AFAIK this is only on my machine. I'll do some cleanup and see if I can get
things to go more smoothly. I only asked about the indentation because most
of that code is pretty greek to me and I needed a starting point to
understand the error. I'll look at it again with your explanation and see
if can grok it a bit more.
On Tue, Sep 9, 2008 at 1:07 PM, Christopher Lee <[EMAIL PROTECTED]> wrote:
>
>
> On Sep 9, 2008, at 12:42 PM, Rob Kirkpatrick wrote:
>
> > Hi Guys,
> >
> > I've run into this error when trying to run some of Jenny's
> > doctests. When I look in the code of sqlgraph.py", line 269 seems
> > to be at the wrong indentation level. I get a new set of errors
> > when I indent that line, so I'm not sure if this is part of my
> > problem or not... Comments?
>
> Hi Rob,
> what makes you think line 269 is mis-indented? It looks right to me;
> __init__() must always bind its itemClass as a subclass, which is what
> self.objclass() does... Note that if itemClass is None,
> self.objclass() just uses self.itemClass (typically provided by the
> class definition).
>
> more comments below...
>
> >
> >
> > **********************************************************************
> > File "/Users/Robby/pyensembl-0.1.0/build/lib/ensembl/adaptor.py",
> > line 274, in ensembl.adaptor.ExonAdaptor
> > Failed example:
> > slice = coreDBAdaptor.fetch_slice_by_region('chromosome', '1',
> > end=100000, strand = -1)
> > Exception raised:
> > Traceback (most recent call last):
> > File "/Library/Frameworks/Python.framework/Versions/2.5/lib/
> > python2.5/doctest.py", line 1212, in __run
> > compileflags, 1) in test.globs
> > File "<doctest ensembl.adaptor.ExonAdaptor[5]>", line 1, in
> > <module>
> > slice = coreDBAdaptor.fetch_slice_by_region('chromosome',
> > '1', end=100000, strand = -1)
> > File "/Users/Robby/pyensembl-0.1.0/build/lib/ensembl/
> > adaptor.py", line 688, in fetch_slice_by_region
> > sr = self._get_seqregion()
> > File "/Users/Robby/pyensembl-0.1.0/build/lib/ensembl/
> > adaptor.py", line 584, in _get_seqregion
> > seqRegion = self._create_seqregion()
> > File "/Users/Robby/pyensembl-0.1.0/build/lib/ensembl/
> > adaptor.py", line 565, in _create_seqregion
> > dnaAdaptor = self.get_adaptor('dna')
> > File "/Users/Robby/pyensembl-0.1.0/build/lib/ensembl/
> > adaptor.py", line 460, in get_adaptor
> > tbAdaptor = adaptorClass(name, itemClass=rowClass,
> > serverInfo=self.conn)
> > File "/Users/Robby/pyensembl-0.1.0/build/lib/ensembl/
> > adaptor.py", line 214, in __init__
> > sqlgraph.SQLTable.__init__(self, name,
> > itemSliceClass=seqdb.SeqDBSlice, attrAlias=dict(seq='sequence'),
> > **kwargs)
> > File "/Library/Frameworks/Python.framework/Versions/2.5/lib/
> > python2.5/site-packages/pygr-0.7-py2.5-macosx-10.3-fat.egg/pygr/
> > sqlgraph.py", line 269, in __init__
> > self.objclass(itemClass) # NEED TO SUBCLASS OUR ITEM CLASS
> > File "/Library/Frameworks/Python.framework/Versions/2.5/lib/
> > python2.5/site-packages/pygr-0.7-py2.5-macosx-10.3-fat.egg/pygr/
> > sqlgraph.py", line 352, in objclass
> > subclassArgs=dict(db=self)) # bind itemClass
> > File "/Library/Frameworks/Python.framework/Versions/2.5/lib/
> > python2.5/site-packages/pygr-0.7-py2.5-macosx-10.3-fat.egg/pygr/
> > classutil.py", line 217, in get_bound_subclass
> > subclass_init(**subclassArgs)
> > TypeError: unbound method _init_subclass() must be called with
> > shadowClass instance as first argument (got nothing instead)
>
> This error message seems to say that the itemClass has an
> _init_subclass() attribute that is callable, but which has not been
> "decorated" as a classmethod as it must be. For correct examples of
> how to do this, see seqdb.FileDBSequence or sqlgraph.TupleO. I guess
> I would need to scrutinize Jenny's rowClass code to verify if I'm
> interpreting this right.
>
> I don't see how this error could pass a test suite; it will die
> whenever it tries to construct an instance of this table class. Is
> this only happening on your computer, or does Jenny get the same error?
>
> -- Chris
>
> >
>
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