[Biopython-dev] [Bug 2405] New: BioSQL gives UserWarning: ... not recognised as database type: temporarily accepting key

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2405

           Summary: BioSQL gives UserWarning: ... not recognised as database
                    type: temporarily accepting key
           Product: Biopython
           Version: 1.44
          Platform: All
        OS/Version: All
            Status: NEW
          Severity: normal
          Priority: P2
         Component: BioSQL
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: biopython-bugzilla at maubp.freeserve.co.uk


This can be demonstrated by the new unit test:

$python run_tests.py test_BioSQL_SeqIO.py

The test should pass, but prints lots of warnings to the console, e.g.:

.../BioSQL/Loader.py:500: UserWarning: LocusID not recognised as database type:
temporarily accepting key
  warnings.warn("%s not recognised as database type: temporarily accepting key"
% key)

We need to update the dictionary (which is now) in BioSQL/__init__.py to cope
with these - but whatever mapping we use should be compatible with BioPerl,
BioJava, etc.


-- 
Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email
------- You are receiving this mail because: -------
You are the assignee for the bug, or are watching the assignee.