db/00117/AddAerialRasterDSMCvterms.pm

   1 #!/usr/bin/env perl
   2
   3
   4 =head1 NAME
   5
   6  AddAerialRasterDSMCvterms
   7
   8 =head1 SYNOPSIS
   9
  10 mx-run AddAerialRasterDSMCvterms [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 This patch adds cvterms for phenotype spreadsheet associated images
  17 This subclass uses L<Moose>. The parent class uses L<MooseX::Runnable>
  18
  19 =head1 AUTHOR
  20
  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 AddAerialRasterDSMCvterms;
  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 This patch adds cvterms for phenotype spreadsheet associated images
  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 CV TERMS...\n";
  62
  63     my $terms = {
  64         'project_md_image' => [
  65             'observation_unit_polygon_raster_dsm_imagery',
  66             'threshold_background_removed_stitched_drone_imagery_raster_dsm',
  67             'observation_unit_polygon_raster_dsm_background_removed_threshold_imagery',
  68             'raw_boundaries_top_left_drone_imagery',
  69             'raw_boundaries_top_right_drone_imagery',
  70             'raw_boundaries_bottom_left_drone_imagery',
  71             'raw_boundaries_bottom_right_drone_imagery'
  72         ],
  73         'project_property' => [
  74             'drone_run_raw_images_saved_micasense_stacks',
  75             'drone_run_band_plot_polygons_partial'
  76         ]
  77     };
  78
  79         foreach my $t (keys %$terms){
  80                 foreach (@{$terms->{$t}}){
  81                         $schema->resultset("Cv::Cvterm")->create_with({
  82                                 name => $_,
  83                                 cv => $t
  84                         });
  85                 }
  86         }
  87
  88
  89     print "You're done!\n";
  90 }
  91
  92
  93 ####
  94 1; #
  95 ####