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 fastaInput2records = ">Foo\n"\r
  67                         + "MTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV"\r
  68                         + "\n>Bar\n"\r
  69                         + "ASDAAPEHPGIALWLHALEDAGQAEAAAAYTRAHQLLPEEPYITAQLLNAVA\n";\r
  70         public static final String fastaInput1record = ">Foo\n"\r
  71                         + "MTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV"\r
  72                         + "\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(2);\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(int nLines) {\r
  93                 try {\r
  94                         if (nLines == 1) {\r
  95                                 return SequenceUtil.readFasta(new ByteArrayInputStream(fastaInput1record.getBytes()));\r
  96                         }\r
  97                         return SequenceUtil.readFasta(new ByteArrayInputStream(fastaInput2records.getBytes()));\r
  98                 } catch (IOException ignored) {\r
  99                         // Should not happen as a source is not a external stream\r
 100                         ignored.printStackTrace();\r
 101                 }\r
 102                 return null;\r
 103         }\r
 104 \r
 105         /**\r
 106          * Converting input to a form accepted by WS\r
 107          * \r
 108          * @return List of FastaSequence records\r
 109          */\r
 110         private static List<FastaSequence> loadAlignment() {\r
 111                 try {\r
 112                         return SequenceUtil.readFasta(new ByteArrayInputStream(\r
 113                                         fastaAlignment.getBytes()));\r
 114                 } catch (IOException ignored) {\r
 115                         // Should not happen as a source is not a external stream\r
 116                         ignored.printStackTrace();\r
 117                 }\r
 118                 return null;\r
 119         }\r
 120 \r
 121         private final PrintWriter writer;\r
 122         private final String hostname;\r
 123 \r
 124         /**\r
 125          * Construct an instance of JABAWS tester\r
 126          * \r
 127          * @param hostname\r
 128          *            - fully qualified host and context name of JABAWS e.g.\r
 129          *            http://nanna.cluster.lifesci.dundee.ac.uk:8080/jaba\r
 130          * @param writer\r
 131          *            a PrintWriter instance to writer test log to.\r
 132          */\r
 133         public WSTester(String hostname, PrintWriter writer) {\r
 134                 if (Util.isEmpty(hostname)) {\r
 135                         throw new NullPointerException("Hostname must be provided!");\r
 136                 }\r
 137                 this.hostname = hostname;\r
 138                 this.writer = writer;\r
 139         }\r
 140 \r
 141         /**\r
 142          * Prints usage\r
 143          */\r
 144         static void printUsage() {\r
 145                 System.out.println("Usage: <Class or Jar file name> " + hostkey\r
 146                                 + pseparator + "host_and_context " + "<" + servicekey\r
 147                                 + pseparator + "serviceName>");\r
 148                 System.out.println();\r
 149                 System.out.println(hostkey\r
 150                                                 + pseparator\r
 151                                                 + "<host_and_context> - a full URL to the JABAWS web server including context path e.g. http://10.31.1.159:8080/ws");\r
 152                 System.out.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("JABAService instance must be provided!");\r
 228                         }\r
 229 \r
 230                         if (wservice instanceof MsaWS) {\r
 231                                 return testMsaWS((MsaWS<T>) wservice);\r
 232                         } else if (wservice instanceof SequenceAnnotation) {\r
 233                                 return testSequenceAnnotationWS(\r
 234                                                 (SequenceAnnotation<T>) wservice, service);\r
 235                         } else {\r
 236                                 throw new UnsupportedOperationException("The service: " + wservice.getClass() + " is not supported! ");\r
 237                         }\r
 238                 } catch (Exception e) {\r
 239                         reportException(e);\r
 240                         return false;\r
 241                 }\r
 242         }\r
 243 \r
 244         private <T> boolean testSequenceAnnotationWS(\r
 245                         SequenceAnnotation<T> wservice, Services service) throws Exception {\r
