[Biopython-dev] BioSQL
Michiel De Hoon
mdehoon at c2b2.columbia.edu
Tue Nov 20 02:34:09 UTC 2007
With the Biopython currently in CVS, I get an error from test_BioSQL:
======================================================================
FAIL: test_BioSQL
----------------------------------------------------------------------
Traceback (most recent call last):
File "run_tests.py", line 151, in runTest
self.runSafeTest()
File "run_tests.py", line 188, in runSafeTest
expected_handle)
File "run_tests.py", line 289, in compare_output
"\nOutput : "+`output_line` + "\nExpected: "+`expected_line`
AssertionError:
Output : 'Load SeqRecord objects into a BioSQL database. ... ERROR\n'
Expected: 'Load SeqRecord objects into a BioSQL database. ... ok\n'
----------------------------------------------------------------------
If I run test_BioSQL.py directly, I expect to get a
Bio.MissingExternalDependencyError (as with Biopython 1.44):
Traceback (most recent call last):
File "test_BioSQL.py", line 40, in <module>
raise Bio.MissingExternalDependencyError(message)
Bio.MissingExternalDependencyError: Enable tests in Tests/test_BioSQL.py (not
im
portant if you do not plan to use BioSQL).
---------------------------------------------------------------------------
With Biopython now in CVS, test_BioSQL.py generates the following output:
$ python test_BioSQL.py
Load SeqRecord objects into a BioSQL database. ... ERROR
Get a list of all items in the database. ... ERROR
Test retrieval of items using various ids. ... ERROR
Make sure Seqs from BioSQL implement the right interface. ... ERROR
Check SeqFeatures of a sequence. ... ERROR
Make sure SeqRecords from BioSQL implement the right interface. ... ERROR
Check that slices of sequences are retrieved properly. ... ERROR
Make sure all records are correctly loaded. ... ERROR
Indepth check that SeqFeatures are transmitted through the db. ... ERROR
======================================================================
ERROR: Load SeqRecord objects into a BioSQL database.
----------------------------------------------------------------------
Traceback (most recent call last):
File "test_BioSQL.py", line 275, in setUp
create_database()
File "test_BioSQL.py", line 56, in create_database
host = DBHOST)
File "/usr/lib/python2.5/site-packages/BioSQL/BioSeqDatabase.py", line 28,
in
open_database
module = __import__(driver)
File "build/bdist.cygwin-1.5.24-i686/egg/MySQLdb/__init__.py", line 19, in
<mo
dule>
File "build/bdist.cygwin-1.5.24-i686/egg/_mysql.py", line 7, in <module>
File "build/bdist.cygwin-1.5.24-i686/egg/_mysql.py", line 6, in
__bootstrap__
ImportError: Permission denied
======================================================================
ERROR: Get a list of all items in the database.
----------------------------------------------------------------------
Traceback (most recent call last):
File "test_BioSQL.py", line 128, in setUp
load_database(gb_handle)
File "test_BioSQL.py", line 102, in load_database
create_database()
File "test_BioSQL.py", line 56, in create_database
host = DBHOST)
File "/usr/lib/python2.5/site-packages/BioSQL/BioSeqDatabase.py", line 28,
in
open_database
module = __import__(driver)
File "build/bdist.cygwin-1.5.24-i686/egg/MySQLdb/__init__.py", line 19, in
<mo
dule>
File "build/bdist.cygwin-1.5.24-i686/egg/_mysql.py", line 7, in <module>
File "build/bdist.cygwin-1.5.24-i686/egg/_mysql.py", line 6, in
__bootstrap__
ImportError: Permission denied
======================================================================
ERROR: Test retrieval of items using various ids.
----------------------------------------------------------------------
Traceback (most recent call last):
File "test_BioSQL.py", line 128, in setUp
load_database(gb_handle)
File "test_BioSQL.py", line 102, in load_database
create_database()
File "test_BioSQL.py", line 56, in create_database
host = DBHOST)
File "/usr/lib/python2.5/site-packages/BioSQL/BioSeqDatabase.py", line 28,
in
open_database
module = __import__(driver)
File "build/bdist.cygwin-1.5.24-i686/egg/MySQLdb/__init__.py", line 19, in
<mo
dule>
File "build/bdist.cygwin-1.5.24-i686/egg/_mysql.py", line 7, in <module>
File "build/bdist.cygwin-1.5.24-i686/egg/_mysql.py", line 6, in
__bootstrap__
ImportError: Permission denied
======================================================================
ERROR: Make sure Seqs from BioSQL implement the right interface.
----------------------------------------------------------------------
Traceback (most recent call last):
File "test_BioSQL.py", line 179, in setUp
load_database(gb_handle)
File "test_BioSQL.py", line 102, in load_database
create_database()
File "test_BioSQL.py", line 56, in create_database
host = DBHOST)
File "/usr/lib/python2.5/site-packages/BioSQL/BioSeqDatabase.py", line 28,
in
open_database
module = __import__(driver)
File "build/bdist.cygwin-1.5.24-i686/egg/MySQLdb/__init__.py", line 19, in
<mo
dule>
File "build/bdist.cygwin-1.5.24-i686/egg/_mysql.py", line 7, in <module>
File "build/bdist.cygwin-1.5.24-i686/egg/_mysql.py", line 6, in
__bootstrap__
ImportError: Permission denied
======================================================================
ERROR: Check SeqFeatures of a sequence.
