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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18 package compbio.ws.server;
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20 import java.security.InvalidParameterException;
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21 import java.util.ArrayList;
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22 import java.util.HashSet;
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23 import java.util.List;
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24 import java.util.Set;
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26 import org.apache.log4j.Logger;
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28 import compbio.data.sequence.FastaSequence;
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29 import compbio.data.sequence.ScoreManager;
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30 import compbio.runner.RunnerUtil;
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31 import compbio.engine.AsyncExecutor;
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32 import compbio.engine.Configurator;
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33 import compbio.engine.ProgressGetter;
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34 import compbio.engine.client.ConfiguredExecutable;
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35 import compbio.engine.client.EngineUtil;
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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.LimitExceededException;
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41 import compbio.metadata.Option;
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42 import compbio.metadata.ResultNotAvailableException;
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43 import compbio.ws.client.Services;
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44 import compbio.ws.client.ServicesUtil;
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46 public final class WSUtil {
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48 public static final void validateJobId(String jobId)
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49 throws InvalidParameterException {
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50 if (!EngineUtil.isValidJobId(jobId)) {
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51 throw new InvalidParameterException("JobId is not provided or cannot be recognised! Given value: " + jobId);
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55 public static final void validateFastaInput(List<FastaSequence> sequences)
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56 throws JobSubmissionException {
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57 if (sequences == null || sequences.isEmpty()) {
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58 throw new JobSubmissionException("List of fasta sequences required but not provided! ");
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60 Set<String> names = new HashSet<String>();
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61 for (FastaSequence fs : sequences) {
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62 boolean unique = names.add(fs.getId());
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64 throw new JobSubmissionException(
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65 "Input sequences must have unique names! \nSequence " + fs.getId() + " is a duplicate!");
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67 if (fs.getLength() == 0) {
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68 throw new JobSubmissionException("Sequence must not be empty! Sequence: " + fs.getId() + " was empty");
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73 public static JobStatus getJobStatus(String jobId) {
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74 AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);
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75 return asyncEngine.getJobStatus(jobId);
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78 public static ChunkHolder pullFile(String file, long position) {
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79 return ProgressGetter.pull(file, position);
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82 public static byte getProgress(String jobId) {
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83 throw new UnsupportedOperationException();
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86 public static AsyncExecutor getEngine(ConfiguredExecutable<?> confClustal) {
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87 assert confClustal != null;
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88 return Configurator.getAsyncEngine(confClustal);
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91 public static boolean cancelJob(String jobId) {
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92 AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);
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93 return asyncEngine.cancelJob(jobId);
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96 public static <T> String align(List<FastaSequence> sequences,
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97 ConfiguredExecutable<T> confExec, Logger logger,
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98 String callingMethod, Limit<T> limit)
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99 throws LimitExceededException, JobSubmissionException {
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101 if (limit != null && limit.isExceeded(sequences)) {
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102 throw LimitExceededException.newLimitExceeded(limit, sequences);
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104 RunnerUtil.writeInput(sequences, confExec);
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105 AsyncExecutor engine = Configurator.getAsyncEngine(confExec);
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106 String jobId = engine.submitJob(confExec);
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107 reportUsage(confExec, logger);
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112 static <T> void reportUsage(ConfiguredExecutable<T> confExec, Logger logger) {
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113 if (GAUtils.IS_GA_ENABLED) {
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114 Services service = ServicesUtil.getServiceByRunner(confExec.getExecutable().getClass());
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115 GAUtils.reportUsage(service);
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116 logger.info("Reporting GA usage for " + service);
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120 public static <T> String analize(List<FastaSequence> sequences,
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121 ConfiguredExecutable<T> confExec, Logger log, String method,
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122 Limit<T> limit) throws JobSubmissionException {
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123 if (limit != null && limit.isExceeded(sequences)) {
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124 throw LimitExceededException.newLimitExceeded(limit, sequences);
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126 RunnerUtil.writeInput(sequences, confExec);
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127 AsyncExecutor engine = Configurator.getAsyncEngine(confExec);
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128 String jobId = engine.submitJob(confExec);
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129 reportUsage(confExec, log);
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133 // Same as analize(...) but RNAalifold takes clustal input not fasta
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134 // An if condition in the above method might be a better solution but
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135 // you need a way of finding out the type of confExec at runtime
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137 public static <T> String fold(List<FastaSequence> sequences,
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138 ConfiguredExecutable<T> confExec, Logger log, String method,
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139 Limit<T> limit) throws JobSubmissionException {
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140 if (limit != null && limit.isExceeded(sequences)) {
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141 throw LimitExceededException.newLimitExceeded(limit, sequences);
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143 RunnerUtil.writeClustalInput(sequences, confExec, '-');
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144 AsyncExecutor engine = Configurator.getAsyncEngine(confExec);
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145 String jobId = engine.submitJob(confExec);
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146 reportUsage(confExec, log);
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151 * TODO Rewrite using purely CommandBuilder. This is breaking encapsulation
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153 public static final <T> List<String> getCommands(List<Option<T>> options,
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154 String keyValueSeparator) {
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155 List<String> oList = new ArrayList<String>();
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156 for (Option<T> o : options) {
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157 oList.add(o.toCommand(keyValueSeparator));
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162 public static void validateAAConInput(List<FastaSequence> sequences)
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163 throws JobSubmissionException {
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164 validateFastaInput(sequences);
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166 for (FastaSequence fs : sequences) {
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168 len = fs.getLength();
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171 if (fs.getLength() != len) {
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172 throw new JobSubmissionException(
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173 "All sequences must be of the same length. Please align the sequences " +
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174 " prior to submission! The first sequence length is : " + len +
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175 " but the sequence '" + fs.getId() + "' length is " + fs.getLength());
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180 // public static void validateJpredInput(List<FastaSequence> sequences)
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181 // throws JobSubmissionException {
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182 // validateFastaInput(sequences);
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184 // for (FastaSequence fs : sequences) {
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186 // len = fs.getLength();
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189 // if (fs.getLength() != len) {
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190 // System.out.println("FASTA rec: id = " + fs.getId() + ": seq = " + fs.getSequence());
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191 // throw new JobSubmissionException(
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192 // "All sequences must be of the same length. Please align the sequences " +
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193 // " prior to submission! The first sequence length is : " + len +
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194 // " but the sequence '" + fs.getId() + "' length is " + fs.getLength());
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199 public static <T> ScoreManager getAnnotation(String jobId, Logger log)
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200 throws ResultNotAvailableException {
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201 WSUtil.validateJobId(jobId);
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202 AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);
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203 ConfiguredExecutable<T> aacon = (ConfiguredExecutable<T>) asyncEngine.getResults(jobId);
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204 ScoreManager mas = aacon.getResults();
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205 log.trace(jobId + " getConservation : " + mas);
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