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.HashMap;\r
  41 import java.util.HashSet;\r
  42 import java.util.List;\r
  43 import java.util.Map;\r
  44 import java.util.logging.Level;\r
  45 import java.util.logging.Logger;\r
  46 \r
  47 import javax.xml.ws.Service;\r
  48 import javax.xml.ws.WebServiceException;\r
  49 \r
  50 import compbio.data.msa.JABAService;\r
  51 import compbio.data.msa.Metadata;\r
  52 import compbio.data.msa.MsaWS;\r
  53 import compbio.data.msa.SequenceAnnotation;\r
  54 import compbio.data.sequence.Alignment;\r
  55 import compbio.data.sequence.FastaSequence;\r
  56 import compbio.data.sequence.Score;\r
  57 import compbio.data.sequence.SequenceUtil;\r
  58 import compbio.data.sequence.UnknownFileFormatException;\r
  59 import compbio.metadata.JobSubmissionException;\r
  60 import compbio.metadata.Option;\r
  61 import compbio.metadata.Preset;\r
  62 import compbio.metadata.ResultNotAvailableException;\r
  63 import compbio.metadata.WrongParameterException;\r
  64 \r
  65 /**\r
  66  * A command line client for JAva Bioinformatics Analysis Web Services\r
  67  * \r
  68  * @author pvtroshin\r
  69  * @version 1.0\r
  70  */\r
  71 public class Jws2Client {\r
  72 \r
  73         /*\r
  74          * Use java.util.Logger instead of log4j logger to reduce the size of the\r
  75          * client package\r
  76          */\r
  77         private static final Logger log = Logger.getLogger(Jws2Client.class\r
  78                         .getCanonicalName());\r
  79 \r
  80         // JABAWS version 1.0 service name\r
  81         static final String QUALIFIED_SERVICE_NAME = "http://msa.data.compbio/01/01/2010/";\r
  82 \r
  83         // JABAWS version 2.0 service name\r
  84         static final String V2_QUALIFIED_SERVICE_NAME = "http://msa.data.compbio/01/12/2010/";\r
  85 \r
  86         /**\r
  87          * Attempt to construct the URL object from the string\r
  88          * \r
  89          * @param urlstr\r
  90          * @return true if it succeed false otherwise\r
  91          */\r
  92         public static boolean validURL(String urlstr) {\r
  93                 try {\r
  94                         if (urlstr == null || urlstr.trim().length() == 0) {\r
  95                                 return false;\r
  96                         }\r
  97                         new URL(urlstr);\r
  98                 } catch (MalformedURLException e) {\r
  99                         return false;\r
 100                 }\r
 101                 return true;\r
 102         }\r
 103 \r
 104         /**\r
 105          * Connects to the service and do the job as requested, if something goes\r
 106          * wrong reports or/and prints usage help.\r
 107          * \r
 108          * @param <T>\r
 109          *            web service type\r
 110          * @param cmd\r
 111          *            command line options\r
 112          * @throws IOException\r
 113          */\r
 114         <T> Jws2Client(String[] cmd) throws IOException {\r
 115 \r
 116                 String hostname = CmdHelper.getHost(cmd);\r
 117                 if (hostname == null) {\r
 118                         System.out.println("Host name is not provided!");\r
 119                         printUsage(1);\r
 120                 }\r
 121 \r
 122                 if (!validURL(hostname)) {\r
 123                         System.out.println("Host name is not valid!");\r
 124                         printUsage(1);\r
 125                 }\r
 126                 String serviceName = CmdHelper.getServiceName(cmd);\r
 127                 if (serviceName == null) {\r
 128                         System.out.println("Service name is no provided!");\r
 129                         printUsage(1);\r
 130                 }\r
 131                 Services service = Services.getService(serviceName);\r
 132                 if (service == null) {\r
 133                         System.out.println("Service " + serviceName\r
 134                                         + " is no supported! Valid values are: "\r
 135                                         + Arrays.toString(Services.values()));\r
 136                         printUsage(1);\r
 137                 }\r
 138                 File inputFile = IOHelper.getFile(cmd, inputkey, true);\r
 139                 File outFile = IOHelper.getFile(cmd, outputkey, false);\r
 140                 File parametersFile = IOHelper.getFile(cmd, paramFile, true);\r
 141                 String presetName = CmdHelper.getPresetName(cmd);\r
 142 \r
 143                 Metadata<T> msaws = (Metadata<T>) connect(hostname, service);\r
 144                 Preset<T> preset = null;\r
 145                 if (presetName != null) {\r
 146                         preset = MetadataHelper.getPreset(msaws, presetName);\r
 147                 }\r
