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.ClustalW;
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49 import compbio.util.Timer;
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50 import compbio.ws.client.Services;
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52 @WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = "http://msa.data.compbio/01/01/2010/", serviceName = "ClustalWS")
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53 public class ClustalWS implements MsaWS<ClustalW> {
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55 // Ask for resource injection
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57 private WebServiceContext wsContext;
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59 private static Logger log = Logger.getLogger(ClustalWS.class);
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61 private static volatile WSLogger logger;
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63 private static final RunnerConfig<ClustalW> clustalOptions = Util
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64 .getSupportedOptions(ClustalW.class);
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66 private static final PresetManager<ClustalW> clustalPresets = Util
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67 .getPresets(ClustalW.class);
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69 private static final LimitsManager<ClustalW> limitMan = compbio.engine.client.Util
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70 .getLimits(new ClustalW().getType());
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73 * Initialise the logger. This cannot be done in the constructor as the
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74 * WebServiceContext is not available at the object construction time
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76 private WSLogger getLogger() {
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77 if (logger == null) {
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78 synchronized (ClustalWS.class) {
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79 if (logger == null) {
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80 logger = WSLogger.getStatLogger(Services.ClustalWS,
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89 public String align(List<FastaSequence> sequences)
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90 throws JobSubmissionException {
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92 WSUtil.validateFastaInput(sequences);
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93 ConfiguredExecutable<ClustalW> confClust = init(sequences);
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94 return WSUtil.align(sequences, confClust, getLogger(), "align",
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98 ConfiguredExecutable<ClustalW> init(List<FastaSequence> dataSet)
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99 throws JobSubmissionException {
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100 ClustalW clustal = new ClustalW();
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101 ConfiguredExecutable<ClustalW> confClust = Configurator
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102 .configureExecutable(clustal, dataSet);
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107 public String presetAlign(List<FastaSequence> sequences,
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108 Preset<ClustalW> preset) throws JobSubmissionException,
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109 WrongParameterException {
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110 WSUtil.validateFastaInput(sequences);
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111 if (preset == null) {
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112 throw new WrongParameterException("Preset must be provided!");
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114 Limit<ClustalW> limit = getLimit(preset.getName());
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115 ConfiguredExecutable<ClustalW> confClust = init(sequences);
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116 confClust.addParameters(preset.getOptions());
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117 return WSUtil.align(sequences, confClust, getLogger(), "presetAlign",
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122 public String customAlign(List<FastaSequence> sequences,
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123 List<Option<ClustalW>> options) throws JobSubmissionException,
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124 WrongParameterException {
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125 WSUtil.validateFastaInput(sequences);
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126 ConfiguredExecutable<ClustalW> confClust = init(sequences);
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127 List<String> params = WSUtil.getCommands(options,
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128 ClustalW.KEY_VALUE_SEPARATOR);
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129 confClust.addParameters(params);
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130 log.info("Setting parameters: " + params);
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131 return WSUtil.align(sequences, confClust, getLogger(), "customAlign",
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136 public RunnerConfig<ClustalW> getRunnerOptions() {
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137 Timer timer = Timer.getMilliSecondsTimer();
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138 getLogger().logAll(timer, "getRunnerOptions");
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139 return clustalOptions;
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142 @SuppressWarnings("unchecked")
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144 public Alignment getResult(String jobId) throws ResultNotAvailableException {
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145 Timer timer = Timer.getMilliSecondsTimer();
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146 WSUtil.validateJobId(jobId);
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147 AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);
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148 ConfiguredExecutable<ClustalW> clustal = (ConfiguredExecutable<ClustalW>) asyncEngine
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149 .getResults(jobId);
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150 Alignment al = clustal.getResults();
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151 getLogger().log(timer, "getResults", jobId);
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156 public Limit<ClustalW> getLimit(String presetName) {
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157 Timer timer = Timer.getMilliSecondsTimer();
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158 if (limitMan == null) {
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159 // No limit is configured
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162 Limit<ClustalW> limit = limitMan.getLimitByName(presetName);
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163 getLogger().logAll(timer, "getLimit");
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168 public LimitsManager<ClustalW> getLimits() {
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173 public boolean cancelJob(String jobId) {
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174 Timer timer = Timer.getMilliSecondsTimer();
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175 WSUtil.validateJobId(jobId);
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176 boolean result = WSUtil.cancelJob(jobId);
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177 getLogger().logFine(timer, "Cancel");
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182 public JobStatus getJobStatus(String jobId) {
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183 Timer timer = Timer.getMilliSecondsTimer();
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184 WSUtil.validateJobId(jobId);
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185 JobStatus status = WSUtil.getJobStatus(jobId);
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186 getLogger().logFine(timer, "getJobStatus");
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191 public PresetManager<ClustalW> getPresets() {
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192 Timer timer = Timer.getMilliSecondsTimer();
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193 getLogger().logAll(timer, "pullExecStatistics");
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194 return clustalPresets;
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198 public ChunkHolder pullExecStatistics(String jobId, long position) {
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199 Timer timer = Timer.getMilliSecondsTimer();
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200 WSUtil.validateJobId(jobId);
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201 String file = Configurator.getWorkDirectory(jobId) + File.separator
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202 + ClustalW.getStatFile();
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203 ChunkHolder cholder = WSUtil.pullFile(file, position);
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204 getLogger().logFine(timer, "pullExecStatistics");
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