db/00085/UpdateNewProjectProps.pm

   1 #!/usr/bin/env perl
   2
   3
   4 =head1 NAME
   5
   6  UpdateNewProjectProps
   7
   8 =head1 SYNOPSIS
   9
  10 mx-run ThisPackageName [options] -H hostname -D dbname -u username [-F]
  11
  12 this is a subclass of L<CXGN::Metadata::Dbpatch>
  13 see the perldoc of parent class for more details.
  14
  15 =head1 DESCRIPTION
  16
  17 This patch updates cvterm name from
  18 Genetic Gain to genetic_gain_trial,
  19 Health Status to health_status_trial,
  20 Heterosis to heterosis_trial
  21 Storage to storage_trial
  22
  23 This subclass uses L<Moose>. The parent class uses L<MooseX::Runnable>
  24
  25 =head1 AUTHOR
  26
  27  Alex Ogbonna<aco46@cornell.edu>
  28
  29 =head1 COPYRIGHT & LICENSE
  30
  31 Copyright 2010 Boyce Thompson Institute for Plant Research
  32
  33 This program is free software; you can redistribute it and/or modify
  34 it under the same terms as Perl itself.
  35
  36 =cut
  37
  38
  39 package UpdateNewProjectProps;
  40
  41 use Moose;
  42 use Bio::Chado::Schema;
  43 use Try::Tiny;
  44
  45 extends 'CXGN::Metadata::Dbpatch';
  46
  47
  48 has '+description' => ( default => <<'' );
  49 This patch will update the cvterm name of
  50 Genetic Gain -> genetic_gain_trial
  51 Health Status -> health_status_trial
  52 Heterosis -> heterosis_trial
  53 Storage -> storage_trial
  54
  55
  56 has '+prereq' => (
  57     default => sub {
  58         ['AddNewProjectType'],
  59     },
  60   );
  61
  62   sub patch {
  63       my $self=shift;
  64
  65       print STDOUT "Executing the patch:\n " .   $self->name . ".\n\nDescription:\n  ".  $self->description . ".\n\nExecuted by:\n " .  $self->username . " .";
  66
  67       print STDOUT "\nChecking if this db_patch was executed before or if previous db_patches have been executed.\n";
  68
  69       print STDOUT "\nExecuting the SQL commands.\n";
  70       my $schema = Bio::Chado::Schema->connect( sub { $self->dbh->clone } );
  71
  72       my $coderef = sub {
  73                my $cvterm_rs = $schema->resultset("Cv::Cvterm");
  74                my $cv_rs = $schema->resultset("Cv::Cv");
  75                my $project_type_cv = $cv_rs->find( { name => 'project_type' });
  76
  77           my %cvterm_hash = (
  78                                'Genetic Gain' => 'genetic_gain_trial',
  79                                'Health Status' => 'health_status_trial',
  80                                'Heterosis'     => 'heterosis_trial',
  81                                'Storage'       => 'storage_trial',
  82                            );
  83
  84         foreach my $key (keys %cvterm_hash) {
  85              my $cvterm = $cvterm_rs->search( { name => $key ,  cv_id => $project_type_cv->cv_id() });
  86              if ( $cvterm != 0 ) {
  87               print STDERR "Updating cvterm $key to " . $cvterm_hash{$key} . "\n";
  88               my $cvterm_row = $cvterm->first();
  89               $cvterm->update( { name => $cvterm_hash{$key} } ) ;
  90              }
  91              else { print "Cannot find cvterm $key in the database \n" ; }
  92         }
  93
  94         if ($self->trial) {
  95             print "Trial mode! Rolling back transaction\n\n";
  96             $schema->txn_rollback;
  97             return 0;
  98         }
  99         return 1;
 100       };
 101
 102       try {
 103           $schema->txn_do($coderef);
 104
 105       } catch {
 106           die "Load failed! " . $_ .  "\n" ;
 107       };
 108
 109
 110       print "You're done!\n";
 111   }
 112
 113   ####
 114   1; #
 115   ####
 116