 148                 List<Option<T>> customOptions = null;\r
 149                 if (parametersFile != null) {\r
 150                         List<String> prms = IOHelper.loadParameters(parametersFile);\r
 151                         customOptions = MetadataHelper.processParameters(prms,\r
 152                                         msaws.getRunnerOptions());\r
 153                 }\r
 154                 Alignment alignment = null;\r
 155                 if (inputFile != null) {\r
 156                         OutputStream outStream = null;\r
 157                         if (outFile != null) {\r
 158                                 outStream = IOHelper.getOutStream(outFile);\r
 159                         } else {\r
 160                                 // this stream is going to be closed later which is fine as\r
 161                                 // std.out will not be\r
 162                                 outStream = System.out;\r
 163                         }\r
 164                         if (service.getServiceType() == SequenceAnnotation.class) {\r
 165                                 Map<String, HashSet<Score>> result = analize(inputFile,\r
 166                                                 ((SequenceAnnotation<T>) msaws), preset, customOptions);\r
 167                                 assert result != null && !result.values().isEmpty() : "No Result reported!";\r
 168                                 IOHelper.writeOut(outStream, result);\r
 169                         } else {\r
 170                                 alignment = align(inputFile, (MsaWS<T>) msaws, preset,\r
 171                                                 customOptions);\r
 172                                 IOHelper.writeOut(outStream, alignment);\r
 173                         }\r
 174                         outStream.close();\r
 175                 }\r
 176 \r
 177                 boolean listParameters = CmdHelper.listParameters(cmd);\r
 178                 if (listParameters) {\r
 179                         System.out.println(MetadataHelper.getParametersList(msaws));\r
 180                 }\r
 181                 boolean listPreset = CmdHelper.listPresets(cmd);\r
 182                 if (listPreset) {\r
 183                         System.out.println(MetadataHelper.getPresetList(msaws));\r
 184                 }\r
 185                 boolean listLimits = CmdHelper.listLimits(cmd);\r
 186                 if (listLimits) {\r
 187                         System.out.println(MetadataHelper.getLimits(msaws));\r
 188                 }\r
 189                 log.fine("Disconnecting...");\r
 190                 ((Closeable) msaws).close();\r
 191                 log.fine("Disconnected successfully!");\r
 192         }\r
 193         /**\r
 194          * Calculate conservation for sequences loaded from the file\r
 195          * \r
 196          * @param wsproxy\r
 197          *            a web service proxy\r
 198          * @param file\r
 199          *            the file to read the results from\r
 200          * @param preset\r
 201          *            Preset to use optional\r
 202          * @param customOptions\r
 203          *            the list of options\r
 204          * @return Set<Score> the conservation scores\r
 205          * @throws UnknownFileFormatException\r
 206          */\r
 207         <T> HashMap<String, HashSet<Score>> analize(File file,\r
 208                         SequenceAnnotation<T> wsproxy, Preset<T> preset,\r
 209                         List<Option<T>> customOptions) {\r
 210 \r
 211                 List<FastaSequence> fastalist = null;\r
 212                 HashMap<String, HashSet<Score>> scores = null;\r
 213                 try {\r
 214                         fastalist = SequenceUtil.openInputStream(file.getAbsolutePath());\r
 215 \r
 216                         String jobId = null;\r
 217                         if (customOptions != null && preset != null) {\r
 218                                 System.out\r
 219                                                 .println("WARN: Parameters (-f) are defined together with a preset (-r) ignoring preset!");\r
 220                         }\r
 221                         if (customOptions != null) {\r
 222                                 jobId = wsproxy.customAnalize(fastalist, customOptions);\r
 223                         } else if (preset != null) {\r
 224                                 jobId = wsproxy.presetAnalize(fastalist, preset);\r
 225                         } else {\r
 226                                 jobId = wsproxy.analize(fastalist);\r
 227                         }\r
 228                         Thread.sleep(2000);\r
 229                         scores = wsproxy.getAnnotation(jobId);\r
 230                         assert scores != null && !scores.values().isEmpty() : "Scores are NULL";\r
 231 \r
