webservices/compbio/ws/server/ClustalOWS.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.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 \r
  51 @WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = JABAService.V2_SERVICE_NAMESPACE, serviceName = "ClustalOWS")\r
  52 public class ClustalOWS implements MsaWS<ClustalO> {\r
  53 \r
  54         private static Logger log = Logger.getLogger(ClustalOWS.class);\r
  55 \r
  56         private static final RunnerConfig<ClustalO> clustalOptions = Util\r
  57                         .getSupportedOptions(ClustalO.class);\r
  58 \r
  59         private static final PresetManager<ClustalO> clustalPresets = Util\r
  60                         .getPresets(ClustalO.class);\r
  61 \r
  62         private static final LimitsManager<ClustalO> limitMan = compbio.engine.client.Util\r
  63                         .getLimits(new ClustalO().getType());\r
  64 \r
  65         @Override\r
  66         public String align(List<FastaSequence> sequences)\r
  67                         throws JobSubmissionException {\r
  68 \r
  69                 WSUtil.validateFastaInput(sequences);\r
  70                 ConfiguredExecutable<ClustalO> confClust = init(sequences);\r
  71                 return WSUtil.align(sequences, confClust, log, "align", getLimit(""));\r
  72         }\r
  73 \r
  74         ConfiguredExecutable<ClustalO> init(List<FastaSequence> dataSet)\r
  75                         throws JobSubmissionException {\r
  76                 ClustalO clustal = new ClustalO();\r
  77                 clustal.setInput(SkeletalExecutable.INPUT)\r
  78                                 .setOutput(SkeletalExecutable.OUTPUT)\r
  79                                 .setError(SkeletalExecutable.ERROR);\r
  80                 ConfiguredExecutable<ClustalO> confClust = Configurator\r
  81                                 .configureExecutable(clustal, dataSet);\r
  82                 // Set the number of threads for the cluster execution from conf file\r
  83                 if (confClust.getExecProvider() == Executable.ExecProvider.Cluster) {\r
  84                         int clusterCpuNum = SkeletalExecutable.getClusterCpuNum(clustal\r
  85                                         .getType());\r
  86                         if (clusterCpuNum != 0) {\r
  87                                 clustal.setNCore(clusterCpuNum);\r
  88                         }\r
  89                 }\r
  90 \r
  91                 return confClust;\r
  92         }\r
  93 \r
  94         @Override\r
  95         public String presetAlign(List<FastaSequence> sequences,\r
  96                         Preset<ClustalO> preset) throws JobSubmissionException,\r
  97                         WrongParameterException {\r
  98                 WSUtil.validateFastaInput(sequences);\r
  99                 if (preset == null) {\r
 100                         throw new WrongParameterException("Preset must be provided!");\r
 101                 }\r
 102                 Limit<ClustalO> limit = getLimit(preset.getName());\r
 103                 ConfiguredExecutable<ClustalO> confClust = init(sequences);\r
 104                 confClust.addParameters(preset.getOptions());\r
 105                 return WSUtil.align(sequences, confClust, log, "presetAlign", limit);\r
 106         }\r
 107 \r
 108         @Override\r
 109         public String customAlign(List<FastaSequence> sequences,\r
 110                         List<Option<ClustalO>> options) throws JobSubmissionException,\r
 111                         WrongParameterException {\r
 112                 WSUtil.validateFastaInput(sequences);\r
 113                 ConfiguredExecutable<ClustalO> confClust = init(sequences);\r
 114                 List<String> params = WSUtil.getCommands(options,\r
 115                                 ClustalO.KEY_VALUE_SEPARATOR);\r
 116                 confClust.addParameters(params);\r
 117                 log.info("Setting parameters: " + params);\r
 118                 return WSUtil.align(sequences, confClust, log, "customAlign",\r
 119                                 getLimit(""));\r
 120         }\r
 121 \r
 122         @Override\r
 123         public RunnerConfig<ClustalO> getRunnerOptions() {\r
 124                 return clustalOptions;\r
 125         }\r
 126 \r
 127         @SuppressWarnings("unchecked")\r
 128         @Override\r
 129         public Alignment getResult(String jobId) throws ResultNotAvailableException {\r
 130 \r
 131                 WSUtil.validateJobId(jobId);\r
 132                 AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);\r
 133                 ConfiguredExecutable<ClustalO> clustal = (ConfiguredExecutable<ClustalO>) asyncEngine\r
 134                                 .getResults(jobId);\r
 135                 Alignment al = clustal.getResults();\r
 136 \r
 137                 return al;\r
 138         }\r
 139 \r
 140         @Override\r
 141         public Limit<ClustalO> getLimit(String presetName) {\r
 142                 if (limitMan == null) {\r
 143                         // No limit is configured\r
 144                         return null;\r
 145                 }\r
 146                 Limit<ClustalO> limit = limitMan.getLimitByName(presetName);\r
 147                 return limit;\r
 148         }\r
 149 \r
 150         @Override\r
 151         public LimitsManager<ClustalO> getLimits() {\r
 152                 return limitMan;\r
 153         }\r
 154 \r
 155         @Override\r
 156         public boolean cancelJob(String jobId) {\r
 157                 WSUtil.validateJobId(jobId);\r
 158                 boolean result = WSUtil.cancelJob(jobId);\r
 159                 return result;\r
 160         }\r
 161 \r
 162         @Override\r
 163         public JobStatus getJobStatus(String jobId) {\r
 164                 WSUtil.validateJobId(jobId);\r
 165                 JobStatus status = WSUtil.getJobStatus(jobId);\r
 166                 return status;\r
 167         }\r
 168 \r
 169         @Override\r
 170         public PresetManager<ClustalO> getPresets() {\r
 171                 return clustalPresets;\r
 172         }\r
 173 \r
 174         @Override\r
 175         public ChunkHolder pullExecStatistics(String jobId, long position) {\r
 176 \r
 177                 WSUtil.validateJobId(jobId);\r
 178                 String file = Configurator.getWorkDirectory(jobId) + File.separator\r
 179                                 + ClustalO.getStatFile();\r
 180                 ChunkHolder cholder = WSUtil.pullFile(file, position);\r
 181                 return cholder;\r
 182         }\r
 183 \r
 184 }\r