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.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.Executable;\r
  37 import compbio.engine.client.SkeletalExecutable;\r
  38 import compbio.engine.client.EngineUtil;\r
  39 import compbio.metadata.ChunkHolder;\r
  40 import compbio.metadata.JobStatus;\r
  41 import compbio.metadata.JobSubmissionException;\r
  42 import compbio.metadata.Limit;\r
  43 import compbio.metadata.LimitsManager;\r
  44 import compbio.metadata.Option;\r
  45 import compbio.metadata.Preset;\r
  46 import compbio.metadata.PresetManager;\r
  47 import compbio.metadata.ResultNotAvailableException;\r
  48 import compbio.metadata.RunnerConfig;\r
  49 import compbio.metadata.WrongParameterException;\r
  50 import compbio.runner.RunnerUtil;\r
  51 import compbio.runner.msa.ClustalO;\r
  52 \r
  53 @WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = JABAService.V2_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         private static final RunnerConfig<ClustalO> clustalOptions = RunnerUtil.getSupportedOptions(ClustalO.class);\r
  58         private static final PresetManager<ClustalO> clustalPresets = RunnerUtil.getPresets(ClustalO.class);\r
  59         private static final LimitsManager<ClustalO> limitMan = EngineUtil.getLimits(new ClustalO().getType());\r
  60 \r
  61         @Override\r
  62         public String align(List<FastaSequence> sequences)\r
  63                         throws JobSubmissionException {\r
  64                 WSUtil.validateFastaInput(sequences);\r
  65                 ConfiguredExecutable<ClustalO> confClust = init(sequences);\r
  66                 return WSUtil.align(sequences, confClust, log, "align", getLimit(""));\r
  67         }\r
  68 \r
  69         ConfiguredExecutable<ClustalO> init(List<FastaSequence> dataSet)\r
  70                         throws JobSubmissionException {\r
  71                 ClustalO clustal = new ClustalO();\r
  72                 clustal.setInput(SkeletalExecutable.INPUT);\r
  73                 clustal.setOutput(SkeletalExecutable.OUTPUT);\r
  74                 clustal.setError(SkeletalExecutable.ERROR);\r
  75                 ConfiguredExecutable<ClustalO> confClust = Configurator.configureExecutable(clustal, dataSet);\r
  76                 // Set the number of threads for the cluster execution from conf file\r
  77                 if (confClust.getExecProvider() == Executable.ExecProvider.Cluster) {\r
  78                         int clusterCpuNum = SkeletalExecutable.getClusterCpuNum(clustal.getType());\r
  79                         if (clusterCpuNum != 0) {\r
  80                                 clustal.setNCore(clusterCpuNum);\r
  81                         }\r
  82                 }\r
  83                 return confClust;\r
  84         }\r
  85 \r
  86         @Override\r
  87         public String presetAlign(List<FastaSequence> sequences,\r
  88                         Preset<ClustalO> preset) throws JobSubmissionException,\r
  89                         WrongParameterException {\r
  90                 WSUtil.validateFastaInput(sequences);\r
  91                 if (preset == null) {\r
  92                         throw new WrongParameterException("Preset must be provided!");\r
  93                 }\r
  94                 Limit<ClustalO> limit = getLimit(preset.getName());\r
  95                 ConfiguredExecutable<ClustalO> confClust = init(sequences);\r
  96                 confClust.addParameters(preset.getOptions());\r
  97                 return WSUtil.align(sequences, confClust, log, "presetAlign", limit);\r
  98         }\r
  99 \r
 100         @Override\r
 101         public String customAlign(List<FastaSequence> sequences,\r
 102                         List<Option<ClustalO>> options) throws JobSubmissionException,\r
 103                         WrongParameterException {\r
 104                 WSUtil.validateFastaInput(sequences);\r
 105                 ConfiguredExecutable<ClustalO> confClust = init(sequences);\r
 106                 List<String> params = WSUtil.getCommands(options, ClustalO.KEY_VALUE_SEPARATOR);\r
 107                 confClust.addParameters(params);\r
 108                 log.info("Setting parameters: " + params);\r
 109                 return WSUtil.align(sequences, confClust, log, "customAlign", getLimit(""));\r
 110         }\r
 111 \r
 112         @Override\r
 113         public RunnerConfig<ClustalO> getRunnerOptions() {\r
 114                 return clustalOptions;\r
 115         }\r
 116 \r
 117         @SuppressWarnings("unchecked")\r
 118         @Override\r
 119         public Alignment getResult(String jobId) throws ResultNotAvailableException {\r
 120                 WSUtil.validateJobId(jobId);\r
 121                 AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);\r
 122                 ConfiguredExecutable<ClustalO> clustal = (ConfiguredExecutable<ClustalO>) asyncEngine.getResults(jobId);\r
 123                 Alignment al = clustal.getResults();\r
 124                 return new Alignment (al.getSequences(),Program.ClustalO, '-');\r
 125         }\r
 126 \r
 127         @Override\r
 128         public Limit<ClustalO> getLimit(String presetName) {\r
 129                 if (limitMan == null) {\r
 130                         // No limit is configured\r
 131                         return null;\r
 132                 }\r
 133                 Limit<ClustalO> limit = limitMan.getLimitByName(presetName);\r
 134                 return limit;\r
 135         }\r
 136 \r
 137         @Override\r
 138         public LimitsManager<ClustalO> getLimits() {\r
 139                 return limitMan;\r
 140         }\r
 141 \r
 142         @Override\r
 143         public boolean cancelJob(String jobId) {\r
 144                 WSUtil.validateJobId(jobId);\r
 145                 boolean result = WSUtil.cancelJob(jobId);\r
 146                 return result;\r
 147         }\r
 148 \r
 149         @Override\r
 150         public JobStatus getJobStatus(String jobId) {\r
 151                 WSUtil.validateJobId(jobId);\r
 152                 JobStatus status = WSUtil.getJobStatus(jobId);\r
 153                 return status;\r
 154         }\r
 155 \r
 156         @Override\r
 157         public PresetManager<ClustalO> getPresets() {\r
 158                 return clustalPresets;\r
 159         }\r
 160 \r
 161         @Override\r
 162         public ChunkHolder pullExecStatistics(String jobId, long position) {\r
 163                 WSUtil.validateJobId(jobId);\r
 164                 String file = Configurator.getWorkDirectory(jobId) + File.separator + ClustalO.getStatFile();\r
 165                 ChunkHolder cholder = WSUtil.pullFile(file, position);\r
 166                 return cholder;\r
 167         }\r
 168 \r
 169 }\r