webservices/compbio/ws/server/SequenceAnnotationService.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.util.List;\r
  21 \r
  22 import org.apache.log4j.Logger;\r
  23 \r
  24 import compbio.data.sequence.FastaSequence;\r
  25 import compbio.data.sequence.ScoreManager;\r
  26 import compbio.engine.client.ConfiguredExecutable;\r
  27 import compbio.engine.client.SkeletalExecutable;\r
  28 import compbio.metadata.JobSubmissionException;\r
  29 import compbio.metadata.Limit;\r
  30 import compbio.metadata.LimitExceededException;\r
  31 import compbio.metadata.Option;\r
  32 import compbio.metadata.Preset;\r
  33 import compbio.metadata.ResultNotAvailableException;\r
  34 import compbio.metadata.UnsupportedRuntimeException;\r
  35 import compbio.metadata.WrongParameterException;\r
  36 import compbio.runner.conservation.AACon;\r
  37 \r
  38 /**\r
  39  * Common methods for all SequenceAnnotation web services\r
  40  * \r
  41  * @author pvtroshin\r
  42  * \r
  43  * @param <T>\r
  44  * \r
  45  * @version 1.0 June 2011\r
  46  * @since 2.0\r
  47  */\r
  48 public abstract class SequenceAnnotationService<T> extends GenericMetadataService {\r
  49 \r
  50         /*\r
  51          * FIXME - instances of the Runner (?) and their types should be defined in\r
  52          * Executable IF\r
  53          */\r
  54         SequenceAnnotationService(SkeletalExecutable<T> exec, Logger log) {\r
  55                 super(exec, log);\r
  56         }\r
  57 \r
  58         public ScoreManager getAnnotation(String jobId)\r
  59                         throws ResultNotAvailableException {\r
  60                 return WSUtil.getAnnotation(jobId, log);\r
  61         }\r
  62 \r
  63         public String analize(List<FastaSequence> sequences)\r
  64                         throws UnsupportedRuntimeException, LimitExceededException,\r
  65                         JobSubmissionException {\r
  66                 WSUtil.validateFastaInput(sequences);\r
  67                 ConfiguredExecutable<T> confIUPred = init(sequences);\r
  68                 return WSUtil.analize(sequences, confIUPred, log, "analize",\r
  69                                 getLimit(""));\r
  70         }\r
  71 \r
  72         public String customAnalize(List<FastaSequence> sequences,\r
  73                         List<Option<T>> options) throws UnsupportedRuntimeException,\r
  74                         LimitExceededException, JobSubmissionException,\r
  75                         WrongParameterException {\r
  76                 WSUtil.validateAAConInput(sequences);\r
  77                 ConfiguredExecutable<T> confAACon = init(sequences);\r
  78                 // Could not do that! Space separated values\r
  79                 // will all be treated as keys! thus duplicates removed\r
  80                 // String params = cbuilder.getCommand();\r
  81                 List<String> params = WSUtil.getCommands(options,\r
  82                                 AACon.KEY_VALUE_SEPARATOR);\r
  83                 confAACon.addParameters(params);\r
  84                 return WSUtil.analize(sequences, confAACon, log, "customAnalize",\r
  85                                 getLimit(""));\r
  86         }\r
  87 \r
  88         public String presetAnalize(List<FastaSequence> sequences, Preset<T> preset)\r
  89                         throws UnsupportedRuntimeException, LimitExceededException,\r
  90                         JobSubmissionException, WrongParameterException {\r
  91                 WSUtil.validateAAConInput(sequences);\r
  92                 if (preset == null) {\r
  93                         throw new WrongParameterException("Preset must be provided!");\r
  94                 }\r
  95                 ConfiguredExecutable<T> confAAcon = init(sequences);\r
  96                 confAAcon.addParameters(preset.getOptions());\r
  97                 Limit<T> limit = getLimit(preset.getName());\r
  98                 return WSUtil\r
  99                                 .analize(sequences, confAAcon, log, "presetAnalize", limit);\r
 100         }\r
 101 \r
 102 }\r