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Better integrate the @ArgumentCollection into the command-line argument parser. Walkers can now specify their own @ArgumentCollections. Also cleaned up a bit of the CommandLineProgram template method pattern to minimize duplicate code. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1746 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-09-29 22:23:19 +00:00
parent b1c321f161
commit 70e1aef550
13 changed files with 198 additions and 38 deletions
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6
java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java
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@ -47,7 +47,6 @@ import java.util.Arrays;
public abstract class CommandLineExecutable extends CommandLineProgram {
public Object GATKResult = null;
/**
* The actual engine which performs the analysis.
*/
@ -77,19 +76,16 @@ public abstract class CommandLineExecutable extends CommandLineProgram {
}
protected Object executeGATK() {
GATKArgumentCollection arguments = getArgumentCollection();
Walker<?,?> mWalker = GATKEngine.getWalkerByName(getAnalysisName());
// load the arguments into the walkers
loadArgumentsIntoObject(arguments);
loadArgumentsIntoObject(mWalker);
// process any arguments that need a second pass
GATKArgumentCollection arguments = getArgumentCollection();
processArguments(arguments);
// set the analysis name in the argument collection
arguments.analysisName = getAnalysisName();
return GATKEngine.execute(arguments, mWalker);
}

6
java/src/org/broadinstitute/sting/gatk/GATKArgumentCollection.java
View File

@ -47,9 +47,6 @@ public class GATKArgumentCollection {
public GATKArgumentCollection() {
}
@Element(required = false)
public String analysisName = null;
@ElementMap(entry = "analysis_argument", key = "key", attribute = true, inline = true, required = false)
public Map<String, String> walkerArgs = new HashMap<String, String>();
@ -235,9 +232,6 @@ public class GATKArgumentCollection {
if (!other.intervals.equals(this.intervals)) {
return false;
}
if (!other.analysisName.equals(this.analysisName)) {
return false;
}
if (!other.DBSNPFile.equals(this.DBSNPFile)) {
return false;
}

4
java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
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@ -105,6 +105,7 @@ public class GenomeAnalysisEngine {
* Actually run the GATK with the specified walker.
* @param args the argument collection, where we get all our setup information from
* @param my_walker Walker to run over the dataset. Must not be null.
* @return the value of this traversal.
*/
public Object execute(GATKArgumentCollection args, Walker<?,?> my_walker) {
// validate our parameters
@ -225,7 +226,7 @@ public class GenomeAnalysisEngine {
Utils.scareUser(String.format("Read-based traversals require a reference file but none was given"));
microScheduler = MicroScheduler.create(my_walker, readsDataSource, referenceDataSource, rodDataSources, argCollection.numberOfThreads);
} else {
Utils.scareUser(String.format("Unable to create the appropriate TraversalEngine for analysis type " + argCollection.analysisName));
Utils.scareUser(String.format("Unable to create the appropriate TraversalEngine for analysis type %s", WalkerManager.getWalkerName(my_walker.getClass())));
}
return microScheduler;
@ -615,6 +616,7 @@ public class GenomeAnalysisEngine {
* Initialize the output streams as specified by the user.
*
* @param walker the walker to initialize output streams for
* @param outputTracker the tracker supplying the initialization data.
*/
private void initializeOutputStreams(Walker walker, OutputTracker outputTracker) {
if( argCollection.outErrFileName != null )

4
java/src/org/broadinstitute/sting/gatk/io/OutputTracker.java
View File

@ -103,7 +103,7 @@ public abstract class OutputTracker {
targetValue = builder.build();
}
JVMUtils.setField( targetField.field, walker, targetValue );
JVMUtils.setFieldValue( targetField.field, walker, targetValue );
}
}
@ -171,6 +171,6 @@ public abstract class OutputTracker {
*/
private void installStub( Walker walker, String fieldName, OutputStream outputStream ) {
Field field = JVMUtils.findField( walker.getClass(), fieldName );
JVMUtils.setField( field, walker, outputStream );
JVMUtils.setFieldValue( field, walker, outputStream );
}
}

