webservices/compbio/ws/server/JpredWS.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.JpredAlignment;\r
  32 import compbio.data.sequence.FastaSequence;\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.predictors.Jpred;\r
  52 \r
  53 @WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = JABAService.SERVICE_NAMESPACE, serviceName = "JpredWS")\r
  54 public class JpredWS implements MsaWS<Jpred> {\r
  55 \r
  56         private static Logger log = Logger.getLogger(JpredWS.class);\r
  57 \r
  58         private static final RunnerConfig<Jpred> jpredOptions = RunnerUtil.getSupportedOptions(Jpred.class);\r
  59         private static final PresetManager<Jpred> jpredPresets = RunnerUtil.getPresets(Jpred.class);\r
  60         private static final LimitsManager<Jpred> limitMan = EngineUtil.getLimits(new Jpred().getType());\r
  61 \r
  62         @Override\r
  63         public String align(List<FastaSequence> sequences)\r
  64                         throws JobSubmissionException {\r
  65                 WSUtil.validateFastaInput(sequences);\r
  66                 ConfiguredExecutable<Jpred> confClust = init(sequences);\r
  67                 return WSUtil.align(sequences, confClust, log, "align", getLimit(""));\r
  68         }\r
  69 \r
  70         ConfiguredExecutable<Jpred> init(List<FastaSequence> dataSet)\r
  71                         throws JobSubmissionException {\r
  72                 Jpred jpred = new Jpred();\r
  73                 jpred.setInput(SkeletalExecutable.INPUT);\r
  74                 jpred.setOutput(SkeletalExecutable.OUTPUT);\r
  75                 jpred.setError(SkeletalExecutable.ERROR);\r
  76                 ConfiguredExecutable<Jpred> confJpred = Configurator.configureExecutable(jpred, dataSet);\r
  77                 // Set the number of threads for the cluster execution from conf file\r
  78                 if (confJpred.getExecProvider() == Executable.ExecProvider.Cluster) {\r
  79                         int clusterCpuNum = SkeletalExecutable.getClusterCpuNum(jpred.getType());\r
  80                         if (clusterCpuNum != 0) {\r
  81                                 jpred.setNCore(clusterCpuNum);\r
  82                         }\r
  83                 }\r
  84                 return confJpred;\r
  85         }\r
  86 \r
  87         @Override\r
  88         public String presetAlign(List<FastaSequence> sequences,\r
  89                         Preset<Jpred> preset) throws JobSubmissionException,\r
  90                         WrongParameterException {\r
  91                 WSUtil.validateFastaInput(sequences);\r
  92                 if (preset == null) {\r
  93                         throw new WrongParameterException("Preset must be provided!");\r
  94                 }\r
  95                 Limit<Jpred> limit = getLimit(preset.getName());\r
  96                 ConfiguredExecutable<Jpred> confClust = init(sequences);\r
  97                 confClust.addParameters(preset.getOptions());\r
  98                 return WSUtil.align(sequences, confClust, log, "presetAlign", limit);\r
  99         }\r
 100 \r
 101         @Override\r
 102         public String customAlign(List<FastaSequence> sequences,\r
 103                         List<Option<Jpred>> options) throws JobSubmissionException,\r
 104                         WrongParameterException {\r
 105                 WSUtil.validateFastaInput(sequences);\r
 106                 ConfiguredExecutable<Jpred> confClust = init(sequences);\r
 107                 List<String> params = WSUtil.getCommands(options, Jpred.KEY_VALUE_SEPARATOR);\r
 108                 confClust.addParameters(params);\r
 109                 log.info("Setting parameters: " + params);\r
 110                 return WSUtil.align(sequences, confClust, log, "customAlign", getLimit(""));\r
 111         }\r
 112 \r
 113         @Override\r
 114         public RunnerConfig<Jpred> getRunnerOptions() {\r
 115                 return jpredOptions;\r
 116         }\r
 117 \r
 118         @SuppressWarnings("unchecked")\r
 119         @Override\r
 120         public Alignment getResult(String jobId) throws ResultNotAvailableException {\r
 121                 WSUtil.validateJobId(jobId);\r
 122                 AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);\r
 123                 ConfiguredExecutable<Jpred> jpred = (ConfiguredExecutable<Jpred>) asyncEngine.getResults(jobId);\r
 124                 return (Alignment)jpred.getResults();\r
 125         }\r
 126 \r
 127         @Override\r
 128         public Limit<Jpred> getLimit(String presetName) {\r
 129                 if (limitMan == null) {\r
 130                         // No limit is configured\r
 131                         return null;\r
 132                 }\r
 133                 Limit<Jpred> limit = limitMan.getLimitByName(presetName);\r
 134                 return limit;\r
 135         }\r
 136 \r
 137         @Override\r
 138         public LimitsManager<Jpred> 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<Jpred> getPresets() {\r
 158                 return jpredPresets;\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 + Jpred.getStatFile();\r
 165                 ChunkHolder cholder = WSUtil.pullFile(file, position);\r
 166                 return cholder;\r
 167         }\r
 168 \r
 169 }\r