cgi-bin/chado/publication.pl

   1 package CXGN::Chado::PublicationDetailPage;
   2
   3 use base qw/CXGN::Page::Form::SimpleFormPage/;
   4
   5 use strict;
   6 use warnings;
   7
   8 use CXGN::Page;
   9 use CXGN::Page::FormattingHelpers qw/info_section_html
  10                                      page_title_html
  11                                      columnar_table_html
  12                                      info_table_html
  13                                      html_optional_show
  14                                      tooltipped_text
  15                                    /;
  16 use CXGN::People::Person;
  17 use CXGN::Chado::Publication;
  18 use CXGN::Chado::Pubauthor;
  19 use CXGN::Phenome::Locus;
  20 use CXGN::Phenome::Locus::LocusRanking;
  21 use CXGN::Phenome::Allele;
  22 use CXGN::Chado::Dbxref;
  23 use CXGN::Contact;
  24 use CXGN::People::PageComment;
  25 use CXGN::Tools::Text qw/ sanitize_string /;
  26
  27 my $publication_detail_page=CXGN::Chado::PublicationDetailPage->new();
  28
  29 sub new {
  30     my $class=shift;
  31     my $self= $class->SUPER::new(@_);
  32     $self->set_script_name("publication.pl");
  33     return $self;
  34 }
  35
  36
  37 sub define_object {
  38     my $self=shift;
  39     $self->set_dbh(CXGN::DB::Connection->new() );
  40     my %args= $self->get_args();
  41     foreach my $k (keys %args) {
  42         $args{$k} = sanitize_string($args{$k});
  43     }
  44     my $pub_id= $args{pub_id};
  45
  46     unless (!$pub_id || $pub_id =~m /^\d+$/) { $self->get_page->message_page("No publication exists for identifier: $pub_id"); }
  47     $self->set_object_id($pub_id);
  48     $self->set_object(CXGN::Chado::Publication->new($self->get_dbh, $self->get_object_id));
  49
  50     $self->set_primary_key("pub_id");
  51     $self->set_owners();
  52 }
  53
  54
  55 sub display_page {
  56     my $self=shift;
  57     my %args = $self->get_args();
  58     my $publication=$self->get_object();
  59     my $pub_id = $self->get_object_id();
  60     my $pub_title = $publication->get_title();
  61     my $page="/chado/publication.pl?pub_id=?";
  62     my $action= $args{action} || "";
  63
  64     #import javascript libraries
  65     $self->get_page()->jsan_use("jquery");
  66     $self->get_page()->jsan_use("CXGN.Phenome.Locus");
  67     $self->get_page()->jsan_use("CXGN.Phenome.Publication");
  68
  69     if (!$pub_title && $action ne 'new' && $action ne  'store') { $self->get_page->message_page("No publication exists for this identifier");}
  70
  71
  72     $self->get_page->header("SGN publication $pub_title");
  73     print page_title_html("Publication:\t$pub_title\n");
  74
  75     my $edit_links=$self->get_edit_links();
  76
  77     my $pub_html=$edit_links. "<br />". $self->get_form->as_table_string(). "<br />";
  78     if ($action eq 'new') { print qq |<p><b><a href = "/chado/add_publication.pl?action=new&amp;type=$args{type}&amp;type_id=$args{type_id}&amp;reffering_page=$args{reffering_page}">Store PubMed publication.</a></b></p>|; }
  79     print info_section_html(title    => 'Publication details',
  80                             contents => $pub_html ,
  81                             );
  82     if ($args{refering_page}) { print qq |<a href="$args{refering_page}">Go back to refering page.</a><br />|; }
  83
  84     my $dbxref_html=$self->get_dbxref_html($publication->get_dbxrefs());
  85
  86     print info_section_html(title    => 'External resources',
  87                             contents => $dbxref_html ,
  88                             );
  89     my $loci_link;
  90     my @loci= $publication->get_loci();
  91     foreach my $locus(@loci)  {
  92         my $locus_id = $locus->get_locus_id();
  93         my $locus_symbol= $locus->get_locus_symbol();
  94         my $cname=$locus->get_common_name();
  95         $loci_link .= qq|<a href="/phenome/locus_display.pl?locus_id=$locus_id">$cname '$locus_symbol'</a><br />| if $locus->get_obsolete() eq 'f';
  96     }
  97     print info_section_html(title    => 'Associated loci',
  98                             contents => $loci_link ,
  99                             );
 100     my $user_type= $self->get_user()->get_user_type();
 101     if ($args{get_ranked_loci} && $user_type eq 'curator' ) { $self->rank_loci_now(); }
 102
 103     my $ranked_loci= $self->get_ranked_loci();
