lib/CXGN/Genotype/Search.pm

   1 package CXGN::Genotype::Search;
   2
   3 =head1 NAME
   4
   5 CXGN::Genotype::Search - an object to handle searching genotypes for stocks
   6
   7 =head1 USAGE
   8
   9 my $genotypes_search = CXGN::Genotype::Search->new({
  10     bcs_schema=>$schema,
  11     accession_list=>$accession_list,
  12     trial_list=>$trial_list,
  13     protocol_id=>$protocol_id
  14 });
  15 my $resultset = $genotypes_search->get_genotype_info();
  16 my $genotypes = $resultset->{genotypes};
  17
  18 =head1 DESCRIPTION
  19
  20
  21 =head1 AUTHORS
  22
  23  Nicolas Morales <nm529@cornell.edu>
  24  With code moved from CXGN::BreederSearch
  25  Lukas Mueller <lam87@cornell.edu>
  26  Aimin Yan <ay247@cornell.edu>
  27
  28 =cut
  29
  30 use strict;
  31 use warnings;
  32 use Moose;
  33 use Try::Tiny;
  34 use Data::Dumper;
  35 use SGN::Model::Cvterm;
  36 use CXGN::Trial;
  37
  38 has 'bcs_schema' => ( isa => 'Bio::Chado::Schema',
  39     is => 'rw',
  40     required => 1,
  41 );
  42
  43 has 'accession_list' => (
  44     isa => 'ArrayRef[Int]|Undef',
  45     is => 'ro',
  46 );
  47
  48 has 'trial_list' => (
  49     isa => 'ArrayRef[Int]|Undef',
  50     is => 'ro',
  51 );
  52
  53 has 'protocol_id' => (
  54     isa => 'Int',
  55     is => 'rw',
  56     required => 1,
  57 );
  58
  59 has 'limit' => (
  60     isa => 'Int',
  61     is => 'rw',
  62 );
  63
  64 has 'offset' => (
  65     isa => 'Int',
  66     is => 'rw',
  67 );
  68
  69 =head2 get_genotype_info
  70
  71 returns: an array with genotype information
  72
  73 =cut
  74
  75 sub get_genotype_info {
  76     my $self = shift;
  77     my $schema = $self->bcs_schema;
  78     my $trial_list = $self->trial_list;
  79     my $protocol_id = $self->protocol_id;
  80     my $accession_list = $self->accession_list;
  81     my $limit = $self->limit;
  82     my $offset = $self->offset;
  83     my @data;
  84     my %search_params;
  85
  86     my $snp_genotyping_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($self->bcs_schema, 'snp genotyping', 'genotype_property')->cvterm_id();
  87
  88     my @trials_accessions;
  89     foreach (@$trial_list){
  90         my $trial = CXGN::Trial->new({bcs_schema=>$schema, trial_id=>$_});
  91         my $accessions = $trial->get_accessions();
  92         foreach (@$accessions){
  93             push @trials_accessions, $_->{stock_id};
  94         }
  95     }
  96
  97     #If accessions are explicitly given, then accessions found from trials will not be added to the search.
  98     if (!$accession_list || scalar(@$accession_list)==0) {
  99         push @$accession_list, @trials_accessions;
 100     }
 101
 102     #For projects inserted into database during the addition of genotypes and genotypeprops
 103     if (scalar(@trials_accessions)==0){
 104         if ($trial_list && scalar(@$trial_list)>0) {
 105             $search_params{'nd_experiment_projects.project_id'} = { -in => $trial_list };
 106         }
 107     }
 108
 109     $search_params{'genotypeprops.type_id'} = $snp_genotyping_cvterm_id;
 110     $search_params{'nd_protocol.nd_protocol_id'} = $protocol_id;
 111     if ($accession_list && scalar(@$accession_list)>0) {
 112         $search_params{'stock.stock_id'} = { -in => $accession_list };
 113     }
 114
 115     my @select_list = ('genotypeprops.genotypeprop_id', 'genotypeprops.value', 'nd_protocol.name', 'stock.stock_id', 'stock.uniquename', 'genotype.uniquename');
 116     my @select_as_list = ('genotypeprop_id', 'value', 'protocol_name', 'stock_id', 'uniquename', 'genotype_uniquename');
 117     #$self->bcs_schema->storage->debug(1);
 118     my $rs = $self->bcs_schema->resultset('NaturalDiversity::NdExperiment')->search(
 119         \%search_params,
 120         {join=> [{'nd_experiment_genotypes' => {'genotype' => 'genotypeprops'} }, {'nd_experiment_protocols' => 'nd_protocol' }, 'nd_experiment_projects', {'nd_experiment_stocks' => 'stock'} ],
 121         select=> \@select_list,
 122         as=> \@select_as_list,
 123         order_by=>{ -asc=>'genotypeprops.genotypeprop_id' }
 124         }
 125     );
 126
 127     if ($rs) {
 128         if ($limit && defined($offset)){
 129             my $rs_slice = $rs->slice($offset, $limit);
 130             $rs = $rs_slice;
 131         }
 132         while (my $row = $rs->next()) {
 133             my $genotype_json = $row->get_column('value');
 134             my $genotype = JSON::Any->decode($genotype_json);
 135
 136             push @data, {
 137                 markerProfileDbId => $row->get_column('genotypeprop_id'),
 138                 germplasmDbId => $row->get_column('stock_id'),
 139                 germplasmName => $row->get_column('uniquename'),
 140                 genotypeUniquename => $row->get_column('genotype_uniquename'),
 141                 analysisMethod => $row->get_column('protocol_name'),
 142                 genotype_hash => $genotype,
 143                 resultCount => scalar(keys(%$genotype))
 144             };
 145         }
 146     }
 147     #print STDERR Dumper \@data;
 148
 149     my $total_count = $rs->count();
 150
 151     return ($total_count, \@data);
 152 }
 153
 154
 155
 156 1;