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.SkeletalExecutable;
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37 import compbio.engine.client.EngineUtil;
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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.RunnerUtil;
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50 import compbio.runner.msa.Mafft;
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52 @WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = JABAService.SERVICE_NAMESPACE, serviceName = "MafftWS")
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53 public class MafftWS implements MsaWS<Mafft> {
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55 private static Logger log = Logger.getLogger(MafftWS.class);
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56 private static final RunnerConfig<Mafft> mafftOptions = RunnerUtil.getSupportedOptions(Mafft.class);
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57 private static final PresetManager<Mafft> mafftPresets = RunnerUtil.getPresets(Mafft.class);
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58 private static final LimitsManager<Mafft> limitMan = EngineUtil.getLimits(new Mafft().getType());
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61 public String align(List<FastaSequence> sequences)
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62 throws JobSubmissionException {
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63 WSUtil.validateFastaInput(sequences);
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64 ConfiguredExecutable<Mafft> confMafft = init(sequences);
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65 return WSUtil.align(sequences, confMafft, log, "align", getLimit(""));
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68 ConfiguredExecutable<Mafft> init(List<FastaSequence> dataSet)
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69 throws JobSubmissionException {
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70 Mafft mafft = new Mafft();
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71 mafft.setInput(SkeletalExecutable.INPUT);
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72 mafft.setOutput(SkeletalExecutable.OUTPUT);
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73 mafft.setError(SkeletalExecutable.ERROR);
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74 return Configurator.configureExecutable(mafft, dataSet);
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78 public String customAlign(List<FastaSequence> sequences,
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79 List<Option<Mafft>> options) throws JobSubmissionException,
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80 WrongParameterException {
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81 WSUtil.validateFastaInput(sequences);
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82 ConfiguredExecutable<Mafft> confMafft = init(sequences);
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83 List<String> params = WSUtil.getCommands(options, Mafft.KEY_VALUE_SEPARATOR);
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84 log.info("Setting parameters: " + params);
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85 confMafft.addParameters(params);
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86 return WSUtil.align(sequences, confMafft, log, "customAlign", getLimit(""));
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90 public String presetAlign(List<FastaSequence> sequences,
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91 Preset<Mafft> preset) throws JobSubmissionException,
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92 WrongParameterException {
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93 WSUtil.validateFastaInput(sequences);
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94 if (preset == null) {
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95 throw new WrongParameterException("Preset must be provided!");
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97 ConfiguredExecutable<Mafft> confMafft = init(sequences);
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98 confMafft.addParameters(preset.getOptions());
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99 // This will return default limit if a specific the limit for a
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100 // particular preset is not found
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101 Limit<Mafft> limit = getLimit(preset.getName());
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103 return WSUtil.align(sequences, confMafft, log, "presetAlign", limit);
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106 @SuppressWarnings("unchecked")
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108 public Alignment getResult(String jobId) throws ResultNotAvailableException {
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109 WSUtil.validateJobId(jobId);
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110 AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);
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111 ConfiguredExecutable<Mafft> mafft = (ConfiguredExecutable<Mafft>) asyncEngine
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112 .getResults(jobId);
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113 Alignment al = mafft.getResults();
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114 return new Alignment (al.getSequences(), Program.Mafft, '-');
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118 public Limit<Mafft> getLimit(String presetName) {
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119 if (limitMan == null) {
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120 // Limit is not defined
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123 return limitMan.getLimitByName(presetName);
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127 public LimitsManager<Mafft> getLimits() {
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132 public ChunkHolder pullExecStatistics(String jobId, long position) {
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133 WSUtil.validateJobId(jobId);
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134 String file = Configurator.getWorkDirectory(jobId) + File.separator
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135 + new Mafft().getError();
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136 return WSUtil.pullFile(file, position);
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140 public boolean cancelJob(String jobId) {
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141 WSUtil.validateJobId(jobId);
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142 return WSUtil.cancelJob(jobId);
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146 public JobStatus getJobStatus(String jobId) {
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147 WSUtil.validateJobId(jobId);
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148 return WSUtil.getJobStatus(jobId);
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152 public PresetManager<Mafft> getPresets() {
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153 return mafftPresets;
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157 public RunnerConfig<Mafft> getRunnerOptions() {
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158 return mafftOptions;
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