webservices/compbio/ws/client/Jws2Client.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.inputkey;\r
  22 import static compbio.ws.client.Constraints.outputkey;\r
  23 import static compbio.ws.client.Constraints.paramFile;\r
  24 \r
  25 import java.io.Closeable;\r
  26 import java.io.File;\r
  27 import java.io.FileInputStream;\r
  28 import java.io.IOException;\r
  29 import java.io.PrintWriter;\r
  30 import java.io.Writer;\r
  31 import java.net.ConnectException;\r
  32 import java.net.MalformedURLException;\r
  33 import java.net.URL;\r
  34 import java.util.Arrays;\r
  35 import java.util.Collections;\r
  36 import java.util.List;\r
  37 import java.util.Set;\r
  38 import java.util.logging.Level;\r
  39 import java.util.logging.Logger;\r
  40 \r
  41 import javax.xml.namespace.QName;\r
  42 import javax.xml.ws.Service;\r
  43 import javax.xml.ws.WebServiceException;\r
  44 \r
  45 import compbio.data.msa.JABAService;\r
  46 import compbio.data.msa.Metadata;\r
  47 import compbio.data.msa.MsaWS;\r
  48 import compbio.data.msa.RegistryWS;\r
  49 import compbio.data.msa.SequenceAnnotation;\r
  50 import compbio.data.sequence.Alignment;\r
  51 import compbio.data.sequence.FastaSequence;\r
  52 import compbio.data.sequence.ScoreManager;\r
  53 import compbio.data.sequence.SequenceUtil;\r
  54 import compbio.data.sequence.UnknownFileFormatException;\r
  55 import compbio.metadata.JobSubmissionException;\r
  56 import compbio.metadata.Option;\r
  57 import compbio.metadata.Preset;\r
  58 import compbio.metadata.ResultNotAvailableException;\r
  59 import compbio.metadata.WrongParameterException;\r
  60 import compbio.util.FileUtil;\r
  61 \r
  62 /**\r
  63  * A command line client for JAva Bioinformatics Analysis Web Services\r
  64  * \r
  65  * @author pvtroshin\r
  66  * @version 1.0\r
  67  */\r
  68 public class Jws2Client {\r
  69 \r
  70         /*\r
  71          * Use java.util.Logger instead of log4j logger to reduce the size of the\r
  72          * client package\r
  73          */\r
  74         private static final Logger log = Logger.getLogger(Jws2Client.class\r
  75                         .getCanonicalName());\r
  76 \r
  77         /**\r
  78          * Attempt to construct the URL object from the string\r
  79          * \r
  80          * @param urlstr\r
  81          * @return true if it succeed false otherwise\r
  82          */\r
  83         public static boolean validURL(String urlstr) {\r
  84                 try {\r
  85                         if (urlstr == null || urlstr.trim().length() == 0) {\r
  86                                 return false;\r
  87                         }\r
  88                         new URL(urlstr);\r
  89                 } catch (MalformedURLException e) {\r
  90                         return false;\r
  91                 }\r
  92                 return true;\r
  93         }\r
  94 \r
  95         /**\r
  96          * Connects to the service and do the job as requested, if something goes\r
  97          * wrong reports or/and prints usage help.\r
  98          * \r
  99          * @param <T>\r
 100          *            web service type\r
 101          * @param cmd\r
 102          *            command line options\r
 103          * @throws IOException\r
 104          */\r
 105         <T> Jws2Client(String[] cmd) throws IOException {\r
 106 \r
 107                 String hostname = CmdHelper.getHost(cmd);\r
 108                 if (hostname == null) {\r
 109                         System.err.println("Host name is not provided!");\r
 110                         printUsage(1);\r
 111                 }\r
 112 \r
 113                 if (!validURL(hostname)) {\r
 114                         System.err.println("Host name is not valid!");\r
 115                         printUsage(1);\r
 116                 }\r
 117                 // Just list available services and quit\r
 118                 boolean listServices = CmdHelper.listServices(cmd);\r
 119                 if (listServices) {\r
 120                         listServices(hostname);\r
 121                         System.exit(0);\r
 122                 }\r
 123 \r
 124                 String serviceName = CmdHelper.getServiceName(cmd);\r
 125                 if (serviceName == null) {\r
 126                         System.err.println("Service name is no provided!");\r
 127                         printUsage(1);\r
 128                 }\r
 129                 Services service = Services.getService(serviceName);\r
 130                 if (service == null) {\r
 131                         System.err.println("Service " + serviceName\r
 132                                         + " is no recognized! Valid values are: "\r
 133                                         + Arrays.toString(Services.values()));\r
