[Biopython] help with ncbiWWW

[Jocelyne]

FYI, I ran into the same issue and had to have try catch with a timeout on
the request. I think Nabeel's explanation should cover it. Note that
catching request timeout exceptions in python 2 is a bit of a pain...

--sent from my not-so-new-yet-still-awesome galaxy note edge

On Jul 26, 2017 11:50, "Peter Cock" <p.j.a.cock at googlemail.com> wrote:

> Hi Pej.
>
> Hmm. Maybe setting the timeout is not going to solve your
> problem. I was hoping that would be a neat solution.
>
> Can you show us the stack trace when you had to stop a job
> please?
>
> I assume you are using control+c to do this, in which case
> Python ought to stop with the exception KeyboardInterrupt.
> What I am interested in here is where in the code Python
> is getting stuck. That would be a good clue.
>
> Peter
>
> On Wed, Jul 26, 2017 at 2:47 PM, Pejvak Moghimi
> <pejvak.moghimi at york.ac.uk> wrote:
> > Hi Peter,
> >
> > That solution, so far, does not seem to have worked nor with 10 neither
> with
> > 30 second options.
> >
> > Cheers,
> > Pej.
> >
> > On 26 July 2017 at 13:29, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> >>
> >> I am hoping that putting this near the start of your script will
> >> apply the default timeout to all your BLAST calls (or other
> >> network calls, e.g. NCBI Entrez):
> >>
> >> import socket
> >> socket.setdefaulttimeout(30)  # timeout in seconds
> >>
> >> Peter
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