can you send me a script that causes the problem?
On Tue, Sep 16, 2008 at 11:00:36AM -0700, Rob Kirkpatrick wrote:
-> Looks like I'm getting the error specifically when I try to store the dna
-> table. If my code looks like:
->
-> serverRegistry = get_registry(host='ensembldb.ensembl.org',
-> user='anonymous')
-> coreDBAdaptor = serverRegistry.get_DBAdaptor('homo_sapiens', 'core',
-> '47_36i')
-> import pdb; pdb.set_trace()
-> aslice = coreDBAdaptor.fetch_slice_by_region('chromosome', '1', end=100000,
-> strand = -1)
->
-> And I set a breakpoint like this:
->
-> (Pdb) b pygr.classutil.get_bound_subclass
-> Breakpoint 1 at
->
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/pygr-0.7-py2.5-macosx-10.3-i386.egg/pygr/classutil.py:189
->
-> Then during the first "iteration" to save seqregion, things go fine, it then
-> chokes when it tries to save the DNA table....
->
-> (Pdb) c
-> >
->
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/pygr-0.7-py2.5-macosx-10.3-i386.egg/pygr/classutil.py(192)get_bound_subclass()
-> -> targetClass = getattr(obj,classattr)
-> (Pdb) l
-> 187
-> 188
-> 189 B def get_bound_subclass(obj, classattr='__class__', subname=None,
-> factories=(),
-> 190 attrDict=None, subclassArgs=None):
-> 191 'create a subclass specifically for obj to bind its shadow
-> attributes'
-> 192 -> targetClass = getattr(obj,classattr)
-> 193 try:
-> 194 if targetClass._shadowOwner is obj:
-> 195 return targetClass # already shadowed, so nothing to do
-> 196 except AttributeError: # not a shadow class, so just shadow it
-> 197 pass
-> (Pdb) print obj
-> <SQL table homo_sapiens_core_47_36i.seq_region>
-> (Pdb) print classattr
-> itemClass
-> (Pdb) print subname
-> homo_sapiens_core_47_36i.seq_region
-> (Pdb) print factories
-> ()
-> (Pdb) print attrDict
-> None
-> (Pdb) print subclassArgs
-> {'db': <SQL table homo_sapiens_core_47_36i.seq_region>}
-> (Pdb) c
-> >
->
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/pygr-0.7-py2.5-macosx-10.3-i386.egg/pygr/classutil.py(192)get_bound_subclass()
-> -> targetClass = getattr(obj,classattr)
-> (Pdb) print obj
-> <SQL table homo_sapiens_core_47_36i.dna>
-> (Pdb) print classattr
-> itemClass
-> (Pdb) print subname
-> homo_sapiens_core_47_36i.dna
-> (Pdb) print factories
-> ()
-> (Pdb) print attrDict
-> None
-> (Pdb) print subclassArgs
-> {'db': <SQL table homo_sapiens_core_47_36i.dna>}
-> (Pdb) c
-> TypeError: 'unbound method _init_subclass() must be called with shadowClass
-> instance as first argument (got nothing instead)'
-> > /Users/goober/pygr-dev/bin/python(23)<module>()
-> -> execfile(sys.argv[0])
-> (Pdb)
->
->
-> I'll keep looking to see if I can figure anything out...
->
-> ->
--
C. Titus Brown, [EMAIL PROTECTED]
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