webservices/compbio/ws/server/JpredWS.java

   1 /* Copyright (c) 2011 Peter Troshin\r
   2  * Copyright (c) 2013 Alexander Sherstnev\r
   3  *  \r
   4  *  JAva Bioinformatics Analysis Web Services (JABAWS)\r
   5  *  @version: 2.5     \r
   6  * \r
   7  *  This library is free software; you can redistribute it and/or modify it under the terms of the\r
   8  *  Apache License version 2 as published by the Apache Software Foundation\r
   9  * \r
  10  *  This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
  11  *  even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
  12  *  License for more details.\r
  13  * \r
  14  *  A copy of the license is in apache_license.txt. It is also available here:\r
  15  * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
  16  * \r
  17  * Any republication or derived work distributed in source code form\r
  18  * must include this copyright and license notice.\r
  19  */\r
  20 package compbio.ws.server;\r
  21 \r
  22 import java.io.File;\r
  23 import java.util.Arrays;\r
  24 import java.util.List;\r
  25 \r
  26 import javax.jws.WebService;\r
  27 \r
  28 import org.apache.log4j.Logger;\r
  29 \r
  30 import compbio.data.msa.JABAService;\r
  31 import compbio.data.msa.SequenceAnnotation;\r
  32 import compbio.data.sequence.FastaSequence;\r
  33 import compbio.engine.Configurator;\r
  34 import compbio.engine.client.ConfiguredExecutable;\r
  35 import compbio.metadata.ChunkHolder;\r
  36 import compbio.metadata.JobSubmissionException;\r
  37 import compbio.metadata.LimitExceededException;\r
  38 import compbio.metadata.Option;\r
  39 import compbio.metadata.Preset;\r
  40 import compbio.metadata.UnsupportedRuntimeException;\r
  41 import compbio.metadata.WrongParameterException;\r
  42 import compbio.runner.predictors.Jpred;\r
  43 \r
  44 @WebService(endpointInterface = "compbio.data.msa.SequenceAnnotation", targetNamespace = JABAService.V2_SERVICE_NAMESPACE, serviceName = "JpredWS")\r
  45 public class JpredWS extends SequenceAnnotationService<Jpred>\r
  46                 implements SequenceAnnotation<Jpred> {\r
  47 \r
  48         private static Logger log = Logger.getLogger(JpredWS.class);\r
  49 \r
  50         public JpredWS() {\r
  51                 super(new Jpred(), log);\r
  52         }\r
  53 \r
  54         @Override\r
  55         public String analize(List<FastaSequence> sequences)\r
  56                         throws UnsupportedRuntimeException, LimitExceededException, JobSubmissionException {\r
  57                 WSUtil.validateJpredInput(sequences);\r
  58                 ConfiguredExecutable<Jpred> confpred = init(sequences);\r
  59 \r
  60                 // set default conservation method to fastest - SHENKIN\r
  61                 // TODO: This violates encapsulation, should be moved to the runners\r
  62                 // level.\r
  63                 //confpred.addParameters(Arrays.asList("-m=SHENKIN"));\r
  64                 return WSUtil.analize(sequences, confpred, log, "JpredWS analize", getLimit(""));\r
  65         }\r
  66 \r
  67         @Override\r
  68         public String customAnalize(List<FastaSequence> sequences, List<Option<Jpred>> options) \r
  69                                         throws UnsupportedRuntimeException, LimitExceededException, JobSubmissionException, WrongParameterException {\r
  70                 WSUtil.validateJpredInput(sequences);\r
  71                 return super.customAnalize(sequences, options);\r
  72         }\r
  73 \r
  74         @Override\r
  75         public String presetAnalize(List<FastaSequence> sequences, Preset<Jpred> preset)\r
  76                         throws UnsupportedRuntimeException, LimitExceededException, JobSubmissionException, WrongParameterException {\r
  77                 WSUtil.validateJpredInput(sequences);\r
  78                 return super.presetAnalize(sequences, preset);\r
  79         }\r
  80 \r
  81         @Override\r
  82         public ChunkHolder pullExecStatistics(String jobId, long position) {\r
  83                 WSUtil.validateJobId(jobId);\r
  84                 String file = Configurator.getWorkDirectory(jobId) + File.separator + Jpred.getStatFile();\r
  85                 return WSUtil.pullFile(file, position);\r
  86         }\r
  87 \r
  88 }\r