/*
* Copyright (c) 2012 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.gatk.engine.io.stubs;
import org.broadinstitute.gatk.utils.commandline.*;
import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
import org.broadinstitute.gatk.utils.exceptions.DynamicClassResolutionException;
import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
import java.io.File;
import java.io.OutputStream;
import java.lang.reflect.Constructor;
import java.lang.reflect.Type;
/**
* Insert an OutputStreamStub instead of a full-fledged concrete OutputStream implementations.
*/
public class OutputStreamArgumentTypeDescriptor extends ArgumentTypeDescriptor {
/**
* The engine into which output stubs should be fed.
*/
private final GenomeAnalysisEngine engine;
/**
* The default output stream to write to write this info if
*/
private final OutputStream defaultOutputStream;
/**
* Create a new OutputStream argument, notifying the given engine when that argument has been created.
* @param engine Engine to add SAMFileWriter output to.
* @param defaultOutputStream Default target for output file.
*/
public OutputStreamArgumentTypeDescriptor(GenomeAnalysisEngine engine,OutputStream defaultOutputStream) {
this.engine = engine;
this.defaultOutputStream = defaultOutputStream;
}
@Override
public boolean supports( Class type ) {
return getConstructorForClass(type) != null;
}
@Override
public boolean createsTypeDefault(ArgumentSource source) {
return !source.isRequired() && source.defaultsToStdout();
}
@Override
public String typeDefaultDocString(ArgumentSource source) {
return "stdout";
}
@Override
public Object createTypeDefault(ParsingEngine parsingEngine,ArgumentSource source, Type type) {
if(source.isRequired() || !source.defaultsToStdout())
throw new ReviewedGATKException("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((Class)type,stub);
}
@Override
public Object parse( ParsingEngine parsingEngine, ArgumentSource source, Type type, ArgumentMatches matches ) {
ArgumentDefinition definition = createDefaultArgumentDefinition(source);
String fileName = getArgumentValue( definition, matches ).asString();
// 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);
Object result = createInstanceOfClass(makeRawTypeIfNecessary(type),stub);
// WARNING: Side effects required by engine!
parsingEngine.addTags(result,getArgumentTags(matches));
return result;
}
/**
* Retrieves the constructor for an object that takes exactly one argument: an output stream.
* @param type Type for which to go constructor spelunking.
* @return Constructor, if available. Null, if not.
*/
private Constructor<OutputStream> getConstructorForClass( Class type ) {
try {
return type.getConstructor( OutputStream.class );
}
catch( NoSuchMethodException ex ) {
return null;
}
}
/**
* Creat a new instance of the class accepting a single outputstream constructor.
* @param type Type of object to create.
* @param outputStream resulting output stream.
* @return A new instance of the outputstream-derived class.
*/
private Object createInstanceOfClass(Class type,OutputStream outputStream) {
try {
return getConstructorForClass(type).newInstance(outputStream);
} catch (Exception e) {
throw new DynamicClassResolutionException(type, e);
}
}
}