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 org.apache.log4j.Logger;\r
  33 \r
  34 import compbio.data.msa.JABAService;\r
  35 import compbio.data.msa.Metadata;\r
  36 import compbio.data.msa.MsaWS;\r
  37 import compbio.data.msa.SequenceAnnotation;\r
  38 import compbio.data.sequence.Alignment;\r
  39 import compbio.data.sequence.FastaSequence;\r
  40 import compbio.data.sequence.ScoreManager;\r
  41 import compbio.data.sequence.SequenceUtil;\r
  42 import compbio.metadata.JobStatus;\r
  43 import compbio.metadata.JobSubmissionException;\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.ResultNotAvailableException;\r
  50 import compbio.metadata.RunnerConfig;\r
  51 import compbio.metadata.UnsupportedRuntimeException;\r
  52 import compbio.metadata.WrongParameterException;\r
  53 import compbio.util.FileUtil;\r
  54 import compbio.util.Util;\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         private 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         private 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         private final String hostname;\r
 121 \r
 122         public WSTester(String hostname, PrintWriter writer) {\r
 123                 if (Util.isEmpty(hostname)) {\r
 124                         throw new NullPointerException("Hostname must be provided!");\r
 125                 }\r
 126                 this.hostname = hostname;\r
 127                 this.writer = writer;\r
 128         }\r
 129 \r
 130         /**\r
 131          * Prints usage\r
 132          */\r
 133         static void printUsage() {\r
 134                 System.out.println("Usage: <Class or Jar file name> " + hostkey\r
 135                                 + pseparator + "host_and_context " + "<" + servicekey\r
 136                                 + pseparator + "serviceName>");\r
 137                 System.out.println();\r
 138                 System.out\r
 139                                 .println(hostkey\r
 140                                                 + pseparator\r
 141                                                 + "<host_and_context> - a full URL to the JABAWS web server including context path e.g. http://10.31.1.159:8080/ws");\r
 142                 System.out\r
 143                                 .println(servicekey\r
 144                                                 + pseparator\r
 145                                                 + "<ServiceName> - optional if unspecified all services are tested otherwise one of "\r
 146                                                 + Arrays.toString(Services.values()));\r
 147                 System.out.println();\r
 148 \r
 149         }\r
 150 \r
 151         /**\r
 152          * Calls alignment with preset\r
 153          * \r
 154          * @param <T>\r
 155          * @param msaws\r
 156          * @param presets\r
 157          *            list of the Preset\r
 158          * @throws UnsupportedRuntimeException\r
 159          */\r
 160         private <T> boolean presetAlign(MsaWS<T> msaws, List<Preset<T>> presets)\r
 161                         throws UnsupportedRuntimeException {\r
 162                 boolean succeed = false;\r
 163                 for (Preset<T> preset : presets) {\r
 164                         writer.print("Aligning with preset '" + preset.getName() + "'... ");\r
 165                         Alignment al = null;\r
 166                         try {\r
 167                                 String taskId = msaws.presetAlign(seqs, preset);\r
 168                                 al = msaws.getResult(taskId);\r
 169                                 if (al != null) {\r
 170                                         writer.println(OK);\r
 171                                 }\r
 172                                 succeed = true;\r
 173                         } catch (UnsupportedRuntimeException e) {\r
 174                                 writer.println(FAILED);\r
 175                                 // If executable is not supported than none of the presets are\r
 176                                 // going to work\r
 177                                 throw new UnsupportedRuntimeException(e);\r
 178                         } catch (JobSubmissionException 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 (WrongParameterException 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                         } catch (ResultNotAvailableException e) {\r
 193                                 // TODO custom message\r
 194                                 writer.println(FAILED);\r
 195                                 writer.println();\r
 196                                 writer.println(e.getLocalizedMessage());\r
