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 java.io.ByteArrayInputStream;\r
  22 import java.io.Closeable;\r
  23 import java.io.IOException;\r
  24 import java.util.Arrays;\r
  25 import java.util.List;\r
  26 \r
  27 import javax.xml.ws.WebServiceException;\r
  28 \r
  29 import compbio.data.msa.MsaWS;\r
  30 import compbio.data.sequence.Alignment;\r
  31 import compbio.data.sequence.FastaSequence;\r
  32 import compbio.data.sequence.SequenceUtil;\r
  33 import compbio.metadata.JobStatus;\r
  34 import compbio.metadata.JobSubmissionException;\r
  35 import compbio.metadata.Limit;\r
  36 import compbio.metadata.LimitsManager;\r
  37 import compbio.metadata.Preset;\r
  38 import compbio.metadata.PresetManager;\r
  39 import compbio.metadata.ResultNotAvailableException;\r
  40 import compbio.metadata.RunnerConfig;\r
  41 import compbio.metadata.UnsupportedRuntimeException;\r
  42 import compbio.metadata.WrongParameterException;\r
  43 \r
  44 /**\r
  45  * Class for testing web services\r
  46  * \r
  47  * @author pvtroshin\r
  48  * \r
  49  * @version 1.0 February 2010\r
  50  */\r
  51 public class WSTester {\r
  52 \r
  53         /**\r
  54          * Sequences to be used as input for all WS\r
  55          */\r
  56         static final String fastaInput = ">Foobar\n"\r
  57                         + "MTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAVARLGRVRWTQQRHAEAAVLLQQASDAAPEHPGIALWLGHALEDAGQAEAAAAAYTRAHQLLPEEPYITAQLLNWRRRLCDWRALDVLSAQVRAAVAQGVGAVEPFAFLSEDASAAEQLACARTRAQAIAASVRPLAPTRVRSKGPLRVGFVSNGFGAHPTGLLTVALFEALQRRQPDLQMHLFATSGDDGSTLRTRLAQASTLHDVTALGHLATAKHIRHHGIDLLFDLRGWGGGGRPEVFALRPAPVQVNWLAYPGTSGAPWMDYVLGDAFALPPALEPFYSEHVLRLQGAFQPSDTSRVVAEPPSRTQCGLPEQGVVLCCFNNSYKLNPQSMARMLAVLREVPDSVLWLLSGPGEADARLRAFAHAQGVDAQRLVFMPKLPHPQYLARYRHADLFLDTHPYNAHTTASDALWTGCPVLTTPGETFAARVAGSLNHHLGLDEMNVADDAAFVAKA"\r
  58                         + "\n>Barbar\n"\r
  59                         + "ASDAAPEHPGIALWLHALEDAGQAEAAAAYTRAHQLLPEEPYITAQLLNAVAQGVGAVEPFAFLSEDASAAESVRPLAPTRVRSKGPLRVGFVSNGFGAHPTGLLTVALFEALQRRQPDLQMHLFATSGDDGSTLRTRLAQASTLHDVTALGHLATAKHIRHHGIDLLFDLRGWGGGGRPEVFALRPAPVQVNWLAYPGTSGAPWMDYVLGDAFALPPALEPFYSEHVLRLQGAFQPSDTSRVVAEPPSRTQCGLPEQGVVLCCFNNSYKLNPQSMARMLAVLREVPDSVLWLLSGPGEADARLRAFAHAQGVDAQRLVFMPKLPHPQYLARYRHADLFLDTHPYNAHTTASDALWTGCPVLTTPGETFAARVAGSLNHHLGLDEMNVADDAAFVAKAVALASDPAALTALHARVDVLRRESGVFEMDGFADDFGALLQALARRHGWLGI"\r
  60                         + "\n>Foofriend\n"\r
  61                         + "MTADGPRELLQLRAAVRHRPQDVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAVARLGRVRWTQQRHAEAAVLLQQASDAAPEHPGIALWLGHALEDHQLLPEEPYITAQLDVLSAQVRAAVAQGVGAVEPFAFLSEDASAAEQLACARTRAQAIAASVRPLAPTRVRSKGPLRVGFVSNGFGAHPTGLLTVALFEALQRRQPDLQMHLFATSGDDGSTLRTRLAQASTLHDVTALGHLATAKHIRHHGIDLLFDLRGWGGGGRPEVFALRPAPVQVNWLAYPGTSGAPWMDYVLGDAFALPPALEPFYSEHVLRLQGAFQPSDTSRVVAEPPSRTQCGLPEQGVVLCCFNNSYKLNPQSMARMLAVLREVPDSVLWLLSGPGEADARLRAFAHAQGVDAQRLVFMPKLPHPQYLARYRHADLFLDTHPYNAHTTASDALWTGCPVLTTPGETFAARVAGSLNHHLGLDEMNVADDAAFVAKAVALASDPAALTALHARVDVLRRESI\n";\r
  62 \r
  63         static final List<FastaSequence> seqs = loadSeqs();\r
  64 \r
  65         private static final String FAILED = "FAILED";\r
  66         private static final String OK = "OK";\r
  67 \r
  68         /**\r
  69          * Converting input to a form accepted by WS\r
  70          * \r
  71          * @return List of FastaSequence records\r
  72          */\r
  73         static List<FastaSequence> loadSeqs() {\r
  74                 try {\r
  75                         return SequenceUtil.readFasta(new ByteArrayInputStream(fastaInput\r
  76                                         .getBytes()));\r
  77                 } catch (IOException ignored) {\r
  78                         // Should not happen as a source is not a external stream\r
  79                         ignored.printStackTrace();\r
  80                 }\r
  81                 return null;\r
  82         }\r
  83 \r
  84         /**\r
  85          * Prints usage\r
  86          */\r
  87         static void printUsage() {\r
  88                 System.out.println("Usage: <Class or Jar file name> "\r
  89                                 + Jws2Client.hostkey + Jws2Client.pseparator\r
  90                                 + "host_and_context " + "<" + Jws2Client.servicekey\r
  91                                 + Jws2Client.pseparator + "serviceName>");\r
  92                 System.out.println();\r
  93                 System.out\r
  94                                 .println(Jws2Client.hostkey\r
  95                                                 + Jws2Client.pseparator\r
