20e6eff593096b1ec381de4ee5058c5edafd2bba
mmaddren
  Tue Aug 30 15:47:54 2011 -0700
added protocol checking functionality, partial support for deprecated, and revised the error messages to be more consistent
diff --git python/programs/cvValidate/cvValidate python/programs/cvValidate/cvValidate
index 6deec4d..8bee272 100755
--- python/programs/cvValidate/cvValidate
+++ python/programs/cvValidate/cvValidate
@@ -1,22 +1,31 @@
 #!/hive/groups/encode/dcc/bin/python
 import sys
+import argparse
 from ucscgenomics.cvfile.CvFile import *
 
 class validate(object):
 	"""validation script that calls cv.validate and then puts all its errors into a list"""
 
 	def __init__(self):
+	
+		parser = argparse.ArgumentParser(description = 'Validates the controlled vocabulary file')
+		parser.add_argument('-t', '--trackPath', help='Overrides the default track path ~/kent/src/hg/makeDb/trackDb/')
+		parser.add_argument('-p', '--protocolPath', help='Overrides the default protocol path ~/htdocsExtras/ENCODE/')
+		parser.add_argument('-n', '--nowarn', action='store_true', default=False, help='Suppress all warnings, only display breaking errors')
+		
+		args = parser.parse_args(sys.argv[1:])
+	
 		self.errors = list()
-		self.cv = CvFile(sys.argv[1], self.addtoerrs)	
+		self.cv = CvFile(args.trackPath, self.addtoerrs, args.protocolPath)	
 		self.cv.validate()
 		
 		for err in self.errors:
 			print err
 			
 	def addtoerrs(self, exception):
 		self.errors.append(exception)
 
 if __name__ == '__main__':
     val = validate()