lib/CXGN/Trial/TrialLayout.pm

   1 package CXGN::Trial::TrialLayout;
   2
   3 =head1 NAME
   4
   5 CXGN::Trial::TrialLayout - Module to get layout information about a trial
   6
   7 =head1 SYNOPSIS
   8
   9     This object has been converted to a factory object that will produce different classes
  10     based on the experiment_type. The usage has been kept the same for backwards compatibility,
  11     but a cleaner factory object implementation should be adopted in the future.
  12
  13  my $trial_layout = CXGN::Trial::TrialLayout->new({
  14     schema => $schema,
  15     trial_id => $trial_id,
  16     experiment_type => $experiment_type #Either 'field_layout' or 'genotyping_layout'
  17  });
  18  my $tl = $trial_layout->get_design();
  19
  20  This module handles both retrieval of field_layout and genotyping_layout experiments.
  21
  22  If experiment_type is field_layout, get_design returns a hash representing
  23  all the plots, with their design info and plant info and samples info. The return is
  24  a HashRef of HashRef where the keys are the plot_number such as:
  25
  26  {
  27     '1001' => {
  28         "plot_name" => "plot1",
  29         "plot_number" => 1001,
  30         "plot_id" => 1234,
  31         "accession_name" => "accession1",
  32         "accession_id" => 2345,
  33         "block_number" => 1,
  34         "row_number" => 2,
  35         "col_number" => 3,
  36         "rep_number" => 1,
  37         "is_a_control" => 1,
  38         "seedlot_name" => "seedlot1",
  39         "seedlot_stock_id" => 3456,
  40         "num_seed_per_plot" => 12,
  41         "seed_transaction_operator" => "janedoe",
  42         "plant_names" => ["plant1", "plant2"],
  43         "plant_ids" => [3456, 3457],
  44         "plot_geo_json" => {}
  45     }
  46  }
  47
  48  If experiment_type is genotyping_layout, get_design returns a hash representing
  49  all wells in a plate, with the tissue_sample name in each well and its accession.
  50  The return is a HashRef of HashRef where the keys are the well number such as:
  51
  52  {
  53     'A01' => {
  54         "plot_name" => "mytissuesample_A01",
  55         "stock_name" => "accession1",
  56         "plot_number" => "A01",
  57         "row_number" => "A",
  58         "col_number" => "1",
  59         "is_blank" => 0,
  60         "concentration" => "2",
  61         "volume" => "4",
  62         "dna_person" => "nmorales",
  63         "acquisition_date" => "2018/01/09",
  64         "tissue_type" => "leaf",
  65         "extraction" => "ctab",
  66         "ncbi_taxonomy_id" => "1001",
  67         "source_observation_unit_name" => "plant1",
  68         "source_observation_unit_id" => "9091"
  69     }
  70  }
  71
  72  By using get_design(), this module attempts to get the design from a
  73  projectprop called 'trial_layout_json', but if it cannot be found it calls
  74  generate_and_cache_layout() to generate the design, return it, and store it
  75  using that projectprop.
  76
  77 --------------------------------------------------------------------------
  78
  79 This can also be used the verify that a layout has a physical map covering all
  80 plots, as well as verifying that the relationships between entities are valid
  81 by doing:
  82
  83 my $trial_layout = CXGN::Trial::TrialLayout->new({
  84     schema => $schema,
  85     trial_id => $c->stash->{trial_id},
  86     experiment_type => $experiment_type, #Either 'field_layout' or 'genotyping_layout'
  87     verify_layout=>1,
  88     verify_physical_map=>1
  89 });
  90 my $trial_errors = $trial_layout->generate_and_cache_layout();
  91
  92 If there are errors, $trial_errors is a HashRef like:
  93
  94 {
  95     "errors" =>
  96         {
  97             "layout_errors" => [ "the accession between plot 1 and seedlot 1 is out of sync", "the accession between plot 1 and plant 1 is out of sync" ],
  98             "seedlot_errors" => [ "plot1 does not have a seedlot linked" ],
  99             "physical_map_errors" => [ "plot 1 does not have a row_number", "plot 1 does not have a col_number"]
 100         }
 101 }
 102
 103 =head1 DESCRIPTION
 104
 105
 106 =head1 AUTHORS
 107
 108  Jeremy D. Edwards (jde22@cornell.edu)
 109
 110 =cut
 111
 112
 113 # use Moose;
 114 # use MooseX::FollowPBP;
 115 # use Moose::Util::TypeConstraints;
 116 # use Try::Tiny;
 117 # use CXGN::Stock::StockLookup;
 118 # use CXGN::Location::LocationLookup;
 119 # use Data::Dumper;
 120 # use SGN::Model::Cvterm;
 121 # use CXGN::Chado::Stock;
 122 # use JSON;
 123
 124 use CXGN::Trial::TrialLayoutFactory;
 125
 126
 127 # has 'schema' => (
 128 #     is       => 'rw',
 129 #     isa      => 'DBIx::Class::Schema',
 130 #     required => 1,
 131 # );
 132
 133 # has 'trial_id' => (
 134 #     isa => 'Int',
 135 #     is => 'rw',
 136 #     predicate => 'has_trial_id',
 137 #     trigger => \&_lookup_trial_id,
 138 #     required => 1
 139 # );
 140
 141 # has 'experiment_type' => (
 142 #     is       => 'rw',
 143 #     isa     => 'Str', #field_layout or genotyping_layout
 144 #     required => 1,
 145 # );
 146
 147
 148
 149
 150 sub new {
 151     my $class = shift;
 152
 153     my $args = shift;
 154
 155     my $factory = CXGN::Trial::TrialLayoutFactory->new();
 156
 157     my $object = $factory->create( $args );
 158
 159     return $object;
 160
 161 }
 162
 163
 164 1;