[Biopython-dev] [Bug 2681] BioSQL: record annotations enhancements

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2681


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

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------- Comment #7 from biopython-bugzilla at maubp.freeserve.co.uk  2008-12-13 19:11 EST -------
(In reply to comment #4)
> (In reply to comment #2)
> > (In reply to comment #0)
> > > 1) Fixed date/dates typo.
> > 
> > Why is it a typo?  Change not checked in.
> 
> The function _load_bioentry_date in Loader.py inserts the annotation 'date',
> if present, or the current date if not, into the bioentry_qualifier_value
> table. This is pulled by BioSeq.py _retrieve_qualifier_value and stored as
> the attribute 'dates'. Hence I considered line 307 in BioSeq.py to be a typo,
> which should be 'date' and not 'dates'.

OK, that does make sense.  However...

> Also, because Loader.py handles dates separately, they should not be
> handled by the function load_annotations.

That would make sense if we make the above "dates"/"date" change.

If we tested a record with a "date" annotation, I guess currently it would get
recorded twice - once under "date_changed" by _load_bioentry_date (retrieved as
"dates") and again but under "date" by _load_annotations (retrieved as "date").

Right now, I'm wondering why _load_bioentry_date exists in the first place ...
perhaps this special annotation entry "date_changed" is to mimic BioPerl?


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