cgi-bin/phenome/associate_ontology_term.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 use CXGN::Feed;
  10
  11 use CXGN::Phenome::LocusDbxref;
  12 use CXGN::Phenome::Locus::LocusDbxrefEvidence;
  13 use CXGN::Phenome::Individual::IndividualDbxref;
  14 use CXGN::Phenome::Individual::IndividualDbxrefEvidence;
  15
  16 use JSON;
  17
  18
  19 my $dbh = CXGN::DB::Connection->new();
  20
  21 my($login_person_id,$login_user_type)=CXGN::Login->new($dbh)->verify_session();
  22
  23 if ($login_user_type eq 'curator' || $login_user_type eq 'submitter' || $login_user_type eq 'sequencer') {
  24     my $doc = CXGN::Scrap::AjaxPage->new();
  25     $doc->send_http_header();
  26
  27     my %error = ();
  28     my $json = JSON->new();
  29
  30
  31     my ($type, $object_id, $dbxref_id,  $relationship_id, $evidence_code_id, $evidence_description_id, $evidence_with_id, $reference_id ) = $doc->get_encoded_arguments("type", "object_id", "dbxref_id", "relationship_id", "evidence_code_id", "evidence_description_id", "evidence_with_id", "reference_id");
  32
  33     if (!$evidence_with_id) {$evidence_with_id = undef};
  34     if (!$evidence_description_id) {$evidence_description_id = undef};
  35     if (!$reference_id) {$reference_id = CXGN::Chado::Publication::get_curator_ref($dbh)};
  36
  37     my $link;
  38     eval {
  39         #print STDERR "trying to store a new $type _dbxref ! \n\n";
  40         my ($object_dbxref, $object_dbxref_id, $object_dbxref_evidence);
  41         my @evidences;
  42         if ($type eq 'locus') {
  43             $object_dbxref_id= CXGN::Phenome::LocusDbxref::locus_dbxref_exists($dbh,$object_id, $dbxref_id);
  44             $object_dbxref=CXGN::Phenome::LocusDbxref->new($dbh, $object_dbxref_id);
  45             $object_dbxref->set_locus_id($object_id);
  46
  47             $object_dbxref_evidence= CXGN::Phenome::Locus::LocusDbxrefEvidence->new($dbh); ##
  48             $link= "http://www.sgn.cornell.edu/phenome/locus_display.pl?locus_id=$object_id";
  49
  50         }elsif ($type eq 'individual') {
  51             $object_dbxref_id= CXGN::Phenome::Individual::IndividualDbxref::individual_dbxref_exists($dbh,$object_id, $dbxref_id);
  52             $object_dbxref=CXGN::Phenome::Individual::IndividualDbxref->new($dbh, $object_dbxref_id);
  53             $object_dbxref->set_individual_id($object_id);
  54             $object_dbxref_evidence= CXGN::Phenome::Individual::IndividualDbxrefEvidence->new($dbh);
  55
  56
  57             $link= "http://www.sgn.cornell.edu/phenome/individual.pl?individual_id=$object_id";
  58         }
  59
  60         $object_dbxref->set_dbxref_id($dbxref_id);
  61         $object_dbxref->set_sp_person_id($login_person_id);
  62
  63         #this store should insert a new locus_dbxref if !$locus_dbxref_id
  64         #update obsolete to 'f' if $locus_dbxref_id and obsolete ='t'
  65         #do nothing if $locus_dbxref_id and obsolete = 'f'
  66         my $obsolete = $object_dbxref->get_obsolete();
  67
  68         #print STDERR "associate_ontology.pl is about to store a new $type _dbxref...\n";
  69
  70         #if the dbxref exists this should just return the database id to be used for storing a  dbxref_evidence
  71         $object_dbxref_id=$object_dbxref->store();
  72         print STDERR "object_dbxref_id = $object_dbxref_id ! \n";
  73         if ($type eq 'locus') { $object_dbxref_evidence->set_object_dbxref_id($object_dbxref_id); }
  74         elsif ($type eq 'individual') { $object_dbxref_evidence->set_individual_dbxref_id($object_dbxref_id); }
  75
  76         $object_dbxref_evidence->set_relationship_type_id($relationship_id);
  77         $object_dbxref_evidence->set_evidence_code_id($evidence_code_id);
  78         $object_dbxref_evidence->set_evidence_description_id($evidence_description_id);
  79         $object_dbxref_evidence->set_evidence_with($evidence_with_id);
  80         $object_dbxref_evidence->set_reference_id($reference_id);
  81         $object_dbxref_evidence->set_sp_person_id($login_person_id);
  82
  83         #$object_dbxref_evidence->set_updated_by($login_person_id); # evidences are now handled directly.
  84         #see update_ontology_evidence.pl
  85
  86         #if the evidence code already exists for this annotation, do not  store
  87         #if   ($object_dbxref_evidence->evidence_exists()  ) {
  88             #return here some javascript error code...
  89         #    $error{"error"} = "associate_ontology_term.pl failed. Evidence code already exists in db...(relationship_id = $relationship_id, evidence_code_id = $evidence_code_id, $type _dbxref_id = $object_dbxref_id \n";
  90
  91         #LocusDbxrefEvidence->store() should unobsolete if the evidence exists with obsolete= 't'
  92         my $object_dbxref_evidence_id= $object_dbxref_evidence->store() ;
  93
  94     };
  95     if ($@) {
  96         $error{"error"} =  'Failed associating ontology term! An email message has been sent to the SGN development team. We are working on fixing this problem.';
  97         CXGN::Contact::send_email('associate_ontology_term.pl died',"$@ \n params: relationship_id=$relationship_id\n evidence_code_id= $evidence_code_id\n evidence_description_id =$evidence_description_id\nevidence_with_id=$evidence_with_id \n reference_id=$reference_id\n sp_person_id=$login_person_id\n type=$type\n object_id= $object_id\n  dbxref_id=$dbxref_id", 'sgn-bugs@sgn.cornell.edu');
  98         warn "associating ontology term failed!  $@";
  99     }
 100     else  {
 101
 102         my $subject="[New ontology term loaded] $type $object_id";
 103         my $person= CXGN::People::Person->new($dbh, $login_person_id);
 104         my $user=$person->get_first_name()." ".$person->get_last_name();
 105         my $user_link = qq |http://www.sgn.cornell.edu/solpeople/personal-info.pl?sp_person_id=$login_person_id|;
 106
 107         my $fdbk_body="$user ($user_link has submitted a new ontology term for $type $object_id  \n
 108         $link";
 109         CXGN::Contact::send_email($subject,$fdbk_body, 'sgn-db-curation@sgn.cornell.edu');
 110         CXGN::Feed::update_feed($subject,$fdbk_body);
 111     }
 112     my $jobj = $json->encode(\%error);
 113     print  $jobj;
 114
 115
 116 }
 117
 118
 119