zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Fixed: GSA-392 @arguments with just a short name get the wrong argument bindings 

-- Now blows up if an argument begins with -.  Implementation isn't pretty, as it actually blows up during Queue extension creation with a somewhat obscure error message but at least its something.
This commit is contained in:
Mark DePristo 2012-08-17 10:35:25 -04:00
parent 4c0f198d48
commit a3d2764d11
1 changed files with 17 additions and 0 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

17
public/java/src/org/broadinstitute/sting/commandline/ArgumentDefinition.java
View File

@ -26,6 +26,7 @@
package org.broadinstitute.sting.commandline; package org.broadinstitute.sting.commandline;
import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import java.lang.annotation.Annotation; import java.lang.annotation.Annotation;
import java.util.List; import java.util.List;
@ -147,6 +148,9 @@ public class ArgumentDefinition {
this.exclusiveOf = exclusiveOf; this.exclusiveOf = exclusiveOf;
this.validation = validation; this.validation = validation;
this.validOptions = validOptions; this.validOptions = validOptions;
validateName(shortName);
validateName(fullName);
} }
/** /**
@ -192,6 +196,9 @@ public class ArgumentDefinition {
else else
shortName = null; shortName = null;
validateName(shortName);
validateName(fullName);
this.ioType = ioType; this.ioType = ioType;
this.argumentType = argumentType; this.argumentType = argumentType;
this.fullName = fullName; this.fullName = fullName;
@ -277,4 +284,14 @@ public class ArgumentDefinition {
String validation = (String)CommandLineUtils.getValue(annotation, "validation"); String validation = (String)CommandLineUtils.getValue(annotation, "validation");
return validation.trim().length() > 0 ? validation.trim() : null; return validation.trim().length() > 0 ? validation.trim() : null;
} }
/**
* Make sure the argument's name is valid
*
* @param name
*/
private void validateName(final String name) {
if ( name != null && name.startsWith("-") )
throw new ReviewedStingException("Invalid argument definition: " + name + " begins with a -");
}
} }