lib/CXGN/BreedersToolbox/StocksFuzzySearch.pm

   1 package CXGN::BreedersToolbox::StocksFuzzySearch;
   2
   3 =head1 NAME
   4
   5 CXGN::BreedersToolbox::StocksFuzzySearch - an object to find approximate matches in the database to a query list of stock names.
   6
   7 =head1 USAGE
   8
   9  my $fuzzy_stock_search = CXGN::BreedersToolbox::StocksFuzzySearch->new({schema => $schema});
  10  my $fuzzy_search_result = $fuzzy_stock_search->get_matches(\@stock_list, $max_distance, $stock_type);
  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 $stock_list_ref = shift;
  40     my $max_distance = shift;
  41     my $stock_type = shift;
  42     my $schema = $self->get_schema();
  43     my @stock_list = @{$stock_list_ref};
  44     my %synonym_uniquename_lookup;
  45     my $fuzzy_string_search = CXGN::String::FuzzyMatch->new( { case_insensitive => 0} );
  46     my @fuzzy_stocks;
  47     my @absent_stocks;
  48     my @found_stocks;
  49     my %results;
  50     my $error = '';
  51     print STDERR "FuzzySearch 1".localtime()."\n";
  52
  53     my $synonym_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'stock_synonym', 'stock_property')->cvterm_id();
  54     my $stock_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, $stock_type, 'stock_type')->cvterm_id();
  55     my $q = "SELECT stock.uniquename, stockprop.value, stockprop.type_id FROM stock LEFT JOIN stockprop USING(stock_id) WHERE stock.type_id=$stock_type_id";
  56     my $h = $schema->storage->dbh()->prepare($q);
  57     $h->execute();
  58     my %uniquename_hash;
  59     while (my ($uniquename, $synonym, $type_id) = $h->fetchrow_array()) {
  60         $uniquename_hash{$uniquename}++;
  61         if ($type_id){
  62             if ($type_id == $synonym_type_id){
  63                 push @{$synonym_uniquename_lookup{$synonym}}, $uniquename;
  64             }
  65         }
  66     }
  67
  68     my @stock_names = keys %uniquename_hash;
  69     my @synonym_names = keys %synonym_uniquename_lookup;
  70     push (@stock_names, @synonym_names);
  71
  72     my @lowercased_names;
  73     my %lowercase_name_lookup;
  74     foreach (@stock_names){
  75         push @lowercased_names, lc($_);
  76         $lowercase_name_lookup{lc($_)} = $_;
  77     }
  78
  79     my @lowercased_synonyms;
  80     my %lowercase_synonym_lookup;
  81     foreach (@synonym_names){
  82         push @lowercased_synonyms, lc($_);
  83         $lowercase_synonym_lookup{lc($_)} = $_;
  84     }
  85     print STDERR "FuzzySearch 2".localtime()."\n";
  86
  87     foreach my $stock_name (@stock_list) {
  88         #lookup case insensitive stock names#
  89         my $lc_name = lc($stock_name);
  90         if (exists($lowercase_name_lookup{$lc_name})){
  91             my $uniquename = $lowercase_name_lookup{$lc_name};
  92             push @found_stocks, {matched_string => $stock_name, unique_name => $uniquename};
  93             next;
  94         }
  95         #lookup cases insensitive stock synonyms#
  96         if (exists($lowercase_synonym_lookup{$lc_name})){
  97             my %match_info;
  98             if (scalar(@{$lowercase_synonym_lookup{$lc_name}}) > 1){
  99                 my $synonym_lookup_uniquename = join ',', @{$lowercase_synonym_lookup{$lc_name}};
 100                 $error .= "This synonym $stock_name has more than one uniquename $synonym_lookup_uniquename. This should not happen!";
 101                 next;
 102             } elsif (scalar(@{$lowercase_synonym_lookup{$lc_name}}) == 1){
 103                 $match_info{matched_string} = $stock_name." (SYNONYM OF ".$lowercase_synonym_lookup{$lc_name}->[0].")";
 104                 $match_info{is_synonym} = 1;
 105                 $match_info{unique_name} = $lowercase_synonym_lookup{$lc_name}->[0];
 106             }
 107             push @found_stocks, \%match_info;
 108             next;
 109         }
 110
 111         my @search_stock_names;
 112         foreach (@lowercased_names){
 113             #if there is a difference in length greater than 10, it will not fuzzy search over that name
 114             if (abs(length($_) - length($stock_name)) <= 10){
 115                 push @search_stock_names, $_;
 116             }
 117         }
 118
 119        #####case-sensitive matches are exact_match
 120         my @stock_matches = @{$fuzzy_string_search->get_matches(lc($stock_name), \@search_stock_names, $max_distance)};
 121
 122         if (scalar(@stock_matches) == 0) {
 123             push (@absent_stocks, $stock_name);
 124         } else {
 125             my @matches;
 126             foreach (@stock_matches){
 127                 my %match_info;
 128                 my $matched_name = $_->{string};
 129                 my $original_matched_name = $lowercase_name_lookup{$matched_name};
 130                 $match_info{'name'} = $original_matched_name;
 131                 $match_info{'distance'} = $_->{distance};
 132                 my $synonym_lookup_of_matched_string = $synonym_uniquename_lookup{$original_matched_name} || [];
 133                 if (scalar(@$synonym_lookup_of_matched_string) > 1){
 134                     my $synonym_lookup_uniquename = join ',', @$synonym_lookup_of_matched_string;
 135                     $error .= "This synonym $matched_name has more than one uniquename $synonym_lookup_uniquename. This should not happen!";
 136                     next;
 137                 } elsif (scalar(@$synonym_lookup_of_matched_string) == 1){
 138                     $match_info{'unique_names'} = [$original_matched_name];
 139                     $match_info{'is_synonym'} = 1;
 140                     $match_info{'synonym_of'} = $synonym_lookup_of_matched_string->[0];
 141                 } else {
 142                     $match_info{'unique_names'} = [$original_matched_name];
 143                 }
 144                 push @matches, \%match_info;
 145             }
 146             push @fuzzy_stocks, {
 147                 name => $stock_name,
 148                 matches => \@matches
 149             };
 150         }
 151     }
 152
 153     if ($error){
 154         print STDERR "FUZZY ERRORS: $error\n";
 155         $results{'error'} = $error;
 156     }
 157
 158     $results{'found'} = \@found_stocks;
 159     $results{'fuzzy'} = \@fuzzy_stocks;
 160     $results{'absent'} = \@absent_stocks;
 161     return \%results;
 162 }
 163
 164 ###
 165 1;
 166 ###