 134                         printUsage(1);\r
 135                 }\r
 136                 // Test service and quit\r
 137                 boolean testService = CmdHelper.testService(cmd);\r
 138                 if (testService) {\r
 139                         testService(hostname, service, new PrintWriter(System.out, true));\r
 140                         System.exit(0);\r
 141                 }\r
 142 \r
 143                 File inputFile = IOHelper.getFile(cmd, inputkey, true);\r
 144                 File outFile = IOHelper.getFile(cmd, outputkey, false);\r
 145                 File parametersFile = IOHelper.getFile(cmd, paramFile, true);\r
 146                 String presetName = CmdHelper.getPresetName(cmd);\r
 147 \r
 148                 Metadata<T> msaws = (Metadata<T>) connect(hostname, service);\r
 149                 Preset<T> preset = null;\r
 150                 if (presetName != null) {\r
 151                         preset = MetadataHelper.getPreset(msaws, presetName);\r
 152                 }\r
 153                 List<Option<T>> customOptions = null;\r
 154                 if (parametersFile != null) {\r
 155                         List<String> prms = IOHelper.loadParameters(parametersFile);\r
 156                         customOptions = MetadataHelper.processParameters(prms,\r
 157                                         msaws.getRunnerOptions());\r
 158                 }\r
 159                 Alignment alignment = null;\r
 160                 if (inputFile != null) {\r
 161                         Writer writer = null;\r
 162                         if (outFile != null) {\r
 163                                 writer = IOHelper.getWriter(outFile);\r
 164                         } else {\r
 165                                 // this stream is going to be closed later which is fine as\r
 166                                 // std.out will not be\r
 167                                 writer = new PrintWriter(System.out, true);\r
 168                         }\r
 169                         if (service.getServiceType() == SequenceAnnotation.class) {\r
 170                                 ScoreManager result = analize(inputFile,\r
 171                                                 ((SequenceAnnotation<T>) msaws), preset, customOptions);\r
 172 \r
 173                                 IOHelper.writeOut(writer, result);\r
 174                         } else {\r
 175                                 alignment = align(inputFile, (MsaWS<T>) msaws, preset,\r
 176                                                 customOptions);\r
 177                                 IOHelper.writeOut(writer, alignment);\r
 178                         }\r
 179                         writer.close();\r
 180                 }\r
 181 \r
 182                 boolean listParameters = CmdHelper.listParameters(cmd);\r
 183                 if (listParameters) {\r
 184                         System.out.println(MetadataHelper.getParametersList(msaws));\r
 185                 }\r
 186                 boolean listPreset = CmdHelper.listPresets(cmd);\r
 187                 if (listPreset) {\r
 188                         System.out.println(MetadataHelper.getPresetList(msaws));\r
 189                 }\r
 190                 boolean listLimits = CmdHelper.listLimits(cmd);\r
 191                 if (listLimits) {\r
 192                         System.out.println(MetadataHelper.getLimits(msaws));\r
 193                 }\r
 194                 log.fine("Disconnecting...");\r
 195                 ((Closeable) msaws).close();\r
 196                 log.fine("Disconnected successfully!");\r
 197         }\r
 198 \r
 199         /**\r
 200          * Asks registry to test the service on the host hostname\r
 201          * \r
 202          * @param hostname\r
 203          * @param service\r
 204          * @param writer\r
 205          * @throws ConnectException\r
 206          * @throws WebServiceException\r
 207          */\r
 208         public static void testService(String hostname, Services service,\r
 209                         PrintWriter writer) throws ConnectException, WebServiceException {\r
 210                 RegistryWS registry = connectToRegistry(hostname);\r
 211                 if (registry != null) {\r
 212                         String message = registry.testService(service);\r
 213                         writer.println("Service " + service + " testing results: ");\r
 214                         writer.println(message);\r
 215                         FileUtil.closeSilently(((Closeable) registry));\r
 216                 }\r
 217                 writer.flush();\r
 218         }\r
 219 \r
 220         public static Set<Services> getServices(String hostname)\r
