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Encapsulate output tracking a bit. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@570 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-04-30 15:12:13 +00:00
parent 3bf3c21ddd
commit 7f173af2ea
4 changed files with 250 additions and 39 deletions
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61
java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
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@ -45,7 +45,7 @@ public class GenomeAnalysisTK extends CommandLineProgram {
public String DOWNSAMPLE_COVERAGE = null;
public String INTERVALS_FILE = null;
// our walker manager
private WalkerManager walkerManager = null;
@ -73,19 +73,12 @@ public class GenomeAnalysisTK extends CommandLineProgram {
/**
* How many threads should be allocated to this analysis.
*/
public int numThreads = 1;
public int numThreads = 1;
/**
* The output stream, initialized from OUTFILENAME / OUTERRFILENAME.
* Used by the walker.
* Collection of output streams used by the walker.
*/
public PrintStream out = System.out;
/**
* The output stream, initialized from ERRFILENAME / OUTERRFILENAME.
* Used by the walker.
*/
public PrintStream err = System.err;
private OutputTracker outputTracker = null;
/**
* our log, which we want to capture anything from this class
@ -121,7 +114,7 @@ public class GenomeAnalysisTK extends CommandLineProgram {
m_parser.addOptionalArg("out", "o", "An output file presented to the walker. Will overwrite contents if file exists.", "outFileName" );
m_parser.addOptionalArg("err", "e", "An error output file presented to the walker. Will overwrite contents if file exists.", "errFileName" );
m_parser.addOptionalArg("outerr", "oe", "A joint file for 'normal' and error output presented to the walker. Will overwrite contents if file exists.", "outErrFileName");
m_parser.addOptionalArg("numthreads", "nt", "How many threads should be allocated to running this analysis.", "numThreads");
m_parser.addOptionalFlag("disablethreading", "dt", "Disable experimental threading support.", "DISABLE_THREADING");
@ -179,7 +172,7 @@ public class GenomeAnalysisTK extends CommandLineProgram {
/**
* Convenience function that binds RODs using the old-style command line parser to the new style list for
* a uniform processing.
*
*
* @param name
* @param type
* @param file
@ -227,7 +220,7 @@ public class GenomeAnalysisTK extends CommandLineProgram {
if ( HAPMAP_CHIP_FILE != null ) bindConvenienceRods("hapmap-chip", "GFF", HAPMAP_CHIP_FILE);
ReferenceOrderedData.parseBindings(logger, ROD_BINDINGS, rods);
initializeOutputStreams();
Walker<?,?> my_walker = null;
@ -267,7 +260,7 @@ public class GenomeAnalysisTK extends CommandLineProgram {
this.engine = microScheduler.getTraversalEngine();
}
else {
logger.warn("Preliminary threading support DISABLED");
logger.warn("Preliminary threading support DISABLED");
this.engine = new TraverseByLociByReference(INPUT_FILES, REF_FILE_ARG, rods);
}
}
@ -345,30 +338,24 @@ public class GenomeAnalysisTK extends CommandLineProgram {
* Initialize the output streams as specified by the user.
*/
private void initializeOutputStreams() {
out = System.out;
err = System.err;
outputTracker = (outErrFileName != null) ? new OutputTracker( outErrFileName, outErrFileName )
: new OutputTracker( outFileName, errFileName );
}
if( outErrFileName != null && (outFileName != null || errFileName != null) )
throw new IllegalArgumentException("Can't set output/error output file with either out file name or err file name");
/**
* Get the output stream to be used with this walker.
* @return Output stream used with this walker.
*/
public PrintStream getWalkerOutputStream() {
return outputTracker.getOutStream();
}
try {
if( outErrFileName != null ) {
PrintStream outErrStream = new PrintStream( outErrFileName );
out = outErrStream;
err = outErrStream;
}
if ( outFileName != null ) {
out = new PrintStream( outFileName );
}
if( errFileName != null ) {
err = new PrintStream( errFileName );
}
}
catch( FileNotFoundException ex ) {
throw new RuntimeException("Unable to open a walker output file.", ex);
}
/**
* Get the output stream to be used with this walker.
