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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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.List;
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24 import org.apache.log4j.Logger;
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26 import compbio.data.sequence.FastaSequence;
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27 import compbio.engine.AsyncExecutor;
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28 import compbio.engine.Configurator;
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29 import compbio.engine.ProgressGetter;
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30 import compbio.engine.client.ConfiguredExecutable;
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31 import compbio.metadata.ChunkHolder;
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32 import compbio.metadata.JobStatus;
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33 import compbio.metadata.JobSubmissionException;
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34 import compbio.metadata.Limit;
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35 import compbio.metadata.LimitExceededException;
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36 import compbio.metadata.Option;
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37 import compbio.util.Timer;
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39 public final class WSUtil {
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41 private static Logger log = Logger.getLogger(WSUtil.class);
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43 public static final void validateJobId(String jobId)
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44 throws InvalidParameterException {
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45 if (!compbio.engine.client.Util.isValidJobId(jobId)) {
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46 throw new InvalidParameterException(
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47 "JobId is not provided or cannot be recognised! Given value: "
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52 public static final void validateFastaInput(List<FastaSequence> sequences)
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53 throws InvalidParameterException {
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54 if (sequences == null || sequences.isEmpty()) {
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55 throw new InvalidParameterException(
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56 "List of fasta sequences required but not provided! ");
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60 public static JobStatus getJobStatus(String jobId) {
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61 AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);
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62 return asyncEngine.getJobStatus(jobId);
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65 public static ChunkHolder pullFile(String file, long position) {
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66 return ProgressGetter.pull(file, position);
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69 public static byte getProgress(String jobId) {
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70 throw new UnsupportedOperationException();
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73 public static AsyncExecutor getEngine(ConfiguredExecutable<?> confClustal) {
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74 assert confClustal != null;
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75 return Configurator.getAsyncEngine(confClustal);
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78 public static boolean cancelJob(String jobId) {
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79 AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);
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80 return asyncEngine.cancelJob(jobId);
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83 public static <T> String align(List<FastaSequence> sequences,
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84 ConfiguredExecutable<T> confExec, WSLogger logger,
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85 String callingMethod, Limit<T> limit)
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86 throws LimitExceededException, JobSubmissionException {
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87 Timer timer = Timer.getMilliSecondsTimer();
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88 if (limit != null && limit.isExceeded(sequences)) {
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89 throw LimitExceededException.newLimitExceeded(limit, sequences);
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91 compbio.runner.Util.writeInput(sequences, confExec);
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92 AsyncExecutor engine = Configurator.getAsyncEngine(confExec);
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93 String jobId = engine.submitJob(confExec);
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94 if (logger != null) {
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95 logger.log(timer, callingMethod, jobId);
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101 * TODO Rewrite using purely CommandBuilder. This is breaking encapsulation
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103 public static final <T> List<String> getCommands(List<Option<T>> options,
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104 String keyValueSeparator) {
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105 List<String> oList = new ArrayList<String>();
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106 for (Option<T> o : options) {
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107 oList.add(o.toCommand(keyValueSeparator));
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