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Oops. While writing command-line argument docs, I realized I introduced 

a regression in default value handling.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@226 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-03-30 18:51:39 +00:00
parent 875802e8fc
commit 36f851362e
2 changed files with 47 additions and 10 deletions
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1
java/src/org/broadinstitute/sting/utils/cmdLine/Argument.java
View File

@ -24,4 +24,5 @@ public @interface Argument {
String doc() default "";
boolean required() default true;
String exclusive() default "";
String defaultValue() default "";
}

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

@ -297,17 +297,17 @@ public class ArgumentParser {
// logger.info("We have " + opts.size() + " options");
for (Option opt : opts) {
//logger.info("looking at " + m_storageLocations.get(opt.getLongOpt()));
Field field = m_storageLocations.get(opt.getLongOpt());
// Check to see if the object contains the specified field. Iterate through
// the array rather than doing a name lookup in case field names overlap between
// multiple classes in the application.
List<Field> fieldsInObj = Arrays.asList(obj.getClass().getFields());
if( !fieldsInObj.contains(field) )
continue;
if (cmd.hasOption(opt.getOpt())) {
//logger.info("looking at " + m_storageLocations.get(opt.getLongOpt()));
Field field = m_storageLocations.get(opt.getLongOpt());
// Check to see if the object contains the specified field. Iterate through
// the array rather than doing a name lookup in case field names overlap between
// multiple classes in the application.
List<Field> fieldsInObj = Arrays.asList(obj.getClass().getFields());
if( !fieldsInObj.contains(field) )
continue;
try {
if (opt.hasArg())
field.set(obj, constructFromString(field, cmd.getOptionValues(opt.getOpt())));
@ -318,9 +318,45 @@ public class ArgumentParser {
throw new RuntimeException("processArgs: Failed conversion " + e.getMessage());
}
}
else {
if( hasDefaultValue( field ) ) {
try {
field.set(obj, constructFromString(field, new String[] { getDefaultValue(field) }) );
}
catch (IllegalAccessException e) {
logger.fatal("processArgs: cannot convert field " + field.toString());
throw new RuntimeException("processArgs: Failed conversion " + e.getMessage());
}
}
}
}
}
/**
* Returns whether this field is annotated with a default value.
* @param f the field to check for a default.
* @return whether a default value exists.
*/
private boolean hasDefaultValue( Field f ) {
return getDefaultValue( f ) != null;
}
/**
* Gets the String representation for the default value of a given argument.
* @return The string of a default value, or null if no default exists.
*/
private String getDefaultValue( Field f ) {
Argument arg = f.getAnnotation( Argument.class );
if( arg == null )
return null;
String defaultValue = arg.defaultValue().trim();
if( defaultValue.length() == 0 )
return null;
return defaultValue;
}
/**
* Simple class to wrap the posix parser and get access to the parsed cmd object.
*/