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