webservices/compbio/ws/client/WSTester.java

   1 /* Copyright (c) 2011 Peter Troshin\r
   2  * Copyright (c) 2013 Alexander Sherstnev\r
   3  *  \r
   4  *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0\r
   5  * \r
   6  *  This library is free software; you can redistribute it and/or modify it under the terms of the\r
   7  *  Apache License version 2 as published by the Apache Software Foundation\r
   8  * \r
   9  *  This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
  10  *  even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
  11  *  License for more details.\r
  12  * \r
  13  *  A copy of the license is in apache_license.txt. It is also available here:\r
  14  * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
  15  * \r
  16  * Any republication or derived work distributed in source code form\r
  17  * must include this copyright and license notice.\r
  18  */\r
  19 \r
  20 package compbio.ws.client;\r
  21 \r
  22 import static compbio.ws.client.Constraints.hostkey;\r
  23 import static compbio.ws.client.Constraints.pseparator;\r
  24 import static compbio.ws.client.Constraints.servicekey;\r
  25 \r
  26 import java.io.ByteArrayInputStream;\r
  27 import java.io.Closeable;\r
  28 import java.io.IOException;\r
  29 import java.io.PrintWriter;\r
  30 import java.net.ConnectException;\r
  31 import java.net.MalformedURLException;\r
  32 import java.net.URL;\r
  33 import java.util.Arrays;\r
  34 import java.util.List;\r
  35 import java.util.logging.Level;\r
  36 \r
  37 import javax.xml.ws.Service;\r
  38 import javax.xml.ws.WebServiceException;\r
  39 \r
  40 import compbio.data.msa.JABAService;\r
  41 import compbio.data.msa.Metadata;\r
  42 import compbio.data.msa.MsaWS;\r
  43 import compbio.data.msa.SequenceAnnotation;\r
  44 import compbio.data.sequence.Alignment;\r
  45 import compbio.data.sequence.FastaSequence;\r
  46 import compbio.data.sequence.ScoreManager;\r
  47 import compbio.data.sequence.SequenceUtil;\r
  48 import compbio.metadata.JobStatus;\r
  49 import compbio.metadata.Limit;\r
  50 import compbio.metadata.LimitsManager;\r
  51 import compbio.metadata.Option;\r
  52 import compbio.metadata.Preset;\r
  53 import compbio.metadata.PresetManager;\r
  54 import compbio.metadata.RunnerConfig;\r
  55 import compbio.metadata.UnsupportedRuntimeException;\r
  56 import compbio.util.FileUtil;\r
  57 import compbio.util.Util;\r
  58 \r
  59 /**\r
  60  * Class for testing web services\r
  61  * \r
  62  * @author pvtroshin\r
  63  * \r
  64  * @version 1.5 February 2013\r
  65  */\r
  66 public class WSTester {\r
  67 \r
  68         /**\r
  69          * Test sequences to be used as input for WS\r
  70          */\r
  71         public static final String fastaInput2records = \r
  72                         ">Foo\nMTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV\n"\r
  73                 +   ">Bar\nASDAAPEHPGIALWLHALEDAGQAEAAAAYTRAHQLLPEEPYITAQLLNAVA\n";\r
  74         public static final String fastaInput1record = \r
  75                         ">Foo\nMTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV\n";\r
  76         public static final String fastaAlignment = \r
  77                         ">Foo\nMTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV--------\n"\r
  78                 +   ">Bar\nASDAAPEH------------PGIALWLHALE-DAGQAEAAA---AYTRAHQLLPEEPYITAQLLNAVA\n";\r
  79         public static final String fastaRNAAlignment = \r
  80                         ">Foo\nC-UUGCGUUAAUGAGAACAGAAACG-UAAA--CUAUAA-CCUAG-G-GGUUUCUGUUGGAUGGUUG----GCAAC\n"\r
  81                 +   ">Bar\nG-UGGCGCUUAUGACGCAGUUGUCU-UAAA-CUCGAAC--UCGA-GCGGGCAAUUGCUGAU-UACGAUUAACCAC\n";\r
  82 \r
  83         /**\r
  84          * Status strings\r
  85          */\r
  86         private static final String FAILED = "FAILED";\r
  87         private static final String OK = "OK";\r
  88         private static final String UNSUPPORTED = "UNSUPPORTED";\r
  89 \r
  90         /**\r
  91          * Converting input to a form accepted by WS\r
  92          * \r
  93          * @return List of FastaSequence records\r
  94          */\r
  95         private static List<FastaSequence> loadSeqs(int nLines) {\r
  96                 try {\r
  97                         if (nLines == 1) {\r
  98                                 return SequenceUtil.readFasta(new ByteArrayInputStream(fastaInput1record.getBytes()));\r
  99                         }\r
