ok spotted it - you just need to change the tags in the Registry file from RegistryDBPointer to MartDBLocation. If you look at the example in exampleSimpleMartRegistry.xml in the same dir you will get the idea. Other than that the registry is probably fine
cheers Damian On Fri, 12 May 2006, allank wrote: > 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 > >> > >> > >> > >> > > > > > > > >
