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.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.Mafft;
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50 @WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = "http://msa.data.compbio/01/01/2010/", serviceName = "MafftWS")
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51 public class MafftWS implements MsaWS<Mafft> {
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53 // Ask for resource injection
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55 WebServiceContext wsContext;
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57 private static Logger statLog = Logger.getLogger("MafftWS-stats");
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59 private static Logger log = Logger.getLogger(MafftWS.class);
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61 private static final RunnerConfig<Mafft> mafftOptions = Util
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62 .getSupportedOptions(Mafft.class);
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64 private static final PresetManager<Mafft> mafftPresets = Util
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65 .getPresets(Mafft.class);
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68 public String align(List<FastaSequence> sequences)
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69 throws JobSubmissionException {
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70 WSUtil.validateFastaInput(sequences);
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71 ConfiguredExecutable<Mafft> confMafft = init(sequences);
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72 return WSUtil.align(sequences, confMafft, null, "align", getLimit(""));
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75 ConfiguredExecutable<Mafft> init(List<FastaSequence> dataSet)
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76 throws JobSubmissionException {
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77 Mafft mafft = new Mafft();
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78 mafft.setInput("fasta.in").setOutput("fasta.out");
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79 return Configurator.configureExecutable(mafft, dataSet);
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83 public String customAlign(List<FastaSequence> sequences,
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84 List<Option<Mafft>> options) throws JobSubmissionException,
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85 WrongParameterException {
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86 WSUtil.validateFastaInput(sequences);
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87 ConfiguredExecutable<Mafft> confMafft = init(sequences);
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88 List<String> params = WSUtil.getCommands(options,
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89 Mafft.KEY_VALUE_SEPARATOR);
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90 log.info("Setting parameters: " + params);
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91 confMafft.addParameters(params);
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92 return WSUtil.align(sequences, confMafft, null, "customAlign",
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97 public String presetAlign(List<FastaSequence> sequences,
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98 Preset<Mafft> preset) throws JobSubmissionException,
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99 WrongParameterException {
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100 WSUtil.validateFastaInput(sequences);
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101 if (preset == null) {
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102 throw new WrongParameterException("Preset must be provided!");
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104 ConfiguredExecutable<Mafft> confMafft = init(sequences);
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105 confMafft.addParameters(preset.getOptions());
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106 // This will return default limit if a specific the limit for a
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107 // particular preset is not found
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108 Limit<Mafft> limit = getLimit(preset.getName());
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110 return WSUtil.align(sequences, confMafft, null, "presetAlign", limit);
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113 @SuppressWarnings("unchecked")
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115 public Alignment getResult(String jobId) throws ResultNotAvailableException {
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116 WSUtil.validateJobId(jobId);
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117 AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);
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118 ConfiguredExecutable<Mafft> mafft = (ConfiguredExecutable<Mafft>) asyncEngine
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119 .getResults(jobId);
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120 Alignment al = mafft.getResults();
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121 //log(jobId, "getResults");
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126 public Limit<Mafft> getLimit(String presetName) {
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127 return new Mafft().getLimit(presetName);
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131 public LimitsManager<Mafft> getLimits() {
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132 return new Mafft().getLimits();
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136 public ChunkHolder pullExecStatistics(String jobId, long position) {
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137 WSUtil.validateJobId(jobId);
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138 String file = Configurator.getWorkDirectory(jobId) + File.separator
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139 + new Mafft().getError();
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140 return WSUtil.pullFile(file, position);
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144 public boolean cancelJob(String jobId) {
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145 WSUtil.validateJobId(jobId);
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146 return 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 return WSUtil.getJobStatus(jobId);
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156 public PresetManager<Mafft> getPresets() {
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157 return mafftPresets;
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161 public RunnerConfig<Mafft> getRunnerOptions() {
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162 return mafftOptions;
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