cgi-bin/phenome/obsolete_object_dbxref.pl

   1 use strict;
   2 use warnings;
   3
   4 use CXGN::Scrap::AjaxPage;
   5 use CXGN::DB::Connection;
   6 use CXGN::Phenome::LocusDbxref;
   7 use CXGN::Login;
   8 use CXGN::Contact;
   9 use CXGN::People::Person;
  10 use JSON;
  11
  12 my $dbh = CXGN::DB::Connection->new();
  13 my($login_person_id,$login_user_type)=CXGN::Login->new($dbh)->verify_session();
  14 my $json = JSON->new();
  15 my %error=();
  16
  17
  18 if ($login_user_type eq 'curator' || $login_user_type eq 'submitter' || $login_user_type eq 'sequencer') {
  19
  20     my $doc = CXGN::Scrap::AjaxPage->new();
  21     $doc->send_http_header();
  22     my ($object_dbxref_id, $type, $action) = $doc->get_encoded_arguments("object_dbxref_id", "type", "action");
  23     my  $link;
  24
  25     eval {
  26         if ($type eq 'locus') {
  27             my $locus_dbxref=CXGN::Phenome::LocusDbxref->new($dbh, $object_dbxref_id);
  28             if ($action eq 'unobsolete' ) {
  29                 $locus_dbxref->unobsolete();
  30             }else { $locus_dbxref->obsolete(); }
  31             my $locus_id = $locus_dbxref->get_locus_id();
  32             $link = "http://solgenomics.net/phenome/locus_display.pl?locus_id=$locus_id";
  33         }elsif ($type eq 'individual') {
  34             my $individual_dbxref=CXGN::Phenome::Individual::IndividualDbxref->new($dbh, $object_dbxref_id);
  35             if ($action eq 'unobsolete' ) { $individual_dbxref->unobsolete(); }
  36             else { $individual_dbxref->obsolete(); }
  37
  38             my $individual_id = $individual_dbxref->get_individual_id();
  39             $link = "http://solgenomics.net/phenome/individual.pl?individual_id=$individual_id";
  40         }
  41     };
  42     if ($@) {
  43         warn "$action ontology term association failed!  $@";
  44         $error{error} =  "$action annotation for $type failed!  $@";
  45     }
  46     else  {
  47         $error{response} =  "$action annotation for $type worked!";
  48
  49         my $subject="[Ontology-$type association $action] ";
  50         my $person= CXGN::People::Person->new($dbh, $login_person_id);
  51         my $user=$person->get_first_name()." ".$person->get_last_name();
  52         my $user_link = qq |http://solgenomics.net/solpeople/personal-info.pl?sp_person_id=$login_person_id|;
  53
  54         my $fdbk_body="$user ($user_link) just $action ontology-$type association from phenome. $type - dbxref\n
  55          id=$object_dbxref_id  \n $link";
  56         CXGN::Contact::send_email($subject,$fdbk_body, 'sgn-db-curation@sgn.cornell.edu');
  57     }
  58
  59 } else {
  60     $error{error} =  "User type $login_user_type does not have permissions to obsolete ! ";
  61 }
  62
  63 my $jobj = $json->encode(\%error);
  64 print  $jobj;