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?
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
>
The information in this message is commercial in confidence and may be
privileged. It is intended for the addressee(s) only. Access to this
message by anyone else is strictly prohibited. If you have received this
message in error, please inform the sender immediately.Please note that
messages sent or received by the Tessella e-mail system may be monitored
and stored in an information retrieval system.
TESSELLA [EMAIL PROTECTED]
__/__/__/ Tessella Support Services plc
__/__/__/ Building 26, Granta Park, Great Abington, Cambridge CB1 6GP
__/__/__/ Tel: (44)(0)1223-897770
www.tessella.com Registered in England No. 1466429