 100                         return SequenceUtil.readFasta(new ByteArrayInputStream(fastaInput2records.getBytes()));\r
 101                 } catch (IOException ignored) {\r
 102                         // Should not happen as a source is not a external stream\r
 103                         ignored.printStackTrace();\r
 104                 }\r
 105                 return null;\r
 106         }\r
 107 \r
 108         /**\r
 109          * Converting input to a form accepted by WS\r
 110          * \r
 111          * @return List of FastaSequence records\r
 112          */\r
 113         private static List<FastaSequence> loadAlignment() {\r
 114                 try {\r
 115                         return SequenceUtil.readFasta(new ByteArrayInputStream(\r
 116                                         fastaAlignment.getBytes()));\r
 117                 } catch (IOException ignored) {\r
 118                         // Should not happen as a source is not a external stream\r
 119                         ignored.printStackTrace();\r
 120                 }\r
 121                 return null;\r
 122         }\r
 123         /**\r
 124          * Converting input to a form accepted by WS\r
 125          * \r
 126          * @return List of FastaSequence records with aligned RNA sequences\r
 127          */\r
 128         private static List<FastaSequence> loadRNAAlignment() {\r
 129                 try {\r
 130                         return SequenceUtil.readFasta(new ByteArrayInputStream(fastaRNAAlignment.getBytes()));\r
 131                 } catch (IOException ignored) {\r
 132                         // Should not happen as a source is not a external stream\r
 133                         ignored.printStackTrace();\r
 134                 }\r
 135                 return null;\r
 136         }\r
 137 \r
 138         private final PrintWriter writer;\r
 139         private final String hostname;\r
 140 \r
 141         /**\r
 142          * Construct an instance of JABAWS tester\r
 143          * \r
 144          * @param hostname\r
 145          *            - fully qualified host and context name of JABAWS e.g.\r
 146          *            http://nanna.cluster.lifesci.dundee.ac.uk:8080/jaba\r
 147          * @param writer\r
 148          *            a PrintWriter instance to writer test log to.\r
 149          */\r
 150         public WSTester(String hostname, PrintWriter writer) {\r
 151                 if (Util.isEmpty(hostname)) {\r
 152                         throw new NullPointerException("Hostname must be provided!");\r
 153                 }\r
 154                 this.hostname = hostname;\r
 155                 this.writer = writer;\r
 156         }\r
 157 \r
 158         /**\r
 159          * Prints usage\r
 160          */\r
 161         static void printUsage() {\r
 162                 System.out.println("Usage: <Class or Jar file name> " + hostkey\r
 163                                 + pseparator + "host_and_context " + "<" + servicekey\r
 164                                 + pseparator + "serviceName>");\r
 165                 System.out.println();\r
 166                 System.out.println(hostkey\r
 167                                                 + pseparator\r
 168                                                 + "<host_and_context> - a full URL to the JABAWS web server including context path e.g. http://10.31.1.159:8080/ws");\r
 169                 System.out.println(servicekey\r
 170                                                 + pseparator\r
 171                                                 + "<ServiceName> - optional if unspecified all services are tested otherwise one of "\r
 172                                                 + Arrays.toString(Services.values()));\r
 173                 System.out.println();\r
 174 \r
 175         }\r
 176 \r
 177         /**\r
 178          * Calls alignment with preset\r
 179          * \r
 180          * @param <T>\r
 181          * @param msaws\r
 182          * @param presets\r
 183          *            list of the Preset\r
 184          * @throws UnsupportedRuntimeException\r
 185          */\r
 186         private <T> boolean presetAlign(MsaWS<T> msaws, List<Preset<T>> presets)\r
 187                         throws UnsupportedRuntimeException {\r
 188                 boolean succeed = false;\r
 189                 for (Preset<T> preset : presets) {\r
