cgi-bin/solpeople/personal-info.pl

   1 # Evan, 1 / 15 / 07: combines contact-info.pl and research-info.pl
   2
   3 #if a user is logged in, look at the logged-in user's info;
   4 #else, can call with an id parameter to get a read-only view of any user's info
   5 #(if no login and no 'id=', no good)
   6
   7 #(we don't want to encourage users to go directly to this page to edit their own info;
   8 # they should go through top-level.pl, so they'll already be logged in when they get here)
   9
  10 use strict;
  11 use CXGN::Login;
  12
  13 my $contact_info_page = new SolPeoplePersonalInfoPage();
  14
  15 package SolPeoplePersonalInfoPage;
  16
  17 use CXGN::Page;
  18 use CXGN::Page::FormattingHelpers qw/page_title_html/;
  19 use CXGN::People;
  20 use File::Spec;
  21 use HTML::Entities;
  22 use CXGN::Phenome::Locus;
  23
  24 use base qw | CXGN::Page::Form::SimpleFormPage |;
  25
  26 sub new {
  27         my $class = shift;
  28         my $person_id = shift;
  29         my $self = $class->SUPER::new(); #arguments are parsed from the Page here
  30         my (undef, undef, $this_script_filename) = File::Spec->splitpath($0); #$0 contains current filename with some path or other prepended
  31         $self->set_script_name($this_script_filename);
  32         return $self;
  33 }
  34
  35 sub define_object {
  36         my $self = shift;
  37         # call set_object_id, set_object and set_primary_key here
  38         my %args = $self->get_args();
  39         $self->set_object_id($args{sp_person_id});
  40         $self->set_object(new CXGN::People::Person($self->get_dbh(), $args{sp_person_id}));
  41         $self->set_primary_key("sp_person_id");
  42         $self->set_owners($self->get_object()->get_sp_person_id());
  43 }
  44
  45 #specified in SimpleFormPage
  46 sub check_modify_privileges {
  47     my $self = shift;
  48
  49     # implement quite strict access controls by default
  50     #
  51     my $person_id = $self->get_login()->has_session();
  52     my $user =  CXGN::People::Person->new($self->get_dbh(), $person_id);
  53     my $user_id = $user->get_sp_person_id();
  54     if ($user->get_user_type() eq 'curator') {
  55         return 0;
  56     }
  57
  58     # check the owner only if the action is not new
  59     #
  60     my @owners= $self->get_owners();
  61
  62
  63     if (!(grep {/^$user_id$/} @owners ))
  64     {
  65         $self->get_page()->message_page("You do not have rights to modify this database entry because you do not own it. [$user_id, @owners]");
  66     }
  67     else {
  68         return 0;
  69     }
  70
  71
  72     # override to check privileges for edit, store, delete.
  73     # return 0 for allow, 1 for not allow.
  74     return 0;
  75
  76 }
  77
  78 #specified in SimpleFormPage
  79 sub validate_parameters_before_store
  80 {
  81         my $self = shift;
  82         my %args = $self->get_args();
  83
  84         my ($keywords, $format, $research_interests, $organism_codes_str, $unlisted_organisms_str) =
  85                 @args{qw(keywords format research_interests organisms unlisted_organisms)};
  86         $format = "auto" unless $format eq "html";
  87
  88         #after checking for legal values, do the actual storing of existing organism IDs here
  89         my @organism_codes = map {$_ =~ tr/[0-9]//cds; $_} split(/\0/, $organism_codes_str);
  90         foreach my $c ( @organism_codes )
  91         {
  92                 my $test = new CXGN::People::Organism($self->get_dbh(), $c);
  93                 if(!defined($test))
  94                 {
  95                         $self->get_page()->message_page("Organism code \"$_\" is not defined in the database.\n");
  96                 }
  97         }
  98         my %selected_organisms = map {$_ => 1} @organism_codes; #ids of only those organisms selected with the multiselect appear in the hash
  99         my $person = $self->get_object();
 100         foreach my $o ($person->get_organisms())
 101         {
 102                 $o->set_selected(0);
 103                 if($selected_organisms{$o->get_sp_organism_id()})
 104                 {
 105                         $o->set_selected(1);
 106                 }
 107         }
 108
 109         #deal with unlisted organisms
 110         my @unlisted_organisms;
 111         foreach (split(/;/, $unlisted_organisms_str))
 112         {
 113                 if(m/^\s*((\S.*\S)|\S)\s*$/) #remove leading and trailing spaces
 114                 {
 115                         push @unlisted_organisms, $1;
 116                 }
 117         }
 118         my $unlisted_organisms = join("\0", @unlisted_organisms);
 119
 120         # Quick, dirty hack method of defenestrating disallowed HTML tags in
 121         # research interest statements: replace allowed tags with a marker string,
 122         # then delete all tokens of the form "<[^>]+>", then replace the marker string
 123         # with the original tag.
