[BioMart Users] Problem importing tables with user-defined types?

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[BioMart Users] Problem importing tables with user-defined types?

Thomas TRIPLET
Hello,

I am trying to create a virtual mart, and I am having some trouble with a few tables, for no apparent reason. When I add specific tables from a RDBMS data source (from postgres), I am consistently getting the following error message :

org.biomart.common.exceptions.AssociationException: A relation between these two keys already exists.

One of the the table in question is :

Column Type Not Null

goTermWID bigint NOT NULL PK
name character varying(255)                 NOT NULL
namespace namespace NOT NULL
acc character varying(7)                 NOT NULL U
isObsolete boolean NOT NULL
isRoot boolean NOT NULL
comments text

There are also a number of table that are just ignored, without error message, like this one :

Column Type Not Null

ecNodeWID bigint NOT NULL
ecNumber ltree NOT NULL
acceptedName character varying(500) NOT NULL
systematicName character varying(500) NOT NULL
comments text NOT NULL
obsolete boolean NOT NULL
parentNodeWID bigint


Those 2 tables look very ordinary, so I'm not quite sure what's wrong here.


I thought for a while that the problem came from tables with user-defined types. But I found instances of such tables that were imported without any trouble. Could let me know if this is indeed the case and if so, if there is a way around it (besides converting the types in the underlying database).

Thanks for your input!

Thomas

--
Thomas Triplet, Ph.D.
http://www.thomastriplet.net

Centre for Structural and Functional Genomics
Concordia University
7141 West Sherbrooke St
Montreal QC H4B 1R6





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Re: [BioMart Users] [yong] Problem importing tables with user-defined types?

Arek Kasprzyk
Hi Yong,
could you help Thomas to investigate this  problem please? Probably best if he sends  you his XML


a

On Thu, Oct 6, 2011 at 5:52 PM, Thomas TRIPLET <[hidden email]> wrote:
Hello,

I am trying to create a virtual mart, and I am having some trouble with a few tables, for no apparent reason. When I add specific tables from a RDBMS data source (from postgres), I am consistently getting the following error message :

org.biomart.common.exceptions.AssociationException: A relation between these two keys already exists.

One of the the table in question is :

Column Type Not Null

goTermWID bigint NOT NULL PK
name character varying(255)                 NOT NULL
namespace namespace NOT NULL
acc character varying(7)                 NOT NULL U
isObsolete boolean NOT NULL
isRoot boolean NOT NULL
comments text

There are also a number of table that are just ignored, without error message, like this one :

Column Type Not Null

ecNodeWID bigint NOT NULL
ecNumber ltree NOT NULL
acceptedName character varying(500) NOT NULL
systematicName character varying(500) NOT NULL
comments text NOT NULL
obsolete boolean NOT NULL
parentNodeWID bigint


Those 2 tables look very ordinary, so I'm not quite sure what's wrong here.


I thought for a while that the problem came from tables with user-defined types. But I found instances of such tables that were imported without any trouble. Could let me know if this is indeed the case and if so, if there is a way around it (besides converting the types in the underlying database).

Thanks for your input!

Thomas

--
Thomas Triplet, Ph.D.
http://www.thomastriplet.net

Centre for Structural and Functional Genomics
Concordia University
7141 West Sherbrooke St
Montreal QC H4B 1R6





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Users mailing list
[hidden email]
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