[Biopython] help with ncbiWWW

[Peter Cock]

If there is an exception, sure :)

Perhaps I misunderstood, but I thought here there was no
exception - the loop just keeps happening - checking the
NCBI every two minutes but not ending.

Peter


On Wed, Jul 26, 2017 at 8:50 PM, Jocelyne <jocelyne at gmail.com> wrote:
> 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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