cgi-bin/chado/add_publication.pl

   1
   2 use strict;
   3
   4 my $add_publication_page = CXGN::Chado::AddPublicationPage->new();
   5
   6 package CXGN::Chado::AddPublicationPage;
   7
   8
   9 use CXGN::Page;
  10 use CXGN::Page::FormattingHelpers qw / info_section_html page_title_html html_optional_show/;
  11 use CXGN::Chado::Publication;
  12 use CXGN::Phenome::Locus;
  13 use CXGN::Phenome::Allele;
  14
  15 use CXGN::People;
  16 use CXGN::Contact;
  17 use CXGN::Tools::Pubmed;
  18 use CXGN::Tools::Text qw / sanitize_string /;
  19 use Bio::Chado::Schema;
  20 use CXGN::Chado::Stock;
  21 use CatalystX::GlobalContext qw( $c );
  22
  23 use base qw / CXGN::Page::Form::SimpleFormPage /;
  24
  25 sub new {
  26     my $class = shift;
  27     my $self = $class->SUPER::new(@_);
  28     $self->set_script_name("add_publication.pl");
  29     return $self;
  30 }
  31
  32
  33 sub define_object {
  34     my $self = shift;
  35
  36     # call set_object_id, set_object and set_primary_key here
  37     # with the appropriate parameters.
  38     #
  39     my %args = $self->get_args();
  40     $self->set_object_id($args{pub_id});
  41     $self->set_object(CXGN::Chado::Publication->new( $self->get_dbh(), $self->get_object_id() )
  42                       );
  43     $self->set_primary_key("pub_id");
  44 #    $self->set_object_owner($self->get_object()->get_sp_person_id); #publications do not have owners, but object_dbxref linking tables do!
  45
  46     $self->set_owners( ());
  47     $self->set_schema($c->dbic_schema('Bio::Chado::Schema', 'sgn_chado') );
  48 }
  49
  50 # override store to check if a publication with the submitted ID (pubmed accession?) already exists
  51
  52 sub store {
  53     my $self = shift;
  54
  55     my $publication = $self->get_object();
  56     my $sp_person_id=$self->get_user()->get_sp_person_id();
  57
  58     my %args = $self->get_args();
  59
  60
  61     my $action=$args{action};
  62     my $refering_page=$args{refering_page};
  63     my $type= $args{type};  #locus or allele or stock...?
  64     my $type_id = $args{type_id}; #the database id of the refering object (locus..)
  65     my $accession= sanitize_string($args{accession});
  66     my $script_name= $self->get_script_name();
  67
  68     my ($locus, $allele, $pop, $ind, $stock);
  69
  70     if ($type eq 'locus') {  $locus= CXGN::Phenome::Locus->new($self->get_dbh(), $type_id); }
  71     elsif ($type eq 'allele') { $allele= CXGN::Phenome::Allele->new($self->get_dbh(), $type_id); }
  72     elsif ($type eq 'stock') { $stock= CXGN::Chado::Stock->new($self->get_schema(), $type_id); }
  73
  74     my $pub_id;
  75     my $dbxref_id=undef;
  76     my $existing_publication= CXGN::Chado::Publication->get_pub_by_accession($self->get_dbh(),$accession );
  77     if ($pub_id = $existing_publication->get_pub_id) {
  78         #if the publication is already stored in dbxref, we need it's dbxref_id for storing it in the object_dbxref linking table
  79         $publication=CXGN::Chado::Publication->new($self->get_dbh(), $pub_id);
  80         $dbxref_id= $publication->get_dbxref_id_by_db('PMID');
  81     }
  82     $publication->set_accession($accession);
  83     $publication->add_dbxref("PMID:$accession");
  84
  85     #dbxref object...
  86     my $dbxref= CXGN::Chado::Dbxref->new($self->get_dbh(), $dbxref_id);
  87
  88     #now check if the publication exists and associated and if it has been obsoleted..
