webservices/compbio/ws/client/Jws2Client.java

   1 /* Copyright (c) 2011 Peter Troshin\r
   2  *  \r
   3  *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0     \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.FoldWS;\r
  47 import compbio.data.msa.Metadata;\r
  48 import compbio.data.msa.MsaWS;\r
  49 import compbio.data.msa.RegistryWS;\r
  50 import compbio.data.msa.SequenceAnnotation;\r
  51 import compbio.data.sequence.Alignment;\r
  52 import compbio.data.sequence.FastaSequence;\r
  53 import compbio.data.sequence.RNAstruct;\r
  54 import compbio.data.sequence.ScoreManager;\r
  55 import compbio.data.sequence.ClustalAlignmentUtil;\r
  56 import compbio.data.sequence.SequenceUtil;\r
  57 import compbio.data.sequence.UnknownFileFormatException;\r
  58 import compbio.metadata.JobSubmissionException;\r
  59 import compbio.metadata.Option;\r
  60 import compbio.metadata.Preset;\r
  61 import compbio.metadata.ResultNotAvailableException;\r
  62 import compbio.metadata.WrongParameterException;\r
  63 import compbio.util.FileUtil;\r
  64 \r
  65 /**\r
  66  * A command line client for JAva Bioinformatics Analysis Web Services\r
  67  * \r
  68  * @author pvtroshin\r
  69  * @version 1.0\r
  70  */\r
  71 public class Jws2Client {\r
  72 \r
  73         /*\r
  74          * Use java.util.Logger instead of log4j logger to reduce the size of the\r
  75          * client package\r
  76          */\r
  77         private static final Logger log = Logger.getLogger(Jws2Client.class\r
  78                         .getCanonicalName());\r
  79 \r
  80         /**\r
  81          * Attempt to construct the URL object from the string\r
  82          * \r
  83          * @param urlstr\r
  84          * @return true if it succeed false otherwise\r
  85          */\r
  86         public static boolean validURL(String urlstr) {\r
  87                 try {\r
  88                         if (urlstr == null || urlstr.trim().length() == 0) {\r
  89                                 return false;\r
  90                         }\r
  91                         new URL(urlstr);\r
  92                 } catch (MalformedURLException e) {\r
  93                         return false;\r
  94                 }\r
  95                 return true;\r
  96         }\r
  97 \r
  98         /**\r
  99          * Connects to the service and do the job as requested, if something goes\r
 100          * wrong reports or/and prints usage help.\r
 101          * \r
 102          * @param <T>\r
 103          *            web service type\r
 104          * @param cmd\r
 105          *            command line options\r
 106          * @throws IOException\r
 107          */\r
 108         <T> Jws2Client(String[] cmd) throws IOException {\r
 109                 \r
 110 \r
 111                 String hostname = CmdHelper.getHost(cmd);\r
 112                 if (hostname == null) {\r
 113                         System.err.println("Host name is not provided!");\r
 114                         printUsage(1);\r
 115                 }\r
 116 \r
 117                 if (!validURL(hostname)) {\r
 118                         System.err.println("Host name is not valid!");\r
 119                         printUsage(1);\r
 120                 }\r
 121                 // Just list available services and quit\r
 122                 boolean listServices = CmdHelper.listServices(cmd);\r
 123                 if (listServices) {\r
 124                         listServices(hostname);\r
 125                         System.exit(0);\r
 126                 }\r
 127 \r
 128                 String serviceName = CmdHelper.getServiceName(cmd);\r
 129                 if (serviceName == null) {\r
 130                         System.err.println("Service name is no provided!");\r
 131                         printUsage(1);\r
 132                 }\r
 133                 Services service = Services.getService(serviceName);\r
 134                 if (service == null) {\r
 135                         System.err.println("Service " + serviceName\r
 136                                         + " is no recognized! Valid values are: "\r
 137                                         + Arrays.toString(Services.values()));\r
 138                         printUsage(1);\r
 139                 }\r
 140                 // Test service and quit\r
 141                 boolean testService = CmdHelper.testService(cmd);\r
 142                 if (testService) {\r
 143                         testService(hostname, service, new PrintWriter(System.out, true));\r
 144                         System.exit(0);\r
 145                 }\r
 146 \r
 147                 File inputFile = IOHelper.getFile(cmd, inputkey, true);\r
 148                 File outFile = IOHelper.getFile(cmd, outputkey, false);\r
 149                 File parametersFile = IOHelper.getFile(cmd, paramFile, true);\r
 150                 String presetName = CmdHelper.getPresetName(cmd);\r
 151 \r
 152                 Metadata<T> msaws = (Metadata<T>) connect(hostname, service);\r
 153                 Metadata<T> foldws = (Metadata<T>) connect(hostname, service);\r
 154                 Preset<T> preset = null;\r
 155                 if (presetName != null) {\r
 156                         preset = MetadataHelper.getPreset(msaws, presetName);\r
 157                 }\r
 158                 List<Option<T>> customOptions = null;\r
 159                 if (parametersFile != null) {\r
