webservices/compbio/ws/client/AAConClient.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.limitList;\r
  23 import static compbio.ws.client.Constraints.outputkey;\r
  24 import static compbio.ws.client.Constraints.paramFile;\r
  25 import static compbio.ws.client.Constraints.paramList;\r
  26 import static compbio.ws.client.Constraints.presetList;\r
  27 import static compbio.ws.client.Constraints.presetkey;\r
  28 import static compbio.ws.client.Constraints.pseparator;\r
  29 \r
  30 import java.io.Closeable;\r
  31 import java.io.File;\r
  32 import java.io.FileInputStream;\r
  33 import java.io.IOException;\r
  34 import java.io.OutputStream;\r
  35 import java.net.MalformedURLException;\r
  36 import java.net.URL;\r
  37 import java.util.Arrays;\r
  38 import java.util.List;\r
  39 import java.util.Set;\r
  40 import java.util.logging.Level;\r
  41 import java.util.logging.Logger;\r
  42 \r
  43 import javax.xml.namespace.QName;\r
  44 import javax.xml.ws.Service;\r
  45 import javax.xml.ws.WebServiceException;\r
  46 \r
  47 import compbio.data.msa.Annotation;\r
  48 import compbio.data.sequence.FastaSequence;\r
  49 import compbio.data.sequence.Score;\r
  50 import compbio.data.sequence.SequenceUtil;\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 import compbio.ws.server.AAConWS;\r
  57 \r
  58 /**\r
  59  * A command line client for AACon web service\r
  60  * \r
  61  * @author pvtroshin\r
  62  * @version 1.0\r
  63  */\r
  64 public class AAConClient {\r
  65 \r
  66         /*\r
  67          * Use java.util.Logger instead of log4j logger to reduce the size of the\r
  68          * client package\r
  69          */\r
  70         private static final Logger log = Logger.getLogger(AAConClient.class\r
  71                         .getCanonicalName());\r
  72 \r
  73         static final String QUALIFIED_SERVICE_NAME = "http://msa.data.compbio/01/12/2010/";\r
  74 \r
  75         // static final String hostname = "http://www.compbio.dundee.ac.uk/aacon";\r
  76         static final String hostname = "http://localhost:8080/jabaws";\r
  77 \r
  78         static final String serviceName = "AAConWS";\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 <AAConWS>\r
 103          *            web service type\r
 104          * @param cmd\r
 105          *            command line options\r
 106          * @throws IOException\r
 107          */\r
 108         @SuppressWarnings("unchecked")\r
 109         AAConClient(String[] cmd) throws IOException {\r
 110 \r
 111                 Services service = Services.getService(serviceName);\r
 112                 if (service == null) {\r
 113                         System.out.println("Service " + serviceName\r
 114                                         + " is no supported! Valid values are: "\r
 115                                         + Arrays.toString(Services.values()));\r
 116                         printUsage(1);\r
 117                 }\r
 118                 File inputFile = IOHelper.getFile(cmd, inputkey, true);\r
 119                 File outFile = IOHelper.getFile(cmd, outputkey, false);\r
 120                 File parametersFile = IOHelper.getFile(cmd, paramFile, true);\r
 121                 String presetName = CmdHelper.getPresetName(cmd);\r
 122 \r
 123                 Annotation<AAConWS> msaws = connect(hostname, service);\r
 124                 Preset<AAConWS> preset = null;\r
 125                 if (presetName != null) {\r
 126                         preset = MetadataHelper.getPreset(msaws, presetName);\r
 127                 }\r
 128                 List<Option<AAConWS>> customOptions = null;\r
 129                 if (parametersFile != null) {\r
 130                         List<String> prms = IOHelper.loadParameters(parametersFile);\r
 131                         customOptions = MetadataHelper.processParameters(prms,\r
 132                                         msaws.getRunnerOptions());\r
 133                 }\r
 134                 Set<Score> result = null;\r
 135                 if (inputFile != null) {\r
 136                         System.out.println("calc conserv!");\r
 137                         result = analize(inputFile, msaws, preset, customOptions);\r
 138                         OutputStream outStream = null;\r
 139                         if (outFile != null) {\r
 140                                 outStream = IOHelper.getOutStream(outFile);\r
 141                         } else {\r
 142                                 // this stream is going to be closed later which is fine as\r
 143                                 // std.out will not be\r
 144                                 outStream = System.out;\r
 145                         }\r
 146                         writeOut(outStream, result);\r
 147                         // stream is closed in the method no need to close it here\r
 148                 }\r
 149 \r
 150                 boolean listParameters = CmdHelper.listParameters(cmd);\r
 151                 if (listParameters) {\r
 152                         System.out.println(MetadataHelper.getParametersList(msaws));\r
 153                 }\r
 154                 boolean listPreset = CmdHelper.listPresets(cmd);\r
 155                 if (listPreset) {\r
 156                         System.out.println(MetadataHelper.getPresetList(msaws));\r
 157                 }\r
 158                 boolean listLimits = CmdHelper.listLimits(cmd);\r
 159                 if (listLimits) {\r
 160                         System.out.println(MetadataHelper.getLimits(msaws));\r
 161                 }\r
 162                 log.fine("Disconnecting...");\r
 163                 ((Closeable) msaws).close();\r
 164                 log.fine("Disconnected successfully!");\r
 165         }\r
 166 \r
 167         /**\r
