On 21 Dec 2006, at 13:44, Marina Olhovsky wrote:
Sorry about that, Arek!
This is what I asked:
I've set up a mart and am trying to configure Martview for searching.
I am using PostgreSQL on localhost. My source database used to
generate the mart is called "reagent_tracker" residing in 'public'
schema. I've placed the generated mart in a new schema that I've also
named "reagent_tracker". It contains two datasets (reagents_tbl and
wells_tbl) in the following tables:
reagent_tracker.meta_conf__dataset__main
reagent_tracker.meta_template__xml__dm
reagent_tracker.reagents_tbl__reagentproplist_tbl__dm
reagent_tracker.meta_conf__interface__dm
reagent_tracker.meta_version__version__main
reagent_tracker.reagents_tbl__reagents_tbl__main
reagent_tracker.meta_conf__user__dm
reagent_tracker.reagents_tbl__association_tbl__dm
reagent_tracker.wells_tbl__prep_tbl__dm
reagent_tracker.meta_conf__xml__dm
reagent_tracker.reagents_tbl__experiment_tbl__dm
reagent_tracker.wells_tbl__wells_tbl__main
reagent_tracker.meta_template__template__main
reagent_tracker.reagents_tbl__packets_tbl__dm
This is what my registry file looks like:
<MartRegistry>
<virtualSchema name="default" visible="1" default="1">
<MartDBLocation
name="reagent_tracker"
displayName="Reagent Tracker"
databaseType="postgres"
host="localhost"
database="reagent_tracker"
port="5432"
schema="reagent_tracker"
user="olhovsky"
password="my_passwd"
includeDatasets=""
martUser = ""
/>
</virtualSchema>
</MartRegistry>
I get the following error on configuration:
perl bin/configure.pl -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/sbin/httpd2
[1]:
Got usable Apache in /usr/sbin/httpd2, 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
Processing Cached Registry:
/home/olhovsky/biomart-perl/conf/cachedRegistries/
myRegistry.xml.cached
Can't use an undefined value as an ARRAY reference at
/home/olhovsky/biomart-perl/bin/configureBioMart.pl line 375.
This is the output of running config with --clean option:
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/sbin/httpd2
[1]:
Got usable Apache in /usr/sbin/httpd2, 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 visible in MartDBLocation
location:reagent_tracker not defined - setting to default values
Optional setting for default in MartDBLocation
location:reagent_tracker not defined - setting to default values
[NEW CONFIGURATION] .... WITH MEMORY [default]
default ... Reagent Tracker .......... 001/001 ... reagents_tbl
.............................. (RDBMS) localhost:5432
................ OK
Setting possible links between datasets
....(scanning) 100%
....(linking) 100%
....(sorting) 100%
....(clustering) 1/1 - 0 remain
....(resolving) 100%
Building templates for visible datasets
Uh-oh, got some non-fatal warnings:
Use of uninitialized value in print at
/home/olhovsky/biomart-perl/bin/configureBioMart.pl line 353.
Hi Marina,
yes this looks a bit weird. Your xml is pulled out ok but then it dies
on templates.
There is nothing that immidiately strikes me as being a possible problem
Is there a chance that you could send us (off the list) your xml so we
could investigate
a bit here?
(you need to use MEditor, connect to your mart and 'save all' to the
file) and please
send us this file (probably tar.gz)
thanks
a.
Thank you very much.
Marina.
-----Original Message-----
From: Arek Kasprzyk [mailto:[EMAIL PROTECTED]
Sent: Thu 12/21/2006 3:27 AM
To: Marina Olhovsky
Subject: Re: [mart-dev] RE: Configuration error
On 20 Dec 2006, at 23:31, Marina Olhovsky wrote:
you need to try again :)
has your mail client got the 'Format->make plain text' option?
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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