webservices/compbio/ws/server/ClustalOWS.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.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.engine.AsyncExecutor;\r
  33 import compbio.engine.Configurator;\r
  34 import compbio.engine.client.ConfiguredExecutable;\r
  35 import compbio.engine.client.Executable;\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.ClustalO;\r
  50 import compbio.runner.msa.ClustalW;\r
  51 import compbio.runner.msa.Tcoffee;\r
  52 \r
  53 @WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = JABAService.SERVICE_NAMESPACE, serviceName = "ClustalOWS")\r
  54 public class ClustalOWS implements MsaWS<ClustalO> {\r
  55 \r
  56         private static Logger log = Logger.getLogger(ClustalOWS.class);\r
  57 \r
  58         private static final RunnerConfig<ClustalO> clustalOptions = Util\r
  59                         .getSupportedOptions(ClustalO.class);\r
  60 \r
  61         private static final PresetManager<ClustalO> clustalPresets = Util\r
  62                         .getPresets(ClustalO.class);\r
  63 \r
  64         private static final LimitsManager<ClustalO> limitMan = compbio.engine.client.Util\r
  65                         .getLimits(new ClustalO().getType());\r
  66 \r
  67         @Override\r
  68         public String align(List<FastaSequence> sequences)\r
  69                         throws JobSubmissionException {\r
  70 \r
  71                 WSUtil.validateFastaInput(sequences);\r
  72                 ConfiguredExecutable<ClustalO> confClust = init(sequences);\r
  73                 return WSUtil.align(sequences, confClust, log, "align", getLimit(""));\r
  74         }\r
  75 \r
  76         ConfiguredExecutable<ClustalO> init(List<FastaSequence> dataSet)\r
  77                         throws JobSubmissionException {\r
  78                 ClustalO clustal = new ClustalO();\r
  79                 clustal.setInput(SkeletalExecutable.INPUT)\r
  80                                 .setOutput(SkeletalExecutable.OUTPUT)\r
  81                                 .setError(SkeletalExecutable.ERROR);\r
  82                 ConfiguredExecutable<ClustalO> confClust = Configurator\r
  83                                 .configureExecutable(clustal, dataSet);\r
  84                 // Set the number of threads for the cluster execution from conf file\r
  85                 if (confClust.getExecProvider() == Executable.ExecProvider.Cluster) {\r
  86                         int clusterCpuNum = SkeletalExecutable.getClusterCpuNum(clustal.getType());\r
  87                         if (clusterCpuNum != 0) {\r
  88                                 clustal.setNCore(clusterCpuNum);\r
  89                         }\r
  90                 }\r
  91 \r
  92                 return confClust;\r
  93         }\r
  94 \r
  95         @Override\r
  96         public String presetAlign(List<FastaSequence> sequences,\r
  97                         Preset<ClustalO> preset) throws JobSubmissionException,\r
  98                         WrongParameterException {\r
  99                 WSUtil.validateFastaInput(sequences);\r
 100                 if (preset == null) {\r
 101                         throw new WrongParameterException("Preset must be provided!");\r
 102                 }\r
 103                 Limit<ClustalO> limit = getLimit(preset.getName());\r
 104                 ConfiguredExecutable<ClustalO> confClust = init(sequences);\r
 105                 confClust.addParameters(preset.getOptions());\r
 106                 return WSUtil.align(sequences, confClust, log, "presetAlign", limit);\r
 107         }\r
 108 \r
 109         @Override\r
 110         public String customAlign(List<FastaSequence> sequences,\r
 111                         List<Option<ClustalO>> options) throws JobSubmissionException,\r
 112                         WrongParameterException {\r
 113                 WSUtil.validateFastaInput(sequences);\r
 114                 ConfiguredExecutable<ClustalO> confClust = init(sequences);\r
 115                 List<String> params = WSUtil.getCommands(options,\r
 116                                 ClustalO.KEY_VALUE_SEPARATOR);\r
 117                 confClust.addParameters(params);\r
 118                 log.info("Setting parameters: " + params);\r
 119                 return WSUtil.align(sequences, confClust, log, "customAlign",\r
 120                                 getLimit(""));\r
 121         }\r
 122 \r
 123         @Override\r
 124         public RunnerConfig<ClustalO> getRunnerOptions() {\r
 125                 return clustalOptions;\r
 126         }\r
 127 \r
 128         @SuppressWarnings("unchecked")\r
 129         @Override\r
 130         public Alignment getResult(String jobId) throws ResultNotAvailableException {\r
 131 \r
 132                 WSUtil.validateJobId(jobId);\r
 133                 AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);\r
 134                 ConfiguredExecutable<ClustalO> clustal = (ConfiguredExecutable<ClustalO>) asyncEngine\r
 135                                 .getResults(jobId);\r
 136                 Alignment al = clustal.getResults();\r
 137 \r
 138                 return al;\r
 139         }\r
 140 \r
 141         @Override\r
 142         public Limit<ClustalO> getLimit(String presetName) {\r
 143                 if (limitMan == null) {\r
 144                         // No limit is configured\r
 145                         return null;\r
 146                 }\r
 147                 Limit<ClustalO> limit = limitMan.getLimitByName(presetName);\r
 148                 return limit;\r
 149         }\r
 150 \r
 151         @Override\r
 152         public LimitsManager<ClustalO> getLimits() {\r
 153                 return limitMan;\r
 154         }\r
 155 \r
 156         @Override\r
 157         public boolean cancelJob(String jobId) {\r
 158                 WSUtil.validateJobId(jobId);\r
 159                 boolean result = WSUtil.cancelJob(jobId);\r
 160                 return result;\r
 161         }\r
 162 \r
 163         @Override\r
 164         public JobStatus getJobStatus(String jobId) {\r
 165                 WSUtil.validateJobId(jobId);\r
 166                 JobStatus status = WSUtil.getJobStatus(jobId);\r
 167                 return status;\r
 168         }\r
 169 \r
 170         @Override\r
 171         public PresetManager<ClustalO> getPresets() {\r
 172                 return clustalPresets;\r
 173         }\r
 174 \r
 175         @Override\r
 176         public ChunkHolder pullExecStatistics(String jobId, long position) {\r
 177 \r
 178                 WSUtil.validateJobId(jobId);\r
 179                 String file = Configurator.getWorkDirectory(jobId) + File.separator\r
 180                                 + ClustalO.getStatFile();\r
 181                 ChunkHolder cholder = WSUtil.pullFile(file, position);\r
 182                 return cholder;\r
 183         }\r
 184 \r
 185 }\r