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.data.sequence.Program;
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33 import compbio.engine.AsyncExecutor;
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34 import compbio.engine.Configurator;
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35 import compbio.engine.client.ConfiguredExecutable;
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36 import compbio.engine.client.Executable;
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37 import compbio.engine.client.SkeletalExecutable;
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38 import compbio.engine.client.EngineUtil;
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39 import compbio.metadata.ChunkHolder;
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40 import compbio.metadata.JobStatus;
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41 import compbio.metadata.JobSubmissionException;
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42 import compbio.metadata.Limit;
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43 import compbio.metadata.LimitsManager;
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44 import compbio.metadata.Option;
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45 import compbio.metadata.Preset;
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46 import compbio.metadata.PresetManager;
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47 import compbio.metadata.ResultNotAvailableException;
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48 import compbio.metadata.RunnerConfig;
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49 import compbio.metadata.WrongParameterException;
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50 import compbio.runner.RunnerUtil;
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51 import compbio.runner.msa.ClustalO;
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53 @WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = JABAService.V2_SERVICE_NAMESPACE, serviceName = "ClustalOWS")
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54 public class ClustalOWS implements MsaWS<ClustalO> {
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56 private static Logger log = Logger.getLogger(ClustalOWS.class);
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57 private static final RunnerConfig<ClustalO> clustalOptions = RunnerUtil.getSupportedOptions(ClustalO.class);
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58 private static final PresetManager<ClustalO> clustalPresets = RunnerUtil.getPresets(ClustalO.class);
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59 private static final LimitsManager<ClustalO> limitMan = EngineUtil.getLimits(new ClustalO().getType());
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62 public String align(List<FastaSequence> sequences)
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63 throws JobSubmissionException {
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64 WSUtil.validateFastaInput(sequences);
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65 ConfiguredExecutable<ClustalO> confClust = init(sequences);
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66 return WSUtil.align(sequences, confClust, log, "align", getLimit(""));
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69 ConfiguredExecutable<ClustalO> init(List<FastaSequence> dataSet)
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70 throws JobSubmissionException {
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71 ClustalO clustal = new ClustalO();
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72 clustal.setInput(SkeletalExecutable.INPUT);
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73 clustal.setOutput(SkeletalExecutable.OUTPUT);
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74 clustal.setError(SkeletalExecutable.ERROR);
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75 ConfiguredExecutable<ClustalO> confClust = Configurator.configureExecutable(clustal, dataSet);
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76 // Set the number of threads for the cluster execution from conf file
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77 if (confClust.getExecProvider() == Executable.ExecProvider.Cluster) {
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78 int clusterCpuNum = SkeletalExecutable.getClusterCpuNum(clustal.getType());
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79 if (clusterCpuNum != 0) {
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80 clustal.setNCore(clusterCpuNum);
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87 public String presetAlign(List<FastaSequence> sequences,
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88 Preset<ClustalO> preset) throws JobSubmissionException,
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89 WrongParameterException {
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90 WSUtil.validateFastaInput(sequences);
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91 if (preset == null) {
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92 throw new WrongParameterException("Preset must be provided!");
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94 Limit<ClustalO> limit = getLimit(preset.getName());
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95 ConfiguredExecutable<ClustalO> confClust = init(sequences);
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96 confClust.addParameters(preset.getOptions());
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97 return WSUtil.align(sequences, confClust, log, "presetAlign", limit);
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101 public String customAlign(List<FastaSequence> sequences,
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102 List<Option<ClustalO>> options) throws JobSubmissionException,
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103 WrongParameterException {
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104 WSUtil.validateFastaInput(sequences);
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105 ConfiguredExecutable<ClustalO> confClust = init(sequences);
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106 List<String> params = WSUtil.getCommands(options, ClustalO.KEY_VALUE_SEPARATOR);
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107 confClust.addParameters(params);
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108 log.info("Setting parameters: " + params);
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109 return WSUtil.align(sequences, confClust, log, "customAlign", getLimit(""));
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113 public RunnerConfig<ClustalO> 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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120 WSUtil.validateJobId(jobId);
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121 AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);
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122 ConfiguredExecutable<ClustalO> clustal = (ConfiguredExecutable<ClustalO>) asyncEngine.getResults(jobId);
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123 Alignment al = clustal.getResults();
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124 return new Alignment (al.getSequences(),Program.ClustalO, '-');
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128 public Limit<ClustalO> getLimit(String presetName) {
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129 if (limitMan == null) {
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130 // No limit is configured
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133 Limit<ClustalO> limit = limitMan.getLimitByName(presetName);
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138 public LimitsManager<ClustalO> getLimits() {
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143 public boolean cancelJob(String jobId) {
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144 WSUtil.validateJobId(jobId);
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145 boolean result = WSUtil.cancelJob(jobId);
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150 public JobStatus getJobStatus(String jobId) {
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151 WSUtil.validateJobId(jobId);
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152 JobStatus status = WSUtil.getJobStatus(jobId);
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157 public PresetManager<ClustalO> getPresets() {
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158 return clustalPresets;
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162 public ChunkHolder pullExecStatistics(String jobId, long position) {
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163 WSUtil.validateJobId(jobId);
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164 String file = Configurator.getWorkDirectory(jobId) + File.separator + ClustalO.getStatFile();
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165 ChunkHolder cholder = WSUtil.pullFile(file, position);
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