 221                         throws WebServiceException, ConnectException {\r
 222                 RegistryWS registry = connectToRegistry(hostname);\r
 223                 Set<Services> services = Collections.EMPTY_SET;\r
 224                 if (registry != null) {\r
 225                         services = registry.getSupportedServices();\r
 226                         FileUtil.closeSilently(((Closeable) registry));\r
 227                 }\r
 228                 return services;\r
 229         }\r
 230 \r
 231         private static void listServices(String hostname)\r
 232                         throws WebServiceException, IOException {\r
 233                 Set<Services> services = Jws2Client.getServices(hostname);\r
 234                 if (!services.isEmpty()) {\r
 235                         System.out.println("Supported services are: "\r
 236                                         + Services.toString(services));\r
 237                 } else {\r
 238                         System.out.println("Failed to connect to the registry! ");\r
 239                 }\r
 240         }\r
 241 \r
 242         /**\r
 243          * Calculate conservation for sequences loaded from the file\r
 244          * \r
 245          * @param wsproxy\r
 246          *            a web service proxy\r
 247          * @param file\r
 248          *            the file to read the results from\r
 249          * @param preset\r
 250          *            Preset to use optional\r
 251          * @param customOptions\r
 252          *            the list of options\r
 253          * @return Set<Score> the conservation scores\r
 254          * @throws UnknownFileFormatException\r
 255          */\r
 256         static <T> ScoreManager analize(List<FastaSequence> fastalist,\r
 257                         SequenceAnnotation<T> wsproxy, Preset<T> preset,\r
 258                         List<Option<T>> customOptions) {\r
 259 \r
 260                 ScoreManager scores = null;\r
 261                 try {\r
 262                         String jobId = null;\r
 263                         if (customOptions != null && preset != null) {\r
 264                                 System.out\r
 265                                                 .println("WARN: Parameters (-f) are defined together with a preset (-r) ignoring preset!");\r
 266                         }\r
 267                         if (customOptions != null) {\r
 268                                 jobId = wsproxy.customAnalize(fastalist, customOptions);\r
 269                         } else if (preset != null) {\r
 270                                 jobId = wsproxy.presetAnalize(fastalist, preset);\r
 271                         } else {\r
 272                                 jobId = wsproxy.analize(fastalist);\r
 273                         }\r
 274                         System.out.println("\n\ncalling analise.........");\r
 275                         Thread.sleep(1000);\r
 276                         scores = wsproxy.getAnnotation(jobId);\r
 277 \r
 278                 } catch (JobSubmissionException e) {\r
 279                         System.err\r
 280                                         .println("Exception while submitting job to a web server. "\r
 281                                                         + "Exception details are below:");\r
 282                         e.printStackTrace();\r
 283                 } catch (ResultNotAvailableException e) {\r
 284                         System.err.println("Exception while waiting for results. "\r
 285                                         + "Exception details are below:");\r
 286                         e.printStackTrace();\r
 287                 } catch (InterruptedException e) {\r
 288                         // ignore and propagate an interruption\r
 289                         Thread.currentThread().interrupt();\r
 290                         System.err.println("Exception while waiting for results. "\r
 291                                         + "Exception details are below:");\r
 292                         e.printStackTrace();\r
 293                 } catch (WrongParameterException e) {\r
 294                         System.err\r
 295                                         .println("Exception while parsing the web method input parameters. "\r
 296                                                         + "Exception details are below:");\r
 297                         e.printStackTrace();\r
 298                 }\r
 299                 return scores;\r
 300 \r
 301         }\r
 302 \r
 303         /**\r
 304          * Calculate conservation for sequences loaded from the file\r
 305          * \r
 306          * @param wsproxy\r
 307          *            a web service proxy\r
