Hi Dzu,
the value of "schema" must match that of "database".
Hope this helps!
Regards,
Anthony
On 10/19/2010 04:24 PM, vile...@vt.edu wrote:
Hi, I am having problems connecting to the Biomart databases using the example
perl script given off of the site, I tried writing my own registry file and had
some suggestions on how to get it working but all I get are errors so far, here
is my registry file:
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE MartRegistry>
<MartRegistry>
<MartDBLocation
databaseType="mysql"
host="martdb.ensembl.org"
database="ensembl_mart_49"
name="ensembl"
displayName="ENSEMBL 59 GENE (SANGER UK)"
port="5316"
schema="snp_mart_59"
user="anonymous"
password=""
visible="1"
default="1"
martUser=""
includeDatasets="" />
</MartRegistry>
And I recieve this error when running Perl:
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
COULD NOT CONNECT TO DATABASE ensembl_mart_49.CHECK YOUR SETTINGS
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Problems with the retrieval of dataset configuration
Please check:
that your mart Registry files contains correct connection
params,
that you are using the correct version on XML::Simple,
that BioMart databases contain a populated meta_conf tables and
that you have set martUser correctly if you are running in
restricted data
access mode (populated meta_conf__user__dm)
Is there a syntax error in my registry file or am I doing something else wrong?
Thank you.
Dzu
