cgi-bin/phenome/locus_browser.pl

   1 use CatalystX::GlobalContext qw( $c );
   2 use strict;
   3 use warnings;
   4
   5 use CXGN::Scrap::AjaxPage;
   6 use CXGN::DB::Connection;
   7 use CXGN::Login;
   8 use CXGN::Contact;
   9 use CXGN::People::Person;
  10
  11 use CXGN::Phenome::LocusgroupMember;
  12 use CXGN::Phenome::Locus;
  13 use CXGN::Chado::Cvterm;
  14 use CXGN::Feed;
  15 use CXGN::Tools::Organism;
  16
  17 use JSON;
  18
  19
  20 my $doc = CXGN::Scrap::AjaxPage->new();
  21 $doc->send_http_header();
  22
  23 my ($type, $locus_name, $object_id, $organism, $subject_id,  $relationship_id, $evidence_id, $reference_id, $lgm_id) = $doc->get_encoded_arguments("type", "locus_name", "object_id", "organism", "locus_id", "locus_relationship_id", "locus_evidence_code_id", "locus_reference_id", "lgm_id");
  24
  25
  26
  27 my $dbh = CXGN::DB::Connection->new();
  28 my $sp_person_id = $c->user() ? $c->user->get_object()->get_sp_person_id() : undef;
  29 my $schema=  $c->dbic_schema('CXGN::Phenome::Schema', undef, $sp_person_id);
  30
  31 my ($login_person_id, $login_user_type)=CXGN::Login->new($dbh)->verify_session();
  32
  33 if ($login_user_type eq 'curator' || $login_user_type eq 'submitter' || $login_user_type eq 'sequencer') {
  34
  35     if ($type eq 'browse locus') {
  36         if (!$organism) {  ($locus_name, $organism) = split(/,\s*/,  $locus_name); }
  37         $locus_name =~ /(\w+)/;
  38         $locus_name =$1;
  39         if (($locus_name) && ($organism)) {
  40             my $locus_query = "SELECT locus_id, locus_symbol, locus_name, common_name FROM phenome.locus
  41                                    JOIN sgn.common_name USING (common_name_id)
  42                                    WHERE (locus_symbol ILIKE '$locus_name%' OR locus_name ILIKE '%$locus_name%') AND (locus_id != $object_id) AND (common_name ILIKE '$organism%') AND locus.obsolete='f'";
  43             my $sth = $dbh->prepare($locus_query);
  44             $sth->execute();
  45             my ($obj_id, $symbol, $name, $obj_organism) = $sth->fetchrow_array();
  46             my $available_loci;
  47             while($symbol) {
  48                 $available_loci .= "$obj_id*$obj_organism -- $symbol -- $name|";
  49                 ($obj_id, $symbol, $name, $obj_organism) = $sth->fetchrow_array();
  50             }
  51             print "$available_loci";
  52         }
  53     }
  54
  55 }