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 \r
  76         /**\r
  77          * Status strings\r
  78          */\r
  79         private static final String FAILED = "FAILED";\r
  80         private static final String OK = "OK";\r
  81         private static final String UNSUPPORTED = "UNSUPPORTED";\r
  82 \r
  83         /**\r
  84          * Converting input to a form accepted by WS\r
  85          * \r
  86          * @return List of FastaSequence records\r
  87          */\r
  88         private static List<FastaSequence> loadSeqs(int nLines) {\r
  89                 try {\r
  90                         if (nLines == 1) {\r
  91                                 return SequenceUtil.readFasta(new ByteArrayInputStream(fastaInput1record.getBytes()));\r
  92                         }\r
  93                         return SequenceUtil.readFasta(new ByteArrayInputStream(fastaInput2records.getBytes()));\r
  94                 } catch (IOException ignored) {\r
  95                         // Should not happen as a source is not a external stream\r
  96                         ignored.printStackTrace();\r
  97                 }\r
  98                 return null;\r
  99         }\r
 100 \r
 101         /**\r
 102          * Converting input to a form accepted by WS\r
 103          * \r
 104          * @return List of FastaSequence records\r
 105          */\r
 106         private static List<FastaSequence> loadAlignment() {\r
 107                 try {\r
 108                         return SequenceUtil.readFasta(new ByteArrayInputStream(\r
 109                                         fastaAlignment.getBytes()));\r
 110                 } catch (IOException ignored) {\r
 111                         // Should not happen as a source is not a external stream\r
 112                         ignored.printStackTrace();\r
 113                 }\r
 114                 return null;\r
 115         }\r
 116 \r
 117         private final PrintWriter writer;\r
 118         private final String hostname;\r
 119 \r
 120         /**\r
 121          * Construct an instance of JABAWS tester\r
 122          * \r
 123          * @param hostname\r
 124          *            - fully qualified host and context name of JABAWS e.g.\r
 125          *            http://nanna.cluster.lifesci.dundee.ac.uk:8080/jaba\r
 126          * @param writer\r
 127          *            a PrintWriter instance to writer test log to.\r
 128          */\r
 129         public WSTester(String hostname, PrintWriter writer) {\r
 130                 if (Util.isEmpty(hostname)) {\r
 131                         throw new NullPointerException("Hostname must be provided!");\r
 132                 }\r
 133                 this.hostname = hostname;\r
 134                 this.writer = writer;\r
 135         }\r
 136 \r
 137         /**\r
 138          * Prints usage\r
 139          */\r
 140         static void printUsage() {\r
 141                 System.out.println("Usage: <Class or Jar file name> " + hostkey\r
 142                                 + pseparator + "host_and_context " + "<" + servicekey\r
 143                                 + pseparator + "serviceName>");\r
 144                 System.out.println();\r
 145                 System.out.println(hostkey\r
 146                                                 + pseparator\r
 147                                                 + "<host_and_context> - a full URL to the JABAWS web server including context path e.g. http://10.31.1.159:8080/ws");\r
 148                 System.out.println(servicekey\r
 149                                                 + pseparator\r
 150                                                 + "<ServiceName> - optional if unspecified all services are tested otherwise one of "\r
 151                                                 + Arrays.toString(Services.values()));\r
 152                 System.out.println();\r
 153 \r
 154         }\r
 155 \r
 156         /**\r
 157          * Calls alignment with preset\r
 158          * \r
 159          * @param <T>\r
 160          * @param msaws\r
 161          * @param presets\r
 162          *            list of the Preset\r
 163          * @throws UnsupportedRuntimeException\r
 164          */\r
 165         private <T> boolean presetAlign(MsaWS<T> msaws, List<Preset<T>> presets)\r
 166                         throws UnsupportedRuntimeException {\r
 167                 boolean succeed = false;\r
 168                 for (Preset<T> preset : presets) {\r
 169                         writer.print("Aligning with preset '" + preset.getName() + "'... ");\r
 170                         Alignment al = null;\r
