[Biopython-dev] BioSQL test code on Postgres

[Cymon Cox]

Hi Folks,

The current test code in test_BioSQL.py fails on PostgreSQL;

ERROR: Check list, keys, length etc
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/cymon/git/biopython-github-master/Tests/test_BioSQL.py", line
187, in test_get_db_items
    del db["non-existant-name"]
  File "/home/cymon/git/biopython-github-master/BioSQL/BioSeqDatabase.py",
line 519, in __delitem__
    if key not in self:
  File "/home/cymon/git/biopython-github-master/BioSQL/BioSeqDatabase.py",
line 539, in __contains__
    (self.dbid, value))[0])
  File "/home/cymon/git/biopython-github-master/BioSQL/BioSeqDatabase.py",
line 423, in execute_and_fetch_col0
    self.execute(sql, args or ())
  File "/home/cymon/git/biopython-github-master/BioSQL/BioSeqDatabase.py",
line 404, in execute
    self.dbutils.execute(self.cursor, sql, args)
  File "/home/cymon/git/biopython-github-master/BioSQL/DBUtils.py", line 33,
in execute
    cursor.execute(sql, args or ())
DataError: invalid input syntax for integer: "non-existant-name"
LINE 1: ...M bioentry WHERE biodatabase_id=1 AND bioentry_id=E'non-exis...

Because when trying to delete a bioentry_id that is a string type, ie.
"non-existant-name" (line 188 on test_BioSQL.py),  postgres throws an error
rather than returning a long (0,1) as in sqlite (and presumably MySQL (I
havent tried it)).

Should we be type checking in __delitem__ (line 517) in BioSeqDatabase.py so
that trying to delete a bioentry_id that is a string throws an appropriate
error?

Otherwise the BioSQL tests pass on PostGreSQL.

The default DBDRIVER PostgreSQL driver in setup.py should be changed to
"pyscopg2"

Cheers, Cymon