webservices/compbio/ws/client/Jws2Client.java

   1 /* Copyright (c) 2009 Peter Troshin\r
   2  *  \r
   3  *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0     \r
   4  * \r
   5  *  This library is free software; you can redistribute it and/or modify it under the terms of the\r
   6  *  Apache License version 2 as published by the Apache Software Foundation\r
   7  * \r
   8  *  This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
   9  *  even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
  10  *  License for more details.\r
  11  * \r
  12  *  A copy of the license is in apache_license.txt. It is also available here:\r
  13  * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
  14  * \r
  15  * Any republication or derived work distributed in source code form\r
  16  * must include this copyright and license notice.\r
  17  */\r
  18 \r
  19 package compbio.ws.client;\r
  20 \r
  21 import static compbio.ws.client.Constraints.hostkey;\r
  22 import static compbio.ws.client.Constraints.inputkey;\r
  23 import static compbio.ws.client.Constraints.limitList;\r
  24 import static compbio.ws.client.Constraints.outputkey;\r
  25 import static compbio.ws.client.Constraints.paramFile;\r
  26 import static compbio.ws.client.Constraints.paramList;\r
  27 import static compbio.ws.client.Constraints.presetList;\r
  28 import static compbio.ws.client.Constraints.presetkey;\r
  29 import static compbio.ws.client.Constraints.pseparator;\r
  30 import static compbio.ws.client.Constraints.servicekey;\r
  31 \r
  32 import java.io.Closeable;\r
  33 import java.io.File;\r
  34 import java.io.FileInputStream;\r
  35 import java.io.IOException;\r
  36 import java.io.OutputStream;\r
  37 import java.net.MalformedURLException;\r
  38 import java.net.URL;\r
  39 import java.util.Arrays;\r
  40 import java.util.List;\r
  41 import java.util.logging.Level;\r
  42 import java.util.logging.Logger;\r
  43 \r
  44 import javax.xml.ws.Service;\r
  45 import javax.xml.ws.WebServiceException;\r
  46 \r
  47 import compbio.data.msa.JABAService;\r
  48 import compbio.data.msa.Metadata;\r
  49 import compbio.data.msa.MsaWS;\r
  50 import compbio.data.sequence.Alignment;\r
  51 import compbio.data.sequence.FastaSequence;\r
  52 import compbio.data.sequence.SequenceUtil;\r
  53 import compbio.metadata.JobSubmissionException;\r
  54 import compbio.metadata.Option;\r
  55 import compbio.metadata.Preset;\r
  56 import compbio.metadata.ResultNotAvailableException;\r
  57 import compbio.metadata.WrongParameterException;\r
  58 \r
  59 /**\r
  60  * A command line client for JAva Bioinformatics Analysis Web Services\r
  61  * \r
  62  * @author pvtroshin\r
  63  * @version 1.0\r
  64  */\r
  65 public class Jws2Client {\r
  66 \r
  67         /*\r
  68          * Use java.util.Logger instead of log4j logger to reduce the size of the\r
  69          * client package\r
  70          */\r
  71         private static final Logger log = Logger.getLogger(Jws2Client.class\r
  72                         .getCanonicalName());\r
  73 \r
  74         // JABAWS version 1.0 service name\r
  75         static final String QUALIFIED_SERVICE_NAME = "http://msa.data.compbio/01/01/2010/";\r
  76 \r
  77         // JABAWS version 2.0 service name\r
  78         static final String V2_QUALIFIED_SERVICE_NAME = "http://msa.data.compbio/01/12/2010/";\r
  79 \r
  80         /**\r
  81          * Attempt to construct the URL object from the string\r
  82          * \r
  83          * @param urlstr\r
  84          * @return true if it succeed false otherwise\r
  85          */\r
  86         public static boolean validURL(String urlstr) {\r
  87                 try {\r
  88                         if (urlstr == null || urlstr.trim().length() == 0) {\r
  89                                 return false;\r
  90                         }\r
  91                         new URL(urlstr);\r
  92                 } catch (MalformedURLException e) {\r
  93                         return false;\r
  94                 }\r
  95                 return true;\r
  96         }\r
  97 \r
  98         /**\r
  99          * Connects to the service and do the job as requested, if something goes\r
 100          * wrong reports or/and prints usage help.\r
 101          * \r
 102          * @param <T>\r
 103          *            web service type\r
 104          * @param cmd\r
 105          *            command line options\r
 106          * @throws IOException\r
 107          */\r
 108         <T> Jws2Client(String[] cmd) throws IOException {\r
 109 \r
 110                 String hostname = CmdHelper.getHost(cmd);\r
 111                 if (hostname == null) {\r
 112                         System.out.println("Host name is not provided!");\r
 113                         printUsage(1);\r
 114                 }\r
 115 \r
 116                 if (!validURL(hostname)) {\r
 117                         System.out.println("Host name is not valid!");\r
