webservices/compbio/ws/server/ClustalWS.java

   1 /* Copyright (c) 2009 Peter Troshin\r
   2  *  \r
   3  *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0   \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.annotation.Resource;\r
  25 import javax.jws.WebService;\r
  26 import javax.xml.ws.WebServiceContext;\r
  27 \r
  28 import org.apache.log4j.Logger;\r
  29 \r
  30 import compbio.data.msa.MsaWS;\r
  31 import compbio.data.sequence.Alignment;\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.metadata.ChunkHolder;\r
  37 import compbio.metadata.JobStatus;\r
  38 import compbio.metadata.JobSubmissionException;\r
  39 import compbio.metadata.Limit;\r
  40 import compbio.metadata.LimitsManager;\r
  41 import compbio.metadata.Option;\r
  42 import compbio.metadata.Preset;\r
  43 import compbio.metadata.PresetManager;\r
  44 import compbio.metadata.ResultNotAvailableException;\r
  45 import compbio.metadata.RunnerConfig;\r
  46 import compbio.metadata.WrongParameterException;\r
  47 import compbio.runner.Util;\r
  48 import compbio.runner.msa.ClustalW;\r
  49 import compbio.util.Timer;\r
  50 import compbio.ws.client.Services;\r
  51 \r
  52 @WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = "http://msa.data.compbio/01/01/2010/", serviceName = "ClustalWS")\r
  53 public class ClustalWS implements MsaWS<ClustalW> {\r
  54 \r
  55         // Ask for resource injection\r
  56         @Resource\r
  57         private WebServiceContext wsContext;\r
  58 \r
  59         private static Logger log = Logger.getLogger(ClustalWS.class);\r
  60 \r
  61         private static volatile WSLogger logger;\r
  62 \r
  63         private static final RunnerConfig<ClustalW> clustalOptions = Util\r
  64                         .getSupportedOptions(ClustalW.class);\r
  65 \r
  66         private static final PresetManager<ClustalW> clustalPresets = Util\r
  67                         .getPresets(ClustalW.class);\r
  68 \r
  69         private static final LimitsManager<ClustalW> limitMan = compbio.engine.client.Util\r
  70                         .getLimits(new ClustalW().getType());\r
  71 \r
  72         /*\r
  73          * Initialise the logger. This cannot be done in the constructor as the\r
  74          * WebServiceContext is not available at the object construction time\r
  75          */\r
  76         private WSLogger getLogger() {\r
  77                 if (logger == null) {\r
  78                         synchronized (ClustalWS.class) {\r
  79                                 if (logger == null) {\r
  80                                         logger = WSLogger.getStatLogger(Services.ClustalWS,\r
  81                                                         wsContext);\r
  82                                 }\r
  83                         }\r
  84                 }\r
  85                 return logger;\r
  86         }\r
  87 \r
  88         @Override\r
  89         public String align(List<FastaSequence> sequences)\r
  90                         throws JobSubmissionException {\r
  91 \r
  92                 WSUtil.validateFastaInput(sequences);\r
  93                 ConfiguredExecutable<ClustalW> confClust = init(sequences);\r
  94                 return WSUtil.align(sequences, confClust, getLogger(), "align",\r
  95                                 getLimit(""));\r
  96         }\r
  97 \r
  98         ConfiguredExecutable<ClustalW> init(List<FastaSequence> dataSet)\r
  99                         throws JobSubmissionException {\r
 100                 ClustalW clustal = new ClustalW();\r
 101                 ConfiguredExecutable<ClustalW> confClust = Configurator\r
 102                                 .configureExecutable(clustal, dataSet);\r
 103                 return confClust;\r
 104         }\r
 105 \r
 106         @Override\r
 107         public String presetAlign(List<FastaSequence> sequences,\r
 108                         Preset<ClustalW> preset) throws JobSubmissionException,\r
 109                         WrongParameterException {\r
 110                 WSUtil.validateFastaInput(sequences);\r
 111                 if (preset == null) {\r
 112                         throw new WrongParameterException("Preset must be provided!");\r
 113                 }\r
 114                 Limit<ClustalW> limit = getLimit(preset.getName());\r
 115                 ConfiguredExecutable<ClustalW> confClust = init(sequences);\r