 124         #
 125         # Using the marker string allows us to "save" the information about the tag
 126         # that is allowed -- changing it to a token that won't match the "<[^>]+>"
 127         # pattern. Using a random marker string prevents a user learning (through a
 128         # website error or something that reveals a static marker string) the marker
 129         # and trying to insert illegal tags by typing the marker into their statement
 130         # manually. This is further guarded against by only recognizing marker strings
 131         # with allowed tags encoded. (Yes, I am paranoid)
 132         #
 133         # The main problem with this is if someone happens to use both a literal "<"
 134         # and a matching ">" in their research statement -- if that happens, the
 135         # text flanked by these will be deleted -- they'll need to use &lt; and &gt;
 136         # instead.
 137         my $tag_marker = $self->get_page()->tempname();
 138         my $formatted_interests = $research_interests;
 139         $formatted_interests =~ s/<(\/{0,1})([pbi]|br)>/$1-$2-$tag_marker/g;
 140         $formatted_interests =~ s/\<[^>]+\>//g;
 141         $formatted_interests =~ s/(\/{0,1})-([pbi]|br)-$tag_marker/<$1$2>/g;
 142
 143         # This is stored separately in the database, without tags, for full-text searching.
 144         $research_interests =~ s/\<[^>]+\>//g;
 145
 146         if ($format eq "auto")
 147         {
 148                 $formatted_interests =~ s/\r{0,1}\n\r{0,1}\n/<\/p><p>/g;
 149                 $formatted_interests = "<p>$formatted_interests</p>";
 150         }
 151
 152         $args{keywords} = HTML::Entities::encode_entities($keywords);
 153         $args{format} = $format;
 154         $args{research_interests} = ($format eq "auto") ? HTML::Entities::encode_entities($research_interests) : $formatted_interests;
 155         $args{unlisted_organisms} = $unlisted_organisms;
 156         $self->set_args(%args); #necessary if you want to affect the arguments that will be stored
 157 }
 158
 159 sub generate_form
 160 {
 161         my $self = shift;
 162
 163         my %args = $self->get_args();
 164         my $person = $self->get_object();
 165
 166         $self->init_form();
 167         my $form = $self->get_form();
 168         if ($form->is_editable()) {
 169                 $form->set_submit_method('post'); #avoid long URLs caused by research interests
 170         }
 171
 172         my ($displayed_first_name, $displayed_last_name) = ($person->get_first_name(), $person->get_last_name());
 173         #i added some html into empty name fields asking people to update their blank entries in the database.
 174         #if we encounter one of these, do not fill in the field for their name with the html! --john
 175         if($displayed_first_name=~/^</){$displayed_first_name='';}
 176         if($displayed_last_name=~/^</){$displayed_last_name='';}
 177
 178         my @organisms = $person->get_organisms();
 179         my @organism_ids = map {$_->get_organism_id()} @organisms;
 180         my @organism_names = map {$_->get_organism_name()} @organisms;
 181         my @organism_selections = map {$_->is_selected() ? '1' : '0'} @organisms;
 182
 183         #element IDs for the source elements for the preview panes
 184         $self->{html_source_element_id} = 'html_source';
 185         $self->{organisms_source_element_id} = 'organisms_source';
 186
 187         my $default_field_length = 22;
 188         if($form->is_editable()) {
 189             $form->add_label(display_name => "",
 190                              field_name => "lbl1",
 191                              contents => "If you would like to enter or update information at this time but do not want it displayed publically, check this option.");
 192
 193             $form->add_checkbox(display_name => "Censor contact information from directory search and public display",
 194                                 field_name => "censor",
 195                                 contents => "1",
 196                                 selected => $person->get_censored(),
 197                                 object => $person,
 198                                 getter => "get_censored",
 199                                 setter => "set_censor");
 200
 201             $form->add_label(display_name => "",
 202                              field_name => "lbl2",
 203                              contents => "The first and last names you enter here will be displayed in the SGN directory (if not censored using the box above)."
