zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Fix issue where non-required file inputs can throw a NullPointerException 

rather than a UserException when an the input argument is specified without
an argument value. 
The magnitude of code required to fix this points to a need to give the
command-line argument system a good spring cleaning.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4714 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2010-11-22 01:49:17 +00:00
parent b9a59ea54f
commit 8ca5edf89f
6 changed files with 82 additions and 27 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java
View File

@ -322,7 +322,7 @@ class SimpleArgumentTypeDescriptor extends ArgumentTypeDescriptor {
// if their argument has no value and there's no default, throw a missing argument value exception.
// TODO: Clean this up so that null values never make it to this point. To fix this, we'll have to clean up the implementation of -U.
else if (value == null)
throw new MissingArgumentValueException(Collections.singleton(createDefaultArgumentDefinition(source)));
throw new MissingArgumentValueException(createDefaultArgumentDefinition(source));
else
throw new UnknownEnumeratedValueException(createDefaultArgumentDefinition(source),value);
} else {

51
java/src/org/broadinstitute/sting/commandline/MissingArgumentValueException.java 100644
View File

@ -0,0 +1,51 @@
/*
* Copyright (c) 2010, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.commandline;
import org.broadinstitute.sting.utils.Utils;
import java.util.Collection;
/**
* Specifies that a value was missing when attempting to populate an argument.
*/
public class MissingArgumentValueException extends ArgumentException {
public MissingArgumentValueException( ArgumentDefinition... missingArguments ) {
super( formatArguments(missingArguments) );
}
private static String formatArguments( ArgumentDefinition... missingArguments ) {
StringBuilder sb = new StringBuilder();
for( ArgumentDefinition missingArgument: missingArguments ) {
if( missingArgument.shortName != null )
sb.append( String.format("%nValue for argument with name '--%s' (-%s) is missing.", missingArgument.fullName, missingArgument.shortName) );
else
sb.append( String.format("%nValue for argument with name '--%s' is missing.", missingArgument.fullName) );
if(missingArgument.validOptions != null)
sb.append( String.format(" Valid options are (%s).", Utils.join(",",missingArgument.validOptions)));
}
return sb.toString();
}
}

19
java/src/org/broadinstitute/sting/commandline/ParsingEngine.java
View File

@ -490,25 +490,6 @@ class MissingArgumentException extends ArgumentException {
}
}
class MissingArgumentValueException extends ArgumentException {
public MissingArgumentValueException( Collection<ArgumentDefinition> missingArguments ) {
super( formatArguments(missingArguments) );
}
private static String formatArguments( Collection<ArgumentDefinition> missingArguments ) {
StringBuilder sb = new StringBuilder();
for( ArgumentDefinition missingArgument: missingArguments ) {
if( missingArgument.shortName != null )
sb.append( String.format("%nValue for argument with name '--%s' (-%s) is missing.", missingArgument.fullName, missingArgument.shortName) );
else
sb.append( String.format("%nValue for argument with name '--%s' is missing.", missingArgument.fullName) );
if(missingArgument.validOptions != null)
sb.append( String.format(" Valid options are (%s).", Utils.join(",",missingArgument.validOptions)));
}
return sb.toString();
}
}
/**
* An exception for undefined arguments.
*/

10
java/src/org/broadinstitute/sting/gatk/io/stubs/OutputStreamArgumentTypeDescriptor.java
View File

