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.MalformedURLException;\r
  32 import java.net.URL;\r
  33 import java.util.Arrays;\r
  34 import java.util.List;\r
  35 import java.util.Set;\r
  36 import java.util.logging.Level;\r
  37 import java.util.logging.Logger;\r
  38 \r
  39 import javax.xml.namespace.QName;\r
  40 import javax.xml.ws.Service;\r
  41 import javax.xml.ws.WebServiceException;\r
  42 \r
  43 import compbio.data.msa.JABAService;\r
  44 import compbio.data.msa.Metadata;\r
  45 import compbio.data.msa.MsaWS;\r
  46 import compbio.data.msa.RegistryWS;\r
  47 import compbio.data.msa.SequenceAnnotation;\r
  48 import compbio.data.sequence.Alignment;\r
  49 import compbio.data.sequence.FastaSequence;\r
  50 import compbio.data.sequence.ScoreManager;\r
  51 import compbio.data.sequence.SequenceUtil;\r
  52 import compbio.data.sequence.UnknownFileFormatException;\r
  53 import compbio.metadata.JobSubmissionException;\r
  54 import compbio.metadata.Option;\r
  55 import compbio.metadata.Preset;\r
  56 import compbio.metadata.ResultNotAvailableException;\r
  57 import compbio.metadata.WrongParameterException;\r
  58 \r
  59 /**\r
  60  * A command line client for JAva Bioinformatics Analysis Web Services\r
  61  * \r
  62  * @author pvtroshin\r
  63  * @version 1.0\r
  64  */\r
  65 public class Jws2Client {\r
  66 \r
  67         /*\r
  68          * Use java.util.Logger instead of log4j logger to reduce the size of the\r
  69          * client package\r
  70          */\r
  71         private static final Logger log = Logger.getLogger(Jws2Client.class\r
  72                         .getCanonicalName());\r
  73 \r
  74         // JABAWS version 1.0 service name\r
  75         static final String QUALIFIED_SERVICE_NAME = "http://msa.data.compbio/01/01/2010/";\r
  76 \r
  77         // JABAWS version 2.0 service name\r
  78         static final String V2_QUALIFIED_SERVICE_NAME = "http://msa.data.compbio/01/12/2010/";\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                 String hostname = CmdHelper.getHost(cmd);\r
 111                 if (hostname == null) {\r
 112                         System.err.println("Host name is not provided!");\r
 113                         printUsage(1);\r
 114                 }\r
 115 \r
 116                 if (!validURL(hostname)) {\r
 117                         System.err.println("Host name is not valid!");\r
 118                         printUsage(1);\r
 119                 }\r
 120                 // Just list available services and quit\r
 121                 boolean listServices = CmdHelper.listServices(cmd);\r
 122                 if (listServices) {\r
 123                         listServices(hostname);\r
 124                         System.exit(0);\r
 125                 }\r
 126 \r
 127                 String serviceName = CmdHelper.getServiceName(cmd);\r
 128                 if (serviceName == null) {\r
 129                         System.err.println("Service name is no provided!");\r
 130                         printUsage(1);\r
 131                 }\r
 132                 Services service = Services.getService(serviceName);\r
 133                 if (service == null) {\r
 134                         System.err.println("Service " + serviceName\r
 135                                         + " is no recognized! Valid values are: "\r
 136                                         + Arrays.toString(Services.values()));\r
 137                         printUsage(1);\r
 138                 }\r
 139                 // Test service and quit\r
 140                 boolean testService = CmdHelper.testService(cmd);\r
 141                 if (testService) {\r
 142                         testService(hostname, service);\r
 143                         System.exit(0);\r
 144                 }\r
 145 \r
 146                 File inputFile = IOHelper.getFile(cmd, inputkey, true);\r
 147                 File outFile = IOHelper.getFile(cmd, outputkey, false);\r
 148                 File parametersFile = IOHelper.getFile(cmd, paramFile, true);\r
 149                 String presetName = CmdHelper.getPresetName(cmd);\r
 150 \r
 151                 Metadata<T> msaws = (Metadata<T>) connect(hostname, service);\r
 152                 Preset<T> preset = null;\r
 153                 if (presetName != null) {\r
 154                         preset = MetadataHelper.getPreset(msaws, presetName);\r
 155                 }\r
 156                 List<Option<T>> customOptions = null;\r
 157                 if (parametersFile != null) {\r
 158                         List<String> prms = IOHelper.loadParameters(parametersFile);\r
 159                         customOptions = MetadataHelper.processParameters(prms,\r
 160                                         msaws.getRunnerOptions());\r
 161                 }\r
 162                 Alignment alignment = null;\r
 163                 if (inputFile != null) {\r
 164                         Writer writer = null;\r
 165                         if (outFile != null) {\r
