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 /solpeople/profile/<sp_person_id>, 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 use Digest::MD5 qw | md5_hex |;
  24
  25 use base qw | CXGN::Page::Form::SimpleFormPage |;
  26
  27 sub new {
  28         my $class = shift;
  29         my $person_id = shift;
  30         my $self = $class->SUPER::new(); #arguments are parsed from the Page here
  31         my (undef, undef, $this_script_filename) = File::Spec->splitpath($0); #$0 contains current filename with some path or other prepended
  32         $self->set_script_name($this_script_filename);
  33         return $self;
  34 }
  35
  36 sub define_object {
  37         my $self = shift;
  38         # call set_object_id, set_object and set_primary_key here
  39         my %args = $self->get_args();
  40         $self->set_object_id($args{sp_person_id});
  41         $self->set_object(new CXGN::People::Person($self->get_dbh(), $args{sp_person_id}));
  42         $self->set_primary_key("sp_person_id");
  43         $self->set_owners($self->get_object()->get_sp_person_id());
  44 }
  45
  46 #specified in SimpleFormPage
  47 sub check_modify_privileges {
  48     my $self = shift;
  49
  50     # implement quite strict access controls by default
  51     #
  52     my $person_id = $self->get_login()->has_session();
  53     my $user =  CXGN::People::Person->new($self->get_dbh(), $person_id);
  54     my $user_id = $user->get_sp_person_id();
  55     if ($user->get_user_type() eq 'curator') {
  56         return 0;
  57     }
  58
  59     # check the owner only if the action is not new
  60     #
  61     my @owners= $self->get_owners();
  62
  63
  64     if (!(grep {/^$user_id$/} @owners ))
  65     {
  66         $self->get_page()->message_page("You do not have rights to modify this database entry because you do not own it. [$user_id, @owners]");
  67     }
  68     else {
  69         return 0;
  70     }
  71
  72
  73     # override to check privileges for edit, store, delete.
  74     # return 0 for allow, 1 for not allow.
  75     return 0;
  76
  77 }
  78
  79 #specified in SimpleFormPage
  80 sub validate_parameters_before_store
  81 {
  82         my $self = shift;
  83         my %args = $self->get_args();
  84
  85         my ($keywords, $format, $research_interests, $organism_codes_str, $unlisted_organisms_str) =
  86                 @args{qw(keywords format research_interests organisms unlisted_organisms)};
  87         $format = "auto" unless $format eq "html";
  88
  89         #after checking for legal values, do the actual storing of existing organism IDs here
  90         my @organism_codes = map {$_ =~ tr/[0-9]//cds; $_} split(/\0/, $organism_codes_str);
  91         foreach my $c ( @organism_codes )
  92         {
  93                 my $test = new CXGN::People::Organism($self->get_dbh(), $c);
  94                 if(!defined($test))
  95                 {
  96                         $self->get_page()->message_page("Organism code \"$_\" is not defined in the database.\n");
  97                 }
  98         }
  99         my %selected_organisms = map {$_ => 1} @organism_codes; #ids of only those organisms selected with the multiselect appear in the hash
 100         my $person = $self->get_object();
 101         foreach my $o ($person->get_organisms())
 102         {
 103                 $o->set_selected(0);
 104                 if($selected_organisms{$o->get_sp_organism_id()})
 105                 {
 106                         $o->set_selected(1);
 107                 }
 108         }
 109
 110         #deal with unlisted organisms
 111         my @unlisted_organisms;
 112         foreach (split(/;/, $unlisted_organisms_str))
 113         {
 114                 if(m/^\s*((\S.*\S)|\S)\s*$/) #remove leading and trailing spaces
 115                 {
 116                         push @unlisted_organisms, $1;
 117                 }
 118         }
 119         my $unlisted_organisms = join("\0", @unlisted_organisms);
 120
 121         # Quick, dirty hack method of defenestrating disallowed HTML tags in
 122         # research interest statements: replace allowed tags with a marker string,
 123         # then delete all tokens of the form "<[^>]+>", then replace the marker string
 124         # with the original tag.
