lib/CXGN/BreedersToolbox/AccessionsFuzzySearch.pm

   1 package CXGN::BreedersToolbox::AccessionsFuzzySearch;
   2
   3 =head1 NAME
   4
   5 CXGN::BreedersToolbox::AccessionsFuzzySearch - an object to find approximate matches in the database to a query accession name.
   6
   7 =head1 USAGE
   8
   9  my $fuzzy_accession_search = CXGN::BreedersToolbox::AccessionsFuzzySearch->new({schema => $schema});
  10  my $fuzzy_search_result = $fuzzy_accession_search->get_matches(\@accession_list, $max_distance)};
  11
  12 =head1 DESCRIPTION
  13
  14
  15 =head1 AUTHORS
  16
  17  Jeremy D. Edwards (jde22@cornell.edu)
  18
  19 =cut
  20
  21 use strict;
  22 use warnings;
  23 use Moose;
  24 use MooseX::FollowPBP;
  25 use Moose::Util::TypeConstraints;
  26 use CXGN::String::FuzzyMatch;
  27 use SGN::Model::Cvterm;
  28 #use Data::Dumper;
  29
  30 has 'schema' => (
  31                  is       => 'rw',
  32                  isa      => 'DBIx::Class::Schema',
  33                  required => 1,
  34                 );
  35
  36
  37 sub get_matches {
  38         my $self = shift;
  39         my $accession_list_ref = shift;
  40         my $max_distance = shift;
  41         my $schema = $self->get_schema();
  42         my @accession_list = @{$accession_list_ref};
  43         my %synonym_uniquename_lookup;
  44         my $fuzzy_string_search = CXGN::String::FuzzyMatch->new( { case_insensitive => 0} );
  45         my @fuzzy_accessions;
  46         my @absent_accessions;
  47         my @found_accessions;
  48         my %results;
  49
  50         my $synonym_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'stock_synonym', 'stock_property')->cvterm_id();
  51         my $accession_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'accession', 'stock_type')->cvterm_id();
  52         my $q = "SELECT stock.uniquename, stockprop.value, stockprop.type_id FROM stock LEFT JOIN stockprop USING(stock_id) WHERE stock.type_id=$accession_type_id";
  53         my $h = $schema->storage->dbh()->prepare($q);
  54         $h->execute();
  55         my %uniquename_hash;
  56         while (my ($uniquename, $synonym, $type_id) = $h->fetchrow_array()) {
  57                 $uniquename_hash{$uniquename} = 1;
  58                 if ($type_id){
  59                         if ($type_id == $synonym_type_id){
  60                                 push @{$synonym_uniquename_lookup{$synonym}}, $uniquename;
  61                         }
  62                 }
  63         }
  64
  65         my @stock_names = keys %uniquename_hash;
  66         my @synonym_names = keys %synonym_uniquename_lookup;
  67         push (@stock_names, @synonym_names);
  68         my %stock_names_hash = map {$_ => 1} @stock_names;
  69
  70   foreach my $accession_name (@accession_list) {
  71           if (exists($stock_names_hash{$accession_name})){
  72                   push @found_accessions, {"matched_string" => $accession_name, "unique_name" => $accession_name};
  73                   next;
  74           }
  75     my @matches;
  76     my @accession_matches = @{$fuzzy_string_search->get_matches($accession_name, \@stock_names, $max_distance)};
  77     my $more_than_one_perfect_match = 0;
  78     my $more_than_one_unique_name_for_synonym = 0;
  79     my $has_one_unique_match = 0;
  80
  81     if (scalar @accession_matches eq 0) {
  82       push (@absent_accessions, $accession_name);
  83     } else {
  84       my $matched_string = $accession_matches[0]->{'string'};
  85       my $synonym_lookup_of_matched_string = $synonym_uniquename_lookup{$matched_string};
  86
  87       #Make sure that there isn't more than one perfect match
  88       if ($accession_matches[1]) {
  89         my $next_matched_string = $accession_matches[1]->{'string'};
  90         if ($next_matched_string eq $accession_name) {
  91           $more_than_one_perfect_match = 1;
  92         }
  93       }
  94
  95       #Make sure that there isn't more than one unique name for the searched string if synonym
  96       if ($synonym_lookup_of_matched_string) {
  97         if (scalar @{$synonym_lookup_of_matched_string} > 1) {
  98           $more_than_one_unique_name_for_synonym = 1;
  99         }
 100       }
 101
 102       #Store accession name to found list if there is one unique match
 103       if ( $matched_string eq $accession_name && !$more_than_one_perfect_match && !$more_than_one_unique_name_for_synonym) {
 104         my %found_accession_and_uniquename;
 105         $found_accession_and_uniquename{'matched_string'} = $accession_name;
 106
 107         #when there is a synonym, store the unique name and the searched string
 108         if ($synonym_lookup_of_matched_string) {
 109           my @unique_names_of_synonym;
 110           @unique_names_of_synonym = @{$synonym_lookup_of_matched_string};
 111           #should not be more than one unique name for synonym because checked array length earlier
 112           $found_accession_and_uniquename{'unique_name'} = $unique_names_of_synonym[0];
 113         } else {
 114           $found_accession_and_uniquename{'unique_name'} = $accession_name;
 115         }
 116         push (@found_accessions, \%found_accession_and_uniquename);
 117         $has_one_unique_match = 1;
 118       }
 119
 120       if (!$has_one_unique_match) {
 121         foreach my $match (@accession_matches) {
 122           my $matched_name = $match->{'string'};
 123           my $distance = $match->{'distance'};
 124           my %match_info;
 125           $match_info{'name'} = $matched_name;
 126           $match_info{'distance'} = $distance;
 127           if ($synonym_uniquename_lookup{$matched_name}) {
 128             $match_info{'unique_names'} = $synonym_uniquename_lookup{$matched_name};
 129           } else {
 130             my @unique_names_array = [$matched_name];
 131             $match_info{'unique_names'} = \@unique_names_array;
 132           }
 133           push (@matches, \%match_info);
 134         }
 135         my %accession_and_fuzzy_matches;
 136         $accession_and_fuzzy_matches{'name'} = $accession_name;
 137         $accession_and_fuzzy_matches{'matches'} = \@matches;
 138         push (@fuzzy_accessions, \%accession_and_fuzzy_matches);
 139       }
 140     }
 141   }
 142   $results{'found'} = \@found_accessions;
 143   $results{'fuzzy'} = \@fuzzy_accessions;
 144   $results{'absent'} = \@absent_accessions;
 145   return \%results;
 146 }
 147 ###
 148 1;
 149 ###