 118                         printUsage(1);\r
 119                 }\r
 120                 String serviceName = CmdHelper.getServiceName(cmd);\r
 121                 if (serviceName == null) {\r
 122                         System.out.println("Service name is no provided!");\r
 123                         printUsage(1);\r
 124                 }\r
 125                 Services service = Services.getService(serviceName);\r
 126                 if (service == null) {\r
 127                         System.out.println("Service " + serviceName\r
 128                                         + " is no supported! Valid values are: "\r
 129                                         + Arrays.toString(Services.values()));\r
 130                         printUsage(1);\r
 131                 }\r
 132                 File inputFile = IOHelper.getFile(cmd, inputkey, true);\r
 133                 File outFile = IOHelper.getFile(cmd, outputkey, false);\r
 134                 File parametersFile = IOHelper.getFile(cmd, paramFile, true);\r
 135                 String presetName = CmdHelper.getPresetName(cmd);\r
 136 \r
 137                 Metadata<T> msaws = (Metadata<T>) connect(hostname, service);\r
 138                 Preset<T> preset = null;\r
 139                 if (presetName != null) {\r
 140                         preset = MetadataHelper.getPreset(msaws, presetName);\r
 141                 }\r
 142                 List<Option<T>> customOptions = null;\r
 143                 if (parametersFile != null) {\r
 144                         List<String> prms = IOHelper.loadParameters(parametersFile);\r
 145                         customOptions = MetadataHelper.processParameters(prms,\r
 146                                         msaws.getRunnerOptions());\r
 147                 }\r
 148                 Alignment alignment = null;\r
 149                 if (inputFile != null) {\r
 150                         if (service == Services.AAConWS) {\r
 151                                 System.out.println("calc conserv!");\r
 152                         } else {\r
 153 \r
 154                                 alignment = align(inputFile, (MsaWS<T>) msaws, preset,\r
 155                                                 customOptions);\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                                 IOHelper.writeOut(outStream, alignment);\r
 165                                 // stream is closed in the method no need to close it here\r
 166                         }\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         /**\r
 187          * Connects to a web service by the host and the service name\r
 188          * \r
 189          * @param <T>\r
 190          *            web service type\r
 191          * @param host\r
 192          * @param service\r
 193          * @return MsaWS<T>\r
 194          * @throws WebServiceException\r
 195          */\r
 196         public static JABAService connect(String host, Services service)\r
 197                         throws WebServiceException {\r
 198                 URL url = null;\r
 199                 log.log(Level.FINE, "Attempting to connect...");\r
 200                 try {\r
 201                         url = new URL(host + "/" + service.toString() + "?wsdl");\r
 202                 } catch (MalformedURLException e) {\r
 203                         e.printStackTrace();\r
 204                         // ignore as the host name is already verified\r
 205                 }\r
 206                 Service serv = null;\r
 207                 try {\r
 208                         serv = service.getService(url, QUALIFIED_SERVICE_NAME);\r
 209                 } catch (WebServiceException wse) {\r
 210                         System.out.println("Conecting to JABAWS version 2 service");\r
 211                         if (isV2service(wse)) {\r
 212                                 serv = service.getService(url, V2_QUALIFIED_SERVICE_NAME);\r
 213                         }\r
 214                 }\r
 215                 JABAService serviceIF = service.getInterface(serv);\r
 216                 log.log(Level.FINE, "Connected successfully!");\r
 217 \r
 218                 return serviceIF;\r
 219         }\r
 220 \r
 221         static boolean isV2service(WebServiceException wse) {\r
 222                 String message = wse.getMessage();\r
 223                 int idx = message.indexOf("not a valid service");\r
 224                 if (idx > 0) {\r
 225                         if (message.substring(idx).contains(V2_QUALIFIED_SERVICE_NAME)) {\r
 226                                 return true;\r
 227                         }\r
 228                 }\r
 229                 return false;\r
 230         }\r
 231 \r
 232         /**\r
 233          * Align sequences from the file using MsaWS\r
 234          * \r
 235          * @param <T>\r
 236          *            web service type e.g. Clustal\r