25
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeCalculationModelFactory.java
View File

@ -1,3 +1,28 @@
/*
* Copyright (c) 2009 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.gatk.walkers.genotyper;
import static org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeCalculationModel.Model.*;

25
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
View File

@ -1,3 +1,28 @@
/*
* Copyright (c) 2009 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.gatk.walkers.genotyper;
import org.broadinstitute.sting.utils.cmdLine.Argument;

25
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
View File

@ -1,3 +1,28 @@
/*
* Copyright (c) 2009 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.gatk.walkers.genotyper;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;

18
java/src/org/broadinstitute/sting/utils/JVMUtils.java
View File

@ -75,7 +75,7 @@ public class JVMUtils {
* @param instance Instance in which to set the field.
* @param value The value to which to set the given field in the given instance.
*/
public static void setField( Field field, Object instance, Object value ) {
public static void setFieldValue( Field field, Object instance, Object value ) {
try {
field.setAccessible(true);
field.set(instance, value);
@ -85,4 +85,20 @@ public class JVMUtils {
}
}
/**
* Gets the value stored in the provided field in the given instance.
* @param field Field to set in the given object.
* @param instance Instance in which to set the field.
* @return Value currently stored in the given field.
*/
public static Object getFieldValue( Field field, Object instance ) {
try {
field.setAccessible(true);
return field.get(instance);
}
catch( IllegalAccessException ex ) {
throw new StingException(String.format("Could not retrieve %s in instance %s",field.getName(),instance.getClass().getName()));
}
}
}

10
java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentMatches.java
View File

@ -124,6 +124,7 @@ public class ArgumentMatches implements Iterable<ArgumentMatch> {
/**
* Find all successful matches (a 'successful' match is one paired with a definition).
* @return All successful matches.
*/
ArgumentMatches findSuccessfulMatches() {
ArgumentMatches matches = new ArgumentMatches();
@ -151,7 +152,6 @@ public class ArgumentMatches implements Iterable<ArgumentMatch> {
* Merges the given argument match into the set of existing argument matches.
* If multiple arguments are present, those arguments will end up grouped.
* @param match The match to merge into.
* @return The merged match.
*/
void mergeInto( ArgumentMatch match ) {
boolean definitionExists = false;
@ -228,6 +228,14 @@ class ArgumentMatch implements Iterable<ArgumentMatch> {
indices.put(index,values );
}
/**
* Return a string representation of the given argument match, for debugging purposes.
* @return String representation of the match.
*/
public String toString() {
return label;
}
/**
* Creates an iterator that walks over each individual match at each position of a given argument.
* @return An iterator over the individual matches in this argument. Will not be null.

17
java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentSource.java
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@ -25,8 +25,6 @@
package org.broadinstitute.sting.utils.cmdLine;
import org.broadinstitute.sting.utils.StingException;
import java.lang.reflect.Field;
import java.util.Collection;
import java.util.List;
@ -96,11 +94,12 @@ public class ArgumentSource {
}
/**
* Injects the specified value into the selected field of the instance.
* @param targetInstance Instance into which to inject the parsed value.
* Parses the specified value based on the specified type.
* @param source The type of value to be parsed.
* @param values String representation of all values passed.
* @return the parsed value of the object.
*/
public Object parse( ArgumentSource source, Object targetInstance, ArgumentMatches values ) {
public Object parse( ArgumentSource source, ArgumentMatches values ) {
Object value = null;
if( !isFlag() ) {
ArgumentTypeDescriptor typeDescriptor = ArgumentTypeDescriptor.create( field.getType() );
@ -128,4 +127,12 @@ public class ArgumentSource {
Class argumentType = field.getType();
return Collection.class.isAssignableFrom(argumentType) || field.getType().isArray();
}
/**
* Gets a string representation of the argument source for debugging.
* @return String representation of the argument source.
*/
public String toString() {
return clazz.getSimpleName() + ": " + field.getName();
}
}