 197                                 e.printStackTrace(writer);\r
 198                                 continue;\r
 199                         }\r
 200                 }\r
 201                 return succeed;\r
 202         }\r
 203 \r
 204         private <T> boolean testMsaWS(MsaWS<T> msaws)\r
 205                         throws UnsupportedRuntimeException {\r
 206                 assert msaws != null;\r
 207 \r
 208                 boolean succeed = testDefaultAlignment(msaws);\r
 209                 // If exception above is thrown than the tests below is not run\r
 210 \r
 211                 PresetManager<T> pmanager = msaws.getPresets();\r
 212                 if (pmanager != null && pmanager.getPresets().size() > 0) {\r
 213                         writer.println("Testing alignment with presets:");\r
 214                         List<Preset<T>> plist = pmanager.getPresets();\r
 215                         succeed = !succeed ? presetAlign(msaws, plist) : succeed;\r
 216                 }\r
 217                 testMetadata(msaws);\r
 218                 return succeed;\r
 219         }\r
 220         /**\r
 221          * Call most of web services functions and check the output\r
 222          * \r
 223          * @param <T>\r
 224          *            web service type\r
 225          * @param msaws\r
 226          * @throws UnsupportedRuntimeException\r
 227          *             is thrown if the connection to a web service was made, but\r
 228          *             the web service is not functional. e.g. when native\r
 229          *             executable does not exists for a server platform\r
 230          */\r
 231         @SuppressWarnings("unchecked")\r
 232         private <T> boolean checkService(JABAService wservice) {\r
 233                 try {\r
 234                         if (wservice == null) {\r
 235                                 throw new NullPointerException(\r
 236                                                 "JABAService instance must be provided!");\r
 237                         }\r
 238 \r
 239                         if (wservice instanceof MsaWS) {\r
 240                                 return testMsaWS((MsaWS<T>) wservice);\r
 241                         } else if (wservice instanceof SequenceAnnotation) {\r
 242                                 return testSequenceAnnotationWS((SequenceAnnotation<T>) wservice);\r
 243                         } else {\r
 244                                 throw new UnsupportedOperationException("The service: "\r
 245                                                 + wservice.getClass() + " is not supported! ");\r
 246                         }\r
 247                 } catch (UnsupportedRuntimeException e) {\r
 248                         writer.println(e.getLocalizedMessage());\r
 249                         e.printStackTrace(writer);\r
 250                         return false;\r
 251                 }\r
 252         }\r
 253 \r
 254         private <T> boolean testSequenceAnnotationWS(SequenceAnnotation<T> wservice)\r
 255                         throws UnsupportedRuntimeException {\r
 256                 writer.println("Calling analyse.........");\r
 257                 boolean success = testDefaultAnalyse(loadAlignment(), wservice, null,\r
 258                                 null);\r
 259 \r
 260                 PresetManager<T> presetman = wservice.getPresets();\r
 261                 if (presetman != null) {\r
 262                         List<Preset<T>> presets = presetman.getPresets();\r
 263                         if (presets != null && !presets.isEmpty()) {\r
 264                                 Preset<T> preset = presets.get(0);\r
 265                                 writer.println("Calling analyse with Preset.........");\r
 266                                 success = testDefaultAnalyse(loadAlignment(), wservice, preset,\r
 267                                                 null);\r
 268                         }\r
 269                 }\r
 270                 testMetadata(wservice);\r
 271                 return success;\r
 272         }\r
 273 \r
 274         private <T> boolean testDefaultAnalyse(List<FastaSequence> fastalist,\r
 275                         SequenceAnnotation<T> wsproxy, Preset<T> preset,\r
 276                         List<Option<T>> customOptions) throws UnsupportedRuntimeException {\r
 277 \r
 278                 ScoreManager scores = null;\r
 279                 try {\r
 280                         String jobId = null;\r
 281                         if (customOptions != null) {\r
 282                                 jobId = wsproxy.customAnalize(fastalist, customOptions);\r
 283                         } else if (preset != null) {\r