 104     print info_section_html(title    => 'Matched loci',
 105                             contents => $ranked_loci ,
 106                             collapsible=>1,
 107                             collapsed =>1,
 108                             );
 109     ########
 110     if ($user_type eq 'curator') {
 111         # the text-indexing function does not do the right thing now
 112         # have to modify it so the search will be against just the current  publication
 113         print info_section_html(title    => 'Curator Tools',
 114                                 contents => $self->get_curator_tools(),
 115                                 );
 116     }
 117     #######
 118     my $page_comment_obj = CXGN::People::PageComment->new($self->get_dbh(), "pub", $pub_id, $self->get_page()->{request}->uri()."?".$self->get_page()->{request}->args());
 119     print $page_comment_obj->get_html();
 120
 121     $self->get_page()->footer();
 122 }
 123
 124 sub store {
 125
 126     my $self = shift;
 127
 128     my $publication = $self->get_object();
 129     my $sp_person_id=$self->get_user()->get_sp_person_id();
 130
 131     my %args = $self->get_args();
 132
 133     my $action=$args{action};
 134     my $refering_page=$args{refering_page};
 135     my $type= $args{type};  #locus or allele or stock or...?
 136     my $type_id = $args{type_id}; #the database id of the refering object (locus..)
 137     my $script_name= $self->get_script_name();
 138     my $db_name= "SGN_ref";
 139
 140     #db_name, accession, and uniquename will not be changed when updating..
 141     if (!$publication->get_db_name()) {  $publication->set_db_name($db_name); }
 142     #########
 143     $publication->set_cvterm_name('journal'); #this should be implemented in the form framework- maybe a drop down list with publication types from cvterm table??
 144     ########
 145
 146     $self->SUPER::store(1);
 147
 148     my @dbxrefs=$publication->get_dbxrefs();
 149     foreach my $dbxref(@dbxrefs) {
 150         my ($locus, $allele);
 151         if ($type eq 'locus') {
 152             $locus= CXGN::Phenome::Locus->new($self->get_dbh(), $type_id);
 153             $locus->add_locus_dbxref($dbxref, undef, $sp_person_id);
 154         }
 155         elsif ($type eq 'allele') {
 156             $allele= CXGN::Phenome::Allele->new($self->get_dbh(), $type_id);
 157             $allele->add_allele_dbxref($dbxref, undef, $sp_person_id);
 158         }
 159     }
 160     my $pub_id= $publication->get_pub_id();
 161     if ($type eq 'stock' ) {
 162         my $pub = $publication->bcs_pub;
 163         $pub->find_or_create_related('stock_pubs', {
 164             stock_id => $type_id
 165                                      });
 166     }
 167     if ($refering_page) {
 168         $self->get_page()->client_redirect("/chado/add_publication.pl?type=$type&type_id=$type_id&refering_page=$refering_page&action=new");
 169     }else {
 170         $self->get_page()->client_redirect("/chado/publication.pl?pub_id=$pub_id");
 171     }
 172 }
 173
 174 sub generate_form {
 175     my $self=shift;
 176     $self->init_form();
 177     my $publication=$self->get_object();
 178
 179     my %args=$self->get_args();
 180     my $type = $args{type};
 181     my $type_id = $args{type_id};
 182     my $refering_page= $args{refering_page};
 183
 184    my $author_example = tooltipped_text('Authors', 'Author names should be entered in the order of  last name, followed by "," then first name followed by ".". e.g Darwin, Charles. van Rijn, Henk. Giorgio,AB');
 185
 186     $self->get_form()->add_textarea(
 187                                  display_name => "Title",
 188                                  field_name  => "title",
 189                                  object => $publication,
 190                                  getter => "get_title",
 191                                  setter => "set_title",
 192                                  validate=>'string',
 193                                  columns => 80,
 194                                  rows => 1,
 195                               );
 196
 197     $self->get_form()->add_field(
 198                                  display_name => "Series name",
 199                                  field_name  => "series_name",
 200                                  object => $publication,
 201                                  getter => "get_series_name",
