webservices/compbio/ws/server/TcoffeeWS.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.Tcoffee;\r
  52 \r
  53 @WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = JABAService.SERVICE_NAMESPACE, serviceName = "TcoffeeWS")\r
  54 public class TcoffeeWS implements MsaWS<Tcoffee> {\r
  55 \r
  56         private static Logger log = Logger.getLogger(TcoffeeWS.class);\r
  57         private static final RunnerConfig<Tcoffee> tcoffeeOptions = RunnerUtil.getSupportedOptions(Tcoffee.class);\r
  58         private static final PresetManager<Tcoffee> tcoffeePresets = RunnerUtil.getPresets(Tcoffee.class);\r
  59         private static final LimitsManager<Tcoffee> limitMan = EngineUtil.getLimits(new Tcoffee().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<Tcoffee> confTcoffee = init(sequences);\r
  66                 return WSUtil.align(sequences, confTcoffee, log, "align", getLimit(""));\r
  67         }\r
  68 \r
  69         ConfiguredExecutable<Tcoffee> init(List<FastaSequence> sequences)\r
  70                         throws JobSubmissionException {\r
  71                 Tcoffee tcoffee = new Tcoffee();\r
  72                 tcoffee.setInput(SkeletalExecutable.INPUT)\r
  73                                 .setOutput(SkeletalExecutable.OUTPUT)\r
  74                                 .setError(SkeletalExecutable.ERROR);\r
  75 \r
  76                 ConfiguredExecutable<Tcoffee> confCoffee = Configurator\r
  77                                 .configureExecutable(tcoffee, sequences);\r
  78                 if (confCoffee.getExecProvider() == Executable.ExecProvider.Cluster) {\r
  79                         int clusterCpuNum = SkeletalExecutable\r
  80                                         .getClusterCpuNum(Tcoffee.class);\r
  81                         if (clusterCpuNum != 0) {\r
  82                                 tcoffee.setNCore(clusterCpuNum);\r
  83                         }\r
  84                 }\r
  85                 return confCoffee;\r
  86         }\r
  87 \r
  88         @Override\r
  89         public String customAlign(List<FastaSequence> sequences,\r
  90                         List<Option<Tcoffee>> options) throws JobSubmissionException,\r
  91                         WrongParameterException {\r
  92 \r
  93                 WSUtil.validateFastaInput(sequences);\r
  94                 ConfiguredExecutable<Tcoffee> confTcoffee = init(sequences);\r
  95                 List<String> params = WSUtil.getCommands(options, Tcoffee.KEY_VALUE_SEPARATOR);\r
  96                 log.info("Setting parameters:" + params);\r
  97                 confTcoffee.addParameters(params);\r
  98                 return WSUtil.align(sequences, confTcoffee, log, "customAlign", getLimit(""));\r
  99         }\r
 100 \r
 101         @Override\r
 102         public String presetAlign(List<FastaSequence> sequences,\r
 103                         Preset<Tcoffee> preset) throws JobSubmissionException,\r
 104                         WrongParameterException {\r
 105                 WSUtil.validateFastaInput(sequences);\r
 106                 if (preset == null) {\r
 107                         throw new WrongParameterException("Preset must be provided!");\r
 108                 }\r
 109                 ConfiguredExecutable<Tcoffee> confTcoffee = init(sequences);\r
 110                 confTcoffee.addParameters(preset.getOptions());\r
 111                 Limit<Tcoffee> limit = getLimit(preset.getName());\r
 112                 return WSUtil.align(sequences, confTcoffee, log, "presetAlign", limit);\r
 113         }\r
 114 \r
 115         @SuppressWarnings("unchecked")\r
 116         @Override\r
 117         public Alignment getResult(String jobId) throws ResultNotAvailableException {\r
 118                 WSUtil.validateJobId(jobId);\r
 119                 AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);\r
 120                 ConfiguredExecutable<Tcoffee> tcoffee = (ConfiguredExecutable<Tcoffee>) asyncEngine\r
 121                                 .getResults(jobId);\r
 122                 Alignment al = tcoffee.getResults();\r
 123                 return new Alignment (al.getSequences(), Program.Tcoffee, '-');\r
 124         }\r
 125 \r
 126         @Override\r
 127         public Limit<Tcoffee> getLimit(String presetName) {\r
 128                 if (limitMan == null) {\r
 129                         // Limit is not defined\r
 130                         return null;\r
 131                 }\r
 132                 return limitMan.getLimitByName(presetName);\r
 133         }\r
 134 \r
 135         @Override\r
 136         public LimitsManager<Tcoffee> getLimits() {\r
 137                 return limitMan;\r
 138         }\r
 139 \r
 140         @Override\r
 141         public ChunkHolder pullExecStatistics(String jobId, long position) {\r
 142                 WSUtil.validateJobId(jobId);\r
 143                 String file = Configurator.getWorkDirectory(jobId) + File.separator\r
 144                                 + new Tcoffee().getError();\r
 145                 return WSUtil.pullFile(file, position);\r
 146         }\r
 147 \r
 148         @Override\r
 149         public boolean cancelJob(String jobId) {\r
 150                 WSUtil.validateJobId(jobId);\r
 151                 return WSUtil.cancelJob(jobId);\r
 152         }\r
 153 \r
 154         @Override\r
 155         public JobStatus getJobStatus(String jobId) {\r
 156                 WSUtil.validateJobId(jobId);\r
 157                 return WSUtil.getJobStatus(jobId);\r
 158         }\r
 159 \r
 160         @Override\r
 161         public PresetManager<Tcoffee> getPresets() {\r
 162                 return tcoffeePresets;\r
 163         }\r
 164 \r
 165         @Override\r
 166         public RunnerConfig<Tcoffee> getRunnerOptions() {\r
 167                 return tcoffeeOptions;\r
 168         }\r
 169 \r
 170 }\r