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