 166                                 writer = IOHelper.getWriter(outFile);\r
 167                         } else {\r
 168                                 // this stream is going to be closed later which is fine as\r
 169                                 // std.out will not be\r
 170                                 writer = new PrintWriter(System.out, true);\r
 171                         }\r
 172                         if (service.getServiceType() == SequenceAnnotation.class) {\r
 173                                 ScoreManager result = analize(inputFile,\r
 174                                                 ((SequenceAnnotation<T>) msaws), preset, customOptions);\r
 175 \r
 176                                 IOHelper.writeOut(writer, result);\r
 177                         } else {\r
 178                                 alignment = align(inputFile, (MsaWS<T>) msaws, preset,\r
 179                                                 customOptions);\r
 180                                 IOHelper.writeOut(writer, alignment);\r
 181                         }\r
 182                         writer.close();\r
 183                 }\r
 184 \r
 185                 boolean listParameters = CmdHelper.listParameters(cmd);\r
 186                 if (listParameters) {\r
 187                         System.out.println(MetadataHelper.getParametersList(msaws));\r
 188                 }\r
 189                 boolean listPreset = CmdHelper.listPresets(cmd);\r
 190                 if (listPreset) {\r
 191                         System.out.println(MetadataHelper.getPresetList(msaws));\r
 192                 }\r
 193                 boolean listLimits = CmdHelper.listLimits(cmd);\r
 194                 if (listLimits) {\r
 195                         System.out.println(MetadataHelper.getLimits(msaws));\r
 196                 }\r
 197                 log.fine("Disconnecting...");\r
 198                 ((Closeable) msaws).close();\r
 199                 log.fine("Disconnected successfully!");\r
 200         }\r
 201 \r
 202         private void testService(String hostname, Services service)\r
 203                         throws IOException {\r
 204                 RegistryWS registry = connectToRegistry(hostname);\r
 205                 if (registry != null) {\r
 206                         String message = registry.testService(service);\r
 207                         System.out.println("Service " + service + " testing results: ");\r
 208                         System.out.println(message);\r
 209                         ((Closeable) registry).close();\r
 210                 }\r
 211         }\r
 212 \r
 213         private void listServices(String hostname) throws IOException {\r
 214                 RegistryWS registry = connectToRegistry(hostname);\r
 215                 if (registry != null) {\r
 216                         Set<Services> services = registry.getSupportedServices();\r
 217                         System.out.println("Supported services are: "\r
 218                                         + Services.toString(services));\r
 219                         ((Closeable) registry).close();\r
 220                 } else {\r
 221                         System.out.println("Failed to connect to the registry! ");\r
 222                 }\r
 223         }\r
 224 \r
 225         /**\r
 226          * Calculate conservation for sequences loaded from the file\r
 227          * \r
 228          * @param wsproxy\r
 229          *            a web service proxy\r
 230          * @param file\r
 231          *            the file to read the results from\r
 232          * @param preset\r
 233          *            Preset to use optional\r
 234          * @param customOptions\r
 235          *            the list of options\r
 236          * @return Set<Score> the conservation scores\r
 237          * @throws UnknownFileFormatException\r
 238          */\r
 239         static <T> ScoreManager analize(List<FastaSequence> fastalist,\r
 240                         SequenceAnnotation<T> wsproxy, Preset<T> preset,\r
 241                         List<Option<T>> customOptions) {\r
 242 \r
 243                 ScoreManager scores = null;\r
 244                 try {\r
 245                         String jobId = null;\r
 246                         if (customOptions != null && preset != null) {\r
 247                                 System.out\r
 248                                                 .println("WARN: Parameters (-f) are defined together with a preset (-r) ignoring preset!");\r
 249                         }\r
 250                         if (customOptions != null) {\r
 251                                 jobId = wsproxy.customAnalize(fastalist, customOptions);\r
 252                         } else if (preset != null) {\r
 253                                 jobId = wsproxy.presetAnalize(fastalist, preset);\r
 254                         } else {\r
 255                                 jobId = wsproxy.analize(fastalist);\r
 256                         }\r
