cgi-bin/phenome/locus_synonym.pl

   1
   2 use strict;
   3
   4 my $locus_synonym_detail_page = CXGN::Phenome::LocusSynonymDetailPage->new();
   5
   6 package CXGN::Phenome::LocusSynonymDetailPage;
   7
   8
   9 use CXGN::Page;
  10 use CXGN::Page::FormattingHelpers qw / info_section_html page_title_html /;
  11 use CXGN::Phenome::LocusSynonym;
  12 use CXGN::Phenome::Locus;
  13 use CXGN::Feed;
  14
  15 use base qw / CXGN::Page::Form::SimpleFormPage /;
  16
  17 sub new {
  18     my $class = shift;
  19     my $self = $class->SUPER::new(@_);
  20     $self->set_script_name("locus_synonym.pl");
  21
  22     return $self;
  23 }
  24
  25
  26 sub define_object {
  27     my $self = shift;
  28     # call set_object_id, set_object and set_primary_key here
  29     # with the appropriate parameters.
  30     #
  31     my %args = $self->get_args();
  32     $self->set_object_id($args{locus_alias_id});
  33     $self->set_object(CXGN::Phenome::LocusSynonym->new($self->get_dbh(), $self->get_object_id())
  34                       );
  35     $self->set_primary_key("locus_alias_id");
  36     $self->set_owners();
  37 }
  38
  39 # override store to check if a locus synonym with the submitted name already exists
  40
  41 sub store {
  42     my $self = shift;
  43
  44     my $locus_synonym = $self->get_object();
  45
  46     my $locus_synonym_id = $self->get_object_id();
  47     my %args = $self->get_args();
  48
  49     my $not_new_locus_synonym = "";
  50     my ($existing_id, $obsolete) = CXGN::Phenome::LocusSynonym::exists_locus_synonym_named($self->get_dbh(), $args{locus_alias}, $args{locus_id});
  51     if ($existing_id && $obsolete == 0) {
  52
  53         $self->get_page()->header();
  54         print $not_new_locus_synonym = "Locus synonym '".$args{locus_alias}. "' already exists <br />";
  55         print qq { <a href="javascript:history.back(1)">back to locus synonyms</a> };
  56         $self->get_page()->footer();
  57         exit();
  58     }else {
  59         $self->SUPER::store(1);
  60         $self->send_synonym_email();
  61     }
  62
  63     my $locus_id= $args{locus_id};
  64     $self->get_page()->client_redirect("/phenome/locus_synonym.pl?locus_id=$locus_id&action=new");
  65 }
  66
  67 sub delete_dialog {
  68     my $self  = shift;
  69     $self->delete();
  70 }
  71
  72 sub delete {
  73     my $self = shift;
  74     my %args = $self->get_args();
  75
  76     $self->check_modify_privileges();
  77
  78     my $locus;
  79     my $locus_name;
  80     my $image;
  81     my $image_name;
  82
  83     my $locus_synonym_name = $self->get_object()->get_locus_alias();
  84
  85     if ($args{locus_id}) {
  86         $locus = CXGN::Phenome::Locus->new($self->get_dbh(), $args{locus_id});
  87         $locus_name = $locus->get_locus_name();
  88         $locus->remove_locus_alias($args{locus_alias_id});
  89         $self->send_synonym_email('delete');
  90     }
  91     if ($locus) {
  92         my $locus_id= $args{locus_id};
  93         $self->get_page()->client_redirect("/phenome/locus_synonym.pl?locus_id=$locus_id&action=new");
  94     }
  95 }
  96
  97 sub generate_form {
  98     my $self = shift;
  99
 100     my %args = $self->get_args();
 101     my $locus_synonym = $self->get_object();
 102     my $locus_synonym_id = $self->get_object_id();
 103
 104     $self->init_form();
 105
 106     # generate the form with the appropriate values filled in.
 107     # if we view, then take the data straight out of the database
 108     # if we edit, take data from database and override with what's
 109     # in the submitted form parameters.
 110     # if we store, only take the form parameters into account.
 111     # for new, we don't do anything - we present an empty form.
