lib/CXGN/PhenotypingTrial.pm

   1
   2 package CXGN::PhenotypingTrial;
   3
   4 use Moose;
   5
   6 extends 'CXGN::Project';
   7
   8 use SGN::Model::Cvterm;
   9
  10 =head2 function set_field_trials_source_field_trials()
  11
  12  Usage:
  13  Desc:         sets associated source field trials for the current field trial
  14  Ret:          returns an arrayref [ id, name ] of arrayrefs
  15  Args:         an arrayref [source_trial_id1, source_trial_id2]
  16  Side Effects:
  17  Example:
  18
  19 =cut
  20
  21 sub set_field_trials_source_field_trials {
  22     my $self = shift;
  23     my $source_field_trial_ids = shift;
  24     my $schema = $self->bcs_schema;
  25     my $field_trial_from_field_trial_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'field_trial_from_field_trial', 'project_relationship')->cvterm_id();
  26
  27     foreach (@$source_field_trial_ids){
  28         if ($_){
  29             my $trial_rs= $self->bcs_schema->resultset('Project::ProjectRelationship')->create({
  30                 'subject_project_id' => $self->get_trial_id(),
  31                 'object_project_id' => $_,
  32                 'type_id' => $field_trial_from_field_trial_cvterm_id
  33             });
  34         }
  35     }
  36     my $projects = $self->get_field_trials_source_field_trials();
  37     return $projects;
  38 }
  39
  40 =head2 function get_field_trials_source_field_trials()
  41
  42  Usage:
  43  Desc:         return associated source field trials for the current field trial
  44  Ret:          returns an arrayref [ id, name ] of arrayrefs
  45  Args:
  46  Side Effects:
  47  Example:
  48
  49 =cut
  50
  51 sub get_field_trials_source_field_trials {
  52     my $self = shift;
  53     my $schema = $self->bcs_schema;
  54     my $field_trial_from_field_trial_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'field_trial_from_field_trial', 'project_relationship')->cvterm_id();
  55
  56     my $trial_rs= $self->bcs_schema->resultset('Project::ProjectRelationship')->search({
  57         'me.subject_project_id' => $self->get_trial_id(),
  58         'me.type_id' => $field_trial_from_field_trial_cvterm_id
  59     }, {
  60         join => 'object_project', '+select' => ['object_project.name'], '+as' => ['source_trial_name']
  61     });
  62
  63     my @projects;
  64     while (my $r = $trial_rs->next) {
  65         push @projects, [ $r->object_project_id, $r->get_column('source_trial_name') ];
  66     }
  67     return  \@projects;
  68 }
  69
  70 =head2 function get_field_trials_sourced_from_field_trials()
  71
  72  Usage:
  73  Desc:         return associated source field trials for the current field trial
  74  Ret:          returns an arrayref [ id, name ] of arrayrefs
  75  Args:
  76  Side Effects:
  77  Example:
  78
  79 =cut
  80
  81 sub get_field_trials_sourced_from_field_trials {
  82     my $self = shift;
  83     my $schema = $self->bcs_schema;
  84     my $field_trial_from_field_trial_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'field_trial_from_field_trial', 'project_relationship')->cvterm_id();
  85
  86     my $trial_rs= $self->bcs_schema->resultset('Project::ProjectRelationship')->search({
  87         'me.object_project_id' => $self->get_trial_id(),
  88         'me.type_id' => $field_trial_from_field_trial_cvterm_id
  89     }, {
  90         join => 'subject_project', '+select' => ['subject_project.name'], '+as' => ['trial_name']
  91     });
  92
  93     my @projects;
  94     while (my $r = $trial_rs->next) {
  95         push @projects, [ $r->subject_project_id, $r->get_column('trial_name') ];
  96     }
  97     return  \@projects;
  98 }
  99
 100 =head2 function get_drone_run_bands_from_field_trial()
 101
 102  Usage:
 103  Desc:         return associated drone_run_band projects for the current field trial
 104  Ret:          returns an arrayref [ id, name ] of arrayrefs
 105  Args:
 106  Side Effects:
 107  Example:
 108
 109 =cut
 110
 111 sub get_drone_run_bands_from_field_trial {