 257                         System.out.println("\n\ncalling analise.........");\r
 258                         Thread.sleep(1000);\r
 259                         scores = wsproxy.getAnnotation(jobId);\r
 260 \r
 261                 } catch (JobSubmissionException e) {\r
 262                         System.err\r
 263                                         .println("Exception while submitting job to a web server. "\r
 264                                                         + "Exception details are below:");\r
 265                         e.printStackTrace();\r
 266                 } catch (ResultNotAvailableException e) {\r
 267                         System.err.println("Exception while waiting for results. "\r
 268                                         + "Exception details are below:");\r
 269                         e.printStackTrace();\r
 270                 } catch (InterruptedException e) {\r
 271                         // ignore and propagate an interruption\r
 272                         Thread.currentThread().interrupt();\r
 273                         System.err.println("Exception while waiting for results. "\r
 274                                         + "Exception details are below:");\r
 275                         e.printStackTrace();\r
 276                 } catch (WrongParameterException e) {\r
 277                         System.err\r
 278                                         .println("Exception while parsing the web method input parameters. "\r
 279                                                         + "Exception details are below:");\r
 280                         e.printStackTrace();\r
 281                 }\r
 282                 return scores;\r
 283 \r
 284         }\r
 285 \r
 286         /**\r
 287          * Calculate conservation for sequences loaded from the file\r
 288          * \r
 289          * @param wsproxy\r
 290          *            a web service proxy\r
 291          * @param file\r
 292          *            the file to read the results from\r
 293          * @param preset\r
 294          *            Preset to use optional\r
 295          * @param customOptions\r
 296          *            the list of options\r
 297          * @return Set<Score> the conservation scores\r
 298          * @throws IOException\r
 299          * @throws UnknownFileFormatException\r
 300          */\r
 301         static <T> ScoreManager analize(File file, SequenceAnnotation<T> wsproxy,\r
 302                         Preset<T> preset, List<Option<T>> customOptions) {\r
 303                 List<FastaSequence> fastalist = null;\r
 304                 try {\r
 305                         fastalist = SequenceUtil.openInputStream(file.getAbsolutePath());\r
 306                         assert !fastalist.isEmpty() : "Input is empty!";\r
 307                 } catch (IOException e) {\r
 308                         System.err\r
 309                                         .println("Exception while reading the input file. "\r
 310                                                         + "Check that the input file contains a list of fasta formatted sequences! "\r
 311                                                         + "Exception details are below:");\r
 312                         e.printStackTrace();\r
 313                 } catch (UnknownFileFormatException e) {\r
 314                         System.err\r
 315                                         .println("Exception while attempting to read the input file "\r
 316                                                         + "Exception details are below:");\r
 317                         System.out.println(e.getMessage());\r
 318                         e.printStackTrace();\r
 319                 }\r
 320                 return analize(fastalist, wsproxy, preset, customOptions);\r
 321         }\r
 322         /**\r
 323          * Connects to a web service by the host and the service name\r
 324          * \r
 325          * @param T\r
 326          *            web service type\r
 327          * @param host\r
 328          * @param service\r
 329          * @return MsaWS<T>\r
 330          * @throws WebServiceException\r
 331          */\r
 332         public static JABAService connect(String host, Services service)\r
 333                         throws WebServiceException {\r
 334                 URL url = null;\r
 335                 log.log(Level.FINE, "Attempting to connect...");\r
 336                 try {\r
 337                         url = new URL(host + "/" + service.toString() + "?wsdl");\r
 338                 } catch (MalformedURLException e) {\r
 339                         e.printStackTrace();\r
 340                         // ignore as the host name is already verified\r
 341                 }\r
 342                 Service serv = null;\r
 343                 try {\r
 344                         serv = service.getService(url, QUALIFIED_SERVICE_NAME);\r
 345                 } catch (WebServiceException wse) {\r
 346                         System.out.println("Connecting to JABAWS version 2 service");\r
