[Biopython-dev] [Bug 2833] Features insertion on previous bioentry_id

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2833


biopython-bugzilla at maubp.freeserve.co.uk changed:

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------- Comment #25 from biopython-bugzilla at maubp.freeserve.co.uk  2009-06-04 06:08 EST -------
(From update of attachment 1319)
(In reply to comment #24)
> Ive added a patch against biopython on GitHub.
> 
> I hope it address all the points made so far... it now passes all tests
> in test_BioSQL.py (although Ive not added more).

It looked sensible to me. It isn't very elegant (maybe we should move this
hack into Loader.py?), but I can live with it until Hilmar fixes Bug 2839.

Checked in as BioSQL/BioSeqDatabase.py CVS revision 1.23 - thanks!

> One thing we've not yet discussed is the other PostgreSQL driver PyGresql.
> It appears that the project is still active ... I'll open a bug.

Let's discuss that on the new Bug 2849.

> Also, Ive added a create_database() in a setUp() to the ClosedLoopTest
> unittest case because if this suite is called first (as it is for me -
> what actually governs which unittests are called first?) then if a test
> database is missing the suite is going to fail.

Good point, although I added a create_database() to the module itself instead.
The unit tests order is from sorting their description (first line of the
docstring) alphabetically.

See Tests/test_BioSQL.py CVS revision 1.41

We may want to add a few more duplicate tests (using the accession and
identifier) before closing this bug...

Peter


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