 232                 } catch (IOException e) {\r
 233                         System.err\r
 234                                         .println("Exception while reading the input file. "\r
 235                                                         + "Check that the input file contains a list of fasta formatted sequences! "\r
 236                                                         + "Exception details are below:");\r
 237                         e.printStackTrace();\r
 238                 } catch (JobSubmissionException e) {\r
 239                         System.err\r
 240                                         .println("Exception while submitting job to a web server. "\r
 241                                                         + "Exception details are below:");\r
 242                         e.printStackTrace();\r
 243                 } catch (ResultNotAvailableException e) {\r
 244                         System.err.println("Exception while waiting for results. "\r
 245                                         + "Exception details are below:");\r
 246                         e.printStackTrace();\r
 247                 } catch (InterruptedException ignored) {\r
 248                         // ignore and propagate an interruption\r
 249                         Thread.currentThread().interrupt();\r
 250                 } catch (WrongParameterException e) {\r
 251                         System.err\r
 252                                         .println("Exception while parsing the web method input parameters. "\r
 253                                                         + "Exception details are below:");\r
 254                         e.printStackTrace();\r
 255                 } catch (UnknownFileFormatException e) {\r
 256                         System.err\r
 257                                         .println("Exception while attempting to read the input file "\r
 258                                                         + "Exception details are below:");\r
 259                         System.out.println(e.getMessage());\r
 260                         e.printStackTrace();\r
 261                 }\r
 262                 return scores;\r
 263         }\r
 264 \r
 265         /**\r
 266          * Connects to a web service by the host and the service name\r
 267          * \r
 268          * @param T\r
 269          *            web service type\r
 270          * @param host\r
 271          * @param service\r
 272          * @return MsaWS<T>\r
 273          * @throws WebServiceException\r
 274          */\r
 275         public static JABAService connect(String host, Services service)\r
 276                         throws WebServiceException {\r
 277                 URL url = null;\r
 278                 log.log(Level.FINE, "Attempting to connect...");\r
 279                 try {\r
 280                         url = new URL(host + "/" + service.toString() + "?wsdl");\r
 281                 } catch (MalformedURLException e) {\r
 282                         e.printStackTrace();\r
 283                         // ignore as the host name is already verified\r
 284                 }\r
 285                 Service serv = null;\r
 286                 try {\r
 287                         serv = service.getService(url, QUALIFIED_SERVICE_NAME);\r
 288                 } catch (WebServiceException wse) {\r
 289                         System.out.println("Conecting to JABAWS version 2 service");\r
 290                         if (isV2service(wse)) {\r
 291                                 serv = service.getService(url, V2_QUALIFIED_SERVICE_NAME);\r
 292                         }\r
 293                 }\r
 294                 if (serv == null) {\r
 295                         System.err.println("Could not connect to " + url);\r
 296                         // FIXME\r
 297                 }\r
 298                 JABAService serviceIF = service.getInterface(serv);\r
 299                 log.log(Level.FINE, "Connected successfully!");\r
 300 \r
 301                 return serviceIF;\r
 302         }\r
 303 \r
 304         static boolean isV2service(WebServiceException wse) {\r
 305                 String message = wse.getMessage();\r
 306                 int idx = message.indexOf("not a valid service");\r
 307                 if (idx > 0) {\r
 308                         if (message.substring(idx).contains(V2_QUALIFIED_SERVICE_NAME)) {\r
 309                                 return true;\r
 310                         }\r
 311                 }\r
 312                 return false;\r
 313         }\r
 314 \r
 315         /**\r
 316          * Align sequences from the file using MsaWS\r
 317          * \r
 318          * @param <T>\r
 319          *            web service type e.g. Clustal\r
 320          * @param file\r
 321          *            to write the resulting alignment to\r
 322          * @param msaws\r
