webservices/compbio/ws/server/ClustalWS.java

   1 /* Copyright (c) 2009 Peter Troshin\r
   2  *  \r
   3  *  JAva Bioinformatics Analysis Web Services (JABAWS) @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.server;\r
  20 \r
  21 import java.io.File;\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.MsaWS;\r
  29 import compbio.data.sequence.Alignment;\r
  30 import compbio.data.sequence.FastaSequence;\r
  31 import compbio.engine.AsyncExecutor;\r
  32 import compbio.engine.Configurator;\r
  33 import compbio.engine.client.ConfiguredExecutable;\r
  34 import compbio.engine.client.SkeletalExecutable;\r
  35 import compbio.metadata.ChunkHolder;\r
  36 import compbio.metadata.JobStatus;\r
  37 import compbio.metadata.JobSubmissionException;\r
  38 import compbio.metadata.Limit;\r
  39 import compbio.metadata.LimitsManager;\r
  40 import compbio.metadata.Option;\r
  41 import compbio.metadata.Preset;\r
  42 import compbio.metadata.PresetManager;\r
  43 import compbio.metadata.ResultNotAvailableException;\r
  44 import compbio.metadata.RunnerConfig;\r
  45 import compbio.metadata.WrongParameterException;\r
  46 import compbio.runner.Util;\r
  47 import compbio.runner.msa.ClustalW;\r
  48 \r
  49 @WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = "http://msa.data.compbio/01/01/2010/", serviceName = "ClustalWS")\r
  50 public class ClustalWS implements MsaWS<ClustalW> {\r
  51 \r
  52         private static Logger log = Logger.getLogger(ClustalWS.class);\r
  53 \r
  54         private static final RunnerConfig<ClustalW> clustalOptions = Util\r
  55                         .getSupportedOptions(ClustalW.class);\r
  56 \r
  57         private static final PresetManager<ClustalW> clustalPresets = Util\r
  58                         .getPresets(ClustalW.class);\r
  59 \r
  60         private static final LimitsManager<ClustalW> limitMan = compbio.engine.client.Util\r
  61                         .getLimits(new ClustalW().getType());\r
  62 \r
  63         @Override\r
  64         public String align(List<FastaSequence> sequences)\r
  65                         throws JobSubmissionException {\r
  66 \r
  67                 WSUtil.validateFastaInput(sequences);\r
  68                 ConfiguredExecutable<ClustalW> confClust = init(sequences);\r
  69                 return WSUtil.align(sequences, confClust, log, "align", getLimit(""));\r
  70         }\r
  71 \r
  72         ConfiguredExecutable<ClustalW> init(List<FastaSequence> dataSet)\r
  73                         throws JobSubmissionException {\r
  74                 ClustalW clustal = new ClustalW();\r
  75                 clustal.setInput(SkeletalExecutable.INPUT)\r
  76                                 .setOutput(SkeletalExecutable.OUTPUT)\r
  77                                 .setError(SkeletalExecutable.ERROR);\r
  78                 ConfiguredExecutable<ClustalW> confClust = Configurator\r
  79                                 .configureExecutable(clustal, dataSet);\r
  80                 return confClust;\r
  81         }\r
  82 \r
  83         @Override\r
  84         public String presetAlign(List<FastaSequence> sequences,\r
  85                         Preset<ClustalW> preset) throws JobSubmissionException,\r
  86                         WrongParameterException {\r
  87                 WSUtil.validateFastaInput(sequences);\r
  88                 if (preset == null) {\r
  89                         throw new WrongParameterException("Preset must be provided!");\r
  90                 }\r
  91                 Limit<ClustalW> limit = getLimit(preset.getName());\r
  92                 ConfiguredExecutable<ClustalW> confClust = init(sequences);\r
  93                 confClust.addParameters(preset.getOptions());\r
  94                 return WSUtil.align(sequences, confClust, log, "presetAlign", limit);\r
  95         }\r
  96 \r
  97         @Override\r
  98         public String customAlign(List<FastaSequence> sequences,\r
  99                         List<Option<ClustalW>> options) throws JobSubmissionException,\r
 100                         WrongParameterException {\r
 101                 WSUtil.validateFastaInput(sequences);\r
 102                 ConfiguredExecutable<ClustalW> confClust = init(sequences);\r
 103                 List<String> params = WSUtil.getCommands(options,\r
 104                                 ClustalW.KEY_VALUE_SEPARATOR);\r
 105                 confClust.addParameters(params);\r
 106                 log.info("Setting parameters: " + params);\r
 107                 return WSUtil.align(sequences, confClust, log, "customAlign",\r
 108                                 getLimit(""));\r
 109         }\r
 110 \r
 111         @Override\r
 112         public RunnerConfig<ClustalW> getRunnerOptions() {\r
 113                 return clustalOptions;\r
 114         }\r
 115 \r
 116         @SuppressWarnings("unchecked")\r
 117         @Override\r
 118         public Alignment getResult(String jobId) throws ResultNotAvailableException {\r
 119 \r
 120                 WSUtil.validateJobId(jobId);\r
 121                 AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);\r
 122                 ConfiguredExecutable<ClustalW> clustal = (ConfiguredExecutable<ClustalW>) asyncEngine\r
 123                                 .getResults(jobId);\r
 124                 Alignment al = clustal.getResults();\r
 125 \r
 126                 return al;\r
 127         }\r
 128 \r
 129         @Override\r
 130         public Limit<ClustalW> getLimit(String presetName) {\r
 131                 if (limitMan == null) {\r
 132                         // No limit is configured\r
 133                         return null;\r
 134                 }\r
 135                 Limit<ClustalW> limit = limitMan.getLimitByName(presetName);\r
 136                 return limit;\r
 137         }\r
 138 \r
 139         @Override\r
 140         public LimitsManager<ClustalW> getLimits() {\r
 141                 return limitMan;\r
 142         }\r
 143 \r
 144         @Override\r
 145         public boolean cancelJob(String jobId) {\r
 146                 WSUtil.validateJobId(jobId);\r
 147                 boolean result = WSUtil.cancelJob(jobId);\r
 148                 return result;\r
 149         }\r
 150 \r
 151         @Override\r
 152         public JobStatus getJobStatus(String jobId) {\r
 153                 WSUtil.validateJobId(jobId);\r
 154                 JobStatus status = WSUtil.getJobStatus(jobId);\r
 155                 return status;\r
 156         }\r
 157 \r
 158         @Override\r
 159         public PresetManager<ClustalW> getPresets() {\r
 160                 return clustalPresets;\r
 161         }\r
 162 \r
 163         @Override\r
 164         public ChunkHolder pullExecStatistics(String jobId, long position) {\r
 165 \r
 166                 WSUtil.validateJobId(jobId);\r
 167                 String file = Configurator.getWorkDirectory(jobId) + File.separator\r
 168                                 + ClustalW.getStatFile();\r
 169                 ChunkHolder cholder = WSUtil.pullFile(file, position);\r
 170                 return cholder;\r
 171         }\r
 172 \r
 173 }\r