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

[Andreas Kusalananda Kähäri]

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
>>
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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