 171                         try {\r
 172                                 String taskId = msaws.presetAlign(loadSeqs(2), preset);\r
 173                                 al = msaws.getResult(taskId);\r
 174                                 if (al != null) {\r
 175                                         writer.println(OK);\r
 176                                 }\r
 177                                 succeed = true;\r
 178                         } catch (Exception e) {\r
 179                                 if (e instanceof UnsupportedRuntimeException) {\r
 180                                         // If executable is not supported than none of the presets\r
 181                                         // are\r
 182                                         // going to work\r
 183                                         throw (UnsupportedRuntimeException) e;\r
 184                                 } else {\r
 185                                         reportException(e);\r
 186                                 }\r
 187                                 continue;\r
 188                         }\r
 189                 }\r
 190                 return succeed;\r
 191         }\r
 192 \r
 193         private <T> boolean testMsaWS(MsaWS<T> msaws, Services service) throws Exception {\r
 194                 assert msaws != null;\r
 195 \r
 196                 boolean succeed = testDefaultAlignment(msaws, service);\r
 197                 // If exception above is thrown than the tests below is not run\r
 198 \r
 199                 PresetManager<T> pmanager = msaws.getPresets();\r
 200                 if (pmanager != null && pmanager.getPresets().size() > 0) {\r
 201                         writer.println("Testing alignment with presets:");\r
 202                         List<Preset<T>> plist = pmanager.getPresets();\r
 203                         succeed = !succeed ? presetAlign(msaws, plist) : succeed;\r
 204                 }\r
 205                 testMetadata(msaws);\r
 206                 return succeed;\r
 207         }\r
 208         /**\r
 209          * Call most of web services functions and check the output\r
 210          * \r
 211          * @param <T>\r
 212          *            web service type\r
 213          * @param msaws\r
 214          * @throws UnsupportedRuntimeException\r
 215          *             is thrown if the connection to a web service was made, but\r
 216          *             the web service is not functional. e.g. when native\r
 217          *             executable does not exists for a server platform\r
 218          */\r
 219         @SuppressWarnings("unchecked")\r
 220         private <T> boolean checkService(JABAService wservice, Services service) {\r
 221                 try {\r
 222                         if (wservice == null) {\r
 223                                 throw new NullPointerException("JABAService instance must be provided!");\r
 224                         }\r
 225 \r
 226                         if (wservice instanceof MsaWS) {\r
 227                                 return testMsaWS((MsaWS<T>) wservice, service);\r
 228                         } else if (wservice instanceof SequenceAnnotation) {\r
 229                                 return testSequenceAnnotationWS(\r
 230                                                 (SequenceAnnotation<T>) wservice, service);\r
 231                         } else {\r
 232                                 throw new UnsupportedOperationException("The service: " + wservice.getClass() + " is not supported! ");\r
 233                         }\r
 234                 } catch (Exception e) {\r
 235                         reportException(e);\r
 236                         return false;\r
 237                 }\r
 238         }\r
 239 \r
 240         private <T> boolean testSequenceAnnotationWS(\r
 241                         SequenceAnnotation<T> wservice, Services service) throws Exception {\r
 242                 writer.print("Calling analyse.........");\r
 243 \r
 244                 List<FastaSequence> input = loadSeqs(2);\r
 245                 if (service == Services.AAConWS) {\r
 246                         input = loadAlignment();\r
 247                 }\r
 248                 boolean success = testDefaultAnalyse(input, wservice, null, null);\r
 249 \r
 250                 PresetManager<T> presetman = wservice.getPresets();\r
 251                 if (presetman != null) {\r
 252                         List<Preset<T>> presets = presetman.getPresets();\r
 253                         if (presets != null && !presets.isEmpty()) {\r
 254                                 Preset<T> preset = presets.get(0);\r
