You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
What steps will reproduce the problem?
Set attrAlias when instantiating sqlgraph.SQLGraph.
What is the expected output? What do you see instead?
Should get a SQLGraph object. Instead, get error:
In [10]: attrAlias
Out[10]: {'edge_id': 'cid', 'source_id': 'ensGtp_gene', 'target_id': 'cid'}
In [11]: g = sqlgraph.SQLGraph("MOUSE_mm9_ensGene", serverInfo=server_info,
attrAlias=attrAlias)
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
/home/kdaily/<ipython console> in <module>()
/home/dock/shared_libraries/lx64/pkgs/pythonsandbox/2.6.2/lib/python2.6/s
ite-packages/pygr-0.8.1-py2.6-linux-x86_64.egg/pygr/sqlgraph.py in
__init__(self, name, *l, **kwargs)
1477 except KeyError:
1478 pass
-> 1479 SQLTableMultiNoCache.__init__(self, name, *l, **tableArgs)
1480 self.sourceSQL = self._attrSQL('source_id')
1481 self.targetSQL = self._attrSQL('target_id')
/home/dock/shared_libraries/lx64/pkgs/pythonsandbox/2.6.2/lib/python2.6/s
ite-packages/pygr-0.8.1-py2.6-linux-x86_64.egg/pygr/sqlgraph.py in
__init__(self, *args, **kwargs)
1170 def __init__(self, *args, **kwargs):
1171 SQLTableBase.__init__(self, *args, **kwargs)
-> 1172 self.distinct_key = self._attrSQL(self._distinct_key)
1173 if not self.orderBy:
1174 self.orderBy = 'GROUP BY %s ORDER BY %s' %
(self.distinct_key,
/home/dock/shared_libraries/lx64/pkgs/pythonsandbox/2.6.2/lib/python2.6/s
ite-packages/pygr-0.8.1-py2.6-linux-x86_64.egg/pygr/sqlgraph.py in
_attrSQL(self, attr, sqlColumn, columnNumber)
678 except KeyError:
679 raise AttributeError('attribute %s not a valid column \
--> 680 or alias in %s' % (attr, self.name))
681 if sqlColumn: # ENSURE THAT THIS TRULY MAPS TO A
COLUMN NAME IN THE DB
682 try: # CHECK IF field IS COLUMN NUMBER
AttributeError: attribute source_id not a valid column
or alias in MOUSE_mm9_ensGene
Please use labels and text to provide additional information.
Looks like the attrAlias isn't getting put into the right keyword arguments
set: in SQLGraph.__init__
Looking at the values of the output of split_kwargs:
tableArgs = {'serverInfo': <pygr.sqlgraph.MySQLServerInfo object at
0xf85ed0>}
graphArgs = {'attrAlias': {'source_id': 'ensGtp_gene', 'target_id': 'cid',
'edge_id': 'cid'}}
AttrAlias = None
I changed from:
def __init__(self, name, *l, **kwargs):
graphArgs, tableArgs = split_kwargs(kwargs,
('attrAlias', 'defaultColumnType', 'columnAttrs',
'sourceDB', 'targetDB', 'edgeDB', 'simpleKeys',
'unpack_edge', 'edgeDictClass', 'graph'))
to:
def __init__(self, name, *l, **kwargs):
graphArgs, tableArgs = split_kwargs(kwargs,
('defaultColumnType', 'columnAttrs',
'sourceDB', 'targetDB', 'edgeDB', 'simpleKeys',
'unpack_edge', 'edgeDictClass', 'graph'))
and it worked!
Original issue reported on code.google.com by kmda...@gmail.com on 27 May 2010 at 10:17
The text was updated successfully, but these errors were encountered:
Original issue reported on code.google.com by
kmda...@gmail.com
on 27 May 2010 at 10:17The text was updated successfully, but these errors were encountered: