1 /* Copyright (c) 2009 Peter Troshin
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3 * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0
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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.annotation.Resource;
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25 import javax.jws.WebService;
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26 import javax.xml.ws.WebServiceContext;
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28 import org.apache.log4j.Logger;
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30 import compbio.data.msa.MsaWS;
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31 import compbio.data.sequence.Alignment;
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32 import compbio.data.sequence.FastaSequence;
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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.metadata.ChunkHolder;
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39 import compbio.metadata.JobStatus;
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40 import compbio.metadata.JobSubmissionException;
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41 import compbio.metadata.Limit;
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42 import compbio.metadata.LimitsManager;
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43 import compbio.metadata.Option;
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44 import compbio.metadata.Preset;
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45 import compbio.metadata.PresetManager;
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46 import compbio.metadata.ResultNotAvailableException;
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47 import compbio.metadata.RunnerConfig;
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48 import compbio.metadata.WrongParameterException;
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49 import compbio.runner.Util;
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50 import compbio.runner.msa.Tcoffee;
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52 @WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = "http://msa.data.compbio/01/01/2010/", serviceName = "TcoffeeWS")
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53 public class TcoffeeWS implements MsaWS<Tcoffee> {
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55 // Ask for resource injection
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57 WebServiceContext wsContext;
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59 private static Logger statLog = Logger.getLogger("TcoffeeWS-stats");
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61 private static Logger log = Logger.getLogger(TcoffeeWS.class);
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63 private static final RunnerConfig<Tcoffee> tcoffeeOptions = Util
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64 .getSupportedOptions(Tcoffee.class);
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66 private static final PresetManager<Tcoffee> tcoffeePresets = Util
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67 .getPresets(Tcoffee.class);
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69 private static final LimitsManager<Tcoffee> limitMan = compbio.runner.Util
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70 .getLimits(new Tcoffee().getType());
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73 public String align(List<FastaSequence> sequences)
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74 throws JobSubmissionException {
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75 WSUtil.validateFastaInput(sequences);
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76 ConfiguredExecutable<Tcoffee> confTcoffee = init(sequences);
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78 .align(sequences, confTcoffee, null, "align", getLimit(""));
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81 ConfiguredExecutable<Tcoffee> init(List<FastaSequence> sequences)
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82 throws JobSubmissionException {
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83 Tcoffee tcoffee = new Tcoffee();
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84 ConfiguredExecutable<Tcoffee> confCoffee = Configurator
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85 .configureExecutable(tcoffee, sequences);
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86 if (confCoffee.getExecProvider() == Executable.ExecProvider.Cluster) {
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87 int clusterCpuNum = SkeletalExecutable
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88 .getClusterCpuNum(Tcoffee.class);
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89 if (clusterCpuNum != 0) {
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90 tcoffee.setNCore(clusterCpuNum);
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97 public String customAlign(List<FastaSequence> sequences,
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98 List<Option<Tcoffee>> options) throws JobSubmissionException,
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99 WrongParameterException {
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101 WSUtil.validateFastaInput(sequences);
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102 ConfiguredExecutable<Tcoffee> confTcoffee = init(sequences);
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103 List<String> params = WSUtil.getCommands(options,
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104 Tcoffee.KEY_VALUE_SEPARATOR);
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105 log.info("Setting parameters:" + params);
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106 confTcoffee.addParameters(params);
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107 return WSUtil.align(sequences, confTcoffee, null, "customAlign",
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112 public String presetAlign(List<FastaSequence> sequences,
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113 Preset<Tcoffee> preset) throws JobSubmissionException,
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114 WrongParameterException {
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115 WSUtil.validateFastaInput(sequences);
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116 if (preset == null) {
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117 throw new WrongParameterException("Preset must be provided!");
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119 ConfiguredExecutable<Tcoffee> confTcoffee = init(sequences);
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120 confTcoffee.addParameters(preset.getOptions());
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121 Limit<Tcoffee> limit = getLimit(preset.getName());
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122 return WSUtil.align(sequences, confTcoffee, null, "presetAlign", limit);
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125 @SuppressWarnings("unchecked")
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127 public Alignment getResult(String jobId) throws ResultNotAvailableException {
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128 WSUtil.validateJobId(jobId);
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129 AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);
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130 ConfiguredExecutable<Tcoffee> tcoffee = (ConfiguredExecutable<Tcoffee>) asyncEngine
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131 .getResults(jobId);
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132 Alignment al = tcoffee.getResults();
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133 // log(jobId, "getResults");
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138 public Limit<Tcoffee> getLimit(String presetName) {
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139 if (limitMan == null) {
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140 // Limit is not defined
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143 return limitMan.getLimitByName(presetName);
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147 public LimitsManager<Tcoffee> getLimits() {
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152 public ChunkHolder pullExecStatistics(String jobId, long position) {
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153 WSUtil.validateJobId(jobId);
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154 String file = Configurator.getWorkDirectory(jobId) + File.separator
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155 + new Tcoffee().getError();
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156 return WSUtil.pullFile(file, position);
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160 public boolean cancelJob(String jobId) {
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161 WSUtil.validateJobId(jobId);
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162 return WSUtil.cancelJob(jobId);
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166 public JobStatus getJobStatus(String jobId) {
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167 WSUtil.validateJobId(jobId);
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168 return WSUtil.getJobStatus(jobId);
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172 public PresetManager<Tcoffee> getPresets() {
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173 return tcoffeePresets;
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177 public RunnerConfig<Tcoffee> getRunnerOptions() {
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178 return tcoffeeOptions;
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