61
java/src/org/broadinstitute/sting/utils/cmdLine/ParsingEngine.java
View File

@ -88,7 +88,7 @@ public class ParsingEngine {
*/
public void addArgumentSource( String sourceName, Class sourceClass ) {
List<ArgumentDefinition> argumentsFromSource = new ArrayList<ArgumentDefinition>();
for( ArgumentSource argumentSource: extractArgumentSources(sourceClass,true) )
for( ArgumentSource argumentSource: extractArgumentSources(sourceClass) )
argumentsFromSource.addAll( argumentSource.createArgumentDefinitions() );
argumentDefinitions.add( new ArgumentDefinitionGroup(sourceName, argumentsFromSource) );
}
@ -246,31 +246,46 @@ public class ParsingEngine {
* @param object Object into which to add arguments.
*/
public void loadArgumentsIntoObject( Object object ) {
// Get a list of argument sources, not including the children of this argument. For now, skip loading
// arguments into the object recursively.
List<ArgumentSource> argumentSources = extractArgumentSources( object.getClass(), false );
List<ArgumentSource> argumentSources = extractArgumentSources(object.getClass());
for( ArgumentSource argumentSource: argumentSources )
loadMatchesIntoObject( argumentSource, object, argumentMatches.findMatches(argumentSource) );
}
/**
* Loads a single argument into the object.
* Loads a single argument into the object and that objects children.
* @param argumentMatches Argument matches to load into the object.
* @param target
* @param source Argument source to load into the object.
* @param instance Object into which to inject the value. The target might be in a container within the instance.
*/
private void loadMatchesIntoObject( ArgumentSource source, Object target, ArgumentMatches argumentMatches ) {
private void loadMatchesIntoObject( ArgumentSource source, Object instance, ArgumentMatches argumentMatches ) {
// Nothing to load
if( argumentMatches.size() == 0 )
return;
if( source.clazz.isAssignableFrom(target.getClass()) ) {
Object value = source.parse( source, target, argumentMatches );
JVMUtils.setField( source.field, target, value );
// Target instance into which to inject the value.
List<Object> targets = new ArrayList<Object>();
// Check to see whether the instance itself can be the target.
if( source.clazz.isAssignableFrom(instance.getClass()) ) {
targets.add(instance);
}
// Check to see whether a contained class can be the target.
targets.addAll(getContainersMatching(instance,source.clazz));
// Abort if no home is found for the object.
if( targets.size() == 0 )
throw new StingException("Internal command-line parser error: unable to find a home for argument matches " + argumentMatches);
for( Object target: targets ) {
Object value = source.parse( source, argumentMatches );
JVMUtils.setFieldValue( source.field, target, value );
}
}
/**
* Prints out the help associated with these command-line argument definitions.
* @param applicationDetails Details about the specific GATK-based application being run.
*/
public void printHelp( ApplicationDetails applicationDetails ) {
new HelpFormatter().printHelp(applicationDetails,argumentDefinitions);
@ -279,18 +294,17 @@ public class ParsingEngine {
/**
* Extract all the argument sources from a given object.
* @param sourceClass class to act as sources for other arguments.
* @param recursive Whether to recursively look for argument collections and add their contents.
* @return A list of sources associated with this object and its aggregated objects.
*/
private List<ArgumentSource> extractArgumentSources( Class sourceClass, boolean recursive ) {
private List<ArgumentSource> extractArgumentSources(Class sourceClass) {
List<ArgumentSource> argumentSources = new ArrayList<ArgumentSource>();
while( sourceClass != null ) {
Field[] fields = sourceClass.getDeclaredFields();
for( Field field: fields ) {
if( field.isAnnotationPresent(Argument.class) )
argumentSources.add( new ArgumentSource(sourceClass,field) );
if( field.isAnnotationPresent(ArgumentCollection.class) && recursive )
argumentSources.addAll( extractArgumentSources(field.getType(),recursive) );
if( field.isAnnotationPresent(ArgumentCollection.class) )
argumentSources.addAll( extractArgumentSources(field.getType()) );
}
sourceClass = sourceClass.getSuperclass();
}
@ -314,6 +328,7 @@ public class ParsingEngine {
/**
* Parse a short name into an ArgumentMatch.
* @param token The token to parse. The token should pass the isLongArgumentForm test.
* @param position The position of the token in question.
* @return ArgumentMatch associated with this token, or null if no match exists.
*/
private ArgumentMatch parseArgument( String token, int position ) {
@ -328,6 +343,24 @@ public class ParsingEngine {
// No parse results found.
return null;
}
/**
* Gets a list of the container instances of the given type stored within the given target.
* @param target Class holding the container.
* @param type Container type.
* @return A list of containers matching the given type.
*/
private List<Object> getContainersMatching(Object target, Class<?> type) {
List<Object> containers = new ArrayList<Object>();
Field[] fields = target.getClass().getDeclaredFields();
for( Field field: fields ) {
if( field.isAnnotationPresent(ArgumentCollection.class) && type.isAssignableFrom(field.getType()) )
containers.add(JVMUtils.getFieldValue(field,target));
}
return containers;
}
}
/**