  89     my ($associated_publication, $obsolete);
  90     #for stocks
  91     my $stock_pub;
  92     if ($type eq 'locus') {
  93         $associated_publication= $locus->get_locus_dbxref($dbxref)->get_object_dbxref_id();
  94         $obsolete = $locus->get_locus_dbxref($dbxref)->get_obsolete();
  95     }elsif ($type eq 'allele') {
  96         $associated_publication= $allele->get_allele_dbxref($dbxref)->get_allele_dbxref_id();
  97         $obsolete = $allele->get_allele_dbxref($dbxref)->get_obsolete();
  98     }
  99 #       ##the publication exists but not associated with the object
 100     if ($dbxref_id ) {
 101         if ($type eq 'locus') {$locus->add_locus_dbxref($dbxref, $associated_publication, $sp_person_id); }
 102         elsif ($type eq 'allele') { $allele->add_allele_dbxref($dbxref, $associated_publication, $sp_person_id);}
 103         elsif ($type eq 'stock') { $stock->get_object_row->find_or_create_related('stock_pubs' , {
 104             pub_id => $pub_id } );
 105         }
 106         $self->send_publication_email();
 107         if (!$type && !$type_id) {
 108             $self->get_page()->client_redirect("/publication/$pub_id/view");
 109         } else {
 110             $self->get_page()->client_redirect("$script_name?type=$type&amp;type_id=$type_id&amp;refering_page=$refering_page&amp;action=new");
 111         }
 112     }
 113     #fetch the publication from pubmed:
 114     my $pubmed= CXGN::Tools::Pubmed->new($publication);
 115     my $e_id = $publication->get_eid;
 116     if ($e_id) {
 117         $publication->add_dbxref("DOI:$e_id");
 118     }
 119     $self->SUPER::store(1); #this gives the publication a  dbxref id, and stores it in pub, pub_dbxref pubabstract(change to pubprop!!), and pub_author
 120
 121     #instantiate a new dbxref object
 122     my $dbxref= CXGN::Chado::Dbxref->new($self->get_dbh(), $publication->get_dbxref_id_by_db('PMID') );
 123
 124     #store the new locus_dbxref..
 125     if ($type eq 'locus') { $locus->add_locus_dbxref($dbxref, undef, $sp_person_id); }
 126     elsif ($type eq 'allele') { $allele->add_allele_dbxref($dbxref, undef, $sp_person_id); }
 127     elsif ($type eq 'stock') { $stock->get_object_row->find_or_create_related('stock_pubs' , {
 128         pub_id => $publication->get_pub_id } );
 129     }
 130     $self->send_publication_email();
 131     if ($type && $type_id) { #if the publication is also associated with another object
 132         $self->get_page()->client_redirect("$script_name?type=$type&amp;type_id=$type_id&amp;refering_page=$refering_page&amp;action=new");
 133     }else {
 134         my $pub_id  = $publication->get_pub_id();
 135         $self->get_page()->client_redirect("/publication/$pub_id/view");
 136     }
 137 }
 138
 139
 140 sub delete {
 141     my $self  = shift;
 142     $self->check_modify_privileges();
 143     my $script_name= $self->get_script_name();
 144     my %args= $self->get_args();
 145     my $type= $args{type};
 146     my $type_id= $args{type_id};
 147     my $refering_page=$args{refering_page};
 148
 149     my $publication = $self->get_object();
 150
 151     if ($type eq 'locus') {
 152         my $locus_dbxref_obj=CXGN::Phenome::LocusDbxref->new($self->get_dbh, $args{object_dbxref_id});
 153         $locus_dbxref_obj->obsolete();
 154
 155     } elsif ($type eq 'allele') {
 156         my $allele_dbxref_obj=CXGN::Phenome::AlleleDbxref->new($self->get_dbh, $args{object_dbxref_id});
 157         $allele_dbxref_obj->delete();
 158
 159     } elsif ($type eq 'stock') {
 160         #need to pass the stock_pub_id as object_pub_id arg
 161         $self->get_schema->resultset("Stock::StockPub")->find( { stock_pub_id => $args{object_pub_id} } )
 162             ->delete;
 163
 164     }else { print qq | <h3> What are you trying to delete here? </h3>| };
 165
 166     $self->send_publication_email();
 167     $self->get_page()->client_redirect("$script_name?type=$type&amp;type_id=$type_id&amp;refering_page=$refering_page&amp;action=new");
 168
 169 }
 170
 171 sub delete_dialog {
 172     my $self = shift;
 173     my %args = $self->get_args();
 174     $self->check_modify_privileges();
 175
 176     my $title = shift;
 177     my $object_name = shift;
 178     my $field_name = shift;
 179     my $object_id = shift;
 180
 181     my $type = $args{type};
 182     my $type_id= $args{type_id}; #the id of the object we want to associate to the publication
 183
