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.util.Arrays;\r
  32 import java.util.List;\r
  33 \r
  34 import javax.xml.ws.WebServiceException;\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.Limit;\r
  46 import compbio.metadata.LimitsManager;\r
  47 import compbio.metadata.Option;\r
  48 import compbio.metadata.Preset;\r
  49 import compbio.metadata.PresetManager;\r
  50 import compbio.metadata.RunnerConfig;\r
  51 import compbio.metadata.UnsupportedRuntimeException;\r
  52 import compbio.util.FileUtil;\r
  53 import compbio.util.Util;\r
  54 \r
  55 /**\r
  56  * Class for testing web services\r
  57  * \r
  58  * @author pvtroshin\r
  59  * \r
  60  * @version 1.5 February 2013\r
  61  */\r
  62 public class WSTester {\r
  63 \r
  64         /**\r
  65          * Test sequences to be used as input for WS\r
  66          */\r
  67         public static final String fastaInput2records = \r
  68                         ">Foo\nMTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV\n"\r
  69                 +   ">Bar\nASDAAPEHPGIALWLHALEDAGQAEAAAAYTRAHQLLPEEPYITAQLLNAVA\n";\r
  70         public static final String fastaInput1record = \r
  71                         ">Foo\nMTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV\n";\r
  72         public static final String fastaAlignment = \r
  73                         ">Foo\nMTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV--------\n"\r
  74                 +   ">Bar\nASDAAPEH------------PGIALWLHALE-DAGQAEAAA---AYTRAHQLLPEEPYITAQLLNAVA\n";\r
  75         public static final String fastaRNAAlignment = \r
  76                         ">Foo\nC-UUGCGUUAAUGAGAACAGAAACG-UAAA--CUAUAA-CCUAG-G-GGUUUCUGUUGGAUGGUUG----GCAAC\n"\r
  77                 +   ">Bar\nG-UGGCGCUUAUGACGCAGUUGUCU-UAAA-CUCGAAC--UCGA-GCGGGCAAUUGCUGAU-UACGAUUAACCAC\n";\r
  78 \r
  79         /**\r
  80          * Status strings\r
  81          */\r
  82         private static final String FAILED = "FAILED";\r
  83         private static final String OK = "OK";\r
  84         private static final String UNSUPPORTED = "UNSUPPORTED";\r
  85 \r
  86         /**\r
  87          * Converting input to a form accepted by WS\r
  88          * \r
  89          * @return List of FastaSequence records\r
  90          */\r
  91         private static List<FastaSequence> loadSeqs(int nLines) {\r
  92                 try {\r
  93                         if (nLines == 1) {\r
  94                                 return SequenceUtil.readFasta(new ByteArrayInputStream(fastaInput1record.getBytes()));\r
  95                         }\r
  96                         return SequenceUtil.readFasta(new ByteArrayInputStream(fastaInput2records.getBytes()));\r
  97                 } catch (IOException ignored) {\r
  98                         // Should not happen as a source is not a external stream\r
  99                         ignored.printStackTrace();\r
 100                 }\r
 101                 return null;\r
 102         }\r
 103 \r
 104         /**\r
 105          * Converting input to a form accepted by WS\r
 106          * \r
 107          * @return List of FastaSequence records\r
 108          */\r
 109         private static List<FastaSequence> loadAlignment() {\r
 110                 try {\r
 111                         return SequenceUtil.readFasta(new ByteArrayInputStream(\r
 112                                         fastaAlignment.getBytes()));\r
 113                 } catch (IOException ignored) {\r
 114                         // Should not happen as a source is not a external stream\r
 115                         ignored.printStackTrace();\r
 116                 }\r
 117                 return null;\r
 118         }\r
 119         /**\r
 120          * Converting input to a form accepted by WS\r
 121          * \r
 122          * @return List of FastaSequence records with aligned RNA sequences\r
 123          */\r
 124         private static List<FastaSequence> loadRNAAlignment() {\r
 125                 try {\r
 126                         return SequenceUtil.readFasta(new ByteArrayInputStream(fastaRNAAlignment.getBytes()));\r
 127                 } catch (IOException ignored) {\r
 128                         // Should not happen as a source is not a external stream\r
 129                         ignored.printStackTrace();\r
 130                 }\r
 131                 return null;\r
 132         }\r
 133 \r
 134         private final PrintWriter writer;\r
 135         private final String hostname;\r
 136 \r
 137         /**\r
 138          * Construct an instance of JABAWS tester\r
 139          * \r
 140          * @param hostname\r
 141          *            - fully qualified host and context name of JABAWS e.g.\r
