Hi,
I checked out the most up-to-date copy of pygr code from the git
repository. Then I ran the Python Ensembl API doctests with it. Sadly,
nearly all of the doctests failed. Last night, all of the tests passed just
fine. And I have not touched any of the ensembl modules ever since. The
first error message I got was the following:
File "/home/qing/workspace2008/pygr_new/pygr/ensembl/datamodel.py", line
267, in ensembl.datamodel.Exon
Failed example:
exonAdaptor = coreDBAdaptor.get_adaptor('exon')
Exception raised:
Traceback (most recent call last):
File "/usr/lib/python2.5/doctest.py", line 1228, in __run
compileflags, 1) in test.globs
File "<doctest ensembl.datamodel.Exon[2]>", line 1, in <module>
exonAdaptor = coreDBAdaptor.get_adaptor('exon')
File "/home/qing/workspace2008/pygr_new/pygr/ensembl/adaptor.py", line
468, in get_adaptor
tbAdaptor = adaptorClass(name, itemClass=rowClass,
serverInfo=self.conn)
File "/home/qing/workspace2008/pygr_new/pygr/pygr/sqlgraph.py", line
234, in __init__
cursor = serverInfo.cursor()
File "/home/qing/workspace2008/pygr_new/pygr/pygr/sqlgraph.py", line
1399, in cursor
self._cursor = connect(**self.kwargs).cursor()
File "/var/lib/python-support/python2.5/MySQLdb/__init__.py", line 74,
in Connect
return Connection(*args, **kwargs)
File "/var/lib/python-support/python2.5/MySQLdb/connections.py", line
170, in __init__
super(Connection, self).__init__(*args, **kwargs2)
OperationalError: (2013, "Lost connection to MySQL server at 'reading
authorization packet', system error: 0")
Any suggestion will be highly appreciated.
jenny
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