  96                                                 + "<host_and_context> - a full URL to the JABAWS web server including context path e.g. http://10.31.1.159:8080/ws");\r
  97                 System.out\r
  98                                 .println(Jws2Client.servicekey\r
  99                                                 + Jws2Client.pseparator\r
 100                                                 + "<ServiceName> - optional if unspecified all services are tested otherwise one of "\r
 101                                                 + Arrays.toString(Services.values()));\r
 102                 System.out.println();\r
 103 \r
 104         }\r
 105 \r
 106         /**\r
 107          * Calls alignment with preset\r
 108          * \r
 109          * @param <T>\r
 110          * @param msaws\r
 111          * @param presets\r
 112          *            list of the Preset\r
 113          * @throws UnsupportedRuntimeException\r
 114          */\r
 115         static <T> boolean presetAlign(MsaWS<T> msaws, List<Preset<T>> presets)\r
 116                         throws UnsupportedRuntimeException {\r
 117                 boolean succeed = false;\r
 118                 for (Preset<T> preset : presets) {\r
 119                         System.out.print("Aligning with preset '" + preset.getName()\r
 120                                         + "'... ");\r
 121                         Alignment al = null;\r
 122                         try {\r
 123                                 String taskId = msaws.presetAlign(seqs, preset);\r
 124                                 al = msaws.getResult(taskId);\r
 125                                 if (al != null) {\r
 126                                         System.out.println(OK);\r
 127                                 }\r
 128                                 succeed = true;\r
 129                         } catch (UnsupportedRuntimeException e) {\r
 130                                 System.out.println(FAILED);\r
 131                                 // If executable is not supported than none of the presets are\r
 132                                 // going to work\r
 133                                 throw new UnsupportedRuntimeException(e);\r
 134                         } catch (JobSubmissionException e) {\r
 135                                 // TODO custom message\r
 136                                 System.out.println(FAILED);\r
 137                                 System.out.println();\r
 138                                 e.printStackTrace();\r
 139                                 continue;\r
 140                         } catch (WrongParameterException e) {\r
 141                                 // TODO custom message\r
 142                                 System.out.println(FAILED);\r
 143                                 System.out.println();\r
 144                                 e.printStackTrace();\r
 145                                 continue;\r
 146                         } catch (ResultNotAvailableException e) {\r
 147                                 // TODO custom message\r
 148                                 System.out.println(FAILED);\r
 149                                 System.out.println();\r
 150                                 e.printStackTrace();\r
 151                                 continue;\r
 152                         }\r
 153                 }\r
 154                 return succeed;\r
 155         }\r
 156 \r
 157         /**\r
 158          * Call most of web services functions and check the output\r
 159          * \r
 160          * @param <T>\r
 161          *            web service type\r
 162          * @param msaws\r
 163          * @throws UnsupportedRuntimeException\r
 164          *             is thrown if the connection to a web service was made, but\r
 165          *             the web service is not functional. e.g. when native\r
 166          *             executable does not exists for a server platform\r
 167          */\r
 168         static <T> boolean checkService(MsaWS<T> msaws)\r
 169                         throws UnsupportedRuntimeException {\r
 170 \r
 171                 boolean succeed = testDefaultAlignment(msaws);\r
 172 \r
 173                 // If exception above is thrown than the tests below is not run\r
 174 \r
 175                 PresetManager<T> pmanager = msaws.getPresets();\r
 176                 if (pmanager != null && pmanager.getPresets().size() > 0) {\r
 177                         System.out.println("Testing alignment with presets:");\r
 178                         List<Preset<T>> plist = pmanager.getPresets();\r