 112     my $self = shift;
 113     my $bcs_schema = $self->bcs_schema;
 114
 115     my $project_start_date_type_id = SGN::Model::Cvterm->get_cvterm_row($bcs_schema, 'project_start_date', 'project_property')->cvterm_id();
 116     my $design_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($bcs_schema, 'design', 'project_property')->cvterm_id();
 117     my $drone_run_band_type_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($bcs_schema, 'drone_run_band_project_type', 'project_property')->cvterm_id();
 118     my $project_relationship_type_id = SGN::Model::Cvterm->get_cvterm_row($bcs_schema, 'drone_run_on_field_trial', 'project_relationship')->cvterm_id();
 119     my $drone_run_band_relationship_type_id = SGN::Model::Cvterm->get_cvterm_row($bcs_schema, 'drone_run_band_on_drone_run', 'project_relationship')->cvterm_id();
 120
 121     my $q = "SELECT drone_run_band.project_id, drone_run_band.name, drone_run_band.description, drone_run_band_type.value, project.project_id, project.name, project.description, project_start_date.value, field_trial.project_id, field_trial.name, field_trial.description
 122         FROM project AS drone_run_band
 123         JOIN projectprop AS drone_run_band_type ON(drone_run_band.project_id=drone_run_band_type.project_id AND drone_run_band_type.type_id=$drone_run_band_type_cvterm_id)
 124         JOIN project_relationship AS drone_run_band_rel ON(drone_run_band.project_id=drone_run_band_rel.subject_project_id AND drone_run_band_rel.type_id=$drone_run_band_relationship_type_id)
 125         JOIN project ON (drone_run_band_rel.object_project_id = project.project_id)
 126         JOIN projectprop AS project_start_date ON (project.project_id=project_start_date.project_id AND project_start_date.type_id=$project_start_date_type_id)
 127         JOIN project_relationship ON (project.project_id = project_relationship.subject_project_id AND project_relationship.type_id=$project_relationship_type_id)
 128         JOIN project AS field_trial ON (field_trial.project_id=project_relationship.object_project_id)
 129         WHERE field_trial.project_id = ?
 130         ORDER BY project.project_id;";
 131
 132     my $calendar_funcs = CXGN::Calendar->new({});
 133
 134     my $h = $bcs_schema->storage->dbh()->prepare($q);
 135     $h->execute($self->get_trial_id());
 136     my @result;
 137     while (my ($drone_run_band_project_id, $drone_run_band_name, $drone_run_band_description, $drone_run_band_type, $drone_run_project_id, $drone_run_project_name, $drone_run_project_description, $drone_run_date, $field_trial_project_id, $field_trial_project_name, $field_trial_project_description) = $h->fetchrow_array()) {
 138         my $drone_run_date_display = $drone_run_date ? $calendar_funcs->display_start_date($drone_run_date) : '';
 139         push @result, [$drone_run_band_project_id, $drone_run_band_name, $drone_run_band_description, $drone_run_band_type, $drone_run_project_id, $drone_run_project_name, $drone_run_project_description, $drone_run_date_display, $field_trial_project_id, $field_trial_project_name, $field_trial_project_description];
 140     }
 141     return \@result;
 142 }
 143
 144 =head2 function get_trial_stock_type()
 145
 146  Usage:
 147  Desc:         Get stock type used in trial
 148  Ret:
 149  Args:
 150  Side Effects:
 151  Example:
 152
 153 =cut
 154
 155 sub get_trial_stock_type {
 156     my $self = shift;
 157     my $trial_stock_type_cvterm = SGN::Model::Cvterm->get_cvterm_row($self->bcs_schema, 'trial_stock_type', 'project_property');
 158     my $type_id = $trial_stock_type_cvterm->cvterm_id();
 159
 160     my $stock_type_rs = $self->bcs_schema->resultset('Project::Project')->search( { 'me.project_id' => $self->get_trial_id() })->search_related('projectprops', { type_id => $type_id } );
 161
 162     if ($stock_type_rs->count() == 0) {
 163         return undef;
 164     } else {
 165         return $stock_type_rs->first()->value();
 166     }
 167 }
 168
 169
 170 1;