trouble getting biomart to configure to registryFile

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trouble getting biomart to configure to registryFile

Cynthia Lee
Hello,

I'm trying to install BioMart 0.7, but I'm having trouble getting it to configure to my registry file. I created the mart (on oracle) using martbuilder, and am able to open it using mart editor, but when I run the 

>>perl bin/configure.pl -r conf/biomart.xml

command, it keeps giving me the "Problems with the retrieval of dataset configuration" error (pasted below.) I was able to get it running using the sample XML file that came with it (martDBLocation.xml) and when I replace default defaultMartRegistry.xml file in martj0.7, I am able to load it up using martrunner and query around in it just fine... so I don't think the mart is ill-formatted.. 

Was wondering if someone had any idea as to what's going on, or could offer any insight?

here is my registry file: (the host, database and password fields are normally filled in) 
<?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE MartRegistry>
 <MartRegistry>
   <virtualSchema name="default">
   <MartDBLocation
          name         = "bm"
          displayName  = "biomart"
          databaseType = "oracle"
          host         = "(host)"
          port         = "1521"
          database     = "(database)"
          schema       = "bm"
          user         = "bm"
          password     = "(password)"
          visible      = "1"
          default      = ""
          includeDatasets = ""
   />
  </virtualSchema>
 </MartRegistry>


here is the error:
[bash $]# perl bin/configure.pl -r conf/biomart.xml 

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

Checking prerequisites ...[Looks good] 

{excerpt}

Got usable Apache in /usr/local/apache-2.2.13/bin/httpd, probing for version & ModPerl configuration
Have Apache DSO-support and ModPerl library file present, configuring ModPerl in httpd.conf.
Libdir /var/www/biomart/lib is not in @INC, adding to @INC

Cached Registry Unavailable...

Running Complete Clean...


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

 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
                
 COULD NOT CONNECT TO DATABASE bm.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 /var/www/biomart/bin/../lib/BioMart/Initializer.pm line 254
BioMart::Initializer::_init('BioMart::Initializer=HASH(0x12745040)', 'registryFile', '/var/www/biomart/conf/biomart.xml', 'action', 'cached', 'mode', 'memory') called at /var/www/biomart/bin/../lib/BioMart/Initializer.pm line 377
BioMart::Initializer::init_clean('BioMart::Initializer=HASH(0x12745040)', 'registryFile', '/var/www/biomart/conf/biomart.xml', 'action', 'cached', 'mode', 'memory') called at /var/www/biomart/bin/../lib/BioMart/Initializer.pm line 328
BioMart::Initializer::init_cached('BioMart::Initializer=HASH(0x12745040)', 'registryFile', '/var/www/biomart/conf/biomart.xml', 'action', 'cached', 'mode', 'memory') called at /var/www/biomart/bin/../lib/BioMart/Initializer.pm line 168
BioMart::Initializer::_new('BioMart::Initializer=HASH(0x12745040)', 'registryFile', '/var/www/biomart/conf/biomart.xml', 'action', 'cached', 'mode', 'memory') called at /var/www/biomart/bin/../lib/BioMart/RootI.pm line 64
BioMart::RootI::new('BioMart::Initializer', 'registryFile', '/var/www/biomart/conf/biomart.xml', 'action', 'cached', 'mode', 'memory') called at /var/www/biomart/bin/configureBioMart.pl line 331
eval {...} at /var/www/biomart/bin/configureBioMart.pl line 330

Thanks in advance,
Cynthia Lee

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Re: trouble getting biomart to configure to registryFile

Arek Kasprzyk-2
Re: [mart-dev] trouble getting biomart to configure to registryFile Hi Cynthia,
Please check if you have DBI DBD::Oracle installed correctly on your machine. First check if it is installed at all and if so, if it works correctly (you can write a one perl one liner to see if you can connect to the database from the machine that you are running biomart-perl


a


On 30/09/10 6:55 PM, "Cynthia Lee" <leech@...> wrote:

Hello,

I'm trying to install BioMart 0.7, but I'm having trouble getting it to configure to my registry file. I created the mart (on oracle) using martbuilder, and am able to open it using mart editor, but when I run the 

>>perl bin/configure.pl <http://configure.pl>  -r conf/biomart.xml

command, it keeps giving me the "Problems with the retrieval of dataset configuration" error (pasted below.) I was able to get it running using the sample XML file that came with it (martDBLocation.xml) and when I replace default defaultMartRegistry.xml file in martj0.7, I am able to load it up using martrunner and query around in it just fine... so I don't think the mart is ill-formatted.. 

Was wondering if someone had any idea as to what's going on, or could offer any insight?

here is my registry file: (the host, database and password fields are normally filled in) 
<?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE MartRegistry>
 <MartRegistry>
   <virtualSchema name="default">
   <MartDBLocation
          name         = "bm"
          displayName  = "biomart"
          databaseType = "oracle"
          host         = "(host)"
          port         = "1521"
          database     = "(database)"
          schema       = "bm"
          user         = "bm"
          password     = "(password)"
          visible      = "1"
          default      = ""
          includeDatasets = ""
   />
  </virtualSchema>
 </MartRegistry>


here is the error:
[bash $]# perl bin/configure.pl <http://configure.pl>  -r conf/biomart.xml 

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

Checking prerequisites ...[Looks good] 

{excerpt}

Got usable Apache in /usr/local/apache-2.2.13/bin/httpd, probing for version & ModPerl configuration
Have Apache DSO-support and ModPerl library file present, configuring ModPerl in httpd.conf.
Libdir /var/www/biomart/lib is not in @INC, adding to @INC

Cached Registry Unavailable...

Running Complete Clean...


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

 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
                
 COULD NOT CONNECT TO DATABASE bm.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 /var/www/biomart/bin/../lib/BioMart/Initializer.pm line 254
BioMart::Initializer::_init('BioMart::Initializer=HASH(0x12745040)', 'registryFile', '/var/www/biomart/conf/biomart.xml', 'action', 'cached', 'mode', 'memory') called at /var/www/biomart/bin/../lib/BioMart/Initializer.pm line 377
BioMart::Initializer::init_clean('BioMart::Initializer=HASH(0x12745040)', 'registryFile', '/var/www/biomart/conf/biomart.xml', 'action', 'cached', 'mode', 'memory') called at /var/www/biomart/bin/../lib/BioMart/Initializer.pm line 328
BioMart::Initializer::init_cached('BioMart::Initializer=HASH(0x12745040)', 'registryFile', '/var/www/biomart/conf/biomart.xml', 'action', 'cached', 'mode', 'memory') called at /var/www/biomart/bin/../lib/BioMart/Initializer.pm line 168
BioMart::Initializer::_new('BioMart::Initializer=HASH(0x12745040)', 'registryFile', '/var/www/biomart/conf/biomart.xml', 'action', 'cached', 'mode', 'memory') called at /var/www/biomart/bin/../lib/BioMart/RootI.pm line 64
BioMart::RootI::new('BioMart::Initializer', 'registryFile', '/var/www/biomart/conf/biomart.xml', 'action', 'cached', 'mode', 'memory') called at /var/www/biomart/bin/configureBioMart.pl line 331
eval {...} at /var/www/biomart/bin/configureBioMart.pl line 330

Thanks in advance,
Cynthia Lee






Arek Kasprzyk
Director, Bioinformatics Operations and Principal Investigator

Ontario Institute for Cancer Research
MaRS Centre, South Tower
101 College Street, Suite 800
Toronto, Ontario, Canada M5G 0A3
            
Tel:                        416-673-8559
Toll-free:             1-866-678-6427
www.oicr.on.ca
 
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