Hi Syed,
This is the trace of the command:
Checking prerequisites ...[Looks good]
rm /home/cropdesign/biomart/biomart-perl/conf/templates/default/*.ttcrm:
cannot remove
`/home/cropdesign/biomart/biomart-perl/conf/templates/default/*.ttc': No
such file or directory
APACHE: /usr/sbin/apache2
HOST: localhost
PORT: 80
PROXY:
LOCATION: biomart
APXS/2:
You can change the above configuration by editing
"biomart-perl/conf/settings.conf"
Got usable Apache in /usr/sbin/apache2, probing for version & ModPerl
configuration
Have Apache DSO-support and ModPerl library file present, configuring
ModPerl in httpd.conf.
Libdir /home/cropdesign/biomart/biomart-perl/lib is not in @INC, adding to
@INC
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
COULD NOT CONNECT TO DATABASE Testsysbio.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
/home/cropdesign/biomart/biomart-perl/bin/../lib/BioMart/Initializer.pm
line 254
BioMart::Initializer::_init('BioMart::Initializer=HASH(0xabf42b0)',
'registryFile',
'/home/cropdesign/biomart/biomart-perl/conf/martDBLocation.xml', 'action',
'clean', 'mode', 'memory') called at
/home/cropdesign/biomart/biomart-perl/bin/../lib/BioMart/Initializer.pm
line 377
BioMart::Initializer::init_clean('BioMart::Initializer=HASH(0xabf42b0)',
'registryFile',
'/home/cropdesign/biomart/biomart-perl/conf/martDBLocation.xml', 'action',
'clean', 'mode', 'memory') called at
/home/cropdesign/biomart/biomart-perl/bin/../lib/BioMart/Initializer.pm
line 144
BioMart::Initializer::_new('BioMart::Initializer=HASH(0xabf42b0)',
'registryFile',
'/home/cropdesign/biomart/biomart-perl/conf/martDBLocation.xml', 'action',
'clean', 'mode', 'memory') called at
/home/cropdesign/biomart/biomart-perl/bin/../lib/BioMart/RootI.pm line 64
BioMart::RootI::new('BioMart::Initializer', 'registryFile',
'/home/cropdesign/biomart/biomart-perl/conf/martDBLocation.xml', 'action',
'clean', 'mode', 'memory') called at
/home/cropdesign/biomart/biomart-perl/bin/configureBioMart.pl line 330
eval {...} at
/home/cropdesign/biomart/biomart-perl/bin/configureBioMart.pl line 329
Thanks,
Bérénice
Berenice Wulbrecht
Phone: +32 9 242 9172, E-Mail: [email protected]
Postal Address: CropDesign N.V., - - CD2, 9052 Gent (Zwijnaarde), Belgium
CropDesign N.V. - A BASF Plant Science Company
CropDesign N.V.
Technologiepark 3
B-9052 Gent
Belgium
General Telephone: +32-9-241 50 80
Fax: +32-9-241 50 89
Confidentiality notice: The information contained in this e-mail is
confidential and may be the subject of legal professional privilege. It is
intended for the authorized use of the individual or entity addressed. If
the receiver or reader of this message is not the intended recipient, you
are hereby notified that any disclosure, copying, distribution or use of
the contents of this message is prohibited. If this email is received in
error, please accept our apologies, delete all copies from your system,
and notify us at [email protected].
"Syed Haider" <[email protected]>
20/02/2009 16:12
To
[email protected]
cc
"Syed Haider" <[email protected]>, [email protected]
Subject
Re: [mart-dev] Error Stating MartView
Hi Berenice,
Firstly, please focus on martDBLocation for your local database. Could you
please send me the trace when you configure with martDBLocation.xml as
mentioned below:
perl bin/configure.pl -r conf/martDBLocation.xml --clean
Thanks
Syed
> Hi Syed,
>
> I verified all my registry files, I corrected an error on my database
> location but there is still a problem.
> You could find here the trace and my registry files.
>
> Checking prerequisites ...[Looks good]
>
> APACHE: /usr/sbin/apache2
> HOST: localhost
> PORT: 80
> PROXY:
> LOCATION: biomart
> APXS/2:
>
> You can change the above configuration by editing
> "biomart-perl/conf/settings.conf"
>
> Got usable Apache in /usr/sbin/apache2, probing for version & ModPerl
> configuration
> Have Apache DSO-support and ModPerl library file present, configuring
> ModPerl in httpd.conf.
> Libdir /home/cropdesign/biomart/biomart-perl/lib is not in @INC, adding
to
> @INC
>
> Cached Registry Unavailable...
>
> Running Complete Clean...