 125         #
 126         # Using the marker string allows us to "save" the information about the tag
 127         # that is allowed -- changing it to a token that won't match the "<[^>]+>"
 128         # pattern. Using a random marker string prevents a user learning (through a
 129         # website error or something that reveals a static marker string) the marker
 130         # and trying to insert illegal tags by typing the marker into their statement
 131         # manually. This is further guarded against by only recognizing marker strings
 132         # with allowed tags encoded. (Yes, I am paranoid)
 133         #
 134         # The main problem with this is if someone happens to use both a literal "<"
 135         # and a matching ">" in their research statement -- if that happens, the
 136         # text flanked by these will be deleted -- they'll need to use &lt; and &gt;
 137         # instead.
 138         my $tag_marker = $self->get_page()->tempname();
 139         my $formatted_interests = $research_interests;
 140         $formatted_interests =~ s/<(\/{0,1})([pbi]|br)>/$1-$2-$tag_marker/g;
 141         $formatted_interests =~ s/\<[^>]+\>//g;
 142         $formatted_interests =~ s/(\/{0,1})-([pbi]|br)-$tag_marker/<$1$2>/g;
 143
 144         # This is stored separately in the database, without tags, for full-text searching.
 145         $research_interests =~ s/\<[^>]+\>//g;
 146
 147         if ($format eq "auto")
 148         {
 149                 $formatted_interests =~ s/\r{0,1}\n\r{0,1}\n/<\/p><p>/g;
 150                 $formatted_interests = "<p>$formatted_interests</p>";
 151         }
 152
 153         $args{keywords} = HTML::Entities::encode_entities($keywords);
 154         $args{format} = $format;
 155         $args{research_interests} = ($format eq "auto") ? HTML::Entities::encode_entities($research_interests) : $formatted_interests;
 156         $args{unlisted_organisms} = $unlisted_organisms;
 157         $self->set_args(%args); #necessary if you want to affect the arguments that will be stored
 158 }
 159
 160 sub generate_form
 161 {
 162         my $self = shift;
 163
 164         my %args = $self->get_args();
 165         my $person = $self->get_object();
 166
 167         $self->init_form();
 168         my $form = $self->get_form();
 169         if ($form->is_editable()) {
 170                 $form->set_submit_method('post'); #avoid long URLs caused by research interests
 171         }
 172
 173         my ($displayed_first_name, $displayed_last_name) = ($person->get_first_name(), $person->get_last_name());
 174         #i added some html into empty name fields asking people to update their blank entries in the database.
 175         #if we encounter one of these, do not fill in the field for their name with the html! --john
 176         if($displayed_first_name=~/^</){$displayed_first_name='';}
 177         if($displayed_last_name=~/^</){$displayed_last_name='';}
 178
 179         my @organisms = $person->get_organisms();
 180         my @organism_ids = map {$_->get_organism_id()} @organisms;
 181         my @organism_names = map {$_->get_organism_name()} @organisms;
 182         my @organism_selections = map {$_->is_selected() ? '1' : '0'} @organisms;
 183
 184         #element IDs for the source elements for the preview panes
 185         $self->{html_source_element_id} = 'html_source';
 186         $self->{organisms_source_element_id} = 'organisms_source';
 187
 188         my $default_field_length = 22;
 189         if($form->is_editable()) {
 190             $form->add_label(display_name => "",
 191                              field_name => "lbl1",
 192                              contents => "If you would like to enter or update information at this time but do not want it displayed publically, check this option.");
 193
 194             $form->add_checkbox(display_name => "Censor contact information from directory search and public display",
 195                                 field_name => "censor",
 196                                 contents => "1",
 197                                 selected => $person->get_censored(),
 198                                 object => $person,
 199                                 getter => "get_censored",
 200                                 setter => "set_censor");
 201
 202             $form->add_label(display_name => "",
 203                              field_name => "lbl2",
 204                              contents => "The first and last names you enter here will be displayed in the SGN directory (if not censored using the box above)."
