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