webservices/compbio/ws/server/ProbconsWS.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.Probcons;\r
  49 \r
  50 @WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = "http://msa.data.compbio/01/01/2010/", serviceName = "ProbconsWS")\r
  51 public class ProbconsWS implements MsaWS<Probcons> {\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("ProbconsWS-stats");\r
  58 \r
  59     private static Logger log = Logger.getLogger(ProbconsWS.class);\r
  60 \r
  61     private static final RunnerConfig<Probcons> probconsOptions = Util\r
  62             .getSupportedOptions(Probcons.class);\r
  63 \r
  64     @Override\r
  65     public String align(List<FastaSequence> sequences)\r
  66             throws JobSubmissionException {\r
  67         WSUtil.validateFastaInput(sequences);\r
  68         ConfiguredExecutable<Probcons> confProbcons = init(sequences);\r
  69         return WSUtil.align(sequences, confProbcons, null, "align",\r
  70                 getLimit(""));\r
  71     }\r
  72 \r
  73     ConfiguredExecutable<Probcons> init(List<FastaSequence> dataSet)\r
  74             throws JobSubmissionException {\r
  75         Probcons probcons = new Probcons();\r
  76         probcons.setInput("fasta.in").setOutput("alignment.out");\r
  77         return Configurator.configureExecutable(probcons, dataSet);\r
  78     }\r
  79 \r
  80     @Override\r
  81     public String customAlign(List<FastaSequence> sequences,\r
  82             List<Option<Probcons>> options) throws JobSubmissionException,\r
  83             WrongParameterException {\r
  84         WSUtil.validateFastaInput(sequences);\r
  85         ConfiguredExecutable<Probcons> confProbcons = init(sequences);\r
  86         List<String> params = WSUtil.getCommands(options,\r
  87                 Probcons.KEY_VALUE_SEPARATOR);\r
  88         log.info("Setting parameters:" + params);\r
  89         confProbcons.addParameters(params);\r
  90         return WSUtil.align(sequences, confProbcons, null, "customAlign",\r
  91                 getLimit(""));\r
  92     }\r
  93 \r
  94     @Override\r
  95     public String presetAlign(List<FastaSequence> sequences,\r
  96             Preset<Probcons> preset) throws JobSubmissionException,\r
  97             WrongParameterException {\r
  98         WSUtil.validateFastaInput(sequences);\r
  99         if (preset == null) {\r
 100             throw new WrongParameterException("Preset must be provided!");\r
 101         }\r
 102         ConfiguredExecutable<Probcons> confProbcons = init(sequences);\r
 103         confProbcons.addParameters(preset.getOptions());\r
 104         Limit<Probcons> limit = getLimit(preset.getName());\r
 105         return WSUtil\r
 106                 .align(sequences, confProbcons, null, "presetAlign", limit);\r
 107     }\r
 108 \r
 109     @SuppressWarnings("unchecked")\r
 110     @Override\r
 111     public Alignment getResult(String jobId) throws ResultNotAvailableException {\r
 112         WSUtil.validateJobId(jobId);\r
 113         AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);\r
 114         ConfiguredExecutable<Probcons> probcons = (ConfiguredExecutable<Probcons>) asyncEngine\r
 115                 .getResults(jobId);\r
 116         Alignment al = probcons.getResults();\r
 117         //log(jobId, "getResults");\r
 118         return al;\r
 119     }\r
 120 \r
 121     @Override\r
 122     public Limit<Probcons> getLimit(String presetName) {\r
 123         return new Probcons().getLimit(presetName);\r
 124     }\r
 125 \r
 126     @Override\r
 127     public LimitsManager<Probcons> getLimits() {\r
 128         return new Probcons().getLimits();\r
 129     }\r
 130 \r
 131     @Override\r
 132     public ChunkHolder pullExecStatistics(String jobId, long position) {\r
 133         WSUtil.validateJobId(jobId);\r
 134         // TODO check if output is the one to return\r
 135         String file = Configurator.getWorkDirectory(jobId) + File.separator\r
 136                 + new Probcons().getError();\r
 137         return WSUtil.pullFile(file, position);\r
 138     }\r
 139 \r
 140     @Override\r
 141     public boolean cancelJob(String jobId) {\r
 142         WSUtil.validateJobId(jobId);\r
 143         return WSUtil.cancelJob(jobId);\r
 144     }\r
 145 \r
 146     @Override\r
 147     public JobStatus getJobStatus(String jobId) {\r
 148         WSUtil.validateJobId(jobId);\r
 149         return WSUtil.getJobStatus(jobId);\r
 150     }\r
 151 \r
 152     @Override\r
 153     public PresetManager<Probcons> getPresets() {\r
 154         return null;\r
 155     }\r
 156 \r
 157     @Override\r
 158     public RunnerConfig<Probcons> getRunnerOptions() {\r
 159         return probconsOptions;\r
 160     }\r
 161 \r
 162 }\r