webservices/compbio/ws/server/TcoffeeWS.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.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.Tcoffee;\r
  51 \r
  52 @WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = "http://msa.data.compbio/01/01/2010/", serviceName = "TcoffeeWS")\r
  53 public class TcoffeeWS implements MsaWS<Tcoffee> {\r
  54 \r
  55         // Ask for resource injection\r
  56         @Resource\r
  57         WebServiceContext wsContext;\r
  58 \r
  59         private static Logger statLog = Logger.getLogger("TcoffeeWS-stats");\r
  60 \r
  61         private static Logger log = Logger.getLogger(TcoffeeWS.class);\r
  62 \r
  63         private static final RunnerConfig<Tcoffee> tcoffeeOptions = Util\r
  64                         .getSupportedOptions(Tcoffee.class);\r
  65 \r
  66         private static final PresetManager<Tcoffee> tcoffeePresets = Util\r
  67                         .getPresets(Tcoffee.class);\r
  68 \r
  69         private static final LimitsManager<Tcoffee> limitMan = compbio.engine.client.Util\r
  70                         .getLimits(new Tcoffee().getType());\r
  71 \r
  72         @Override\r
  73         public String align(List<FastaSequence> sequences)\r
  74                         throws JobSubmissionException {\r
  75                 WSUtil.validateFastaInput(sequences);\r
  76                 ConfiguredExecutable<Tcoffee> confTcoffee = init(sequences);\r
  77                 return WSUtil\r
  78                                 .align(sequences, confTcoffee, null, "align", getLimit(""));\r
  79         }\r
  80 \r
  81         ConfiguredExecutable<Tcoffee> init(List<FastaSequence> sequences)\r
  82                         throws JobSubmissionException {\r
  83                 Tcoffee tcoffee = new Tcoffee();\r
  84                 ConfiguredExecutable<Tcoffee> confCoffee = Configurator\r
  85                                 .configureExecutable(tcoffee, sequences);\r
  86                 if (confCoffee.getExecProvider() == Executable.ExecProvider.Cluster) {\r
  87                         int clusterCpuNum = SkeletalExecutable\r
  88                                         .getClusterCpuNum(Tcoffee.class);\r
  89                         if (clusterCpuNum != 0) {\r
  90                                 tcoffee.setNCore(clusterCpuNum);\r
  91                         }\r
  92                 }\r
  93                 return confCoffee;\r
  94         }\r
  95 \r
  96         @Override\r
  97         public String customAlign(List<FastaSequence> sequences,\r
  98                         List<Option<Tcoffee>> options) throws JobSubmissionException,\r
  99                         WrongParameterException {\r
 100 \r
 101                 WSUtil.validateFastaInput(sequences);\r
 102                 ConfiguredExecutable<Tcoffee> confTcoffee = init(sequences);\r
 103                 List<String> params = WSUtil.getCommands(options,\r
 104                                 Tcoffee.KEY_VALUE_SEPARATOR);\r
 105                 log.info("Setting parameters:" + params);\r
 106                 confTcoffee.addParameters(params);\r
 107                 return WSUtil.align(sequences, confTcoffee, null, "customAlign",\r
 108                                 getLimit(""));\r
 109         }\r
 110 \r
 111         @Override\r
 112         public String presetAlign(List<FastaSequence> sequences,\r
 113                         Preset<Tcoffee> preset) throws JobSubmissionException,\r
 114                         WrongParameterException {\r
 115                 WSUtil.validateFastaInput(sequences);\r
 116                 if (preset == null) {\r
 117                         throw new WrongParameterException("Preset must be provided!");\r
 118                 }\r
 119                 ConfiguredExecutable<Tcoffee> confTcoffee = init(sequences);\r
 120                 confTcoffee.addParameters(preset.getOptions());\r
 121                 Limit<Tcoffee> limit = getLimit(preset.getName());\r
 122                 return WSUtil.align(sequences, confTcoffee, null, "presetAlign", limit);\r
 123         }\r
 124 \r
 125         @SuppressWarnings("unchecked")\r
 126         @Override\r
 127         public Alignment getResult(String jobId) throws ResultNotAvailableException {\r
 128                 WSUtil.validateJobId(jobId);\r
 129                 AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);\r
 130                 ConfiguredExecutable<Tcoffee> tcoffee = (ConfiguredExecutable<Tcoffee>) asyncEngine\r
 131                                 .getResults(jobId);\r
 132                 Alignment al = tcoffee.getResults();\r
 133                 // log(jobId, "getResults");\r
 134                 return al;\r
 135         }\r
 136 \r
 137         @Override\r
 138         public Limit<Tcoffee> getLimit(String presetName) {\r
 139                 if (limitMan == null) {\r
 140                         // Limit is not defined\r
 141                         return null;\r
 142                 }\r
 143                 return limitMan.getLimitByName(presetName);\r
 144         }\r
 145 \r
 146         @Override\r
 147         public LimitsManager<Tcoffee> getLimits() {\r
 148                 return limitMan;\r
 149         }\r
 150 \r
 151         @Override\r
 152         public ChunkHolder pullExecStatistics(String jobId, long position) {\r
 153                 WSUtil.validateJobId(jobId);\r
 154                 String file = Configurator.getWorkDirectory(jobId) + File.separator\r
 155                                 + new Tcoffee().getError();\r
 156                 return WSUtil.pullFile(file, position);\r
 157         }\r
 158 \r
 159         @Override\r
 160         public boolean cancelJob(String jobId) {\r
 161                 WSUtil.validateJobId(jobId);\r
 162                 return WSUtil.cancelJob(jobId);\r
 163         }\r
 164 \r
 165         @Override\r
 166         public JobStatus getJobStatus(String jobId) {\r
 167                 WSUtil.validateJobId(jobId);\r
 168                 return WSUtil.getJobStatus(jobId);\r
 169         }\r
 170 \r
 171         @Override\r
 172         public PresetManager<Tcoffee> getPresets() {\r
 173                 return tcoffeePresets;\r
 174         }\r
 175 \r
 176         @Override\r
 177         public RunnerConfig<Tcoffee> getRunnerOptions() {\r
 178                 return tcoffeeOptions;\r
 179         }\r
 180 \r
 181 }\r