Re: [mart-dev] Problem retrieving datasets for mart uniprot_mart

2010-10-13 Thread Nelson Ndegwa 

Morning Damian,
Yes, the type on all the DatasetConfig files are  TableSet.
You can pass by and have a look.
Thanks
Nelson


Damian Smedley wrote:

Hi Nelson,

Probably the configuration has lost its type setting on the 
DatasetConfig node. It should be set to TableSet. Do you see this in 
MartEditor? If you can't see it then something may have gone wrong in 
the export process - I can come and find you in person and help you 
fix it.


Cheers
Damian


On Tue, Oct 12, 2010 at 5:24 PM, Nelson Ndegwa nnde...@ebi.ac.uk 
mailto:nnde...@ebi.ac.uk wrote:


Hi All,
I am having problems reconfiguring my previously working MartView.
I was attempting to link two datasets using two attributes/filters
instead of the usual one attribute/filter using MartEditor.
On trying to revert back to the old configuration after deleting
my changes, i still get the same error (below)
Any ideas?
Thanks,
Nelson






  /[biomart-perl]$ perl bin/configure.pl http://configure.pl
--clean -r conf/reactomeEwas.xml/

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

  /Checking prerequisites ...[Looks good] /

  /APACHE: /homes/nn/soft/biomart/apache/bin/httpd/
  /HOST: localhost/
  /PORT: 9000/
  /PROXY:/
  /LOCATION: biomart/
  /Use of uninitialized value in print at
 
/automount/nas10b_vol-vol1-homes/nn/soft/biomart/biomart-perl/bin/configureBioMart.pl

  line 147./
  /APXS/2:/

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



  /Got usable Apache in /homes/nn/soft/biomart/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
  /automount/nas10b_vol-vol1-homes/nn/soft/biomart/biomart-perl/lib is
  not in @INC, adding to @INC/

  /Cached Registry Unavailable.../

  /Running Complete Clean.../

  /Connection parameters of [REACTOME] [ OK ]/
  /Connection parameters of [ENSEMBL 44 GENES (SANGER)][ OK ]/
  /Connection parameters of [UNIPROT (EBI UK)] [ OK ]/
  /Connection parameters of [PRIDE BioMart][ OK ]/


  /ERROR something wrong with your registry: could not load module
  BioMart::Dataset::Problem retrieving datasets for mart uniprot_mart,
  check your parameters: syntax error at (eval 131) line 1, near
  require BioMart::Dataset::Problem retrieving datasets /


  /Trace begun at
 
/automount/nas10b_vol-vol1-homes/nn/soft/biomart/biomart-perl/bin/../lib/BioMart/Root.pm

  line 191/
  /BioMart::Root::loadModule('BioMart::Initializer=HASH(0x4353ce8)',
  'BioMart::Dataset::Problem retrieving datasets for mart
  uniprot_mart, check your parameters') called at
 
/automount/nas10b_vol-vol1-homes/nn/soft/biomart/biomart-perl/bin/../lib/BioMart/Initializer.pm

  line 1162/
 
/BioMart::Initializer::_populateRegistry('BioMart::Initializer=HASH(0x4353ce8)')

  called at
 
/automount/nas10b_vol-vol1-homes/nn/soft/biomart/biomart-perl/bin/../lib/BioMart/Initializer.pm

  line 228/
  /BioMart::Initializer::_init('BioMart::Initializer=HASH(0x4353ce8)',
  'registryFile',
 
'/automount/nas10b_vol-vol1-homes/nn/soft/biomart/biomart-perl/conf/reactomeEwas.xml',

  'action', 'cached', 'mode', 'memory') called at
 
/automount/nas10b_vol-vol1-homes/nn/soft/biomart/biomart-perl/bin/../lib/BioMart/Initializer.pm

  line 377/
 
/BioMart::Initializer::init_clean('BioMart::Initializer=HASH(0x4353ce8)',

  'registryFile',
 
'/automount/nas10b_vol-vol1-homes/nn/soft/biomart/biomart-perl/conf/reactomeEwas.xml',

  'action', 'cached', 'mode', 'memory') called at
 
/automount/nas10b_vol-vol1-homes/nn/soft/biomart/biomart-perl/bin/../lib/BioMart/Initializer.pm

  line 328/
 
/BioMart::Initializer::init_cached('BioMart::Initializer=HASH(0x4353ce8)',

  'registryFile',
 
'/automount/nas10b_vol-vol1-homes/nn/soft/biomart/biomart-perl/conf/reactomeEwas.xml',

  'action', 'cached', 'mode', 'memory') called at
 
/automount/nas10b_vol-vol1-homes/nn/soft/biomart/biomart-perl/bin/../lib/BioMart/Initializer.pm

  line 168/
  /BioMart::Initializer::_new('BioMart::Initializer=HASH(0x4353ce8)',
  'registryFile',
 
'/automount/nas10b_vol-vol1-homes/nn/soft/biomart/biomart-perl/conf/reactomeEwas.xml',

  'action', 'cached', 'mode', 'memory') called at
 
/automount/nas10b_vol-vol1-homes/nn/soft/biomart/biomart-perl/bin/../lib/BioMart/RootI.pm

  line 64/
  /BioMart::RootI::new('BioMart::Initializer', 'registryFile',
 
'/automount/nas10b_vol-vol1-homes/nn/soft/biomart/biomart-perl/conf/reactomeEwas.xml',

  'action', 'cached', 'mode', 'memory') called at

Re: [mart-dev] Problem retrieving datasets for mart uniprot_mart

2010-10-12 Thread Damian Smedley 
Hi Nelson,

Probably the configuration has lost its type setting on the DatasetConfig
node. It should be set to TableSet. Do you see this in MartEditor? If you
can't see it then something may have gone wrong in the export process - I
can come and find you in person and help you fix it.