 190                         writer.print("Aligning with preset '" + preset.getName() + "'... ");\r
 191                         Alignment al = null;\r
 192                         try {\r
 193                                 String taskId = msaws.presetAlign(loadSeqs(2), preset);\r
 194                                 al = msaws.getResult(taskId);\r
 195                                 if (al != null) {\r
 196                                         writer.println(OK);\r
 197                                 }\r
 198                                 succeed = true;\r
 199                         } catch (Exception e) {\r
 200                                 if (e instanceof UnsupportedRuntimeException) {\r
 201                                         // If executable is not supported than none of the presets\r
 202                                         // are\r
 203                                         // going to work\r
 204                                         throw (UnsupportedRuntimeException) e;\r
 205                                 } else {\r
 206                                         reportException(e);\r
 207                                 }\r
 208                                 continue;\r
 209                         }\r
 210                 }\r
 211                 return succeed;\r
 212         }\r
 213 \r
 214         private <T> boolean testMsaWS(MsaWS<T> msaws, Services service) throws Exception {\r
 215                 assert msaws != null;\r
 216 \r
 217                 boolean succeed = testDefaultAlignment(msaws, service);\r
 218                 // If exception above is thrown than the tests below is not run\r
 219 \r
 220                 PresetManager<T> pmanager = msaws.getPresets();\r
 221                 if (pmanager != null && pmanager.getPresets().size() > 0) {\r
 222                         writer.println("Testing alignment with presets:");\r
 223                         List<Preset<T>> plist = pmanager.getPresets();\r
 224                         succeed = !succeed ? presetAlign(msaws, plist) : succeed;\r
 225                 }\r
 226                 testMetadata(msaws);\r
 227                 return succeed;\r
 228         }\r
 229         /**\r
 230          * Call most of web services functions and check the output\r
 231          * \r
 232          * @param <T>\r
 233          *            web service type\r
 234          * @param msaws\r
 235          * @throws UnsupportedRuntimeException\r
 236          *             is thrown if the connection to a web service was made, but\r
 237          *             the web service is not functional. e.g. when native\r
 238          *             executable does not exists for a server platform\r
 239          */\r
 240         @SuppressWarnings("unchecked")\r
 241         private <T> boolean checkService(JABAService wservice, Services service) {\r
 242                 try {\r
 243                         if (wservice == null) {\r
 244                                 throw new NullPointerException("JABAService instance must be provided!");\r
 245                         }\r
 246 \r
 247                         if (wservice instanceof MsaWS) {\r
 248                                 return testMsaWS((MsaWS<T>) wservice, service);\r
 249                         } else if (wservice instanceof SequenceAnnotation) {\r
 250                                 return testSequenceAnnotationWS(\r
 251                                                 (SequenceAnnotation<T>) wservice, service);\r
 252                         } else {\r
 253                                 throw new UnsupportedOperationException("The service: " + 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 annotation test.........");\r
 264 \r
 265                 List<FastaSequence> input = loadSeqs(2);\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. Exception details are below:");\r
 312                 writer.println(e.getLocalizedMessage());\r
 313                 e.printStackTrace(writer);\r
 314         }\r
 315 \r
 316         private <T> void testMetadata(Metadata<T> msaws)\r
 317                         throws UnsupportedRuntimeException {\r
 318 \r
 319                 writer.print("Querying presets...");\r
 320                 PresetManager<T> pmanager = msaws.getPresets();\r
 321                 if (pmanager != null && pmanager.getPresets().size() > 0) {\r
 322                         writer.println(OK);\r
 323                 } else {\r
