webservices/compbio/ws/server/AAConWS.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 package compbio.ws.server;\r
  19 \r
  20 import java.io.File;\r
  21 import java.util.Arrays;\r
  22 import java.util.List;\r
  23 \r
  24 import javax.jws.WebService;\r
  25 \r
  26 import org.apache.log4j.Logger;\r
  27 \r
  28 import compbio.data.msa.JABAService;\r
  29 import compbio.data.msa.SequenceAnnotation;\r
  30 import compbio.data.sequence.FastaSequence;\r
  31 import compbio.engine.Configurator;\r
  32 import compbio.engine.client.ConfiguredExecutable;\r
  33 import compbio.metadata.ChunkHolder;\r
  34 import compbio.metadata.JobSubmissionException;\r
  35 import compbio.metadata.LimitExceededException;\r
  36 import compbio.metadata.Option;\r
  37 import compbio.metadata.Preset;\r
  38 import compbio.metadata.UnsupportedRuntimeException;\r
  39 import compbio.metadata.WrongParameterException;\r
  40 import compbio.runner.conservation.AACon;\r
  41 \r
  42 @WebService(endpointInterface = "compbio.data.msa.SequenceAnnotation", targetNamespace = JABAService.V2_SERVICE_NAMESPACE, serviceName = "AAConWS")\r
  43 public class AAConWS extends SequenceAnnotationService<AACon>\r
  44                 implements\r
  45                         SequenceAnnotation<AACon> {\r
  46 \r
  47         private static Logger log = Logger.getLogger(AAConWS.class);\r
  48 \r
  49         public AAConWS() {\r
  50                 super(new AACon(), log);\r
  51         }\r
  52 \r
  53         /*\r
  54          * @SuppressWarnings("unchecked") public JalviewAnnotation\r
  55          * getJalviewAnnotation(String jobId) throws ResultNotAvailableException {\r
  56          * MultiAnnotatedSequence<Method> result = getResult(jobId); // TODO //\r
  57          * log(jobId, "getResults"); return result.toJalviewAnnotation(); }\r
  58          */\r
  59 \r
  60         @Override\r
  61         public String analize(List<FastaSequence> sequences)\r
  62                         throws UnsupportedRuntimeException, LimitExceededException,\r
  63                         JobSubmissionException {\r
  64                 WSUtil.validateAAConInput(sequences);\r
  65                 ConfiguredExecutable<AACon> confAAcon = init(sequences);\r
  66 \r
  67                 // set default conservation method to fastest - SHENKIN\r
  68                 // TODO: This violates encapsulation, should be moved to the runners\r
  69                 // level.\r
  70                 confAAcon.addParameters(Arrays.asList("-m=SHENKIN"));\r
  71                 return WSUtil.analize(sequences, confAAcon, log, "AAConWS analize",\r
  72                                 getLimit(""));\r
  73         }\r
  74 \r
  75         @Override\r
  76         public String customAnalize(List<FastaSequence> sequences,\r
  77                         List<Option<AACon>> options) throws UnsupportedRuntimeException,\r
  78                         LimitExceededException, JobSubmissionException,\r
  79                         WrongParameterException {\r
  80                 WSUtil.validateAAConInput(sequences);\r
  81                 return super.customAnalize(sequences, options);\r
  82         }\r
  83 \r
  84         @Override\r
  85         public String presetAnalize(List<FastaSequence> sequences,\r
  86                         Preset<AACon> preset) throws UnsupportedRuntimeException,\r
  87                         LimitExceededException, JobSubmissionException,\r
  88                         WrongParameterException {\r
  89                 WSUtil.validateAAConInput(sequences);\r
  90                 return super.presetAnalize(sequences, preset);\r
  91         }\r
  92 \r
  93         @Override\r
  94         public ChunkHolder pullExecStatistics(String jobId, long position) {\r
  95                 WSUtil.validateJobId(jobId);\r
  96                 String file = Configurator.getWorkDirectory(jobId) + File.separator\r
  97                                 + AACon.getStatFile();\r
  98                 return WSUtil.pullFile(file, position);\r
  99         }\r
 100 \r
 101 }\r