 323          *            MsaWS required\r
 324          * @param preset\r
 325          *            Preset to use optional\r
 326          * @param customOptions\r
 327          *            file which contains new line separated list of options\r
 328          * @return Alignment\r
 329          */\r
 330         static <T> Alignment align(File file, MsaWS<T> msaws, Preset<T> preset,\r
 331                         List<Option<T>> customOptions) {\r
 332                 FileInputStream instream = null;\r
 333                 List<FastaSequence> fastalist = null;\r
 334                 Alignment alignment = null;\r
 335                 try {\r
 336                         instream = new FileInputStream(file);\r
 337                         fastalist = SequenceUtil.readFasta(instream);\r
 338                         instream.close();\r
 339                         String jobId = null;\r
 340                         if (customOptions != null && preset != null) {\r
 341                                 System.out\r
 342                                                 .println("WARN: Parameters (-f) are defined together with a preset (-r) ignoring preset!");\r
 343                         }\r
 344                         if (customOptions != null) {\r
 345                                 jobId = msaws.customAlign(fastalist, customOptions);\r
 346                         } else if (preset != null) {\r
 347                                 jobId = msaws.presetAlign(fastalist, preset);\r
 348                         } else {\r
 349                                 jobId = msaws.align(fastalist);\r
 350                         }\r
 351                         Thread.sleep(1000);\r
 352                         alignment = msaws.getResult(jobId);\r
 353 \r
 354                 } catch (IOException e) {\r
 355                         System.err\r
 356                                         .println("Exception while reading the input file. "\r
 357                                                         + "Check that the input file contains a list of fasta formatted sequences! "\r
 358                                                         + "Exception details are below:");\r
 359                         e.printStackTrace();\r
 360                 } catch (JobSubmissionException e) {\r
 361                         System.err\r
 362                                         .println("Exception while submitting job to a web server. "\r
 363                                                         + "Exception details are below:");\r
 364                         e.printStackTrace();\r
 365                 } catch (ResultNotAvailableException e) {\r
 366                         System.err.println("Exception while waiting for results. "\r
 367                                         + "Exception details are below:");\r
 368                         e.printStackTrace();\r
 369                 } catch (InterruptedException ignored) {\r
 370                         // ignore and propagate an interruption\r
 371                         Thread.currentThread().interrupt();\r
 372                 } catch (WrongParameterException e) {\r
 373                         e.printStackTrace();\r
 374                 } finally {\r
 375                         if (instream != null) {\r
 376                                 try {\r
 377                                         instream.close();\r
 378                                 } catch (IOException ignored) {\r
 379                                         // ignore\r
 380                                 }\r
 381                         }\r
 382                 }\r
 383                 return alignment;\r
 384         }\r
 385 \r
 386         /**\r
 387          * Prints Jws2Client usage information to standard out\r
 388          * \r
 389          * @param exitStatus\r
 390          */\r
 391         static void printUsage(int exitStatus) {\r
 392                 System.out.println();\r
 393                 System.out.println("Usage: <Class or Jar file name> " + hostkey\r
 394                                 + pseparator + "host_and_context " + servicekey + pseparator\r
 395                                 + "serviceName ACTION [OPTIONS] ");\r
 396                 System.out.println();\r
 397                 System.out\r
 398                                 .println(hostkey\r
 399                                                 + pseparator\r
 400                                                 + "<host_and_context> - a full URL to the JWS2 web server including context path e.g. http://10.31.1.159:8080/ws");\r
 401                 System.out.println(servicekey + pseparator + "<ServiceName> - one of "\r
 402                                 + Arrays.toString(Services.values()));\r
 403                 System.out.println();\r