 202                                  setter => "set_series_name",
 203                                  validate=>'string',
 204                                  );
 205     $self->get_form()->add_field(
 206                                  display_name => "Volume",
 207                                  field_name  => "volume",
 208                                  object => $publication,
 209                                  getter => "get_volume",
 210                                  setter => "set_volume",
 211                                  validate=>'integer',
 212                                  );
 213     $self->get_form()->add_field(
 214                                  display_name => "Issue",
 215                                  field_name  => "issue",
 216                                  object => $publication,
 217                                  getter => "get_issue",
 218                                  setter => "set_issue",
 219                                  );
 220
 221     $self->get_form()->add_field (
 222                                   display_name => "Year",
 223                                   field_name  => "pyear",
 224                                   object => $publication,
 225                                   getter => "get_pyear",
 226                                   setter => "set_pyear",
 227                                   validate => 'integer',
 228                                   );
 229     $self->get_form()->add_field (
 230                                   display_name => "Pages",
 231                                   field_name  => "pages",
 232                                   object => $publication,
 233                                   getter => "get_pages",
 234                                   setter => "set_pages",
 235                                   validate => 'string',
 236         );
 237     $self->get_form()->add_textarea (
 238                                         display_name=> $author_example,
 239                                         field_name => "author",
 240                                         object => $publication,
 241                                         getter => "get_authors_as_string",
 242                                         setter => "set_author_string",
 243                                         columns => 80,
 244                                         rows =>1,
 245         );
 246     $self->get_form()->add_textarea (
 247                                      display_name=> "Abstract",
 248                                      field_name => "abstract",
 249                                      object => $publication,
 250                                      getter => "get_abstract",
 251                                      setter => "set_abstract",
 252                                      columns => 80,
 253                                      rows => =>12,
 254                                      );
 255     $self->get_form()->add_hidden (
 256                                    field_name => "pub_id",
 257                                    contents   =>$args{pub_id},
 258                                    object => $publication,
 259                                    getter => "get_pub_id",
 260                                    setter => "set_pub_id",
 261         );
 262
 263     $self->get_form()->add_hidden (
 264                                    field_name => "type",
 265                                    contents   => $type,
 266                                    );
 267     $self->get_form()->add_hidden (
 268                                    field_name => "type_id",
 269                                    contents   =>$type_id,
 270         );
 271     $self->get_form()->add_hidden(
 272                                    field_name=>"refering_page",
 273                                    contents=>$refering_page,
 274         );
 275     $self->get_form()->add_hidden( field_name=>"action", contents=>"store" );
 276
 277     if ($self->get_action=~ /view|edit/) {
 278         $self->get_form->from_database();
 279     }
 280     elsif ($self->get_action=~ /store/) {
 281         $self->get_form->from_request($self->get_args());
 282         $self->send_publication_email('store');
 283     }
 284 }
 285
 286 sub delete {
 287     my $self = shift;
