On Tue, Sep 09, 2008 at 01:14:29PM -0700, Rob Kirkpatrick wrote:
-> 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.
Hi, Rob,
using
% nosetests --with-doctest
everything works for me with the latest version of pygr.
cheers,
--titus
-> > > 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
-> >
-> > >
-> >
->
-> ->
--
C. Titus Brown, [EMAIL PROTECTED]
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