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