 237          * @param file\r
 238          *            to write the resulting alignment to\r
 239          * @param msaws\r
 240          *            MsaWS required\r
 241          * @param preset\r
 242          *            Preset to use optional\r
 243          * @param customOptions\r
 244          *            file which contains new line separated list of options\r
 245          * @return Alignment\r
 246          */\r
 247         static <T> Alignment align(File file, MsaWS<T> msaws, Preset<T> preset,\r
 248                         List<Option<T>> customOptions) {\r
 249                 FileInputStream instream = null;\r
 250                 List<FastaSequence> fastalist = null;\r
 251                 Alignment alignment = null;\r
 252                 try {\r
 253                         instream = new FileInputStream(file);\r
 254                         fastalist = SequenceUtil.readFasta(instream);\r
 255                         instream.close();\r
 256                         String jobId = null;\r
 257                         if (customOptions != null && preset != null) {\r
 258                                 System.out\r
 259                                                 .println("WARN: Parameters (-f) are defined together with a preset (-r) ignoring preset!");\r
 260                         }\r
 261                         if (customOptions != null) {\r
 262                                 jobId = msaws.customAlign(fastalist, customOptions);\r
 263                         } else if (preset != null) {\r
 264                                 jobId = msaws.presetAlign(fastalist, preset);\r
 265                         } else {\r
 266                                 jobId = msaws.align(fastalist);\r
 267                         }\r
 268                         Thread.sleep(1000);\r
 269                         alignment = msaws.getResult(jobId);\r
 270 \r
 271                 } catch (IOException e) {\r
 272                         System.err\r
 273                                         .println("Exception while reading the input file. "\r
 274                                                         + "Check that the input file contains a list of fasta formatted sequences! "\r
 275                                                         + "Exception details are below:");\r
 276                         e.printStackTrace();\r
 277                 } catch (JobSubmissionException e) {\r
 278                         System.err\r
 279                                         .println("Exception while submitting job to a web server. "\r
 280                                                         + "Exception details are below:");\r
 281                         e.printStackTrace();\r
 282                 } catch (ResultNotAvailableException e) {\r
 283                         System.err.println("Exception while waiting for results. "\r
 284                                         + "Exception details are below:");\r
 285                         e.printStackTrace();\r
 286                 } catch (InterruptedException ignored) {\r
 287                         // ignore and propagate an interruption\r
 288                         Thread.currentThread().interrupt();\r
 289                 } catch (WrongParameterException e) {\r
 290                         e.printStackTrace();\r
 291                 } finally {\r
 292                         if (instream != null) {\r
 293                                 try {\r
 294                                         instream.close();\r
 295                                 } catch (IOException ignored) {\r
 296                                         // ignore\r
 297                                 }\r
 298                         }\r
 299                 }\r
 300                 return alignment;\r
 301         }\r
 302 \r
 303         /**\r
 304          * Prints Jws2Client usage information to standard out\r
 305          * \r
 306          * @param exitStatus\r
 307          */\r
 308         static void printUsage(int exitStatus) {\r
 309                 System.out.println();\r
 310                 System.out.println("Usage: <Class or Jar file name> " + hostkey\r
 311                                 + pseparator + "host_and_context " + servicekey + pseparator\r
 312                                 + "serviceName ACTION [OPTIONS] ");\r
 313                 System.out.println();\r
 314                 System.out\r
 315                                 .println(hostkey\r
 316                                                 + pseparator\r
 317                                                 + "<host_and_context> - a full URL to the JWS2 web server including context path e.g. http://10.31.1.159:8080/ws");\r
 318                 System.out.println(servicekey + pseparator + "<ServiceName> - one of "\r
 319                                 + Arrays.toString(Services.values()));\r
