[Biopython-dev] [Bug 2475] BioSQL.Loader should reuse existing taxon entries in lineage

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2475





------- Comment #33 from biopython-bugzilla at maubp.freeserve.co.uk  2008-05-19 05:30 EST -------
This bug is also linked to Bug 2494 (currently titled "_retrieve_taxon in
BioSQL.py needs urgent optimization") which is about not using the left/right
values when reteiving data from the database.

This is important because changes made in this bug (i.e. Bug 2475) may leave
the left/right values NULL when writing new lineages.

Also, in repley to comment 31, all of the other _get_...() methods of the
Loader class can also add things to the database (e.g. qualifier keys).  Once
you know this, the fact that _get_taxon_id() goes this too isn't a shock. 
Also, yes, the _get_taxon_id() function is getting far too long, and should
probably be restructured as part of this bug.


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