lib/CXGN/Marker/SearchBrAPI.pm

   1 package CXGN::Marker::SearchBrAPI;
   2
   3 =head1 NAME
   4
   5 CXGN::Marker::SearchBrAPI - an object to handle searching for markers given criteria
   6
   7 =head1 USAGE
   8
   9 my $marker_search = CXGN::Marker::SearchBrAPI->new({
  10     bcs_schema=>$schema,
  11     marker_ids=>\@marker_ids,
  12     marker_names=>\@marker_names,
  13     get_synonyms=>$synonyms,
  14     match_method=>$method,
  15     types=>\@types,
  16     offset=>$page_size*$page,
  17     limit=>$page_size
  18 });
  19 my ($result, $total_count) = $marker_search->search();
  20
  21 =head1 DESCRIPTION
  22
  23
  24 =head1 AUTHORS
  25
  26
  27 =cut
  28
  29 use strict;
  30 use warnings;
  31 use Moose;
  32 use Try::Tiny;
  33 use Data::Dumper;
  34
  35 use CXGN::Marker;
  36 use CXGN::Marker::LocMarker;
  37 use CXGN::Marker::Tools qw(clean_marker_name);
  38 use SGN::Model::Cvterm;
  39 use CXGN::Trial;
  40 use JSON;
  41
  42 has 'bcs_schema' => (
  43     isa => 'Bio::Chado::Schema',
  44     is => 'rw',
  45     required => 1,
  46 );
  47
  48 has 'nd_protocol_id' => (
  49     isa => 'Int',
  50     is => 'rw',
  51 );
  52
  53 has 'marker_ids' => (
  54     isa => 'ArrayRef[Int]|Undef',
  55     is => 'rw',
  56 );
  57
  58 has 'marker_names' => (
  59     isa => 'ArrayRef[Int]|Undef',
  60     is => 'rw'
  61 );
  62
  63 has 'get_synonyms' => (
  64     isa => 'Bool|Undef',
  65     is => 'rw',
  66     default => 0
  67 );
  68
  69 has 'match_method' => (
  70     isa => 'Str|Undef',
  71     is => 'rw'
  72 );
  73
  74 has 'types' => (
  75     isa => 'ArrayRef[Int]|Undef',
  76     is => 'rw'
  77 );
  78
  79 has 'limit' => (
  80     isa => 'Int|Undef',
  81     is => 'rw'
  82 );
  83
  84 has 'offset' => (
  85     isa => 'Int|Undef',
  86     is => 'rw'
  87 );
  88
  89
  90 sub search {
  91     my $self = shift;
  92     my $schema = $self->bcs_schema();
  93     my $marker_ids = $self->marker_ids;
  94     my $marker_names = $self->marker_names;
  95     my $get_synonyms = $self->get_synonyms;
  96     my $match_method = $self->match_method;
  97     my $types = $self->types;
  98     my $limit = $self->limit;
  99     my $offset = $self->offset;
 100     my @where_clause;
 101     my $comparison;
 102
 103     if ($match_method eq 'exact'){ $comparison = 'in';}
 104     elsif ($match_method eq 'case_insensitive'){ $comparison = 'ilike'; }
 105     else { $comparison = 'like'; }
 106
 107     if ($marker_ids && scalar(@$marker_ids)>0) {
 108         my $sql = join ("," , @$marker_ids);
 109         push @where_clause, "marker.marker_id in ($sql)";
 110     }
 111
 112     if ($marker_names && scalar(@$marker_names)>0) {
 113         my $sql = join ("," , @$marker_names);
 114         push @where_clause, "marker_names.name in ($sql)";
 115     }
 116
 117     if ($types && scalar(@$types)>0) {
 118         my $sql = join ("," , @$types);
 119         push @where_clause, "protocol in ($sql)";
 120     }
 121
 122     my $where_clause = scalar(@where_clause)>0 ? " WHERE " . (join (" AND " , @where_clause)) : '';
 123
 124
 125     my $subquery = "SELECT distinct m2m.marker_id,name,alias,protocol,organism_name,common_name.common_name FROM sgn.marker
 126         LEFT JOIN sgn.marker_to_map as m2m using(marker_id)
 127         INNER JOIN sgn.accession ON(parent_1 = accession.accession_id OR parent_2 = accession.accession_id)
 128         INNER JOIN sgn.organism using(organism_id)
 129         INNER JOIN sgn.common_name USING(common_name_id)
 130         INNER JOIN marker_names ON(m2m.marker_id=marker_names.marker_id)
 131         INNER JOIN marker_alias ON(m2m.marker_id=marker_alias.marker_id) $where_clause";
 132
 133     my $h = $schema->storage->dbh()->prepare($subquery);
 134     $h->execute();
 135
 136     my @result;
 137     my $total_count = 0;
 138     my $subtract_count = 0;
 139
 140     while (my ($marker_id, $marker_name, $reference, $alias, $protocol, $full_count) = $h->fetchrow_array()) {
 141         push @result, {
 142             marker_id => $marker_id,
 143             marker_name => $marker_name,
 144             method => $protocol,
 145             references => $reference,
 146             synonyms => $alias,
 147             type => $protocol
 148         };
 149         $total_count = $full_count;
 150     }
 151
 152     my @data_window;
 153     if (($limit && defined($limit) || ($offset && defined($offset)))){
 154         my $start = $offset;
 155         my $end = $offset + $limit - 1;
 156         for( my $i = $start; $i <= $end; $i++ ) {
 157             if ($result[$i]) {
 158                 push @data_window, $result[$i];
 159             }
 160         }
 161     } else {
 162         @data_window = @result;
 163     }
 164
 165     $total_count = $total_count-$subtract_count;
 166     return (\@data_window, $total_count);
 167
 168 }
 169
 170 1;