 347                         if (isV2service(wse)) {\r
 348                                 serv = service.getService(url, V2_QUALIFIED_SERVICE_NAME);\r
 349                         }\r
 350                 }\r
 351                 if (serv == null) {\r
 352                         System.err.println("Could not connect to " + url\r
 353                                         + " the server is down?");\r
 354                         // FIXME\r
 355                 }\r
 356                 JABAService serviceIF = service.getInterface(serv);\r
 357                 log.log(Level.INFO, "Connected successfully!");\r
 358 \r
 359                 return serviceIF;\r
 360         }\r
 361 \r
 362         static boolean isV2service(WebServiceException wse) {\r
 363                 String message = wse.getMessage();\r
 364                 int idx = message.indexOf("not a valid service");\r
 365                 if (idx > 0) {\r
 366                         if (message.substring(idx).contains(V2_QUALIFIED_SERVICE_NAME)) {\r
 367                                 return true;\r
 368                         }\r
 369                 }\r
 370                 return false;\r
 371         }\r
 372 \r
 373         public static compbio.data.msa.RegistryWS connectToRegistry(String host)\r
 374                         throws WebServiceException {\r
 375                 URL url = null;\r
 376                 String service = "RegistryWS";\r
 377                 log.log(Level.FINE, "Attempting to connect...");\r
 378 \r
 379                 try {\r
 380                         url = new URL(host + "/" + service + "?wsdl");\r
 381                 } catch (MalformedURLException e) {\r
 382                         e.printStackTrace();\r
 383                         // ignore as the host name is already verified\r
 384                 }\r
 385                 QName qname = new QName(V2_QUALIFIED_SERVICE_NAME, service);\r
 386                 Service serv = Service.create(url, qname);\r
 387 \r
 388                 if (serv == null) {\r
 389                         System.err.println("Could not connect to " + url\r
 390                                         + " the server is down?");\r
 391                 }\r
 392 \r
 393                 QName portName = new QName(serv.getServiceName().getNamespaceURI(),\r
 394                                 service + "Port");\r
 395                 compbio.data.msa.RegistryWS serviceIF = serv.getPort(portName,\r
 396                                 compbio.data.msa.RegistryWS.class);\r
 397 \r
 398                 log.log(Level.INFO, "Connected to " + service + " successfully!");\r
 399 \r
 400                 return serviceIF;\r
 401         }\r
 402 \r
 403         /**\r
 404          * Align sequences from the file using MsaWS\r
 405          * \r
 406          * @param <T>\r
 407          *            web service type e.g. Clustal\r
 408          * @param file\r
 409          *            to write the resulting alignment to\r
 410          * @param msaws\r
 411          *            MsaWS required\r
 412          * @param preset\r
 413          *            Preset to use optional\r
 414          * @param customOptions\r
 415          *            file which contains new line separated list of options\r
 416          * @return Alignment\r
 417          */\r
 418         static <T> Alignment align(File file, MsaWS<T> msaws, Preset<T> preset,\r
 419                         List<Option<T>> customOptions) {\r
 420                 FileInputStream instream = null;\r
 421                 List<FastaSequence> fastalist = null;\r
 422                 Alignment alignment = null;\r
 423                 try {\r
 424                         instream = new FileInputStream(file);\r
 425                         fastalist = SequenceUtil.readFasta(instream);\r
 426                         instream.close();\r
 427                         String jobId = null;\r
 428                         if (customOptions != null && preset != null) {\r
 429                                 System.out\r
 430                                                 .println("WARN: Parameters (-f) are defined together with a preset (-r) ignoring preset!");\r
 431                         }\r
 432                         if (customOptions != null) {\r
 433                                 jobId = msaws.customAlign(fastalist, customOptions);\r
 434                         } else if (preset != null) {\r
 435                                 jobId = msaws.presetAlign(fastalist, preset);\r
 436                         } else {\r
 437                                 jobId = msaws.align(fastalist);\r
 438                         }\r
 439                         System.out.println("\n\ncalling align.........");\r
 440                         Thread.sleep(1000);\r
 441                         alignment = msaws.getResult(jobId);\r
 442 \r
 443                 } catch (IOException e) {\r
 444                         System.err\r
