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Support for more complex command-line types: arrays, untyped collections, typed collections, interfaces to typed and untyped collections. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@194 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-03-25 20:11:31 +00:00
parent 9840a089ef
commit 4b7bfb284a
2 changed files with 97 additions and 31 deletions
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126
java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentParser.java
View File

@ -3,9 +3,12 @@ package org.broadinstitute.sting.utils.cmdLine;
import org.apache.commons.cli.*;
import org.apache.log4j.Logger;
import java.lang.reflect.Array;
import java.lang.reflect.Constructor;
import java.lang.reflect.Field;
import java.lang.reflect.InvocationTargetException;
import java.lang.reflect.Modifier;
import java.lang.reflect.ParameterizedType;
import java.lang.reflect.Type;
import java.util.ArrayList;
import java.util.Collection;
@ -289,9 +292,10 @@ public class ArgumentParser {
}
catch (UnrecognizedOptionException e) {
// we don't care about unknown exceptions right now
logger.warn(e.getMessage());
if(!allowUnrecognized)
if(!allowUnrecognized) {
logger.warn(e.getMessage());
throw e;
}
}
// Apache CLI can ignore unrecognized arguments with a boolean flag, but
@ -303,33 +307,26 @@ public class ArgumentParser {
// logger.info("We have " + opts.size() + " options");
for (Option opt : opts) {
if (cmd.hasOption(opt.getOpt())) {
if (opt.hasArg()) {
//logger.info("looking at " + m_storageLocations.get(opt.getLongOpt()));
Object obj = m_storageLocations.get(opt.getLongOpt()).first;
Field field = m_storageLocations.get(opt.getLongOpt()).second;
//logger.info("looking at " + m_storageLocations.get(opt.getLongOpt()));
Object obj = m_storageLocations.get(opt.getLongOpt()).first;
Field field = m_storageLocations.get(opt.getLongOpt()).second;
try {
field.set(obj, constructFromString(field, cmd.getOptionValue(opt.getOpt())));
} catch (IllegalAccessException e) {
logger.fatal("processArgs: cannot convert field " + field.toString());
throw new RuntimeException("processArgs: Failed conversion " + e.getMessage());
}
} else {
Object obj = m_storageLocations.get(opt.getLongOpt()).first;
Field field = m_storageLocations.get(opt.getLongOpt()).second;
try {
//logger.fatal("about to parse field " + f.getName());
try {
if (opt.hasArg())
field.set(obj, constructFromString(field, cmd.getOptionValues(opt.getOpt())));
else
field.set(obj, new Boolean(true));
} catch (IllegalAccessException e) {
logger.fatal("processArgs: cannot convert field " + field.toString());
throw new RuntimeException("processArgs: Failed conversion " + e.getMessage());
}
} catch (IllegalAccessException e) {
logger.fatal("processArgs: cannot convert field " + field.toString());
throw new RuntimeException("processArgs: Failed conversion " + e.getMessage());
}
}
}
}
/**
* Simple class to wrap the posix parser and get access to the parsed cmd object.
*/
private class OurPosixParser extends PosixParser {
public CommandLine getCmd() { return cmd; }
}
@ -349,10 +346,19 @@ public class ArgumentParser {
String shortName = (arg.shortName().length() != 0) ? arg.shortName() : fullName.substring(0,1);
if(shortName.length() != 1)
throw new IllegalArgumentException("Invalid short name: " + shortName);
String description = arg.required() ? "(Required Flag) " + arg.doc() : arg.doc();
boolean isFlag = (field.getType() == Boolean.class) || (field.getType() == Boolean.TYPE);
boolean isCollection = field.getType().isArray() || Collection.class.isAssignableFrom(field.getType());
// TODO: Handle flags, handle lists
OptionBuilder ob = OptionBuilder.withLongOpt(fullName).withArgName(fullName).hasArg();
if( isFlag && isCollection )
throw new IllegalArgumentException("Can't have an array of flags.");
String description = arg.doc();
if( arg.required() )
