[BioMart Users] worm mart is not functioning

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[BioMart Users] worm mart is not functioning

Wang, Juan
To whom it may concern,
 
I have problem with retrieving gene sequences with wormmart: it says:
Serious Error: returning undef ... missing attributes for your exportable?

ERROR: caught BioMart::Exception::Query: returning undef ... missing attributes for your exportable?

If you repeatedly get directed to this error page, there may be a problem with your current session parameters. To clear your session and start with a clean slate, please click the New button below.

Stacktrace:
Exception::Class::Base::throw /home/ruihua/download/biomart-perl/lib/BioMart/ResultTable.pm:134
BioMart::ResultTable::_new /home/ruihua/download/biomart-perl/lib/BioMart/RootI.pm:64
BioMart::RootI::new /home/ruihua/download/biomart-perl/lib/BioMart/DatasetI.pm:1105
BioMart::DatasetI::getResultTable /home/ruihua/download/biomart-perl/lib/BioMart/QueryRunner.pm:630
BioMart::QueryRunner::_processPath /home/ruihua/download/biomart-perl/lib/BioMart/QueryRunner.pm:374
BioMart::QueryRunner::_getResultTable /home/ruihua/download/biomart-perl/lib/BioMart/QueryRunner.pm:194
BioMart::QueryRunner::execute /home/ruihua/download/biomart-perl/lib/BioMart/Web.pm:2433
(eval) /home/ruihua/download/biomart-perl/lib/BioMart/Web.pm:2198
BioMart::Web::handle_request /home/ruihua/download/biomart-perl/cgi-bin/martview:100
(eval) /home/ruihua/download/biomart-perl/cgi-bin/martview:99
ModPerl::ROOT::ModPerl::Registry::home_ruihua_download_biomart_2dperl_cgi_2dbin_martview::handler /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi/ModPerl/RegistryCooker.pm:204
(eval) /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi/ModPerl/RegistryCooker.pm:204
ModPerl::RegistryCooker::run /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi/ModPerl/RegistryCooker.pm:170
ModPerl::RegistryCooker::default_handler /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi/ModPerl/Registry.pm:31
ModPerl::Registry::handler -e:0
(eval) -e:0

<IFRAME id=countIFrameId style="VISIBILITY: hidden; WIDTH: 0px; HEIGHT: 0px" name=count_hiddenIFrame src="about:blank" onload=getCountAjax();><IFRAME id=resultsIFrameId style="VISIBILITY: hidden; WIDTH: 0px; HEIGHT: 0px" name=results_hiddenIFrame src="about:blank" onload=getResultsAjax();>
Thank you!
 
Juan

~~~~~~~~~~~~~~~~~~~~~~

Juan Wang, Ph D

Postdoctoral Researcher

Maureen Barr Laboratory

Genetics Department

Rutgers, the State University of New Jersey

145 Bevier Rd

Piscataway, NJ, 08854

USA

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

 


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Re: [BioMart Users] worm mart is not functioning

Jonathan Guberman
Juan,

WormMart seems to be undergoing some sort of maintenance; their servers were down for a while, and now they are back up with what appears to be a developmental and testing site. It's difficult for us to maintain a valid connection when their servers are under development, so it's likely that the connection through Central Portal will be unreliable until they stabilize their servers.

In the meantime, you can try to access it directly through their website: http://www.wormbase.org/ You can see the "WormMart" link in the menubar at the top of the website.

On 2011-02-01, at 3:46 PM, Wang, Juan wrote:

To whom it may concern,
 
I have problem with retrieving gene sequences with wormmart: it says:

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Re: [BioMart Users] worm mart is not functioning

Jonathan Guberman
In reply to this post by Wang, Juan
Juan,

WormMart seems to be undergoing some sort of maintenance; their servers were down for a while, and now they are back up with what appears to be a developmental and testing site. It's difficult for us to maintain a valid connection when their servers are under development, so it's likely that the connection through Central Portal will be unreliable until they stabilize their servers.

In the meantime, you can try to access it directly through their website: http://www.wormbase.org/ You can see the "WormMart" link in the menubar at the top of the website.

Jonathan Guberman, PhD
Application Programmer

Ontario Institute for Cancer Research
MaRS Centre, South Tower
101 College Street, Suite 800
TorontoOntarioCanada M5G 0A3

Tel:         647-260-7818
Toll-free: 1-866-678-6427

On 2011-02-01, at 3:46 PM, Wang, Juan wrote:

To whom it may concern,
 
I have problem with retrieving gene sequences with wormmart


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Re: [BioMart Users] Fwd: worm mart is not functioning

rfang
In reply to this post by Jonathan Guberman
Hello,
   Thanks to Paul for forwarding this message to me.  I am currently
working on building WormMart-WS220.  The testing server at
http://caprica.caltech.edu:9002 in reality is acting like the
production server.  This can also be accessed through the usual
WormMart tab on the top panel of wormbase site.  I will be periodically
updating the site with bug fixing and user requested features.  I will
also migrate the previous stable WormMart releases (i.e.
WormMart-WS195, WS190, WS180, WS170, WS160) from the old production
server to this server by the end of Feb.
   I am not doing development on this server and actually will do
development on another server and only interrupt the testing server
when I need to migrate the dataset from my development server to this
testing server.
    After a period of time, maybe a month, if no serious complain from
users, this testing site will be turn into production server.
    You mentioned that "it's difficult for us to maintain a
valid connection when their servers are under development, so it's
ikely that the connection through Central Portal will be unreliable
until they stabilize their servers".  Please let me know what I need to do
so your Central Portal connection can be reliable.

Thanks and have a nice day,
Ruihua

Ruihua Fang, PhD
WormBase
Biology Division
California Institute of Technology
Pasadena, CA 91125



> This has just been posted on the mart development list. We should probably
> post a reply
>
> P.
>
> Sent from my iPhone
>
> Begin forwarded message:
>
>> From: Jonathan Guberman <[hidden email]>
>> Date: 2 February 2011 06:36:41 PST
>> To: "Wang, Juan" <[hidden email]>
>> Cc: "[hidden email]" <[hidden email]>
>> Subject: Re: [BioMart Users] worm mart is not functioning
>>
>
>> Juan,
>>
>> WormMart seems to be undergoing some sort of maintenance; their servers
>> were down for a while, and now they are back up with what appears to be
>> a developmental and testing site. It's difficult for us to maintain a
>> valid connection when their servers are under development, so it's
>> likely that the connection through Central Portal will be unreliable
>> until they stabilize their servers.
>>
>> In the meantime, you can try to access it directly through their
>> website: http://www.wormbase.org/ You can see the "WormMart" link in the
>> menubar at the top of the website.
>>
>> On 2011-02-01, at 3:46 PM, Wang, Juan wrote:
>>
>>> To whom it may concern,
>>>
>>> I have problem with retrieving gene sequences with wormmart: it says:
>> _______________________________________________
>> Users mailing list
>> [hidden email]
>> https://lists.biomart.org/mailman/listinfo/users
>


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