Problems updating Biomart

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Problems updating Biomart

Rebecca Ewing
Hi

I am trying to update our mart to the use the latest version of our data but keep getting an error message when trying to run the configure script. I have already updated our data in a test mart using the same registry file which worked fine but it won't work for our live mart. The error I am getting is:

Use of uninitialized value in string eq at MartURLLocation.pm line 135.

ERROR something wrong with your registry:
syntax error at line 1, column 0, byte 0 at Parser.pm line 187

Thanks

Rebecca

--
 The Wellcome Trust Sanger Institute is operated by Genome Research
 Limited, a charity registered in England with number 1021457 and a
 company registered in England with number 2742969, whose registered
 office is 215 Euston Road, London, NW1 2BE.
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Re: Problems updating Biomart

Steven Rosanoff
Rebecca,

It looks like there is an issue with some of your configuration files.
Take a look at the following files to make sure the connection details
are setup properly. Your test mart is probably running on a different
host and port as compared to your production mart.

biomart/biomart-perl/conf/setting.conf
biomart/biomart-perl/conf/martDBLocation.xml
biomart/biomart-perl/conf/martURLLocation.xml

Steve

On 04/08/2010 11:41: AM, Rebecca Shepherd wrote:

> Hi
>
> I am trying to update our mart to the use the latest version of our data but keep getting an error message when trying to run the configure script. I have already updated our data in a test mart using the same registry file which worked fine but it won't work for our live mart. The error I am getting is:
>
> Use of uninitialized value in string eq at MartURLLocation.pm line 135.
>
> ERROR something wrong with your registry:
> syntax error at line 1, column 0, byte 0 at Parser.pm line 187
>
> Thanks
>
> Rebecca
>
>    


--
Steven Rosanoff
Software Engineer
EMBL-European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD, UK
Phone: +44 (0)1223 494565
Email: [hidden email]

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Re: Problems updating Biomart

Syed Haider
In reply to this post by Rebecca Ewing
Hi Rebecca,

Thi indicates that your registry XML file is malformed. please see for
any typos.

Best
Syed

On 04/08/2010 11:41, Rebecca Shepherd wrote:

> Hi
>
> I am trying to update our mart to the use the latest version of our data but keep getting an error message when trying to run the configure script. I have already updated our data in a test mart using the same registry file which worked fine but it won't work for our live mart. The error I am getting is:
>
> Use of uninitialized value in string eq at MartURLLocation.pm line 135.
>
> ERROR something wrong with your registry:
> syntax error at line 1, column 0, byte 0 at Parser.pm line 187
>
> Thanks
>
> Rebecca
>
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Re: Problems updating Biomart

Rebecca Ewing
Hi

I am using the exact same registry file as I used for the test mart. Also, the mart has been live for several months now and I haven't changed any settings. It has updated successfully several times before now.

Rebecca

On 4 Aug 2010, at 13:05, Syed Haider wrote:

> Hi Rebecca,
>
> Thi indicates that your registry XML file is malformed. please see for any typos.
>
> Best
> Syed
>
> On 04/08/2010 11:41, Rebecca Shepherd wrote:
>> Hi
>>
>> I am trying to update our mart to the use the latest version of our data but keep getting an error message when trying to run the configure script. I have already updated our data in a test mart using the same registry file which worked fine but it won't work for our live mart. The error I am getting is:
>>
>> Use of uninitialized value in string eq at MartURLLocation.pm line 135.
>>
>> ERROR something wrong with your registry:
>> syntax error at line 1, column 0, byte 0 at Parser.pm line 187
>>
>> Thanks
>>
>> Rebecca
>>



--
 The Wellcome Trust Sanger Institute is operated by Genome Research
 Limited, a charity registered in England with number 1021457 and a
 company registered in England with number 2742969, whose registered
 office is 215 Euston Road, London, NW1 2BE.