On 4 Oct 2006, at 16:18, Twigger Simon wrote:
Hi Richard,
Thanks for trying this, I suspect the permissions are at fault too.
I've been using the same value (the SID) for database and schema as
this is what I do for MySQL (I use the mysql database name for both
fields), but from what you say this will not work with Oracle. We'll
try tweaking this and see if that addresses the problem.
Many thanks for your help,
Simon.
PS Is the the development version of 0.5 available anywhere (I know
its coming 'real soon now' so I'm wondering if now is a good time to
start playing with it)
everything is available from the cvs, the pointers are at
www.biomart.org (you need to go for the main trunk and loose the '-r'
switch)
However I'd advise a two weeks patience with that before trying :-)
a.
--
Simon N. Twigger, Ph.D.
Assistant Professor, Department of Physiology
Medical College of Wisconsin
8701 Watertown Plank Road,
Milwaukee, WI, USA
tel: 414-456-8802
fax: 414-456-6595
AIM/iChat: simontatmcw
On Oct 4, 2006, at 4:15 AM, Richard Holland wrote:
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Hi there.
I created these tables exactly as you describe below in my local
Oracle
Express instance, then downloaded martj-0.4 as described on
biomart.org
and ran MartEditor from that download, and it worked fine. I also
tried
MartEditor from my development copy of martj-0.5, and that worked
fine too.
All I can think of is that you may have permissions problems (you
could
double-check the connection settings you gave MartEditor to check
this -
database should be SID, schema should be the actual owner of the
tables,
e.g. scott, username/password are obvious), or these tables are
actually
synonyms to tables in another schema in which case the mechanism we
use
to search for tables would not find them.
I'm not sure where to go from here. Maybe you could describe what you
are doing in a bit more detail and something might jump out.
cheers,
Richard
Arek Kasprzyk wrote:
On 4 Oct 2006, at 05:33, Twigger Simon wrote:
hi Arek,
Took me a little while to get all the details. We have one main
table:
RGD_GENES__GENES__MAIN
--------------------------------------------
RGD_ID_KEY NUMBER
GENE_SYMBOL VARCHAR2
GENE_NAME VARCHAR2
GENE_DESC VARCHAR2
It has data in it (23k rows), the RGD_ID_KEY is set as the primary
key
for the table. We have a number of other dimension tables, all named
RGD_GENES__xxxxx__DM, here's a representative example:
RGD_GENES__GENOME_V3_1_MAP__DM
-------------------------------------------------------------
RGD_ID_KEY NUMBER
MAP_NAME VARCHAR2
CHROMOSOME VARCHAR2
STRAND VARCHAR2
START_POS NUMBER
STOP_POS NUMBER
These also all have data in them, dumped directly from the RGD
schema
via SQL. We havent defined foreign key constraints between the
RGD_ID_KEY values in the __DM tables back to the RGD_ID_KEY in the
__MAIN table but we could certainly add those in.
From what I can see, assuming that the case doesnt matter, the
tables
are named correctly, the keys are named correctly (presumably NUMBER
is the correct datatype?), there is data in the tables, the biomart
user Im connecting with has appropriate privileges and it should
work
- at least based on my experience with MySQL versions.
When I connect to the database using marteditor (v4) I get this
message:
"No datasets available, is this a biomart compatible schema"
The tables on my MySQL version are essentially the same but all
lower
case and they worked fine.
Let me know if anyone can see anything obvious that could be causing
the problems
Thanks in advance!
Hi Simon,
your tables look perfectly fine to me.
Let us investigate more and we'll come back to you
a.
Simon.
--
Simon N. Twigger, Ph.D.
Assistant Professor, Department of Physiology
Medical College of Wisconsin
8701 Watertown Plank Road,
Milwaukee, WI, USA
tel: 414-456-8802
fax: 414-456-6595
AIM/iChat: simontatmcw
On Sep 29, 2006, at 1:51 PM, Arek Kasprzyk wrote:
On 29 Sep 2006, at 18:16, Twigger Simon wrote:
Hi there,
We're moving a mart over to oracle and we've got a main table
called:
RGD_GENES__GENES__MAIN
When I try and do the naive setup it cant find a dataset and asks
if
this is a biomart compatible schema... The schema used to work
fine
on MySQL, I wondering if the case change from
rgd_genes__genes__main
is causing the problem? Do Biomart table and attribute names have
to
be lowercase, or at least the parts that biomart is relying on
(__main, __dm for tables, _key, etc for attributes)
Thanks in advance for any thoughts on this.
Simon,
could you describe your table for us?
Also for MEditor to work you need to have at least one entry in
this
table.
Could you check that?
a.
Simon.
--
Simon N. Twigger, Ph.D.
Assistant Professor, Department of Physiology
Medical College of Wisconsin
8701 Watertown Plank Road,
Milwaukee, WI, USA
tel: 414-456-8802
fax: 414-456-6595
AIM/iChat: simontatmcw
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------------
Arek Kasprzyk
EMBL-European Bioinformatics Institute.
Wellcome Trust Genome Campus, Hinxton,
Cambridge CB10 1SD, UK.
Tel: +44-(0)1223-494606
Fax: +44-(0)1223-494468
-------------------------------------------------------------------
------------
---------------------------------------------------------------------
----------
Arek Kasprzyk
EMBL-European Bioinformatics Institute.
Wellcome Trust Genome Campus, Hinxton,
Cambridge CB10 1SD, UK.
Tel: +44-(0)1223-494606
Fax: +44-(0)1223-494468
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Arek Kasprzyk
EMBL-European Bioinformatics Institute.
Wellcome Trust Genome Campus, Hinxton,
Cambridge CB10 1SD, UK.
Tel: +44-(0)1223-494606
Fax: +44-(0)1223-494468
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