----------------------------------------------------------------------
Traceback (most recent call last):
File "test_BioSQL.py", line 179, in setUp
load_database(gb_handle)
File "test_BioSQL.py", line 102, in load_database
create_database()
File "test_BioSQL.py", line 56, in create_database
host = DBHOST)
File "/usr/lib/python2.5/site-packages/BioSQL/BioSeqDatabase.py", line 28,
in
open_database
module = __import__(driver)
File "build/bdist.cygwin-1.5.24-i686/egg/MySQLdb/__init__.py", line 19, in
<mo
dule>
File "build/bdist.cygwin-1.5.24-i686/egg/_mysql.py", line 7, in <module>
File "build/bdist.cygwin-1.5.24-i686/egg/_mysql.py", line 6, in
__bootstrap__
ImportError: Permission denied
======================================================================
ERROR: Make sure SeqRecords from BioSQL implement the right interface.
----------------------------------------------------------------------
Traceback (most recent call last):
File "test_BioSQL.py", line 179, in setUp
load_database(gb_handle)
File "test_BioSQL.py", line 102, in load_database
create_database()
File "test_BioSQL.py", line 56, in create_database
host = DBHOST)
File "/usr/lib/python2.5/site-packages/BioSQL/BioSeqDatabase.py", line 28,
in
open_database
module = __import__(driver)
File "build/bdist.cygwin-1.5.24-i686/egg/MySQLdb/__init__.py", line 19, in
<mo
dule>
File "build/bdist.cygwin-1.5.24-i686/egg/_mysql.py", line 7, in <module>
File "build/bdist.cygwin-1.5.24-i686/egg/_mysql.py", line 6, in
__bootstrap__
ImportError: Permission denied
======================================================================
ERROR: Check that slices of sequences are retrieved properly.
----------------------------------------------------------------------
Traceback (most recent call last):
File "test_BioSQL.py", line 179, in setUp
load_database(gb_handle)
File "test_BioSQL.py", line 102, in load_database
create_database()
File "test_BioSQL.py", line 56, in create_database
host = DBHOST)
File "/usr/lib/python2.5/site-packages/BioSQL/BioSeqDatabase.py", line 28,
in
open_database
module = __import__(driver)
File "build/bdist.cygwin-1.5.24-i686/egg/MySQLdb/__init__.py", line 19, in
<mo
dule>
File "build/bdist.cygwin-1.5.24-i686/egg/_mysql.py", line 7, in <module>
File "build/bdist.cygwin-1.5.24-i686/egg/_mysql.py", line 6, in
__bootstrap__
ImportError: Permission denied
======================================================================
ERROR: Make sure all records are correctly loaded.
----------------------------------------------------------------------
Traceback (most recent call last):
File "test_BioSQL.py", line 329, in setUp
load_database(gb_handle)
File "test_BioSQL.py", line 102, in load_database
create_database()
File "test_BioSQL.py", line 56, in create_database
host = DBHOST)
File "/usr/lib/python2.5/site-packages/BioSQL/BioSeqDatabase.py", line 28,
in
open_database
module = __import__(driver)
File "build/bdist.cygwin-1.5.24-i686/egg/MySQLdb/__init__.py", line 19, in
<mo
dule>
File "build/bdist.cygwin-1.5.24-i686/egg/_mysql.py", line 7, in <module>
File "build/bdist.cygwin-1.5.24-i686/egg/_mysql.py", line 6, in
__bootstrap__
ImportError: Permission denied
======================================================================
ERROR: Indepth check that SeqFeatures are transmitted through the db.
----------------------------------------------------------------------
Traceback (most recent call last):
File "test_BioSQL.py", line 329, in setUp
load_database(gb_handle)
File "test_BioSQL.py", line 102, in load_database
create_database()
File "test_BioSQL.py", line 56, in create_database
host = DBHOST)
File "/usr/lib/python2.5/site-packages/BioSQL/BioSeqDatabase.py", line 28,
in
open_database
module = __import__(driver)
File "build/bdist.cygwin-1.5.24-i686/egg/MySQLdb/__init__.py", line 19, in
<mo
dule>
File "build/bdist.cygwin-1.5.24-i686/egg/_mysql.py", line 7, in <module>
File "build/bdist.cygwin-1.5.24-i686/egg/_mysql.py", line 6, in
__bootstrap__
ImportError: Permission denied
----------------------------------------------------------------------
Ran 9 tests in 0.140s
FAILED (errors=9)
Michiel de Hoon
Center for Computational Biology and Bioinformatics
Columbia University
1150 St Nicholas Avenue
New York, NY 10032
-----Original Message-----
From: biopython-dev-bounces at lists.open-bio.org on behalf of Peter
Sent: Mon 11/19/2007 9:05 AM
To: biopython-dev at lists.open-bio.org
Subject: [Biopython-dev] BioSQL
Dear list members,
As some of you may have guessed from recent bug activity, I've got
BioSQL up and running on my machine, using MySQL. I've even made a
start at updating the documentation:
http://www.biopython.org/wiki/BioSQL
Annoyingly the unit test (test_BioSQL.py) wasn't working, but I believe
that I have fixed that now in CVS. If any of the other developers have
BioSQL setup, could you please check out the latest code and double
check this for me. If you use something other than MySQL that would be
of particular interest.
Also, comments on the MySQL commit issue in Bug 2395 welcome!
http://bugzilla.open-bio.org/show_bug.cgi?id=2395
Peter
P.S. I've not yet sorted out bug 2396, I want to study how BioPerl
and/or BioJava handle this to make sure what ever I do is compatible.
http://bugzilla.open-bio.org/show_bug.cgi?id=2396
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