Thanks Damian, for the input, I've modified the defaultMartRegistry.xml
file but the error persists.
This is what I have in the meta_user table.
mysql> select * from meta_user;
+-----------+---------+
| datasetID | user |
+-----------+---------+
| 1 | default |
+-----------+---------+
1 row in set (0.04 sec)
mysql>
And this is the revised "defaultMartRegistry.xml" file
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE MartRegistry>
<MartRegistry>
<MartDBLocation
name = "msd_mart_4"
displayName = "My BioMart Database"
databaseType = "mysql"
host = "localhost"
port = "3306"
instanceName = "msd_mart_4"
database = "msd_mart_4"
schema = "msd_mart_4"
user = "test"
password = "test"
visible = "1"
default = "1"
includeDatasets = "msd_mart_4"
martUser="default"
/>
</MartRegistry>
And this is the attempt to deploy the site along with the error output.
[EMAIL PROTECTED] ~]$ date;time /usr/local/ASF/httpd/apache_1.3.35/bin/httpd
-d /usr/local/src/biomart/biomart-web.other/biomart-web;date;
Mon May 15 17:23:41 SAST 2006
Starting up Ensembl server on host: fusion.sanbi.ac.za:9999
Loading perl startup file...
==============================================================================
[MARTCONF][INFO] Retrieving configuration:
------------------------------------------------------------------------------
Use of uninitialized value in concatenation (.) or string at
/usr/local/src/biomart/biomart-web.other/biomart-web/biomart-plib/BioMart/Configuration/DBLocation.pm
line 113.
WARNING: Could not connect to database msd_mart_4:
SKIPPING at
/usr/local/src/biomart/biomart-web.other/biomart-web/biomart-plib/BioMart/Configuration/DBLocation.pm
line 113.
Had to create DBD::mysql::dr::imp_data_size unexpectedly at
/usr/lib/perl5/vendor_perl/5.8.6/i386-linux-thread-multi/DBI.pm line 1167.
Had to create DBD::mysql::db::imp_data_size unexpectedly at
/usr/lib/perl5/vendor_perl/5.8.6/i386-linux-thread-multi/DBI.pm line 1167.
Use of uninitialized value in concatenation (.) or string at
/usr/local/src/biomart/biomart-web.other/biomart-web/biomart-plib/BioMart/Configuration/DBLocation.pm
line 113.
WARNING: Could not connect to database msd_mart_4:
SKIPPING at
/usr/local/src/biomart/biomart-web.other/biomart-web/biomart-plib/BioMart/Configuration/DBLocation.pm
line 113.
Syntax error on line 246 of
/usr/local/src/biomart/biomart-web.other/biomart-web/conf/httpd.conf:
Can't call method "prepare" on an undefined value at
/usr/local/src/biomart/biomart-web.other/biomart-web/biomart-plib/BioMart/Configuration/MartDBLocation.pm
line 143.
Compilation failed in require at
/usr/local/src/biomart/biomart-web.other/biomart-web/conf/httpd.conf
line 241.
real 0m0.755s
user 0m0.636s
sys 0m0.052s
Mon May 15 17:23:42 SAST 2006
[EMAIL PROTECTED] ~]$
Damian Smedley wrote:
do you have a entry in the meta_user table for "test" - otherwise set the
martUser = "" or whatever you have in that table
cheers
Damian
On Fri, 12 May 2006, allank wrote:
The error persist, this time the error messages look a little different.
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE MartRegistry>
<MartRegistry>
<MartDBLocation
name = "msd_mart_4"
displayName = "My BioMart Database"
databaseType = "mysql"
host = "localhost"
port = "3306"
database = "msd_mart_4"
schema = "msd_mart_4"
user = "test"
password = "test"
visible = "1"
default = ""
includeDatasets = ""
martUser = "test"
/>
</MartRegistry>
[EMAIL PROTECTED] XML-Simple-2.13]$ date;time
/usr/local/ASF/httpd/apache_1.3.35/bin/httpd -d
/usr/local/src/biomart/biomart-web.other/biomart-web;date;
Fri May 12 17:21:04 SAST 2006
Starting up Ensembl server on host: fusion.sanbi.ac.za:9999
Loading perl startup file...
==============================================================================
[MARTCONF][INFO] Retrieving configuration:
------------------------------------------------------------------------------
Use of uninitialized value in concatenation (.) or string at
/usr/local/src/biomart/biomart-web.other/biomart-web/biomart-plib/BioMart/Configuration/DBLocation.pm
line 113.
WARNING: Could not connect to database msd_mart_4:
SKIPPING at
/usr/local/src/biomart/biomart-web.other/biomart-web/biomart-plib/BioMart/Configuration/DBLocation.pm
line 113.
Had to create DBD::mysql::dr::imp_data_size unexpectedly at
/usr/lib/perl5/vendor_perl/5.8.6/i386-linux-thread-multi/DBI.pm line 1167.
Had to create DBD::mysql::db::imp_data_size unexpectedly at
/usr/lib/perl5/vendor_perl/5.8.6/i386-linux-thread-multi/DBI.pm line 1167.