 246                 writer.print("Calling analyse.........");\r
 247 \r
 248                 List<FastaSequence> input = loadSeqs(2);\r
 249                 if (service == Services.AAConWS) {\r
 250                         input = loadAlignment();\r
 251                 }\r
 252                 if (service == Services.JpredWS) {\r
 253                         input = loadSeqs(1);\r
 254                 }\r
 255                 boolean success = testDefaultAnalyse(input, wservice, null, null);\r
 256 \r
 257                 PresetManager<T> presetman = wservice.getPresets();\r
 258                 if (presetman != null) {\r
 259                         List<Preset<T>> presets = presetman.getPresets();\r
 260                         if (presets != null && !presets.isEmpty()) {\r
 261                                 Preset<T> preset = presets.get(0);\r
 262                                 writer.print("Calling analyse with Preset.........");\r
 263                                 success = testDefaultAnalyse(input, wservice, preset, null);\r
 264                         }\r
 265                 }\r
 266                 testMetadata(wservice);\r
 267                 return success;\r
 268         }\r
 269 \r
 270         private <T> boolean testDefaultAnalyse(List<FastaSequence> fastalist,\r
 271                         SequenceAnnotation<T> wsproxy, Preset<T> preset,\r
 272                         List<Option<T>> customOptions) throws Exception {\r
 273 \r
 274                 ScoreManager scores = null;\r
 275 \r
 276                 String jobId = null;\r
 277                 if (customOptions != null) {\r
 278                         jobId = wsproxy.customAnalize(fastalist, customOptions);\r
 279                 } else if (preset != null) {\r
 280                         jobId = wsproxy.presetAnalize(fastalist, preset);\r
 281                 } else {\r
 282                         jobId = wsproxy.analize(fastalist);\r
 283                 }\r
 284                 Thread.sleep(1000);\r
 285                 scores = wsproxy.getAnnotation(jobId);\r
 286                 if (scores != null) {\r
 287                         writer.println(OK);\r
 288                 }\r
 289 \r
 290                 return scores != null;\r
 291         }\r
 292 \r
 293         private void reportException(Exception e) {\r
 294                 writer.println(FAILED);\r
 295                 writer.println("Exception while waiting for results. "\r
 296                                 + "Exception details are below:");\r
 297                 writer.println(e.getLocalizedMessage());\r
 298                 e.printStackTrace(writer);\r
 299         }\r
 300 \r
 301         private <T> void testMetadata(Metadata<T> msaws)\r
 302                         throws UnsupportedRuntimeException {\r
 303 \r
 304                 writer.print("Querying presets...");\r
 305                 PresetManager<T> pmanager = msaws.getPresets();\r
 306                 if (pmanager != null && pmanager.getPresets().size() > 0) {\r
 307                         writer.println(OK);\r
 308                 } else {\r
 309                         writer.println(UNSUPPORTED);\r
 310                 }\r
 311 \r
 312                 writer.print("Querying Parameters...");\r
 313                 RunnerConfig<T> options = msaws.getRunnerOptions();\r
 314                 if (options != null && options.getArguments().size() > 0) {\r
 315                         writer.println(OK);\r
 316                 } else {\r
 317                         writer.println(UNSUPPORTED);\r
 318                 }\r
 319 \r
 320                 writer.print("Querying Limits...");\r
 321                 LimitsManager<T> limits = msaws.getLimits();\r
 322                 if (limits != null && limits.getLimits().size() > 0) {\r
 323                         writer.println(OK);\r
 324                         // writer.println("Limits details: \n" + limits.toString());\r
 325                 } else {\r
 326                         writer.println(UNSUPPORTED);\r
 327                 }\r
 328 \r
 329                 writer.print("Querying Local Engine Limits...");\r
 330                 Limit<T> localLimit = msaws\r
 331                                 .getLimit(PresetManager.LOCAL_ENGINE_LIMIT_PRESET);\r
 332                 if (localLimit != null) {\r
 333                         writer.println(OK);\r
 334                 } else {\r
 335                         writer.println(UNSUPPORTED);\r
 336                 }\r
 337         }\r
 338 \r
 339         /**\r
 340          * Align using default settings\r
 341          * \r
 342          * @param <T>\r
 343          * @param msaws\r
 344          * @throws UnsupportedRuntimeException\r
 345          */\r
