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