 168          * Outputs clustal formatted alignment into the file represented by the\r
 169          * outStream\r
 170          * \r
 171          * @param outStream\r
 172          * @param align\r
 173          *            the alignment to output\r
 174          */\r
 175         static void writeOut(OutputStream outStream, Set<Score> result) {\r
 176                 try {\r
 177                         Score.write(result, outStream);\r
 178                 } catch (IOException e) {\r
 179                         System.err\r
 180                                         .println("Problems writing output file! Stack trace is below: ");\r
 181                         e.printStackTrace();\r
 182                 } finally {\r
 183                         if (outStream != null) {\r
 184                                 try {\r
 185                                         outStream.close();\r
 186                                 } catch (IOException ignored) {\r
 187                                         // e.printStackTrace();\r
 188                                 }\r
 189                         }\r
 190                 }\r
 191         }\r
 192 \r
 193         /**\r
 194          * Connects to a web service by the host and the service name\r
 195          * \r
 196          * @param T\r
 197          *            web service type\r
 198          * @param host\r
 199          * @param service\r
 200          * @return MsaWS<T>\r
 201          * @throws WebServiceException\r
 202          */\r
 203         public static Annotation<AAConWS> connect(String host, Services service)\r
 204                         throws WebServiceException {\r
 205                 URL url = null;\r
 206                 log.log(Level.FINE, "Attempting to connect...");\r
 207                 try {\r
 208                         url = new URL(host + "/" + service.toString() + "?wsdl");\r
 209                 } catch (MalformedURLException e) {\r
 210                         e.printStackTrace();\r
 211                         // ignore as the host name is already verified\r
 212                 }\r
 213                 Service serv = service.getService(url, QUALIFIED_SERVICE_NAME);\r
 214                 @SuppressWarnings("unchecked")\r
 215                 QName portName = new QName(QUALIFIED_SERVICE_NAME, "AAConWS" + "Port");\r
 216 \r
 217                 Annotation<AAConWS> serviceIF = serv\r
 218                                 .getPort(portName, Annotation.class);\r
 219 \r
 220                 log.log(Level.FINE, "Connected successfully!");\r
 221                 return serviceIF;\r
 222         }\r
 223 \r
 224         /**\r
 225          * Align sequences from the file using MsaWS\r
 226          * \r
 227          * @param <T>\r
 228          *            web service type e.g. Clustal\r
 229          * @param file\r
 230          *            to write the resulting alignment to\r
 231          * @param wsproxy\r
 232          *            MsaWS required\r
 233          * @param preset\r
 234          *            Preset to use optional\r
 235          * @param customOptions\r
 236          *            file which contains new line separated list of options\r
 237          * @return Alignment\r
 238          */\r
 239         static <AAConWS> Set<Score> analize(File file, Annotation<AAConWS> wsproxy,\r
 240                         Preset<AAConWS> preset, List<Option<AAConWS>> customOptions) {\r
 241                 FileInputStream instream = null;\r
 242                 List<FastaSequence> fastalist = null;\r
 243                 Set<Score> scores = null;\r
 244                 try {\r
 245                         instream = new FileInputStream(file);\r
 246                         fastalist = SequenceUtil.readFasta(instream);\r
 247                         instream.close();\r
 248                         String jobId = null;\r
 249                         if (customOptions != null && preset != null) {\r
 250                                 System.out\r
 251                                                 .println("WARN: Parameters (-f) are defined together with a preset (-r) ignoring preset!");\r
 252                         }\r
 253                         if (customOptions != null) {\r
 254                                 jobId = wsproxy.customAnalize(fastalist, customOptions);\r
 255                         } else if (preset != null) {\r
 256                                 jobId = wsproxy.presetAnalize(fastalist, preset);\r
 257                         } else {\r
 258                                 jobId = wsproxy.analize(fastalist);\r
 259                         }\r
 260                         Thread.sleep(1000);\r
 261                         scores = wsproxy.getAnnotation(jobId);\r
 262 \r
 263                 } catch (IOException e) {\r
 264                         System.err\r
 265                                         .println("Exception while reading the input file. "\r
 266                                                         + "Check that the input file contains a list of fasta formatted sequences! "\r
 267                                                         + "Exception details are below:");\r
 268                         e.printStackTrace();\r
 269                 } catch (JobSubmissionException e) {\r
 270                         System.err\r
 271                                         .println("Exception while submitting job to a web server. "\r
 272                                                         + "Exception details are below:");\r
 273                         e.printStackTrace();\r
 274                 } catch (ResultNotAvailableException e) {\r
 275                         System.err.println("Exception while waiting for results. "\r
 276                                         + "Exception details are below:");\r
