db/00163/AddGenomicPredictionStatCvterms.pm

   1 #!/usr/bin/env perl
   2
   3 =head1 NAME
   4
   5 AddGenomicPredictionStatCvterms.pm
   6
   7 =head1 SYNOPSIS
   8
   9 mx-run ThisPackageName [options] -H hostname -D dbname -u username [-F]
  10
  11 this is a subclass of L<CXGN::Metadata::Dbpatch>
  12 see the perldoc of parent class for more details.
  13
  14 =head1 DESCRIPTION
  15 This patch adds genomic prediction analysis statistics cvterms.
  16 This subclass uses L<Moose>. The parent class uses L<MooseX::Runnable>
  17
  18 =head1 AUTHOR
  19
  20 Isaak Y Tecle<iyt2@cornell.edu>
  21
  22 =head1 COPYRIGHT & LICENSE
  23
  24 Copyright 2010 Boyce Thompson Institute for Plant Research
  25
  26 This program is free software; you can redistribute it and/or modify
  27 it under the same terms as Perl itself.
  28
  29 =cut
  30
  31
  32 package AddGenomicPredictionStatCvterms;
  33
  34 use Moose;
  35 use Bio::Chado::Schema;
  36 use Try::Tiny;
  37 extends 'CXGN::Metadata::Dbpatch';
  38
  39
  40 has '+description' => ( default => <<'' );
  41 Description of this patch goes here
  42
  43 has '+prereq' => (
  44         default => sub {
  45         [],
  46     },
  47
  48   );
  49
  50 sub patch {
  51     my $self=shift;
  52
  53     print STDOUT "Executing the patch:\n " .   $self->name . ".\n\nDescription:\n  ".  $self->description . ".\n\nExecuted by:\n " .  $self->username . " .";
  54
  55     print STDOUT "\nChecking if this db_patch was executed before or if previous db_patches have been executed.\n";
  56
  57     print STDOUT "\nExecuting the SQL commands.\n";
  58     my $schema = Bio::Chado::Schema->connect( sub { $self->dbh->clone } );
  59
  60
  61     print STDERR "INSERTING Genomic Prediction statistics TERMS...\n";
  62     my $dbhost = $self->dbhost;
  63     my $dbname = $self->dbname;
  64
  65     `perl ~/cxgn/chado_tools/chado/bin/gmod_load_cvterms.pl -H $dbhost -D $dbname -r postgres  -s SGNSTAT -d Pg  ~/cxgn/sgn/ontology/cxgn_statistics.obo`;
  66
  67     print "\nYou're done!\n\n";
  68
  69 }
  70
  71
  72 ####
  73 1; #
  74 ####