On 14 Feb 2007, at 17:02, trevor paterson ((RI)) wrote:
hi Arek
this error was in the martbuilder auto generated sql for making a
dataset from one table in my postgresql database...
out of the 45 or so temporary tables used in the script - this is the
only one that has an error ( and it is in the first temporary table! )
the sql error thrown is
No such attribute a.user_id_key
because the name in the original source table is "a.user_id" not "
a.user_id_key"
if I change the sql FROM "on a.user_id_key=b.accession;" TO "on
a.user_id=b.accession;"
the whole script works ok and the dataset is made ok, with all the
correct tables made and data loaded
so it would seem to me ( as a complete newbie ;) that it is the
autogeneration algorithm that is causing this naming error rather than
some error of mine...( cos I haven't done anything at all
configuration wise). The error is consistently repeatable...
apart from this one error everything is working very impressively so
far, and i can generate datasets and explore them through the java
tools!
ok, I understand now :) somehow MBuilder mention escaped my attention :)
apologies, we'll try to correct this and we'll get back to you
thanks for reporting this,
a.
thanks
Trevor Paterson
Bioinformatics
Roslin Institute
Scotland EH25 9PS
phone +44 (0) 131 5274477
http://www.roslin.ac.uk/
http://www.thearkdb.org/
http://www.comparagrid.org/
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-----Original Message-----
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On
Behalf Of Arek Kasprzyk
Sent: 14 February 2007 16:40
To: trevor paterson (RI)
Cc: andy law (RI); mart-dev
Subject: [mart-dev] Re: biomart newbie
On 14 Feb 2007, at 14:05, trevor paterson ((RI)) wrote:
Hi
I am looking for a bit of help trying to start using biomart
the very first dataset i try to create has an sql error in it, in the
very first table, which to my mind looks like an error in the
autogeneration - not something I have configured
create table testbiomart.TEMP__1 as select a.email_address as
email_address,a.first_name as first_name,a.institution as
institution,a.password as password,a.surname as surname,a.user_id as
user_id_key,b.created as created,b.name as name,b.type_name as
type_name,b.user_id as user_id_core_object from public.users as a left
join public.core_object as b on a.user_id_key=b.accession;
the last condition refers to a non existant column a.user_id_key,
which should actually be a.user_id ( because user_id_key is the name
generated for the new field, not the original datasource name...)
i suspect it is not easy to recongifure things like this - but am i
missing something??
I am registering for the dev list - but this seems to be 'non-instant'
Hi Trevor,
hmm ... it should be instant :)
I have subscribed you now
your table looks perfectly ok, apart from the fact that it does not
comply with biomart naming convention but this would only cause
problems later on during configuration step.
In fact 'create table as select ...'
is is how we generate all our marts
Could you send us the exact SQL error you seeing?
we'll see if we can help
(just a guess ... perhaps 'from public.users as a' is not correct,
maybe 'from public.users a' should be ok?) what rdbms are you working
with?
a.
ta
Trevor Paterson
Bioinformatics
Roslin Institute
Scotland EH25 9PS
phone +44 (0) 131 5274477
http://www.roslin.ac.uk/
http://www.thearkdb.org/
http://www.comparagrid.org/
Roslin Institute is a company limited by guarantee, registered in
Scotland (registered number SC157100) and a Scottish Charity
(registered number SC023592). Our registered office is at Roslin,
Midlothian, EH25 9PS. VAT registration number 847380013.
The information contained in this e-mail (including any attachments)
is confidential and is intended for the use of the addressee only.
The opinions expressed within this e-mail (including any attachments)
are the opinions of the sender and do not necessarily constitute those
of Roslin Institute (Edinburgh) ("the Institute") unless specifically
stated by a sender who is duly authorised to do so on behalf of the
Institute
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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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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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