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