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.runner.disorder;
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21 import java.io.File;
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22 import java.io.FileInputStream;
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23 import java.io.FileNotFoundException;
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24 import java.io.IOException;
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25 import java.io.InputStream;
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26 import java.util.Arrays;
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27 import java.util.List;
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29 import org.apache.log4j.Logger;
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31 import compbio.data.sequence.AnnotatedSequence;
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32 import compbio.data.sequence.SequenceUtil;
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33 import compbio.data.sequence.UnknownFileFormatException;
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34 import compbio.engine.client.CommandBuilder;
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35 import compbio.engine.client.Executable;
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36 import compbio.engine.client.SkeletalExecutable;
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37 import compbio.metadata.Limit;
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38 import compbio.metadata.LimitsManager;
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39 import compbio.metadata.ResultNotAvailableException;
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40 import compbio.runner.Util;
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45 * java -Xmx512 -jar jronn_v3.jar -i=test_seq.txt -n=1 -o=out.txt -s=stat.out
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50 public class Jronn extends SkeletalExecutable<Jronn> {
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52 private static Logger log = Logger.getLogger(Jronn.class);
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55 * Number of cores to use, defaults to 1 for local execution or the value of
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56 * "jronn.cluster.cpunum" property for cluster execution
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58 private int ncoreNumber = 0;
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60 private final String ncorePrm = "-n=";
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62 // Cache for Limits information
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63 private static LimitsManager<Jronn> limits;
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65 public static final String KEY_VALUE_SEPARATOR = Util.SPACE;
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66 public static final String STAT_FILE = "stat.txt";
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69 addParameters(Arrays.asList("-jar", getLibPath(), "-s=" + STAT_FILE,
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73 @SuppressWarnings("unchecked")
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75 public List<AnnotatedSequence> getResults(String workDirectory)
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76 throws ResultNotAvailableException {
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77 List<AnnotatedSequence> sequences = null;
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79 InputStream inStream = new FileInputStream(new File(workDirectory,
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81 sequences = SequenceUtil.readJRonn(inStream);
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83 } catch (FileNotFoundException e) {
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84 log.error(e.getMessage(), e.getCause());
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85 throw new ResultNotAvailableException(e);
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86 } catch (IOException e) {
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87 log.error(e.getMessage(), e.getCause());
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88 throw new ResultNotAvailableException(e);
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89 } catch (UnknownFileFormatException e) {
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90 log.error(e.getMessage(), e.getCause());
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91 throw new ResultNotAvailableException(e);
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92 } catch (NullPointerException e) {
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93 log.error(e.getMessage(), e.getCause());
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94 throw new ResultNotAvailableException(e);
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99 private static String getLibPath() {
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101 String settings = ph.getProperty("jronn.jar.file");
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102 if (compbio.util.Util.isEmpty(settings)) {
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103 throw new NullPointerException(
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104 "Please define jronn.jar.file property in Executable.properties file"
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105 + "and initialize it with the location of jronn jar file");
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107 if (new File(settings).isAbsolute()) {
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108 // Jronn jar can be found so no actions necessary
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109 // no further actions is necessary
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112 return compbio.engine.client.Util.convertToAbsolute(settings);
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116 public List<String> getCreatedFiles() {
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117 return Arrays.asList(getOutput(), getError());
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121 public Jronn setInput(String inFile) {
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122 super.setInput(inFile);
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123 cbuilder.setParam("-i=" + inFile);
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128 public Jronn setOutput(String outFile) {
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129 super.setOutput(outFile);
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130 cbuilder.setParam("-o=" + outFile);
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135 public Limit<Jronn> getLimit(String presetName) {
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136 if (limits == null) {
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137 limits = getLimits();
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139 Limit<Jronn> limit = null;
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140 if (limits != null) {
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141 // this returns default limit if preset is undefined!
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142 limit = limits.getLimitByName(presetName);
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144 // If limit is not defined for a particular preset, then return default
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146 if (limit == null) {
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147 log.debug("Limit for the preset " + presetName
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148 + " is not found. Using default");
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149 limit = limits.getDefaultLimit();
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155 public LimitsManager<Jronn> getLimits() {
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156 // synchronise on static field
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157 synchronized (log) {
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158 if (limits == null) {
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159 limits = Util.getLimits(this.getClass());
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166 public Class<? extends Executable<?>> getType() {
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167 return this.getClass();
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170 public static String getStatFile() {
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174 public void setNCore(int ncoreNumber) {
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175 if (ncoreNumber < 1 || ncoreNumber > 100) {
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176 throw new IndexOutOfBoundsException(
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177 "Number of cores must be within 1 and 100 ");
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179 this.ncoreNumber = ncoreNumber;
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180 cbuilder.setParam(ncorePrm + Integer.toString(getNCore()));
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184 return ncoreNumber;
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188 public CommandBuilder<Jronn> getParameters(ExecProvider provider) {
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189 // If number of cores is provided, set it for the cluster execution only!
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190 if (provider == Executable.ExecProvider.Cluster) {
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191 int cpunum = SkeletalExecutable.getClusterCpuNum(getType());
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192 cpunum = (cpunum==0) ? 1 : cpunum;
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195 // Limit number of cores to 1 for ANY execution which does not set
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196 // Ncores explicitly using setNCore method or is run on local VM
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197 if(ncoreNumber==0) {
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201 return super.getParameters(provider);
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