Re: [BioMart Users] [DCC] Error has occurred

classic Classic list List threaded Threaded
1 message Options
Reply | Threaded
Open this post in threaded view
|

Re: [BioMart Users] [DCC] Error has occurred

Junjun Zhang
Hi Nuria,

Jonathan helped locating the problems.

The problem with drag&drop failed for some of the items is likely a bug, we tried it using BioMart 0.8 RC7 (an internal release), it works fine.

Problem with queries end up with "Error occurred" is due to missing pseudo attribute used in linkouturl in the configured access point. See the screenshot below:



In the linkouturl, there is a pseudo attribute 'exturl' (attribute that is not based on a database table column). But in this access point, such pseudo attribute is not presented. It does exist in the source config (left-side panel), you will need to drag&drop it from left to right.

Hope this helps.

Junjun



From: "[hidden email]" <[hidden email]>
Date: Thu, 10 Nov 2011 08:58:23 -0500
To: jzhang <[hidden email]>
Subject: RE: [DCC] [BioMart Users] Error has occurred

Hi Junjun,

 

There it goes the mysql schema. Thank you so much!

 

Regards,

Núria


De: Junjun Zhang [[hidden email]]
Enviado el: miércoles, 09 de noviembre de 2011 20:22
Para: QUERALT, NURIA (IDIBAPS)
Asunto: Re: [DCC] [BioMart Users] Error has occurred

 

Hi Nuria,

 

If you can send me the mysql schema dump (no data), it would be very helpful.

 

Thanks,

Junjun

 

 

From: Jonathan Guberman <[hidden email]>
Date: Wed, 9 Nov 2011 09:21:57 -0500
To: jzhang <[hidden email]>
Cc: "[hidden email]" <[hidden email]>
Subject: Re: [DCC] [BioMart Users] Error has occurred

 

The mart in question points to their local MySQL DB, so I'm unable to reproduce the problem.

 

On 2011-11-09, at 9:12 AM, Junjun Zhang wrote:



Hi Jonathan,
Can you pls have a look into this?

Junjun
Sent from my BBerry

 

From: [hidden email] [[hidden email]]
Sent: Wednesday, November 09, 2011 04:08 AM
To: Junjun Zhang
Subject: RE: [BioMart Users] Error has occurred
 

Dear Junjun,

 

There it goes the registry file.

 

The first configuration ‘Ensembl + DDK’ is giving the error when I query it filtering: DDK Database -> Differential Expression -> HGNC Gene Symbol = ADIPOQ, andsetting the attribute: DDK Database -> Experiments -> Title. The second configuration ‘Ensembl + DDK’ is the one that I commented in the prior email trying to link DDK to Ensembl. Two things in this case: I don’t understand why couldn’t I copy all the Ensembl folders to the DDK config; and an error appears when the filter ‘DDK Database -> Differential Expression -> HGNC Gene Symbol = ADIPOQ’ I set and the attribute ‘ENSEMBL -> Features ->GENE -> Ensembl -> Ensembl Gene ID’ is request. Many thanks in advance.

 

Best regards,

Núria

 

 

 

Núria


De: Junjun Zhang [[hidden email]]
Enviado el: miércoles, 09 de noviembre de 2011 4:20
Para: QUERALT, NURIA (IDIBAPS)
CC: [hidden email]
Asunto: Re: [BioMart Users] Errorhas occurred

 

Hi Núria,

 

We would need reproduce the problems here, is it possible to send me (off the list) the registry file so we can test it out?

 

Best regards,

Junjun

 

 

From: Yong Liang <[hidden email]>
Date: Tue, 8 Nov 2011 12:31:48 -0500
To: Arek Kasprzyk <[hidden email]>, "[hidden email]" <[hidden email]>
Cc: "[hidden email]" <[hidden email]>
Subject: Re: [BioMart Users] Error has occurred

 

I think Junjun may be the best person to help on this issue. 

 

From: Arek Kasprzyk <[hidden email]>
Date: Tue, 8 Nov 2011 11:53:33 -0500
To: "[hidden email]" <[hidden email]>
Cc: "[hidden email]" <[hidden email]>
Subject: Re: [BioMart Users] Error has occurred

 

Hi Nuria,
I think we need Yong's (our MConfigurator expert) advice because this does not seem to be a very informative error message. Yong: would you be able to point Nuria in the right direction if she sent you the error log?


a



On Tue, Nov 8, 2011 at 6:58 AM, <[hidden email]> wrote:

Dear all,

 

I linked Ensembl mart with a local virtual mart, being Ensembl configuration the one i am editing and our local virtual mart config the source for creating the link to the Ensembl configuration and ‘Ensembl Gene ID’ the attribute chosen for the link. I’m detecting that when I query this configuration the message “Error hasoccurred” comes up, but only when a specific attribute from our localmart is set as attribute. This attribute is the same used for creating the report based on the previously existing local virtual mart configuration. How could i trace this error to find out why is happening?

 

For more information, I tried to overcome this error doing the reverse link: editing the local virtual mart configuration and linking it to Ensembl mart config by means of ‘Ensembl Gene ID’ attribute that is common in the two marts. But in this case the error emerges when ‘Ensembl Gene ID’ from Ensembl mart is set as attribute. Moreover, once the link is set, when i edited the virtual mart configuration moving all the foldersfrom Ensembl config to virtual mart config, not all the folders are available to be copied. Why is this happening?

 

Many thanks in advance.

 

Regards,

Núria

 


_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users




<DDKproblems8NOV2011>_______________________________________________
DCC mailing list
[hidden email]
https://lists.oicr.on.ca/mailman/listinfo/dcc

 


_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users