cgi-bin/phenome/add_dbxref.pl

   1 use strict;
   2 use warnings;
   3
   4 use CXGN::Scrap::AjaxPage;
   5 use CXGN::DB::Connection;
   6 use CXGN::Login;
   7 use CXGN::People::Person;
   8 use CXGN::Contact;
   9
  10 use CXGN::Chado::Dbxref;
  11 use CXGN::Phenome::Locus;
  12 use CXGN::Phenome::Locus::LocusRanking;
  13 use CXGN::Feed;
  14
  15 my $dbh = CXGN::DB::Connection->new();
  16 my($login_person_id,$login_user_type)=CXGN::Login->new($dbh)->verify_session();
  17
  18 if ($login_user_type eq 'curator' || $login_user_type eq 'submitter' || $login_user_type eq 'sequencer') {
  19     my $doc = CXGN::Scrap::AjaxPage->new();
  20     my ($type,$object_id,$dbxref_id,$validate)= $doc->get_encoded_arguments("type","object_id","dbxref_id","validate");
  21
  22     my $dbxref= CXGN::Chado::Dbxref->new($dbh, $dbxref_id);
  23     my $pub_id=$dbxref->get_publication()->get_pub_id();
  24     my $link;
  25     eval {
  26         my ($object, $object_dbxref, $object_dbxref_id);
  27         if ($type eq 'locus') {
  28             $link= "http://www.sgn.cornell.edu/phenome/locus_display.pl?locus_id=$object_id";
  29
  30             $object=CXGN::Phenome::Locus->new($dbh, $object_id);
  31             my $pub_rank= CXGN::Phenome::Locus::LocusRanking->new($dbh, $object_id, $pub_id);
  32             $pub_rank->set_validate($validate);
  33             $pub_rank->store_validate(); #store locus_pub_ranking_validate
  34             my $locus_dbxref_id =$object->get_locus_dbxref($dbxref)->get_object_dbxref_id();
  35             if ($validate eq 'yes') { $object->add_locus_dbxref($dbxref,$locus_dbxref_id,$login_person_id); }
  36             elsif ($validate eq 'no') { $object->get_locus_dbxref($dbxref)->obsolete(); }
  37
  38
  39         }elsif ($type eq 'individual') {
  40             $object_dbxref_id= CXGN::Phenome::Individual::IndividualDbxref::individual_dbxref_exists($dbh,$object_id, $dbxref_id);
  41             $object_dbxref=CXGN::Phenome::Individual::IndividualDbxref->new($dbh, $object_dbxref_id);
  42             $object_dbxref->set_individual_id($object_id);
  43             $link= "http://www.sgn.cornell.edu/phenome/individual.pl?individual_id=$object_id";
  44         }
  45
  46         #this store should insert a new locus_dbxref if !$locus_dbxref_id
  47         #update obsolete to 'f' if $locus_dbxref_id and obsolete ='t'
  48         #do nothing if $locus_dbxref_id and obsolete = 'f'
  49         #my $obsolete = $object_dbxref->get_obsolete();
  50         #if ($obsolete eq 'f' && $object_dbxref_id) {
  51         #    print STDERR "********associate_ontology_term.pl exiting ***** $obsolete, $object_dbxref_id, $type\n\n";
  52         #    exit();
  53         #}
  54
  55     };
  56     if ($@) { warn "***********dbxref association failed! \n $@ \n "; }
  57     else  {
  58
  59         my $subject="[New locus_dbxref term loaded] $type $object_id";
  60         my $person= CXGN::People::Person->new($dbh, $login_person_id);
  61         my $user=$person->get_first_name()." ".$person->get_last_name();
  62         my $user_link = qq |http://www.sgn.cornell.edu/solpeople/personal-info.pl?sp_person_id=$login_person_id|;
  63
  64         my $fdbk_body="$user ($user_link has submitted a new dbxref (id=$dbxref_id) for $type $object_id  \n
  65         $link";
  66         CXGN::Contact::send_email($subject,$fdbk_body, 'sgn-db-curation@sgn.cornell.edu');
  67         CXGN::Feed::update_feed($subject,$fdbk_body);
  68     }
  69 }
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  72