 205                              . " Your username for this interface is not displayed.");
 206         }
 207         $form->add_select(display_name => "Salutation",
 208                           field_name => "salutation",
 209                           contents => $person->get_salutation(),
 210                           object => $person,
 211                           getter => "get_salutation",
 212                           setter => "set_salutation",
 213                           select_list_ref => [qw(None Prof. Dr. Mr. Ms. Mrs.)],
 214                           select_id_list_ref => ['', qw(Prof. Dr. Mr. Ms. Mrs.)]);
 215         $form->add_field(display_name => "First name",
 216                          field_name => "first_name",
 217                          contents => $displayed_first_name,
 218                          length => $default_field_length,
 219                          object => $person,
 220                          getter => "get_first_name",
 221                          setter => "set_first_name",
 222                          validate => "string");
 223         $form->add_field(display_name => "Last name",
 224                          field_name => "last_name",
 225                          contents => $displayed_last_name,
 226                          length => $default_field_length,
 227                          object => $person,
 228                          getter => "get_last_name",
 229                          setter => "set_last_name",
 230                          validate => "string");
 231         $form->add_field(display_name => "Organization",
 232                          field_name => "organization",
 233                          contents => $person->get_organization(),
 234                          length => 50,
 235                          object => $person,
 236                          getter => "get_organization",
 237                          setter => "set_organization");
 238         $form->add_textarea(display_name => "Address",
 239                             field_name => "address",
 240                             contents => $person->get_address(),
 241                             rows => 4,
 242                             columns => 50,
 243                             object => $person,
 244                             getter => "get_address",
 245                             setter => "set_address");
 246         $form->add_field(display_name => "Country",
 247                          field_name => "country",
 248                          contents => $person->get_country(),
 249                          length => $default_field_length,
 250                          object => $person,
 251                          getter => "get_country",
 252                          setter => "set_country");
 253         if($form->is_editable()) {
 254             $form->add_label(display_name => "",
 255                              field_name => "lbl3",
 256                              contents => "If you wish to be contacted via telephone or fax by interested parties who found your directory entry on SGN, please enter"
 257                              . " telephone numbers here. These numbers will be displayed publically to all SGN users who view your entry.");
 258         }
 259         $form->add_field(display_name => "Phone",
 260                          field_name => "phone",
 261                          contents => $person->get_phone_number(),
 262                          length => $default_field_length,
 263                          object => $person,
 264                          getter => "get_phone_number",
 265                          setter => "set_phone_number");
 266         $form->add_field(display_name => "Fax",
 267                                                         field_name => "fax",
 268                                                         contents => $person->get_fax(),
 269                                                         length => $default_field_length,
 270                                                         object => $person,
 271                                                         getter => "get_fax",
 272                                                         setter => "set_fax");
 273         if($form->is_editable())
 274         {
 275                 $form->add_label(display_name => "",
 276                                                                 field_name => "lbl4",
 277                                                                 contents => "If you would like to be contacted via email by interested parties who found your directory entry on SGN, please enter"
 278                                                                 . " an address here. This address will be displayed publically to all SGN users who view your entry.");
 279         }
 280         $form->add_field(display_name => "Contact E-mail",
 281                                                         field_name => "contact_email",
 282                                                         contents => $person->get_contact_email(),
 283                                                         length => $default_field_length,
 284                                                         object => $person,
 285                                                         getter => "get_contact_email",
 286                                                         setter => "set_contact_email");
 287         $form->add_field(display_name => "Website",
 288                                                         field_name => "webpage",
 289                                                         contents => $person->get_webpage(),
