cgi-bin/phenome/unigene_browser.pl

   1
   2 #!/usr/bin/perl -w
   3
   4 use strict;
   5 use warnings;
   6
   7 use CXGN::Scrap::AjaxPage;
   8 use CXGN::Phenome::Locus;
   9 use CXGN::Transcript::Unigene;
  10 use CXGN::DB::Connection;
  11 use CXGN::Login;
  12 use CXGN::People::Person;
  13 use CXGN::Feed;
  14 use JSON;
  15
  16
  17
  18 my %error = ();
  19 my $json = JSON->new();
  20
  21 my $dbh = CXGN::DB::Connection->new();
  22 my $doc = CXGN::Scrap::AjaxPage->new();
  23 $doc->send_http_header();
  24
  25 my ($type, $locus_id, $unigene_id, $sp_person_id, $locus_unigene_id) = $doc->get_encoded_arguments("type", "locus_id", "unigene_id", "sp_person_id", "locus_unigene_id");
  26
  27 my $locus= CXGN::Phenome::Locus->new($dbh, $locus_id);
  28
  29 $unigene_id =~/(\d+)/;
  30 $unigene_id =$1;
  31 $unigene_id =~ s/\s//;
  32 my $unigene_link = qq |http://www.sgn.cornell.edu/search/unigene.pl?unigene_id=SGN-U$unigene_id|;
  33
  34 my($login_person_id, $login_user_type)=CXGN::Login->new($dbh)->verify_session();
  35
  36 if ($login_user_type eq 'curator' || $login_user_type eq 'submitter' || $login_user_type eq 'sequencer') {
  37
  38     my $person= CXGN::People::Person->new($dbh, $login_person_id);
  39     my $user=$person->get_first_name()." ".$person->get_last_name();
  40     my $user_link = qq |http://www.sgn.cornell.edu/solpeople/personal-info.pl?sp_person_id=$sp_person_id|;
  41
  42     if (length($unigene_id)>1) {
  43         if ($type eq 'associate') {
  44             eval {
  45                 my $id = $locus->add_unigene($unigene_id, $sp_person_id);
  46             };
  47
  48             if ($@) {
  49                 $error{"error"} =  $@;
  50                 CXGN::Contact::send_email('unigene_browser.pl died',"locus-unigene association failed (locus_id = $locus_id, unigene_id = $unigene_id , person_id = $sp_person_id . $@", 'sgn-bugs@sgn.cornell.edu');
  51             }
  52             else  {
  53                 my $subject="[New unigene associated] locus $locus_id";
  54                 my $fdbk_body="$user ($user_link) has associated\n unigene $unigene_link\n with locus http://www.sgn.cornell.edu/phenome/locus_display.pl?locus_id=$locus_id";
  55                 CXGN::Contact::send_email($subject,$fdbk_body, 'sgn-db-curation@sgn.cornell.edu');
  56                 CXGN::Feed::update_feed($subject,$fdbk_body);
  57             }
  58         }
  59
  60         elsif ($type eq 'browse') {
  61
  62             my $organism = $locus->get_common_name();
  63             my $unigene = CXGN::Transcript::Unigene->new($dbh, $unigene_id);
  64             my $available_unigenes = "";
  65
  66             if (defined($unigene)) {
  67                 my $build_nr = $unigene->get_build_nr();
  68                 my $nr_members = $unigene->get_nr_members();
  69                 my $unigene_build = $unigene->get_unigene_build();
  70                 my $unigene_organism = $unigene_build->get_common_name();
  71                 my $build_status = $unigene_build->get_status();
  72
  73                 if (($unigene_organism eq $organism) && ($build_status eq "C")) {
  74
  75                     $available_unigenes .="$unigene_id*$unigene_id -- $unigene_organism -- build $build_nr -- $nr_members members|";
  76                     $error{"response"} = $available_unigenes;
  77                 }
  78             }
  79         }
  80     }elsif ($locus_unigene_id && $type eq 'obsolete') {
  81
  82         eval {
  83             $locus->obsolete_unigene($locus_unigene_id);
  84         };
  85
  86         if ($@) {
  87             $error{"error"} =  $@;
  88             CXGN::Contact::send_email('unigene_browser.pl died',"Obsoleting unigene faild. $@", 'sgn-bugs@sgn.cornell.edu');
  89         }else {
  90             $error{"response"} = "Obsoleting locus_unigene $locus_unigene_id succeeded!";
  91             my $subject="[Locus-unigene obsoleted] locus $locus_id";
  92             my $fdbk_body="$user ($user_link) has obsoleted\n unigene $unigene_link\n link from locus http://www.sgn.cornell.edu/phenome/locus_display.pl?locus_id=$locus_id";
  93             CXGN::Contact::send_email($subject,$fdbk_body, 'sgn-db-curation@sgn.cornell.edu');
  94             CXGN::Feed::update_feed($subject,$fdbk_body);
  95         }
  96     }
  97
  98     my $jobj = $json->encode(\%error);
  99     print $jobj;
 100 }
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 102