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 org.apache.log4j.Logger;\r
  36 \r
  37 import compbio.data.msa.JABAService;\r
  38 import compbio.data.msa.Metadata;\r
  39 import compbio.data.msa.MsaWS;\r
  40 import compbio.data.msa.SequenceAnnotation;\r
  41 import compbio.data.sequence.Alignment;\r
  42 import compbio.data.sequence.FastaSequence;\r
  43 import compbio.data.sequence.ScoreManager;\r
  44 import compbio.data.sequence.SequenceUtil;\r
  45 import compbio.metadata.JobStatus;\r
  46 import compbio.metadata.Limit;\r
  47 import compbio.metadata.LimitsManager;\r
  48 import compbio.metadata.Option;\r
  49 import compbio.metadata.Preset;\r
  50 import compbio.metadata.PresetManager;\r
  51 import compbio.metadata.RunnerConfig;\r
  52 import compbio.metadata.UnsupportedRuntimeException;\r
  53 import compbio.util.FileUtil;\r
  54 import compbio.util.Util;\r
  55 \r
  56 /**\r
  57  * Class for testing web services\r
  58  * \r
  59  * @author pvtroshin\r
  60  * \r
  61  * @version 1.0 February 2010\r
  62  */\r
  63 public class WSTester {\r
  64 \r
  65         private static Logger log = Logger.getLogger(WSTester.class);\r
  66         /**\r
  67          * Sequences to be used as input for all WS\r
  68          */\r
  69         public static final String fastaInput = ">Foo\n"\r
  70                         + "MTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV"\r
  71                         + "\n>Bar\n"\r
  72                         + "ASDAAPEHPGIALWLHALEDAGQAEAAAAYTRAHQLLPEEPYITAQLLNAVA\n";\r
  73 \r
  74         public static final String fastaAlignment = ">Foo\n"\r
  75                         + "MTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV--------\n"\r
  76                         + ">Bar\n"\r
  77                         + "ASDAAPEH------------PGIALWLHALE-DAGQAEAAA---AYTRAHQLLPEEPYITAQLLNAVA\n"\r
  78                         + "";\r
  79 \r
  80         static final List<FastaSequence> seqs = loadSeqs();\r
  81 \r
  82         private static final String FAILED = "FAILED";\r
  83         private static final String OK = "OK";\r
  84 \r
  85         private static final String UNSUPPORTED = "UNSUPPORTED";\r
  86 \r
  87         /**\r
  88          * Converting input to a form accepted by WS\r
  89          * \r
  90          * @return List of FastaSequence records\r
  91          */\r
  92         private static List<FastaSequence> loadSeqs() {\r
  93                 try {\r
  94                         return SequenceUtil.readFasta(new ByteArrayInputStream(fastaInput\r
  95                                         .getBytes()));\r
  96                 } catch (IOException ignored) {\r
  97                         // Should not happen as a source is not a external stream\r
  98                         ignored.printStackTrace();\r
  99                 }\r
 100                 return null;\r
 101         }\r
 102 \r
 103         /**\r
 104          * Converting input to a form accepted by WS\r
 105          * \r
 106          * @return List of FastaSequence records\r
 107          */\r
 108         private static List<FastaSequence> loadAlignment() {\r
 109                 try {\r
 110                         return SequenceUtil.readFasta(new ByteArrayInputStream(\r
 111                                         fastaAlignment.getBytes()));\r
 112                 } catch (IOException ignored) {\r
 113                         // Should not happen as a source is not a external stream\r
 114                         ignored.printStackTrace();\r
 115                 }\r
 116                 return null;\r
 117         }\r
 118 \r
 119         private final PrintWriter writer;\r
 120         private final String hostname;\r
 121 \r
 122         /**\r
 123          * Construct an instance of JABAWS tester\r
 124          * \r
 125          * @param hostname\r
 126          *            - fully qualified host and context name of JABAWS e.g.\r
 127          *            http://nanna.cluster.lifesci.dundee.ac.uk:8080/jaba\r
 128          * @param writer\r
 129          *            a PrintWriter instance to writer test log to.\r
 130          */\r
 131         public WSTester(String hostname, PrintWriter writer) {\r
 132                 if (Util.isEmpty(hostname)) {\r
 133                         throw new NullPointerException("Hostname must be provided!");\r
 134                 }\r
 135                 this.hostname = hostname;\r
 136                 this.writer = writer;\r
 137         }\r
 138 \r
 139         /**\r
 140          * Prints usage\r
 141          */\r
 142         static void printUsage() {\r
 143                 System.out.println("Usage: <Class or Jar file name> " + hostkey\r
 144                                 + pseparator + "host_and_context " + "<" + servicekey\r
 145                                 + pseparator + "serviceName>");\r
 146                 System.out.println();\r
 147                 System.out\r
 148                                 .println(hostkey\r
 149                                                 + pseparator\r
