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 JWS2 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