Hi Arek and Damian,
I have finally managed to connect the local database using biomart-web.
In the earlier situation, I ran a small perl script to connect to the
database (as advised by Arek) and it seemed I had a problem with
DBD::mysql on my setup
(http://dev.mysql.com/doc/refman/5.0/en/perl-support-problems.html) I
configured and installed mysql from source and then installed the
failing DBD::mysql module, I ran the “make test” before the installation
of DBD::mysql and all tests were successful. I installed the msd_mart_4
database, I set my $LD_LIBRARY_PATH to include the mysql directory where
the shared libraries reside. The site now starts without errors. Thank
you all for your assistance.
Allan.
Arek Kasprzyk wrote:
On 16 May 2006, at 13:40, allank wrote:
Hi Alan,
I am not sure if this is of much help but I just downloaded the full
content
of what we have on msd_mart_4 under current on my laptop.
Imported it with no problems:
bigmac: ~/Desktop/msd_ftp/msd_mart_4[arek] mysql -uroot msd_current
<table.sql
bigmac: ~/Desktop/msd_ftp/msd_mart_4[arek] mysqlimport -uroot -L
msd_current *txt
msd_current.meta_conf__dataset__main: Records: 1 Deleted: 0 Skipped: 0
Warnings: 0
msd_current.meta_conf__interface__dm: Records: 1 Deleted: 0 Skipped: 0
Warnings: 0
msd_current.meta_conf__user__dm: Records: 1 Deleted: 0 Skipped: 0
Warnings: 0
msd_current.meta_conf__xml__dm: Records: 1 Deleted: 0 Skipped: 0
Warnings: 0
msd_current.meta_configuration: Records: 1 Deleted: 0 Skipped: 0
Warnings: 0
msd_current.meta_interface: Records: 0 Deleted: 0 Skipped: 0 Warnings: 0
msd_current.meta_user: Records: 0 Deleted: 0 Skipped: 0 Warnings: 0
msd_current.meta_version__version__main: Records: 1 Deleted: 0
Skipped: 0 Warnings: 0
msd_current.msd__assembly__main: Records: 40306 Deleted: 0 Skipped: 0
Warnings: 0
msd_current.msd__assembly_type__look: Records: 36 Deleted: 0 Skipped:
0 Warnings: 0
msd_current.msd__cath__dm: Records: 186629 Deleted: 0 Skipped: 0
Warnings: 0
msd_current.msd__chain__main: Records: 162438 Deleted: 0 Skipped: 0
Warnings: 0
msd_current.msd__ec__dm: Records: 34374 Deleted: 0 Skipped: 0 Warnings: 0
msd_current.msd__entry__main: Records: 32537 Deleted: 0 Skipped: 0
Warnings: 0
msd_current.msd__exp_type__look: Records: 15 Deleted: 0 Skipped: 0
Warnings: 0
msd_current.msd__go__dm: Records: 0 Deleted: 0 Skipped: 0 Warnings: 0
msd_current.msd__hetgroup__dm: Records: 60769 Deleted: 0 Skipped: 0
Warnings: 0
msd_current.msd__interpro__dm: Records: 105098 Deleted: 0 Skipped: 0
Warnings: 0
msd_current.msd__journal__dm: Records: 56478 Deleted: 0 Skipped: 0
Warnings: 0
msd_current.msd__keyword__dm: Records: 107177 Deleted: 0 Skipped: 0
Warnings: 0
msd_current.msd__pfam__dm: Records: 55703 Deleted: 0 Skipped: 0
Warnings: 0
msd_current.msd__scop__dm: Records: 181621 Deleted: 0 Skipped: 0
Warnings: 0
msd_current.msd__sws__dm: Records: 175741 Deleted: 0 Skipped: 0
Warnings: 0
msd_current.msd__taxonomy__dm: Records: 162438 Deleted: 0 Skipped: 0
Warnings: 0
started the up to date server v. 0.4 _without_ any additional editing
anywhere:
bigmac: ~/websites/biomart-04/biomart-web[arek] apachem .
Starting up Ensembl server on host: bigmac:9999
Loading perl startup file...
========================================================================
======
[MARTCONF][INFO] Removed 3 HTML template files
[MARTCONF][INFO] Retrieving configuration:
------------------------------------------------------------------------
------
Software/configuration version check: 0.4 My BioMart Database OK
DATASET default ... My BioMart Database ..... 001/001 ... msd
....................................... (RDBMS) 127.0.0.1:3306
................ OK
------------------------------------------------------------------------
------
[MARTCONF][INFO] Writing Configuration to
/Users/arek/websites/biomart-04/biomart-web/conf/martconf.packed at
/Users/arek/websites/biomart-04/biomart-web/conf/perl.startup line 92.
------------------------------------------------------------------------
------
with the following mart registry file:
bigmac: ~/websites/biomart-04/biomart-web[arek] cat
biomart-plib/conf/defaultMartRegistry.xml
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE MartRegistry>
<MartRegistry>
<MartDBLocation
name = "msd_mart_4"
displayName = " My BioMart Database"
databaseType = "mysql"
host = "127.0.0.1"
port = "3306"
database = "msd_current"
schema = "msd_current"
user = "root"
password = ""
visible = "1"
default = ""
includeDatasets = ""
martUser = ""
/>
</MartRegistry>
did a few queries and everything appears to be working correctly
a.
------------------------------------------------------------------------
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Arek Kasprzyk
EMBL-European Bioinformatics Institute.
Wellcome Trust Genome Campus, Hinxton,
Cambridge CB10 1SD, UK.
Tel: +44-(0)1223-494606
Fax: +44-(0)1223-494468
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