webservices/compbio/ws/client/AAConClient.java

   1 /* Copyright (c) 2010 Peter Troshin\r
   2  *  \r
   3  *  Amino Acid Conservation Web Service client @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.IOException;\r
  33 import java.io.OutputStream;\r
  34 import java.net.MalformedURLException;\r
  35 import java.net.URL;\r
  36 import java.util.HashSet;\r
  37 import java.util.List;\r
  38 import java.util.Map;\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.SequenceAnnotation;\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.data.sequence.UnknownFileFormatException;\r
  52 import compbio.metadata.JobSubmissionException;\r
  53 import compbio.metadata.Option;\r
  54 import compbio.metadata.Preset;\r
  55 import compbio.metadata.ResultNotAvailableException;\r
  56 import compbio.metadata.WrongParameterException;\r
  57 import compbio.ws.server.AAConWS;\r
  58 \r
  59 /**\r
  60  * A command line client for AACon web service\r
  61  * \r
  62  * @author pvtroshin\r
  63  * @version 1.0\r
  64  */\r
  65 public class AAConClient {\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(AAConClient.class\r
  72                         .getCanonicalName());\r
  73 \r
  74         /**\r
  75          * The fully qualified web service namespace\r
  76          */\r
  77         static final String QUALIFIED_SERVICE_NAME = "http://msa.data.compbio/01/12/2010/";\r
  78 \r
  79         /**\r
  80          * Web service host\r
  81          */\r
  82         static final String hostname = "http://www.compbio.dundee.ac.uk/aacon";\r
  83         // static final String hostname = "http://localhost:8080/jabaws";\r
  84 \r
  85         /**\r
  86          * Web service name\r
  87          */\r
  88         static final String serviceName = "AAConWS";\r
  89 \r
  90         /**\r
  91          * Connects to the service and do the job as requested, if something goes\r
  92          * wrong reports or/and prints usage help.\r
  93          * \r
  94          * @param cmd\r
  95          *            command line options\r
  96          * @throws IOException\r
  97          *             if the system cannot read/write from/into the file system\r
  98          */\r
  99         @SuppressWarnings("unchecked")\r
 100         AAConClient(String[] cmd) throws IOException {\r
 101 \r
 102                 File inputFile = IOHelper.getFile(cmd, inputkey, true);\r
 103                 File outFile = IOHelper.getFile(cmd, outputkey, false);\r
 104                 File parametersFile = IOHelper.getFile(cmd, paramFile, true);\r
 105                 String presetName = CmdHelper.getPresetName(cmd);\r
 106 \r
 107                 SequenceAnnotation<AAConWS> msaws = connect();\r
 108                 Preset<AAConWS> preset = null;\r
 109                 if (presetName != null) {\r
 110                         preset = MetadataHelper.getPreset(msaws, presetName);\r
 111                 }\r
 112                 List<Option<AAConWS>> customOptions = null;\r
 113                 if (parametersFile != null) {\r
 114                         List<String> prms = IOHelper.loadParameters(parametersFile);\r
 115                         customOptions = MetadataHelper.processParameters(prms,\r
 116                                         msaws.getRunnerOptions());\r
 117                 }\r
 118                 Map<String, HashSet<Score>> result = null;\r
 119                 if (inputFile != null) {\r
 120                         System.out.println("Calculating conservation...");\r
 121                         result = analize(inputFile, msaws, preset, customOptions);\r
 122                         OutputStream outStream = null;\r
 123                         if (outFile != null) {\r
 124                                 outStream = IOHelper.getOutStream(outFile);\r
 125                         } else {\r
 126                                 // this stream is going to be closed later which is fine as\r
 127                                 // std.out will not be\r
 128                                 outStream = System.out;\r
 129                         }\r
 130                         writeOut(outStream, result);\r
 131                         // stream is closed in the method no need to close it here\r
 132                 }\r
 133 \r
 134                 boolean listParameters = CmdHelper.listParameters(cmd);\r
 135                 if (listParameters) {\r
 136                         System.out.println(MetadataHelper.getParametersList(msaws));\r
 137                 }\r
 138                 boolean listPreset = CmdHelper.listPresets(cmd);\r
 139                 if (listPreset) {\r
 140                         System.out.println(MetadataHelper.getPresetList(msaws));\r
 141                 }\r
 142                 boolean listLimits = CmdHelper.listLimits(cmd);\r
 143                 if (listLimits) {\r
 144                         System.out.println(MetadataHelper.getLimits(msaws));\r
 145                 }\r
 146                 log.fine("Disconnecting...");\r
 147                 ((Closeable) msaws).close();\r
 148                 log.fine("Disconnected successfully!");\r
 149         }\r
 150 \r
 151         /**\r
 152          * Outputs AAcon results into the file represented by the outStream\r
 153          * \r
 154          * @param outStream\r
 155          * @param result\r
 156          *            the AACon scores to output\r
 157          */\r
 158         static void writeOut(OutputStream outStream,\r
 159                         Map<String, HashSet<Score>> result) {\r
 160                 try {\r
 161                         for (Map.Entry<String, ? extends Set<Score>> entry : result\r
 162                                         .entrySet()) {\r