 204                              . " Your username for this interface is not displayed.");
 205         }
 206         $form->add_select(display_name => "Salutation",
 207                           field_name => "salutation",
 208                           contents => $person->get_salutation(),
 209                           object => $person,
 210                           getter => "get_salutation",
 211                           setter => "set_salutation",
 212                           select_list_ref => [qw(None Prof. Dr. Mr. Ms. Mrs.)],
 213                           select_id_list_ref => ['', qw(Prof. Dr. Mr. Ms. Mrs.)]);
 214         $form->add_field(display_name => "First name",
 215                          field_name => "first_name",
 216                          contents => $displayed_first_name,
 217                          length => $default_field_length,
 218                          object => $person,
 219                          getter => "get_first_name",
 220                          setter => "set_first_name",
 221                          validate => "string");
 222         $form->add_field(display_name => "Last name",
 223                          field_name => "last_name",
 224                          contents => $displayed_last_name,
 225                          length => $default_field_length,
 226                          object => $person,
 227                          getter => "get_last_name",
 228                          setter => "set_last_name",
 229                          validate => "string");
 230         $form->add_field(display_name => "Organization",
 231                          field_name => "organization",
 232                          contents => $person->get_organization(),
 233                          length => 50,
 234                          object => $person,
 235                          getter => "get_organization",
 236                          setter => "set_organization");
 237         $form->add_textarea(display_name => "Address",
 238                             field_name => "address",
 239                             contents => $person->get_address(),
 240                             rows => 4,
 241                             columns => 50,
 242                             object => $person,
 243                             getter => "get_address",
 244                             setter => "set_address");
 245         $form->add_field(display_name => "Country",
 246                          field_name => "country",
 247                          contents => $person->get_country(),
 248                          length => $default_field_length,
 249                          object => $person,
 250                          getter => "get_country",
 251                          setter => "set_country");
 252         if($form->is_editable()) {
 253             $form->add_label(display_name => "",
 254                              field_name => "lbl3",
 255                              contents => "If you wish to be contacted via telephone or fax by interested parties who found your directory entry on SGN, please enter"
 256                              . " telephone numbers here. These numbers will be displayed publically to all SGN users who view your entry.");
 257         }
 258         $form->add_field(display_name => "Phone",
 259                          field_name => "phone",
 260                          contents => $person->get_phone_number(),
 261                          length => $default_field_length,
 262                          object => $person,
 263                          getter => "get_phone_number",
 264                          setter => "set_phone_number");
 265         $form->add_field(display_name => "Fax",
 266                                                         field_name => "fax",
 267                                                         contents => $person->get_fax(),
 268                                                         length => $default_field_length,
 269                                                         object => $person,
 270                                                         getter => "get_fax",
 271                                                         setter => "set_fax");
 272         if($form->is_editable())
 273         {
 274                 $form->add_label(display_name => "",
 275                                                                 field_name => "lbl4",
 276                                                                 contents => "If you would like to be contacted via email by interested parties who found your directory entry on SGN, please enter"
 277                                                                 . " an address here. This address will be displayed publically to all SGN users who view your entry.");
 278         }
 279         $form->add_field(display_name => "Contact E-mail",
 280                                                         field_name => "contact_email",
 281                                                         contents => $person->get_contact_email(),
 282                                                         length => $default_field_length,
 283                                                         object => $person,
 284                                                         getter => "get_contact_email",
 285                                                         setter => "set_contact_email");
 286         $form->add_field(display_name => "Website",
 287                                                         field_name => "webpage",
 288                                                         contents => $person->get_webpage(),
