webservices/compbio/ws/client/AAConClient.java

   1 /* Copyright (c) 2011 Peter Troshin\r
   2  *  \r
   3  *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0     \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.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 \r
  81         /**\r
  82          * Web service name\r
  83          */\r
  84         static final String serviceName = "AAConWS";\r
  85 \r
  86         /**\r
  87          * Connects to the service and do the job as requested, if something goes\r
  88          * wrong reports or/and prints usage help.\r
  89          * \r
  90          * @param cmd\r
  91          *            command line options\r
  92          * @throws IOException\r
  93          *             if the system cannot read/write from/into the file system\r
  94          */\r
  95         @SuppressWarnings("unchecked")\r
  96         AAConClient(String[] cmd) throws IOException {\r
  97                 File inputFile = IOHelper.getFile(cmd, inputkey, true);\r
  98                 File outFile = IOHelper.getFile(cmd, outputkey, false);\r
  99                 File parametersFile = IOHelper.getFile(cmd, paramFile, true);\r
 100                 String presetName = CmdHelper.getPresetName(cmd);\r
 101 \r
 102                 SequenceAnnotation<AAConWS> msaws = connect();\r
 103                 Preset<AAConWS> preset = null;\r
 104                 if (presetName != null) {\r
 105                         preset = MetadataHelper.getPreset(msaws, presetName);\r
 106                 }\r
 107                 List<Option<AAConWS>> customOptions = null;\r
 108                 if (parametersFile != null) {\r
 109                         List<String> prms = IOHelper.loadParameters(parametersFile);\r
 110                         customOptions = MetadataHelper.processParameters(prms, msaws.getRunnerOptions());\r
 111                 }\r
 112                 ScoreManager result = null;\r
 113                 if (inputFile != null) {\r
 114                         System.out.println("Calculating conservation...");\r
 115                         result = analize(inputFile, msaws, preset, customOptions);\r
 116                         Writer outStream = null;\r
 117                         if (outFile != null) {\r
 118                                 outStream = IOHelper.getWriter(outFile);\r
 119                         } else {\r
 120                                 // this stream is going to be closed later which is fine as\r
 121                                 // std.out will not be\r
 122                                 outStream = new PrintWriter(System.out, true);\r
 123                         }\r
 124                         writeOut(outStream, result);\r
 125                         // stream is closed in the method no need to close it here\r
 126                 }\r
 127 \r
 128                 boolean listParameters = CmdHelper.listParameters(cmd);\r
 129                 if (listParameters) {\r
 130                         System.out.println(MetadataHelper.getParametersList(msaws));\r
 131                 }\r
 132                 boolean listPreset = CmdHelper.listPresets(cmd);\r
 133                 if (listPreset) {\r
 134                         System.out.println(MetadataHelper.getPresetList(msaws));\r
 135                 }\r
 136                 boolean listLimits = CmdHelper.listLimits(cmd);\r
 137                 if (listLimits) {\r
 138                         System.out.println(MetadataHelper.getLimits(msaws));\r
 139                 }\r
 140                 log.fine("Disconnecting...");\r
 141                 ((Closeable) msaws).close();\r
 142                 log.fine("Disconnected successfully!");\r
 143         }\r
 144 \r
 145         /**\r
 146          * Outputs AAcon results into the file represented by the outStream\r
 147          * \r
 148          * @param outStream\r
 149          * @param result\r
 150          *            the AACon scores to output\r
 151          */\r
 152         static void writeOut(Writer writer, ScoreManager result) {\r
 153                 try {\r
 154                         result.writeOut(writer);\r
 155                 } catch (IOException e) {\r
 156                         System.err.println("Problems writing output file! Stack trace is below: ");\r
 157                         e.printStackTrace();\r
 158                 } finally {\r
 159                         if (writer != null) {\r
 160                                 try {\r
 161                                         writer.close();\r
 162                                 } catch (IOException ignored) {\r
 163                                         // e.printStackTrace();\r
 164                                 }\r
