471059f48d7e0d93419bebfb79c379dde343fcb1
mmaddren
  Tue Apr 10 12:11:08 2012 -0700
removed CRLF from encode and fixed a small error in cv.py
diff --git python/lib/ucscgenomics/cv.py python/lib/ucscgenomics/cv.py
index 7709a32..0fc7b9f 100644
--- python/lib/ucscgenomics/cv.py
+++ python/lib/ucscgenomics/cv.py
@@ -57,31 +57,31 @@
         '''wrapper function for raising exception'''
         raise exception
 
     def readStanza(self, stanza, key=None):
         '''overriden method from RaFile which makes specialized stanzas based on type'''
         entry = CvStanza()
 
         key, val = entry.readStanza(stanza)
         return key, val, entry
 
 
     def validate(self):
         '''base validation method which calls all stanzas' validate'''
         for stanza in self.itervalues():
             stanza.validate(self)
-        print self.missingTypes
+        #print self.missingTypes
 
     def getTypeOfTermStanza(self, type):
         types = self.filter(lambda s: s['term'] == type and s['type'] == 'typeOfTerm', lambda s: s)
         if len(types) != 1:
             return None
         return types[0]
                 
 class CvStanza(ra.RaStanza):
     '''base class for a single stanza in the cv, which adds validation'''
     
     def __init__(self):
         ra.RaStanza.__init__(self)
 
     def readStanza(self, stanza):
         '''
@@ -129,33 +129,30 @@
             else:
                 self[raKey] = raVal
         
     def validate(self, cvfile):
         type = self['type']
         if self['type'] == 'Cell Line': # :(
             if 'organism' in self and self['organism'] == 'human':
                 type = 'cellType'
             elif 'organism' in self and self['organism'] == 'mouse':
                 type = 'mouseCellType'
             else:
                 cvfile.handler(OrganismError(self))
         
         typeStanza = cvfile.getTypeOfTermStanza(type)
         if typeStanza == None:
-            #print cvfile.filter2(lambda s: s['type'] == 'typeOfTerm').keys()
-            #print '>%s<' % cvfile['mouseCellType ']['term']
-            #print '>%s<' % cvfile['mouseCellType ']['type']
             cvfile.handler(InvalidTypeError(self, self['type'] + '(%s)' % type))
             return
         required = list()
         if 'requiredVars' in typeStanza:
             required = extractList(typeStanza['requiredVars'])
         optional = list()
         if 'optionalVars' in typeStanza:
             optional = extractList(typeStanza['optionalVars'])
         
         self.checkMandatory(cvfile, required)
         required.extend(optional)
         self.checkExtraneous(cvfile, required)
         self.checkDuplicates(cvfile)
         
         for key in self.iterkeys():