[ensembl-dev] Region report tool / Registry - only works for mysql users without password?

[Nick Langridge]

I've tested with an external mysql instance too and I see the same issue.
It works fine for user accounts that do not require a password, but 
fails if a password is used.

On 01/05/2012 14:28, Nick Langridge wrote:
> Hi Kieron,
>
> Thanks for the reply.
>
> No luck using 127.0.0.1 - same error as before, it still isn't using 
> the password.
> Any other suggestions?
>
> Also, i'm sorry to say that I'm not really using this on the command 
> line, just for debugging my ensembl instance :)
> The command was built by the ensembl webcode - I guess it doesn't 
> check for the duplication of the connection details.
>
> Cheers,
> Nick
>
>
>
> On 30/04/2012 16:28, Kieron Taylor wrote:
>> Hi Nick, I'm glad to see someone is using the Region report tool from 
>> the command line.
>>
>> There is a bug that we know of in the secondary host connection code, 
>> which is being fixed, but there are a couple of things we have 
>> noticed in your parameter specification.
>>
>> Firstly, pointing the tool at the same server twice redundant. The 
>> feature is in place to assist in situations (such as on our main 
>> public servers) where data must be spread across several hosts. 
>> Hopefully you are just masking your true connection settings.
>>
>> Secondly, MySQL behaves badly with "localhost" as a target. It tends 
>> to assume socket connections instead of by http, which can cause no 
>> end of connection issues. Sockets are treated differently for valid 
>> users and authentication than through HTTP. Try feeding it 127.0.0.1 
>> as a host instead.
>>
>>
>> Kieron
>>
>> On 30/04/12 16:00, Nick Langridge wrote:
>>> Hi,
>>>
>>> I'm trying to use the region report tool but it seems to ignore the
>>> mysql password that I supply in the options:
>>>
>>> perl region_report.pl --species=Anopheles_gambiae 
>>> --input=/tmp/inputfile
>>> --include=gt --report --host=localhost --port=3306 --db_version=66
>>> --user=myuser --password=mypass --secondaryhost=localhost
>>> --secondaryport=3306 --db_version=66 --secondaryuser=myuser
>>> --secondarypassword=mypass --output=/tmp/outputfile
>>>
>>> I see error:
>>>
>>> connect: DBI:mysql:host=localhost;port=3306 myuser at
>>> /ensembl/www-live/VB-2012-03/ensembl/modules/Bio/EnsEMBL/Registry.pm
>>> line 1566.
>>> DBI connect('host=localhost;port=3306','myuser',...) failed: Access
>>> denied for user 'myuser'@'localhost' (using password: NO) at
>>> /ensembl/www-live/VB-2012-03/ensembl/modules/Bio/EnsEMBL/Registry.pm
>>> line 1567
>>>
>>> -------------------- EXCEPTION --------------------
>>> MSG: Cannot connect to the Ensembl MySQL server at localhost:3306; 
>>> check
>>> your settings & DBI error message: Access denied for user
>>> 'myuser'@'localhost' (using password: NO)
>>> STACK Bio::EnsEMBL::Registry::load_registry_from_db
>>> /ensembl/www-live/VB-2012-03/ensembl/modules/Bio/EnsEMBL/Registry.pm:1567 
>>>
>>> STACK Bio::EnsEMBL::Registry::load_registry_from_multiple_dbs
>>> /ensembl/www-live/VB-2012-03/ensembl/modules/Bio/EnsEMBL/Registry.pm:2296 
>>>
>>> STACK toplevel
>>> /ensembl/www-live/VB-2012-03/ensembl-tools/scripts/region_reporter/region_report.pl:176 
>>>
>>>
>>> Ensembl API version = 66
>>> ---------------------------------------------------
>>>
>>> As far as I can see, the region report script calls
>>> Bio::Ensembl::Registry->load_registry_from_multiple_dbs() with the
>>> password present, but the registry seems to ignore it.
>>>
>>> Is this the expected behaviour?
>>>
>>> Cheers,
>>> Nick
>>>
>>>
>>>
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>>
>>
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