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/
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Arek Kasprzyk
EMBL-European Bioinformatics Institute.
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