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