 163                                 System.out.println(">" + entry.getKey());\r
 164                                 Score.write(entry.getValue(), outStream);\r
 165                         }\r
 166                 } catch (IOException e) {\r
 167                         System.err\r
 168                                         .println("Problems writing output file! Stack trace is below: ");\r
 169                         e.printStackTrace();\r
 170                 } finally {\r
 171                         if (outStream != null) {\r
 172                                 try {\r
 173                                         outStream.close();\r
 174                                 } catch (IOException ignored) {\r
 175                                         // e.printStackTrace();\r
 176                                 }\r
 177                         }\r
 178                 }\r
 179         }\r
 180 \r
 181         /**\r
 182          * Connects to a AACon web service by the host and the service name\r
 183          * \r
 184          * \r
 185          * @return {@link AlignmentAnnotation}\r
 186          * @throws WebServiceException\r
 187          *             if cannot connect to a web service\r
 188          */\r
 189         public static SequenceAnnotation<AAConWS> connect()\r
 190                         throws WebServiceException {\r
 191                 URL url = null;\r
 192                 log.log(Level.FINE, "Attempting to connect...");\r
 193                 try {\r
 194                         url = new URL(hostname + "/" + "AAConWS" + "?wsdl");\r
 195                 } catch (MalformedURLException e) {\r
 196                         e.printStackTrace();\r
 197                         // ignore as the host name is already verified\r
 198                 }\r
 199                 QName qname = new QName(QUALIFIED_SERVICE_NAME, "AAConWS");\r
 200                 Service serv = Service.create(url, qname);\r
 201                 QName portName = new QName(QUALIFIED_SERVICE_NAME, "AAConWS" + "Port");\r
 202 \r
 203                 @SuppressWarnings("unchecked")\r
 204                 SequenceAnnotation<AAConWS> serviceIF = serv.getPort(portName,\r
 205                                 SequenceAnnotation.class);\r
 206 \r
 207                 log.log(Level.FINE, "Connected successfully!");\r
 208                 return serviceIF;\r
 209         }\r
 210 \r
 211         /**\r
 212          * Calculate conservation for sequences loaded from the file\r
 213          * \r
 214          * @param wsproxy\r
 215          *            a web service proxy\r
 216          * @param file\r
 217          *            the file to read the results from\r
 218          * @param preset\r
 219          *            Preset to use optional\r
 220          * @param customOptions\r
 221          *            the list of options\r
 222          * @return Set<Score> the conservation scores\r
 223          * @throws UnknownFileFormatException\r
 224          */\r
 225         static Map<String, HashSet<Score>> analize(File file,\r
 226                         SequenceAnnotation<AAConWS> wsproxy, Preset<AAConWS> preset,\r
 227                         List<Option<AAConWS>> customOptions) {\r
 228 \r
 229                 List<FastaSequence> fastalist = null;\r
 230                 Map<String, HashSet<Score>> scores = null;\r
 231                 try {\r
 232                         fastalist = SequenceUtil.openInputStream(file.getAbsolutePath());\r
 233 \r
 234                         String jobId = null;\r
 235                         if (customOptions != null && preset != null) {\r
 236                                 System.out\r
 237                                                 .println("WARN: Parameters (-f) are defined together with a preset (-r) ignoring preset!");\r
 238                         }\r
 239                         if (customOptions != null) {\r
 240                                 jobId = wsproxy.customAnalize(fastalist, customOptions);\r
 241                         } else if (preset != null) {\r
 242                                 jobId = wsproxy.presetAnalize(fastalist, preset);\r
 243                         } else {\r
 244                                 jobId = wsproxy.analize(fastalist);\r
 245                         }\r
 246                         Thread.sleep(1000);\r
 247                         scores = wsproxy.getAnnotation(jobId);\r
 248 \r
 249                 } catch (IOException e) {\r
 250                         System.err\r
 251                                         .println("Exception while reading the input file. "\r
 252                                                         + "Check that the input file contains a list of fasta formatted sequences! "\r
 253                                                         + "Exception details are below:");\r
 254                         e.printStackTrace();\r
 255                 } catch (JobSubmissionException e) {\r
 256                         System.err\r
 257                                         .println("Exception while submitting job to a web server. "\r
 258                                                         + "Exception details are below:");\r
 259                         e.printStackTrace();\r
 260                 } catch (ResultNotAvailableException e) {\r
 261                         System.err.println("Exception while waiting for results. "\r
 262                                         + "Exception details are below:");\r
 263                         e.printStackTrace();\r
 264                 } catch (InterruptedException ignored) {\r
 265                         // ignore and propagate an interruption\r
 266                         Thread.currentThread().interrupt();\r
