lib/SGN/Controller/BreedersToolbox/Trial.pm

   1
   2 package SGN::Controller::BreedersToolbox::Trial;
   3
   4 use Moose;
   5 use CXGN::Trial::TrialLayout;
   6 use CXGN::BreedersToolbox::Projects;
   7
   8 BEGIN { extends 'Catalyst::Controller'; }
   9
  10
  11 sub trial_info : Path('/breeders_toolbox/trial') Args(1) {
  12     my $self = shift;
  13     my $c = shift;
  14     my $trial_id = shift;
  15     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
  16     my $trial_layout = CXGN::Trial::TrialLayout->new({schema => $schema, trial_id => $trial_id} );
  17     my $program_object = CXGN::BreedersToolbox::Projects->new( { schema => $schema });
  18     my $breeding_program = $program_object->get_breeding_program_with_trial($trial_id);
  19     my $trial_name =  $trial_layout->get_trial_name();
  20     my $trial_description =  $trial_layout->get_trial_description();
  21     my $trial_year =  $trial_layout->get_trial_year();
  22     my $design_type = $trial_layout->get_design_type();
  23     my $plot_names_ref = $trial_layout->get_plot_names();
  24     my $accession_names_ref = $trial_layout->get_accession_names();
  25     my $control_names_ref = $trial_layout->get_control_names();
  26     my $block_numbers = $trial_layout->get_block_numbers();
  27     my $replicate_numbers = $trial_layout->get_replicate_numbers();
  28
  29
  30     my @plot_names;
  31     if ($plot_names_ref) {
  32       @plot_names = @{$trial_layout->get_plot_names()};
  33     }
  34
  35     $c->stash->{design_type} = $design_type;
  36     $c->stash->{accession_names} = $accession_names_ref;
  37     $c->stash->{control_names} = $control_names_ref;
  38     $c->stash->{plot_names} = $plot_names_ref;
  39     $c->stash->{design_type} = $design_type;
  40     $c->stash->{trial_description} = $trial_description;
  41     $c->stash->{trial_id} = $trial_id;
  42     my $number_of_blocks;
  43     if ($block_numbers) {
  44       $number_of_blocks = scalar(@{$block_numbers});
  45     }
  46     $c->stash->{number_of_blocks} = $number_of_blocks;
  47     my $number_of_replicates;
  48     if ($replicate_numbers) {
  49       $number_of_replicates = scalar(@{$replicate_numbers});
  50     }
  51     $c->stash->{number_of_replicates} = $number_of_replicates;
  52
  53     my $user = $c->user();
  54     if (!$user) {
  55         $c->stash->{template} = '/generic_message.mas';
  56         $c->stash->{message}  = 'You must be logged in to access this page.';
  57         return;
  58     }
  59     my $dbh = $c->dbc->dbh();
  60
  61     my $h = $dbh->prepare("SELECT project.name FROM project WHERE project_id=?");
  62     $h->execute($trial_id);
  63
  64     my ($name) = $h->fetchrow_array();
  65
  66     $c->stash->{trial_name} = $name;
  67
  68     $h = $dbh->prepare("SELECT distinct(nd_geolocation.nd_geolocation_id), nd_geolocation.description, count(*) FROM nd_geolocation JOIN nd_experiment USING(nd_geolocation_id) JOIN nd_experiment_project USING (nd_experiment_id) JOIN project USING (project_id) WHERE project_id=? GROUP BY nd_geolocation_id, nd_geolocation.description");
  69     $h->execute($trial_id);
  70
  71     my @location_data = ();
  72     while (my ($id, $desc, $count) = $h->fetchrow_array()) {
  73         push @location_data, [$id, $desc, $count];
  74     }
  75
  76     $c->stash->{location_data} = \@location_data;
  77
  78     $h = $dbh->prepare("SELECT distinct(cvterm.name), count(*) FROM cvterm JOIN phenotype ON (cvterm_id=cvalue_id) JOIN nd_experiment_phenotype USING(phenotype_id) JOIN nd_experiment_project USING(nd_experiment_id) WHERE project_id=? GROUP BY cvterm.name");
  79
  80     $h->execute($trial_id);
  81
  82     my @phenotype_data;
  83     while (my ($trait, $count) = $h->fetchrow_array()) {
  84         push @phenotype_data, [$trait, $count];
  85     }
  86     $c->stash->{phenotype_data} = \@phenotype_data;
  87
  88     $h = $dbh->prepare("SELECT distinct(projectprop.value) FROM projectprop WHERE project_id=? AND type_id=(SELECT cvterm_id FROM cvterm WHERE name='project year')");
  89     $h->execute($trial_id);
  90
  91     my @years;
  92     while (my ($year) = $h->fetchrow_array()) {
  93         push @years, $year;
  94     }
  95
  96     $c->stash->{user_can_modify} = $user->check_roles("submitter");
  97
  98     $c->stash->{breeding_program} = $breeding_program;
  99
 100     $c->stash->{years} = \@years;
 101
 102     $c->stash->{plot_data} = [];
 103
 104     $c->stash->{trial_id} = $trial_id;
 105
 106     $c->stash->{template} = '/breeders_toolbox/trial.mas';
 107 }
 108
 109
 110 1;