 160                         List<String> prms = IOHelper.loadParameters(parametersFile);\r
 161                         customOptions = MetadataHelper.processParameters(prms,\r
 162                                         msaws.getRunnerOptions());\r
 163                 }\r
 164 //              System.out.println("The Options read from the command line: " + customOptions);\r
 165                 \r
 166                 Alignment alignment = null;\r
 167                 String rnastruct = null;\r
 168                 if (inputFile != null) {\r
 169                         Writer writer = null;\r
 170                         if (outFile != null) {\r
 171                                 writer = IOHelper.getWriter(outFile);\r
 172                         } else {\r
 173                                 // this stream is going to be closed later which is fine as\r
 174                                 // std.out will not be\r
 175                                 writer = new PrintWriter(System.out, true);\r
 176                         }\r
 177                         if (service.getServiceType() == SequenceAnnotation.class) {\r
 178                                 ScoreManager result = analize(inputFile,\r
 179                                                 ((SequenceAnnotation<T>) msaws), preset, customOptions);\r
 180 \r
 181                                 IOHelper.writeOut(writer, result);\r
 182                         } else if (service.getServiceType() == MsaWS.class) {\r
 183                                 alignment = align(inputFile, (MsaWS<T>) msaws, preset,\r
 184                                                 customOptions);\r
 185                                 IOHelper.writeOut(writer, alignment);\r
 186                         } else if (service.getServiceType() == FoldWS.class) {\r
 187                                 rnastruct = fold(inputFile, (FoldWS<T>) foldws, preset, customOptions);\r
 188                                 // No IOHelper method for rnastruct/String yet\r
 189                                 if (writer != null) {\r
 190                                         writer.write(rnastruct);\r
 191                                 }\r
 192                         }\r
 193                         writer.close();\r
 194                 }\r
 195 \r
 196                 boolean listParameters = CmdHelper.listParameters(cmd);\r
 197                 if (listParameters) {\r
 198                         System.out.println(MetadataHelper.getParametersList(msaws));\r
 199                 }\r
 200                 boolean listPreset = CmdHelper.listPresets(cmd);\r
 201                 if (listPreset) {\r
 202                         System.out.println(MetadataHelper.getPresetList(msaws));\r
 203                 }\r
 204                 boolean listLimits = CmdHelper.listLimits(cmd);\r
 205                 if (listLimits) {\r
 206                         System.out.println(MetadataHelper.getLimits(msaws));\r
 207                 }\r
 208                 log.fine("Disconnecting...");\r
 209                 ((Closeable) msaws).close();\r
 210                 log.fine("Disconnected successfully!");\r
 211         }\r
 212 \r
 213         /**\r
 214          * Asks registry to test the service on the host hostname\r
 215          * \r
 216          * @param hostname\r
 217          * @param service\r
 218          * @param writer\r
 219          * @throws ConnectException\r
 220          * @throws WebServiceException\r
 221          */\r
 222         public static void testService(String hostname, Services service,\r
 223                         PrintWriter writer) throws ConnectException, WebServiceException {\r
 224                 RegistryWS registry = connectToRegistry(hostname);\r
 225                 if (registry != null) {\r
 226                         String message = registry.testService(service);\r
 227                         writer.println("Service " + service + " testing results: ");\r
 228                         writer.println(message);\r
 229                         FileUtil.closeSilently(((Closeable) registry));\r
 230                 }\r
 231                 writer.flush();\r
 232         }\r
 233 \r
 234         public static Set<Services> getServices(String hostname)\r
 235                         throws WebServiceException, ConnectException {\r
 236                 RegistryWS registry = connectToRegistry(hostname);\r
 237                 Set<Services> services = Collections.EMPTY_SET;\r
 238                 if (registry != null) {\r
 239                         services = registry.getSupportedServices();\r
 240                         FileUtil.closeSilently(((Closeable) registry));\r
 241                 }\r
 242                 return services;\r
 243         }\r
 244 \r
 245         private static void listServices(String hostname)\r
 246                         throws WebServiceException, IOException {\r
 247                 Set<Services> services = Jws2Client.getServices(hostname);\r
 248                 if (!services.isEmpty()) {\r
 249                         System.out.println("Supported services are: "\r
 250                                         + Services.toString(services));\r
 251                 } else {\r
 252                         System.out.println("Failed to connect to the registry! ");\r
 253                 }\r
 254         }\r
 255 \r
 256         /**\r
 257          * Calculate conservation for sequences loaded from the file\r
