On 21 Jul 2006, at 09:11, [EMAIL PROTECTED] wrote:
Hi Alexandre,
I don't know if you have your __main tables sorted yet. We have a
BioMart with three __main tables but what I didn't realise from the
doc was
that a subsequent __main table must be a subset of a previous __main
table
ie. include all the previous fields including the __key column. That's
right isn't it Damian?
yes, this is exactly the case. We frequently refer to it as each
subsequent
main table is a subclass of the previous one. We need to improve the
docs :)
a.
Hope this helps,
Robert
To: Alexandre Gattiker <[EMAIL PROTECTED]>
cc: [email protected]
bcc:
Subject: Re: [mart-dev] marteditor hangs on bad db design
@
20/07/2006 21:02 CET
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
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