[Biopython-dev] SQLite test failure on Windows, OperationalError: unable to open database file

[Peter Cock]

Hi all,

About a week ago most of the Windows nightly tests broke - e.g.
here on the same revision (!) 79f9054e5246ba30816ff93a775d594ae7da6fc6
https://github.com/biopython/biopython/commit/79f9054e5246ba30816ff93a775d594ae7da6fc6

Worked, Fri Mar 14
http://testing.open-bio.org/biopython/builders/Windows%20XP%20-%20Python%202.6/builds/1129

Failed, Sat Mar 15
http://testing.open-bio.org/biopython/builders/Windows%20XP%20-%20Python%202.6/builds/1130
...
test_BioSQL_sqlite3 ... FAIL
...
======================================================================
ERROR: Check list, keys, length etc
----------------------------------------------------------------------
Traceback (most recent call last):
  File "c:\repositories\BuildBotBiopython\win26\build\Tests\common_BioSQL.py",
line 193, in setUp
    load_database(gb_handle)
  File "c:\repositories\BuildBotBiopython\win26\build\Tests\common_BioSQL.py",
line 166, in load_database
    create_database()
  File "c:\repositories\BuildBotBiopython\win26\build\Tests\common_BioSQL.py",
line 148, in create_database
    server.load_database_sql(SQL_FILE)
  File "c:\repositories\BuildBotBiopython\win26\build\build\lib.win32-2.6\BioSQL\BioSeqDatabase.py",
line 281, in load_database_sql
    self.adaptor.cursor.execute(sql_line)
OperationalError: unable to open database file

(etc)

Presumably something changed on the machine itself - perhaps a
Windows security update? Any guesses for what might be wrong
and why it broke on Python 2.6, PyPy 1.9, 2.0, 2.1 - yet works
fine on Python 2.7, Python 3.3, PyPy 2.2 and Jython 2.7?

Logged into this machine, I can reproduce the error with:

c:\python26\python test_BioSQL_sqlite3.py

Thanks,

Peter