 258          * \r
 259          * @param wsproxy\r
 260          *            a web service proxy\r
 261          * @param file\r
 262          *            the file to read the results from\r
 263          * @param preset\r
 264          *            Preset to use optional\r
 265          * @param customOptions\r
 266          *            the list of options\r
 267          * @return Set<Score> the conservation scores\r
 268          * @throws UnknownFileFormatException\r
 269          */\r
 270         static <T> ScoreManager analize(List<FastaSequence> fastalist,\r
 271                         SequenceAnnotation<T> wsproxy, Preset<T> preset,\r
 272                         List<Option<T>> customOptions) {\r
 273 \r
 274                 ScoreManager scores = null;\r
 275                 try {\r
 276                         String jobId = null;\r
 277                         if (customOptions != null && preset != null) {\r
 278                                 System.out\r
 279                                                 .println("WARN: Parameters (-f) are defined together with a preset (-r) ignoring preset!");\r
 280                         }\r
 281                         if (customOptions != null) {\r
 282                                 jobId = wsproxy.customAnalize(fastalist, customOptions);\r
 283                         } else if (preset != null) {\r
 284                                 jobId = wsproxy.presetAnalize(fastalist, preset);\r
 285                         } else {\r
 286                                 jobId = wsproxy.analize(fastalist);\r
 287                         }\r
 288                         System.out.println("\n\ncalling analise.........");\r
 289                         Thread.sleep(1000);\r
 290                         scores = wsproxy.getAnnotation(jobId);\r
 291 \r
 292                 } catch (JobSubmissionException e) {\r
 293                         System.err\r
 294                                         .println("Exception while submitting job to a web server. "\r
 295                                                         + "Exception details are below:");\r
 296                         e.printStackTrace();\r
 297                 } catch (ResultNotAvailableException e) {\r
 298                         System.err.println("Exception while waiting for results. "\r
 299                                         + "Exception details are below:");\r
 300                         e.printStackTrace();\r
 301                 } catch (InterruptedException e) {\r
 302                         // ignore and propagate an interruption\r
 303                         Thread.currentThread().interrupt();\r
 304                         System.err.println("Exception while waiting for results. "\r
 305                                         + "Exception details are below:");\r
 306                         e.printStackTrace();\r
 307                 } catch (WrongParameterException e) {\r
 308                         System.err\r
 309                                         .println("Exception while parsing the web method input parameters. "\r
 310                                                         + "Exception details are below:");\r
 311                         e.printStackTrace();\r
 312                 }\r
 313                 return scores;\r
 314 \r
 315         }\r
 316 \r
 317         /**\r
 318          * Calculate conservation for sequences loaded from the file\r
 319          * \r
 320          * @param wsproxy\r
 321          *            a web service proxy\r
 322          * @param file\r
 323          *            the file to read the results from\r
 324          * @param preset\r
 325          *            Preset to use optional\r
 326          * @param customOptions\r
 327          *            the list of options\r
 328          * @return Set<Score> the conservation scores\r
 329          * @throws IOException\r
 330          * @throws UnknownFileFormatException\r
 331          */\r
 332         static <T> ScoreManager analize(File file, SequenceAnnotation<T> wsproxy,\r
 333                         Preset<T> preset, List<Option<T>> customOptions) {\r
 334                 List<FastaSequence> fastalist = null;\r
 335                 try {\r
 336                         fastalist = SequenceUtil.openInputStream(file.getAbsolutePath());\r
 337                         assert !fastalist.isEmpty() : "Input is empty!";\r
 338                 } catch (IOException e) {\r
 339                         System.err\r
 340                                         .println("Exception while reading the input file. "\r
 341                                                         + "Check that the input file contains a list of fasta formatted sequences! "\r
 342                                                         + "Exception details are below:");\r
 343                         e.printStackTrace();\r
 344                 } catch (UnknownFileFormatException e) {\r
 345                         System.err\r
 346                                         .println("Exception while attempting to read the input file "\r
 347                                                         + "Exception details are below:");\r
 348                         System.out.println(e.getMessage());\r
 349                         e.printStackTrace();\r
 350                 }\r
 351                 return analize(fastalist, wsproxy, preset, customOptions);\r