 289                                                         length => $default_field_length,
 290                                                         object => $person,
 291                                                         getter => "get_webpage",
 292                                                         setter => "set_webpage");
 293         if($form->is_editable())
 294         {
 295                 $form->add_label(display_name => "",
 296                                                                 field_name => "lbl5",
 297                                                                 contents => "Enter research keywords (for searching) and a fuller explanation of your research interests (for searching and displaying) below.");
 298         }
 299         $form->add_field(display_name => "Keywords",
 300                                                         field_name => "keywords",
 301                                                         contents => $person->get_research_keywords(),
 302                                                         length => 60,
 303                                                         object => $person,
 304                                                         getter => 'get_research_keywords',
 305                                                         setter => 'set_research_keywords');
 306         if($form->is_editable())
 307         {
 308                 $form->add_label(display_name => "",
 309                                                                 field_name => "lbl6",
 310                                                                 contents => "Please separate terms with a <b>semicolon</b>. Do not use quotation marks or other punctuation. (Example: fruit development;"
 311                                                                                                 . " host pathogen interaction; drought tolerance)");
 312         }
 313         $form->add_multiselect(display_name => "Research Organisms",
 314                                                                         field_name => "organisms",
 315                                                                         choices => \@organism_ids,
 316                                                                         labels => \@organism_names,
 317                                                                         contents => \@organism_selections,
 318                                                                         object => $person,
 319                                                                         getter => 'get_organism_id_string');
 320         if($form->is_editable())
 321         {
 322                 $form->add_label(display_name => "",
 323                                                                 field_name => "lbl7",
 324                                                                 contents => "You may select multiple organisms by clicking on more than one while holding the control key down. If an organism is not listed"
 325                                                                                                 . " in the selection box, please specify your additional organisms by their official Latin names in the text entry box below, in"
 326                                                                                                 . " a <b>semicolon</b>-separated list.");
 327                 #the contents will be edited by the pre-storing validation function; notice this field never needs to be gotten, only sotten
 328                 $form->add_field(display_name => "Unlisted Organisms",
 329                                                                 field_name => "unlisted_organisms",
 330                                                                 id => $self->{organisms_source_element_id},
 331                                                                 contents => "",
 332                                                                 length => 60,
 333                                                                 object => $person,
 334                                                                 setter => 'add_organisms');
 335         }
 336
 337         if($form->is_editable()) {
 338             $form->add_radio_list(display_name => "",
 339                                   field_name => "format",
 340                                   id_prefix => "format_",
 341                                   choices => ["auto", "html"],
 342                                   labels => ["Auto-format (entry is plain text)", "Use HTML markup tags"],
 343                                   contents => $person->get_user_format(),
 344                                   object => $person,
 345                                   getter => 'get_user_format',
 346                                   setter => 'set_user_format');
 347
 348             $form->add_label(display_name => "",
 349                              field_name => "lbl8",
 350                              contents => "For auto-formatted plain text entries, separate paragraphs by a single empty line. For HTML entries, please use only paragraph"
 351                              . " tags (&lt;p&gt;), bold and italic tags (&lt;b&gt;, &lt;i&gt;), and break tags (&lt;br&gt;). All other tags will be removed.");
 352         }
 353         $form->add_textarea(display_name => "Interests",
 354                             field_name => "research_interests",
 355                             id => $self->{html_source_element_id},
 356                             contents => $person->get_research_interests(),