 284                                 jobId = wsproxy.presetAnalize(fastalist, preset);\r
 285                         } else {\r
 286                                 jobId = wsproxy.analize(fastalist);\r
 287                         }\r
 288                         Thread.sleep(1000);\r
 289                         scores = wsproxy.getAnnotation(jobId);\r
 290 \r
 291                 } catch (JobSubmissionException e) {\r
 292                         writer.println("Exception while submitting job to a web server. "\r
 293                                         + "Exception details are below:");\r
 294                         e.printStackTrace(writer);\r
 295                 } catch (ResultNotAvailableException e) {\r
 296                         writer.println("Exception while waiting for results. "\r
 297                                         + "Exception details are below:");\r
 298                         e.printStackTrace(writer);\r
 299                 } catch (InterruptedException e) {\r
 300                         // ignore and propagate an interruption\r
 301                         Thread.currentThread().interrupt();\r
 302                         writer.println("Exception while waiting for results. "\r
 303                                         + "Exception details are below:");\r
 304                         e.printStackTrace(writer);\r
 305                 } catch (WrongParameterException e) {\r
 306                         writer.println("Exception while parsing the web method input parameters. "\r
 307                                         + "Exception details are below:");\r
 308                         e.printStackTrace(writer);\r
 309                 }\r
 310                 return scores != null;\r
 311         }\r
 312 \r
 313         private <T> void testMetadata(Metadata<T> msaws)\r
 314                         throws UnsupportedRuntimeException {\r
 315 \r
 316                 writer.print("Querying presets...");\r
 317                 PresetManager<T> pmanager = msaws.getPresets();\r
 318                 if (pmanager != null && pmanager.getPresets().size() > 0) {\r
 319                         writer.println(OK);\r
 320                 } else {\r
 321                         writer.println(UNSUPPORTED);\r
 322                 }\r
 323 \r
 324                 writer.print("Querying Parameters...");\r
 325                 RunnerConfig<T> options = msaws.getRunnerOptions();\r
 326                 if (options != null && options.getArguments().size() > 0) {\r
 327                         writer.println(OK);\r
 328                 } else {\r
 329                         writer.println(UNSUPPORTED);\r
 330                 }\r
 331 \r
 332                 writer.print("Querying Limits...");\r
 333                 LimitsManager<T> limits = msaws.getLimits();\r
 334                 if (limits != null && limits.getLimits().size() > 0) {\r
 335                         writer.println(OK);\r
 336                 } else {\r
 337                         writer.println(UNSUPPORTED);\r
 338                 }\r
 339 \r
 340                 writer.print("Querying Local Engine Limits...");\r
 341                 Limit<T> localLimit = msaws\r
 342                                 .getLimit(PresetManager.LOCAL_ENGINE_LIMIT_PRESET);\r
 343                 if (localLimit != null) {\r
 344                         writer.println(OK);\r
 345                 } else {\r
 346                         writer.println(UNSUPPORTED);\r
 347                 }\r
 348         }\r
 349 \r
 350         /**\r
 351          * Align using default settings\r
 352          * \r
 353          * @param <T>\r
 354          * @param msaws\r
 355          * @throws UnsupportedRuntimeException\r
 356          */\r
 357         private <T> boolean testDefaultAlignment(MsaWS<T> msaws)\r
 358                         throws UnsupportedRuntimeException {\r
 359                 writer.print("Testing alignment with default parameters:");\r
 360                 Alignment al = null;\r
 361                 boolean succeed = false;\r
 362                 try {\r
 363                         String taskId = msaws.align(seqs);\r
 364                         writer.print("\nQuerying job status...");\r
 365                         JobStatus status = msaws.getJobStatus(taskId);\r
 366                         while (status != JobStatus.FINISHED) {\r
 367                                 Thread.sleep(1000);\r
 368                                 status = msaws.getJobStatus(taskId);\r
 369                         }\r
 370                         writer.println(OK);\r
 371                         writer.print("Retrieving results...");\r
 372                         al = msaws.getResult(taskId);\r
