[ensembl-dev] Problem with using ensembl API when called via the web

Thu Oct 20 04:44:32 BST 2011

Hi Andreas and Anne,

Thank you so much for your replies.

Firstly, as Andreas suggested, I will get a local copy of the database 
before I proceed.
Thank you for pointing this out. And yes, the web service and command 
line calls are
run on the same machine.

Anne, if I connect directly from command line it works perfectly fine. I 
have tested it
a few times over a few days, and it always works from command line, and 
doesn't
work when I call the script via the web. So, I'm pretty sure it's not a 
problem with
the database.

I will try it with a local copy of the db and see if I have the same 
problem...

Thank you so much!

Regards,
Natascha

On Wednesday 19,October,2011 04:53 PM, Anne Parker wrote:
> We were having problems yesterday afternoon with someone "spamming" the public database server with badly-optimised queries. This may well account for your database connection issues. Can you try connecting directly from a command line, and let us know if that works?
>
> Cheers
>
> Anne
>
>
>
> On 19 Oct 2011, at 09:48, Andreas Kusalananda Kähäri wrote:
>
>> Just throwing in another thought about this:
>>
>> The point in the code where your program breaks is just after failing
>> to establish a connection to the database. There might be too many
>> connections open by others for you to connect. In this case, waiting
>> for others to finish fetching their data and then trying again would
>> solve the problem.
>>
>> Kind regards,
>> AKK
>>
>> On 19 October 2011 09:24, Andreas Kusalananda Kähäri<ak at ebi.ac.uk>  wrote:
>>> Hi Natascha,
>>>
>>> I can't see anything obviously wrong with your code. If you get as far
>>> as trying to connect, all modules are most likely loaded ok.
>>>
>>> The environment from which the program is executing when running from
>>> the command line is obviously different in some way from when you're
>>> running the program via the web server, but I can't see in what way.
>>> I'm wondering if proxies makes a difference on this level or not, but
>>> unfortunately I'm not experienced enough with web services to make a
>>> proper diagnosis.
>>>
>>> Are you running the web service from the same machine as when you run
>>> the program from the command line? If not, do they both have the same
>>> connectivity to external hosts (e.g., ensembldb)?
>>>
>>>
>>> By the way, if you're developing a web application using the Ensembl
>>> API, I would strongly advise to point it to local copies of the
>>> databases, not at our public database server as this is likely to slow
>>> interactiveness down for you (and possibly slow down access for our
>>> other users).
>>>
>>>
>>> Kind regards,
>>> Andreas Kusalananda Kähäri
>>>
>>>
>>> On 19 October 2011 05:44, Natascha May<natascha at tll.org.sg>  wrote:
>>>> Hello everyone,
>>>>
>>>> I am new to using the ensembl perl API (version 63). I would really
>>>> appreciate some help for a problem I'm having with my perl script.
>>>>
>>>> The perl script basically connects to the DB and uses the slice method to
>>>> retrieve some information. If I run this perl script
>>>> from my terminal, it works fine, and I am able to get results from ensembl.
>>>> However, if I call this perl script via a php script
>>>> (because I am trying to develop a web based tool), the MySQL connection
>>>> fails.
>>>>
>>>> Error message in httpd/error_log:
>>>>
>>>> DBI connect('host=ensembldb.ensembl.org;port=5306','anonymous',...) failed:
>>>> Can't connect to MySQL server on
>>>> 'ensembldb.ensembl.org' (13) at
>>>> /var/www/cgi-bin/tll_blat/ensembl-src/ensembl/modules/Bio/EnsEMBL/Registry.pm
>>>> line 1452
>>>> Can't call method "selectall_arrayref" on an undefined value at
>>>> /var/www/cgi-bin/tll_blat/ensembl-src/ensembl/modules/Bio/EnsEMBL/Registry.pm
>>>> line 1455.
>>>>
>>>> I have explicitly set the location of the ensembl and perl modules at the
>>>> top of my perl script as follows:
>>>>
>>>> use warnings;
>>>>
>>>> use lib '/var/www/cgi-bin/tll_blat/ensembl-src/bioperl-1.2.3';
>>>> use lib '/var/www/cgi-bin/tll_blat/ensembl-src/ensembl/modules';
>>>>
>>>> use Bio::EnsEMBL::Registry;
>>>>
>>>> $registry = 'Bio::EnsEMBL::Registry';
>>>> $slice='Bio::EnsEMBL::Slice';
>>>> $gene='Bio::EnsEMBL::Gene';
>>>>
>>>> $registry->load_registry_from_db(-host =>  'ensembldb.ensembl.org', -user =>
>>>> 'anonymous');
>>>>
>>>> All this works when I run it from command line, but not via the web.
>>>> Where could I be going wrong...?
>>>>
>>>> Thank you so much!
>>>>
>>>> ~ Natascha
>>>>
>>>> Information in this email is confidential and may also be privileged. It is
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>>>> _______________________________________________
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>>>>
>>>>
>>>
>>>
>>> --
>>> Andreas Kusalananda Kähäri, Ensembl Software Developer
>>> European Bioinformatics Institute (EMBL-EBI)
>>> Wellcome Trust Genome Campus, Hinxton
>>> Cambridge CB10 1SD, United Kingdom
>>>
>>
>>
>> -- 
>> Andreas Kusalananda Kähäri, Ensembl Software Developer
>> European Bioinformatics Institute (EMBL-EBI)
>> Wellcome Trust Genome Campus, Hinxton
>> Cambridge CB10 1SD, United Kingdom
>>
>> _______________________________________________
>> Dev mailing list    Dev at ensembl.org
>> List admin (including subscribe/unsubscribe): http://lists.ensembl.org/mailman/listinfo/dev
>> Ensembl Blog: http://www.ensembl.info/
> Anne Parker
> Ensembl Web Production Manager
> http://www.ensembl.org
>
>
>
>
>

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