 184     my $object_name;
 185     my $object_pub_id = $args{object_pub_id};
 186     my $object_dbxref_id= $args{object_dbxref_id};
 187
 188     if ( $object_dbxref_id ) {
 189         if ($type eq 'locus') {
 190             my $locus = CXGN::Phenome::Locus->new($self->get_dbh(), $type_id);
 191             $object_name = $locus->get_locus_name();
 192         }elsif ($type eq 'allele') {
 193             my $allele = CXGN::Phenome::Allele->new($self->get_dbh(), $type_id);
 194             $object_name = $allele->get_allele_name();
 195         }
 196         $object_dbxref_id= $args{object_dbxref_id};
 197     }
 198     if ( $object_pub_id ) {
 199         if ($type eq 'stock') {
 200             my $stock = $self->get_schema->resultset("Stock::Stock")->find( {
 201                 stock_id => $type_id } );
 202             $object_name = $stock->name;
 203         }
 204     }
 205     my $back_link= qq |<a href="javascript:history.back(1)">Go back without deleting</a> |;
 206
 207     $self->get_page()->header();
 208
 209     page_title_html();
 210     print qq {
 211         <form>
 212             Delete publication association with $type ($object_name)?
 213             <input type="hidden" name="action" value="delete" />
 214             <input type="hidden" name="$field_name" value="$object_id" />
 215             <input type="hidden" name="type" value="$type" />
 216             <input type="hidden" name="type_id" value="$type_id" />
 217             <input type="hidden" name="object_dbxref_id" value="$object_dbxref_id" />
 218             <input type="hidden" name="object_pub_id" value="$object_pub_id" />
 219             <input type="hidden" name="refering_page" value="$args{refering_page}" />
 220             <input type="submit" value="Delete" />
 221             </form>
 222
 223             $back_link
 224         };
 225
 226     $self->get_page()->footer();
 227 }
 228
 229
 230 sub generate_form {
 231     my $self = shift;
 232
 233     my %args = $self->get_args();
 234     my $publication = $self->get_object();
 235     my $pub_id = $self->get_object_id();
 236
 237     $self->init_form();
 238
 239     # generate the form with the appropriate values filled in.
 240     # if we view, then take the data straight out of the database
 241     # if we edit, take data from database and override with what's
 242     # in the submitted form parameters.
 243     # if we store, only take the form parameters into account.
 244     # for new, we don't do anything - we present an empty form.
 245     #
 246
 247     # add form elements
 248     #
 249     $self->get_form()->add_field(display_name=>"Enter a PubMed ID: ",
 250                                  field_name=>"accession",
 251                                  length=>20,
 252                                  object=>$publication,
 253                                  getter=>"get_accession",
 254                                  setter=>"set_accession",
 255                                  validate=>"token"
 256                                  );
 257
 258
 259     $self->get_form()->add_hidden( field_name=>"action", contents=>"confirm_store" );
 260     $self->get_form()->add_hidden( field_name=>"pub_id", contents=>$pub_id );
 261
 262     $self->get_form()->add_hidden( field_name=>"type_id",
 263                                    contents=>$args{type_id}  );
 264
 265     $self->get_form()->add_hidden( field_name=>"type",
 266                                    contents=>$args{type}  );
 267
 268     $self->get_form()->add_hidden( field_name=>"refering_page",
 269                                    contents=>$args{refering_page}  );
 270
 271
 272     if ($self->get_action()=~/store/i) {
 273         $self->get_form()->from_request(%args);
 274     }
 275
 276
 277 }
 278
 279 sub display_page {
 280     my $self = shift;
 281     my %args = $self->get_args();
 282     #my $cvterm_name = $args{cvterm_name};
 283     # generate an appropriate edit link
 284     #
 285
 286     $self->get_page->jsan_use("CXGN.Phenome.Tools");
 287     $self->get_page->jsan_use("MochiKit.DOM");
 288     $self->get_page->jsan_use("Prototype");
 289
 290     my $script_name = $self->get_script_name();
 291     my @publications = ();
 292     my @obsoleted= ();
 293     my ($locus, $allele, $pop, $ind, @dbxref_objs, $object_dbxref_id, $obsolete, $name_dbxref_id, $stock, $pubs); #add vars here if you want this script to work with other object types..