 142          *            http://nanna.cluster.lifesci.dundee.ac.uk:8080/jaba\r
 143          * @param writer\r
 144          *            a PrintWriter instance to writer test log to.\r
 145          */\r
 146         public WSTester(String hostname, PrintWriter writer) {\r
 147                 if (Util.isEmpty(hostname)) {\r
 148                         throw new NullPointerException("Hostname must be provided!");\r
 149                 }\r
 150                 this.hostname = hostname;\r
 151                 this.writer = writer;\r
 152         }\r
 153 \r
 154         /**\r
 155          * Prints usage\r
 156          */\r
 157         static void printUsage() {\r
 158                 System.out.println("Usage: <Class or Jar file name> " + hostkey\r
 159                                 + pseparator + "host_and_context " + "<" + servicekey\r
 160                                 + pseparator + "serviceName>");\r
 161                 System.out.println();\r
 162                 System.out.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.println(servicekey\r
 166                                                 + pseparator\r
 167                                                 + "<ServiceName> - optional if unspecified all services are tested otherwise one of "\r
 168                                                 + Arrays.toString(Services.values()));\r
 169                 System.out.println();\r
 170 \r
 171         }\r
 172 \r
 173         /**\r
 174          * Calls alignment with preset\r
 175          * \r
 176          * @param <T>\r
 177          * @param msaws\r
 178          * @param presets\r
 179          *            list of the Preset\r
 180          * @throws UnsupportedRuntimeException\r
 181          */\r
 182         private <T> boolean presetAlign(MsaWS<T> msaws, List<Preset<T>> presets)\r
 183                         throws UnsupportedRuntimeException {\r
 184                 boolean succeed = false;\r
 185                 for (Preset<T> preset : presets) {\r
 186                         writer.print("Aligning with preset '" + preset.getName() + "'... ");\r
 187                         Alignment al = null;\r
 188                         try {\r
 189                                 String taskId = msaws.presetAlign(loadSeqs(2), preset);\r
 190                                 al = msaws.getResult(taskId);\r
 191                                 if (al != null) {\r
 192                                         writer.println(OK);\r
 193                                 }\r
 194                                 succeed = true;\r
 195                         } catch (Exception e) {\r
 196                                 if (e instanceof UnsupportedRuntimeException) {\r
 197                                         // If executable is not supported than none of the presets\r
 198                                         // are\r
 199                                         // going to work\r
 200                                         throw (UnsupportedRuntimeException) e;\r
 201                                 } else {\r
 202                                         reportException(e);\r
 203                                 }\r
 204                                 continue;\r
 205                         }\r
 206                 }\r
 207                 return succeed;\r
 208         }\r
 209 \r
 210         private <T> boolean testMsaWS(MsaWS<T> msaws, Services service) throws Exception {\r
 211                 assert msaws != null;\r
 212 \r
 213                 boolean succeed = testDefaultAlignment(msaws, service);\r
 214                 // If exception above is thrown than the tests below is not run\r
 215 \r
 216                 PresetManager<T> pmanager = msaws.getPresets();\r
 217                 if (pmanager != null && pmanager.getPresets().size() > 0) {\r
 218                         writer.println("Testing alignment with presets:");\r
 219                         List<Preset<T>> plist = pmanager.getPresets();\r
 220                         succeed = !succeed ? presetAlign(msaws, plist) : succeed;\r
 221                 }\r
 222                 testMetadata(msaws);\r
 223                 return succeed;\r
 224         }\r
 225         /**\r
 226          * Call most of web services functions and check the output\r
 227          * \r
 228          * @param <T>\r
 229          *            web service type\r
 230          * @param msaws\r
 231          * @throws UnsupportedRuntimeException\r
 232          *             is thrown if the connection to a web service was made, but\r
 233          *             the web service is not functional. e.g. when native\r
 234          *             executable does not exists for a server platform\r
