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