 308          * @param file\r
 309          *            the file to read the results from\r
 310          * @param preset\r
 311          *            Preset to use optional\r
 312          * @param customOptions\r
 313          *            the list of options\r
 314          * @return Set<Score> the conservation scores\r
 315          * @throws IOException\r
 316          * @throws UnknownFileFormatException\r
 317          */\r
 318         static <T> ScoreManager analize(File file, SequenceAnnotation<T> wsproxy,\r
 319                         Preset<T> preset, List<Option<T>> customOptions) {\r
 320                 List<FastaSequence> fastalist = null;\r
 321                 try {\r
 322                         fastalist = SequenceUtil.openInputStream(file.getAbsolutePath());\r
 323                         assert !fastalist.isEmpty() : "Input is empty!";\r
 324                 } catch (IOException e) {\r
 325                         System.err\r
 326                                         .println("Exception while reading the input file. "\r
 327                                                         + "Check that the input file contains a list of fasta formatted sequences! "\r
 328                                                         + "Exception details are below:");\r
 329                         e.printStackTrace();\r
 330                 } catch (UnknownFileFormatException e) {\r
 331                         System.err\r
 332                                         .println("Exception while attempting to read the input file "\r
 333                                                         + "Exception details are below:");\r
 334                         System.out.println(e.getMessage());\r
 335                         e.printStackTrace();\r
 336                 }\r
 337                 return analize(fastalist, wsproxy, preset, customOptions);\r
 338         }\r
 339         /**\r
 340          * Connects to a web service by the host and the service name web service\r
 341          * type\r
 342          * \r
 343          * @param host\r
 344          *            the fully qualified name of JABAWS server including JABAWS\r
 345          *            context name e.g\r
 346          *            http://nanna.cluster.lifesci.dundee.ac.uk:8080/jaba\r
 347          * @param service\r
 348          *            the name of the JABAWS service to connect to\r
 349          * @return JABAService<T>\r
 350          * @throws WebServiceException\r
 351          * @throws ConnectException\r
 352          *             if fails to connect to the service on the host\r
 353          */\r
 354         public static JABAService connect(String host, Services service)\r
 355                         throws WebServiceException, ConnectException {\r
 356                 URL url = null;\r
 357                 log.log(Level.FINE, "Attempting to connect...");\r
 358                 try {\r
 359                         url = new URL(host + "/" + service.toString() + "?wsdl");\r
 360                 } catch (MalformedURLException e) {\r
 361                         e.printStackTrace();\r
 362                         // ignore as the host name is already verified\r
 363                 }\r
 364                 Service serv = null;\r
 365                 try {\r
 366                         serv = service.getService(url, JABAService.SERVICE_NAMESPACE);\r
 367                 } catch (WebServiceException wse) {\r
 368                         System.out.println("Connecting to JABAWS version 2 service");\r
 369                         if (isV2service(wse)) {\r
 370                                 serv = service\r
 371                                                 .getService(url, JABAService.V2_SERVICE_NAMESPACE);\r
 372                         }\r
 373                 }\r
 374                 if (serv == null) {\r
 375                         throw new ConnectException("Could not connect to " + url\r
 376                                         + " the server is down?");\r
 377                 }\r
 378                 JABAService serviceIF = service.getInterface(serv);\r
 379                 log.log(Level.INFO, "Connected successfully!");\r
 380 \r
 381                 return serviceIF;\r
 382         }\r
 383 \r
 384         static boolean isV2service(WebServiceException wse) {\r
 385                 String message = wse.getMessage();\r
 386                 int idx = message.indexOf("not a valid service");\r
 387                 if (idx > 0) {\r
 388                         if (message.substring(idx).contains(\r
 389                                         JABAService.V2_SERVICE_NAMESPACE)) {\r
 390                                 return true;\r
 391                         }\r