 290                                                         length => $default_field_length,
 291                                                         object => $person,
 292                                                         getter => "get_webpage",
 293                                                         setter => "set_webpage");
 294         if($form->is_editable())
 295         {
 296                 $form->add_label(display_name => "",
 297                                                                 field_name => "lbl5",
 298                                                                 contents => "Enter research keywords (for searching) and a fuller explanation of your research interests (for searching and displaying) below.");
 299         }
 300         $form->add_field(display_name => "Keywords",
 301                                                         field_name => "keywords",
 302                                                         contents => $person->get_research_keywords(),
 303                                                         length => 60,
 304                                                         object => $person,
 305                                                         getter => 'get_research_keywords',
 306                                                         setter => 'set_research_keywords');
 307         if($form->is_editable())
 308         {
 309                 $form->add_label(display_name => "",
 310                                                                 field_name => "lbl6",
 311                                                                 contents => "Please separate terms with a <b>semicolon</b>. Do not use quotation marks or other punctuation. (Example: fruit development;"
 312                                                                                                 . " host pathogen interaction; drought tolerance)");
 313         }
 314         $form->add_multiselect(display_name => "Research Organisms",
 315                                                                         field_name => "organisms",
 316                                                                         choices => \@organism_ids,
 317                                                                         labels => \@organism_names,
 318                                                                         contents => \@organism_selections,
 319                                                                         object => $person,
 320                                                                         getter => 'get_organism_id_string');
 321         if($form->is_editable())
 322         {
 323                 $form->add_label(display_name => "",
 324                                                                 field_name => "lbl7",
 325                                                                 contents => "You may select multiple organisms by clicking on more than one while holding the control key down. If an organism is not listed"
 326                                                                                                 . " in the selection box, please specify your additional organisms by their official Latin names in the text entry box below, in"
 327                                                                                                 . " a <b>semicolon</b>-separated list.");
 328                 #the contents will be edited by the pre-storing validation function; notice this field never needs to be gotten, only sotten
 329                 $form->add_field(display_name => "Unlisted Organisms",
 330                                                                 field_name => "unlisted_organisms",
 331                                                                 id => $self->{organisms_source_element_id},
 332                                                                 contents => "",
 333                                                                 length => 60,
 334                                                                 object => $person,
 335                                                                 setter => 'add_organisms');
 336         }
 337
 338         if($form->is_editable()) {
 339             $form->add_radio_list(display_name => "",
 340                                   field_name => "format",
 341                                   id_prefix => "format_",
 342                                   choices => ["auto", "html"],
 343                                   labels => ["Auto-format (entry is plain text)", "Use HTML markup tags"],
 344                                   contents => $person->get_user_format(),
 345                                   object => $person,
 346                                   getter => 'get_user_format',
 347                                   setter => 'set_user_format');
 348
 349             $form->add_label(display_name => "",
 350                              field_name => "lbl8",
 351                              contents => "For auto-formatted plain text entries, separate paragraphs by a single empty line. For HTML entries, please use only paragraph"
 352                              . " 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.");
 353         }
 354         $form->add_textarea(display_name => "Interests",
 355                             field_name => "research_interests",
 356                             id => $self->{html_source_element_id},
 357                             contents => $person->get_research_interests(),
 358                             rows => 20,
 359                             columns => 80,
 360                             object => $person,
