[pygr-notify] Issue 47 in pygr: KeyError on deleting pygr.Data resource

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Issue 47: KeyError on deleting pygr.Data resource
http://code.google.com/p/pygr/issues/detail?id=47

New issue report by robert.d.kirkpatrick:
What steps will reproduce the problem?
1. Save a resource to pygr.Data with no SCHEMA
2. Delete the resource (i.e. via pygr.Data.deleteResource )


What is the expected output? What do you see instead?
Expected output is nothing.  We see a KeyError instead:

Traceback (most recent call last):
   File "/Users/Robby/pygr-dev/bin/python", line 23, in <module>
     execfile(sys.argv[0])
   File "/Users/Robby/Desktop/delete-resource-schema-error.py", line 32, in
<module>
     remRes()
   File "/Users/Robby/Desktop/delete-resource-schema-error.py", line 26, in
remRes
     pygr.Data.deleteResource(sqltab)
   File
"/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/pygr-0.7-py2.5-macosx-10.3-fat.egg/pygr/Data.py",
line 864, in deleteResource
     self.delSchema(id,layer)
   File
"/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/pygr-0.7-py2.5-macosx-10.3-fat.egg/pygr/Data.py",
line 1019, in delSchema
     d=db.getschema(id) # GET THE EXISTING SCHEMA
   File
"/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/pygr-0.7-py2.5-macosx-10.3-fat.egg/pygr/Data.py",
line 536, in getschema
     return self.db['SCHEMA.'+id]
   File
"/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/shelve.py",  
line
112, in __getitem__
     f = StringIO(self.dict[key])
   File
"/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/bsddb/__init__.py",
line 223, in __getitem__
     return _DeadlockWrap(lambda: self.db[key])  # self.db[key]
   File
"/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/bsddb/dbutils.py",
line 62, in DeadlockWrap
     return function(*_args, **_kwargs)
   File
"/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/bsddb/__init__.py",
line 223, in <lambda>
     return _DeadlockWrap(lambda: self.db[key])  # self.db[key]
KeyError: 'SCHEMA.Bio.Seq.Genome.ECOLI'


What version of the product are you using? On what operating system?
Using MacOS v10.4 or v10.5
git commit # c42925322ab8258b40bd09fd9bf0c871c6ebf75a


Please provide any additional information below.
The pygr.Data resource does in fact get deleted but a call is made to
delSchema() with a pygr.Data resource id of 'SCHEMA.name.of.resource'.  If
no schema was ever saved, this resource will never exist and thus retrieval
via "d=db.getschema(id) # GET THE EXISTING SCHEMA" will always produce the
KeyError.

See attached script and modified ecoli 'genome' file to reproduce.



Attachments:
	ECOLI.fna  2.9 KB
	delete-resource-schema-error.py  645 bytes


Issue attributes:
	Status: New
	Owner: ----
	Labels: Type-Defect Priority-Medium

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