[pygr-notify] Issue 54 in pygr: sqlgraph.GraphView unpickle-able error

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Status: Accepted
Owner: jqian.ubc
CC: cjlee112
Labels: Type-Defect Priority-High

New issue 54 by jqian.ubc: sqlgraph.GraphView unpickle-able error
http://code.google.com/p/pygr/issues/detail?id=54

What steps will reproduce the problem?

Python 2.5.2 (r252:60911, Aug  8 2008, 09:22:44)
[GCC 4.3.1] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import pygr.Data
>>> from ensembl import adaptor
>>> from pygr import sqlgraph
>>> conn = pygr.Data.Bio.Server.Ensembl.Ensembldb()
>>> translationTB =
sqlgraph.SQLTable('homo_sapiens_core_47_36i.translation',
itemClass=sqlgraph.TupleO, serverInfo=conn)
>>> exonTB = sqlgraph.SQLTable('homo_sapiens_core_47_36i.exon',
itemClass=sqlgraph.TupleO, serverInfo=conn)
>>> cursor = translationTB.cursor
>>> sql_statement = 'SELECT t3.exon_id FROM
homo_sapiens_core_47_36i.translation AS tr,
homo_sapiens_core_47_36i.exon_transcript AS t1,
homo_sapiens_core_47_36i.exon_transcript AS t2,
homo_sapiens_core_47_36i.exon_transcript AS t3 WHERE tr.translation_id = %s
AND tr.transcript_id = t1.transcript_id AND t1.transcript_id =
t2.transcript_id AND t2.transcript_id = t3.transcript_id AND t1.exon_id =
tr.start_exon_id AND t2.exon_id = tr.end_exon_id AND t3.rank >= t1.rank AND
t3.rank <= t2.rank ORDER BY t3.rank'
>>> translationExons = sqlgraph.GraphView(translationTB, exonTB,
sql_statement, cursor)
>>> translation = translationTB[15121]
>>> exons = translationExons[translation]
>>> for e in exons:
...     print e.id
...
95160
95020
95035
95172
95110
95101
95088
95081
95069
95059
95050
>>> translationExons.__doc__ = 'Ensembl translation -> exons GraphView,
homo_sapiens_core_47_36i'
>>>
pygr.Data.Bio.Ensembl.GraphView.homo_sapiens_core_47_36i.translationExons =
translationExons
>>> pygr.Data.save()

qing at 1[ensembl]$ python -i
Python 2.5.2 (r252:60911, Aug  8 2008, 09:22:44)
[GCC 4.3.1] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import pygr.Data
>>> from ensembl import adaptor
>>> from pygr import sqlgraph
>>> tExons =
pygr.Data.Bio.Ensembl.GraphView.homo_sapiens_core_47_36i.translationExons()
Traceback (most recent call last):
   File "<stdin>", line 1, in <module>
   File "/home/qing/workspace2008/pygr/pygr/Data.py", line 1103, in __call__
     return getResource(self._path,layer=self._layer,*args,**kwargs)
   File "/home/qing/workspace2008/pygr/pygr/Data.py", line 725, in __call__
     obj = db.__getitem__(id,download) # TRY TO OBTAIN FROM THIS DATABASE
   File "/home/qing/workspace2008/pygr/pygr/Data.py", line 479, in  
__getitem__
     obj = self.finder.loads(s) # RUN THE UNPICKLER ON THE STRING
   File "/home/qing/workspace2008/pygr/pygr/Data.py", line 669, in loads
     obj=unpickler.load() # ACTUALLY UNPICKLE THE DATA
   File "/usr/lib/python2.5/pickle.py", line 858, in load
     dispatch[key](self)
   File "/usr/lib/python2.5/pickle.py", line 1217, in load_build
     setstate(state)
   File "/home/qing/workspace2008/pygr/pygr/classutil.py", line 148, in
standard_setstate
     self.__init__(**state)
TypeError: __init__() got an unexpected keyword argument 'serverInfo'


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