 361                             getter => 'get_research_interests',
 362                             setter => 'set_research_interests');
 363         if($form->get_action() =~ /edit|store/)
 364         {
 365                 $form->add_label(display_name => "",
 366                                                                 field_name => "lbl9",
 367                                                                 contents => "The preview feature below (requires JavaScript) shows your current interests statement if you've selected HTML format. Also,"
 368                                                                                                 . " if you need to define new organisms, the preview will show how the website is parsing the text you've entered above.");
 369         }
 370
 371         #for allowing the form to make changes
 372         if($form->is_editable())
 373         {
 374                 $form->add_hidden(display_name => "ID", field_name => "sp_person_id", contents => $person->get_sp_person_id());
 375                 $form->add_hidden(display_name => "Action", field_name => "action", contents => "store");
 376         }
 377
 378         if($form->is_editable())
 379         {
 380                 $form->set_reset_button_text("Clear");
 381                 $form->set_submit_button_text("Submit Changes");
 382         }
 383         if($self->get_action() =~ /view|edit/)
 384         {
 385                 $form->from_database();
 386         }
 387
 388         elsif($self->get_action() =~ /store/)
 389         {
 390                 $form->from_request($self->get_args());
 391         }
 392 }
 393
 394 #no arguments
 395 #return an HTML string for a toolbar with other possible actions for the form
 396 sub get_actions_toolbar
 397 {
 398         my $self = shift;
 399         my $user_id= $self->get_user()->get_sp_person_id();
 400         my @owners= $self->get_owners();
 401
 402         my $script_name = $self->get_script_name();
 403         my $user_is_owner = (grep {/^$user_id$/} @owners);
 404         my %args = $self->get_args();
 405         my $sp_person_id = $args{sp_person_id};
 406
 407         my ($login_user_id, $user_type) = CXGN::Login->new($self->get_dbh())->has_session();
 408         my $home;
 409         if($user_is_owner || $user_type eq 'curator')
 410         {
 411                 $home = qq(<a href="/solpeople/profile/$sp_person_id">[Profile Home]</a>&nbsp;&nbsp;);
 412         }
 413         else
 414         {
 415                 $home = qq(<span class="ghosted">[Directory Update Home]</span>);
 416         }
 417
 418         if($self->get_action() eq "edit")
 419         {
 420                 if($user_is_owner || $user_type eq 'curator')
 421                 {
 422                         return $home . qq(<a href="$script_name?action=view&sp_person_id=$sp_person_id">[Cancel Edit]</a>);
 423                 }
 424                 else
 425                 {
 426                         return $home . qq(<span class="ghosted">[Cancel Edit]</span>);
 427                 }
 428         }
 429         elsif($self->get_action() eq "view")
 430         {
 431                 if($user_is_owner || $user_type eq 'curator')
 432                 {
 433                         return $home . qq(<a href="$script_name?action=edit&sp_person_id=$sp_person_id">[Edit]</a>);
 434                 }
 435                 else
 436                 {
 437                         return $home . qq(<span class="ghosted">[Edit]</span>);
 438                 }
 439         }
 440         elsif($self->get_action() eq "store") {}
 441 }
 442
 443 sub display_page
 444 {
 445         my $self = shift;
 446         my $person = $self->get_object();
 447         my $page = $self->get_page();
 448         #SimpleFormPage takes care of some unknown action strings, but we don't handle the full set of actions it supports
 449         if($self->get_action() !~ /^view|edit|store$/)
 450         {
 451                 $page->message_page("Illegal parameter: action '" . $self->get_action() . "' is not supported by " . $self->get_script_name());
 452                 exit();
 453         }
 454
 455         $page->add_style(text => ".subtitle {font-weight: bold; text-align: center}");
 456         $page->add_style(text => ".invisible {display: none}");
 457         $page->jsan_use("CXGN.DynamicPreviewPane", "MochiKit.DOM", "MochiKit.Signal"); #include javascript modules
 458         $page->header("Sol People: contact and research info");
 459
 460         print qq{<table><tr valign="middle"><td width="670" align="center" valign="middle" ><br />};
 461
 462         print page_title_html("Personal info for " . $person->get_first_name() . " " . $person->get_last_name());
 463
 464         print "</td><td>";
 465
 466
 467         print qq { <a href="https://gravatar.com/" class="footer" ><img src="http://gravatar.com/avatar/}. md5_hex(lc($person->get_contact_email())). qq {?d=mm" /></a>};
 468         print "</td></tr></table>";
 469
 470
 471
 472         print $self->get_actions_toolbar() . "<hr />\n";
 473         print $self->get_form()->as_table_string();
 474
 475
 476         if($self->get_action() =~ /^edit$/) {
 477                 #show the preview panes
 478                 my $html_preview_pane_parent_id = 'html_preview_pane_parent';
 479                 my $organisms_preview_pane_parent_id = 'organisms_preview_pane_parent';
 480                 print <<EOHTML;
 481 <hr width="90%" />
 482 <div class="subtitle">Interests and Organisms Preview</div>
 483 <div id="all_html_preview_stuff">
 484 Your research interests will be displayed on SGN\'s website as shown in the box below (the box will not be displayed).