 324                         writer.println(UNSUPPORTED);\r
 325                 }\r
 326 \r
 327                 writer.print("Querying Parameters...");\r
 328                 RunnerConfig<T> options = msaws.getRunnerOptions();\r
 329                 if (options != null && options.getArguments().size() > 0) {\r
 330                         writer.println(OK);\r
 331                 } else {\r
 332                         writer.println(UNSUPPORTED);\r
 333                 }\r
 334 \r
 335                 writer.print("Querying Limits...");\r
 336                 LimitsManager<T> limits = msaws.getLimits();\r
 337                 if (limits != null && limits.getLimits().size() > 0) {\r
 338                         writer.println(OK);\r
 339                         // writer.println("Limits details: \n" + limits.toString());\r
 340                 } else {\r
 341                         writer.println(UNSUPPORTED);\r
 342                 }\r
 343 \r
 344                 writer.print("Querying Local Engine Limits...");\r
 345                 Limit<T> localLimit = msaws\r
 346                                 .getLimit(PresetManager.LOCAL_ENGINE_LIMIT_PRESET);\r
 347                 if (localLimit != null) {\r
 348                         writer.println(OK);\r
 349                 } else {\r
 350                         writer.println(UNSUPPORTED);\r
 351                 }\r
 352         }\r
 353 \r
 354         /**\r
 355          * Align using default settings\r
 356          * \r
 357          * @param <T>\r
 358          * @param msaws\r
 359          * @throws UnsupportedRuntimeException\r
 360          */\r
 361         private <T> boolean testDefaultAlignment(MsaWS<T> msaws, Services service) throws Exception {\r
 362                 writer.print("Testing alignment with default parameters:");\r
 363                 Alignment al = null;\r
 364                 boolean succeed = false;\r
 365                 String taskId;\r
 366 \r
 367                 if (service == Services.JpredWS) {\r
 368                         taskId = msaws.align(loadAlignment());\r
 369                 } else {\r
 370                         taskId = msaws.align(loadSeqs(2));\r
 371                 }\r
 372                 writer.print("\nQuerying job status...");\r
 373                 JobStatus status = msaws.getJobStatus(taskId);\r
 374                 while (status != JobStatus.FINISHED) {\r
 375                         Thread.sleep(1000);\r
 376                         status = msaws.getJobStatus(taskId);\r
 377                 }\r
 378                 writer.println(OK);\r
 379                 writer.print("Retrieving results...");\r
 380                 al = msaws.getResult(taskId);\r
 381                 succeed = true;\r
 382                 if (al != null) {\r
 383                         writer.println(OK);\r
 384                 }\r
 385                 return succeed;\r
 386         }\r
 387         /**\r
 388          * Test JWS2 web services\r
 389          * \r
 390          * @param <T>\r
 391          *            web service type\r
 392          * @param args\r
 393          *            -h=<Your web application server host name, port and JWS2\r
 394          *            context path>\r
 395          * \r
 396          *            -s=<ServiceName> which is optional. If service name is not\r
 397          *            provided then all known JWS2 web services are tested\r
 398          * @throws IOException\r
 399          */\r
 400         public static <T> void main(String[] args) throws IOException {\r
 401 \r
 402                 if (args == null || args.length < 1) {\r
 403                         WSTester.printUsage();\r
 404                         System.exit(0);\r
 405                 }\r
 406                 String host = CmdHelper.getHost(args);\r
 407                 String serviceName = CmdHelper.getServiceName(args);\r
 408                 if (!Jws2Client.validURL(host)) {\r
 409                         System.err.println("<host_and_context> parameter is not provided or is incorrect!");\r
 410                         System.exit(1);\r
 411                 }\r
 412                 WSTester tester = new WSTester(host, new PrintWriter(System.out, true));\r
 413 \r
 414                 if (serviceName != null) {\r
 415                         Services service = Services.getService(serviceName);\r
 416                         if (service == null) {\r
