[Biopython-dev] Catching more error conditions in Bio.Entrez

[Sean Davis]

On Wed, Jul 2, 2008 at 6:33 AM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> Hello Michiel et al.,
>
> I've already added a few if statements to the end of
> Bio.Entrez._open() to catch a few errors I'd observed, and I've just
> found another example:
>
>>>> from Bio import Entrez
>>>> Entrez.efetch("nucleotide", id="fiction", rettype="fasta").read()
> '\n'
>>>> Entrez.efetch("nucleotide", id="fiction").read()
> '\n'
>
> This seems to happen for any invalid identifier.  Are you happy for me
> to check for this as an error too?  Are there any valid reasons to get
> back an empty dataset like this?

If the ability to use history is added, then an empty dataset could be
a valid return after an empty search.  For id-based-searches, I'm not
sure I would raise an error for an empty set being returned anyway.

Just my $0.02.

Sean

> Also, I was wondering if we should raise a ValueError rather than
> IOError if we are fairly sure the problem is with the arguments rather
> than the network or the sever being unavailable.
>
> Peter
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