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.Set;\r
  42 import java.util.logging.Level;\r
  43 import java.util.logging.Logger;\r
  44 \r
  45 import javax.xml.ws.Service;\r
  46 import javax.xml.ws.WebServiceException;\r
  47 \r
  48 import compbio.data.msa.Annotation;\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.sequence.Alignment;\r
  53 import compbio.data.sequence.FastaSequence;\r
  54 import compbio.data.sequence.Score;\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          * Use java.util.Logger instead of log4j logger to reduce the size of the\r
  73          * 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 == Services.AAConWS) {\r
 163                                 Set<Score> result = analize(inputFile, ((Annotation<T>) msaws),\r
 164                                                 preset, customOptions);\r
 165                                 IOHelper.writeOut(outStream, result);\r
 166                         } else {\r
 167                                 alignment = align(inputFile, (MsaWS<T>) msaws, preset,\r
 168                                                 customOptions);\r
 169                                 IOHelper.writeOut(outStream, alignment);\r
 170                         }\r
 171 \r
 172                         // stream is closed in the method no need to close it here\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         <T> Set<Score> analize(File file, Annotation<T> wsproxy, Preset<T> preset,\r
 206                         List<Option<T>> customOptions) {\r
 207 \r
 208                 List<FastaSequence> fastalist = null;\r
 209                 Set<Score> scores = null;\r
 210                 try {\r
 211                         fastalist = SequenceUtil.openInputStream(file.getAbsolutePath());\r
 212 \r
 213                         String jobId = null;\r
 214                         if (customOptions != null && preset != null) {\r
 215                                 System.out\r
 216                                                 .println("WARN: Parameters (-f) are defined together with a preset (-r) ignoring preset!");\r
 217                         }\r
 218                         if (customOptions != null) {\r
 219                                 jobId = wsproxy.customAnalize(fastalist, customOptions);\r
 220                         } else if (preset != null) {\r
 221                                 jobId = wsproxy.presetAnalize(fastalist, preset);\r
 222                         } else {\r
 223                                 jobId = wsproxy.analize(fastalist);\r
 224                         }\r
 225                         Thread.sleep(1000);\r
 226                         scores = wsproxy.getAnnotation(jobId);\r
 227 \r
 228                 } catch (IOException e) {\r
 229                         System.err\r
 230                                         .println("Exception while reading the input file. "\r
 231                                                         + "Check that the input file contains a list of fasta formatted sequences! "\r
 232                                                         + "Exception details are below:");\r
 233                         e.printStackTrace();\r
 234                 } catch (JobSubmissionException e) {\r
 235                         System.err\r
 236                                         .println("Exception while submitting job to a web server. "\r
 237                                                         + "Exception details are below:");\r
 238                         e.printStackTrace();\r
 239                 } catch (ResultNotAvailableException e) {\r
 240                         System.err.println("Exception while waiting for results. "\r
 241                                         + "Exception details are below:");\r
 242                         e.printStackTrace();\r
 243                 } catch (InterruptedException ignored) {\r
 244                         // ignore and propagate an interruption\r
 245                         Thread.currentThread().interrupt();\r
 246                 } catch (WrongParameterException e) {\r
 247                         System.err\r
 248                                         .println("Exception while parsing the web method input parameters. "\r
 249                                                         + "Exception details are below:");\r
 250                         e.printStackTrace();\r
 251                 } catch (UnknownFileFormatException e) {\r
 252                         System.err\r
 253                                         .println("Exception while attempting to read the input file "\r
 254                                                         + "Exception details are below:");\r
 255                         System.out.println(e.getMessage());\r
 256                         e.printStackTrace();\r
 257                 }\r
 258                 return scores;\r
 259         }\r
 260 \r
 261         /**\r
 262          * Connects to a web service by the host and the service name\r
 263          * \r
 264          * @param T\r
 265          *            web service type\r
 266          * @param host\r
 267          * @param service\r
 268          * @return MsaWS<T>\r
 269          * @throws WebServiceException\r
 270          */\r
 271         public static JABAService connect(String host, Services service)\r
 272                         throws WebServiceException {\r
 273                 URL url = null;\r
 274                 log.log(Level.FINE, "Attempting to connect...");\r
 275                 try {\r
 276                         url = new URL(host + "/" + service.toString() + "?wsdl");\r
 277                 } catch (MalformedURLException e) {\r