 255                                 writer.print("Calling analyse with Preset.........");\r
 256                                 success = testDefaultAnalyse(input, wservice, preset, null);\r
 257                         }\r
 258                 }\r
 259                 testMetadata(wservice);\r
 260                 return success;\r
 261         }\r
 262 \r
 263         private <T> boolean testDefaultAnalyse(List<FastaSequence> fastalist,\r
 264                         SequenceAnnotation<T> wsproxy, Preset<T> preset,\r
 265                         List<Option<T>> customOptions) throws Exception {\r
 266 \r
 267                 ScoreManager scores = null;\r
 268 \r
 269                 String jobId = null;\r
 270                 if (customOptions != null) {\r
 271                         jobId = wsproxy.customAnalize(fastalist, customOptions);\r
 272                 } else if (preset != null) {\r
 273                         jobId = wsproxy.presetAnalize(fastalist, preset);\r
 274                 } else {\r
 275                         jobId = wsproxy.analize(fastalist);\r
 276                 }\r
 277                 Thread.sleep(1000);\r
 278                 scores = wsproxy.getAnnotation(jobId);\r
 279                 if (scores != null) {\r
 280                         writer.println(OK);\r
 281                 }\r
 282 \r
 283                 return scores != null;\r
 284         }\r
 285 \r
 286         private void reportException(Exception e) {\r
 287                 writer.println(FAILED);\r
 288                 writer.println("Exception while waiting for results. "\r
 289                                 + "Exception details are below:");\r
 290                 writer.println(e.getLocalizedMessage());\r
 291                 e.printStackTrace(writer);\r
 292         }\r
 293 \r
 294         private <T> void testMetadata(Metadata<T> msaws)\r
 295                         throws UnsupportedRuntimeException {\r
 296 \r
 297                 writer.print("Querying presets...");\r
 298                 PresetManager<T> pmanager = msaws.getPresets();\r
 299                 if (pmanager != null && pmanager.getPresets().size() > 0) {\r
 300                         writer.println(OK);\r
 301                 } else {\r
 302                         writer.println(UNSUPPORTED);\r
 303                 }\r
 304 \r
 305                 writer.print("Querying Parameters...");\r
 306                 RunnerConfig<T> options = msaws.getRunnerOptions();\r
 307                 if (options != null && options.getArguments().size() > 0) {\r
 308                         writer.println(OK);\r
 309                 } else {\r
 310                         writer.println(UNSUPPORTED);\r
 311                 }\r
 312 \r
 313                 writer.print("Querying Limits...");\r
 314                 LimitsManager<T> limits = msaws.getLimits();\r
 315                 if (limits != null && limits.getLimits().size() > 0) {\r
 316                         writer.println(OK);\r
 317                         // writer.println("Limits details: \n" + limits.toString());\r
 318                 } else {\r
 319                         writer.println(UNSUPPORTED);\r
 320                 }\r
 321 \r
 322                 writer.print("Querying Local Engine Limits...");\r
 323                 Limit<T> localLimit = msaws\r
 324                                 .getLimit(PresetManager.LOCAL_ENGINE_LIMIT_PRESET);\r
 325                 if (localLimit != null) {\r
 326                         writer.println(OK);\r
 327                 } else {\r
 328                         writer.println(UNSUPPORTED);\r
 329                 }\r
 330         }\r
 331 \r
 332         /**\r
 333          * Align using default settings\r
 334          * \r
 335          * @param <T>\r
 336          * @param msaws\r
 337          * @throws UnsupportedRuntimeException\r
 338          */\r
 339         private <T> boolean testDefaultAlignment(MsaWS<T> msaws, Services service) throws Exception {\r
 340                 writer.print("Testing alignment with default parameters:");\r
 341                 Alignment al = null;\r
 342                 boolean succeed = false;\r
 343                 String taskId;\r
 344 \r
 345                 if (service == Services.JpredWS) {\r
 346                         taskId = msaws.align(loadSeqs(1));\r
 347                 } else {\r
 348                         taskId = msaws.align(loadSeqs(2));\r
 349                 }\r
 350                 writer.print("\nQuerying job status...");\r
 351                 JobStatus status = msaws.getJobStatus(taskId);\r
 352                 while (status != JobStatus.FINISHED) {\r
 353                         Thread.sleep(1000);\r
