Hello,
I'm trying to install BioMart 0.7, but I'm having trouble getting it to
configure to my registry file. I created the mart (on oracle) using
martbuilder, and am able to open it using mart editor, but when I run the
>>perl bin/configure.pl -r conf/biomart.xml
command, it keeps giving me the "Problems with the retrieval of dataset
configuration" error (pasted below.) I was able to get it running using the
sample XML file that came with it (martDBLocation.xml) and when I replace
default defaultMartRegistry.xml file in martj0.7, I am able to load it up
using martrunner and query around in it just fine... so I don't think the
mart is ill-formatted..
Was wondering if someone had any idea as to what's going on, or could offer
any insight?
here is my registry file: (the host, database and password fields are
normally filled in)
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE MartRegistry>
<MartRegistry>
<virtualSchema name="default">
<MartDBLocation
name = "bm"
displayName = "biomart"
databaseType = "oracle"
host = "(host)"
port = "1521"
database = "(database)"
schema = "bm"
user = "bm"
password = "(password)"
visible = "1"
default = ""
includeDatasets = ""
/>
</virtualSchema>
</MartRegistry>
here is the error:
[bash $]# perl bin/configure.pl -r conf/biomart.xml
Do you want to install in API only mode [y/n] [n]: n
Checking prerequisites ...[Looks good]
{excerpt}
Got usable Apache in /usr/local/apache-2.2.13/bin/httpd, probing for version
& ModPerl configuration
Have Apache DSO-support and ModPerl library file present, configuring
ModPerl in httpd.conf.
Libdir /var/www/biomart/lib is not in @INC, adding to @INC
Cached Registry Unavailable...
Running Complete Clean...
Optional setting for martUser in MartDBLocation location:bm not defined -
setting to default values
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
COULD NOT CONNECT TO DATABASE bm.CHECK YOUR SETTINGS
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
ERROR something wrong with your registry: Problems with the retrieval 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)
Trace begun at /var/www/biomart/bin/../lib/BioMart/Initializer.pm line 254
BioMart::Initializer::_init('BioMart::Initializer=HASH(0x12745040)',
'registryFile', '/var/www/biomart/conf/biomart.xml', 'action', 'cached',
'mode', 'memory') called at
/var/www/biomart/bin/../lib/BioMart/Initializer.pm line 377
BioMart::Initializer::init_clean('BioMart::Initializer=HASH(0x12745040)',
'registryFile', '/var/www/biomart/conf/biomart.xml', 'action', 'cached',
'mode', 'memory') called at
/var/www/biomart/bin/../lib/BioMart/Initializer.pm line 328
BioMart::Initializer::init_cached('BioMart::Initializer=HASH(0x12745040)',
'registryFile', '/var/www/biomart/conf/biomart.xml', 'action', 'cached',
'mode', 'memory') called at
/var/www/biomart/bin/../lib/BioMart/Initializer.pm line 168
BioMart::Initializer::_new('BioMart::Initializer=HASH(0x12745040)',
'registryFile', '/var/www/biomart/conf/biomart.xml', 'action', 'cached',
'mode', 'memory') called at /var/www/biomart/bin/../lib/BioMart/RootI.pm
line 64
BioMart::RootI::new('BioMart::Initializer', 'registryFile',
'/var/www/biomart/conf/biomart.xml', 'action', 'cached', 'mode', 'memory')
called at /var/www/biomart/bin/configureBioMart.pl line 331
eval {...} at /var/www/biomart/bin/configureBioMart.pl line 330
Thanks in advance,
Cynthia Lee