 278                         e.printStackTrace();\r
 279                         // ignore as the host name is already verified\r
 280                 }\r
 281                 Service serv = null;\r
 282                 try {\r
 283                         serv = service.getService(url, QUALIFIED_SERVICE_NAME);\r
 284                 } catch (WebServiceException wse) {\r
 285                         System.out.println("Conecting to JABAWS version 2 service");\r
 286                         if (isV2service(wse)) {\r
 287                                 serv = service.getService(url, V2_QUALIFIED_SERVICE_NAME);\r
 288                         }\r
 289                 }\r
 290                 JABAService serviceIF = service.getInterface(serv);\r
 291                 log.log(Level.FINE, "Connected successfully!");\r
 292 \r
 293                 return serviceIF;\r
 294         }\r
 295 \r
 296         static boolean isV2service(WebServiceException wse) {\r
 297                 String message = wse.getMessage();\r
 298                 int idx = message.indexOf("not a valid service");\r
 299                 if (idx > 0) {\r
 300                         if (message.substring(idx).contains(V2_QUALIFIED_SERVICE_NAME)) {\r
 301                                 return true;\r
 302                         }\r
 303                 }\r
 304                 return false;\r
 305         }\r
 306 \r
 307         /**\r
 308          * Align sequences from the file using MsaWS\r
 309          * \r
 310          * @param <T>\r
 311          *            web service type e.g. Clustal\r
 312          * @param file\r
 313          *            to write the resulting alignment to\r
 314          * @param msaws\r
 315          *            MsaWS required\r
 316          * @param preset\r
 317          *            Preset to use optional\r
 318          * @param customOptions\r
 319          *            file which contains new line separated list of options\r
 320          * @return Alignment\r
 321          */\r
 322         static <T> Alignment align(File file, MsaWS<T> msaws, Preset<T> preset,\r
 323                         List<Option<T>> customOptions) {\r
 324                 FileInputStream instream = null;\r
 325                 List<FastaSequence> fastalist = null;\r
 326                 Alignment alignment = null;\r
 327                 try {\r
 328                         instream = new FileInputStream(file);\r
 329                         fastalist = SequenceUtil.readFasta(instream);\r
 330                         instream.close();\r
 331                         String jobId = null;\r
 332                         if (customOptions != null && preset != null) {\r
 333                                 System.out\r
 334                                                 .println("WARN: Parameters (-f) are defined together with a preset (-r) ignoring preset!");\r
 335                         }\r
 336                         if (customOptions != null) {\r
 337                                 jobId = msaws.customAlign(fastalist, customOptions);\r
 338                         } else if (preset != null) {\r
 339                                 jobId = msaws.presetAlign(fastalist, preset);\r
 340                         } else {\r
 341                                 jobId = msaws.align(fastalist);\r
 342                         }\r
 343                         Thread.sleep(1000);\r
 344                         alignment = msaws.getResult(jobId);\r
 345 \r
 346                 } catch (IOException e) {\r
 347                         System.err\r
 348                                         .println("Exception while reading the input file. "\r
 349                                                         + "Check that the input file contains a list of fasta formatted sequences! "\r
 350                                                         + "Exception details are below:");\r
 351                         e.printStackTrace();\r
 352                 } catch (JobSubmissionException e) {\r
 353                         System.err\r
 354                                         .println("Exception while submitting job to a web server. "\r
 355                                                         + "Exception details are below:");\r
 356                         e.printStackTrace();\r
 357                 } catch (ResultNotAvailableException e) {\r
 358                         System.err.println("Exception while waiting for results. "\r
 359                                         + "Exception details are below:");\r
 360                         e.printStackTrace();\r
 361                 } catch (InterruptedException ignored) {\r
 362                         // ignore and propagate an interruption\r
 363                         Thread.currentThread().interrupt();\r
 364                 } catch (WrongParameterException e) {\r
 365                         e.printStackTrace();\r
 366                 } finally {\r
 367                         if (instream != null) {\r
 368                                 try {\r
 369                                         instream.close();\r
 370                                 } catch (IOException ignored) {\r
 371                                         // ignore\r
 372                                 }\r
 373                         }\r
 374                 }\r
 375                 return alignment;\r
 376         }\r
 377 \r
 378         /**\r
 379          * Prints Jws2Client usage information to standard out\r
 380          * \r
 381          * @param exitStatus\r
 382          */\r
 383         static void printUsage(int exitStatus) {\r
 384                 System.out.println();\r
