On 11 Jan 2007, at 18:36, Marina Olhovsky wrote:
Hi Arek/Richard,
I'm trying to custommize my Martview to look like the one on your
server, making several datasets available for search. I've changed
the XML config file from MartDBLocation to MartURLLocation as follows:
<MartRegistry>
<MartURLLocation
name = "test_mart"
displayName = "test_mart"
host = "localhost"
port = "5555"
visible = "1"
default = "1"
includeDatasets = "my_dataset"
martUser = ""
/>
</MartRegistry>
I'm getting the following command-line errors:
% perl bin/configure.pl --clean -r conf/myRegistry.xml
Do you want to install in API only mode [y/n] [n]: n
Checking prerequisites ...[Looks good]
DO YOU WANT TO USE EXISTING SERVER CONFIGURATION [y/n] [y]: n
Checking several common Apache locations...done.
Select either one of the detected httpd paths on the list, OR enter
the path you wish to use:
/usr/local/bin/httpd
/usr/sbin/httpd2
[1]:
Got usable Apache in /usr/local/bin/httpd, probing for version &
ModPerl configuration
Have Apache DSO-support and ModPerl library file present, configuring
ModPerl in httpd.conf.
Enter the server host OR default [p53]:
Enter the server port OR default [5555]:
Enter proxy OR default :
Enter the required script location OR default [biomart]:
Libdir /home/olhovsky/biomart-perl/lib is not in @INC, adding to @INC
Optional setting for serverVirtualSchema in MartURLLocation
location:test_mart not defined - setting to default values
Optional setting for path in MartURLLocation location:test_mart not
defined - setting to default values
Use of uninitialized value in string eq at
/home/olhovsky/biomart-perl/bin/../lib/BioMart/Configuration/
MartURLLocation.pm line 135.
ERROR something wrong with your registry:
No datasets available with given parameters for
Location: test_mart
Trace begun at
/home/olhovsky/biomart-perl/bin/../lib/BioMart/Initializer.pm line
1001
BioMart::Initializer::_populateRegistry('BioMart::
Initializer=HASH(0x93a05c4)') called at
/home/olhovsky/biomart-perl/bin/../lib/BioMart/Initializer.pm line 244
BioMart::Initializer::_init('BioMart::Initializer=HASH(0x93a05c4)',
'registryFile', '/home/olhovsky/biomart-perl/conf/myRegistry.xml',
'action', 'clean', 'mode', 'memory') called at
/home/olhovsky/biomart-perl/bin/../lib/BioMart/Initializer.pm line 393
BioMart::Initializer::init_clean('BioMart::
Initializer=HASH(0x93a05c4)', 'registryFile',
'/home/olhovsky/biomart-perl/conf/myRegistry.xml', 'action', 'clean',
'mode', 'memory') called at
/home/olhovsky/biomart-perl/bin/../lib/BioMart/Initializer.pm line 160
BioMart::Initializer::_new('BioMart::Initializer=HASH(0x93a05c4)',
'registryFile', '/home/olhovsky/biomart-perl/conf/myRegistry.xml',
'action', 'clean', 'mode', 'memory') called at
/home/olhovsky/biomart-perl/bin/../lib/BioMart/RootI.pm line 42
BioMart::RootI::new('BioMart::Initializer', 'registryFile',
'/home/olhovsky/biomart-perl/conf/myRegistry.xml', 'action', 'clean',
'mode', 'memory') called at
/home/olhovsky/biomart-perl/bin/configureBioMart.pl line 339
eval {...} at /home/olhovsky/biomart-perl/bin/configureBioMart.pl
line 338
Marina -
this URLLocation will only pick up one dataset called "my_dataset".
(if there is no such dataset on web server localhost:5555 then you will
see the error message as above)
The server you are trying to configure will talk to another
local BioMart server running on port 5555 using a web service.
If you want more than one dataset you need to leave 'includeDatasets'
empty.
However, I am not sure that I understand why you want to talk to
another local BioMart server
rather than talking directly to your postgress instance through
MartDBLocation?
Is it not the case that you need MartDBLocation set to talk to your
postgress database or
MartURLLocation talking to a public server eg. www.biomart.org? Why are
you trying
to 'chain' local servers like that? I simply don't understand what you
are trying to do. Could
you elaborate on this a bit? maybe there is an alternative way of doing
what you are trying to do
a.
Your help is most appreciated.
Best regards,
Marina.
---------------------------------------------------------
Marina Olhovsky
Software Engineer, Pawson Laboratory
Mount Sinai Hospital
600 University Avenue, Room 1060
Toronto, Ontario, M5G 1X5
[EMAIL PROTECTED]
---------------------------------------------------------
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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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