* @return Output stream used with this walker.
*/
public PrintStream getWalkerErrorStream() {
return outputTracker.getErrStream();
}

120
java/src/org/broadinstitute/sting/gatk/OutputTracker.java 100755
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@ -0,0 +1,120 @@
package org.broadinstitute.sting.gatk;
import org.broadinstitute.sting.utils.StingException;
import java.io.FileOutputStream;
import java.io.PrintStream;
import java.io.FileNotFoundException;
/**
* User: hanna
* Date: Apr 30, 2009
* Time: 9:40:09 AM
* BROAD INSTITUTE SOFTWARE COPYRIGHT NOTICE AND AGREEMENT
* Software and documentation are copyright 2005 by the Broad Institute.
* All rights are reserved.
*
* Users acknowledge that this software is supplied without any warranty or support.
* The Broad Institute is not responsible for its use, misuse, or
* functionality.
*/
/**
* Manages the output and err streams that are created specifically for walker
* output.
*/
public class OutputTracker {
/**
* The streams to which walker users should be writing directly.
*/
private PrintStream out;
private PrintStream err;
/**
* Cache the file streams so that reassemblers can use nio to do fast file transfers.
*/
private FileOutputStream outFileStream;
private FileOutputStream errFileStream;
/**
* Create an object to manage output given filenames for the output and error files.
* If no files are specified, returns null.
* @param outFileName Name of the output file.
* @param errFileName Name of the error file.
*/
public OutputTracker( String outFileName, String errFileName ) {
// If the two output streams match and are non-null, initialize them identically.
// Otherwise, initialize them separately.
if( outFileName != null && outFileName.equals(errFileName) ) {
FileOutputStream outputFile = prepareOutputFile( outFileName );
outFileStream = errFileStream = outputFile;
out = err = new PrintStream( outputFile );
}
else {
if( outFileName != null ) {
outFileStream = prepareOutputFile( outFileName );
out = new PrintStream( outFileStream );
}
else
out = System.out;
if( errFileName != null ) {
errFileStream = prepareOutputFile( errFileName );
err = new PrintStream( errFileStream );
}
else
err = System.err;
}
}
/**
* Gets the output stream for the walker.
* @return Output stream; should be either file-backed or System.out.
*/
public PrintStream getOutStream() {
return out;
}
/**
* Gets the error stream for the walker.
* @return Error stream; should be either file-backed or System.err.
*/
public PrintStream getErrStream() {
return err;
}
/**
* Gets the filestream associated with normal output.
* @return FileStream associated with the output; null if not backed by a file.
*/
public FileOutputStream getOutFile() {
return outFileStream;
}
/**
* Gets the filestream associated with error output.
* @return stream associated with error output; null if not backed by a file.
*/
public FileOutputStream getErrFile() {
return errFileStream;
}
/**
* Given a (non-null) filename, open a file for output.
* @param fileName Filename for the stream. Should not be null.
* @return An open output stream associated with the given file.
*/
private FileOutputStream prepareOutputFile( String fileName ) {
FileOutputStream outputFile = null;
try {
outputFile = new FileOutputStream( fileName );
}
catch( FileNotFoundException ex ) {
throw new StingException("Unable to open output file " + fileName, ex);
}
return outputFile;
}
}

4
java/src/org/broadinstitute/sting/gatk/walkers/Walker.java
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@ -35,8 +35,8 @@ public abstract class Walker<MapType, ReduceType> {
protected Walker() {
if( GenomeAnalysisTK.Instance != null ) {
GenomeAnalysisTK.Instance.loadArgumentsIntoObject(this);
out = GenomeAnalysisTK.Instance.out;
err = GenomeAnalysisTK.Instance.err;
out = GenomeAnalysisTK.Instance.getWalkerOutputStream();
err = GenomeAnalysisTK.Instance.getWalkerErrorStream();
}
else {
out = System.out;

104
java/test/org/broadinstitute/sting/gatk/OutputTrackerTest.java 100755
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@ -0,0 +1,104 @@
package org.broadinstitute.sting.gatk;
import org.junit.Test;
import org.junit.After;
import org.junit.Assert;
import java.io.File;
import java.io.FileNotFoundException;
import java.util.Scanner; /**
* User: hanna
* Date: Apr 30, 2009
* Time: 10:20:18 AM
* BROAD INSTITUTE SOFTWARE COPYRIGHT NOTICE AND AGREEMENT
* Software and documentation are copyright 2005 by the Broad Institute.
