[Biopython-dev] [Bug 2866] SQLite support for BioSQL

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2866





------- Comment #14 from cymon.cox at gmail.com  2009-12-12 13:12 EST -------
(In reply to comment #11)
> I will be able to test the effect of your changes on MySQL, hopefully Cymon
> can do this on PostgreSQL - not that I anticipate and regressions, but best
> to be sure ;)

Is SQLite ":memory:" TESTDB working for you on Brads branch?

It fails for me, all else is fin (incl the SQLite file db). 

[cymon at spiro Tests]$ python test_BioSQL_SeqIO.py
Connecting to database
Removing existing sub-database 'biosql-seqio-test' (if exists)
Traceback (most recent call last):
  File "test_BioSQL_SeqIO.py", line 134, in <module>
    if db_name in server.keys():
  File "/home/cymon/git/biopython-github-master/BioSQL/BioSeqDatabase.py", line
123, in keys
    return self.adaptor.list_biodatabase_names()
  File "/home/cymon/git/biopython-github-master/BioSQL/BioSeqDatabase.py", line
306, in list_biodatabase_names
    "SELECT name FROM biodatabase")
  File "/home/cymon/git/biopython-github-master/BioSQL/BioSeqDatabase.py", line
355, in execute_and_fetch_col0
    self.execute(sql, args or ())
  File "/home/cymon/git/biopython-github-master/BioSQL/BioSeqDatabase.py", line
336, in execute
    self.dbutils.execute(self.cursor, sql, args)
  File "/home/cymon/git/biopython-github-master/BioSQL/DBUtils.py", line 53, in
execute
    cursor.execute(sql, args or ())
sqlite3.OperationalError: no such table: biodatabase


Perhaps its my sqlite installation - I'm not familiar with it:

[cymon at spiro BioSQL]$ dpkg -l|egrep sqlite
ii  libmono-sqlite2.0-cil                2.4.2.3+dfsg-2                        
    Mono Sqlite library (for CLI 2.0)
ii  libsqlite0                           2.8.17-6build1                        
    SQLite shared library
ii  libsqlite3-0                         3.6.16-1ubuntu1                       
    SQLite 3 shared library
ii  sqlite3                              3.6.16-1ubuntu1                       
    A command line interface for SQLite 3

C.


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