lib/CXGN/Trial/TrialLayoutDownload/SamplingTrialLayout.pm

   1 package CXGN::Trial::TrialLayoutDownload::SamplingTrialLayout;
   2
   3 =head1 NAME
   4
   5 CXGN::Trial::TrialLayoutDownload::SamplingTrialLayout - an object to handle downloading a sampling trial layout. this should only be called from CXGN::Trial::TrialLayoutDownload
   6
   7 =head1 USAGE
   8
   9 my $plate_layout = CXGN::Trial::TrialLayoutDownload::SamplingTrialLayout->new({
  10     schema => $schema,
  11     trial_id => $trial_id,
  12     data_level => $data_level,
  13     selected_columns => \%selected_cols,
  14     design => $design,
  15     trial => $selected_trial,
  16 });
  17 my $result = $plate_layout->retrieve();
  18
  19 =head1 DESCRIPTION
  20
  21 Will output an array of arrays, where each row is a tissue sample in the sampling trial. the columns are based on the supplied selected_cols. this should only be called from CXGN::Trial::TrialLayoutDownload
  22
  23 =head1 AUTHORS
  24
  25 =cut
  26
  27 use strict;
  28 use warnings;
  29 use Moose;
  30 use Try::Tiny;
  31 use Data::Dumper;
  32 use SGN::Model::Cvterm;
  33 use CXGN::Stock;
  34 use CXGN::Stock::Accession;
  35
  36 extends 'CXGN::Trial::TrialLayoutDownload';
  37
  38 sub retrieve {
  39     my $self = shift;
  40     my $schema = $self->schema();
  41     my %selected_cols = %{$self->selected_columns};
  42     my %design = %{$self->design};
  43     my $trial = $self->trial;
  44     my @output;
  45
  46     my @possible_cols = ('trial_name', 'year', 'location', 'sampling_facility', 'sampling_trial_sample_type', 'acquisition_date', 'tissue_sample_name', 'plot_number', 'rep_number', 'source_observation_unit_name', 'accession_name', 'synonyms', 'dna_person', 'notes', 'tissue_type', 'extraction', 'concentration', 'volume');
  47
  48     my @header;
  49     foreach (@possible_cols){
  50         if ($selected_cols{$_}){
  51             push @header, $_;
  52         }
  53     }
  54     push @output, \@header;
  55
  56     my $trial_name = $trial->get_name ? $trial->get_name : '';
  57     my $location_name = $trial->get_location ? $trial->get_location->[1] : '';
  58     my $trial_year = $trial->get_year ? $trial->get_year : '';
  59     my $sampling_facility_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'sampling_facility', 'project_property')->cvterm_id();
  60     my $sampling_trial_sample_type_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'sampling_trial_sample_type', 'project_property')->cvterm_id();
  61     my $sampling_facility = $schema->resultset("Project::Projectprop")->search({ project_id => $trial->get_trial_id(), type_id => $sampling_facility_cvterm_id } )->first->value();
  62     my $sampling_type = $schema->resultset("Project::Projectprop")->search({ project_id => $trial->get_trial_id(), type_id => $sampling_trial_sample_type_cvterm_id } )->first->value();
  63
  64     my $pedigree_strings = $self->_get_all_pedigrees(\%design);
  65
  66     foreach my $key (sort { $a cmp $b} keys %design) {
  67         my $design_info = $design{$key};
  68         my $line;
  69         foreach (@possible_cols){
  70             if ($selected_cols{$_}){
  71                 if ($_ eq 'trial_name'){
  72                     push @$line, $trial_name;
  73                 } elsif ($_ eq 'year'){
  74                     push @$line, $trial_year;
  75                 } elsif ($_ eq 'location'){
  76                     push @$line, $location_name;
  77                 } elsif ($_ eq 'sampling_facility'){
  78                     push @$line, $sampling_facility;
  79                 } elsif ($_ eq 'sampling_trial_sample_type'){
  80                     push @$line, $sampling_type;
  81                 } elsif ($_ eq 'tissue_sample_name'){
  82                     push @$line, $design_info->{'plot_name'};
  83                 } elsif ($_ eq 'synonyms'){
  84                     my $accession = CXGN::Stock::Accession->new({schema=>$schema, stock_id=>$design_info->{"accession_id"}});
  85                     push @$line, join ',', @{$accession->synonyms}
  86                 } elsif ($_ eq 'pedigree'){
  87                     push @$line, $pedigree_strings->{$design_info->{"accession_name"}};
  88                 } else {
  89                     push @$line, $design_info->{$_};
  90                 }
  91             }
  92         }
  93         push @output, $line;
  94     }
  95
  96     return \@output;
  97 }
  98
  99 1;