db/00080/UpdateProjectDateProps.pm

   1 #!/usr/bin/env perl
   2
   3
   4 =head1 NAME
   5
   6  UpdateProjectDateProps
   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 deletes resundant project_property 'project harvest date' and 'project planting date' , adds 'project_' prefix to the existing cvterms, and updates the rows in teh projectprop table to point to the correct cvterm
  18
  19 This subclass uses L<Moose>. The parent class uses L<MooseX::Runnable>
  20
  21 =head1 AUTHOR
  22
  23  Naama Menda<nm249@cornell.edu>
  24
  25 =head1 COPYRIGHT & LICENSE
  26
  27 Copyright 2010 Boyce Thompson Institute for Plant Research
  28
  29 This program is free software; you can redistribute it and/or modify
  30 it under the same terms as Perl itself.
  31
  32 =cut
  33
  34
  35 package UpdateProjectDateProps;
  36
  37 use Moose;
  38 use Bio::Chado::Schema;
  39 use Try::Tiny;
  40
  41 extends 'CXGN::Metadata::Dbpatch';
  42
  43
  44 has '+description' => ( default => <<'' );
  45 This patch will update the cvterm name of
  46 harvest_date -> project_harvest_date
  47 planting_date -> project_planting_date
  48 and remove the redundant terms
  49 project harvest date
  50 project planting date
  51 Rows in projectprop that point to the redundant cvterms will be updated to point to the correct ones
  52
  53 has '+prereq' => (
  54     default => sub {
  55         [],
  56     },
  57   );
  58
  59 sub patch {
  60     my $self=shift;
  61
  62     print STDOUT "Executing the patch:\n " .   $self->name . ".\n\nDescription:\n  ".  $self->description . ".\n\nExecuted by:\n " .  $self->username . " .";
  63
  64     print STDOUT "\nChecking if this db_patch was executed before or if previous db_patches have been executed.\n";
  65
  66     print STDOUT "\nExecuting the SQL commands.\n";
  67     my $schema = Bio::Chado::Schema->connect( sub { $self->dbh->clone } );
  68
  69     my $coderef = sub {
  70         my $cvterm_rs = $schema->resultset("Cv::Cvterm");
  71         my $cv_rs = $schema->resultset("Cv::Cv");
  72
  73         my $project_property_cv = $cv_rs->find( { name => 'project_property' });
  74
  75         my $harvest_date_cvterm = $cvterm_rs->search(
  76             { name => 'harvest_date', } )->single;
  77
  78         print "Updating existing cvterm 'harvest_date' \n";
  79         if ($harvest_date_cvterm) {
  80             $harvest_date_cvterm->update( { name => 'project_harvest_date' }, );
  81         } else {
  82             $harvest_date_cvterm = $cvterm_rs->search( { name => 'project_harvest_date' } )->single;
  83         }
  84         my $harvest_date_cvterm_id = $harvest_date_cvterm->cvterm_id;
  85
  86
  87         my $planting_date_cvterm = $cvterm_rs->search(
  88             { name => 'planting_date', } )->single;
  89
  90         print "Updating existing cvterm 'planting_date' \n";
  91         if ($planting_date_cvterm) {
  92             $planting_date_cvterm->update( { name => 'project_planting_date'},);
  93         } else {
  94             $planting_date_cvterm = $cvterm_rs->search( { name => 'project_planting_date' } )->single;
  95         }
  96         my $planting_date_cvterm_id = $planting_date_cvterm->cvterm_id;
  97         ####
  98
  99         #redundant cvterms that should nopt be used
 100         my $old_harvest_cvterm = $cvterm_rs->search(
 101             { name => 'project harvest date', } )->single;
 102         my $old_planting_cvterm = $cvterm_rs->search(
 103             { name => 'project planting date' , })->single;
 104
 105         #update type_ids in projecprop table
 106         if ($old_harvest_cvterm ) {
 107             my $harvest_projectprops = $schema->resultset("Project::Projectprop")->search(
 108                 { type_id => $old_harvest_cvterm->cvterm_id , } );
 109             $harvest_projectprops->update( { type_id => $harvest_date_cvterm_id , });
 110             $old_harvest_cvterm->delete;
 111         }
 112         if ($old_planting_cvterm) {
 113             my $planting_projectprops = $schema->resultset("Project::Projectprop")->search(
 114                 { type_id => $old_planting_cvterm->cvterm_id , } );
 115             $planting_projectprops->update( { type_id => $planting_date_cvterm_id , });
 116
 117             #delete redundant cvterms
 118             $old_planting_cvterm->delete;
 119         }
 120         ##############
 121
 122         if ($self->trial) {
 123             print "Trial mode! Rolling back transaction\n\n";
 124             $schema->txn_rollback;
 125             return 0;
 126         }
 127         return 1;
 128     };
 129
 130     try {
 131         $schema->txn_do($coderef);
 132
 133     } catch {
 134         die "Load failed! " . $_ .  "\n" ;
 135     };
 136
 137
 138     print "You're done!\n";
 139 }
 140
 141
 142 ####
 143 1; #
 144 ####