 288     my %args = $self->get_args();
 289     $self->check_modify_privileges();
 290     my $publication=$self->get_object();
 291     my $pub_title;
 292     my $pub_id = $publication->get_pub_id();
 293     if ($pub_id) {
 294         $pub_title = $publication->get_title();
 295         my $message = $publication->delete();
 296         if (!$message) {
 297             $self->send_publication_email('delete');
 298         }else { $self->get_page()->message_page($message) ; }
 299     }
 300     $self->get_page()->message_page("Deleted publication $pub_id ($pub_title) from database");
 301 }
 302
 303
 304 #overriding to allow access only to curators
 305 sub check_modify_privileges {
 306     my $self = shift;
 307     # implement quite strict access controls by default
 308     #
 309     my $person_id = $self->get_login()->verify_session();
 310     my $user =  CXGN::People::Person->new($self->get_dbh(), $person_id);
 311     my $user_id = $user->get_sp_person_id();
 312     if ($user->get_user_type() eq 'curator' || $user->get_user_type() eq 'submitter' || $user->get_user_type eq 'sequencer') {
 313         return 0;
 314     }else {
 315         $self->get_page()->message_page("This page is only available for SGN curators!!");
 316     }
 317 }
 318
 319 sub get_dbxref_html {
 320     my $self=shift;
 321     my @dbxrefs=@_;
 322     my $html;
 323     foreach my $d(@dbxrefs) {
 324         my $db=$d->get_db_name();
 325         if ($db  ne 'SGN_ref') {
 326             my $url = $d->get_urlprefix() . $d->get_url() . $d->get_accession();
 327             $html .=  qq| <a href= "$url" >| . "$db:" . $d->get_accession() . "</a>";
 328         }
 329     }
 330     return $html;
 331 }
 332
 333 sub get_ranked_loci {
 334     my $self=shift;
 335     my $pub=$self->get_object();
 336     my $loci_hash=$pub->get_ranked_loci();
 337     my $pubs="";
 338     my ($val_pubs, $rej_pubs, $pending_pubs, $a_pubs)= ("" x 4);
 339     my $locus_link;
 340     my @pub;
 341     my $user_type= $self->get_user()->get_user_type();
 342
 343     foreach(sort  { $loci_hash->{$b} <=>  $loci_hash->{$a} } keys %$loci_hash )  {
 344         my $locus=CXGN::Phenome::Locus->new($self->get_dbh, $_);
 345         my $locus_symbol= $locus->get_locus_symbol();
 346         my $locus_name= $locus->get_locus_name();
 347         my $common_name= $locus->get_common_name();
 348         my $pub_id = $pub->get_pub_id();
 349         my $dbxref_id = $pub->get_dbxref_id_by_db('PMID');
 350
 351         my $locusRank = CXGN::Phenome::Locus::LocusRanking->new($self->get_dbh(), $_, $pub_id);
 352         my $validated = $locusRank->get_validate() || "";
 353         my $score = $locusRank->get_rank();
 354
 355         my $val_form= "<BR><BR>";
 356         if ($user_type eq 'curator') {
 357             $val_form= qq|
 358               <div id='locusPubForm_$pub_id'>
 359               <div id='pub_dbxref_id_$dbxref_id'>
 360               <input type="hidden"
 361                 value=$dbxref_id
 362                 id="dbxref_id_$pub_id">
 363               <select id="$dbxref_id"  >
 364                 <option value="" selected></option>
 365                 <option value="no">no</option>
 366                 <option value="yes">yes</option>
 367                 <option value="maybe">maybe</option>
 368               </select>
 369              <input type="button"
 370                 id="associate_pub_button"
 371                 value="Validate match"
 372                 onclick="Locus.addLocusDbxref('$_', '$dbxref_id');this.disabled=false;">
 373              </div>
 374              </div>
 375              <BR>
 376            |;
 377         }
 378         my $associated= $pub->is_associated_publication('locus', $_);
 379         my $val_string;
 380         if ($validated) { $val_string = "(validated: $validated)"; }
 381         $locus_link .=  qq| <a href="/phenome/locus_display.pl?locus_id=$_">$locus_symbol.</a> $common_name '$locus_name' <b> Match score = $score </b> $val_string | . $val_form;
 382
 383     }
 384     return $locus_link;
 385 }
 386
 387
 388 sub send_publication_email {
 389     my $self=shift;
 390     my %args= $self->get_args();
 391     my $refering_page=$args{refering_page};
 392     my $type= $args{type};  #locus or allele or stock or...?
 393     my $type_id = $args{type_id}; #the database id of the refering object (locus..)