 150                                                 + "<host_and_context> - a full URL to the JABAWS web server including context path e.g. http://10.31.1.159:8080/ws");\r
 151                 System.out\r
 152                                 .println(servicekey\r
 153                                                 + pseparator\r
 154                                                 + "<ServiceName> - optional if unspecified all services are tested otherwise one of "\r
 155                                                 + Arrays.toString(Services.values()));\r
 156                 System.out.println();\r
 157 \r
 158         }\r
 159 \r
 160         /**\r
 161          * Calls alignment with preset\r
 162          * \r
 163          * @param <T>\r
 164          * @param msaws\r
 165          * @param presets\r
 166          *            list of the Preset\r
 167          * @throws UnsupportedRuntimeException\r
 168          */\r
 169         private <T> boolean presetAlign(MsaWS<T> msaws, List<Preset<T>> presets)\r
 170                         throws UnsupportedRuntimeException {\r
 171                 boolean succeed = false;\r
 172                 for (Preset<T> preset : presets) {\r
 173                         writer.print("Aligning with preset '" + preset.getName() + "'... ");\r
 174                         Alignment al = null;\r
 175                         try {\r
 176                                 String taskId = msaws.presetAlign(seqs, preset);\r
 177                                 al = msaws.getResult(taskId);\r
 178                                 if (al != null) {\r
 179                                         writer.println(OK);\r
 180                                 }\r
 181                                 succeed = true;\r
 182                         } catch (Exception e) {\r
 183                                 if (e instanceof UnsupportedRuntimeException) {\r
 184                                         // If executable is not supported than none of the presets\r
 185                                         // are\r
 186                                         // going to work\r
 187                                         throw (UnsupportedRuntimeException) e;\r
 188                                 } else {\r
 189                                         reportException(e);\r
 190                                 }\r
 191                                 continue;\r
 192                         }\r
 193                 }\r
 194                 return succeed;\r
 195         }\r
 196 \r
 197         private <T> boolean testMsaWS(MsaWS<T> msaws) throws Exception {\r
 198                 assert msaws != null;\r
 199 \r
 200                 boolean succeed = testDefaultAlignment(msaws);\r
 201                 // If exception above is thrown than the tests below is not run\r
 202 \r
 203                 PresetManager<T> pmanager = msaws.getPresets();\r
 204                 if (pmanager != null && pmanager.getPresets().size() > 0) {\r
 205                         writer.println("Testing alignment with presets:");\r
 206                         List<Preset<T>> plist = pmanager.getPresets();\r
 207                         succeed = !succeed ? presetAlign(msaws, plist) : succeed;\r
 208                 }\r
 209                 testMetadata(msaws);\r
 210                 return succeed;\r
 211         }\r
 212         /**\r
 213          * Call most of web services functions and check the output\r
 214          * \r
 215          * @param <T>\r
 216          *            web service type\r
 217          * @param msaws\r
 218          * @throws UnsupportedRuntimeException\r
 219          *             is thrown if the connection to a web service was made, but\r
 220          *             the web service is not functional. e.g. when native\r
 221          *             executable does not exists for a server platform\r
 222          */\r
 223         @SuppressWarnings("unchecked")\r
 224         private <T> boolean checkService(JABAService wservice, Services service) {\r
 225                 try {\r
 226                         if (wservice == null) {\r
 227                                 throw new NullPointerException(\r
 228                                                 "JABAService instance must be provided!");\r
 229                         }\r
 230 \r
 231                         if (wservice instanceof MsaWS) {\r
 232                                 return testMsaWS((MsaWS<T>) wservice);\r
 233                         } else if (wservice instanceof SequenceAnnotation) {\r
 234                                 return testSequenceAnnotationWS(\r
 235                                                 (SequenceAnnotation<T>) wservice, service);\r
 236                         } else {\r
 237                                 throw new UnsupportedOperationException("The service: "\r
 238                                                 + wservice.getClass() + " is not supported! ");\r
 239                         }\r
 240                 } catch (Exception e) {\r
 241                         reportException(e);\r
 242                         return false;\r
 243                 }\r
 244         }\r