 373                         succeed = true;\r
 374                 } catch (Exception e) {\r
 375                         if (e instanceof UnsupportedRuntimeException) {\r
 376                                 throw (UnsupportedRuntimeException) e;\r
 377                         } else {\r
 378                                 writer.println(FAILED);\r
 379                                 writer.println(e.getLocalizedMessage());\r
 380                                 e.printStackTrace(writer);\r
 381                         }\r
 382                 }\r
 383                 if (al != null) {\r
 384                         writer.println(OK);\r
 385                 }\r
 386                 return succeed;\r
 387         }\r
 388 \r
 389         /**\r
 390          * Test JWS2 web services\r
 391          * \r
 392          * @param <T>\r
 393          *            web service type\r
 394          * @param args\r
 395          *            -h=<Your web application server host name, port and JWS2\r
 396          *            context path>\r
 397          * \r
 398          *            -s=<ServiceName> which is optional. If service name is not\r
 399          *            provided then all known JWS2 web services are tested\r
 400          * @throws IOException\r
 401          */\r
 402         public static <T> void main(String[] args) throws IOException {\r
 403 \r
 404                 if (args == null || args.length < 1) {\r
 405                         WSTester.printUsage();\r
 406                         System.exit(0);\r
 407                 }\r
 408                 String host = CmdHelper.getHost(args);\r
 409                 String serviceName = CmdHelper.getServiceName(args);\r
 410                 if (!Jws2Client.validURL(host)) {\r
 411                         System.err\r
 412                                         .println("<host_and_context> parameter is not provided or is incorrect!");\r
 413                         System.exit(1);\r
 414                 }\r
 415                 WSTester tester = new WSTester(host, new PrintWriter(System.out, true));\r
 416 \r
 417                 if (serviceName != null) {\r
 418                         Services service = Services.getService(serviceName);\r
 419                         if (service == null) {\r
 420                                 tester.writer.println("Service '" + serviceName\r
 421                                                 + "' is not supported. Valid values are: "\r
 422                                                 + Arrays.toString(Services.values()));\r
 423                                 tester.writer.println();\r
 424                                 printUsage();\r
 425                                 System.exit(1);\r
 426                         }\r
 427                         tester.checkService(service);\r
 428                         System.exit(0);\r
 429                 }\r
 430 \r
 431                 tester.writer\r
 432                                 .println("<ServiceName> is not provided checking all known services...");\r
 433 \r
 434                 for (Services serv : Services.values()) {\r
 435                         tester.writer.println();\r
 436                         tester.checkService(serv);\r
 437                 }\r
 438 \r
 439         }\r
 440 \r
 441         public boolean checkService(Services service) {\r
 442                 JABAService ws = Jws2Client.connect(hostname, service);\r
 443                 if (ws == null) {\r
 444                         writer.println("Cannot estabilish the connection to host "\r
 445                                         + hostname + " with service " + service.toString());\r
 446                         return false;\r
 447                 }\r
 448                 boolean succeed = false;\r
 449                 try {\r
 450                         writer.println("Checking service " + service.toString());\r
 451                         succeed = checkService(ws);\r
 452                 } finally {\r
 453                         FileUtil.closeSilently(((Closeable) ws));\r
 454                 }\r
 455                 reportResults(service, succeed);\r
 456                 return succeed;\r
 457         }\r
 458 \r
 459         private void reportResults(Services serv, boolean succeed) {\r
 460                 if (succeed) {\r
 461                         writer.println("Check is completed. The Service " + serv\r
 462                                         + " IS WORKING\n");\r
 463                 } else {\r
 464                         writer.println("Check is completed. The Service " + serv\r
 465                                         + " HAS SOME PROBLEMS\n");\r
 466                 }\r
 467         }\r
 468 }\r