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