@ -28,6 +28,7 @@ package org.broadinstitute.sting.gatk.io.stubs;
import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import java.io.OutputStream;
import java.io.File;
@ -64,11 +65,13 @@ public class OutputStreamArgumentTypeDescriptor extends ArgumentTypeDescriptor {
@Override
public boolean createsTypeDefault(ArgumentSource source) {
return true;
return source.isRequired();
}
@Override
public Object createTypeDefault(ParsingEngine parsingEngine,ArgumentSource source) {
if(!source.isRequired())
throw new ReviewedStingException("BUG: tried to create type default for argument type descriptor that can't support a type default.");
OutputStreamStub stub = new OutputStreamStub(defaultOutputStream);
engine.addOutput(stub);
return createInstanceOfClass(source.field.getType(),stub);
@ -79,6 +82,11 @@ public class OutputStreamArgumentTypeDescriptor extends ArgumentTypeDescriptor {
ArgumentDefinition definition = createDefaultArgumentDefinition(source);
String fileName = getArgumentValue( definition, matches );
// This parser has been passed a null filename and the GATK is not responsible for creating a type default for the object;
// therefore, the user must have failed to specify a type default
if(fileName == null && !source.isRequired())
throw new MissingArgumentValueException(definition);
OutputStreamStub stub = new OutputStreamStub(new File(fileName));
engine.addOutput(stub);

15
java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java
View File

@ -29,6 +29,7 @@ import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
import net.sf.samtools.SAMFileWriter;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import java.lang.annotation.Annotation;
@ -83,11 +84,13 @@ public class SAMFileWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor
@Override
public boolean createsTypeDefault(ArgumentSource source) {
return true;
return source.isRequired();
}
@Override
public Object createTypeDefault(ParsingEngine parsingEngine,ArgumentSource source) {
if(!source.isRequired())
throw new ReviewedStingException("BUG: tried to create type default for argument type descriptor that can't support a type default.");
SAMFileWriterStub stub = new SAMFileWriterStub(engine,defaultOutputStream);
engine.addOutput(stub);
return stub;
@ -95,9 +98,13 @@ public class SAMFileWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor
@Override
public Object parse( ParsingEngine parsingEngine, ArgumentSource source, Class type, ArgumentMatches matches ) {
String writerFileName = getArgumentValue( createBAMArgumentDefinition(source), matches );
if( writerFileName == null )
throw new UserException.CommandLineException("SAM file compression was supplied, but no associated writer was supplied with it.");
ArgumentDefinition bamArgumentDefinition = createBAMArgumentDefinition(source);
String writerFileName = getArgumentValue( bamArgumentDefinition, matches );
// This parser has been passed a null filename and the GATK is not responsible for creating a type default for the object;
// therefore, the user must have failed to specify a type default
if(writerFileName == null && !source.isRequired())
throw new MissingArgumentValueException(bamArgumentDefinition);
SAMFileWriterStub stub = new SAMFileWriterStub(engine, new File(writerFileName));

12
java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterArgumentTypeDescriptor.java
View File

@ -104,11 +104,13 @@ public class VCFWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor {
*/
@Override
public boolean createsTypeDefault(ArgumentSource source) {
return true;
return source.isRequired();
}
@Override
public Object createTypeDefault(ParsingEngine parsingEngine,ArgumentSource source) {
if(!source.isRequired())
throw new ReviewedStingException("BUG: tried to create type default for argument type descriptor that can't support a type default.");
VCFWriterStub stub = new VCFWriterStub(engine, defaultOutputStream, false, argumentSources, false);
engine.addOutput(stub);
return stub;
@ -123,10 +125,16 @@ public class VCFWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor {
*/
@Override
public Object parse( ParsingEngine parsingEngine, ArgumentSource source, Class type, ArgumentMatches matches ) {
ArgumentDefinition defaultArgumentDefinition = createDefaultArgumentDefinition(source);
// Get the filename for the genotype file, if it exists. If not, we'll need to send output to out.
String writerFileName = getArgumentValue(createDefaultArgumentDefinition(source),matches);
String writerFileName = getArgumentValue(defaultArgumentDefinition,matches);
File writerFile = writerFileName != null ? new File(writerFileName) : null;
// This parser has been passed a null filename and the GATK is not responsible for creating a type default for the object;
// therefore, the user must have failed to specify a type default
if(writerFile == null && !source.isRequired())
throw new MissingArgumentValueException(defaultArgumentDefinition);
// Should we compress the output stream?
boolean compress = writerFileName != null && SUPPORTED_ZIPPED_SUFFIXES.contains(getFileSuffix(writerFileName));