 112     #
 113
 114     # add form elements
 115     #
 116     $self->get_form()->add_field(display_name=>"Locus synonym: ",
 117                                  field_name=>"locus_alias",
 118                                  length=>20,
 119                                  object=>$locus_synonym,
 120                                  getter=>"get_locus_alias",
 121                                  setter=>"set_locus_alias",
 122                                  validate=>"string"
 123                                  );
 124
 125     $self->get_form()->add_hidden( field_name=>"action", contents=>"store" );
 126     $self->get_form()->add_hidden( field_name=>"locus_alias_id", contents=>$locus_synonym_id );
 127
 128     $self->get_form()->add_hidden( field_name=>"locus_id",
 129                                    contents=>$args{locus_id},
 130                                    object=>$locus_synonym,
 131                                    getter=>"get_locus_id",
 132                                    setter=>"set_locus_id"
 133                                    );
 134     $self->get_form()->add_hidden (
 135                                    field_name => "sp_person_id",
 136                                    contents   =>$self->get_user()->get_sp_person_id(),
 137                                    object     => $locus_synonym,
 138                                    setter     =>"set_sp_person_id",
 139                                    );
 140
 141     # populate the form
 142     # (do nothing here because synonyms cannot be edited).
 143     #if ($self->get_action()=~/view|edit/i) {
 144 #       $self->get_form()->from_database();
 145 #    }
 146     if ($self->get_action()=~/store/i) {
 147         $args{locus_alias}=lc($args{locus_alias}); # somehow this doesn't work -- would like to lowercase all tags...
 148         $self->get_form()->from_request(%args);
 149     }
 150
 151
 152 }
 153
 154 sub display_page {
 155     my $self = shift;
 156     my %args = $self->get_args();
 157
 158     # generate an appropriate edit link
 159     #
 160     my $script_name = $self->get_script_name();
 161
 162     # generate some locus and/or image information
 163     #
 164     my $locus;
 165     my $locus_name;
 166     my $image;
 167     my $image_name;
 168
 169     my @locus_synonyms = ();
 170     my @image_tags = ();
 171     my @experiment_tags = ();
 172
 173     # render the form
 174     #
 175     $self->get_page()->header();
 176
 177     print page_title_html( qq { SGN <a href="/search/direct_search.pl?search=loci">genes</a> database } );
 178
 179     print qq { <b>Locus synonyms</b> };
 180
 181     if ($args{locus_id}) {
 182         $locus = CXGN::Phenome::Locus->new($self->get_dbh(), $args{locus_id});
 183         @locus_synonyms=$locus->get_locus_aliases('f', 'f');
 184         my $locus_id = $locus->get_locus_id();
 185         print "for locus ".$locus->get_locus_name()."<br /><br />\n";
 186         foreach my $ls (@locus_synonyms) {
 187             my $locus_synonym_id = $ls->get_locus_alias_id();
 188             print $ls->get_locus_alias(). qq { \n <a href="locus_synonym.pl?locus_id=$locus_id&amp;locus_alias_id=$locus_synonym_id&amp;action=confirm_delete">[Remove]</a> <br />\n };
 189         }
 190     }
 191
 192     if (!@locus_synonyms && !@image_tags) { print "<b>None found</b><br /><br />\n"; }
 193
 194     print qq { <br /><br /><b>Add another locus synonym</b>: };
 195
 196     print qq { <center> };
 197
 198     $self->get_form()->as_table();
 199
 200     print qq { </center> };
 201
 202     print qq { <a href="/locus/$args{locus_id}/view">back to locus page</a> };
 203
 204     $self->get_page()->footer();
 205 }
 206
 207
 208 sub send_synonym_email {
 209     my $self=shift;
 210     my $action=shift;
 211     my %args = $self->get_args();
 212     my $locus_id= $args{locus_id};
 213
 214     my $locus_synonym_id=$self->get_object()->get_locus_alias_id();
 215     my $locus_synonym_name= $self->get_object->get_locus_alias();
 216
 217     my $username= $self->get_user()->get_first_name()." ".$self->get_user()->get_last_name();
 218     my $sp_person_id=$self->get_user()->get_sp_person_id();
 219     my $usermail=$self->get_user()->get_private_email();
 220     my $locus_link= qq |http://solgenomics.net/locus/$locus_id/view|;
 221     my $user_link = qq |http://solgenomics.net/solpeople/personal-info.pl?sp_person_id=$sp_person_id|;
 222
 223     my $fdbk_body;
 224     my $subject;
 225     if ($action eq 'delete') {
 226         $subject="[A locus synonym deleted] locus $locus_id";
 227         $fdbk_body="$username ($user_link)\n has deleted locus synonym $locus_synonym_name \n from locus ($locus_link)\n"; }
 228     else {
 229         $subject="[New locus synonym stored] locus $locus_id";
 230         $fdbk_body="$username ($user_link)\n has submitted a new synonym $locus_synonym_name \n for locus ($locus_link)\n"; }
 231
 232     CXGN::Contact::send_email($subject,$fdbk_body, 'sgn-db-curation@sgn.cornell.edu');
 233     CXGN::Feed::update_feed($subject,$fdbk_body);
 234 }