Thanks Arek.
I guess that without introducing modifications to the schema relations, I will
not be able to load it as a dataset using Biomart.
Right? (i.e. there is no way of over-riding this exception).
Is there a way figuring out what are the offending columns/relations through
some Biomart generated log, ...etc
Rashad
________________________________
From: Arek Kasprzyk <[email protected]>
To: Rashad <[email protected]>
Cc: "[email protected]" <[email protected]>
Sent: Thursday, December 6, 2012 10:46:25 AM
Subject: Re: [BioMart Users] 3NF Question
Hi Rashad,
Since Postgres supports FKs, you should not make any changes to this schema
through BioMart tools but rather on the RDBMS level. The schema modification
through BioMart tools is primarily for MySQL MyISM which does not support FKs
a
On Thu, Dec 6, 2012 at 3:27 PM, Rashad <[email protected]> wrote:
Hi Arek,
>
>
>No, I was just trying to load an existing schema structure. If you care about
>the schema itself, its part of an open source product:
>https://dev.openclinica.com/tools/db/index.html
>
>But, I do not expect you to look at that. The problem is, I cannot introduce
>any changes to that schema or its relations.
>
>
>Rashad
>
>
>
>
>
>
>
>
>
>________________________________
> From: Arek Kasprzyk <[email protected]>
>To: Rashad <[email protected]>
>Cc: "[email protected]" <[email protected]>
>Sent: Thursday, December 6, 2012 10:17:54 AM
>
>Subject: Re: [BioMart Users] 3NF Question
>
>
>
>Hi Rashad,
>did you try to define your own relationships or were you simply loading the
>existing schema?
>
>
>
>
>a
>
>
>
>On Thu, Dec 6, 2012 at 3:07 PM, Rashad <[email protected]> wrote:
>
>
>>
>>Hi Arek,
>>
>>
>>The RDBMS is PostGres. Let me know what other info might help.
>>
>>
>>
>>
>>
>>________________________________
>> From: Arek Kasprzyk <[email protected]>
>>To: Life Sciences Informatics <[email protected]>
>>Cc: "[email protected]" <[email protected]>
>>Sent: Thursday, December 6, 2012 9:06:07 AM
>>Subject: Re: [BioMart Users] 3NF Question
>>
>>
>>
>>Hi Rashad,
>>we need more details about this problem. What RDBMS are you using: Oracle,
>>Postgres or MySQL, if the latter is it MyISM or InnDB?
>>
>>
>>cheers,
>>a
>>
>>
>>
>>On Wed, Dec 5, 2012 at 9:02 PM, Life Sciences Informatics
>><[email protected]> wrote:
>>
>>This might be a novice's question, but the following exception:
>>>
>>>
>>>Caused by: org.biomart.common.exceptions.AssociationException: A relation
>>>between these two keys already exists.
>>>
>>>
>>>
>>> results in not being able to load a schema, does it mean that some elements
>>>in the schema are not in the 3NF?
>>>Can Biomart tell me what are the offending keys/relations?
>>>Can I over-ride this in Biomart, so it will still load the schema even
>>>though its not perfect for Biomart needs?
>>>
>>>Rashad
>>>
>>>
>>>_______________________________________________
>>>Users mailing list
>>>[email protected]
>>>https://lists.biomart.org/mailman/listinfo/users
>>>
>>>
>>
>>
>>
>
>
>
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