 165                         }\r
 166                 }\r
 167         }\r
 168 \r
 169         /**\r
 170          * Connects to a AACon web service by the host and the service name\r
 171          * \r
 172          * \r
 173          * @return {@link AlignmentAnnotation}\r
 174          * @throws WebServiceException\r
 175          *             if cannot connect to a web service\r
 176          */\r
 177         public static SequenceAnnotation<AAConWS> connect()\r
 178                         throws WebServiceException {\r
 179                 URL url = null;\r
 180                 log.log(Level.FINE, "Attempting to connect...");\r
 181                 try {\r
 182                         url = new URL(hostname + "/" + "AAConWS" + "?wsdl");\r
 183                 } catch (MalformedURLException e) {\r
 184                         e.printStackTrace();\r
 185                         // ignore as the host name is already verified\r
 186                 }\r
 187                 QName qname = new QName(QUALIFIED_SERVICE_NAME, "AAConWS");\r
 188                 Service serv = Service.create(url, qname);\r
 189                 QName portName = new QName(QUALIFIED_SERVICE_NAME, "AAConWS" + "Port");\r
 190 \r
 191                 @SuppressWarnings("unchecked")\r
 192                 SequenceAnnotation<AAConWS> serviceIF = serv.getPort(portName, SequenceAnnotation.class);\r
 193 \r
 194                 log.log(Level.FINE, "Connected successfully!");\r
 195                 return serviceIF;\r
 196         }\r
 197 \r
 198         /**\r
 199          * Calculate conservation for sequences loaded from the file\r
 200          * \r
 201          * @param wsproxy\r
 202          *            a web service proxy\r
 203          * @param file\r
 204          *            the file to read the results from\r
 205          * @param preset\r
 206          *            Preset to use optional\r
 207          * @param customOptions\r
 208          *            the list of options\r
 209          * @return Set<Score> the conservation scores\r
 210          * @throws UnknownFileFormatException\r
 211          */\r
 212         static ScoreManager analize(File file, SequenceAnnotation<AAConWS> wsproxy,\r
 213                         Preset<AAConWS> preset, List<Option<AAConWS>> customOptions) {\r
 214 \r
 215                 List<FastaSequence> fastalist = null;\r
 216                 ScoreManager scores = null;\r
 217                 try {\r
 218                         fastalist = SequenceUtil.openInputStream(file.getAbsolutePath());\r
 219 \r
 220                         String jobId = null;\r
 221                         if (customOptions != null && preset != null) {\r
 222                                 System.out.println("WARN: Parameters (-f) are defined together with a preset (-r) ignoring preset!");\r
 223                         }\r
 224                         if (customOptions != null) {\r
 225                                 jobId = wsproxy.customAnalize(fastalist, customOptions);\r
 226                         } else if (preset != null) {\r
 227                                 jobId = wsproxy.presetAnalize(fastalist, preset);\r
 228                         } else {\r
 229                                 jobId = wsproxy.analize(fastalist);\r
 230                         }\r
 231                         Thread.sleep(1000);\r
 232                         scores = wsproxy.getAnnotation(jobId);\r
 233 \r
 234                 } catch (IOException e) {\r
 235                         System.err.println("Exception while reading the input file. "\r
 236                                                         + "Check that the input file contains a list of fasta formatted sequences! "\r
 237                                                         + "Exception details are below:");\r
 238                         e.printStackTrace();\r
 239                 } catch (JobSubmissionException e) {\r
 240                         System.err.println("Exception while submitting job to a web server. "\r
 241                                                         + "Exception details are below:");\r
 242                         e.printStackTrace();\r
 243                 } catch (ResultNotAvailableException e) {\r
 244                         System.err.println("Exception while waiting for results. "\r
 245                                         + "Exception details are below:");\r
 246                         e.printStackTrace();\r
 247                 } catch (InterruptedException ignored) {\r
 248                         // ignore and propagate an interruption\r
 249                         Thread.currentThread().interrupt();\r
 250                 } catch (WrongParameterException e) {\r
