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