 352         }\r
 353         /**\r
 354          * Connects to a web service by the host and the service name web service\r
 355          * type\r
 356          * \r
 357          * @param host\r
 358          *            the fully qualified name of JABAWS server including JABAWS\r
 359          *            context name e.g\r
 360          *            http://nanna.cluster.lifesci.dundee.ac.uk:8080/jaba\r
 361          * @param service\r
 362          *            the name of the JABAWS service to connect to\r
 363          * @return JABAService<T>\r
 364          * @throws WebServiceException\r
 365          * @throws ConnectException\r
 366          *             if fails to connect to the service on the host\r
 367          */\r
 368         public static JABAService connect(String host, Services service)\r
 369                         throws WebServiceException, ConnectException {\r
 370                 URL url = null;\r
 371                 log.log(Level.FINE, "Attempting to connect...");\r
 372                 try {\r
 373                         url = new URL(host + "/" + service.toString() + "?wsdl");\r
 374                 } catch (MalformedURLException e) {\r
 375                         e.printStackTrace();\r
 376                         // ignore as the host name is already verified\r
 377                 }\r
 378                 Service serv = null;\r
 379                 try {\r
 380                         serv = service.getService(url, JABAService.SERVICE_NAMESPACE);\r
 381                 } catch (WebServiceException wse) {\r
 382                         System.out.println("Connecting to JABAWS version 2 service");\r
 383                         if (isV2service(wse)) {\r
 384                                 serv = service\r
 385                                                 .getService(url, JABAService.V2_SERVICE_NAMESPACE);\r
 386                         }\r
 387                 }\r
 388                 if (serv == null) {\r
 389                         throw new ConnectException("Could not connect to " + url\r
 390                                         + " the server is down?");\r
 391                 }\r
 392                 JABAService serviceIF = service.getInterface(serv);\r
 393                 log.log(Level.INFO, "Connected successfully!");\r
 394 \r
 395                 return serviceIF;\r
 396         }\r
 397 \r
 398         static boolean isV2service(WebServiceException wse) {\r
 399                 String message = wse.getMessage();\r
 400                 int idx = message.indexOf("not a valid service");\r
 401                 if (idx > 0) {\r
 402                         if (message.substring(idx).contains(\r
 403                                         JABAService.V2_SERVICE_NAMESPACE)) {\r
 404                                 return true;\r
 405                         }\r
 406                 }\r
 407                 return false;\r
 408         }\r
 409 \r
 410         /**\r
 411          * Get a connection of JABAWS registry\r
 412          * \r
 413          * @param host\r
 414          *            the fully qualified name of JABAWS server including JABAWS\r
 415          *            context name e.g\r
 416          *            http://nanna.cluster.lifesci.dundee.ac.uk:8080/jaba\r
 417          * @return compbio.data.msa.RegistryWS - instance of a RegistryWS web\r
 418          *         service\r
 419          * @throws WebServiceException\r
 420          * @throws ConnectException\r
 421          */\r
 422         public static compbio.data.msa.RegistryWS connectToRegistry(String host)\r
 423                         throws WebServiceException, ConnectException {\r
 424                 URL url = null;\r
 425                 String service = "RegistryWS";\r
 426                 log.log(Level.FINE, "Attempting to connect...");\r
 427 \r
 428                 try {\r
 429                         url = new URL(host + "/" + service + "?wsdl");\r
 430                 } catch (MalformedURLException e) {\r
 431                         e.printStackTrace();\r
 432                         // ignore as the host name is already verified\r
 433                 }\r
 434                 QName qname = new QName(JABAService.V2_SERVICE_NAMESPACE, service);\r
 435                 Service serv = Service.create(url, qname);\r
 436 \r
 437                 if (serv == null) {\r
 438                         throw new ConnectException("Could not connect to " + url\r
 439                                         + " the server is down?");\r
 440                 }\r
 441 \r
 442                 QName portName = new QName(serv.getServiceName().getNamespaceURI(),\r
 443                                 service + "Port");\r
 444                 compbio.data.msa.RegistryWS serviceIF = serv.getPort(portName,\r
 445                                 compbio.data.msa.RegistryWS.class);\r
 446 \r
 447                 log.log(Level.INFO, "Connected to " + service + " successfully!");\r
 448 \r
 449                 return serviceIF;\r
 450         }\r
 451 \r
 452         /**\r
 453          * Align sequences from the file using MsaWS\r
 454          * \r
 455          * @param <T>\r
 456          *            web service type e.g. Clustal\r
 457          * @param file\r
 458          *            to write the resulting alignment to\r
 459          * @param msaws\r
 460          *            MsaWS required\r
 461          * @param preset\r