 354                         status = msaws.getJobStatus(taskId);\r
 355                 }\r
 356                 writer.println(OK);\r
 357                 writer.print("Retrieving results...");\r
 358                 al = msaws.getResult(taskId);\r
 359                 succeed = true;\r
 360                 if (al != null) {\r
 361                         writer.println(OK);\r
 362                 }\r
 363                 return succeed;\r
 364         }\r
 365         /**\r
 366          * Test JWS2 web services\r
 367          * \r
 368          * @param <T>\r
 369          *            web service type\r
 370          * @param args\r
 371          *            -h=<Your web application server host name, port and JWS2\r
 372          *            context path>\r
 373          * \r
 374          *            -s=<ServiceName> which is optional. If service name is not\r
 375          *            provided then all known JWS2 web services are tested\r
 376          * @throws IOException\r
 377          */\r
 378         public static <T> void main(String[] args) throws IOException {\r
 379 \r
 380                 if (args == null || args.length < 1) {\r
 381                         WSTester.printUsage();\r
 382                         System.exit(0);\r
 383                 }\r
 384                 String host = CmdHelper.getHost(args);\r
 385                 String serviceName = CmdHelper.getServiceName(args);\r
 386                 if (!Jws2Client.validURL(host)) {\r
 387                         System.err.println("<host_and_context> parameter is not provided or is incorrect!");\r
 388                         System.exit(1);\r
 389                 }\r
 390                 WSTester tester = new WSTester(host, new PrintWriter(System.out, true));\r
 391 \r
 392                 if (serviceName != null) {\r
 393                         Services service = Services.getService(serviceName);\r
 394                         if (service == null) {\r
 395                                 tester.writer.println("Service '" + serviceName + "' is not supported. Valid values are: "\r
 396                                                 + Arrays.toString(Services.values()));\r
 397                                 tester.writer.println();\r
 398                                 printUsage();\r
 399                                 System.exit(1);\r
 400                         }\r
 401                         tester.checkService(service);\r
 402                         System.exit(0);\r
 403                 }\r
 404 \r
 405                 tester.writer.println("<ServiceName> is not provided checking all known services...");\r
 406 \r
 407                 for (Services serv : Services.values()) {\r
 408                         tester.writer.println();\r
 409                         tester.checkService(serv);\r
 410                 }\r
 411 \r
 412         }\r
 413 \r
 414         /**\r
 415          * Test JABA web service\r
 416          * \r
 417          * @param service\r
 418          *            the service to test\r
 419          * @return true if the service works as expected, false otherwise\r
 420          * @throws WebServiceException\r
 421          * @throws ConnectException\r
 422          */\r
 423         public boolean checkService(Services service) throws ConnectException,\r
 424                         WebServiceException {\r
 425                 JABAService ws = Jws2Client.connect(hostname, service);\r
 426                 if (ws == null) {\r
 427                         String line = "Cannot estabilish the connection to host " + hostname + " with service ";\r
 428                         writer.println(line + service.toString());\r
 429                         return false;\r
 430                 }\r
 431                 boolean succeed = false;\r
 432                 try {\r
 433                         writer.println("Checking service " + service.toString());\r
 434                         succeed = checkService(ws, service);\r
 435                 } finally {\r
 436                         FileUtil.closeSilently(((Closeable) ws));\r
 437                 }\r
 438                 reportResults(service, succeed);\r
 439                 return succeed;\r
 440         }\r
 441 \r
 442         private void reportResults(Services serv, boolean succeed) {\r
 443                 if (succeed) {\r
 444                         writer.println("Check is completed. The Service " + serv + " IS WORKING\n");\r
 445                 } else {\r
 446                         writer.println("Check is aborted. The Service " + serv + " HAS SOME PROBLEMS\n");\r
 447                 }\r
 448         }\r
 449 }\r