 294
 295     # render the form
 296     $self->get_page()->header();
 297
 298     print page_title_html( qq { SGN publication upload page } );
 299
 300     print qq { <b> Publications list</b> };
 301
 302     if ($args{type} eq 'locus') {
 303         $locus = CXGN::Phenome::Locus->new($self->get_dbh(), $args{type_id});
 304         @dbxref_objs= $locus->get_dbxrefs(); #array of dbxref objects
 305         print "for locus '".$locus->get_locus_name()."'<br /><br />\n";
 306
 307     }elsif ($args{type} eq 'allele') {
 308         $allele = CXGN::Phenome::Allele->new($self->get_dbh(), $args{type_id});
 309         @dbxref_objs=$allele->get_all_allele_dbxrefs(); #array of dbxref objects
 310         print "for allele '".$allele->get_allele_name()."'<br /><br />\n";
 311     }
 312     elsif ($args{type} eq 'stock') {
 313         $stock = CXGN::Chado::Stock->new($self->get_schema, $args{type_id});
 314         $pubs = $stock->get_object_row->search_related('stock_pubs');
 315         $pubs = $pubs->search_related('pub') if $pubs;
 316         print "for stock '".$stock->get_name ."'<br /><br />\n";
 317         if ($pubs) {
 318             while (my $pub = $pubs->next ) {
 319                 my $pub_id = $pub->pub_id;
 320                 my $db_name = $pub->pub_dbxrefs->first->dbxref->db->name;
 321                 my $accession = $pub->pub_dbxrefs->first->dbxref->accession;
 322                 my $author_string = $self->author_string($pub);
 323                 my $object_pub_id = $stock->get_object_row->search_related('stock_pubs', pub_id => $pub_id)->first->stock_pub_id if $stock;
 324                 print "<a href= /publication/$pub_id/view>$db_name:$accession</a> " . $pub->title() . " (" . $pub->pyear() . ") <b>" . $author_string . "</b>" . qq { \n <a href="add_publication.pl?pub_id=$pub_id&amp;type=$args{type}&amp;type_id=$args{type_id}&amp;object_pub_id=$object_pub_id&amp;action=confirm_delete&amp;refering_page=$args{refering_page}">[Remove]</a> <br /><br />\n };
 325             }
 326         }
 327     }
 328     foreach my $dbxref (@dbxref_objs) {
 329         my $db_name=$dbxref->get_db_name();
 330         my $pub= $dbxref->get_publication();
 331
 332         my $pub_id = $pub->get_pub_id();
 333         my $accession= $dbxref->get_accession();
 334
 335         if ($args{type} eq 'locus') {
 336             #$name_dbxref_id= 'locus_dbxref_id';
 337             $object_dbxref_id= $locus->get_locus_dbxref($dbxref)->get_object_dbxref_id();
 338             $obsolete= $locus->get_locus_dbxref($dbxref)->get_obsolete();
 339         }elsif  ($args{type} eq 'allele') {
 340             #$name_dbxref_id= 'allele_dbxref_id';
 341             $object_dbxref_id= $allele->get_allele_dbxref($dbxref)->get_allele_dbxref_id();
 342             $obsolete= $allele->get_allele_dbxref($dbxref)->get_obsolete();
 343         }
 344         if ($db_name eq 'SGN_ref') { $accession= $pub_id; }
 345         if ($obsolete eq 'f') {
 346             if ($pub_id && $object_dbxref_id) {print "<a href= /publication/$pub_id/view>$db_name:$accession</a>" . $pub->get_title() . " (" . $pub->get_pyear() . ") <b>" . $pub->get_authors_as_string() . "</b>" . qq { \n <a href="add_publication.pl?pub_id=$pub_id&amp;type=$args{type}&amp;type_id=$args{type_id}&amp;object_dbxref_id=$object_dbxref_id&amp;action=confirm_delete&amp;refering_page=$args{refering_page}">[Remove]</a> <br /><br />\n }; }
