1 /* Copyright (c) 2011 Peter Troshin
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3 * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0
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5 * This library is free software; you can redistribute it and/or modify it under the terms of the
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6 * Apache License version 2 as published by the Apache Software Foundation
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8 * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without
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9 * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache
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10 * License for more details.
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12 * A copy of the license is in apache_license.txt. It is also available here:
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13 * @see: http://www.apache.org/licenses/LICENSE-2.0.txt
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15 * Any republication or derived work distributed in source code form
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16 * must include this copyright and license notice.
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19 package compbio.ws.server;
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21 import java.io.File;
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22 import java.util.List;
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24 import javax.jws.WebService;
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26 import org.apache.log4j.Logger;
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28 import compbio.data.msa.JABAService;
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29 import compbio.data.msa.MsaWS;
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30 import compbio.data.sequence.Alignment;
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31 import compbio.data.sequence.FastaSequence;
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32 import compbio.engine.AsyncExecutor;
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33 import compbio.engine.Configurator;
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34 import compbio.engine.client.ConfiguredExecutable;
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35 import compbio.engine.client.SkeletalExecutable;
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36 import compbio.metadata.ChunkHolder;
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37 import compbio.metadata.JobStatus;
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38 import compbio.metadata.JobSubmissionException;
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39 import compbio.metadata.Limit;
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40 import compbio.metadata.LimitsManager;
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41 import compbio.metadata.Option;
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42 import compbio.metadata.Preset;
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43 import compbio.metadata.PresetManager;
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44 import compbio.metadata.ResultNotAvailableException;
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45 import compbio.metadata.RunnerConfig;
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46 import compbio.metadata.WrongParameterException;
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47 import compbio.runner.Util;
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48 import compbio.runner.msa.ClustalW;
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50 @WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = JABAService.SERVICE_NAMESPACE, serviceName = "ClustalWS")
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51 public class ClustalWS implements MsaWS<ClustalW> {
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53 private static Logger log = Logger.getLogger(ClustalWS.class);
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55 private static final RunnerConfig<ClustalW> clustalOptions = Util
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56 .getSupportedOptions(ClustalW.class);
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58 private static final PresetManager<ClustalW> clustalPresets = Util
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59 .getPresets(ClustalW.class);
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61 private static final LimitsManager<ClustalW> limitMan = compbio.engine.client.Util
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62 .getLimits(new ClustalW().getType());
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65 public String align(List<FastaSequence> sequences)
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66 throws JobSubmissionException {
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68 WSUtil.validateFastaInput(sequences);
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69 ConfiguredExecutable<ClustalW> confClust = init(sequences);
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70 return WSUtil.align(sequences, confClust, log, "align", getLimit(""));
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73 ConfiguredExecutable<ClustalW> init(List<FastaSequence> dataSet)
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74 throws JobSubmissionException {
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75 ClustalW clustal = new ClustalW();
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76 clustal.setInput(SkeletalExecutable.INPUT)
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77 .setOutput(SkeletalExecutable.OUTPUT)
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78 .setError(SkeletalExecutable.ERROR);
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79 ConfiguredExecutable<ClustalW> confClust = Configurator
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80 .configureExecutable(clustal, dataSet);
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85 public String presetAlign(List<FastaSequence> sequences,
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86 Preset<ClustalW> preset) throws JobSubmissionException,
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87 WrongParameterException {
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88 WSUtil.validateFastaInput(sequences);
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89 if (preset == null) {
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90 throw new WrongParameterException("Preset must be provided!");
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92 Limit<ClustalW> limit = getLimit(preset.getName());
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93 ConfiguredExecutable<ClustalW> confClust = init(sequences);
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94 confClust.addParameters(preset.getOptions());
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95 return WSUtil.align(sequences, confClust, log, "presetAlign", limit);
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99 public String customAlign(List<FastaSequence> sequences,
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100 List<Option<ClustalW>> options) throws JobSubmissionException,
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101 WrongParameterException {
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102 WSUtil.validateFastaInput(sequences);
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103 ConfiguredExecutable<ClustalW> confClust = init(sequences);
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104 List<String> params = WSUtil.getCommands(options,
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105 ClustalW.KEY_VALUE_SEPARATOR);
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106 confClust.addParameters(params);
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107 log.info("Setting parameters: " + params);
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108 return WSUtil.align(sequences, confClust, log, "customAlign",
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113 public RunnerConfig<ClustalW> getRunnerOptions() {
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114 return clustalOptions;
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117 @SuppressWarnings("unchecked")
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119 public Alignment getResult(String jobId) throws ResultNotAvailableException {
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121 WSUtil.validateJobId(jobId);
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122 AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);
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123 ConfiguredExecutable<ClustalW> clustal = (ConfiguredExecutable<ClustalW>) asyncEngine
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124 .getResults(jobId);
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125 Alignment al = clustal.getResults();
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131 public Limit<ClustalW> getLimit(String presetName) {
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132 if (limitMan == null) {
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133 // No limit is configured
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136 Limit<ClustalW> limit = limitMan.getLimitByName(presetName);
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141 public LimitsManager<ClustalW> getLimits() {
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146 public boolean cancelJob(String jobId) {
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147 WSUtil.validateJobId(jobId);
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148 boolean result = WSUtil.cancelJob(jobId);
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153 public JobStatus getJobStatus(String jobId) {
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154 WSUtil.validateJobId(jobId);
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155 JobStatus status = WSUtil.getJobStatus(jobId);
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160 public PresetManager<ClustalW> getPresets() {
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161 return clustalPresets;
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165 public ChunkHolder pullExecStatistics(String jobId, long position) {
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167 WSUtil.validateJobId(jobId);
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168 String file = Configurator.getWorkDirectory(jobId) + File.separator
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169 + ClustalW.getStatFile();
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170 ChunkHolder cholder = WSUtil.pullFile(file, position);
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