 116                 confClust.addParameters(preset.getOptions());\r
 117                 return WSUtil.align(sequences, confClust, getLogger(), "presetAlign",\r
 118                                 limit);\r
 119         }\r
 120 \r
 121         @Override\r
 122         public String customAlign(List<FastaSequence> sequences,\r
 123                         List<Option<ClustalW>> options) throws JobSubmissionException,\r
 124                         WrongParameterException {\r
 125                 WSUtil.validateFastaInput(sequences);\r
 126                 ConfiguredExecutable<ClustalW> confClust = init(sequences);\r
 127                 List<String> params = WSUtil.getCommands(options,\r
 128                                 ClustalW.KEY_VALUE_SEPARATOR);\r
 129                 confClust.addParameters(params);\r
 130                 log.info("Setting parameters: " + params);\r
 131                 return WSUtil.align(sequences, confClust, getLogger(), "customAlign",\r
 132                                 getLimit(""));\r
 133         }\r
 134 \r
 135         @Override\r
 136         public RunnerConfig<ClustalW> getRunnerOptions() {\r
 137                 Timer timer = Timer.getMilliSecondsTimer();\r
 138                 getLogger().logAll(timer, "getRunnerOptions");\r
 139                 return clustalOptions;\r
 140         }\r
 141 \r
 142         @SuppressWarnings("unchecked")\r
 143         @Override\r
 144         public Alignment getResult(String jobId) throws ResultNotAvailableException {\r
 145                 Timer timer = Timer.getMilliSecondsTimer();\r
 146                 WSUtil.validateJobId(jobId);\r
 147                 AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);\r
 148                 ConfiguredExecutable<ClustalW> clustal = (ConfiguredExecutable<ClustalW>) asyncEngine\r
 149                                 .getResults(jobId);\r
 150                 Alignment al = clustal.getResults();\r
 151                 getLogger().log(timer, "getResults", jobId);\r
 152                 return al;\r
 153         }\r
 154 \r
 155         @Override\r
 156         public Limit<ClustalW> getLimit(String presetName) {\r
 157                 Timer timer = Timer.getMilliSecondsTimer();\r
 158                 if (limitMan == null) {\r
 159                         // No limit is configured\r
 160                         return null;\r
 161                 }\r
 162                 Limit<ClustalW> limit = limitMan.getLimitByName(presetName);\r
 163                 getLogger().logAll(timer, "getLimit");\r
 164                 return limit;\r
 165         }\r
 166 \r
 167         @Override\r
 168         public LimitsManager<ClustalW> getLimits() {\r
 169                 return limitMan;\r
 170         }\r
 171 \r
 172         @Override\r
 173         public boolean cancelJob(String jobId) {\r
 174                 Timer timer = Timer.getMilliSecondsTimer();\r
 175                 WSUtil.validateJobId(jobId);\r
 176                 boolean result = WSUtil.cancelJob(jobId);\r
 177                 getLogger().logFine(timer, "Cancel");\r
 178                 return result;\r
 179         }\r
 180 \r
 181         @Override\r
 182         public JobStatus getJobStatus(String jobId) {\r
 183                 Timer timer = Timer.getMilliSecondsTimer();\r
 184                 WSUtil.validateJobId(jobId);\r
 185                 JobStatus status = WSUtil.getJobStatus(jobId);\r
 186                 getLogger().logFine(timer, "getJobStatus");\r
 187                 return status;\r
 188         }\r
 189 \r
 190         @Override\r
 191         public PresetManager<ClustalW> getPresets() {\r
 192                 Timer timer = Timer.getMilliSecondsTimer();\r
 193                 getLogger().logAll(timer, "pullExecStatistics");\r
 194                 return clustalPresets;\r
 195         }\r
 196 \r
 197         @Override\r
 198         public ChunkHolder pullExecStatistics(String jobId, long position) {\r
 199                 Timer timer = Timer.getMilliSecondsTimer();\r
 200                 WSUtil.validateJobId(jobId);\r
 201                 String file = Configurator.getWorkDirectory(jobId) + File.separator\r
 202                                 + ClustalW.getStatFile();\r
 203                 ChunkHolder cholder = WSUtil.pullFile(file, position);\r
 204                 getLogger().logFine(timer, "pullExecStatistics");\r
 205                 return cholder;\r
 206         }\r
 207 \r
 208 }\r