Problem retrieving datasets for mart uniprot_mart

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Problem retrieving datasets for mart uniprot_mart

nndegwa
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]$/

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Re: Problem retrieving datasets for mart uniprot_mart

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 <[hidden email]> 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]$/


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Re: Problem retrieving datasets for mart uniprot_mart

nndegwa
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 <[hidden email]
> <mailto:[hidden email]>> 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
>      
>     /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]$/
>
>