 357                             rows => 20,
 358                             columns => 80,
 359                             object => $person,
 360                             getter => 'get_research_interests',
 361                             setter => 'set_research_interests');
 362         if($form->get_action() =~ /edit|store/)
 363         {
 364                 $form->add_label(display_name => "",
 365                                                                 field_name => "lbl9",
 366                                                                 contents => "The preview feature below (requires JavaScript) shows your current interests statement if you've selected HTML format. Also,"
 367                                                                                                 . " if you need to define new organisms, the preview will show how the website is parsing the text you've entered above.");
 368         }
 369
 370         #for allowing the form to make changes
 371         if($form->is_editable())
 372         {
 373                 $form->add_hidden(display_name => "ID", field_name => "sp_person_id", contents => $person->get_sp_person_id());
 374                 $form->add_hidden(display_name => "Action", field_name => "action", contents => "store");
 375         }
 376
 377         if($form->is_editable())
 378         {
 379                 $form->set_reset_button_text("Clear");
 380                 $form->set_submit_button_text("Submit Changes");
 381         }
 382         if($self->get_action() =~ /view|edit/)
 383         {
 384                 $form->from_database();
 385         }
 386
 387         elsif($self->get_action() =~ /store/)
 388         {
 389                 $form->from_request($self->get_args());
 390         }
 391 }
 392
 393 #no arguments
 394 #return an HTML string for a toolbar with other possible actions for the form
 395 sub get_actions_toolbar
 396 {
 397         my $self = shift;
 398         my $user_id= $self->get_user()->get_sp_person_id();
 399         my @owners= $self->get_owners();
 400
 401         my $script_name = $self->get_script_name();
 402         my $user_is_owner = (grep {/^$user_id$/} @owners);
 403         my %args = $self->get_args();
 404         my $sp_person_id = $args{sp_person_id};
 405
 406         my ($login_user_id, $user_type) = CXGN::Login->new($self->get_dbh())->has_session();
 407         my $home;
 408         if($user_is_owner || $user_type eq 'curator')
 409         {
 410                 $home = qq(<a href="top-level.pl?sp_person_id=$sp_person_id">[Directory Update Home]</a>&nbsp;&nbsp;);
 411         }
 412         else
 413         {
 414                 $home = qq(<span class="ghosted">[Directory Update Home]</span>);
 415         }
 416
 417         if($self->get_action() eq "edit")
 418         {
 419                 if($user_is_owner || $user_type eq 'curator')
 420                 {
 421                         return $home . qq(<a href="$script_name?action=view&sp_person_id=$sp_person_id">[Cancel Edit]</a>);
 422                 }
 423                 else
 424                 {
 425                         return $home . qq(<span class="ghosted">[Cancel Edit]</span>);
 426                 }
 427         }
 428         elsif($self->get_action() eq "view")
 429         {
 430                 if($user_is_owner || $user_type eq 'curator')
 431                 {
 432                         return $home . qq(<a href="$script_name?action=edit&sp_person_id=$sp_person_id">[Edit]</a>);
 433                 }
 434                 else
 435                 {
 436                         return $home . qq(<span class="ghosted">[Edit]</span>);
 437                 }
 438         }
 439         elsif($self->get_action() eq "store") {}
 440 }
 441
 442 sub display_page
 443 {
 444         my $self = shift;
 445         my $person = $self->get_object();
 446         my $page = $self->get_page();
 447         #SimpleFormPage takes care of some unknown action strings, but we don't handle the full set of actions it supports
 448         if($self->get_action() !~ /^view|edit|store$/)
 449         {
 450                 $page->message_page("Illegal parameter: action '" . $self->get_action() . "' is not supported by " . $self->get_script_name());
 451                 exit();
 452         }
 453
 454         $page->add_style(text => ".subtitle {font-weight: bold; text-align: center}");
 455         $page->add_style(text => ".invisible {display: none}");
 456         $page->jsan_use("CXGN.DynamicPreviewPane", "MochiKit.DOM", "MochiKit.Signal"); #include javascript modules
 457         $page->header("Sol People: contact and research info");
 458         print page_title_html("Personal info for " . $person->get_first_name() . " " . $person->get_last_name());
 459         print $self->get_actions_toolbar() . "<hr />\n";
 460         print $self->get_form()->as_table_string();
 461
 462
 463         if($self->get_action() =~ /^edit$/) {
 464                 #show the preview panes
 465                 my $html_preview_pane_parent_id = 'html_preview_pane_parent';
 466                 my $organisms_preview_pane_parent_id = 'organisms_preview_pane_parent';
 467                 print <<EOHTML;
 468 <hr width="90%" />
 469 <div class="subtitle">Interests and Organisms Preview</div>
 470 <div id="all_html_preview_stuff">
 471 Your research interests will be displayed on SGN\'s website as shown in the box below (the box will not be displayed).
 472 <div id="$html_preview_pane_parent_id"></div>
 473 </div>
 474 <br />You have entered the following currently unlisted organisms. Please check that these names are spelled correctly.
