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.V2_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