 346         private <T> boolean testDefaultAlignment(MsaWS<T> msaws) throws Exception {\r
 347                 writer.print("Testing alignment with default parameters:");\r
 348                 Alignment al = null;\r
 349                 boolean succeed = false;\r
 350 \r
 351                 String taskId = msaws.align(seqs);\r
 352                 writer.print("\nQuerying job status...");\r
 353                 JobStatus status = msaws.getJobStatus(taskId);\r
 354                 while (status != JobStatus.FINISHED) {\r
 355                         Thread.sleep(1000);\r
 356                         status = msaws.getJobStatus(taskId);\r
 357                 }\r
 358                 writer.println(OK);\r
 359                 writer.print("Retrieving results...");\r
 360                 al = msaws.getResult(taskId);\r
 361                 succeed = true;\r
 362                 if (al != null) {\r
 363                         writer.println(OK);\r
 364                 }\r
 365                 return succeed;\r
 366         }\r
 367         /**\r
 368          * Test JWS2 web services\r
 369          * \r
 370          * @param <T>\r
 371          *            web service type\r
 372          * @param args\r
 373          *            -h=<Your web application server host name, port and JWS2\r
 374          *            context path>\r
 375          * \r
 376          *            -s=<ServiceName> which is optional. If service name is not\r
 377          *            provided then all known JWS2 web services are tested\r
 378          * @throws IOException\r
 379          */\r
 380         public static <T> void main(String[] args) throws IOException {\r
 381 \r
 382                 if (args == null || args.length < 1) {\r
 383                         WSTester.printUsage();\r
 384                         System.exit(0);\r
 385                 }\r
 386                 String host = CmdHelper.getHost(args);\r
 387                 String serviceName = CmdHelper.getServiceName(args);\r
 388                 if (!Jws2Client.validURL(host)) {\r
 389                         System.err.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 + "' is not supported. Valid values are: "\r
 398                                                 + Arrays.toString(Services.values()));\r
 399                                 tester.writer.println();\r
 400                                 printUsage();\r
 401                                 System.exit(1);\r
 402                         }\r
 403                         tester.checkService(service);\r
 404                         System.exit(0);\r
 405                 }\r
 406 \r
 407                 tester.writer.println("<ServiceName> is not provided checking all known services...");\r
 408 \r
 409                 for (Services serv : Services.values()) {\r
 410                         tester.writer.println();\r
 411                         tester.checkService(serv);\r
 412                 }\r
 413 \r
 414         }\r
 415 \r
 416         /**\r
 417          * Test JABA web service\r
 418          * \r
 419          * @param service\r
 420          *            the service to test\r
 421          * @return true if the service works as expected, false otherwise\r
 422          * @throws WebServiceException\r
 423          * @throws ConnectException\r
 424          */\r
 425         public boolean checkService(Services service) throws ConnectException,\r
 426                         WebServiceException {\r
 427                 JABAService ws = Jws2Client.connect(hostname, service);\r
 428                 if (ws == null) {\r
 429                         String line = "Cannot estabilish the connection to host " + hostname + " with service ";\r
 430                         writer.println(line + service.toString());\r
 431                         return false;\r
 432                 }\r
 433                 boolean succeed = false;\r
 434                 try {\r
 435                         writer.println("Checking service " + service.toString());\r
 436                         succeed = checkService(ws, service);\r
 437                 } finally {\r
 438                         FileUtil.closeSilently(((Closeable) ws));\r
 439                 }\r
 440                 reportResults(service, succeed);\r
 441                 return succeed;\r
 442         }\r
 443 \r
 444         private void reportResults(Services serv, boolean succeed) {\r
 445                 if (succeed) {\r
 446                         writer.println("Check is completed. The Service " + serv + " IS WORKING\n");\r
 447                 } else {\r
 448                         writer.println("Check is aborted. The Service " + serv + " HAS SOME PROBLEMS\n");\r
 449                 }\r
 450         }\r
 451 }\r