Cheers
Damian


On Tue, Oct 12, 2010 at 5:24 PM, Nelson Ndegwa nnde...@ebi.ac.uk wrote:

 Hi All,
 I am having problems reconfiguring my previously working MartView.
 I was attempting to link two datasets using two attributes/filters instead
 of the usual one attribute/filter using MartEditor.
 On trying to revert back to the old configuration after deleting my
 changes, i still get the same error (below)
 Any ideas?
 Thanks,
 Nelson






   /[biomart-perl]$ perl bin/configure.pl --clean -r conf/reactomeEwas.xml/

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

   /Checking prerequisites ...[Looks good] /

   /APACHE: /homes/nn/soft/biomart/apache/bin/httpd/
   /HOST: localhost/
   /PORT: 9000/
   /PROXY:/
   /LOCATION: biomart/
   /Use of uninitialized value in print at

 /automount/nas10b_vol-vol1-homes/nn/soft/biomart/biomart-perl/bin/configureBioMart.pl
   line 147./
   /APXS/2:/

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



   /Got usable Apache in /homes/nn/soft/biomart/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
   /automount/nas10b_vol-vol1-homes/nn/soft/biomart/biomart-perl/lib is
   not in @INC, adding to @INC/

   /Cached Registry Unavailable.../

   /Running Complete Clean.../

   /Connection parameters of [REACTOME] [ OK ]/
   /Connection parameters of [ENSEMBL 44 GENES (SANGER)][ OK ]/
   /Connection parameters of [UNIPROT (EBI UK)] [ OK ]/
   /Connection parameters of [PRIDE BioMart][ OK ]/


   /ERROR something wrong with your registry: could not load module
   BioMart::Dataset::Problem retrieving datasets for mart uniprot_mart,
   check your parameters: syntax error at (eval 131) line 1, near
   require BioMart::Dataset::Problem retrieving datasets /


   /Trace begun at

 /automount/nas10b_vol-vol1-homes/nn/soft/biomart/biomart-perl/bin/../lib/BioMart/Root.pm
   line 191/
   /BioMart::Root::loadModule('BioMart::Initializer=HASH(0x4353ce8)',
   'BioMart::Dataset::Problem retrieving datasets for mart
   uniprot_mart, check your parameters') called at

 /automount/nas10b_vol-vol1-homes/nn/soft/biomart/biomart-perl/bin/../lib/BioMart/Initializer.pm
   line 1162/

 /BioMart::Initializer::_populateRegistry('BioMart::Initializer=HASH(0x4353ce8)')
   called at

 /automount/nas10b_vol-vol1-homes/nn/soft/biomart/biomart-perl/bin/../lib/BioMart/Initializer.pm
   line 228/
   /BioMart::Initializer::_init('BioMart::Initializer=HASH(0x4353ce8)',
   'registryFile',

 '/automount/nas10b_vol-vol1-homes/nn/soft/biomart/biomart-perl/conf/reactomeEwas.xml',
   'action', 'cached', 'mode', 'memory') called at

 /automount/nas10b_vol-vol1-homes/nn/soft/biomart/biomart-perl/bin/../lib/BioMart/Initializer.pm
   line 377/
   /BioMart::Initializer::init_clean('BioMart::Initializer=HASH(0x4353ce8)',
   'registryFile',

 '/automount/nas10b_vol-vol1-homes/nn/soft/biomart/biomart-perl/conf/reactomeEwas.xml',
   'action', 'cached', 'mode', 'memory') called at

 /automount/nas10b_vol-vol1-homes/nn/soft/biomart/biomart-perl/bin/../lib/BioMart/Initializer.pm
   line 328/

 /BioMart::Initializer::init_cached('BioMart::Initializer=HASH(0x4353ce8)',
   'registryFile',

 '/automount/nas10b_vol-vol1-homes/nn/soft/biomart/biomart-perl/conf/reactomeEwas.xml',
   'action', 'cached', 'mode', 'memory') called at

 /automount/nas10b_vol-vol1-homes/nn/soft/biomart/biomart-perl/bin/../lib/BioMart/Initializer.pm
   line 168/
   /BioMart::Initializer::_new('BioMart::Initializer=HASH(0x4353ce8)',
   'registryFile',

 '/automount/nas10b_vol-vol1-homes/nn/soft/biomart/biomart-perl/conf/reactomeEwas.xml',
   'action', 'cached', 'mode', 'memory') called at

 /automount/nas10b_vol-vol1-homes/nn/soft/biomart/biomart-perl/bin/../lib/BioMart/RootI.pm
   line 64/
   /BioMart::RootI::new('BioMart::Initializer', 'registryFile',

 '/automount/nas10b_vol-vol1-homes/nn/soft/biomart/biomart-perl/conf/reactomeEwas.xml',
   'action', 'cached', 'mode', 'memory') called at

 /automount/nas10b_vol-vol1-homes/nn/soft/biomart/biomart-perl/bin/configureBioMart.pl
   line 332/
   /eval {...} at

 /automount/nas10b_vol-vol1-homes/nn/soft/biomart/biomart-perl/bin/configureBioMart.pl
   line 331/

   /[biomart-perl]$/