* All rights are reserved.
*
* Users acknowledge that this software is supplied without any warranty or support.
* The Broad Institute is not responsible for its use, misuse, or
* functionality.
*/
/**
* For the file opening and closing mechanisms.
*/
public class OutputTrackerTest {
public static final String OUTPUT_FILENAME = "OutputTrackerTest.out";
public static final String ERROR_FILENAME = "OutputTrackerTest.err";
@After
public void cleanupTestFiles() {
File outFile = new File( OUTPUT_FILENAME );
File errFile = new File( ERROR_FILENAME );
if( outFile.exists() ) outFile.delete();
if( errFile.exists() ) errFile.delete();
}
@Test
public void testNullInputs() {
OutputTracker ot = new OutputTracker(null,null);
Assert.assertSame("OutputTracker: Output stream incorrectly initialized.", System.out, ot.getOutStream());
Assert.assertSame("OutputTracker: Error stream incorrectly initialized.", System.err, ot.getErrStream());
}
@Test
public void testOutputStreamAlone() throws FileNotFoundException {
OutputTracker ot = new OutputTracker(OUTPUT_FILENAME,null);
final String OUTPUT_TEXT = "out stream test";
ot.getOutStream().append(OUTPUT_TEXT);
Scanner outScanner = new Scanner(new File(OUTPUT_FILENAME));
String outText = outScanner.nextLine();
Assert.assertFalse("Out stream has too much data", outScanner.hasNext());
Assert.assertEquals("OutputTracker: Written output is incorrect", outText, OUTPUT_TEXT);
Assert.assertSame("OutputTracker: Error stream incorrectly initialized.", System.err, ot.getErrStream());
}
@Test
public void testErrorStreamAlone() throws FileNotFoundException {
OutputTracker ot = new OutputTracker(null,ERROR_FILENAME);
final String ERROR_TEXT = "err stream test";
ot.getErrStream().append(ERROR_TEXT);
Scanner errScanner = new Scanner(new File(ERROR_FILENAME));
String errText = errScanner.nextLine();
Assert.assertFalse("Err stream has too much data", errScanner.hasNext());
Assert.assertSame("OutputTracker: Output stream incorrectly initialized.", System.out, ot.getOutStream());
Assert.assertEquals("OutputTracker: Written error text is incorrect", errText, ERROR_TEXT);
}
@Test
public void testIndependentStreams() throws FileNotFoundException {
OutputTracker ot = new OutputTracker(OUTPUT_FILENAME,ERROR_FILENAME);
final String OUTPUT_TEXT = "out stream test";
ot.getOutStream().append(OUTPUT_TEXT);
final String ERROR_TEXT = "err stream test";
ot.getErrStream().append(ERROR_TEXT);
Scanner outScanner = new Scanner(new File(OUTPUT_FILENAME));
String outText = outScanner.nextLine();
Assert.assertFalse("Out stream has too much data", outScanner.hasNext());
Scanner errScanner = new Scanner(new File(ERROR_FILENAME));
String errText = errScanner.nextLine();
Assert.assertFalse("Err stream has too much data", errScanner.hasNext());
Assert.assertEquals("OutputTracker: Written output text is incorrect", outText, OUTPUT_TEXT);
Assert.assertEquals("OutputTracker: Written error text is incorrect", errText, ERROR_TEXT);
}
@Test
public void testIdenticalInputsGetIdenticalResults() {
OutputTracker ot = new OutputTracker(OUTPUT_FILENAME,OUTPUT_FILENAME);
Assert.assertSame("OutputTracker: FileOutputStreams don't match", ot.getOutFile(), ot.getErrFile());
Assert.assertSame("OutputTracker: PrintStreams don't match", ot.getOutStream(), ot.getErrStream());
}
}