 417                                 tester.writer.println("Service '" + serviceName + "' is not supported. Valid values are: "\r
 418                                                 + Arrays.toString(Services.values()));\r
 419                                 tester.writer.println();\r
 420                                 printUsage();\r
 421                                 System.exit(1);\r
 422                         }\r
 423                         tester.checkService(service);\r
 424                         System.exit(0);\r
 425                 }\r
 426 \r
 427                 tester.writer.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         /**\r
 437          * Connects to a web service by the host and the service name web service type\r
 438          * \r
 439          * @param host\r
 440          *            the fully qualified name of JABAWS server including JABAWS\r
 441          *            context name e.g\r
 442          *            http://nanna.cluster.lifesci.dundee.ac.uk:8080/jaba\r
 443          * @param service\r
 444          *            the name of the JABAWS service to connect to\r
 445          * @return JABAService<T>\r
 446          * @throws WebServiceException\r
 447          * @throws ConnectException\r
 448          *             if fails to connect to the service on the host\r
 449          */\r
 450         private JABAService connect(String host, Services service)\r
 451                         throws WebServiceException, ConnectException {\r
 452                 URL url = null;\r
 453                 System.out.println ("Attempting to connect with " + service.toString() + "...");\r
 454                 try {\r
 455                         url = new URL(host + "/" + service.toString() + "?wsdl");\r
 456                         System.out.println ("URL: " + url.toString());\r
 457                 } catch (MalformedURLException e) {\r
 458                         e.printStackTrace();\r
 459                 }\r
 460                 Service serv = null;\r
 461                 try {\r
 462                         serv = service.getService(url, service.getServiceNamespace());\r
 463                 } catch (WebServiceException wse) {\r
 464                         wse.printStackTrace();\r
 465                 }\r
 466                 if (serv == null) {\r
 467                         throw new ConnectException("Could not connect to " + url + ". Is the server down?");\r
 468                 }\r
 469                 JABAService srv = service.getInterface(serv);\r
 470                 System.out.println ("Connected successfully!");\r
 471                 return srv;\r
 472         }\r
 473 \r
 474         /**\r
 475          * Test JABA web service\r
 476          * \r
 477          * @param service\r
 478          *            the service to test\r
 479          * @return true if the service works as expected, false otherwise\r
 480          * @throws WebServiceException\r
 481          * @throws ConnectException\r
 482          */\r
 483         public boolean checkService(Services service) throws ConnectException,\r
 484                         WebServiceException {\r
 485                 JABAService ws = connect(hostname, service);\r
 486                 if (ws == null) {\r
 487                         String line = "Cannot estabilish the connection to host " + hostname + " with service ";\r
 488                         writer.println(line + service.toString());\r
 489                         return false;\r
 490                 }\r
 491                 boolean succeed = false;\r
 492                 try {\r
 493                         writer.println("Checking service " + service.toString());\r
 494                         succeed = checkService(ws, service);\r
 495                 } finally {\r
 496                         FileUtil.closeSilently(((Closeable) ws));\r
 497                 }\r
 498                 reportResults(service, succeed);\r
 499                 return succeed;\r
 500         }\r
 501 \r
 502         private void reportResults(Services serv, boolean succeed) {\r
 503                 if (succeed) {\r
 504                         writer.println("Check is completed. The Service " + serv + " IS WORKING\n");\r
 505                 } else {\r
 506                         writer.println("Check is aborted. The Service " + serv + " HAS SOME PROBLEMS\n");\r
 507                 }\r
 508         }\r
 509 }\r