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.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 = JABAService.SERVICE_NAMESPACE, serviceName = "TcoffeeWS")
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53 public class TcoffeeWS implements MsaWS<Tcoffee> {
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55 private static Logger log = Logger.getLogger(TcoffeeWS.class);
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57 private static final RunnerConfig<Tcoffee> tcoffeeOptions = Util.getSupportedOptions(Tcoffee.class);
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59 private static final PresetManager<Tcoffee> tcoffeePresets = Util.getPresets(Tcoffee.class);
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61 private static final LimitsManager<Tcoffee> limitMan = compbio.engine.client.Util.getLimits(new Tcoffee().getType());
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64 public String align(List<FastaSequence> sequences)
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65 throws JobSubmissionException {
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66 WSUtil.validateFastaInput(sequences);
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67 ConfiguredExecutable<Tcoffee> confTcoffee = init(sequences);
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68 return WSUtil.align(sequences, confTcoffee, log, "align", getLimit(""));
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71 ConfiguredExecutable<Tcoffee> init(List<FastaSequence> sequences)
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72 throws JobSubmissionException {
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73 Tcoffee tcoffee = new Tcoffee();
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74 tcoffee.setInput(SkeletalExecutable.INPUT)
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75 .setOutput(SkeletalExecutable.OUTPUT)
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76 .setError(SkeletalExecutable.ERROR);
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78 ConfiguredExecutable<Tcoffee> confCoffee = Configurator
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79 .configureExecutable(tcoffee, sequences);
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80 if (confCoffee.getExecProvider() == Executable.ExecProvider.Cluster) {
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81 int clusterCpuNum = SkeletalExecutable
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82 .getClusterCpuNum(Tcoffee.class);
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83 if (clusterCpuNum != 0) {
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84 tcoffee.setNCore(clusterCpuNum);
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91 public String customAlign(List<FastaSequence> sequences,
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92 List<Option<Tcoffee>> options) throws JobSubmissionException,
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93 WrongParameterException {
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95 WSUtil.validateFastaInput(sequences);
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96 ConfiguredExecutable<Tcoffee> confTcoffee = init(sequences);
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97 List<String> params = WSUtil.getCommands(options, Tcoffee.KEY_VALUE_SEPARATOR);
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98 log.info("Setting parameters:" + params);
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99 confTcoffee.addParameters(params);
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100 return WSUtil.align(sequences, confTcoffee, log, "customAlign", getLimit(""));
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104 public String presetAlign(List<FastaSequence> sequences,
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105 Preset<Tcoffee> preset) throws JobSubmissionException,
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106 WrongParameterException {
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107 WSUtil.validateFastaInput(sequences);
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108 if (preset == null) {
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109 throw new WrongParameterException("Preset must be provided!");
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111 ConfiguredExecutable<Tcoffee> confTcoffee = init(sequences);
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112 confTcoffee.addParameters(preset.getOptions());
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113 Limit<Tcoffee> limit = getLimit(preset.getName());
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114 return WSUtil.align(sequences, confTcoffee, log, "presetAlign", limit);
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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<Tcoffee> tcoffee = (ConfiguredExecutable<Tcoffee>) asyncEngine
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123 .getResults(jobId);
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124 Alignment al = tcoffee.getResults();
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125 return new Alignment (al.getSequences(), Program.Tcoffee, '-');
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129 public Limit<Tcoffee> getLimit(String presetName) {
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130 if (limitMan == null) {
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131 // Limit is not defined
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134 return limitMan.getLimitByName(presetName);
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138 public LimitsManager<Tcoffee> getLimits() {
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143 public ChunkHolder pullExecStatistics(String jobId, long position) {
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144 WSUtil.validateJobId(jobId);
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145 String file = Configurator.getWorkDirectory(jobId) + File.separator
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146 + new Tcoffee().getError();
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147 return WSUtil.pullFile(file, position);
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151 public boolean cancelJob(String jobId) {
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152 WSUtil.validateJobId(jobId);
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153 return WSUtil.cancelJob(jobId);
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157 public JobStatus getJobStatus(String jobId) {
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158 WSUtil.validateJobId(jobId);
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159 return WSUtil.getJobStatus(jobId);
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163 public PresetManager<Tcoffee> getPresets() {
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164 return tcoffeePresets;
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168 public RunnerConfig<Tcoffee> getRunnerOptions() {
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169 return tcoffeeOptions;
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