2
java/test/org/broadinstitute/sting/gatk/GATKArgumentCollectionTest.java
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@ -1,7 +1,6 @@
package org.broadinstitute.sting.gatk;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.gatk.GATKArgumentCollection;
import org.junit.After;
import static org.junit.Assert.fail;
import org.junit.Before;
@ -83,7 +82,6 @@ public class GATKArgumentCollectionTest extends BaseTest {
collect.maximumEngineIterations = -1;
collect.strictnessLevel = SAMFileReader.ValidationStringency.STRICT;
collect.referenceFile = new File("referenceFile".toLowerCase());
collect.analysisName = "analysisName".toLowerCase();
collect.DBSNPFile = "DBSNPFile".toLowerCase();
collect.HAPMAPFile = "HAPMAPFile".toLowerCase();
collect.HAPMAPChipFile = "HAPMAPChipFile".toLowerCase();

33
java/test/org/broadinstitute/sting/utils/cmdLine/ParsingEngineTest.java
View File

@ -201,7 +201,7 @@ public class ParsingEngineTest extends BaseTest {
Assert.assertEquals("Enum value is not correct", TestEnum.THREE, argProvider.testEnum);
}
public enum TestEnum { ONE, TWO, THREE };
public enum TestEnum { ONE, TWO, THREE }
private class EnumArgProvider {
@Argument(fullName="test_enum",shortName="ti",doc="test enum",required=false)
@ -562,4 +562,35 @@ public class ParsingEngineTest extends BaseTest {
@Argument(doc="value",validation="\\d+")
Integer value;
}
@Test
public void argumentCollectionTest() {
String[] commandLine = new String[] { "--value", "5" };
parsingEngine.addArgumentSource( ArgumentCollectionProvider.class );
parsingEngine.parse( commandLine );
parsingEngine.validate();
ArgumentCollectionProvider argProvider = new ArgumentCollectionProvider();
parsingEngine.loadArgumentsIntoObject(argProvider);
Assert.assertEquals("Argument is not correctly initialized", 5, argProvider.rap.value.intValue() );
}
private class ArgumentCollectionProvider {
@ArgumentCollection
RequiredArgProvider rap = new RequiredArgProvider();
}
@Test(expected=StingException.class)
public void multipleArgumentCollectionTest() {
parsingEngine.addArgumentSource( MultipleArgumentCollectionProvider.class );
}
private class MultipleArgumentCollectionProvider {
@ArgumentCollection
RequiredArgProvider rap1 = new RequiredArgProvider();
@ArgumentCollection
RequiredArgProvider rap2 = new RequiredArgProvider();
}
}