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