 404                 System.out.println("ACTIONS: ");\r
 405                 System.out\r
 406                                 .println(inputkey\r
 407                                                 + pseparator\r
 408                                                 + "<inputFile> - full path to fasta formatted sequence file, from which to align sequences");\r
 409                 System.out.println(paramList\r
 410                                 + " - lists parameters supported by web service");\r
 411                 System.out.println(presetList\r
 412                                 + " - lists presets supported by web service");\r
 413                 System.out.println(limitList + " - lists web services limits");\r
 414                 System.out\r
 415                                 .println("Please note that if input file is specified other actions are ignored");\r
 416 \r
 417                 System.out.println();\r
 418                 System.out.println("OPTIONS (only for use with -i action):");\r
 419 \r
 420                 System.out.println(presetkey + pseparator\r
 421                                 + "<presetName> - name of the preset to use");\r
 422                 System.out\r
 423                                 .println(outputkey\r
 424                                                 + pseparator\r
 425                                                 + "<outputFile> - full path to the file where to write an alignment");\r
 426                 System.out\r
 427                                 .println("-f=<parameterInputFile> - the name of the file with the list of parameters to use.");\r
 428                 System.out\r
 429                                 .println("Please note that -r and -f options cannot be used together. "\r
 430                                                 + "Alignment is done with either preset or a parameters from the file, but not both!");\r
 431 \r
 432                 System.exit(exitStatus);\r
 433         }\r
 434 \r
 435         /**\r
 436          * Starts command line client, if no parameter are supported print help. Two\r
 437          * parameters are required for successful call the JWS2 host name and a\r
 438          * service name.\r
 439          * \r
 440          * @param args\r
 441          *            Usage: <Class or Jar file name> -h=host_and_context\r
 442          *            -s=serviceName ACTION [OPTIONS]\r
 443          * \r
 444          *            -h=<host_and_context> - a full URL to the JWS2 web server\r
 445          *            including context path e.g. http://10.31.1.159:8080/ws\r
 446          * \r
 447          *            -s=<ServiceName> - one of [MafftWS, MuscleWS, ClustalWS,\r
 448          *            TcoffeeWS, ProbconsWS] ACTIONS:\r
 449          * \r
 450          *            -i=<inputFile> - full path to fasta formatted sequence file,\r
 451          *            from which to align sequences\r
 452          * \r
 453          *            -parameters - lists parameters supported by web service\r
 454          * \r
 455          *            -presets - lists presets supported by web service\r
 456          * \r
 457          *            -limits - lists web services limits Please note that if input\r
 458          *            file is specified other actions are ignored\r
 459          * \r
 460          *            OPTIONS: (only for use with -i action):\r
 461          * \r
 462          *            -r=<presetName> - name of the preset to use\r
 463          * \r
 464          *            -o=<outputFile> - full path to the file where to write an\r
 465          *            alignment -f=<parameterInputFile> - the name of the file with\r
 466          *            the list of parameters to use. Please note that -r and -f\r
 467          *            options cannot be used together. Alignment is done with either\r
 468          *            preset or a parameters from the file, but not both!\r
 469          * \r
 470          */\r
 471         public static void main(String[] args) {\r
 472 \r
 473                 if (args == null) {\r
 474                         printUsage(1);\r
 475                 }\r
 476                 if (args.length < 2) {\r
 477                         System.out.println("Host and service names are required!");\r
 478                         printUsage(1);\r
 479                 }\r
 480 \r
 481                 try {\r
 482                         new Jws2Client(args);\r
 483                 } catch (IOException e) {\r
 484                         log.log(Level.SEVERE, "IOException in client! " + e.getMessage(),\r
 485                                         e.getCause());\r
 486                         System.err.println("Cannot write output file! Stack trace: ");\r
 487                         e.printStackTrace();\r
 488                 }\r
 489         }\r
 490 }\r