 462          *            Preset to use optional\r
 463          * @param customOptions\r
 464          *            file which contains new line separated list of options\r
 465          * @return Alignment\r
 466          */\r
 467         static <T> Alignment align(File file, MsaWS<T> msaws, Preset<T> preset,\r
 468                         List<Option<T>> customOptions) {\r
 469                 FileInputStream instream = null;\r
 470                 List<FastaSequence> fastalist = null;\r
 471                 Alignment alignment = null;\r
 472                 try {\r
 473                         instream = new FileInputStream(file);\r
 474                         fastalist = SequenceUtil.readFasta(instream);\r
 475                         instream.close();\r
 476                         String jobId = null;\r
 477                         if (customOptions != null && preset != null) {\r
 478                                 System.out\r
 479                                                 .println("WARN: Parameters (-f) are defined together with a preset (-r) ignoring preset!");\r
 480                         }\r
 481                         if (customOptions != null) {\r
 482                                 jobId = msaws.customAlign(fastalist, customOptions);\r
 483                         } else if (preset != null) {\r
 484                                 jobId = msaws.presetAlign(fastalist, preset);\r
 485                         } else {\r
 486                                 jobId = msaws.align(fastalist);\r
 487                         }\r
 488                         System.out.println("\n\ncalling align.........");\r
 489                         Thread.sleep(1000);\r
 490                         alignment = msaws.getResult(jobId);\r
 491 \r
 492                 } catch (IOException e) {\r
 493                         System.err\r
 494                                         .println("Exception while reading the input file. "\r
 495                                                         + "Check that the input file contains a list of fasta formatted sequences! "\r
 496                                                         + "Exception details are below:");\r
 497                         e.printStackTrace();\r
 498                 } catch (JobSubmissionException e) {\r
 499                         System.err\r
 500                                         .println("Exception while submitting job to a web server. "\r
 501                                                         + "Exception details are below:");\r
 502                         e.printStackTrace();\r
 503                 } catch (ResultNotAvailableException e) {\r
 504                         System.err.println("Exception while waiting for results. "\r
 505                                         + "Exception details are below:");\r
 506                         e.printStackTrace();\r
 507                 } catch (InterruptedException ignored) {\r
 508                         // ignore and propagate an interruption\r
 509                         Thread.currentThread().interrupt();\r
 510                 } catch (WrongParameterException e) {\r
 511                         e.printStackTrace();\r
 512                 } finally {\r
 513                         if (instream != null) {\r
 514                                 try {\r
 515                                         instream.close();\r
 516                                 } catch (IOException ignored) {\r
 517                                         // ignore\r
 518                                 }\r
 519                         }\r
 520                 }\r
 521                 return alignment;\r
 522         }\r
 523         \r
 524         /**\r
 525          * Return RNA secondary structure from a file using FoldWS\r
 526          * \r
 527          * @param <T>\r
 528          *            web service type e.g. Clustal\r
 529          * @param file\r
 530          *            to read the results from\r
 531          * @param foldws\r
 532          *            FoldWS required\r
 533          * @param preset\r
 534          *            Preset to use optional\r
 535          * @param customOptions\r
 536          *            file which contains new line separated list of options\r
 537          * @return String\r
 538          */\r
 539         \r
 540         static <T> String fold(File file, FoldWS<T> foldws, Preset<T> preset,\r
 541                         List<Option<T>> customOptions) {\r
 542                 FileInputStream instream = null;\r
 543                 Alignment alignment = null;\r
 544                 String rnastruct = null;\r
 545                 try {\r
 546                         instream = new FileInputStream(file);\r
 547                         alignment = ClustalAlignmentUtil.readClustalFile(instream);\r
 548                         instream.close();\r
 549                         String jobId = null;\r
 550                         if (customOptions != null && preset != null) {\r
 551                                 System.out.println("WARN: Parameters (-f) are defined together"\r
 552                                                 + "with a preset (-r), ignoring preset! ");\r
 553                         }\r
 554                         if (customOptions != null) {\r
 555                                 jobId = foldws.customFold(alignment, customOptions);\r
 556                         } else if (preset != null) {\r