 320                 System.out.println();\r
 321                 System.out.println("ACTIONS: ");\r
 322                 System.out\r
 323                                 .println(inputkey\r
 324                                                 + pseparator\r
 325                                                 + "<inputFile> - full path to fasta formatted sequence file, from which to align sequences");\r
 326                 System.out.println(paramList\r
 327                                 + " - lists parameters supported by web service");\r
 328                 System.out.println(presetList\r
 329                                 + " - lists presets supported by web service");\r
 330                 System.out.println(limitList + " - lists web services limits");\r
 331                 System.out\r
 332                                 .println("Please note that if input file is specified other actions are ignored");\r
 333 \r
 334                 System.out.println();\r
 335                 System.out.println("OPTIONS (only for use with -i action):");\r
 336 \r
 337                 System.out.println(presetkey + pseparator\r
 338                                 + "<presetName> - name of the preset to use");\r
 339                 System.out\r
 340                                 .println(outputkey\r
 341                                                 + pseparator\r
 342                                                 + "<outputFile> - full path to the file where to write an alignment");\r
 343                 System.out\r
 344                                 .println("-f=<parameterInputFile> - the name of the file with the list of parameters to use.");\r
 345                 System.out\r
 346                                 .println("Please note that -r and -f options cannot be used together. "\r
 347                                                 + "Alignment is done with either preset or a parameters from the file, but not both!");\r
 348 \r
 349                 System.exit(exitStatus);\r
 350         }\r
 351 \r
 352         /**\r
 353          * Starts command line client, if no parameter are supported print help. Two\r
 354          * parameters are required for successfull call the JWS2 host name and a\r
 355          * service name.\r
 356          * \r
 357          * @param args\r
 358          *            Usage: <Class or Jar file name> -h=host_and_context\r
 359          *            -s=serviceName ACTION [OPTIONS]\r
 360          * \r
 361          *            -h=<host_and_context> - a full URL to the JWS2 web server\r
 362          *            including context path e.g. http://10.31.1.159:8080/ws\r
 363          * \r
 364          *            -s=<ServiceName> - one of [MafftWS, MuscleWS, ClustalWS,\r
 365          *            TcoffeeWS, ProbconsWS] ACTIONS:\r
 366          * \r
 367          *            -i=<inputFile> - full path to fasta formatted sequence file,\r
 368          *            from which to align sequences\r
 369          * \r
 370          *            -parameters - lists parameters supported by web service\r
 371          * \r
 372          *            -presets - lists presets supported by web service\r
 373          * \r
 374          *            -limits - lists web services limits Please note that if input\r
 375          *            file is specified other actions are ignored\r
 376          * \r
 377          *            OPTIONS: (only for use with -i action):\r
 378          * \r
 379          *            -r=<presetName> - name of the preset to use\r
 380          * \r
 381          *            -o=<outputFile> - full path to the file where to write an\r
 382          *            alignment -f=<parameterInputFile> - the name of the file with\r
 383          *            the list of parameters to use. Please note that -r and -f\r
 384          *            options cannot be used together. Alignment is done with either\r
 385          *            preset or a parameters from the file, but not both!\r
 386          * \r
 387          */\r
 388         public static void main(String[] args) {\r
 389 \r
 390                 if (args == null) {\r
 391                         printUsage(1);\r
 392                 }\r
 393                 if (args.length < 2) {\r
 394                         System.out.println("Host and service names are required!");\r
 395                         printUsage(1);\r
 396                 }\r
 397 \r
 398                 try {\r
 399                         new Jws2Client(args);\r
 400                 } catch (IOException e) {\r
 401                         log.log(Level.SEVERE, "IOException in client! " + e.getMessage(),\r
 402                                         e.getCause());\r
 403                         System.err.println("Cannot write output file! Stack trace: ");\r
 404                         e.printStackTrace();\r
 405                 }\r
 406         }\r
 407 }\r