 385                 System.out.println("Usage: <Class or Jar file name> " + hostkey\r
 386                                 + pseparator + "host_and_context " + servicekey + pseparator\r
 387                                 + "serviceName ACTION [OPTIONS] ");\r
 388                 System.out.println();\r
 389                 System.out\r
 390                                 .println(hostkey\r
 391                                                 + pseparator\r
 392                                                 + "<host_and_context> - a full URL to the JWS2 web server including context path e.g. http://10.31.1.159:8080/ws");\r
 393                 System.out.println(servicekey + pseparator + "<ServiceName> - one of "\r
 394                                 + Arrays.toString(Services.values()));\r
 395                 System.out.println();\r
 396                 System.out.println("ACTIONS: ");\r
 397                 System.out\r
 398                                 .println(inputkey\r
 399                                                 + pseparator\r
 400                                                 + "<inputFile> - full path to fasta formatted sequence file, from which to align sequences");\r
 401                 System.out.println(paramList\r
 402                                 + " - lists parameters supported by web service");\r
 403                 System.out.println(presetList\r
 404                                 + " - lists presets supported by web service");\r
 405                 System.out.println(limitList + " - lists web services limits");\r
 406                 System.out\r
 407                                 .println("Please note that if input file is specified other actions are ignored");\r
 408 \r
 409                 System.out.println();\r
 410                 System.out.println("OPTIONS (only for use with -i action):");\r
 411 \r
 412                 System.out.println(presetkey + pseparator\r
 413                                 + "<presetName> - name of the preset to use");\r
 414                 System.out\r
 415                                 .println(outputkey\r
 416                                                 + pseparator\r
 417                                                 + "<outputFile> - full path to the file where to write an alignment");\r
 418                 System.out\r
 419                                 .println("-f=<parameterInputFile> - the name of the file with the list of parameters to use.");\r
 420                 System.out\r
 421                                 .println("Please note that -r and -f options cannot be used together. "\r
 422                                                 + "Alignment is done with either preset or a parameters from the file, but not both!");\r
 423 \r
 424                 System.exit(exitStatus);\r
 425         }\r
 426 \r
 427         /**\r
 428          * Starts command line client, if no parameter are supported print help. Two\r
 429          * parameters are required for successfull call the JWS2 host name and a\r
 430          * service name.\r
 431          * \r
 432          * @param args\r
 433          *            Usage: <Class or Jar file name> -h=host_and_context\r
 434          *            -s=serviceName ACTION [OPTIONS]\r
 435          * \r
 436          *            -h=<host_and_context> - a full URL to the JWS2 web server\r
 437          *            including context path e.g. http://10.31.1.159:8080/ws\r
 438          * \r
 439          *            -s=<ServiceName> - one of [MafftWS, MuscleWS, ClustalWS,\r
 440          *            TcoffeeWS, ProbconsWS] ACTIONS:\r
 441          * \r
 442          *            -i=<inputFile> - full path to fasta formatted sequence file,\r
 443          *            from which to align sequences\r
 444          * \r
 445          *            -parameters - lists parameters supported by web service\r
 446          * \r
 447          *            -presets - lists presets supported by web service\r
 448          * \r
 449          *            -limits - lists web services limits Please note that if input\r
 450          *            file is specified other actions are ignored\r
 451          * \r
 452          *            OPTIONS: (only for use with -i action):\r
 453          * \r
 454          *            -r=<presetName> - name of the preset to use\r
 455          * \r
 456          *            -o=<outputFile> - full path to the file where to write an\r
 457          *            alignment -f=<parameterInputFile> - the name of the file with\r
 458          *            the list of parameters to use. Please note that -r and -f\r
 459          *            options cannot be used together. Alignment is done with either\r
 460          *            preset or a parameters from the file, but not both!\r
 461          * \r
 462          */\r
 463         public static void main(String[] args) {\r
 464 \r
 465                 if (args == null) {\r
 466                         printUsage(1);\r
 467                 }\r
 468                 if (args.length < 2) {\r
 469                         System.out.println("Host and service names are required!");\r
 470                         printUsage(1);\r
 471                 }\r
 472 \r
 473                 try {\r
 474                         new Jws2Client(args);\r
 475                 } catch (IOException e) {\r
 476                         log.log(Level.SEVERE, "IOException in client! " + e.getMessage(),\r
 477                                         e.getCause());\r
 478                         System.err.println("Cannot write output file! Stack trace: ");\r
 479                         e.printStackTrace();\r
 480                 }\r
 481         }\r
 482 }\r