAService jabaservice = null;\r
 395                 try {\r
 396                         writer.print("Connecting to service " + service + " on " + host\r
 397                                         + " ... ");\r
 398                         jabaservice = Jws2Client.connect(host, service);\r
 399                         writer.println(OK);\r
 400                 } catch (WebServiceException e) {\r
 401                         writer.println(FAILED);\r
 402                         writer.println(e.getLocalizedMessage());\r
 403                         e.printStackTrace(writer);\r
 404                 }\r
 405                 return jabaservice;\r
 406         }\r
 407 \r
 408         /**\r
 409          * Test JWS2 web services\r
 410          * \r
 411          * @param <T>\r
 412          *            web service type\r
 413          * @param args\r
 414          *            -h=<Your web application server host name, port and JWS2\r
 415          *            context path>\r
 416          * \r
 417          *            -s=<ServiceName> which is optional. If service name is not\r
 418          *            provided then all known JWS2 web services are tested\r
 419          * @throws IOException\r
 420          */\r
 421         public static <T> void main(String[] args) throws IOException {\r
 422                 WSTester tester = new WSTester(new PrintWriter(System.out, true));\r
 423                 if (args == null || args.length < 1) {\r
 424                         tester.printUsage();\r
 425                         System.exit(0);\r
 426                 }\r
 427                 String host = CmdHelper.getHost(args);\r
 428                 String serviceName = CmdHelper.getServiceName(args);\r
 429                 if (!Jws2Client.validURL(host)) {\r
 430                         tester.writer\r
 431                                         .println("<host_and_context> parameter is not provided or is incorrect!");\r
 432                         System.exit(1);\r
 433                 }\r
 434                 boolean succeed = false;\r
 435                 MsaWS<T> msaws = null;\r
 436                 if (serviceName != null) {\r
 437                         Services service = Services.getService(serviceName);\r
 438                         if (service == null) {\r
 439                                 tester.writer.println("Service '" + serviceName\r
 440                                                 + "' is not supported. Valid values are: "\r
 441                                                 + Arrays.toString(Services.values()));\r
 442                                 tester.writer.println();\r
 443                                 tester.printUsage();\r
 444                                 System.exit(1);\r
 445                         }\r
 446 \r
 447                         msaws = (MsaWS<T>) tester.connect(host, service);\r
 448                         if (msaws == null) {\r
 449                                 System.exit(1);\r
 450                         }\r
 451                         try {\r
 452                                 succeed = tester.checkService(msaws);\r
 453                         } finally {\r
 454                                 ((Closeable) msaws).close();\r
 455                         }\r
 456                         // TODO test results printing!\r
 457                         tester.reportResults(service, succeed);\r
 458                         System.exit(0);\r
 459                 }\r
 460 \r
 461                 tester.writer\r
 462                                 .println("<ServiceName> is not provided checking all known services...");\r
 463 \r
 464                 for (Services serv : Services.values()) {\r
 465                         tester.writer.println();\r
 466                         msaws = (MsaWS<T>) tester.connect(host, serv);\r
 467                         if (msaws == null) {\r
 468                                 continue;\r
 469                         }\r
 470                         try {\r
 471                                 succeed = tester.checkService(msaws);\r
 472                         } finally {\r
 473                                 ((Closeable) msaws).close();\r
 474                         }\r
 475                         tester.reportResults(serv, succeed);\r
 476                 }\r
 477 \r
 478         }\r
 479         private void reportResults(Services serv, boolean succeed) {\r
 480                 if (succeed) {\r
 481                         writer.println("Check is completed. The Service " + serv\r
 482                                         + " IS WORKING");\r
 483                 } else {\r
 484                         writer.println("Check is completed. The Service " + serv\r
 485                                         + " HAS SOME PROBLEMS");\r
 486                 }\r
 487         }\r
 488 }\r