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

[Andy Yates]

Hi Nick,

Looks like we've gotten to the bottom of this problem. The tool was not passing the correct password argument to the Registry (it was using -PASSWORD but the argument is -PASS). Apologies for this. A fixed version has been deployed to which you can pickup from branch-ensembl-66. 

All the best,

Andy

Andrew Yates                   Ensembl Core Software Project Leader
EMBL-EBI                       Tel: +44-(0)1223-492538
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensembl.org/

On 1 May 2012, at 15:01, Nick Langridge wrote:

> 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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> 
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