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
  29     # call set_object_id, set_object and set_primary_key here
  30     # with the appropriate parameters.
  31     #
  32     my %args = $self->get_args();
  33     $self->set_object_id($args{locus_alias_id});
  34     $self->set_object(CXGN::Phenome::LocusSynonym->new($self->get_dbh(), $self->get_object_id())
  35                       );
  36     $self->set_primary_key("locus_alias_id");
  37     $self->set_owners();
  38 }
  39
  40 # override store to check if a locus synonym with the submitted name already exists
  41
  42 sub store {
  43     my $self = shift;
  44
  45     my $locus_synonym = $self->get_object();
  46
  47     my $locus_synonym_id = $self->get_object_id();
  48     my %args = $self->get_args();
  49
  50
  51     my $not_new_locus_synonym = "";
  52   #  print STDERR "*** STORING LOCUS SYNONYM ***\n";
  53     my ($existing_id, $obsolete) = CXGN::Phenome::LocusSynonym::exists_locus_synonym_named($self->get_dbh(), $args{locus_alias}, $args{locus_id});
  54     print STDERR "******$existing_id, $obsolete\n";
  55     if ($existing_id && $obsolete == 0) {
  56         print STDERR "**Locus Synonym already exists...\n";
  57
  58         $self->get_page()->header();
  59         print $not_new_locus_synonym = "Locus synonym '".$args{locus_alias}. "' already exists <br />";
  60         print qq { <a href="javascript:history.back(1)">back to locus synonyms</a> };
  61         $self->get_page()->footer();
  62         exit();
  63     }else {
  64         $self->SUPER::store(1);
  65         $self->send_synonym_email();
  66     }
  67
  68     my $locus_id= $args{locus_id};
  69     $self->get_page()->client_redirect("/phenome/locus_synonym.pl?locus_id=$locus_id&action=new");
  70 }
  71
  72 sub delete_dialog {
  73     my $self  = shift;
  74     $self->delete();
  75 }
  76
  77 sub delete {
  78     my $self = shift;
  79     my %args = $self->get_args();
  80
  81     $self->check_modify_privileges();
  82
  83     my $locus;
  84     my $locus_name;
  85     my $image;
  86     my $image_name;
  87
  88     my $locus_synonym_name = $self->get_object()->get_locus_alias();
  89
  90     if ($args{locus_id}) {
  91         $locus = CXGN::Phenome::Locus->new($self->get_dbh(), $args{locus_id});
  92         $locus_name = $locus->get_locus_name();
  93         $locus->remove_locus_alias($args{locus_alias_id});
  94         $self->send_synonym_email('delete');
  95     }
  96
  97
  98     if ($locus) {
  99         my $locus_id= $args{locus_id};
 100         $self->get_page()->client_redirect("/phenome/locus_synonym.pl?locus_id=$locus_id&action=new");
 101     }
 102 }
 103
 104 sub generate_form {
 105     my $self = shift;
 106
 107     my %args = $self->get_args();
 108     my $locus_synonym = $self->get_object();
 109     my $locus_synonym_id = $self->get_object_id();
 110
 111     $self->init_form();
 112
 113     # generate the form with the appropriate values filled in.
 114     # if we view, then take the data straight out of the database
 115     # if we edit, take data from database and override with what's
 116     # in the submitted form parameters.
 117     # if we store, only take the form parameters into account.
 118     # for new, we don't do anything - we present an empty form.
 119     #
 120
 121     # add form elements
 122     #
 123     $self->get_form()->add_field(display_name=>"Locus synonym: ",
 124                                  field_name=>"locus_alias",
 125                                  length=>20,
 126                                  object=>$locus_synonym,
 127                                  getter=>"get_locus_alias",
 128                                  setter=>"set_locus_alias",
 129                                  validate=>"string"
 130                                  );
 131
 132
 133     $self->get_form()->add_hidden( field_name=>"action", contents=>"store" );
 134     $self->get_form()->add_hidden( field_name=>"locus_alias_id", contents=>$locus_synonym_id );
 135
 136     $self->get_form()->add_hidden( field_name=>"locus_id",
 137                                    contents=>$args{locus_id},
 138                                    object=>$locus_synonym,
 139                                    getter=>"get_locus_id",
 140                                    setter=>"set_locus_id"
 141                                    );
 142     $self->get_form()->add_hidden (
 143                                    field_name => "sp_person_id",
 144                                    contents   =>$self->get_user()->get_sp_person_id(),
 145                                    object     => $locus_synonym,
 146                                    setter     =>"set_sp_person_id",
 147                                    );
 148
 149     # populate the form
 150     # (do nothing here because synonyms cannot be edited).