 245 \r
 246         private <T> boolean testSequenceAnnotationWS(\r
 247                         SequenceAnnotation<T> wservice, Services service) throws Exception {\r
 248                 writer.print("Calling analyse.........");\r
 249 \r
 250                 List<FastaSequence> input = loadSeqs();\r
 251                 if (service == Services.AAConWS) {\r
 252                         input = loadAlignment();\r
 253                 }\r
 254                 boolean success = testDefaultAnalyse(input, wservice, null, null);\r
 255 \r
 256                 PresetManager<T> presetman = wservice.getPresets();\r
 257                 if (presetman != null) {\r
 258                         List<Preset<T>> presets = presetman.getPresets();\r
 259                         if (presets != null && !presets.isEmpty()) {\r
 260                                 Preset<T> preset = presets.get(0);\r
 261                                 writer.print("Calling analyse with Preset.........");\r
 262                                 success = testDefaultAnalyse(input, wservice, preset, null);\r
 263                         }\r
 264                 }\r
 265                 testMetadata(wservice);\r
 266                 return success;\r
 267         }\r
 268 \r
 269         private <T> boolean testDefaultAnalyse(List<FastaSequence> fastalist,\r
 270                         SequenceAnnotation<T> wsproxy, Preset<T> preset,\r
 271                         List<Option<T>> customOptions) throws Exception {\r
 272 \r
 273                 ScoreManager scores = null;\r
 274 \r
 275                 String jobId = null;\r
 276                 if (customOptions != null) {\r
 277                         jobId = wsproxy.customAnalize(fastalist, customOptions);\r
 278                 } else if (preset != null) {\r
 279                         jobId = wsproxy.presetAnalize(fastalist, preset);\r
 280                 } else {\r
 281                         jobId = wsproxy.analize(fastalist);\r
 282                 }\r
 283                 Thread.sleep(1000);\r
 284                 scores = wsproxy.getAnnotation(jobId);\r
 285                 if (scores != null) {\r
 286                         writer.println(OK);\r
 287                 }\r
 288 \r
 289                 return scores != null;\r
 290         }\r
 291 \r
 292         private void reportException(Exception e) {\r
 293                 writer.println(FAILED);\r
 294                 writer.println("Exception while waiting for results. "\r
 295                                 + "Exception details are below:");\r
 296                 writer.println(e.getLocalizedMessage());\r
 297                 e.printStackTrace(writer);\r
 298         }\r
 299 \r
 300         private <T> void testMetadata(Metadata<T> msaws)\r
 301                         throws UnsupportedRuntimeException {\r
 302 \r
 303                 writer.print("Querying presets...");\r
 304                 PresetManager<T> pmanager = msaws.getPresets();\r
 305                 if (pmanager != null && pmanager.getPresets().size() > 0) {\r
 306                         writer.println(OK);\r
 307                 } else {\r
 308                         writer.println(UNSUPPORTED);\r
 309                 }\r
 310 \r
 311                 writer.print("Querying Parameters...");\r
 312                 RunnerConfig<T> options = msaws.getRunnerOptions();\r
 313                 if (options != null && options.getArguments().size() > 0) {\r
 314                         writer.println(OK);\r
 315                 } else {\r
 316                         writer.println(UNSUPPORTED);\r
 317                 }\r
 318 \r
 319                 writer.print("Querying Limits...");\r
 320                 LimitsManager<T> limits = msaws.getLimits();\r
 321                 if (limits != null && limits.getLimits().size() > 0) {\r
 322                         writer.println(OK);\r
 323                         // writer.println("Limits details: \n" + limits.toString());\r
 324                 } else {\r
 325                         writer.println(UNSUPPORTED);\r
 326                 }\r
 327 \r
 328                 writer.print("Querying Local Engine Limits...");\r
 329                 Limit<T> localLimit = msaws\r
 330                                 .getLimit(PresetManager.LOCAL_ENGINE_LIMIT_PRESET);\r
 331                 if (localLimit != null) {\r
 332                         writer.println(OK);\r
 333                 } else {\r
 334                         writer.println(UNSUPPORTED);\r
 335                 }\r
 336         }\r
 337 \r
 338         /**\r
 339          * Align using default settings\r
 340          * \r
 341          * @param <T>\r
 342          * @param msaws\r
 343          * @throws UnsupportedRuntimeException\r
 344          */\r
 345         private <T> boolean testDefaultAlignment(MsaWS<T> msaws) throws Exception {\r
 346                 writer.print("Testing alignment with default parameters:");\r
 347                 Alignment al = null;\r
 348                 boolean succeed = false;\r
 349 \r
 350                 String taskId = msaws.align(seqs);\r
