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/* Copyright (c) 2011 Peter Troshin
*
* JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0
*
* This library is free software; you can redistribute it and/or modify it under the terms of the
* Apache License version 2 as published by the Apache Software Foundation
*
* This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without
* even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache
* License for more details.
*
* A copy of the license is in apache_license.txt. It is also available here:
* @see: http://www.apache.org/licenses/LICENSE-2.0.txt
*
* Any republication or derived work distributed in source code form
* must include this copyright and license notice.
*/
package compbio.runner;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.util.List;
import java.util.Map;
import org.apache.log4j.Logger;
import compbio.data.sequence.Alignment;
import compbio.data.sequence.ClustalAlignmentUtil;
import compbio.data.sequence.FastaSequence;
import compbio.data.sequence.RNAStructScoreManager;
import compbio.data.sequence.Score;
import compbio.data.sequence.RNAStructReader;
import compbio.data.sequence.SequenceUtil;
import compbio.data.sequence.UnknownFileFormatException;
import compbio.engine.client.ConfExecutable;
import compbio.engine.client.ConfiguredExecutable;
import compbio.engine.client.Executable;
import compbio.engine.client.EngineUtil;
import compbio.metadata.JobSubmissionException;
import compbio.metadata.PresetManager;
import compbio.metadata.RunnerConfig;
public final class RunnerUtil {
public static Logger log = Logger.getLogger(RunnerUtil.class);
public static synchronized <T> RunnerConfig<T> getSupportedOptions(
Class<? extends Executable<T>> clazz) {
try {
return ConfExecutable.getRunnerOptions(clazz);
} catch (FileNotFoundException e) {
log.error("Could not load " + clazz + " parameters !" + e.getMessage(), e.getCause());
} catch (IOException e) {
log.error("IO exception while reading " + clazz + " parameters !" + e.getMessage(), e.getCause());
}
return null;
}
public static <T> PresetManager<T> getPresets(
Class<? extends Executable<T>> clazz) {
try {
return ConfExecutable.getRunnerPresets(clazz);
} catch (FileNotFoundException e) {
log.warn("No presets are found for " + clazz + "! " + e.getLocalizedMessage(), e.getCause());
} catch (IOException e) {
log.warn("IO exception while reading presets for " + clazz + "! " + e.getLocalizedMessage(), e.getCause());
}
return null;
}
public static final Alignment readClustalFile(String workDirectory, String clustFile)
throws UnknownFileFormatException, IOException, FileNotFoundException, NullPointerException {
assert !compbio.util.Util.isEmpty(workDirectory);
assert !compbio.util.Util.isEmpty(clustFile);
File cfile = new File(EngineUtil.getFullPath(workDirectory, clustFile));
log.trace("CLUSTAL OUTPUT FILE PATH: " + cfile.getAbsolutePath());
if (!(cfile.exists() && cfile.length() > 0)) {
throw new FileNotFoundException("Result for the jobId " + workDirectory + " with file name " + clustFile + " is not found!");
}
return ClustalAlignmentUtil.readClustalFile(cfile);
}
public static final Map<String, Score> readJronnFile(String workDirectory,
String clustFile) throws UnknownFileFormatException, IOException,
FileNotFoundException, NullPointerException {
assert !compbio.util.Util.isEmpty(workDirectory);
assert !compbio.util.Util.isEmpty(clustFile);
File cfile = new File(EngineUtil.getFullPath(workDirectory, clustFile));
log.trace("Jronn OUTPUT FILE PATH: " + cfile.getAbsolutePath());
if (!(cfile.exists() && cfile.length() > 0)) {
throw new FileNotFoundException("Result for the jobId " + workDirectory + " with file name " + clustFile + " is not found!");
}
return SequenceUtil.readJRonn(cfile);
}
public static void writeInput(List<FastaSequence> sequences,
ConfiguredExecutable<?> exec) throws JobSubmissionException {
try {
File filein = new File(exec.getInput());
FileOutputStream fout = new FileOutputStream(filein);
log.debug("File path: " + filein.getAbsolutePath());
SequenceUtil.writeFasta(fout, sequences);
fout.close();
} catch (IOException e) {
log.error("IOException while writing input file into the disk: " + e.getLocalizedMessage(), e);
throw new JobSubmissionException("We are sorry by JABAWS server seems to have a problem! " + e.getLocalizedMessage(), e);
}
}
public static void writeClustalInput(List<FastaSequence> sequences,
ConfiguredExecutable<?> exec, char gapChar) throws JobSubmissionException {
try {
File filein = new File(exec.getInput());
FileOutputStream fout = new FileOutputStream(filein);
log.debug("File path: " + filein.getAbsolutePath());
SequenceUtil.writeClustal(fout, sequences, gapChar);
fout.close();
} catch (IOException e) {
log.error("IOException while writing input file into the disk: " + e.getLocalizedMessage(), e);
throw new JobSubmissionException("We are sorry but JABAWS server seems to have a problem! " + e.getLocalizedMessage(), e);
}
}
public static RNAStructScoreManager readRNAStruct(String workDirectory,
String structFile) throws IOException, FileNotFoundException {
assert !compbio.util.Util.isEmpty(workDirectory);
assert !compbio.util.Util.isEmpty(structFile);
// The stdout from RNAalifold
File sFile = new File(EngineUtil.getFullPath( workDirectory, structFile));
// Base pair probability matrix (-p option)
File aliFile = new File(EngineUtil.getFullPath( workDirectory, "alifold.out"));
// Check that stdout file exists
if(!(sFile.exists() && sFile.length() > 0)) {
throw new FileNotFoundException("Result for the jobId " + workDirectory + "with file name " + structFile + " is not found!");
}
// Check that base pair probability file exists
if(!aliFile.exists()) {
log.warn("The file alifold.out is not found for the jobId "
+ workDirectory + "Is the -p or --MEA option not specified?");
return RNAStructReader.readRNAStructStream(new FileInputStream(sFile));
} else {
return RNAStructReader.readRNAStructStream(new FileInputStream(sFile),
new FileInputStream(aliFile));
}
}
}
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