Re: [mart-dev] biomart0.6 configuration problems

[Li Jin]

Syed,
Only martj-0.6 can be dowloaded by 
ftp://[EMAIL PROTECTED]/pub/software/biomart/martj_current/martj-bin.tgz
what is the release name of martj head?
I am working remotely with ssh, so I could not use the GUI of martEditor. 
That is why I wanted to edit regitry file with hand. I will use martEditor 
locally to generate the configuration files.

-- Li

On Sun, 6 Apr 2008, Syed Haider wrote:

On Sun, 2008-04-06 at 14:02 -0400, Li Jin wrote:
Hi, Syed,
In fact, at beginning when I installed biomart, I did not use MSD data. I
only followed http://www.biomart.org/user-docs.pdf and created a simple
database called mydataset and created only one table and added one record
into the table.

create table mydataset__mycontent__main (
mypk_key int not null,
mynumber int,
mystring varchar2(20)
);

you can create an empty database, add this table with at least one
record and connect to it using martEditor (please use martj Head and not
release-0_6). Run 'naive' from marteditor and export. Details about
MartEditor are in the docs.  The use biomart-perl to see the impact.



But I do not know the meta* table schema so I downloaded msd from biomart.
ftp://ftp.ebi.ac.uk/pub/databases/biomart/current/

I did not dump all data into the database. I am doing it now. I will send
information later to you.

Thanks,
--Li

On Sun, 6 Apr 2008, Syed Haider wrote:

Hi Li,

firstly you need to create  a database (Mart) where you must have at
least one record in your main table. Seems, you have copied the meta
tables from msd. Anyways, if you have copied msd mart, then you are
missing data in meta tables, they should have some data in them.

firstly, please explain how are you approaching Mart building process -
where did you get these tables from ?

syed

On Sun, 2008-04-06 at 13:06 -0400, Li Jin wrote:
Hi, Syed,
a. I did not use martj for configuration. I modify the myRegistry.xml
manually. Sould I have to use martj?

b. I did not use martEditor. SHould I have to use martEditor?

c. I have the following meta* tables in database:
  meta_conf__dataset__main    |
| meta_conf__interface__dm    |
| meta_conf__user__dm         |
| meta_conf__xml__dm          |
| meta_configuration          |
| meta_interface              |
| meta_user                   |
| meta_version__version__main |

mysql> select * from meta_conf__dataset__main;
+----------------+---------+--------------+---------------------+----------+---------+---------------+----------------+
| dataset_id_key | dataset | display_name | description         | type
| visible | version       | modified       |
+----------------+---------+--------------+---------------------+----------+---------+---------------+----------------+
|              1 | msd     | MSD          |  protein structures | TableSet
|       1 | 15-2005_07_28 | 20060124143506 |
+----------------+---------+--------------+---------------------+----------+---------+---------------+----------------+
1 row in set (0.00 sec)

mysql> select * from meta_conf__interface__dm;
Empty set (0.02 sec)
mysql> select * from meta_conf__user__dm ;
+----------------+-----------+
| dataset_id_key | mart_user |
+----------------+-----------+
|              1 | default   |
+----------------+-----------+
1 row in set (0.04 sec)


mysql> select * from meta_conf__xml__dm ;
Empty set (0.02 sec)

mysql> select * from meta_configuration ;
Empty set (0.00 sec)

mysql> select * from  meta_interface ;
Empty set (0.06 sec)

mysql> select * from meta_configuration ;
Empty set (0.00 sec)

mysql> select * from meta_version__version__main;
Empty set (0.03 sec)


Thank you!
--Li



On Sun, 6 Apr 2008, Syed Haider wrote:

Hi Li,

a- which martj version you are using ?

b- could you do 'Save All' from martEditor and send me all the XML
files.

c- could you check your database for tables like 'meta%' and see if you
have any data in them, please confirm.

syed


On Sun, 2008-04-06 at 12:12 -0400, Li Jin wrote:
Hi, Arek and biomart developers,

When I install biomart0.6, I got the problem as
ERROR something wrong with your registry: could not load module
BioMart::Dataset::: Can't locate BioMart/Dataset/.pm in @INC

Anybody can help me? I saw the similiar problem discussed before
http://osdir.com/ml/science.biology.biomart.general/2006-12/msg00014.html.
But I still could not figure it out myself.