>
> Problems with the web server: 404 Not Found
>
> 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
> /home/cropdesign/biomart/biomart-perl/bin/../lib/BioMart/Initializer.pm
> line 254
> BioMart::Initializer::_init('BioMart::Initializer=HASH(0xa8997f8)',
> 'registryFile',
> '/home/cropdesign/biomart/biomart-perl/conf/registryURLPointer.xml',
> 'action', 'cached', 'mode', 'memory') called at
> /home/cropdesign/biomart/biomart-perl/bin/../lib/BioMart/Initializer.pm
> line 377
> BioMart::Initializer::init_clean('BioMart::Initializer=HASH(0xa8997f8)',
> 'registryFile',
> '/home/cropdesign/biomart/biomart-perl/conf/registryURLPointer.xml',
> 'action', 'cached', 'mode', 'memory') called at
> /home/cropdesign/biomart/biomart-perl/bin/../lib/BioMart/Initializer.pm
> line 328
>
BioMart::Initializer::init_cached('BioMart::Initializer=HASH(0xa8997f8)',
> 'registryFile',
> '/home/cropdesign/biomart/biomart-perl/conf/registryURLPointer.xml',
> 'action', 'cached', 'mode', 'memory') called at
> /home/cropdesign/biomart/biomart-perl/bin/../lib/BioMart/Initializer.pm
> line 168
> BioMart::Initializer::_new('BioMart::Initializer=HASH(0xa8997f8)',
> 'registryFile',
> '/home/cropdesign/biomart/biomart-perl/conf/registryURLPointer.xml',
> 'action', 'cached', 'mode', 'memory') called at
> /home/cropdesign/biomart/biomart-perl/bin/../lib/BioMart/RootI.pm line
64
> BioMart::RootI::new('BioMart::Initializer', 'registryFile',
> '/home/cropdesign/biomart/biomart-perl/conf/registryURLPointer.xml',
> 'action', 'cached', 'mode', 'memory') called at
> /home/cropdesign/biomart/biomart-perl/bin/configureBioMart.pl line 330
> eval {...} at
> /home/cropdesign/biomart/biomart-perl/bin/configureBioMart.pl line 329
>
> This is my RegistryURLPointer.xml
> <MartRegistry>
> <RegistryURLPointer name="central_server" host="localhost" port="80"
> path="" includeMarts="AraGene" />
> </MartRegistry>
> This is my RegistryDBPointer.xml, I added here my own mart.
> <?xml version="1.0" encoding="UTF-8" ?>
> <!DOCTYPE MartRegistry (View Source for full doctype...)>
> - <MartRegistry>
> <RegistryDBPointer name="central_registry" host="localhost"
port="3306"
> user="anonymous" password="" database="central_registry" schema="
> central_registry" databaseType="mysql" includeMarts="AraGene" />
> </MartRegistry>
> This is my martURLLocation.xml
> <MartRegistry>
> <MartURLLocation name="AraGene" displayName="AraGene" host="
> machine.whereislocatedthedatabase" port="80" visible="1" default=""
> includeDatasets="" martUser="" />
> </MartRegistry>
> This is my martDBLocation.xml
> <MartRegistry>
> <MartDBLocation name="AraGene" displayName="AraGene"
databaseType="mysql
> " host="machine.whereislocatedthedatabase" port="3306" database="
> Testsysbio" schema="Testsysbio" user="YYYYYYY" password="XXXXXXX"
visible
> ="1" default="" includeDatasets="" martUser="" />
> </MartRegistry>
> And the beginning of the settings conf, what mean 'location'?
> #apacheBinary=/etc/apache2
> apacheBinary=/usr/sbin/apache2
> serverHost=localhost
> #port=9002
> port=80
> # to use proxying set the proxy port below (even if its 80) and set
> serverHost as your proxy host
> proxy=
> # if apxs or apxs2 is not in default directory where httpd lives, you
may
> set this param to point to apxs/2
> apxs=
> location=biomart
>
> Best regards,
>
> Bérénice
>
> Berenice Wulbrecht
> Phone: +32 9 242 9172, E-Mail: [email protected]
> Postal Address: CropDesign N.V., - - CD2, 9052 Gent (Zwijnaarde),
Belgium
> CropDesign N.V. - A BASF Plant Science Company
> CropDesign N.V.
> Technologiepark 3
> B-9052 Gent
> Belgium
> General Telephone: +32-9-241 50 80
> Fax: +32-9-241 50 89
> Confidentiality notice: The information contained in this e-mail is
> confidential and may be the subject of legal professional privilege. It
is
> intended for the authorized use of the individual or entity addressed.
If
> the receiver or reader of this message is not the intended recipient,
you
> are hereby notified that any disclosure, copying, distribution or use of
> the contents of this message is prohibited. If this email is received in
> error, please accept our apologies, delete all copies from your system,
> and notify us at [email protected].
>
>
>
>
>
> Syed Haider <[email protected]>
> 19/02/2009 19:38
>
> To
> [email protected]
> cc
> [email protected]
> Subject
> Re: [mart-dev] Error Stating MartView
>
>
>
>
>
>
> Hi Berenice,
>
> please send me the contents of your registryURLPointer.xml file. It
> seems that you have host set to localhost and port set to 80 which is
> wrong. If you are using your own database (Mart), use the file
> martDBLocation.xml and the credentials in this file should be similar to
> those you used in MartEditor. What you save in database/mart using
> MartEditor is read by perl library, therefore, the martDBLocation.xml
> file should contain the same connection information. The settings.conf
> helps you configure apache server, the webserver where you intend to
> host your MartView. In your case, localhost and port in settings.conf
> are ok.
