[ensembl-dev] cant connect to DB with perl API

[Nicolas Thierry-Mieg]

So I replicated my setup on another computer on a different network and 
it's working! I guess our IT department added some outgoing TCP 
filtering since the last time I used this script...

Thanks!




On 09/13/2019 03:01 PM, Steve Trevanion wrote:
> Hi Nicolas,
> 
> I can connect fine, so there might be a problem at your end. Can you 
> connect via the command line, either port 5306 or port 3306 ?
> 
> Steve
> 
> $ mysql -u anonymous -h ensembldb.ensembl.org
> Welcome to the MariaDB monitor.  Commands end with ; or \g.
> Your MySQL connection id is 102837958
> Server version: 5.6.33 MySQL Community Server (GPL)
> 
> Copyright (c) 2000, 2016, Oracle, MariaDB Corporation Ab and others.
> 
> Type 'help;' or '\h' for help. Type '\c' to clear the current input 
> statement.
> 
> MySQL [(none)]>
> 
> On 13/09/2019 13:33, Nicolas Thierry-Mieg wrote:
>>
>>
>> On 09/13/2019 01:46 PM, Steve Trevanion wrote:
>>> On 12/09/2019 18:25, Marek Szuba wrote:
>>>> On 2019-09-12 19:09, Nicolas Thierry-Mieg wrote:
>>>>
>>>>> $ perl ./ensemblTest.pl
>>>>> DBI connect('host=ensembldb.ensembl.org;port=3306','anonymous',...)
>>>>> failed: Can't connect to MySQL server on 'ensembldb.ensembl.org' (110)
>>>>> at
>>>>> /home/nthierry/Software/VariantEffectPredictor/ensembl-vep//Bio/EnsEMBL/Registry.pm 
>>>>>
>>>>> line 1770.
>>>> It probably is not you, having just tried talking to the server using
>>>> the command-line client, it is barely responsive. Between that, the 
>>>> fact
>>>> that late last week it was not possible to connect to MySQL on
>>>> ensembldb.ensembl.org at all unless one was extremely lucky, and the
>>>> fact there were ~200 active processes when I looked, my guess is 
>>>> that it
>>>> is simply overloaded.
>>>>
>> > Hi Nicolas,
>> >
>> > We've identified and fixed the problem and the server should be 
>> usable now.
>> >
>> > Regards,
>> >
>> > Steve
>> >
>>
>>
>> Thanks for your replies, it's good to know the problem is probably not 
>> on my side.
>> I am still getting the same error messages, but I'll keep trying.
>>
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-- 
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Nicolas Thierry-Mieg
Laboratoire TIMC-IMAG/BCM, CNRS UMR 5525
Pavillon Taillefer, Faculte de Medecine
38700 La Tronche, France
tel: (+33)456.520.067, fax: (+33)456.520.055
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