description = (isFlag ? "(Required Flag) " : "(Required Option) ") + description;
OptionBuilder ob = OptionBuilder.withLongOpt(fullName);
if( !isFlag ) ob = ob.withArgName(fullName);
ob = isCollection ? ob.hasArgs() : ob.hasArg();
if( arg.required() ) ob = ob.isRequired();
if( description.length() != 0 ) ob = ob.withDescription( description );
@ -362,8 +368,68 @@ public class ArgumentParser {
}
}
private Object constructFromString(Field f, String str) {
Type type = f.getType();
private Object constructFromString(Field f, String[] strs) {
Class type = f.getType();
if( Collection.class.isAssignableFrom(type) ) {
Collection collection = null;
Class containedType = null;
// If this is a parameterized collection, find the contained type. If blow up if only one type exists.
if( f.getGenericType() instanceof ParameterizedType ) {
ParameterizedType parameterizedType = (ParameterizedType)f.getGenericType();
if( parameterizedType.getActualTypeArguments().length > 1 )
throw new IllegalArgumentException("Unable to determine collection type of field: " + f.toString());
containedType = (Class)parameterizedType.getActualTypeArguments()[0];
}
else
containedType = String.class;
// If this is a generic interface, pick a concrete implementation to create and pass back.
// Because of type erasure, don't worry about creating one of exactly the correct type.
if( Modifier.isInterface(type.getModifiers()) || Modifier.isAbstract(type.getModifiers()) )
{
if( java.util.List.class.isAssignableFrom(type) ) type = ArrayList.class;
else if( java.util.Queue.class.isAssignableFrom(type) ) type = java.util.ArrayDeque.class;
else if( java.util.Set.class.isAssignableFrom(type) ) type = java.util.TreeSet.class;
}
try
{
collection = (Collection)type.newInstance();
}
catch( Exception ex ) {
// Runtime exceptions are definitely unexpected parsing simple collection classes.
throw new IllegalArgumentException(ex);
}
for( String str: strs )
collection.add( constructSingleElement(f,containedType,str) );
return collection;
}
else if( type.isArray() ) {
Class containedType = type.getComponentType();
Object arr = Array.newInstance(containedType,strs.length);
for( int i = 0; i < strs.length; i++ )
Array.set( arr,i,constructSingleElement(f,containedType,strs[i]) );
return arr;
}
else {
if( strs.length != 1 )
throw new IllegalArgumentException("Passed multiple arguments to an object expecting a single value.");
return constructSingleElement(f,type,strs[0]);
}
}
/**
* Builds a single element of the given type.
* @param f Implies type of data to construct.
* @param str String representation of data.
* @return parsed form of String.
*/
private Object constructSingleElement(Field f, Class type, String str) {
// lets go through the types we support
if (type == Boolean.TYPE) {
boolean b = false;
@ -378,10 +444,11 @@ public class ArgumentParser {
} else if (type == Float.TYPE) {
Float fl = Float.valueOf(str);
return fl;
} else {
}
else {
Constructor ctor = null;
try {
ctor = f.getType().getConstructor(String.class);
ctor = type.getConstructor(String.class);
return ctor.newInstance(str);
} catch (NoSuchMethodException e) {
logger.fatal("constructFromString:NoSuchMethodException: cannot convert field " + f.toString());
@ -396,7 +463,6 @@ public class ArgumentParser {
logger.fatal("constructFromString:InstantiationException: cannot convert field " + f.toString());
throw new RuntimeException("constructFromString:InstantiationException: Failed conversion " + e.getMessage());
}
}
}

2
java/src/org/broadinstitute/sting/utils/cmdLine/CommandLineProgram.java
View File

@ -258,7 +258,7 @@ public abstract class CommandLineProgram {
/**
* Pass along a new set of valid command line arguments. In this case,
* probably a class with @argument or @flag annotations.
* probably a class with @argument annotations.
* @param source
*/
private void addArgumentSource( Object source ) {