lib/CXGN/Trial/TrialDesignStore/SamplingTrial.pm

   1
   2 package CXGN::Trial::TrialDesignStore::SamplingTrial;
   3
   4 use Moose;
   5 use Try::Tiny;
   6
   7 BEGIN { extends 'CXGN::Trial::TrialDesignStore::AbstractTrial';}
   8
   9 sub BUILD {
  10     my $self = shift;
  11     my $args = shift;
  12
  13     print STDERR "BUILD CXGN::Trial::TrialDesignStore::AbstractTrial\n";
  14     $self->set_nd_experiment_type_id(SGN::Model::Cvterm->get_cvterm_row($self->get_bcs_schema(), 'sampling_layout', 'experiment_type')->cvterm_id());
  15     $self->set_stock_type_id($self->get_tissue_sample_cvterm_id);
  16     $self->set_stock_relationship_type_id($self->get_tissue_sample_of_cvterm_id);
  17
  18     $self->set_source_stock_types([
  19         $self->get_accession_cvterm_id,
  20         $self->get_plot_cvterm_id,
  21         $self->get_plant_cvterm_id,
  22         $self->get_tissue_sample_cvterm_id
  23     ]);
  24
  25     $self->set_valid_properties([
  26         'stock_name',
  27         'plot_name',
  28         'block_number',
  29             'rep_number',
  30         'row_number',
  31         'col_number',
  32         'plot_number',
  33         'extraction',
  34         'dna_person',
  35         'concentration',
  36         'volume',
  37         'tissue_type',
  38         'notes',
  39         'acquisition_date',
  40         'ncbi_taxonomy_id'
  41     ]);
  42 }
  43
  44
  45 sub validate_design {
  46     my $self = shift;
  47
  48     print STDERR "validating design\n";
  49
  50     my $chado_schema = $self->get_bcs_schema();
  51     my $design_type = $self->get_design_type();
  52     my %design = %{$self->get_design};
  53     my $error = '';
  54
  55    if ($design_type ne 'sampling_trial') {
  56         $error .= "design_type not equal to 'sampling_trial'";
  57         return $error;
  58     }
  59
  60     my @valid_properties = @{$self->get_valid_properties()};
  61
  62     my %allowed_properties = map {$_ => 1} @valid_properties;
  63
  64     my %seen_stock_names;
  65     my %seen_accession_names;
  66     foreach my $stock (keys %design){
  67         foreach my $property (keys %{$design{$stock}}){
  68             if (!exists($allowed_properties{$property})) {
  69                 $error .= "Property: $property not allowed! ";
  70             }
  71             if ($property eq 'stock_name') {
  72                 my $stock_name = $design{$stock}->{$property};
  73                 $seen_accession_names{$stock_name}++;
  74             }
  75             if ($property eq 'plot_name') {
  76                 my $plot_name = $design{$stock}->{$property};
  77                 $seen_stock_names{$plot_name}++;
  78             }
  79         }
  80     }
  81
  82     my @stock_names = keys %seen_stock_names;
  83     my @accession_names = keys %seen_accession_names;
  84     if(scalar(@stock_names)<1){
  85         $error .= "You cannot create a trial with less than one sample.";
  86     }
  87     if(scalar(@accession_names)<1){
  88         $error .= "You cannot create a trial with less than one accession.";
  89     }
  90     my $subplot_type_id = SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'subplot', 'stock_type')->cvterm_id();
  91     my $accession_type_id = SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'accession', 'stock_type')->cvterm_id();
  92     my $plot_type_id = SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'plot', 'stock_type')->cvterm_id();
  93     my $plant_type_id = SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'plant', 'stock_type')->cvterm_id();
  94     my $tissue_type_id = SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'tissue_sample', 'stock_type')->cvterm_id();
  95     my $stocks = $chado_schema->resultset('Stock::Stock')->search({
  96         type_id=>$tissue_type_id,
  97         uniquename=>{-in=>\@stock_names}
  98     });
  99     while (my $s = $stocks->next()) {
 100         $error .= "Name $s->uniquename already exists in the database.";
 101     }
 102
 103     my @source_stock_types = ($accession_type_id, $plot_type_id, $plant_type_id, $tissue_type_id);
 104
 105     my $rs = $chado_schema->resultset('Stock::Stock')->search({
 106         'is_obsolete' => { '!=' => 't' },
 107         'type_id' => {-in=>\@source_stock_types},
 108         'uniquename' => {-in=>\@accession_names}
 109     });
 110     my %found_data;
 111     while (my $s = $rs->next()) {
 112         $found_data{$s->uniquename} = 1;
 113     }
 114     foreach (@accession_names){
 115         if (!$found_data{$_}){
 116             $error .= "The following name is not in the database: $_ .";
 117         }
 118     }
 119
 120     return $error;
 121 }
 122
 123
 124 1;