 347         }elsif($pub_id)  {
 348             push @obsoleted, [$pub, $object_dbxref_id] ; #an array of obsoletes pub objects
 349         }
 350     }
 351
 352     if (@obsoleted) { $self->print_obsoleted($args{type}, $args{type_id}, @obsoleted) ; }
 353
 354     print qq { <br /><br /><b>Associate a publication with this $args{type}</b>: };
 355     print qq { <center> };
 356     $self->get_form()->as_table();
 357     print qq { </center> };
 358
 359     print qq {<br /> <br /><b> For publications not in Pubmed <a href="/publication/0/new">click here</a> <br /> };
 360
 361     if ($args{refering_page}) { print "<a href=\"$args{refering_page}\">[Go back]</a><br /><br />\n"; }
 362
 363     $self->get_page()->footer();
 364 }
 365
 366
 367 sub print_obsoleted {
 368     my $self=shift;
 369     my $type=shift;
 370     my $type_id=shift;
 371     my @publications=@_;
 372     my $obsoleted_pubs;
 373     foreach my $ref (@publications) {
 374         my $pub= $ref->[0];
 375         my $pub_id= $pub->get_pub_id();
 376         my $db_name= ($pub->get_dbxrefs())[0]->get_db_name();
 377         my $uniquename= $pub->get_uniquename();
 378         my ($accession, $title)= split ':', $uniquename;
 379         #if ($db_name eq 'SGN_ref') { $accession= $pub_id;}
 380         my $url="/publication/$pub_id/view";
 381         $obsoleted_pubs .=  qq |<a href= $url target=blank>$db_name:$accession</a> $uniquename | . $self->unobsolete_pub($type, $ref->[1])."<br />";
 382     }
 383     my $print_obsoleted=
 384         html_optional_show('obsoleted_pubs',
 385                            'Show obsolete',
 386                            qq|<div class="minorbox">$obsoleted_pubs</div> |,
 387                            );
 388
 389     print $print_obsoleted;
 390     #return $print_obsoleted;
 391 }
 392
 393 sub unobsolete_pub {
 394     my $self =shift;
 395     my $type=shift;
 396     my $type_dbxref_id= shift;
 397     my $unobsolete_link = "";
 398
 399     if (($self->get_user()->get_user_type() eq 'submitter') || ($self->get_user()->get_user_type() eq 'curator') || ($self->get_user()->get_user_type() eq 'sequencer')) {
 400         $unobsolete_link=qq|
 401             <a href="javascript:Tools.unobsoleteAnnot('$type', '$type_dbxref_id')">[unobsolete]</a>
 402
 403             <div id='unobsoleteAnnotationForm' style="display: none">
 404             <div id='type_dbxref_id_hidden'>
 405             <input type="hidden"
 406             value=$type_dbxref_id
 407             id="$type_dbxref_id">
 408             </div>
 409             </div>
 410             |;
 411     }
 412     return $unobsolete_link;
 413 }
 414
 415 sub confirm_store {
 416
 417     my $self=shift;
 418     my %args=$self->get_args();
 419     my $refering_page=$args{refering_page};
 420     my $type= $args{type};  #locus or allele or stock...?
 421     my $type_id = $args{type_id}; #the database id of the refering object (locus..)
 422     my $accession= sanitize_string($args{accession});
 423
 424     my $publication= $self->get_object();
 425     $publication->set_accession($accession);
 426
 427 ############
 428     my $dbxref_id=undef;
 429
 430     #need to check if the publication is already in the database and associated with the object (locus..)
