On 18 May 2006, at 09:55, allank wrote:
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.
Hi Alan,
good to know it is working fine for you :)
a.
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.
----------------------------------------------------------------------
-- -------
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
----------------------------------------------------------------------
-- -------
------------------------------------------------------------------------
-------
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
------------------------------------------------------------------------
-------
