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.metadata.ChunkHolder;\r
  38 import compbio.metadata.JobStatus;\r
  39 import compbio.metadata.JobSubmissionException;\r
  40 import compbio.metadata.Limit;\r
  41 import compbio.metadata.LimitsManager;\r
  42 import compbio.metadata.Option;\r
  43 import compbio.metadata.Preset;\r
  44 import compbio.metadata.PresetManager;\r
  45 import compbio.metadata.ResultNotAvailableException;\r
  46 import compbio.metadata.RunnerConfig;\r
  47 import compbio.metadata.WrongParameterException;\r
  48 import compbio.runner.Util;\r
  49 import compbio.runner.msa.Tcoffee;\r
  50 \r
  51 @WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = "http://msa.data.compbio/01/01/2010/", serviceName = "TcoffeeWS")\r
  52 public class TcoffeeWS implements MsaWS<Tcoffee> {\r
  53 \r
  54     // Ask for resource injection\r
  55     @Resource\r
  56     WebServiceContext wsContext;\r
  57 \r
  58     private static Logger statLog = Logger.getLogger("TcoffeeWS-stats");\r
  59 \r
  60     private static Logger log = Logger.getLogger(TcoffeeWS.class);\r
  61 \r
  62     private static final RunnerConfig<Tcoffee> tcoffeeOptions = Util\r
  63             .getSupportedOptions(Tcoffee.class);\r
  64 \r
  65     private static final PresetManager<Tcoffee> tcoffeePresets = Util\r
  66             .getPresets(Tcoffee.class);\r
  67 \r
  68     @Override\r
  69     public String align(List<FastaSequence> sequences)\r
  70             throws JobSubmissionException {\r
  71         WSUtil.validateFastaInput(sequences);\r
  72         ConfiguredExecutable<Tcoffee> confTcoffee = init(sequences);\r
  73         return WSUtil\r
  74                 .align(sequences, confTcoffee, null, "align", getLimit(""));\r
  75     }\r
  76 \r
  77     ConfiguredExecutable<Tcoffee> init(List<FastaSequence> sequences)\r
  78             throws JobSubmissionException {\r
  79         Tcoffee tcoffee = new Tcoffee();\r
  80         tcoffee.setInput("fasta.in").setOutput("fasta.out");\r
  81         ConfiguredExecutable<Tcoffee> confCoffee = Configurator\r
  82                 .configureExecutable(tcoffee, sequences);\r
  83         if (confCoffee.getExecProvider() == Executable.ExecProvider.Cluster) {\r
  84             int clusterCpuNum = Tcoffee.getClusterCpuNum();\r
  85             if (clusterCpuNum != 0) {\r
  86                 tcoffee.setNCore(clusterCpuNum);\r
  87             }\r
  88         }\r
  89         return confCoffee;\r
  90     }\r
  91 \r
  92     @Override\r
  93     public String customAlign(List<FastaSequence> sequences,\r
  94             List<Option<Tcoffee>> options) throws JobSubmissionException,\r
  95             WrongParameterException {\r
  96 \r
  97         WSUtil.validateFastaInput(sequences);\r
  98         ConfiguredExecutable<Tcoffee> confTcoffee = init(sequences);\r
  99         List<String> params = WSUtil.getCommands(options,\r
 100                 Tcoffee.KEY_VALUE_SEPARATOR);\r
 101         log.info("Setting parameters:" + params);\r
 102         confTcoffee.addParameters(params);\r
 103         return WSUtil.align(sequences, confTcoffee, null, "customAlign",\r
 104                 getLimit(""));\r
 105     }\r
 106 \r
 107     @Override\r
 108     public String presetAlign(List<FastaSequence> sequences,\r
 109             Preset<Tcoffee> preset) throws JobSubmissionException,\r
 110             WrongParameterException {\r
 111         WSUtil.validateFastaInput(sequences);\r
 112         if (preset == null) {\r
 113             throw new WrongParameterException("Preset must be provided!");\r
 114         }\r
 115         ConfiguredExecutable<Tcoffee> confTcoffee = init(sequences);\r
 116         confTcoffee.addParameters(preset.getOptions());\r
 117         Limit<Tcoffee> limit = getLimit(preset.getName());\r
 118         return WSUtil.align(sequences, confTcoffee, null, "presetAlign", limit);\r
 119     }\r
 120 \r
 121     @SuppressWarnings("unchecked")\r
 122     @Override\r
 123     public Alignment getResult(String jobId) throws ResultNotAvailableException {\r
 124         WSUtil.validateJobId(jobId);\r
 125         AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);\r
 126         ConfiguredExecutable<Tcoffee> tcoffee = (ConfiguredExecutable<Tcoffee>) asyncEngine\r
 127                 .getResults(jobId);\r
 128         Alignment al = tcoffee.getResults();\r
 129         //log(jobId, "getResults");\r
 130         return al;\r
 131     }\r
 132 \r
 133     @Override\r
 134     public Limit<Tcoffee> getLimit(String presetName) {\r
 135         return new Tcoffee().getLimit(presetName);\r
 136     }\r
 137 \r
 138     @Override\r
 139     public LimitsManager<Tcoffee> getLimits() {\r
 140         return new Tcoffee().getLimits();\r
 141     }\r
 142 \r
 143     @Override\r
 144     public ChunkHolder pullExecStatistics(String jobId, long position) {\r
 145         WSUtil.validateJobId(jobId);\r
 146         String file = Configurator.getWorkDirectory(jobId) + File.separator\r
 147                 + new Tcoffee().getError();\r
 148         return WSUtil.pullFile(file, position);\r
 149     }\r
 150 \r
 151     @Override\r
 152     public boolean cancelJob(String jobId) {\r
 153         WSUtil.validateJobId(jobId);\r
 154         return WSUtil.cancelJob(jobId);\r
 155     }\r
 156 \r
 157     @Override\r
 158     public JobStatus getJobStatus(String jobId) {\r
 159         WSUtil.validateJobId(jobId);\r
 160         return WSUtil.getJobStatus(jobId);\r
 161     }\r
 162 \r
 163     @Override\r
 164     public PresetManager<Tcoffee> getPresets() {\r
 165         return tcoffeePresets;\r
 166     }\r
 167 \r
 168     @Override\r
 169     public RunnerConfig<Tcoffee> getRunnerOptions() {\r
 170         return tcoffeeOptions;\r
 171     }\r
 172 \r
 173 }\r