Thanks,
Li

Here is my myRegistry.xml:

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE MartRegistry>
<MartRegistry>

<virtualSchema name="default" visible="0" default="1">
<MartDBLocation
         name = "example"
         displayName = "example"
         databaseType = "mysql"
         host = "localhost"
         port = "3306"
         database = "mydataset"
         schema = "mydataset"
         user = "lanfei"
         password = "lanfei"
         visible = "1"
         default = ""
         includeDatasets = ""
/>
</virtualSchema>
</MartRegistry>

The following is the problem in detail:

[EMAIL PROTECTED] biomart-perl]# perl bin/configure.pl -r
conf/myRegistry.xml

Do you want to install in API only mode [y/n] [n]:

Checking prerequisites ...[Looks good]

APACHE: /usr/local/apache/bin/httpd
HOST: biomart.hljnys.com
PORT: 80
PROXY:
LOCATION:

You can change the above configuration by editing
"biomart-perl/conf/settings.conf"



Got usable Apache in /usr/local/apache/bin/httpd, probing for version &
ModPerl configuration
Have Apache DSO-support and ModPerl library file present, configuring
ModPerl in httpd.conf.
Have auxiliary Perl libdirs in $PERL5LIB, adding to @INC
Libdir /home/lanfei/biomart-perl/lib is not in @INC, adding to @INC

Cached Registry Unavailable...

Running Complete Clean...


Optional setting for martUser in MartDBLocation location:example not
defined - setting to default values

Connection parameters of [example]      [ OK ]

Use of uninitialized value in sprintf at
/home/lanfei/biomart-perl/bin/../lib/BioMart/Initializer.pm line 1173.

ERROR something wrong with your registry: could not load module
BioMart::Dataset::: Can't locate BioMart/Dataset/.pm in @INC (@INC
contains: /home/lanfei/biomart-perl/bin/../lib
/usr/local/lib/perl5/site_perl/auto
/root/installserver/2bio-perl/bioperl-live
/usr/local/lib/perl5/5.8.8/i686-linux /usr/local/lib/perl5/5.8.8
/usr/local/lib/perl5/site_perl/5.8.8/i686-linux
/usr/local/lib/perl5/site_perl/5.8.8 /usr/local/lib/perl5/site_perl .) at
(eval 118) line 3.


Trace begun at /home/lanfei/biomart-perl/bin/../lib/BioMart/Root.pm line
169
BioMart::Root::loadModule('BioMart::Initializer=HASH(0x9e40658)',
'BioMart::Dataset::') called at
/home/lanfei/biomart-perl/bin/../lib/BioMart/Initializer.pm line 1176
BioMart::Initializer::_populateRegistry('BioMart::Initializer=HASH(0x9e40658)')
called at /home/lanfei/biomart-perl/bin/../lib/BioMart/Initializer.pm line
244
BioMart::Initializer::_init('BioMart::Initializer=HASH(0x9e40658)',
'registryFile', '/home/lanfei/biomart-perl/conf/myRegistry.xml', 'action',
'cached', 'mode', 'memory') called at
/home/lanfei/biomart-perl/bin/../lib/BioMart/Initializer.pm line 393
BioMart::Initializer::init_clean('BioMart::Initializer=HASH(0x9e40658)',
'registryFile', '/home/lanfei/biomart-perl/conf/myRegistry.xml', 'action',
'cached', 'mode', 'memory') called at
/home/lanfei/biomart-perl/bin/../lib/BioMart/Initializer.pm line 344
BioMart::Initializer::init_cached('BioMart::Initializer=HASH(0x9e40658)',
'registryFile', '/home/lanfei/biomart-perl/conf/myRegistry.xml', 'action',
'cached', 'mode', 'memory') called at
/home/lanfei/biomart-perl/bin/../lib/BioMart/Initializer.pm line 184
BioMart::Initializer::_new('BioMart::Initializer=HASH(0x9e40658)',
'registryFile', '/home/lanfei/biomart-perl/conf/myRegistry.xml', 'action',
'cached', 'mode', 'memory') called at
/home/lanfei/biomart-perl/bin/../lib/BioMart/RootI.pm line 42
BioMart::RootI::new('BioMart::Initializer', 'registryFile',
'/home/lanfei/biomart-perl/conf/myRegistry.xml', 'action', 'cached',
'mode', 'memory') called at
/home/lanfei/biomart-perl/bin/configureBioMart.pl line 302
eval {...} at /home/lanfei/biomart-perl/bin/configureBioMart.pl line 301