[Biopython-dev] [Bug 1493] New: Failure to load a MySQL database using BioSQL

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

http://bugzilla.bioperl.org/show_bug.cgi?id=1493

           Summary: Failure to load a MySQL database using BioSQL
           Product: Biopython
           Version: Not Applicable
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: BioSQL
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: idoerg at burnham.org


Hi,

Following a tutorial example on BioSQL, I ran into the followning dump. 
Seems like the taxon_id table does not have a columns "binomial" or "variant".
I used the table definitions for MySQLdb off the CVS on the MySQLDb site. 

Iddo

>>> gdb = server.new_database("px01")
>>> from Bio import GenBank
>>> parser = GenBank.FeatureParser()
>>> iterator =
GenBank.Iterator(open("/usr/home/iddo/results/anthrax_03/px01_gb"),parser)
Traceback (most recent call last):
  File "<stdin>", line 1, in ?
IOError: [Errno 2] No such file or directory:
'/usr/home/iddo/results/anthrax_03/px01_gb'
>>> iterator =\
GenBank.Iterator(open("/usr/home/iddo/results/anthrax_03/px01_03.gb"),parser)
>>> gdb.load(iterator)
Traceback (most recent call last):
  File "<stdin>", line 1, in ?
  File "/home/iddo/biopy_cvs/biopython/BioSQL/BioSeqDatabase.py", line 337, in load
    db_loader.load_seqrecord(cur_record)
  File "/home/iddo/biopy_cvs/biopython/BioSQL/Loader.py", line 30, in load_seqrecord
    bioentry_id = self._load_bioentry_table(record)
  File "/home/iddo/biopy_cvs/biopython/BioSQL/Loader.py", line 173, in
_load_bioentry_table
    taxon_id = self._get_taxon_id(record)
  File "/home/iddo/biopy_cvs/biopython/BioSQL/Loader.py", line 107, in _get_taxon_id
    taxa = self.adaptor.execute_and_fetchall(sql, (binomial, variant))
  File "/home/iddo/biopy_cvs/biopython/BioSQL/BioSeqDatabase.py", line 236, in
execute_and_fetchall
    self.cursor.execute(sql, args)
  File "/usr/lib/python2.2/site-packages/MySQLdb/cursors.py", line 95, in execute
    return self._execute(query, args)
  File "/usr/lib/python2.2/site-packages/MySQLdb/cursors.py", line 114, in _execute
    self.errorhandler(self, exc, value)
  File "/usr/lib/python2.2/site-packages/MySQLdb/connections.py", line 33, in
defaulterrorhandler
    raise errorclass, errorvalue
_mysql_exceptions.OperationalError: (1054, "Unknown column 'binomial' in 'where
clause'")
>>>



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