[Biopython] Skipping over blank/erroneous Entrez.esummary() results

Brad Chapman chapmanb at 50mail.com
Wed Oct 7 12:32:27 UTC 2009


Peter and Michiel;

> > In addition to Michiel's workaround, I checked in a small
> > change which could at least circumvent the error you are
> > reporting:
> > 
> > http://github.com/biopython/biopython/commit/4dca8a24f62a1c28556d4e58f34db66f4b099279

Peter:
> Does "correctly" mean a default value? I see Brad has just commited a change to
> use -1 in this case, but perhaps None is also a good choice? Can we
> alternatively
> leave this bit of the data structure empty?

Michiel:
> Sorry, but that change introduces two bugs. First, we should be able
> to distinguish between -1 and missing values. More importantly, we
> want to be able to add attributes to value. Since -1 is an integer
> instead of an object, it won't allow that.
>
> Can you revert this change?

Thanks guys -- not the best choice. How do you feel about just passing
it along as an empty string and only doing the integer conversion if we
actually have data to convert?

http://github.com/biopython/biopython/commit/1fff8038e4fa9e2643851a70118e3227ccbea44e

So now missing values are empty strings, as passed, instead of any
sort of integer interpretation of them.

Brad



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