 235          */\r
 236         @SuppressWarnings("unchecked")\r
 237         private <T> boolean checkService(JABAService wservice, Services service) {\r
 238                 try {\r
 239                         if (wservice == null) {\r
 240                                 throw new NullPointerException("JABAService instance must be provided!");\r
 241                         }\r
 242 \r
 243                         if (wservice instanceof MsaWS) {\r
 244                                 return testMsaWS((MsaWS<T>) wservice, service);\r
 245                         } else if (wservice instanceof SequenceAnnotation) {\r
 246                                 return testSequenceAnnotationWS(\r
 247                                                 (SequenceAnnotation<T>) wservice, service);\r
 248                         } else {\r
 249                                 throw new UnsupportedOperationException("The service: " + wservice.getClass() + " is not supported! ");\r
 250                         }\r
 251                 } catch (Exception e) {\r
 252                         reportException(e);\r
 253                         return false;\r
 254                 }\r
 255         }\r
 256 \r
 257         private <T> boolean testSequenceAnnotationWS(\r
 258                         SequenceAnnotation<T> wservice, Services service) throws Exception {\r
 259                 writer.print("Calling analyse.........");\r
 260 \r
 261                 List<FastaSequence> input = loadSeqs(2);\r
 262                 if (service == Services.AAConWS ) {\r
 263                         input = loadAlignment();\r
 264                 } else if (service == Services.RNAalifoldWS) {\r
 265                         input = loadRNAAlignment();\r
 266                 }\r
 267                 boolean success = testDefaultAnalyse(input, wservice, null, null);\r
 268 \r
 269                 PresetManager<T> presetman = wservice.getPresets();\r
 270                 if (presetman != null) {\r
 271                         List<Preset<T>> presets = presetman.getPresets();\r
 272                         if (presets != null && !presets.isEmpty()) {\r
 273                                 Preset<T> preset = presets.get(0);\r
 274                                 writer.print("Calling analyse with Preset.........");\r
 275                                 success = testDefaultAnalyse(input, wservice, preset, null);\r
 276                         }\r
 277                 }\r
 278                 testMetadata(wservice);\r
 279                 return success;\r
 280         }\r
 281 \r
 282         private <T> boolean testDefaultAnalyse(List<FastaSequence> fastalist,\r
 283                         SequenceAnnotation<T> wsproxy, Preset<T> preset,\r
 284                         List<Option<T>> customOptions) throws Exception {\r
 285 \r
 286                 ScoreManager scores = null;\r
 287 \r
 288                 String jobId = null;\r
 289                 if (customOptions != null) {\r
 290                         jobId = wsproxy.customAnalize(fastalist, customOptions);\r
 291                 } else if (preset != null) {\r
 292                         jobId = wsproxy.presetAnalize(fastalist, preset);\r
 293                 } else {\r
 294                         jobId = wsproxy.analize(fastalist);\r
 295                 }\r
 296                 Thread.sleep(1000);\r
 297                 scores = wsproxy.getAnnotation(jobId);\r
 298                 if (scores != null) {\r
 299                         writer.println(OK);\r
 300                 }\r
 301 \r
 302                 return scores != null;\r
 303         }\r
 304 \r
 305         private void reportException(Exception e) {\r
 306                 writer.println(FAILED);\r
 307                 writer.println("Exception while waiting for results. "\r
 308                                 + "Exception details are below:");\r
 309                 writer.println(e.getLocalizedMessage());\r
 310                 e.printStackTrace(writer);\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                         // writer.println("Limits details: \n" + limits.toString());\r
 337                 } else {\r
 338                         writer.println(UNSUPPORTED);\r
 339                 }\r
 340 \r
 341                 writer.print("Querying Local Engine Limits...");\r
 342                 Limit<T> localLimit = msaws\r
 343                                 .getLimit(PresetManager.LOCAL_ENGINE_LIMIT_PRESET);\r
 344                 if (localLimit != null) {\r
 345                         writer.println(OK);\r
 346                 } else {\r
 347                         writer.println(UNSUPPORTED);\r
