Hi Damian,
Thanks for the reply, I've populated the meta_interface and meta_user tables as
advised but the error persists.
Attached find the
"/usr/local/src/biomart/biomart-web.other/biomart-web/biomart-plib/conf/defaultMartRegistry.xml"
Allan.
Damian Smedley wrote:
Hi Allan
can you send me your defaultMartRegistry.xml file just to make sure.
Also trying adding values(1,'default') to the meta_interface and meta_user
table. Pretty sure they have to be populated. Let us know if that helps
and we will fix the ftp dump
Best wishes
Damian
On Fri, 12 May 2006, allank wrote:
Hi all,
I am trying to configure Biomart on my workstation. But I am unable a
database connection on biomart-web web application, for martj-0.4, I
have managed to obtain a connection but I receive “no datasets in this
database” message when I attempt an import. When I fire up apache web
server and supply the path to biomart-web directory I get the error
below[^].
For both the biomart-web and martj-0.4, I have modified the
“defaultMartRegistry” accordingly to match the database connection
requirements.
I have setup a local msd_mart_4 database with data and schema definition
from “ftp://ftp.ebi.ac.uk/pub/databases/biomart/current/msd_mart_4/” and
populated all the meta_% tables with the exception of meta_interface and
meta_user tables whose sqldump data files appear to be empty, I however
did not populate the msd_% tables.
Regards,
Allan.
[^]
[EMAIL PROTECTED] biomart-web.other]$ date;time
/usr/local/ASF/httpd/apache_1.3.35/bin/httpd -d
/usr/local/src/biomart/biomart-web.other/biomart-web;date;
Fri May 12 12:01:06 SAST 2006
Starting up Ensembl server on host: fusion.sanbi.ac.za:9999
Loading perl startup file...
==============================================================================
[MARTCONF][INFO] Retrieving configuration:
------------------------------------------------------------------------------
Use of uninitialized value in concatenation (.) or string at
/usr/local/src/biomart/biomart-web.other/biomart-web/biomart-plib/BioMart/Configuration/DBLocation.pm
line 113.
WARNING: Could not connect to database msd_mart_4:
SKIPPING at
/usr/local/src/biomart/biomart-web.other/biomart-web/biomart-plib/BioMart/Configuration/DBLocation.pm
line 113.
WARNING: Could not load Registry from database
dbi:mysql:database=msd_mart_4;host=localhost;port=3306, SKIPPING
Syntax error on line 246 of
/usr/local/src/biomart/biomart-web.other/biomart-web/conf/httpd.conf:
-------------------- EXCEPTION --------------------
DATE: 12-MAY-2006
MSG: Problems with the retrival 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)
STACK BioMart::Initializer::_new
/usr/local/src/biomart/biomart-web.other/biomart-web/biomart-plib/BioMart/Initializer.pm:172
STACK BioMart::RootI::new
/usr/local/src/biomart/biomart-web.other/biomart-web/biomart-plib/BioMart/RootI.pm:54
STACK (eval)
/usr/local/src/biomart/biomart-web.other/biomart-web/conf/perl.startup:86
STACK (eval)
/usr/local/src/biomart/biomart-web.other/biomart-web/conf/httpd.conf:241
STACK toplevel
/usr/local/src/biomart/biomart-web.other/biomart-web/conf/perl.startup:0
-------------------------------------------
at
/usr/local/src/biomart/biomart-web.other/biomart-web/conf/perl.startup
line 86
Compilation failed in require at
/usr/local/src/biomart/biomart-web.other/biomart-web/conf/httpd.conf
line 241.
real 0m2.858s
user 0m0.600s
sys 0m0.148s
Fri May 12 12:01:09 SAST 2006
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