do you have a entry in the meta_user table for "test" - otherwise set the martUser = "" or whatever you have in that table
cheers Damian On Fri, 12 May 2006, allank wrote: > The error persist, this time the error messages look a little different. > > <?xml version="1.0" encoding="UTF-8"?> > <!DOCTYPE MartRegistry> > <MartRegistry> > <MartDBLocation > name = "msd_mart_4" > displayName = "My BioMart Database" > databaseType = "mysql" > host = "localhost" > port = "3306" > database = "msd_mart_4" > schema = "msd_mart_4" > user = "test" > password = "test" > visible = "1" > default = "" > includeDatasets = "" > martUser = "test" > /> > </MartRegistry> > > > [EMAIL PROTECTED] XML-Simple-2.13]$ 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 17:21:04 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. > Had to create DBD::mysql::dr::imp_data_size unexpectedly at > /usr/lib/perl5/vendor_perl/5.8.6/i386-linux-thread-multi/DBI.pm line 1167. > Had to create DBD::mysql::db::imp_data_size unexpectedly at > /usr/lib/perl5/vendor_perl/5.8.6/i386-linux-thread-multi/DBI.pm line 1167. > 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. > Syntax error on line 246 of > /usr/local/src/biomart/biomart-web.other/biomart-web/conf/httpd.conf: > Can't call method "prepare" on an undefined value at > /usr/local/src/biomart/biomart-web.other/biomart-web/biomart-plib/BioMart/Configuration/MartDBLocation.pm > > line 143. > Compilation failed in require at > /usr/local/src/biomart/biomart-web.other/biomart-web/conf/httpd.conf > line 241. > > > real 0m0.719s > user 0m0.556s > sys 0m0.080s > Fri May 12 17:21:05 SAST 2006 > > Damian Smedley wrote: > > >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 > >>>> > >>>> > >>>> > >>>> > >>>> > >>>> > >>> > >>> > >>> > >>> > >> > >> > > > > > > > >
