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