 431     my $existing_publication= CXGN::Chado::Publication->get_pub_by_accession($self->get_dbh(),$accession) ;
 432
 433     if (my $pub_id = $existing_publication->get_pub_id) {
 434         my $publication=CXGN::Chado::Publication->new($self->get_dbh(), $pub_id);
 435         if($publication->is_associated_publication($type, $type_id)) {
 436             $self->get_page()->header();
 437             print  "<h3>Publication '$accession' is already associated with $args{type}  $args{type_id} </h3>";
 438             print qq { <a href="javascript:history.back(1)">back to publications</a> };
 439             $self->get_page()->footer();
 440         }
 441         else { #the publication isn't associated with this object
 442             if (!$type && !$type_id) {
 443                 $self->get_page()->client_redirect("/publication/$pub_id/view");
 444             } else {
 445                 $self->get_page()->header();
 446                 $self->print_confirm_form();
 447             }
 448         }
 449     } else { # the publication doesn't exist in our database
 450         $self->get_page()->header();
 451         $self->print_confirm_form();
 452     }
 453
 454
 455 }
 456
 457
 458 sub print_confirm_form {
 459     my $self=shift;
 460     my %args= $self->get_args();
 461     my $refering_page=$args{refering_page};
 462     my $type= $args{type};  #locus or...?
 463     my $type_id = $args{type_id}; #the database id of the refering object (locus..)
 464     my $accession= sanitize_string($args{accession});
 465
 466     my $script_name= $self->get_script_name();
 467
 468     my $publication= $self->get_object();
 469     $publication->set_accession($accession);
 470
 471 ############
 472     my $dbxref_id=undef;
 473
 474     #first fetch the publication from pubmed:
 475
 476     my $pubmed= CXGN::Tools::Pubmed->new($publication);
 477     my $pub_title=$publication->get_title();
 478
 479     #check if NCBI server is down (See CXGN::Tools::Pubmed for set_message($message)
 480     if ($publication->get_message() ) { $self->get_page->message_page( $publication->get_message() ); }
 481     #add pubmed verification step
 482     if ( !$pub_title ) {
 483         print  qq |<h3> $accession is not a valid pubmed ID. </h3>  |;
 484         print  qq |<a href="$script_name?type=$type&amp;type_id=$type_id&amp;refering_page=$refering_page&amp;action=new">Go back</a>|;
 485         $self->get_page()->footer();
 486         exit(0);
 487     }
 488
 489
 490 ############
 491     my $print_publication ="";
 492     my @authors= $publication->get_authors();
 493     foreach my $a (@authors) {
 494         $print_publication .=$a .", ";
 495     }
 496
 497     chop $print_publication;
 498     chop $print_publication;
 499     $print_publication .= ". (" . $publication->get_pyear() . ") " . $publication->get_title() . " " . $publication->get_series_name(). " (" . $publication->get_volume() . "):" . $publication->get_pages() . ".";
 500
 501     my $pyear= $publication->get_pyear(); #) $publication->get_title(). $publication->get_series_name() . $publication->get_volume() : $publication->get_pages() .  |;
 502
 503     my $print_associations;
 504
 505     my $publication_exists= CXGN::Chado::Publication->get_pub_by_accession($self->get_dbh(), $accession);
 506     $publication->set_pub_id($publication_exists->get_pub_id()) if $publication_exists;
 507
 508     if ($type eq 'locus') {
 509         my $locus= CXGN::Phenome::Locus->new($self->get_dbh(), $type_id);
 510         my $is_associated= $locus->associated_publication($accession);
 511         if ($publication && !$is_associated) {
 512             my @associated_with_loci = $publication->get_loci();
 513             if (@associated_with_loci) {
 514                 $print_associations .= "<br> this publication is already associated with locus:<br> ";
 515                 foreach my $a(@associated_with_loci) {
 516                     my $a_locus_id= $a->get_locus_id;
 517                     my $a_locus_name=$a->get_locus_name;
 518                     $print_associations .= qq | <a href= "/phenome/locus_display.pl?locus_id=$a_locus_id">$a_locus_name<br></a> |;
 519                 }
 520             }
 521         }
 522     }
 523     print qq | <br/> <h3>The following publication will be stored in the database and associated with $args{type}  $args{type_id}: </h3> $print_publication <br> <b> $print_associations </b>|;
 524
 525
 526
 527     $self->init_form();
 528
 529     $self->get_form()->add_hidden( field_name=>"accession", contents=>$accession );
 530     $self->get_form()->add_hidden( field_name=>"type", contents=>$args{type} );
 531     $self->get_form()->add_hidden( field_name=>"type_id", contents=>$args{type_id} );
 532     $self->get_form()->add_hidden( field_name=>"refering_page", contents=>$args{refering_page} );
 533
 534
 535     $self->get_form()->add_hidden( field_name=>"action", contents=>"store" );
 536
 537     page_title_html("Confirm store");
 538
 539
 540
 541     $self->get_form()->as_table();
 542
 543     if ($self->get_action()=~/store/i) {
 544         $self->get_form()->from_request(%args);
 545
 546
 547     }
 548
 549     print qq | <BR> <a href="javascript:history.back(1)">Go back without storing the publication</a> | ;
 550
 551     $self->get_page()->footer();
 552
 553 }
 554
 555 sub send_publication_email {
 556
 557     my $self=shift;
 558     my %args= $self->get_args();
 559     my $refering_page=$args{refering_page};
 560     my $type= $args{type};  #locus or...?
