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