 394     my $accession= $args{accession};
 395
 396     my $action= $self->get_action();
 397     my $username= $self->get_user()->get_first_name()." ".$self->get_user()->get_last_name();
 398     my $sp_person_id=$self->get_user()->get_sp_person_id();
 399
 400     my $user_link = qq | /solpeople/personal-info.pl?sp_person_id=$sp_person_id|;
 401
 402     my $usermail=$self->get_user()->get_contact_email();
 403     my $fdbk_body;
 404     my $subject;
 405
 406     if ($action eq 'store') {
 407         $subject="[New non PubMed  publication associated with $type: $type_id]";
 408         $fdbk_body="$username($user_link) has associated a non pubmed publication $accession with $type : $type_id";
 409     }
 410     elsif($action eq 'delete') {
 411         $subject="[A publication-locus association removed from $type : $type_id]";
 412         $fdbk_body="$username ($user_link) has removed a publication from $type : $type_id ";
 413     }
 414     CXGN::Contact::send_email($subject,$fdbk_body, 'sgn-db-curation@sgn.cornell.edu');
 415 }
 416
 417
 418 sub get_edit_links {
 419     my $self =shift;
 420     my $form_name = shift;
 421     return $self->get_new_link_html($form_name)." ".
 422         $self->get_edit_link_html($form_name) ." ". $self->get_delete_link_html($form_name);
 423
 424 }
 425
 426 sub get_edit_link_html {
 427     my $self = shift;
 428     my $form_name = shift;
 429     my $edit_link = "";
 430     my $script_name = $self->get_script_name();
 431     my $primary_key = $self->get_primary_key();
 432     my $object_id = $self->get_object_id();
 433
 434     my $user_id= $self->get_user()->get_sp_person_id();
 435     if (($self->get_user()->get_user_type() eq "curator") || ($self->get_user()->get_user_type() eq "submitter") || ( $self->get_user()->get_user_type() eq "sequencer") ) {
 436         $edit_link = qq { <a href="$script_name?action=edit&amp;form=$form_name&amp;$primary_key=$object_id">[Edit]</a> };
 437
 438     }else {
 439         $edit_link = qq { <span class="ghosted">[Edit]</span> };
 440     }
 441     if ($self->get_action() eq "edit") {
 442         $edit_link = qq { <a href="$script_name?action=view&amp;form=$form_name&amp;$primary_key=$object_id">[Cancel Edit]</a> };
 443     }
 444     if ($self->get_action() eq "new") {
 445         $edit_link = qq { <span class="ghosted">[Edit]</span> };
 446     }
 447     return $edit_link;
 448 }
 449
 450 sub get_delete_link_html {
 451     my $self = shift;
 452     my $form_name = shift;
 453     my $delete_link = "";
 454     my $script_name = $self->get_script_name();
 455     my $primary_key = $self->get_primary_key();
 456     my $object_id = $self->get_object_id();
 457     my $user_id= $self->get_user()->get_sp_person_id();
 458     if (($self->get_user()->get_user_type() eq "curator") || ($self->get_user()->get_user_type() eq "submitter") || ( $self->get_user()->get_user_type() eq "sequencer") ) {
 459         $delete_link = qq { <a href="$script_name?action=confirm_delete&amp;form=$form_name&amp;$primary_key=$object_id">[Delete]</a> };
 460     }else {
 461         $delete_link = qq { <span class="ghosted">[Delete]</span> };
 462     }
 463     if ($self->get_action() eq "edit") {
 464         $delete_link = qq { <span class="ghosted">[Delete]</span> };
 465     }
 466     if ($self->get_action() eq "new") {
 467         $delete_link = qq { <span class="ghosted">[Delete]</span> };
 468     }
 469     return $delete_link;
 470 }
 471
 472
 473
 474 sub get_curator_tools {
 475     my $self=shift;
 476     my $pub_id= $self->get_object_id();
 477
 478
 479 #add AJAX form for validating publication status. Current status is selected by default
 480     my $stat=$self->get_object()->get_status();
 481     my @stat_options= ("curated","pending", "irrelevant", "no gene");
 482     my $stat_options= qq|<option value=""></option>|;
 483     foreach my $s(@stat_options) {
 484         my $selected = qq|selected="selected"| if $s eq $stat || undef;
 485         $stat_options .= qq|<option value="$s" $selected >$s</option>|
 486     }
 487     my $stats=  qq|<select id="pub_stat" onchange="Publication.updatePubCuratorStat(this.value, $pub_id)">