 445                                         .println("Exception while reading the input file. "\r
 446                                                         + "Check that the input file contains a list of fasta formatted sequences! "\r
 447                                                         + "Exception details are below:");\r
 448                         e.printStackTrace();\r
 449                 } catch (JobSubmissionException e) {\r
 450                         System.err\r
 451                                         .println("Exception while submitting job to a web server. "\r
 452                                                         + "Exception details are below:");\r
 453                         e.printStackTrace();\r
 454                 } catch (ResultNotAvailableException e) {\r
 455                         System.err.println("Exception while waiting for results. "\r
 456                                         + "Exception details are below:");\r
 457                         e.printStackTrace();\r
 458                 } catch (InterruptedException ignored) {\r
 459                         // ignore and propagate an interruption\r
 460                         Thread.currentThread().interrupt();\r
 461                 } catch (WrongParameterException e) {\r
 462                         e.printStackTrace();\r
 463                 } finally {\r
 464                         if (instream != null) {\r
 465                                 try {\r
 466                                         instream.close();\r
 467                                 } catch (IOException ignored) {\r
 468                                         // ignore\r
 469                                 }\r
 470                         }\r
 471                 }\r
 472                 return alignment;\r
 473         }\r
 474 \r
 475         /**\r
 476          * Prints Jws2Client usage information to standard out\r
 477          * \r
 478          * @param exitStatus\r
 479          */\r
 480         static void printUsage(int exitStatus) {\r
 481                 System.out.println(Constraints.help_text);\r
 482                 System.exit(exitStatus);\r
 483         }\r
 484 \r
 485         /**\r
 486          * Starts command line client, if no parameter are supported print help. Two\r
 487          * parameters are required for successful call the JWS2 host name and a\r
 488          * service name.\r
 489          * \r
 490          * @param args\r
 491          *            Usage: <Class or Jar file name> -h=host_and_context\r
 492          *            -s=serviceName ACTION [OPTIONS]\r
 493          * \r
 494          *            -h=<host_and_context> - a full URL to the JWS2 web server\r
 495          *            including context path e.g. http://10.31.1.159:8080/ws\r
 496          * \r
 497          *            -s=<ServiceName> - one of [MafftWS, MuscleWS, ClustalWS,\r
 498          *            TcoffeeWS, ProbconsWS] ACTIONS:\r
 499          * \r
 500          *            -i=<inputFile> - full path to fasta formatted sequence file,\r
 501          *            from which to align sequences\r
 502          * \r
 503          *            -parameters - lists parameters supported by web service\r
 504          * \r
 505          *            -presets - lists presets supported by web service\r
 506          * \r
 507          *            -limits - lists web services limits Please note that if input\r
 508          *            file is specified other actions are ignored\r
 509          * \r
 510          *            OPTIONS: (only for use with -i action):\r
 511          * \r
 512          *            -r=<presetName> - name of the preset to use\r
 513          * \r
 514          *            -o=<outputFile> - full path to the file where to write an\r
 515          *            alignment -f=<parameterInputFile> - the name of the file with\r
 516          *            the list of parameters to use. Please note that -r and -f\r
 517          *            options cannot be used together. Alignment is done with either\r
 518          *            preset or a parameters from the file, but not both!\r
 519          * \r
 520          */\r
 521         public static void main(String[] args) {\r
 522 \r
 523                 if (args == null) {\r
 524                         printUsage(1);\r
 525                 }\r
 526                 if (args.length < 2) {\r
 527                         System.err.println("Host and service names are required!");\r
 528                         printUsage(1);\r
 529                 }\r
 530 \r
 531                 try {\r
 532                         new Jws2Client(args);\r
 533                 } catch (IOException e) {\r
 534                         log.log(Level.SEVERE, "IOException in client! " + e.getMessage(),\r
 535                                         e.getCause());\r
 536                         System.err.println("Cannot write output file! Stack trace: ");\r
 537                         e.printStackTrace();\r
 538                 }\r
 539         }\r
 540 }\r