>From my understanding, if table bbb is a subclass of table main, then
the basic structure should look like this:
id_key references main(id_key)
bbb_id_key
gene
col1
primary key (id_key, bbb_id_key)
ie. it should have an FK that references main, include all the columns
from main, plus additional column(s) of its own which when combined with
the FK create a unique primary key for bbb. Once all this is in place,
you can add extra columns to bbb such as col2.
cheers,
Richard
On Mon, 2006-07-24 at 09:11 +0200, Alexandre Gattiker wrote:
> Hi Damian,
>
> Here is an example schema that is sufficient to hang marteditor.
>
> CREATE TABLE Sc__main__main (
> id_key int auto_increment primary key,
>
> gene varchar(10),
> col1 int
> );
>
> CREATE TABLE Sc__bbb__main (
> id_key int auto_increment primary key,
>
> gene varchar(10),
> col2 int
> );
>
> Making all column names unique didn't seem to solve it.
>
> CREATE TABLE Sc__main__main (
> id_key int auto_increment primary key,
>
> gene varchar(10),
> col1 int
> );
>
> CREATE TABLE Sc__bbb__main (
> id_key2 int auto_increment primary key,
>
> gene2 varchar(10),
> col2 int
> );
>
>
> Best
> Alexandre
>
>
>
>
>
> Damian Smedley wrote:
> > On Thu, 20 Jul 2006, Alexandre Gattiker wrote:
> >
> >> Damian Smedley wrote:
> >>> On Thu, 20 Jul 2006, Alexandre Gattiker wrote:
> >>>
> >>>> Hello,
> >>>>
> >>>> If a mart database accidentally contains two __main tables for the same
> >>>> dataset, marteditor in "Naive" mode hangs in the following loop at
> >>>> DatabaseDatasetConfigUtils.java line 3342.
> >>> do you mean two tables with exactly the same name? All our ensembl
> >>> datasets have two __main tables per dataset so that shouldn't be a
> >>> problem. What are the names of your main tables out of interest - we will
> >>> investigate
> >> my tables were named something like:
> >>
> >> Scerevisiae__aaa__main
> >> Scerevisiae__bbb__main
> >>
> >> According to the doc the part in the middle is irrelevant, and there
> >> should only be one __main table with a given prefix part, if I
> >> understand correctly.
> >
> > guess our docs are a bit misleading on this - we will improve it for the
> > 0_5 release :) Your table names should be fine (eg) in
> > hsapiens_gene_ensembl we have:
> >
> > hsapiens_gene_ensembl__gene__main with gene_id_key
> > hsapiens_gene_ensembl__transcript__main with gene_id_key,
> > transcript_id_key
> >
> > suspect it is the combination of your main tables and keys that is causing
> > the hang rather than the table names - what are your keys?
> >
> > cheers
> > Damian
> >
> >
> >> Cheers
> >> Alexandre
> >>
> >>
> >> --
> >> Alexandre Gattiker
> >> Swiss Institute of Bioinformatics, Genome Bioinformatics Group
> >> Biozentrum Tel. +41 61 267 1579
> >> Klingelbergstrasse 50 Fax +41 61 267 1585
> >> 4056 Basel [EMAIL PROTECTED]
> >> Switzerland http://www.biozentrum.unibas.ch/primig
> >>
> >
>
>
--
Richard Holland (BioMart Team)
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
UNITED KINGDOM
Tel: +44-(0)1223-494416