 561     my $type_id = $args{type_id}; #the database id of the refering object (locus..)
 562     my $accession= sanitize_string($args{accession});
 563     my $deleted_pubid = $args{pub_id};
 564
 565
 566     my $action= $self->get_action();
 567     my $type_link;
 568     my $username= $self->get_user()->get_first_name()." ".$self->get_user()->get_last_name();
 569     my $sp_person_id=$self->get_user()->get_sp_person_id();
 570
 571     if ($type eq 'locus') {
 572         $type_link = qq | solgenomics.net/locus/$type_id/view|;
 573     }
 574     elsif ($type eq 'allele') {
 575         $type_link = qq | solgenomics.net/phenome/allele.pl?allele_id=$type_id|;
 576     }
 577     elsif ($type eq 'stock') {
 578         $type_link = qq | solgenomics.net/stock/view/id/$type_id|;
 579     }
 580
 581     my $user_link = qq | solgenomics.net/solpeople/personal-info.pl?sp_person_id=$sp_person_id|;
 582
 583     my $usermail=$self->get_user()->get_contact_email();
 584     my $fdbk_body;
 585     my $subject;
 586
 587     my $pubmed_link = qq | http://www.ncbi.nlm.nih.gov/pubmed/$accession |;
 588
 589 if ($action eq 'store') {
 590
 591         $subject="[New publication associated with $type: $type_id]";
 592         $fdbk_body="$username ($user_link) has associated publication $pubmed_link \n with $type: $type_link";
 593    }
 594     elsif($action eq 'delete') {
 595
 596         my $deleted_pub = CXGN::Chado::Publication->new($self->get_dbh(), $deleted_pubid);
 597         my $deleted_acc = $deleted_pub->get_accession();
 598         my $deleted_pubmed = qq | http://www.ncbi.nlm.nih.gov/pubmed/$deleted_acc |;
 599         $subject="[A publication-$type association removed from $type: $type_id]";
 600         $fdbk_body="$username ($user_link) has removed publication $deleted_pubmed \n from $type: $type_link";
 601     }
 602
 603     CXGN::Contact::send_email($subject,$fdbk_body, 'sgn-db-curation@sgn.cornell.edu');
 604
 605 }
 606
 607
 608 sub get_schema {
 609   my $self = shift;
 610   return $self->{schema};
 611 }
 612
 613 sub set_schema {
 614   my $self = shift;
 615   $self->{schema} = shift;
 616 }
 617
 618 sub author_string {
 619     my ($self, $pub) = @_;
 620     my $string;
 621     my $authors = $pub->search_related('pubauthors' , {}, { order_by => 'rank' } );
 622     while (my $author = $authors->next) {
 623         my $last_name  = $author->surname();
 624         my $first_names = $author->givennames();
 625
 626         my ($first_name, $name) = split (/,/, $first_names);
 627         if ($name) {
 628             $string .="$last_name, $name. ";
 629         } else { $string .= "$last_name, $first_name. "; }
 630     }
 631     chop $string;
 632     chop $string;
 633     return $string;
 634 }