Hi Arek,
We are trying to get the DDL for the schema I mentioned earlier. But, I do have
another question. The operations that are performed through the
MartConfigurator, like adding a new data set, selecting what tables to include,
...etc. Can all of this be done from the command line or by including some
configuration file? Is there another manual that explains that? Sorry if I have
missed something.
I am accessing/working with a Biomart instance through ssh, and doing things
through the MartConfigurator over X-windows is extremely slow and sometimes
non-responsive, so I am trying to find an alternative.
Regards,
Rashad
________________________________
From: Arek Kasprzyk <[email protected]>
To: Rashad <[email protected]>
Cc: "[email protected]" <[email protected]>
Sent: Friday, December 21, 2012 1:08:07 PM
Subject: Re: [BioMart Users] 3NF Question
Hi Rashad,
you can just send me the schema that caused the exception that you described in
your email.
This should be enough for me
cheers,
a
On Thu, Dec 13, 2012 at 4:41 AM, Rashad <[email protected]> wrote:
Hi Arek,
>
>
>Thanks for your interest in helping. I was not able to create the DDL from the
>DB instance itself, because of lack of enough privileges. I will find another
>way and got it to you.
>
>
>Regards,
>Rashad
>
>
>
>________________________________
> From: Arek Kasprzyk <[email protected]>
>To: Rashad <[email protected]>
>Sent: Wednesday, December 12, 2012 4:53:03 AM
>
>Subject: Re: [BioMart Users] 3NF Question
>
>
>
>Hi Rashad,
>I would like to load this schema locally to try to reproduce the problem that
>you reported. How can i get hold of the DDL file?
>
>
>
>
>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
>>>>
>>>>
>
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