 151     #if ($self->get_action()=~/view|edit/i) {
 152 #       $self->get_form()->from_database();
 153 #    }
 154     if ($self->get_action()=~/store/i) {
 155         $args{locus_alias}=lc($args{locus_alias}); # somehow this doesn't work -- would like to lowercase all tags...
 156         $self->get_form()->from_request(%args);
 157     }
 158
 159
 160 }
 161
 162 sub display_page {
 163     my $self = shift;
 164     my %args = $self->get_args();
 165
 166     # generate an appropriate edit link
 167     #
 168     my $script_name = $self->get_script_name();
 169
 170     # generate some locus and/or image information
 171     #
 172     my $locus;
 173     my $locus_name;
 174     my $image;
 175     my $image_name;
 176
 177     my @locus_synonyms = ();
 178     my @image_tags = ();
 179     my @experiment_tags = ();
 180
 181     # render the form
 182     #
 183     $self->get_page()->header();
 184
 185     print page_title_html( qq { SGN <a href="/search/direct_search.pl?search=loci">genes</a> database } );
 186
 187     print qq { <b>Locus synonyms</b> };
 188
 189     if ($args{locus_id}) {
 190         $locus = CXGN::Phenome::Locus->new($self->get_dbh(), $args{locus_id});
 191         @locus_synonyms=$locus->get_locus_aliases('f', 'f');
 192         my $locus_id = $locus->get_locus_id();
 193         print "for locus ".$locus->get_locus_name()."<br /><br />\n";
 194         foreach my $ls (@locus_synonyms) {
 195             my $locus_synonym_id = $ls->get_locus_alias_id();
 196             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 };
 197         }
 198
 199     }
 200
 201     if (!@locus_synonyms && !@image_tags) { print "<b>None found</b><br /><br />\n"; }
 202
 203     print qq { <br /><br /><b>Add another locus synonym</b>: };
 204
 205     print qq { <center> };
 206
 207     $self->get_form()->as_table();
 208
 209     print qq { </center> };
 210
 211     print qq { <a href="locus_display.pl?locus_id=$args{locus_id}&amp;action=view">back to locus page</a> };
 212
 213     $self->get_page()->footer();
 214
 215
 216 }
 217
 218
 219 sub send_synonym_email {
 220     my $self=shift;
 221     my $action=shift;
 222     my %args = $self->get_args();
 223     my $locus_id= $args{locus_id};
 224
 225     my $locus_synonym_id=$self->get_object()->get_locus_alias_id();
 226     my $locus_synonym_name= $self->get_object->get_locus_alias();
 227
 228     my $username= $self->get_user()->get_first_name()." ".$self->get_user()->get_last_name();
 229     my $sp_person_id=$self->get_user()->get_sp_person_id();
 230     my $usermail=$self->get_user()->get_private_email();
 231     my $locus_link= qq |http://www.sgn.cornell.edu/phenome/locus_display.pl?locus_id=$locus_id|;
 232     my $user_link = qq |http://www.sgn.cornell.edu/solpeople/personal-info.pl?sp_person_id=$sp_person_id|;
 233
 234     my $fdbk_body;
 235     my $subject;
 236     if ($action eq 'delete') {
 237         $subject="[A locus synonym deleted] locus $locus_id";
 238         $fdbk_body="$username ($user_link)\n has deleted locus synonym $locus_synonym_name \n from locus ($locus_link)\n"; }
 239     else {
 240         $subject="[New locus synonym stored] locus $locus_id";
 241         $fdbk_body="$username ($user_link)\n has submitted a new synonym $locus_synonym_name \n for locus ($locus_link)\n"; }
 242
 243
 244     CXGN::Contact::send_email($subject,$fdbk_body, 'sgn-db-curation@sgn.cornell.edu');
 245     CXGN::Feed::update_feed($subject,$fdbk_body);
 246 }