/*
* 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;
import htsjdk.samtools.SAMFileReader;
import htsjdk.samtools.ValidationStringency;
import org.broadinstitute.gatk.utils.commandline.ArgumentSource;
import org.broadinstitute.gatk.engine.io.storage.Storage;
import org.broadinstitute.gatk.engine.io.storage.StorageFactory;
import org.broadinstitute.gatk.engine.io.stubs.OutputStreamStub;
import org.broadinstitute.gatk.engine.io.stubs.Stub;
import org.broadinstitute.gatk.engine.walkers.Walker;
import org.broadinstitute.gatk.utils.classloader.JVMUtils;
import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
import org.broadinstitute.gatk.utils.exceptions.UserException;
import org.broadinstitute.gatk.utils.io.IOUtils;
import org.broadinstitute.gatk.utils.sam.SAMFileReaderBuilder;
import java.io.File;
import java.io.OutputStream;
import java.lang.reflect.Field;
import java.util.HashMap;
import java.util.Map;
/**
* Manages the output and err streams that are created specifically for walker
* output.
*/
public abstract class OutputTracker {
/**
* The streams to which walker users should be reading directly.
*/
protected Map<ArgumentSource, Object> inputs = new HashMap<ArgumentSource,Object>();
/**
* The streams to which walker users should be writing directly.
*/
protected Map<Stub,Storage> outputs = new HashMap<Stub,Storage>();
/**
* Special-purpose stub. Provides a connection to output streams.
*/
protected OutputStreamStub outStub = null;
/**
* Special-purpose stream. Provides a connection to error streams.
*/
protected OutputStreamStub errStub = null;
/**
* Gets the output storage associated with a given stub.
* @param stub The stub for which to find / create the right output stream.
* @param <T> Type of the stream to create.
* @return Storage object with a facade of type T.
*/
public abstract <T> T getStorage( Stub<T> stub );
public void prepareWalker( Walker walker, ValidationStringency strictnessLevel ) {
for( Map.Entry<ArgumentSource,Object> io: inputs.entrySet() ) {
ArgumentSource targetField = io.getKey();
Object targetValue = io.getValue();
// Ghastly hack: reaches in and finishes building out the SAMFileReader.
// TODO: Generalize this, and move it to its own initialization step.
if( targetValue instanceof SAMFileReaderBuilder) {
SAMFileReaderBuilder builder = (SAMFileReaderBuilder)targetValue;
builder.setValidationStringency(strictnessLevel);
targetValue = builder.build();
}
JVMUtils.setFieldValue( targetField.field, walker, targetValue );
}
}
/**
* Provide a mechanism for injecting supplemental streams for external management.
* @param argumentSource source Class / field into which to inject this stream.
* @param stub Stream to manage.
*/
public void addInput( ArgumentSource argumentSource, Object stub ) {
inputs.put(argumentSource,stub);
}
/**
* Provide a mechanism for injecting supplemental streams for external management.
* @param stub Stream to manage.
*/
public <T> void addOutput(Stub<T> stub) {
addOutput(stub,null);
}
/**
* Provide a mechanism for injecting supplemental streams for external management.
* @param stub Stream to manage.
*/
public <T> void addOutput(Stub<T> stub, Storage<T> storage) {
stub.register(this);
outputs.put(stub,storage);
validateOutputPath(stub);
}
/**
* Close down all existing output streams.
*/
public void close() {
for( Stub stub: outputs.keySet() ) {
// If the stream hasn't yet been created, create it so that there's at least an empty file present.
if( outputs.get(stub) == null )
getTargetStream(stub);
// Close down the storage.
outputs.get(stub).close();
}
}
/**
* Collects the target stream for this data.
* @param stub The stub for this stream.
* @param <T> type of stub.
* @return An instantiated file into which data can be written.
*/
protected <T> T getTargetStream( Stub<T> stub ) {
if( !outputs.containsKey(stub) )
throw new ReviewedGATKException("OutputTracker was not notified that this stub exists: " + stub);
Storage<T> storage = outputs.get(stub);
if( storage == null ) {
storage = StorageFactory.createStorage(stub);
outputs.put(stub,storage);
}
return (T)storage;
}
/**
* Ensures that the File associated with this stub (if any) is in a writable location
* @param stub
*/
protected <T> void validateOutputPath(final Stub<T> stub) {
if (stub.getOutputFile() != null && !(IOUtils.isSpecialFile(stub.getOutputFile()))) {
final File parentDir = stub.getOutputFile().getAbsoluteFile().getParentFile();
if (! (parentDir.canWrite() && parentDir.canExecute()))
throw new UserException.CouldNotCreateOutputFile(stub.getOutputFile(),
"either the containing directory doesn't exist or it isn't writable");
}
}
/**
* Install an OutputStreamStub into the given fieldName of the given walker.
* @param walker Walker into which to inject the field name.
* @param fieldName Name of the field into which to inject the stub.
*/
private void installStub( Walker walker, String fieldName, OutputStream outputStream ) {
Field field = JVMUtils.findField( walker.getClass(), fieldName );
JVMUtils.setFieldValue( field, walker, outputStream );
}
}