>
>
> Hope this helps,
> Syed
>
> [email protected] wrote:
>>
>> Hi,
>>
>> I have configured my own dataset, I filled the diffreent registry file
>> in the directory conf on biomart-perl folder.
>> When I lauch the command perl bin/configure.pl
>> conf/registryURLPointer.xml, I get this error.
>>
>> Checking prerequisites ...[Looks good]
>>
>> APACHE: /usr/sbin/apache2
>> HOST: localhost
>> PORT: 80
>> PROXY:
>> LOCATION: biomart
>> APXS/2:
>>
>> You can change the above configuration by editing
>> "biomart-perl/conf/settings.conf"
>>
>>
>>
>> Got usable Apache in /usr/sbin/apache2, probing for version & ModPerl
>> configuration
>> Have Apache DSO-support and ModPerl library file present, configuring
>> ModPerl in httpd.conf.
>> Libdir /home/cropdesign/biomart/biomart-perl/lib is not in @INC,
>> adding to @INC
>>
>> Cached Registry Unavailable...
>>
>> Running Complete Clean...
>>
>>
>> Problems with the web server: 500 Can't connect to localhost:80
>> (connect: Connection refused)
>>
>>
>>
>>
>> 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
>> /home/cropdesign/biomart/biomart-perl/bin/../lib/BioMart/Initializer.pm
>> line 254
>> BioMart::Initializer::_init('BioMart::Initializer=HASH(0xa4a2c68)',
>> 'registryFile',
>> '/home/cropdesign/biomart/biomart-perl/conf/registryURLPointer.xml',
>> 'action', 'cached', 'mode', 'memory') called at
>> /home/cropdesign/biomart/biomart-perl/bin/../lib/BioMart/Initializer.pm
>> line 377
>>
BioMart::Initializer::init_clean('BioMart::Initializer=HASH(0xa4a2c68)',
>
>> 'registryFile',
>> '/home/cropdesign/biomart/biomart-perl/conf/registryURLPointer.xml',
>> 'action', 'cached', 'mode', 'memory') called at
>> /home/cropdesign/biomart/biomart-perl/bin/../lib/BioMart/Initializer.pm
>> line 328
>>
>
BioMart::Initializer::init_cached('BioMart::Initializer=HASH(0xa4a2c68)',
>> 'registryFile',
>> '/home/cropdesign/biomart/biomart-perl/conf/registryURLPointer.xml',
>> 'action', 'cached', 'mode', 'memory') called at
>> /home/cropdesign/biomart/biomart-perl/bin/../lib/BioMart/Initializer.pm
>> line 168
>> BioMart::Initializer::_new('BioMart::Initializer=HASH(0xa4a2c68)',
>> 'registryFile',
>> '/home/cropdesign/biomart/biomart-perl/conf/registryURLPointer.xml',
>> 'action', 'cached', 'mode', 'memory') called at
>> /home/cropdesign/biomart/biomart-perl/bin/../lib/BioMart/RootI.pm line
> 64
>> BioMart::RootI::new('BioMart::Initializer', 'registryFile',
>> '/home/cropdesign/biomart/biomart-perl/conf/registryURLPointer.xml',
>> 'action', 'cached', 'mode', 'memory') called at
>> /home/cropdesign/biomart/biomart-perl/bin/configureBioMart.pl line 330
>> eval {...} at
>> /home/cropdesign/biomart/biomart-perl/bin/configureBioMart.pl line 329
>>
>> Do you have an idea on what could be wrong, I have no errorlog created.
>>
>> Best regards,
>>
>> Bérénice
>>
>>
>> *Berenice Wulbrecht*
>>
>> Phone: +32 9 242 9172, E-Mail: [email protected]
>> Postal Address: CropDesign N.V., - - CD2, 9052 Gent (Zwijnaarde),
> Belgium
>>
>> *CropDesign N.V. - A BASF Plant Science Company*
>>
>> CropDesign N.V.
>> Technologiepark 3
>> B-9052 Gent
>> Belgium
>> General Telephone: +32-9-241 50 80
>> Fax: +32-9-241 50 89
>> Confidentiality notice: The information contained in this e-mail is
>> confidential and may be the subject of legal professional privilege.
>> It is intended for the authorized use of the individual or entity
>> addressed. If the receiver or reader of this message is not the
>> intended recipient, you are hereby notified that any disclosure,
>> copying, distribution or use of the contents of this message is
>> prohibited. If this email is received in error, please accept our
>> apologies, delete all copies from your system, and notify us at
>> [email protected].
>>
>
>
======================================
Syed Haider.
EMBL-European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton,
Cambridge CB10 1SD, UK.
======================================