 277                         e.printStackTrace();\r
 278                 } catch (InterruptedException ignored) {\r
 279                         // ignore and propagate an interruption\r
 280                         Thread.currentThread().interrupt();\r
 281                 } catch (WrongParameterException e) {\r
 282                         e.printStackTrace();\r
 283                 } finally {\r
 284                         if (instream != null) {\r
 285                                 try {\r
 286                                         instream.close();\r
 287                                 } catch (IOException ignored) {\r
 288                                         // ignore\r
 289                                 }\r
 290                         }\r
 291                 }\r
 292                 return scores;\r
 293         }\r
 294 \r
 295         /**\r
 296          * Prints Jws2Client usage information to standard out\r
 297          * \r
 298          * @param exitStatus\r
 299          */\r
 300         static void printUsage(int exitStatus) {\r
 301                 System.out.println();\r
 302                 System.out.println("Usage: <Class or Jar file name> "\r
 303                                 + " ACTION [OPTIONS] ");\r
 304                 System.out.println();\r
 305                 System.out.println("ACTIONS: ");\r
 306                 System.out\r
 307                                 .println(inputkey\r
 308                                                 + pseparator\r
 309                                                 + "<inputFile> - full path to fasta or Clustal formatted alignment file ");\r
 310                 System.out.println(paramList\r
 311                                 + " - lists parameters supported by web service");\r
 312                 System.out.println(presetList\r
 313                                 + " - lists presets supported by web service");\r
 314                 System.out.println(limitList + " - lists web services limits");\r
 315                 System.out\r
 316                                 .println("Please note that if input file is specified other actions are ignored");\r
 317 \r
 318                 System.out.println();\r
 319                 System.out.println("OPTIONS (only for use with -i action):");\r
 320 \r
 321                 System.out.println(presetkey + pseparator\r
 322                                 + "<presetName> - name of the preset to use");\r
 323                 System.out\r
 324                                 .println(outputkey\r
 325                                                 + pseparator\r
 326                                                 + "<outputFile> - full path to the file where to write the result");\r
 327                 System.out\r
 328                                 .println("-f=<parameterInputFile> - the name of the file with the list of parameters to use.");\r
 329                 System.out\r
 330                                 .println("Please note that -r and -f options cannot be used together. "\r
 331                                                 + "Conservation is calculated with either a preset or "\r
 332                                                 + "the parameters from the file, but not both!");\r
 333 \r
 334                 System.exit(exitStatus);\r
 335         }\r
 336 \r
 337         /**\r
 338          * Starts command line client, if no parameter are supported print help. Two\r
 339          * parameters are required for successfull call the JWS2 host name and a\r
 340          * service name.\r
 341          * \r
 342          * @param args\r
 343          *            Usage: <Class or Jar file name> ACTION [OPTIONS]\r
 344          * \r
 345          *            -i=<inputFile> - full path to fasta or Clustal formatted\r
 346          *            alignment file\r
 347          * \r
 348          *            -parameters - lists parameters supported by web service\r
 349          * \r
 350          *            -presets - lists presets supported by web service\r
 351          * \r
 352          *            -limits - lists web services limits. Please note that if input\r
 353          *            file is specified other actions are ignored\r
 354          * \r
 355          *            OPTIONS: (only for use with -i action):\r
 356          * \r
 357          *            -r=<presetName> - name of the preset to use\r
 358          * \r
 359          *            -o=<outputFile> - full path to the file where to write results\r
 360          *            -f=<parameterInputFile> - the name of the file with the list\r
 361          *            of parameters to use. Please note that -r and -f options\r
 362          *            cannot be used together. Conservation is calculated with\r
 363          *            either a preset or parameters from the file, but not both!\r
 364          * \r
 365          */\r
 366         public static void main(String[] args) {\r
 367 \r
 368                 if (args == null) {\r
 369                         printUsage(1);\r
 370                 }\r
 371                 if (args.length < 1) {\r
 372                         System.out.println("No options is specified! ");\r
 373                         printUsage(1);\r
 374                 }\r
 375 \r
 376                 try {\r
 377                         new AAConClient(args);\r
 378                 } catch (IOException e) {\r
 379                         log.log(Level.SEVERE, "IOException in client! " + e.getMessage(),\r
 380                                         e.getCause());\r
 381                         System.err.println("Cannot write output file! Stack trace: ");\r
 382                         e.printStackTrace();\r
 383                 }\r
 384         }\r
 385 }\r