 179                         succeed = !succeed ? presetAlign(msaws, plist) : succeed;\r
 180                 }\r
 181 \r
 182                 System.out.print("Querying presets...");\r
 183 \r
 184                 if (pmanager != null && pmanager.getPresets().size() > 0) {\r
 185                         System.out.println(OK);\r
 186                 } else {\r
 187                         System.out.println("UNSUPPORTED");\r
 188                 }\r
 189 \r
 190                 System.out.print("Querying Parameters...");\r
 191                 RunnerConfig<T> options = msaws.getRunnerOptions();\r
 192                 if (options != null && options.getArguments().size() > 0) {\r
 193                         System.out.println(OK);\r
 194                 } else {\r
 195                         System.out.println(FAILED);\r
 196                         succeed = false;\r
 197                 }\r
 198 \r
 199                 System.out.print("Querying Limits...");\r
 200                 LimitsManager<T> limits = msaws.getLimits();\r
 201                 if (limits != null && limits.getLimits().size() > 0) {\r
 202                         System.out.println(OK);\r
 203                 } else {\r
 204                         System.out.println("UNSUPPORTED");\r
 205                 }\r
 206 \r
 207                 System.out.print("Querying Local Engine Limits...");\r
 208                 Limit<T> localLimit = msaws\r
 209                                 .getLimit(PresetManager.LOCAL_ENGINE_LIMIT_PRESET);\r
 210                 if (localLimit != null) {\r
 211                         System.out.println(OK);\r
 212                 } else {\r
 213                         System.out.println("UNSUPPORTED");\r
 214                 }\r
 215                 return succeed;\r
 216         }\r
 217 \r
 218         /**\r
 219          * Align using default settings\r
 220          * \r
 221          * @param <T>\r
 222          * @param msaws\r
 223          * @throws UnsupportedRuntimeException\r
 224          */\r
 225         static <T> boolean testDefaultAlignment(MsaWS<T> msaws)\r
 226                         throws UnsupportedRuntimeException {\r
 227                 System.out.print("Testing alignment with default parameters:");\r
 228                 Alignment al = null;\r
 229                 boolean succeed = false;\r
 230                 try {\r
 231                         String taskId = msaws.align(seqs);\r
 232                         System.out.print("\nQuerying job status...");\r
 233                         JobStatus status = msaws.getJobStatus(taskId);\r
 234                         while (status != JobStatus.FINISHED) {\r
 235                                 Thread.sleep(1000);\r
 236                                 status = msaws.getJobStatus(taskId);\r
 237                         }\r
 238                         System.out.println(OK);\r
 239                         System.out.print("Retrieving results...");\r
 240                         al = msaws.getResult(taskId);\r
 241                         succeed = true;\r
 242                 } catch (ResultNotAvailableException e) {\r
 243                         System.out.println(FAILED);\r
 244                         e.printStackTrace();\r
 245                 } catch (JobSubmissionException e) {\r
 246                         System.out.println(FAILED);\r
 247                         System.out.println();\r
 248                         e.printStackTrace();\r
 249                 } catch (InterruptedException e) {\r
 250                         System.out.println(FAILED);\r
 251                         System.out.println();\r
 252                         e.printStackTrace();\r
 253                 }\r
 254                 if (al != null) {\r
 255                         System.out.println(OK);\r
 256                 }\r
 257                 return succeed;\r
 258         }\r
 259 \r
 260         /**\r
 261          * Connect to a WS using the host and the service name\r
 262          * \r
 263          * @param <T>\r
 264          * @param host\r
 265          * @param service\r
 266          * @return\r
 267          */\r
 268         static <T> MsaWS<T> connect(String host, Services service) {\r
 269                 MsaWS<T> msaws = null;\r
 270                 try {\r
 271                         System.out.print("Connecting to service " + service + " on " + host\r
 272                                         + " ... ");\r
 273                         msaws = Jws2Client.connect(host, service);\r