 348                 }\r
 349         }\r
 350 \r
 351         /**\r
 352          * Align using default settings\r
 353          * \r
 354          * @param <T>\r
 355          * @param msaws\r
 356          * @throws UnsupportedRuntimeException\r
 357          */\r
 358         private <T> boolean testDefaultAlignment(MsaWS<T> msaws, Services service) throws Exception {\r
 359                 writer.print("Testing alignment with default parameters:");\r
 360                 Alignment al = null;\r
 361                 boolean succeed = false;\r
 362                 String taskId;\r
 363 \r
 364                 if (service == Services.JpredWS) {\r
 365                         taskId = msaws.align(loadAlignment());\r
 366                 } else {\r
 367                         taskId = msaws.align(loadSeqs(2));\r
 368                 }\r
 369                 writer.print("\nQuerying job status...");\r
 370                 JobStatus status = msaws.getJobStatus(taskId);\r
 371                 while (status != JobStatus.FINISHED) {\r
 372                         Thread.sleep(1000);\r
 373                         status = msaws.getJobStatus(taskId);\r
 374                 }\r
 375                 writer.println(OK);\r
 376                 writer.print("Retrieving results...");\r
 377                 al = msaws.getResult(taskId);\r
 378                 succeed = true;\r
 379                 if (al != null) {\r
 380                         writer.println(OK);\r
 381                 }\r
 382                 return succeed;\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.println("<host_and_context> parameter is not provided or is incorrect!");\r
 407                         System.exit(1);\r
 408                 }\r
 409                 WSTester tester = new WSTester(host, new PrintWriter(System.out, true));\r
 410 \r
 411                 if (serviceName != null) {\r
 412                         Services service = Services.getService(serviceName);\r
 413                         if (service == null) {\r
 414                                 tester.writer.println("Service '" + serviceName + "' is not supported. Valid values are: "\r
 415                                                 + Arrays.toString(Services.values()));\r
 416                                 tester.writer.println();\r
 417                                 printUsage();\r
 418                                 System.exit(1);\r
 419                         }\r
 420                         tester.checkService(service);\r
 421                         System.exit(0);\r
 422                 }\r
 423 \r
 424                 tester.writer.println("<ServiceName> is not provided checking all known services...");\r
 425 \r
 426                 for (Services serv : Services.values()) {\r
 427                         tester.writer.println();\r
 428                         tester.checkService(serv);\r
 429                 }\r
 430 \r
 431         }\r
 432 \r
 433         /**\r
 434          * Test JABA web service\r
 435          * \r
 436          * @param service\r
 437          *            the service to test\r
 438          * @return true if the service works as expected, false otherwise\r
 439          * @throws WebServiceException\r
 440          * @throws ConnectException\r
 441          */\r
 442         public boolean checkService(Services service) throws ConnectException,\r
 443                         WebServiceException {\r
 444                 JABAService ws = Jws2Client.connect(hostname, service);\r
 445                 if (ws == null) {\r
 446                         String line = "Cannot estabilish the connection to host " + hostname + " with service ";\r
 447                         writer.println(line + service.toString());\r
 448                         return false;\r
 449                 }\r
 450                 boolean succeed = false;\r
 451                 try {\r
 452                         writer.println("Checking service " + service.toString());\r
 453                         succeed = checkService(ws, service);\r
 454                 } finally {\r
 455                         FileUtil.closeSilently(((Closeable) ws));\r
 456                 }\r
 457                 reportResults(service, succeed);\r
 458                 return succeed;\r
 459         }\r
 460 \r
 461         private void reportResults(Services serv, boolean succeed) {\r
 462                 if (succeed) {\r
 463                         writer.println("Check is completed. The Service " + serv + " IS WORKING\n");\r
 464                 } else {\r
 465                         writer.println("Check is aborted. The Service " + serv + " HAS SOME PROBLEMS\n");\r
 466                 }\r
 467         }\r
 468 }\r