Use of uninitialized value in concatenation (.) or string at
/usr/local/src/biomart/biomart-web.other/biomart-web/biomart-plib/BioMart/Configuration/DBLocation.pm
line 113.
WARNING: Could not connect to database msd_mart_4:
SKIPPING at
/usr/local/src/biomart/biomart-web.other/biomart-web/biomart-plib/BioMart/Configuration/DBLocation.pm
line 113.
Syntax error on line 246 of
/usr/local/src/biomart/biomart-web.other/biomart-web/conf/httpd.conf:
Can't call method "prepare" on an undefined value at
/usr/local/src/biomart/biomart-web.other/biomart-web/biomart-plib/BioMart/Configuration/MartDBLocation.pm
line 143.
Compilation failed in require at
/usr/local/src/biomart/biomart-web.other/biomart-web/conf/httpd.conf
line 241.
real 0m0.719s
user 0m0.556s
sys 0m0.080s
Fri May 12 17:21:05 SAST 2006
Damian Smedley wrote:
ok spotted it - you just need to change the tags in the Registry file from
RegistryDBPointer to MartDBLocation. If you look at the example in
exampleSimpleMartRegistry.xml in the same dir you will get the idea. Other
than that the registry is probably fine
cheers
Damian
On Fri, 12 May 2006, allank wrote:
Hi Damian,
Thanks for the reply, I've populated the meta_interface and meta_user tables as
advised but the error persists.
Attached find the
"/usr/local/src/biomart/biomart-web.other/biomart-web/biomart-plib/conf/defaultMartRegistry.xml"
Allan.
Damian Smedley wrote:
Hi Allan
can you send me your defaultMartRegistry.xml file just to make sure.
Also trying adding values(1,'default') to the meta_interface and meta_user
table. Pretty sure they have to be populated. Let us know if that helps
and we will fix the ftp dump
Best wishes
Damian
On Fri, 12 May 2006, allank wrote:
Hi all,
I am trying to configure Biomart on my workstation. But I am unable a
database connection on biomart-web web application, for martj-0.4, I
have managed to obtain a connection but I receive “no datasets in this
database” message when I attempt an import. When I fire up apache web
server and supply the path to biomart-web directory I get the error
below[^].
For both the biomart-web and martj-0.4, I have modified the
“defaultMartRegistry” accordingly to match the database connection
requirements.
I have setup a local msd_mart_4 database with data and schema definition
from “ftp://ftp.ebi.ac.uk/pub/databases/biomart/current/msd_mart_4/” and
populated all the meta_% tables with the exception of meta_interface and
meta_user tables whose sqldump data files appear to be empty, I however
did not populate the msd_% tables.
Regards,
Allan.
[^]
[EMAIL PROTECTED] biomart-web.other]$ date;time
/usr/local/ASF/httpd/apache_1.3.35/bin/httpd -d
/usr/local/src/biomart/biomart-web.other/biomart-web;date;
Fri May 12 12:01:06 SAST 2006
Starting up Ensembl server on host: fusion.sanbi.ac.za:9999
Loading perl startup file...
==============================================================================
[MARTCONF][INFO] Retrieving configuration:
------------------------------------------------------------------------------
Use of uninitialized value in concatenation (.) or string at
/usr/local/src/biomart/biomart-web.other/biomart-web/biomart-plib/BioMart/Configuration/DBLocation.pm
line 113.
WARNING: Could not connect to database msd_mart_4:
SKIPPING at
/usr/local/src/biomart/biomart-web.other/biomart-web/biomart-plib/BioMart/Configuration/DBLocation.pm
line 113.
WARNING: Could not load Registry from database
dbi:mysql:database=msd_mart_4;host=localhost;port=3306, SKIPPING
Syntax error on line 246 of
/usr/local/src/biomart/biomart-web.other/biomart-web/conf/httpd.conf:
-------------------- EXCEPTION --------------------
DATE: 12-MAY-2006
MSG: Problems with the retrival 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)
STACK BioMart::Initializer::_new
/usr/local/src/biomart/biomart-web.other/biomart-web/biomart-plib/BioMart/Initializer.pm:172
STACK BioMart::RootI::new
/usr/local/src/biomart/biomart-web.other/biomart-web/biomart-plib/BioMart/RootI.pm:54
STACK (eval)
/usr/local/src/biomart/biomart-web.other/biomart-web/conf/perl.startup:86
STACK (eval)
/usr/local/src/biomart/biomart-web.other/biomart-web/conf/httpd.conf:241
STACK toplevel
/usr/local/src/biomart/biomart-web.other/biomart-web/conf/perl.startup:0
-------------------------------------------
at
/usr/local/src/biomart/biomart-web.other/biomart-web/conf/perl.startup
line 86
Compilation failed in require at
/usr/local/src/biomart/biomart-web.other/biomart-web/conf/httpd.conf
line 241.
real 0m2.858s
user 0m0.600s
sys 0m0.148s
Fri May 12 12:01:09 SAST 2006