 488                     $stat_options
 489                     </select>
 490                    |;
 491     #add AJAX form for assigning curator. Assigned curator is selected by default
 492     my $assigned_to_id= $self->get_object()->get_curator_id();
 493     my @curators= CXGN::People::Person::get_curators($self->get_dbh());
 494     my %names = map {$_ => CXGN::People::Person->new($self->get_dbh(), $_)->get_first_name() }  @curators;
 495     my $curator_options=qq|<option value=""></option>|;
 496     for my $curator_id (keys %names) {
 497         my $curator= $names{$curator_id};
 498         my $selected = qq|selected="selected"| if $curator_id==$assigned_to_id || undef;
 499         $curator_options .=qq|<option value="$curator_id" $selected>$curator</option>|;
 500     }
 501     my $curators=qq|<select id="pub_curator_select" onchange="Publication.updatePubCuratorAssigned(this.value, $pub_id)">
 502                      $curator_options
 503                      </select>
 504                     | ;
 505
 506
 507     my $form = qq |
 508         <form action="" method="get">
 509         <input id="" type="hidden" value="1" name="get_ranked_loci"/>
 510         <input id="" type="hidden" value="$pub_id" name="pub_id"/>
 511
 512         <input type="submit" value="Get ranked loci"/>
 513         </form>
 514
 515         |;
 516     my $html = <<EOHTML;
 517     Publications are automatically indexed when inserted into the database. A nightly cron job connects publications with loci based on text matching. You may run the matching algorithm manually to see now the possible matching loci. This might take a few minutes to load. After clicking this link the page will automatically reload. If matching loci are found these will be printed in the 'Matched loci' section above.
 518         $form
 519
 520 EOHTML
 521
 522     my $search = qq|Go back to <a href="/search/pub_search.pl">literature search page</a>.|;
 523     return info_table_html('Publication status'=>$stats,
 524                            'Assigned to curator'=> $curators ,
 525                            'Text index'=> $html)
 526         . $search;
 527 }
 528
 529
 530 sub rank_loci_now {
 531     my $self=shift;
 532     my $pub=$self->get_object();
 533     my $pub_id= $self->get_object_id();
 534     my $title_string= $pub->title_tsvector_string();
 535     $title_string =~ s/\'//g;
 536
 537     print STDERR "title_string = $title_string ! \n";
 538     my @match_words = split (/\s/, $title_string);
 539     #print STDERR "match_words= @match_words\n";
 540     my $abstract_string= $pub->abstract_tsvector_string();
 541     $abstract_string =~ s/\'//g;
 542     push (@match_words, (split /\s/, $abstract_string) );
 543
 544     #hash for storing unique loci.
 545     my %loci_subset=();
 546     MATCH: foreach (@match_words) {
 547         $_= "%$_%";
 548         print STDERR "...matching $_ ...\n";
 549         my $get_loci_q= ("SELECT distinct locus_id FROM phenome.locus WHERE locus_name SIMILAR TO ?
 550                       OR  locus_symbol SIMILAR TO ? OR gene_activity SIMILAR TO ? OR description SIMILAR TO ?
 551                       ORDER BY  locus_id");
 552         my $l_sth=$self->get_dbh()->prepare($get_loci_q);
 553         $l_sth->execute($_, $_, $_, $_);
 554         my (@loci)=$l_sth->fetchrow_array();
 555
 556         ##limiting the number of hits to 20 to keep this function from extremely slowing down the page.
 557         if (scalar(@loci) > 20 ) { print STDERR " Found ". scalar(@loci) . "loci! skipping...\n"; next MATCH; }
 558         else {  foreach(@loci) { $loci_subset{$_}++; } }
 559     }
 560     foreach my $locus_id (sort {$loci_subset{$a} <=> $loci_subset{$b} } keys %loci_subset) {
 561         my $locus = CXGN::Phenome::Locus->new($self->get_dbh(), $locus_id);
 562         eval {
 563             my %pub= $locus->add_locus_pub_rank($pub_id);
 564             #while ( my ($match_type, $value) = each(%pub) ) {
 565             #    print STDERR ("$match_type=> $value\n");
 566             #}
 567         };
 568     }
 569 }