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Fix for GSA-44...don't throw exception when user specifies -h. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@742 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-05-18 00:42:00 +00:00
parent d35e20ce21
commit e6ce80c8e3
2 changed files with 73 additions and 25 deletions
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42
java/src/org/broadinstitute/sting/utils/cmdLine/CommandLineProgram.java
View File

@ -166,17 +166,31 @@ public abstract class CommandLineProgram {
if( clp.canAddArgumentsDynamically() ) {
// if the command-line program can toss in extra args, fetch them and reparse the arguments.
parser.parse(args);
parser.validate( EnumSet.of(ParsingEngine.ValidationType.InvalidArgument) );
// Allow invalid and missing required arguments to pass this validation step.
// - InvalidArgument in case these arguments are specified by plugins.
// - MissingRequiredArgument in case the user requested help. Handle that later, once we've
// determined the full complement of arguments.
parser.validate( EnumSet.of(ParsingEngine.ValidationType.MissingRequiredArgument,
ParsingEngine.ValidationType.InvalidArgument) );
parser.loadArgumentsIntoObject( clp );
Class[] argumentSources = clp.getArgumentSources();
for( Class argumentSource: argumentSources )
parser.addArgumentSource( clp.getArgumentSourceName(argumentSource), argumentSource );
parser.parse(args);
if( isHelpPresent( clp, parser ) )
printHelpAndExit( clp, parser );
parser.validate();
}
else {
parser.parse(args);
if( isHelpPresent( clp, parser ) )
printHelpAndExit( clp, parser );
parser.validate();
parser.loadArgumentsIntoObject( clp );
}
@ -202,12 +216,6 @@ public abstract class CommandLineProgram {
//logger.removeAllAppenders();
}
// they asked for help, give it to them
if (clp.help) {
parser.printHelp( clp.getRunningInstructions() );
System.exit(1);
}
// if they specify a log location, output our data there
if (clp.toFile != null) {
FileAppender appender = null;
@ -337,6 +345,26 @@ public abstract class CommandLineProgram {
System.out.printf("%s%n", msg);
}
/**
* Do a cursory search for the given argument.
* @param clp Instance of the command-line program.
* @param parser Parser
* @return True if help is present; false otherwise.
*/
private static boolean isHelpPresent( CommandLineProgram clp, ParsingEngine parser ) {
return parser.isArgumentPresent("help");
}
/**
* Print help and exit.
* @param clp Instance of the command-line program.
* @param parser True if help is present; false otherwise.
*/
private static void printHelpAndExit( CommandLineProgram clp, ParsingEngine parser ) {
parser.printHelp( clp.getRunningInstructions() );
System.exit(0);
}
/**
* used to indicate an error occured
* @param msg the message to display

56
java/src/org/broadinstitute/sting/utils/cmdLine/ParsingEngine.java
View File

@ -95,6 +95,18 @@ public class ParsingEngine {
argumentDefinitions.add( new ArgumentDefinitionGroup(sourceName, argumentsFromSource) );
}
/**
* Do a cursory search to see if an argument with the given name is present.
* @param argumentFullName full name of the argument.
* @return True if the argument is present. False otherwise.
*/
public boolean isArgumentPresent( String argumentFullName ) {
ArgumentDefinition definition =
argumentDefinitions.findArgumentDefinition(argumentFullName,ArgumentDefinitions.FullNameDefinitionMatcher);
return argumentMatches.hasMatch(definition);
}
/**
* Parse the given set of command-line arguments, returning
* an ArgumentMatches object describing the best fit of these
@ -214,26 +226,34 @@ public class ParsingEngine {
* @param object Object into which to add arguments.
*/
public void loadArgumentsIntoObject( Object object ) {
for( ArgumentMatch match: argumentMatches ) {
ArgumentDefinition definition = match.definition;
for( ArgumentMatch match: argumentMatches )
loadArgumentIntoObject( match, object );
}
// A null definition might be in the list if some invalid arguments were passed in but we
// want to load in a subset of data for better error reporting. Ignore null definitions.
if( definition == null )
continue;
/**
* Loads a single argument into the object.
* @param argument Argument to load into the object.
* @param object Target for the argument.
*/
public void loadArgumentIntoObject( ArgumentMatch argument, Object object ) {
ArgumentDefinition definition = argument.definition;
if( definition.sourceClass.isAssignableFrom(object.getClass()) ) {
try {
definition.sourceField.setAccessible(true);
if( !isArgumentFlag(definition) )
definition.sourceField.set( object, constructFromString( definition.sourceField, match.values() ) );
else
definition.sourceField.set( object, true );
}
catch( IllegalAccessException ex ) {
//logger.fatal("processArgs: cannot convert field " + field.toString());
throw new StingException("processArgs: Failed conversion " + ex.getMessage(), ex);
}
// A null definition might be in the list if some invalid arguments were passed in but we
// want to load in a subset of data for better error reporting. Ignore null definitions.
if( definition == null )
return;
if( definition.sourceClass.isAssignableFrom(object.getClass()) ) {
try {
definition.sourceField.setAccessible(true);
if( !isArgumentFlag(definition) )
definition.sourceField.set( object, constructFromString( definition.sourceField, argument.values() ) );
else
definition.sourceField.set( object, true );
}
catch( IllegalAccessException ex ) {
//logger.fatal("processArgs: cannot convert field " + field.toString());
throw new StingException("processArgs: Failed conversion " + ex.getMessage(), ex);
}
}
}