webservices/compbio/ws/server/MuscleWS.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.Muscle;\r
  49 \r
  50 @WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = "http://msa.data.compbio/01/01/2010/", serviceName = "MuscleWS")\r
  51 public class MuscleWS implements MsaWS<Muscle> {\r
  52 \r
  53     // Ask for resource injection\r
  54     @Resource\r
  55     WebServiceContext wsContext;\r
  56 \r
  57     private static Logger statLog = Logger.getLogger("MuscleWS-stats");\r
  58 \r
  59     private static Logger log = Logger.getLogger(MuscleWS.class);\r
  60 \r
  61     private static final RunnerConfig<Muscle> muscleOptions = Util\r
  62             .getSupportedOptions(Muscle.class);\r
  63 \r
  64     private static final PresetManager<Muscle> musclePresets = Util\r
  65             .getPresets(Muscle.class);\r
  66 \r
  67     @Override\r
  68     public String align(List<FastaSequence> sequences)\r
  69             throws JobSubmissionException {\r
  70         WSUtil.validateFastaInput(sequences);\r
  71         ConfiguredExecutable<Muscle> confMuscle = init(sequences);\r
  72         return WSUtil.align(sequences, confMuscle, null, "align", getLimit(""));\r
  73     }\r
  74 \r
  75     ConfiguredExecutable<Muscle> init(List<FastaSequence> sequences)\r
  76             throws JobSubmissionException {\r
  77         Muscle muscle = new Muscle();\r
  78         muscle.setInput("fasta.in").setOutput("fasta.out");\r
  79         return Configurator.configureExecutable(muscle, sequences);\r
  80     }\r
  81 \r
  82     @Override\r
  83     public String customAlign(List<FastaSequence> sequences,\r
  84             List<Option<Muscle>> options) throws JobSubmissionException,\r
  85             WrongParameterException {\r
  86         WSUtil.validateFastaInput(sequences);\r
  87         ConfiguredExecutable<Muscle> confMuscle = init(sequences);\r
  88         // Could not do that! Space separated values\r
  89         // will all be treated as keys! thus duplicates removed\r
  90         // String params = cbuilder.getCommand();\r
  91         List<String> params = WSUtil.getCommands(options,\r
  92                 Muscle.KEY_VALUE_SEPARATOR);\r
  93         confMuscle.addParameters(params);\r
  94         return WSUtil.align(sequences, confMuscle, null, "customAlign",\r
  95                 getLimit(""));\r
  96     }\r
  97 \r
  98     @Override\r
  99     public String presetAlign(List<FastaSequence> sequences,\r
 100             Preset<Muscle> preset) throws JobSubmissionException,\r
 101             WrongParameterException {\r
 102         WSUtil.validateFastaInput(sequences);\r
 103         if (preset == null) {\r
 104             throw new WrongParameterException("Preset must be provided!");\r
 105         }\r
 106         ConfiguredExecutable<Muscle> confMuscle = init(sequences);\r
 107         confMuscle.addParameters(preset.getOptions());\r
 108         Limit<Muscle> limit = getLimit(preset.getName());\r
 109         return WSUtil.align(sequences, confMuscle, null, "presetAlign", limit);\r
 110     }\r
 111 \r
 112     @SuppressWarnings("unchecked")\r
 113     @Override\r
 114     public Alignment getResult(String jobId) throws ResultNotAvailableException {\r
 115         WSUtil.validateJobId(jobId);\r
 116         AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);\r
 117         ConfiguredExecutable<Muscle> muscle = (ConfiguredExecutable<Muscle>) asyncEngine\r
 118                 .getResults(jobId);\r
 119         Alignment al = muscle.getResults();\r
 120         //log(jobId, "getResults");\r
 121         return al;\r
 122     }\r
 123 \r
 124     @Override\r
 125     public Limit<Muscle> getLimit(String presetName) {\r
 126         return new Muscle().getLimit(presetName);\r
 127     }\r
 128 \r
 129     @Override\r
 130     public LimitsManager<Muscle> getLimits() {\r
 131         return new Muscle().getLimits();\r
 132     }\r
 133 \r
 134     @Override\r
 135     public ChunkHolder pullExecStatistics(String jobId, long position) {\r
 136         WSUtil.validateJobId(jobId);\r
 137         String file = Configurator.getWorkDirectory(jobId) + File.separator\r
 138                 + Muscle.getStatFile();\r
 139         return WSUtil.pullFile(file, position);\r
 140     }\r
 141 \r
 142     @Override\r
 143     public boolean cancelJob(String jobId) {\r
 144         WSUtil.validateJobId(jobId);\r
 145         return WSUtil.cancelJob(jobId);\r
 146     }\r
 147 \r
 148     @Override\r
 149     public JobStatus getJobStatus(String jobId) {\r
 150         WSUtil.validateJobId(jobId);\r
 151         return WSUtil.getJobStatus(jobId);\r
 152     }\r
 153 \r
 154     @Override\r
 155     public PresetManager<Muscle> getPresets() {\r
 156         return musclePresets;\r
 157     }\r
 158 \r
 159     @Override\r
 160     public RunnerConfig<Muscle> getRunnerOptions() {\r
 161         return muscleOptions;\r
 162     }\r
 163 \r
 164 }\r