 251                         System.err.println("Exception while parsing the web method input parameters. "\r
 252                                                         + "Exception details are below:");\r
 253                         e.printStackTrace();\r
 254                 } catch (UnknownFileFormatException e) {\r
 255                         System.err.println("Exception while attempting to read the input file "\r
 256                                                 + "Exception details are below:");\r
 257                         System.out.println(e.getMessage());\r
 258                         e.printStackTrace();\r
 259                 }\r
 260                 return scores;\r
 261         }\r
 262 \r
 263         /**\r
 264          * Prints AAConClient usage information to standard out\r
 265          * \r
 266          * @param exitStatus\r
 267          */\r
 268         static void printUsage(int exitStatus) {\r
 269                 System.out.println();\r
 270                 System.out.println("Usage: <Class or Jar file name>  ACTION [OPTIONS] ");\r
 271                 System.out.println();\r
 272                 System.out.println("ACTIONS: ");\r
 273                 System.out.println(inputkey + pseparator + "<inputFile> - full path to fasta or Clustal formatted alignment file ");\r
 274                 System.out.println(paramList + " - lists parameters supported by web service");\r
 275                 System.out.println(presetList + " - lists presets supported by web service");\r
 276                 System.out.println(limitList + " - lists web services limits");\r
 277                 System.out.println("Please note that if input file is specified other actions are ignored\n");\r
 278                 System.out.println("OPTIONS (only for use with -i action):");\r
 279                 System.out.println(presetkey + pseparator + "<presetName> - name of the preset to use");\r
 280                 System.out.println(outputkey + pseparator + "<outputFile> - full path to the file where to write the result");\r
 281                 System.out.println("-f=<parameterInputFile> - the name of the file with the list of parameters to use.");\r
 282                 System.out.println("Please note that -r and -f options cannot be used together. "\r
 283                                                 + "Conservation is calculated with either a preset or parameters from the file, but not both!");\r
 284                 System.exit(exitStatus);\r
 285         }\r
 286 \r
 287         /**\r
 288          * Starts command line client, if no parameters are supplied prints help.\r
 289          * \r
 290          * @param args\r
 291          *            Usage: <Class or Jar file name> ACTION [OPTIONS]\r
 292          * \r
 293          *            -i=<inputFile> - full path to fasta or Clustal formatted\r
 294          *            alignment file\r
 295          * \r
 296          *            -parameters - lists parameters supported by web service\r
 297          * \r
 298          *            -presets - lists presets supported by web service\r
 299          * \r
 300          *            -limits - lists web services limits. Please note that if input\r
 301          *            file is specified other actions are ignored\r
 302          * \r
 303          *            OPTIONS: (only for use with -i action):\r
 304          * \r
 305          *            -r=<presetName> - name of the preset to use\r
 306          * \r
 307          *            -o=<outputFile> - full path to the file where to write results\r
 308          *            -f=<parameterInputFile> - the name of the file with the list\r
 309          *            of parameters to use. Please note that -r and -f options\r
 310          *            cannot be used together. Conservation is calculated with\r
 311          *            either a preset or parameters from the file, but not both!\r
 312          * \r
 313          */\r
 314         public static void main(String[] args) {\r
 315 \r
 316                 if (args == null) {\r
 317                         printUsage(1);\r
 318                 }\r
 319                 if (args.length < 1) {\r
 320                         System.out.println("No options is specified! ");\r
 321                         printUsage(1);\r
 322                 }\r
 323 \r
 324                 try {\r
 325                         new AAConClient(args);\r
 326                 } catch (IOException e) {\r
 327                         log.log(Level.SEVERE, "IOException in client! " + e.getMessage(), e.getCause());\r
 328                         System.err.println("Cannot write output file! Stack trace: ");\r
 329                         e.printStackTrace();\r
 330                 }\r
 331         }\r
 332 }\r