 475 Once committed, these names cannot be changed by this interface.
 476 If you accidentally save an incorrect organism name, please contact us via <a href="mailto:sgn-feedback\@sgn.cornell.edu">sgn-feedback\@sgn.cornell.edu</a>.
 477 <div id="$organisms_preview_pane_parent_id"></div>
 478 <script type="text/javascript">
 479 DynamicPreviewPane.createPreviewPane('html', '$self->{html_source_element_id}', '$html_preview_pane_parent_id');
 480 DynamicPreviewPane.createPreviewPane('list(;)', '$self->{organisms_source_element_id}', '$organisms_preview_pane_parent_id');
 481
 482 //show or hide the interests preview pane based on user format selection
 483 function makeVisible() {MochiKit.DOM.removeElementClass(this, "invisible");}
 484 function makeInvisible() {MochiKit.DOM.addElementClass(this, "invisible");}
 485 var previewPaneSection = MochiKit.DOM.getElement("all_html_preview_stuff");
 486 MochiKit.Signal.connect("format_auto", "onclick", previewPaneSection, makeInvisible);
 487 MochiKit.Signal.connect("format_html", "onclick", previewPaneSection, makeVisible);
 488 //initialize
 489 if(MochiKit.DOM.getElement("format_auto").checked) MochiKit.DOM.addElementClass("all_html_preview_stuff", "invisible");
 490 </script>
 491 EOHTML
 492         }
 493
 494         my ($locus_annotations, $more_annotations) ;
 495         my @annotated_loci = ();
 496
 497         if ($self->get_action() !~ /^edit$/) {
 498             my $person_id=  $person->get_sp_person_id();
 499             @annotated_loci = CXGN::Phenome::Locus::get_locus_ids_by_editor($self->get_dbh(), $person_id);
 500             my $top= 50;
 501             my $more = 0;
 502             my $max = @annotated_loci;
 503             if (@annotated_loci>24) {
 504                 $more = @annotated_loci-24;
 505                 $max = 24;
 506             }
 507
 508
 509             for (my $i=0; $i<$top; $i++) {
 510                 my $locus = CXGN::Phenome::Locus->new($self->get_dbh(), $annotated_loci[$i]);
 511                 my $symbol = $locus->get_locus_symbol();
 512                 my $locus_id = $locus->get_locus_id();
 513
 514
 515                 if ($locus_id && $symbol) { #deanx jan23 2008
 516                   if ($i<$max)  {
 517                      $locus_annotations .= qq | <a href="/phenome/locus_display.pl?locus_id=$locus_id&amp;action=view">$symbol</a> | }
 518                   else {
 519                     $more_annotations .= qq { <a href="/phenome/locus_display.pl?locus_id=$locus_id&amp;action=view">$symbol</a> };
 520                   }
 521                 }
 522             }
 523
 524             if ($more) {
 525                 $locus_annotations .= qq|<br><b>and <a href="/search/locus_search.pl?w8e4_editor=$person_id">$more more</a></b><br />|;
 526
 527
 528             }
 529         }
 530
 531         if (@annotated_loci) {
 532             print "<hr />\n";
 533             print "Locus editor assignments:&nbsp;\n";
 534             print $locus_annotations;
 535         }
 536
 537         my $pop_list = $self->owner_populations();
 538         if ($pop_list) {
 539             print "<hr />\n $pop_list";
 540         }
 541
 542         $page->footer();
 543 }
 544
 545 sub owner_populations {
 546     my $self = shift;
 547     my $sp_person_id = $self->get_object_id();
 548     my @pops = CXGN::Phenome::Population->my_populations($sp_person_id);
 549     my $pop_list = 'Populations:<br/>';
 550
 551     if (@pops) {
 552         foreach my $pops (@pops) {
 553             my $pop_name = $pops->get_name();
 554             my $pop_id = $pops->get_population_id();
 555             #my $is_public = $pops->get_privacy_status();
 556             #if ($is_public) {$is_public = 'is publicly available';}
 557             #if (!$is_public) {$is_public = 'is not publicly available yet';}
 558             $pop_list .= qq |<a href="/phenome/population.pl?population_id=$pop_id">$pop_name</a><br/>|;
 559         }
 560         return $pop_list;
 561
 562     } else {
 563         return;
 564     }
 565
 566 }