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.
======================================
