/*
* 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;
import org.apache.log4j.Logger;
import org.broadinstitute.gatk.utils.commandline.ArgumentTypeDescriptor;
import org.broadinstitute.gatk.utils.commandline.CommandLineProgram;
import org.broadinstitute.gatk.engine.arguments.GATKArgumentCollection;
import org.broadinstitute.gatk.engine.datasources.reads.SAMReaderID;
import org.broadinstitute.gatk.engine.filters.ReadFilter;
import org.broadinstitute.gatk.engine.io.stubs.OutputStreamArgumentTypeDescriptor;
import org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterArgumentTypeDescriptor;
import org.broadinstitute.gatk.engine.io.stubs.VCFWriterArgumentTypeDescriptor;
import org.broadinstitute.gatk.engine.phonehome.GATKRunReport;
import org.broadinstitute.gatk.engine.refdata.utils.RMDTriplet;
import org.broadinstitute.gatk.engine.walkers.Walker;
import org.broadinstitute.gatk.utils.crypt.CryptUtils;
import org.broadinstitute.gatk.utils.crypt.GATKKey;
import org.broadinstitute.gatk.utils.exceptions.UserException;
import org.broadinstitute.gatk.utils.text.ListFileUtils;
import java.security.PublicKey;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
/**
* @author aaron
*/
public abstract class CommandLineExecutable extends CommandLineProgram {
/**
* The actual engine which performs the analysis.
*/
protected GenomeAnalysisEngine engine = new GenomeAnalysisEngine();
// get the analysis name
public abstract String getAnalysisName();
/**
* Gets the GATK argument bundle.
* @return A structure consisting of whatever arguments should be used to initialize the GATK engine.
*/
protected abstract GATKArgumentCollection getArgumentCollection();
/**
* A list of all the arguments initially used as sources.
*/
private final Collection<Object> argumentSources = new ArrayList<Object>();
protected static Logger logger = Logger.getLogger(CommandLineExecutable.class);
/**
* this is the function that the inheriting class can expect to have called
* when the command line system has initialized.
*
* @return the return code to exit the program with
*/
protected int execute() throws Exception {
engine.setParser(parser);
argumentSources.add(this);
Walker<?,?> walker = engine.getWalkerByName(getAnalysisName());
try {
// Make sure a valid GATK user key is present, if required.
authorizeGATKRun();
engine.setArguments(getArgumentCollection());
// File lists can require a bit of additional expansion. Set these explicitly by the engine.
final Collection<SAMReaderID> bamFileList=ListFileUtils.unpackBAMFileList(getArgumentCollection().samFiles,parser);
engine.setSAMFileIDs(bamFileList);
if(getArgumentCollection().showFullBamList){
logger.info(String.format("Adding the following input SAM Files: %s",bamFileList.toString()));
}
engine.setWalker(walker);
walker.setToolkit(engine);
Collection<ReadFilter> filters = engine.createFilters();
engine.setFilters(filters);
// load the arguments into the walker / filters.
// TODO: The fact that this extra load call exists here when all the parsing happens at the engine
// TODO: level indicates that we're doing something wrong. Turn this around so that the GATK can drive
// TODO: argument processing.
loadArgumentsIntoObject(walker);
argumentSources.add(walker);
Collection<RMDTriplet> rodBindings = ListFileUtils.unpackRODBindings(parser.getRodBindings(), parser);
engine.setReferenceMetaDataFiles(rodBindings);
for (ReadFilter filter: filters) {
loadArgumentsIntoObject(filter);
argumentSources.add(filter);
}
engine.execute();
generateGATKRunReport(walker);
} catch ( Exception e ) {
generateGATKRunReport(walker, e);
throw e;
}
// always return 0
return 0;
}
/**
* Authorizes this run of the GATK by checking for a valid GATK user key, if required.
* Currently, a key is required only if running with the -et NO_ET or -et STDOUT options.
*/
private void authorizeGATKRun() {
if ( getArgumentCollection().phoneHomeType == GATKRunReport.PhoneHomeOption.NO_ET ||
getArgumentCollection().phoneHomeType == GATKRunReport.PhoneHomeOption.STDOUT ) {
if ( getArgumentCollection().gatkKeyFile == null ) {
throw new UserException("Running with the -et NO_ET or -et STDOUT option requires a GATK Key file. " +
"Please see " + UserException.PHONE_HOME_DOCS_URL +
" for more information and instructions on how to obtain a key.");
}
else {
PublicKey gatkPublicKey = CryptUtils.loadGATKDistributedPublicKey();
GATKKey gatkUserKey = new GATKKey(gatkPublicKey, getArgumentCollection().gatkKeyFile);
if ( ! gatkUserKey.isValid() ) {
throw new UserException.KeySignatureVerificationException(getArgumentCollection().gatkKeyFile);
}
}
}
}
/**
* Generate the GATK run report for this walker using the current GATKEngine, if -et is enabled.
* This report will be written to either STDOUT or to the run repository, depending on the options
* for -et.
*
* @param e the exception, can be null if no exception occurred
*/
private void generateGATKRunReport(Walker<?,?> walker, Exception e) {
if ( getArgumentCollection().phoneHomeType != GATKRunReport.PhoneHomeOption.NO_ET ) {
GATKRunReport report = new GATKRunReport(walker, e, engine, getArgumentCollection().phoneHomeType );
report.postReport(getArgumentCollection().phoneHomeType);
}
}
/**
* Convenience method for fully parameterized generateGATKRunReport when an exception has
* not occurred
*
* @param walker
*/
private void generateGATKRunReport(Walker<?,?> walker) {
generateGATKRunReport(walker, null);
}
/**
* Subclasses of CommandLinePrograms can provide their own types of command-line arguments.
* @return A collection of type descriptors generating implementation-dependent placeholders.
*/
protected Collection<ArgumentTypeDescriptor> getArgumentTypeDescriptors() {
return Arrays.asList( new VCFWriterArgumentTypeDescriptor(engine,System.out,argumentSources),
new SAMFileWriterArgumentTypeDescriptor(engine,System.out),
new OutputStreamArgumentTypeDescriptor(engine,System.out) );
}
/**
* GATK can add arguments dynamically based on analysis type.
*
* @return true
*/
@Override
protected boolean canAddArgumentsDynamically() {
return true;
}
/**
* GATK provides the walker as an argument source.
* @return List of walkers to load dynamically.
*/
@Override
protected Class[] getArgumentSources() {
// No walker info? No plugins.
if (getAnalysisName() == null) return new Class[] {};
Collection<Class> argumentSources = new ArrayList<Class>();
Walker walker = engine.getWalkerByName(getAnalysisName());
engine.setArguments(getArgumentCollection());
engine.setWalker(walker);
walker.setToolkit(engine);
argumentSources.add(walker.getClass());
Collection<ReadFilter> filters = engine.createFilters();
for(ReadFilter filter: filters)
argumentSources.add(filter.getClass());
Class[] argumentSourcesAsArray = new Class[argumentSources.size()];
return argumentSources.toArray(argumentSourcesAsArray);
}
@Override
protected String getArgumentSourceName( Class argumentSource ) {
return engine.getWalkerName((Class<Walker>)argumentSource);
}
}