 351                 writer.print("\nQuerying job status...");\r
 352                 JobStatus status = msaws.getJobStatus(taskId);\r
 353                 while (status != JobStatus.FINISHED) {\r
 354                         Thread.sleep(1000);\r
 355                         status = msaws.getJobStatus(taskId);\r
 356                 }\r
 357                 writer.println(OK);\r
 358                 writer.print("Retrieving results...");\r
 359                 al = msaws.getResult(taskId);\r
 360                 succeed = true;\r
 361                 if (al != null) {\r
 362                         writer.println(OK);\r
 363                 }\r
 364                 return succeed;\r
 365         }\r
 366         /**\r
 367          * Test JWS2 web services\r
 368          * \r
 369          * @param <T>\r
 370          *            web service type\r
 371          * @param args\r
 372          *            -h=<Your web application server host name, port and JWS2\r
 373          *            context path>\r
 374          * \r
 375          *            -s=<ServiceName> which is optional. If service name is not\r
 376          *            provided then all known JWS2 web services are tested\r
 377          * @throws IOException\r
 378          */\r
 379         public static <T> void main(String[] args) throws IOException {\r
 380 \r
 381                 if (args == null || args.length < 1) {\r
 382                         WSTester.printUsage();\r
 383                         System.exit(0);\r
 384                 }\r
 385                 String host = CmdHelper.getHost(args);\r
 386                 String serviceName = CmdHelper.getServiceName(args);\r
 387                 if (!Jws2Client.validURL(host)) {\r
 388                         System.err\r
 389                                         .println("<host_and_context> parameter is not provided or is incorrect!");\r
 390                         System.exit(1);\r
 391                 }\r
 392                 WSTester tester = new WSTester(host, new PrintWriter(System.out, true));\r
 393 \r
 394                 if (serviceName != null) {\r
 395                         Services service = Services.getService(serviceName);\r
 396                         if (service == null) {\r
 397                                 tester.writer.println("Service '" + serviceName\r
 398                                                 + "' is not supported. Valid values are: "\r
 399                                                 + Arrays.toString(Services.values()));\r
 400                                 tester.writer.println();\r
 401                                 printUsage();\r
 402                                 System.exit(1);\r
 403                         }\r
 404                         tester.checkService(service);\r
 405                         System.exit(0);\r
 406                 }\r
 407 \r
 408                 tester.writer\r
 409                                 .println("<ServiceName> is not provided checking all known services...");\r
 410 \r
 411                 for (Services serv : Services.values()) {\r
 412                         tester.writer.println();\r
 413                         tester.checkService(serv);\r
 414                 }\r
 415 \r
 416         }\r
 417 \r
 418         /**\r
 419          * Test JABA web service\r
 420          * \r
 421          * @param service\r
 422          *            the service to test\r
 423          * @return true if the service works as expected, false otherwise\r
 424          * @throws WebServiceException\r
 425          * @throws ConnectException\r
 426          */\r
 427         public boolean checkService(Services service) throws ConnectException,\r
 428                         WebServiceException {\r
 429                 JABAService ws = Jws2Client.connect(hostname, service);\r
 430                 if (ws == null) {\r
 431                         writer.println("Cannot estabilish the connection to host "\r
 432                                         + hostname + " with service " + service.toString());\r
 433                         return false;\r
 434                 }\r
 435                 boolean succeed = false;\r
 436                 try {\r
 437                         writer.println("Checking service " + service.toString());\r
 438                         succeed = checkService(ws, service);\r
 439                 } finally {\r
 440                         FileUtil.closeSilently(((Closeable) ws));\r
 441                 }\r
 442                 reportResults(service, succeed);\r
 443                 return succeed;\r
 444         }\r
 445 \r
 446         private void reportResults(Services serv, boolean succeed) {\r
 447                 if (succeed) {\r
 448                         writer.println("Check is completed. The Service " + serv\r
 449                                         + " IS WORKING\n");\r
 450                 } else {\r
 451                         writer.println("Check is aborted. The Service " + serv\r
 452                                         + " HAS SOME PROBLEMS\n");\r
 453                 }\r
 454         }\r
 455 }\r