 392                 }\r
 393                 return false;\r
 394         }\r
 395 \r
 396         /**\r
 397          * Get a connection of JABAWS registry\r
 398          * \r
 399          * @param host\r
 400          *            the fully qualified name of JABAWS server including JABAWS\r
 401          *            context name e.g\r
 402          *            http://nanna.cluster.lifesci.dundee.ac.uk:8080/jaba\r
 403          * @return compbio.data.msa.RegistryWS - instance of a RegistryWS web\r
 404          *         service\r
 405          * @throws WebServiceException\r
 406          * @throws ConnectException\r
 407          */\r
 408         public static compbio.data.msa.RegistryWS connectToRegistry(String host)\r
 409                         throws WebServiceException, ConnectException {\r
 410                 URL url = null;\r
 411                 String service = "RegistryWS";\r
 412                 log.log(Level.FINE, "Attempting to connect...");\r
 413 \r
 414                 try {\r
 415                         url = new URL(host + "/" + service + "?wsdl");\r
 416                 } catch (MalformedURLException e) {\r
 417                         e.printStackTrace();\r
 418                         // ignore as the host name is already verified\r
 419                 }\r
 420                 QName qname = new QName(JABAService.V2_SERVICE_NAMESPACE, service);\r
 421                 Service serv = Service.create(url, qname);\r
 422 \r
 423                 if (serv == null) {\r
 424                         throw new ConnectException("Could not connect to " + url\r
 425                                         + " the server is down?");\r
 426                 }\r
 427 \r
 428                 QName portName = new QName(serv.getServiceName().getNamespaceURI(),\r
 429                                 service + "Port");\r
 430                 compbio.data.msa.RegistryWS serviceIF = serv.getPort(portName,\r
 431                                 compbio.data.msa.RegistryWS.class);\r
 432 \r
 433                 log.log(Level.INFO, "Connected to " + service + " successfully!");\r
 434 \r
 435                 return serviceIF;\r
 436         }\r
 437 \r
 438         /**\r
 439          * Align sequences from the file using MsaWS\r
 440          * \r
 441          * @param <T>\r
 442          *            web service type e.g. Clustal\r
 443          * @param file\r
 444          *            to write the resulting alignment to\r
 445          * @param msaws\r
 446          *            MsaWS required\r
 447          * @param preset\r
 448          *            Preset to use optional\r
 449          * @param customOptions\r
 450          *            file which contains new line separated list of options\r
 451          * @return Alignment\r
 452          */\r
 453         static <T> Alignment align(File file, MsaWS<T> msaws, Preset<T> preset,\r
 454                         List<Option<T>> customOptions) {\r
 455                 FileInputStream instream = null;\r
 456                 List<FastaSequence> fastalist = null;\r
 457                 Alignment alignment = null;\r
 458                 try {\r
 459                         instream = new FileInputStream(file);\r
 460                         fastalist = SequenceUtil.readFasta(instream);\r
 461                         instream.close();\r
 462                         String jobId = null;\r
 463                         if (customOptions != null && preset != null) {\r
 464                                 System.out\r
 465                                                 .println("WARN: Parameters (-f) are defined together with a preset (-r) ignoring preset!");\r
 466                         }\r
 467                         if (customOptions != null) {\r
 468                                 jobId = msaws.customAlign(fastalist, customOptions);\r
 469                         } else if (preset != null) {\r
 470                                 jobId = msaws.presetAlign(fastalist, preset);\r
 471                         } else {\r
 472                                 jobId = msaws.align(fastalist);\r
 473                         }\r
 474                         System.out.println("\n\ncalling align.........");\r
 475                         Thread.sleep(1000);\r
 476                         alignment = msaws.getResult(jobId);\r
 477 \r
 478                 } catch (IOException e) {\r
 479                         System.err\r
 480                                         .println("Exception while reading the input file. "\r
 481                                                         + "Check that the input file contains a list of fasta formatted sequences! "\r
 482                                                         + "Exception details are below:");\r
