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.runner;
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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.FileOutputStream;
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25 import java.io.IOException;
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26 import java.util.List;
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27 import java.util.Map;
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29 import org.apache.log4j.Logger;
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31 import compbio.data.sequence.Alignment;
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32 import compbio.data.sequence.ClustalAlignmentUtil;
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33 import compbio.data.sequence.FastaSequence;
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34 import compbio.data.sequence.RNAStructScoreManager;
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35 import compbio.data.sequence.Score;
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36 import compbio.data.sequence.RNAStructReader;
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37 import compbio.data.sequence.SequenceUtil;
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38 import compbio.data.sequence.UnknownFileFormatException;
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39 import compbio.engine.client.ConfExecutable;
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40 import compbio.engine.client.ConfiguredExecutable;
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41 import compbio.engine.client.Executable;
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42 import compbio.engine.client.EngineUtil;
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43 import compbio.metadata.JobSubmissionException;
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44 import compbio.metadata.PresetManager;
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45 import compbio.metadata.RunnerConfig;
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47 public final class RunnerUtil {
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49 public static Logger log = Logger.getLogger(RunnerUtil.class);
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51 public static synchronized <T> RunnerConfig<T> getSupportedOptions(
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52 Class<? extends Executable<T>> clazz) {
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54 return ConfExecutable.getRunnerOptions(clazz);
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55 } catch (FileNotFoundException e) {
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56 log.error("Could not load " + clazz + " parameters !" + e.getMessage(), e.getCause());
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57 } catch (IOException e) {
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58 log.error("IO exception while reading " + clazz + " parameters !" + e.getMessage(), e.getCause());
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63 public static <T> PresetManager<T> getPresets(
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64 Class<? extends Executable<T>> clazz) {
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66 return ConfExecutable.getRunnerPresets(clazz);
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67 } catch (FileNotFoundException e) {
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68 log.warn("No presets are found for " + clazz + "! " + e.getLocalizedMessage(), e.getCause());
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69 } catch (IOException e) {
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70 log.warn("IO exception while reading presets for " + clazz + "! " + e.getLocalizedMessage(), e.getCause());
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75 public static final Alignment readClustalFile(String workDirectory, String clustFile)
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76 throws UnknownFileFormatException, IOException, FileNotFoundException, NullPointerException {
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77 assert !compbio.util.Util.isEmpty(workDirectory);
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78 assert !compbio.util.Util.isEmpty(clustFile);
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79 File cfile = new File(EngineUtil.getFullPath(workDirectory, clustFile));
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80 log.trace("CLUSTAL OUTPUT FILE PATH: " + cfile.getAbsolutePath());
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81 if (!(cfile.exists() && cfile.length() > 0)) {
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82 throw new FileNotFoundException("Result for the jobId " + workDirectory + " with file name " + clustFile + " is not found!");
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84 return ClustalAlignmentUtil.readClustalFile(cfile);
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87 public static final Map<String, Score> readJronnFile(String workDirectory,
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88 String clustFile) throws UnknownFileFormatException, IOException,
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89 FileNotFoundException, NullPointerException {
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90 assert !compbio.util.Util.isEmpty(workDirectory);
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91 assert !compbio.util.Util.isEmpty(clustFile);
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92 File cfile = new File(EngineUtil.getFullPath(workDirectory, clustFile));
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93 log.trace("Jronn OUTPUT FILE PATH: " + cfile.getAbsolutePath());
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94 if (!(cfile.exists() && cfile.length() > 0)) {
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95 throw new FileNotFoundException("Result for the jobId " + workDirectory + " with file name " + clustFile + " is not found!");
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97 return SequenceUtil.readJRonn(cfile);
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100 public static void writeInput(List<FastaSequence> sequences,
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101 ConfiguredExecutable<?> exec) throws JobSubmissionException {
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103 File filein = new File(exec.getInput());
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104 FileOutputStream fout = new FileOutputStream(filein);
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105 log.debug("File path: " + filein.getAbsolutePath());
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106 SequenceUtil.writeFasta(fout, sequences);
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108 } catch (IOException e) {
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109 log.error("IOException while writing input file into the disk: " + e.getLocalizedMessage(), e);
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110 throw new JobSubmissionException("We are sorry by JABAWS server seems to have a problem! " + e.getLocalizedMessage(), e);
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114 public static void writeClustalInput(List<FastaSequence> sequences,
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115 ConfiguredExecutable<?> exec, char gapChar) throws JobSubmissionException {
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117 File filein = new File(exec.getInput());
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118 FileOutputStream fout = new FileOutputStream(filein);
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119 log.debug("File path: " + filein.getAbsolutePath());
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120 SequenceUtil.writeClustal(fout, sequences, gapChar);
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122 } catch (IOException e) {
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123 log.error("IOException while writing input file into the disk: " + e.getLocalizedMessage(), e);
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124 throw new JobSubmissionException("We are sorry but JABAWS server seems to have a problem! " + e.getLocalizedMessage(), e);
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128 public static RNAStructScoreManager readRNAStruct(String workDirectory,
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129 String structFile) throws IOException, FileNotFoundException {
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131 assert !compbio.util.Util.isEmpty(workDirectory);
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132 assert !compbio.util.Util.isEmpty(structFile);
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133 // The stdout from RNAalifold
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134 File sFile = new File(EngineUtil.getFullPath( workDirectory, structFile));
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135 // Base pair probability matrix (-p option)
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136 File aliFile = new File(EngineUtil.getFullPath( workDirectory, "alifold.out"));
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137 // Check that stdout file exists
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138 if(!(sFile.exists() && sFile.length() > 0)) {
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139 throw new FileNotFoundException("Result for the jobId " + workDirectory + "with file name " + structFile + " is not found!");
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141 // Check that base pair probability file exists
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142 if(!aliFile.exists()) {
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143 log.warn("The file alifold.out is not found for the jobId "
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144 + workDirectory + "Is the -p or --MEA option not specified?");
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145 return RNAStructReader.readRNAStructStream(new FileInputStream(sFile));
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148 return RNAStructReader.readRNAStructStream(new FileInputStream(sFile),
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149 new FileInputStream(aliFile));
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