 557                                 jobId = foldws.presetFold(alignment, preset);\r
 558                         } else {\r
 559                                 jobId = foldws.fold(alignment);\r
 560                         }\r
 561                         System.out.println("\n\ncalling fold.........");\r
 562                         Thread.sleep(1000);\r
 563                         rnastruct = foldws.getResult(jobId);\r
 564                                 \r
 565                 } catch (IOException e) {\r
 566                         System.err.println("Exception while reading the input file. Exception details: ");\r
 567                         e.printStackTrace();\r
 568                 } catch (UnknownFileFormatException e) {\r
 569                         System.err.println("Exception while reading input file. Doesnt look like a Clustal format file");\r
 570                         e.printStackTrace();\r
 571                 } catch (JobSubmissionException e) {\r
 572                         System.err.println("Exception while submitting job to the web server. ");\r
 573                         e.printStackTrace();\r
 574                 } catch (ResultNotAvailableException e) {\r
 575                         System.err.println("Exception while waiting for results. Exception details: ");\r
 576                         e.printStackTrace();\r
 577                 } catch (InterruptedException ignored) {\r
 578                         // ignore and propagate an interruption\r
 579                         Thread.currentThread().interrupt();\r
 580                 } catch (WrongParameterException e) {\r
 581                         e.printStackTrace();\r
 582                 } finally {\r
 583                         if (instream != null) {\r
 584                                 try {\r
 585                                         instream.close();\r
 586                                 } catch (IOException ignored) {\r
 587                                         // ignore\r
 588                                 }\r
 589                         }\r
 590                 }\r
 591                 return rnastruct;\r
 592         }\r
 593                 \r
 594         /**\r
 595          * Prints Jws2Client usage information to standard out\r
 596          * \r
 597          * @param exitStatus\r
 598          */\r
 599         static void printUsage(int exitStatus) {\r
 600                 System.out.println(Constraints.help_text);\r
 601                 System.exit(exitStatus);\r
 602         }\r
 603 \r
 604         /**\r
 605          * Starts command line client, if no parameter are supported print help. Two\r
 606          * parameters are required for successful call the JWS2 host name and a\r
 607          * service name.\r
 608          * \r
 609          * @param args\r
 610          *            Usage: <Class or Jar file name> -h=host_and_context\r
 611          *            -s=serviceName ACTION [OPTIONS]\r
 612          * \r
 613          *            -h=<host_and_context> - a full URL to the JWS2 web server\r
 614          *            including context path e.g. http://10.31.1.159:8080/ws\r
 615          * \r
 616          *            -s=<ServiceName> - one of [MafftWS, MuscleWS, ClustalWS,\r
 617          *            TcoffeeWS, ProbconsWS] ACTIONS:\r
 618          * \r
 619          *            -i=<inputFile> - full path to fasta formatted sequence file,\r
 620          *            from which to align sequences\r
 621          * \r
 622          *            -parameters - lists parameters supported by web service\r
 623          * \r
 624          *            -presets - lists presets supported by web service\r
 625          * \r
 626          *            -limits - lists web services limits Please note that if input\r
 627          *            file is specified other actions are ignored\r
 628          * \r
 629          *            OPTIONS: (only for use with -i action):\r
 630          * \r
 631          *            -r=<presetName> - name of the preset to use\r
 632          * \r
 633          *            -o=<outputFile> - full path to the file where to write an\r
 634          *            alignment -f=<parameterInputFile> - the name of the file with\r
 635          *            the list of parameters to use. Please note that -r and -f\r
 636          *            options cannot be used together. Alignment is done with either\r
 637          *            preset or a parameters from the file, but not both!\r
 638          * \r
 639          */\r
 640         public static void main(String[] args) {\r
 641 \r
 642                 if (args == null) {\r
 643                         printUsage(1);\r
 644                 }\r
 645                 if (args.length < 2) {\r
 646                         System.err.println("Host and service names are required!");\r
 647                         printUsage(1);\r
 648                 }\r
 649 \r
 650                 try {\r
 651                         new Jws2Client(args);\r
 652                 } catch (IOException e) {\r
 653                         log.log(Level.SEVERE, "IOException in client! " + e.getMessage(),\r
 654                                         e.getCause());\r
 655                         System.err.println("Cannot write output file! Stack trace: ");\r
 656                         e.printStackTrace();\r
 657                 }\r
 658         }\r
 659 }\r