 267                 } catch (WrongParameterException e) {\r
 268                         System.err\r
 269                                         .println("Exception while parsing the web method input parameters. "\r
 270                                                         + "Exception details are below:");\r
 271                         e.printStackTrace();\r
 272                 } catch (UnknownFileFormatException e) {\r
 273                         System.err\r
 274                                         .println("Exception while attempting to read the input file "\r
 275                                                         + "Exception details are below:");\r
 276                         System.out.println(e.getMessage());\r
 277                         e.printStackTrace();\r
 278                 }\r
 279                 return scores;\r
 280         }\r
 281 \r
 282         /**\r
 283          * Prints AAConClient usage information to standard out\r
 284          * \r
 285          * @param exitStatus\r
 286          */\r
 287         static void printUsage(int exitStatus) {\r
 288                 System.out.println();\r
 289                 System.out.println("Usage: <Class or Jar file name> "\r
 290                                 + " ACTION [OPTIONS] ");\r
 291                 System.out.println();\r
 292                 System.out.println("ACTIONS: ");\r
 293                 System.out\r
 294                                 .println(inputkey\r
 295                                                 + pseparator\r
 296                                                 + "<inputFile> - full path to fasta or Clustal formatted alignment file ");\r
 297                 System.out.println(paramList\r
 298                                 + " - lists parameters supported by web service");\r
 299                 System.out.println(presetList\r
 300                                 + " - lists presets supported by web service");\r
 301                 System.out.println(limitList + " - lists web services limits");\r
 302                 System.out\r
 303                                 .println("Please note that if input file is specified other actions are ignored");\r
 304 \r
 305                 System.out.println();\r
 306                 System.out.println("OPTIONS (only for use with -i action):");\r
 307 \r
 308                 System.out.println(presetkey + pseparator\r
 309                                 + "<presetName> - name of the preset to use");\r
 310                 System.out\r
 311                                 .println(outputkey\r
 312                                                 + pseparator\r
 313                                                 + "<outputFile> - full path to the file where to write the result");\r
 314                 System.out\r
 315                                 .println("-f=<parameterInputFile> - the name of the file with the list of parameters to use.");\r
 316                 System.out\r
 317                                 .println("Please note that -r and -f options cannot be used together. "\r
 318                                                 + "Conservation is calculated with either a preset or "\r
 319                                                 + "the parameters from the file, but not both!");\r
 320 \r
 321                 System.exit(exitStatus);\r
 322         }\r
 323 \r
 324         /**\r
 325          * Starts command line client, if no parameters are supplied prints help.\r
 326          * \r
 327          * @param args\r
 328          *            Usage: <Class or Jar file name> ACTION [OPTIONS]\r
 329          * \r
 330          *            -i=<inputFile> - full path to fasta or Clustal formatted\r
 331          *            alignment file\r
 332          * \r
 333          *            -parameters - lists parameters supported by web service\r
 334          * \r
 335          *            -presets - lists presets supported by web service\r
 336          * \r
 337          *            -limits - lists web services limits. Please note that if input\r
 338          *            file is specified other actions are ignored\r
 339          * \r
 340          *            OPTIONS: (only for use with -i action):\r
 341          * \r
 342          *            -r=<presetName> - name of the preset to use\r
 343          * \r
 344          *            -o=<outputFile> - full path to the file where to write results\r
 345          *            -f=<parameterInputFile> - the name of the file with the list\r
 346          *            of parameters to use. Please note that -r and -f options\r
 347          *            cannot be used together. Conservation is calculated with\r
 348          *            either a preset or parameters from the file, but not both!\r
 349          * \r
 350          */\r
 351         public static void main(String[] args) {\r
 352 \r
 353                 if (args == null) {\r
 354                         printUsage(1);\r
 355                 }\r
 356                 if (args.length < 1) {\r
 357                         System.out.println("No options is specified! ");\r
 358                         printUsage(1);\r
 359                 }\r
 360 \r
 361                 try {\r
 362                         new AAConClient(args);\r
 363                 } catch (IOException e) {\r
 364                         log.log(Level.SEVERE, "IOException in client! " + e.getMessage(),\r
 365                                         e.getCause());\r
 366                         System.err.println("Cannot write output file! Stack trace: ");\r
 367                         e.printStackTrace();\r
 368                 }\r
 369         }\r
 370 }\r