 483                         e.printStackTrace();\r
 484                 } catch (JobSubmissionException e) {\r
 485                         System.err\r
 486                                         .println("Exception while submitting job to a web server. "\r
 487                                                         + "Exception details are below:");\r
 488                         e.printStackTrace();\r
 489                 } catch (ResultNotAvailableException e) {\r
 490                         System.err.println("Exception while waiting for results. "\r
 491                                         + "Exception details are below:");\r
 492                         e.printStackTrace();\r
 493                 } catch (InterruptedException ignored) {\r
 494                         // ignore and propagate an interruption\r
 495                         Thread.currentThread().interrupt();\r
 496                 } catch (WrongParameterException e) {\r
 497                         e.printStackTrace();\r
 498                 } finally {\r
 499                         if (instream != null) {\r
 500                                 try {\r
 501                                         instream.close();\r
 502                                 } catch (IOException ignored) {\r
 503                                         // ignore\r
 504                                 }\r
 505                         }\r
 506                 }\r
 507                 return alignment;\r
 508         }\r
 509 \r
 510         /**\r
 511          * Prints Jws2Client usage information to standard out\r
 512          * \r
 513          * @param exitStatus\r
 514          */\r
 515         static void printUsage(int exitStatus) {\r
 516                 System.out.println(Constraints.help_text);\r
 517                 System.exit(exitStatus);\r
 518         }\r
 519 \r
 520         /**\r
 521          * Starts command line client, if no parameter are supported print help. Two\r
 522          * parameters are required for successful call the JWS2 host name and a\r
 523          * service name.\r
 524          * \r
 525          * @param args\r
 526          *            Usage: <Class or Jar file name> -h=host_and_context\r
 527          *            -s=serviceName ACTION [OPTIONS]\r
 528          * \r
 529          *            -h=<host_and_context> - a full URL to the JWS2 web server\r
 530          *            including context path e.g. http://10.31.1.159:8080/ws\r
 531          * \r
 532          *            -s=<ServiceName> - one of [MafftWS, MuscleWS, ClustalWS,\r
 533          *            TcoffeeWS, ProbconsWS] ACTIONS:\r
 534          * \r
 535          *            -i=<inputFile> - full path to fasta formatted sequence file,\r
 536          *            from which to align sequences\r
 537          * \r
 538          *            -parameters - lists parameters supported by web service\r
 539          * \r
 540          *            -presets - lists presets supported by web service\r
 541          * \r
 542          *            -limits - lists web services limits Please note that if input\r
 543          *            file is specified other actions are ignored\r
 544          * \r
 545          *            OPTIONS: (only for use with -i action):\r
 546          * \r
 547          *            -r=<presetName> - name of the preset to use\r
 548          * \r
 549          *            -o=<outputFile> - full path to the file where to write an\r
 550          *            alignment -f=<parameterInputFile> - the name of the file with\r
 551          *            the list of parameters to use. Please note that -r and -f\r
 552          *            options cannot be used together. Alignment is done with either\r
 553          *            preset or a parameters from the file, but not both!\r
 554          * \r
 555          */\r
 556         public static void main(String[] args) {\r
 557 \r
 558                 if (args == null) {\r
 559                         printUsage(1);\r
 560                 }\r
 561                 if (args.length < 2) {\r
 562                         System.err.println("Host and service names are required!");\r
 563                         printUsage(1);\r
 564                 }\r
 565 \r
 566                 try {\r
 567                         new Jws2Client(args);\r
 568                 } catch (IOException e) {\r
 569                         log.log(Level.SEVERE, "IOException in client! " + e.getMessage(),\r
 570                                         e.getCause());\r
 571                         System.err.println("Cannot write output file! Stack trace: ");\r
 572                         e.printStackTrace();\r
 573                 }\r
 574         }\r
 575 }\r