 274                         System.out.println(OK);\r
 275                 } catch (WebServiceException e) {\r
 276                         System.out.println(FAILED);\r
 277                 }\r
 278                 return msaws;\r
 279         }\r
 280 \r
 281         /**\r
 282          * Test JWS2 web services\r
 283          * \r
 284          * @param <T>\r
 285          *            web service type\r
 286          * @param args\r
 287          *            -h=<Your web application server host name, port and JWS2\r
 288          *            context path>\r
 289          * \r
 290          *            -s=<ServiceName> which is optional. If service name is not\r
 291          *            provided then all known JWS2 web services are tested\r
 292          * @throws IOException\r
 293          */\r
 294         public static <T> void main(String[] args) throws IOException {\r
 295 \r
 296                 if (args == null || args.length < 1) {\r
 297                         printUsage();\r
 298                         System.exit(0);\r
 299                 }\r
 300                 String host = Jws2Client.getHost(args);\r
 301                 String serviceName = Jws2Client.getServiceName(args);\r
 302                 if (!Jws2Client.validURL(host)) {\r
 303                         System.out\r
 304                                         .println("<host_and_context> parameter is not provided or is incorrect!");\r
 305                         System.exit(1);\r
 306                 }\r
 307                 boolean succeed = false;\r
 308                 MsaWS<T> msaws = null;\r
 309                 if (serviceName != null) {\r
 310                         Services service = Services.getService(serviceName);\r
 311                         if (service == null) {\r
 312                                 System.out.println("Service '" + serviceName\r
 313                                                 + "' is not supported. Valid values are: "\r
 314                                                 + Arrays.toString(Services.values()));\r
 315                                 System.out.println();\r
 316                                 printUsage();\r
 317                                 System.exit(1);\r
 318                         }\r
 319 \r
 320                         msaws = connect(host, service);\r
 321                         if (msaws == null) {\r
 322                                 System.exit(1);\r
 323                         }\r
 324                         try {\r
 325                                 succeed = checkService(msaws);\r
 326                         } catch (UnsupportedRuntimeException ignored) {\r
 327                                 System.exit(1);\r
 328                         } finally {\r
 329                                 ((Closeable) msaws).close();\r
 330                         }\r
 331                         reportResults(service, succeed);\r
 332                         System.exit(0);\r
 333                 }\r
 334 \r
 335                 System.out\r
 336                                 .println("<ServiceName> is not provided checking all known services...");\r
 337 \r
 338                 for (Services serv : Services.values()) {\r
 339                         System.out.println();\r
 340                         msaws = connect(host, serv);\r
 341                         if (msaws == null) {\r
 342                                 continue;\r
 343                         }\r
 344                         try {\r
 345                                 succeed = checkService(msaws);\r
 346                         } catch (UnsupportedRuntimeException ignored) {\r
 347                                 System.out.println("Service " + serv + " IS NOT FUNCTIONAL");\r
 348                                 continue;\r
 349                         } finally {\r
 350                                 ((Closeable) msaws).close();\r
 351                         }\r
 352                         reportResults(serv, succeed);\r
 353                 }\r
 354 \r
 355         }\r
 356 \r
 357         private static void reportResults(Services serv, boolean succeed) {\r
 358                 if (succeed) {\r
 359                         System.out.println("Check is completed. The Service " + serv\r
 360                                         + " IS WORKING");\r
 361                 } else {\r
 362                         System.out.println("Check is completed. The Service " + serv\r
 363                                         + " HAS SOME PROBLEMS");\r
 364                 }\r
 365         }\r
 366 }\r