cgi-bin/chado/ajax_ontology_browser.pl

   1
   2 use strict;
   3 use warnings;
   4
   5 # a new version of the ontology browser by Lukas.
   6
   7 use CXGN::Scrap::AjaxPage;
   8 use CXGN::DB::Connection;
   9 use CXGN::Chado::Ontology;
  10 use CXGN::Chado::Cvterm;
  11 use JSON;
  12
  13
  14 my $json = JSON->new();
  15 my %res=();
  16
  17 my $s   = CXGN::Scrap::AjaxPage->new();
  18 my $dbh = CXGN::DB::Connection->new();
  19
  20 my ( $node, $action, $db_name, $term_name ) =
  21   $s->get_encoded_arguments( "node", "action", "db_name", "term_name" );
  22
  23 my $cvterm = CXGN::Chado::Cvterm->new_with_accession( $dbh, $node );
  24
  25 my $empty_cvterm   = CXGN::Chado::Cvterm->new($dbh);
  26 my @response_nodes = ();
  27 my $error          = "";
  28 if ( $action eq "children" ) {
  29     @response_nodes = $cvterm->get_children();
  30 }
  31 elsif ( $action eq "parents" ) {
  32     @response_nodes = $cvterm->get_recursive_parents();
  33 }
  34 elsif ( $action eq "roots" ) {
  35     my @namespaces = ( 'GO', 'PO', 'SP', 'SO', 'PATO' );
  36     my @roots = ();
  37     foreach (@namespaces) {
  38         push @roots, CXGN::Chado::Cvterm::get_roots( $dbh, $_ );
  39     }
  40     foreach (@roots) { push @response_nodes, [ $_, $empty_cvterm ] }
  41
  42
  43 } elsif ( $action eq "match" ) {
  44     my $synonym_query = $dbh->prepare(
  45         "SELECT  distinct(cvterm.dbxref_id), cv.name, cvterm.name, dbxref.accession, synonym
  46                                    FROM public.cvterm
  47                                    JOIN public.cv USING (cv_id)
  48                                    LEFT JOIN public.cvtermsynonym USING (cvterm_id)
  49                                    JOIN public.dbxref USING (dbxref_id)
  50                                    JOIN public.db USING (db_id)
  51                                    WHERE cvterm.is_obsolete= 0 AND
  52                                    db.name=? AND
  53                                    cvtermsynonym.synonym ilike '%$term_name%'
  54                                   "
  55         );
  56
  57     my $ontology_query = $dbh->prepare(
  58         "SELECT  distinct(cvterm.dbxref_id), cv.name, cvterm.name, dbxref.accession,
  59                                    count(synonym)
  60                                    FROM public.cvterm
  61                                    JOIN public.cv USING (cv_id)
  62                                    LEFT JOIN public.cvtermsynonym USING (cvterm_id)
  63                                    JOIN public.dbxref USING (dbxref_id)
  64                                    JOIN public.db USING (db_id)
  65                                    WHERE cvterm.is_obsolete= 0 AND
  66                                    db.name=? AND
  67                                     (cvterm.name ilike '%$term_name%'
  68                                     OR cvterm.definition ilike '%$term_name%'
  69                                     )
  70                                     GROUP BY cvterm.dbxref_id, cvterm.name, dbxref.accession, cv.name
  71                                     ORDER BY cv.name, cvterm.name
  72                                    "
  73         );
  74     $ontology_query->execute($db_name);
  75     my %terms;
  76     my ( $dbxref_id, $cv_name, $cvterm_name, $accession, $synonym ) =
  77         $ontology_query->fetchrow_array();
  78
  79     while ($cvterm_name) {
  80         $terms{$cv_name}{"$dbxref_id*$cv_name--$db_name:$accession--"} =
  81             $cvterm_name;
  82         ( $dbxref_id, $cv_name, $cvterm_name, $accession, $synonym ) =
  83             $ontology_query->fetchrow_array();
  84     }
  85
  86     $synonym_query->execute($db_name);
  87     my @synonym_terms;
  88     while ( my ( $dbxref_id, $cv_name, $cvterm_name, $accession, $synonym ) =
  89             $synonym_query->fetchrow_array() )
  90     {
  91         if ( $terms{$cv_name}{"$dbxref_id*$cv_name--$db_name:$accession--"} ) {
  92             $terms{$cv_name}{"$dbxref_id*$cv_name--$db_name:$accession--"} .=
  93                 " ($synonym)";
  94         }
  95         else {
  96             $terms{$cv_name}{"$dbxref_id*$cv_name--$db_name:$accession--"} =
  97                 $cvterm_name . " ($synonym)";
  98         }
  99     }
 100
 101     #sort the hash of hashes by keys(cv_name)  and then by values (term names)
 102     my $print_string;
 103
 104     foreach my $cv_name ( sort ( keys %terms ) ) {
 105         foreach my $key (
 106             sort { $terms{$cv_name}{$a} cmp $terms{$cv_name}{$b} }
 107             keys %{ $terms{$cv_name} }
 108             )
 109         {
 110             $print_string .= $key . $terms{$cv_name}{$key};
 111             $print_string .= "|";
 112         }
 113     }
 114     $res{response} = $print_string;
 115
 116 } else { $res{error} = "ERROR. The action parameter is required."; }
 117
 118
 119 my @response_list = ();
 120
 121 if (@response_nodes) {
 122     foreach my $n (@response_nodes) {
 123         my $has_children = 0;
 124         if ( $n->[0]->count_children() > 0 ) { $has_children = 1; }
 125         push @response_list,
 126         ( $n->[0]->get_full_accession() ) . "\*"
 127             . (   $n->[0]->get_cvterm_name() . "\*"
 128                   . ( $n->[0]->get_cvterm_id() )
 129                   . "\*$has_children" . "\*"
 130                   . $n->[1]->get_cvterm_name() );
 131     }
 132     $res{response} = join "#", @response_list;
 133 }
 134
 135
 136 $s->send_http_header();
 137 print $json->encode(\%res);
 138
 139