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.JpredAlignment;
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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.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.predictors.Jpred;
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53 //@WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = JABAService.V2_SERVICE_NAMESPACE, serviceName = "JpredWS")
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54 //public class JpredWS implements MsaWS<Jpred> {
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56 // private static Logger log = Logger.getLogger(JpredWS.class);
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58 // private static final RunnerConfig<Jpred> jpredOptions = RunnerUtil.getSupportedOptions(Jpred.class);
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59 // private static final PresetManager<Jpred> jpredPresets = RunnerUtil.getPresets(Jpred.class);
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60 // private static final LimitsManager<Jpred> limitMan = EngineUtil.getLimits(new Jpred().getType());
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63 // public String align(List<FastaSequence> sequences)
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64 // throws JobSubmissionException {
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65 // WSUtil.validateFastaInput(sequences);
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66 // ConfiguredExecutable<Jpred> confClust = init(sequences);
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67 // return WSUtil.align(sequences, confClust, log, "align", getLimit(""));
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70 // ConfiguredExecutable<Jpred> init(List<FastaSequence> dataSet)
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71 // throws JobSubmissionException {
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72 // Jpred jpred = new Jpred();
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73 // jpred.setInput(SkeletalExecutable.INPUT);
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74 // jpred.setOutput(SkeletalExecutable.OUTPUT);
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75 // jpred.setError(SkeletalExecutable.ERROR);
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76 // ConfiguredExecutable<Jpred> confJpred = Configurator.configureExecutable(jpred, dataSet);
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77 // // Set the number of threads for the cluster execution from conf file
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78 // if (confJpred.getExecProvider() == Executable.ExecProvider.Cluster) {
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79 // int clusterCpuNum = SkeletalExecutable.getClusterCpuNum(jpred.getType());
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80 // if (clusterCpuNum != 0) {
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81 // jpred.setNCore(clusterCpuNum);
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84 // return confJpred;
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88 // public String presetAlign(List<FastaSequence> sequences,
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89 // Preset<Jpred> preset) throws JobSubmissionException,
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90 // WrongParameterException {
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91 // WSUtil.validateFastaInput(sequences);
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92 // if (preset == null) {
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93 // throw new WrongParameterException("Preset must be provided!");
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95 // Limit<Jpred> limit = getLimit(preset.getName());
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96 // ConfiguredExecutable<Jpred> confClust = init(sequences);
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97 // confClust.addParameters(preset.getOptions());
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98 // return WSUtil.align(sequences, confClust, log, "presetAlign", limit);
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102 // public String customAlign(List<FastaSequence> sequences,
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103 // List<Option<Jpred>> options) throws JobSubmissionException,
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104 // WrongParameterException {
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105 // WSUtil.validateFastaInput(sequences);
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106 // ConfiguredExecutable<Jpred> confClust = init(sequences);
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107 // List<String> params = WSUtil.getCommands(options, Jpred.KEY_VALUE_SEPARATOR);
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108 // confClust.addParameters(params);
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109 // log.info("Setting parameters: " + params);
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110 // return WSUtil.align(sequences, confClust, log, "customAlign", getLimit(""));
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114 // public RunnerConfig<Jpred> getRunnerOptions() {
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115 // return jpredOptions;
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118 // @SuppressWarnings("unchecked")
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120 // public Alignment getResult(String jobId) throws ResultNotAvailableException {
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121 // WSUtil.validateJobId(jobId);
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122 // AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);
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123 // ConfiguredExecutable<Jpred> jpred = (ConfiguredExecutable<Jpred>) asyncEngine.getResults(jobId);
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124 // return (Alignment)jpred.getResults();
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128 // public Limit<Jpred> 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<Jpred> limit = limitMan.getLimitByName(presetName);
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138 // public LimitsManager<Jpred> getLimits() {
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139 // return limitMan;
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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<Jpred> getPresets() {
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158 // return jpredPresets;
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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 + Jpred.getStatFile();
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165 // ChunkHolder cholder = WSUtil.pullFile(file, position);
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