 485 <div id="$html_preview_pane_parent_id"></div>
 486 </div>
 487 <br />You have entered the following currently unlisted organisms. Please check that these names are spelled correctly.
 488 Once committed, these names cannot be changed by this interface.
 489 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>.
 490 <div id="$organisms_preview_pane_parent_id"></div>
 491 <script type="text/javascript">
 492 DynamicPreviewPane.createPreviewPane('html', '$self->{html_source_element_id}', '$html_preview_pane_parent_id');
 493 DynamicPreviewPane.createPreviewPane('list(;)', '$self->{organisms_source_element_id}', '$organisms_preview_pane_parent_id');
 494
 495 //show or hide the interests preview pane based on user format selection
 496 function makeVisible() {MochiKit.DOM.removeElementClass(this, "invisible");}
 497 function makeInvisible() {MochiKit.DOM.addElementClass(this, "invisible");}
 498 var previewPaneSection = MochiKit.DOM.getElement("all_html_preview_stuff");
 499 MochiKit.Signal.connect("format_auto", "onclick", previewPaneSection, makeInvisible);
 500 MochiKit.Signal.connect("format_html", "onclick", previewPaneSection, makeVisible);
 501 //initialize
 502 if(MochiKit.DOM.getElement("format_auto").checked) MochiKit.DOM.addElementClass("all_html_preview_stuff", "invisible");
 503 </script>
 504 EOHTML
 505         }
 506
 507         my ($locus_annotations, $more_annotations) ;
 508         my @annotated_loci = ();
 509
 510         if ($self->get_action() !~ /^edit$/) {
 511             my $person_id=  $person->get_sp_person_id();
 512             @annotated_loci = CXGN::Phenome::Locus::get_locus_ids_by_editor($self->get_dbh(), $person_id);
 513             my $top= 50;
 514             my $more = 0;
 515             my $max = @annotated_loci;
 516             if (@annotated_loci>24) {
 517                 $more = @annotated_loci-24;
 518                 $max = 24;
 519             }
 520
 521
 522             for (my $i=0; $i<$top; $i++) {
 523                 my $locus = CXGN::Phenome::Locus->new($self->get_dbh(), $annotated_loci[$i]);
 524                 my $symbol = $locus->get_locus_symbol();
 525                 my $locus_id = $locus->get_locus_id();
 526
 527
 528                 if ($locus_id && $symbol) { #deanx jan23 2008
 529                   if ($i<$max)  {
 530                      $locus_annotations .= qq | <a href="/locus/$locus_id/view">$symbol</a> | }
 531                   else {
 532                     $more_annotations .= qq { <a href="/locus/$locus_id/view">$symbol</a> };
 533                   }
 534                 }
 535             }
 536
 537             if ($more) {
 538                 $locus_annotations .= qq|<br><b>and <a href="/search/locus">$more more</a></b><br />|;
 539
 540
 541             }
 542         }
 543
 544         if (@annotated_loci) {
 545             print "<hr />\n";
 546             print "Locus editor assignments:&nbsp;\n";
 547             print $locus_annotations;
 548         }
 549
 550         my $pop_list = $self->owner_populations();
 551         if ($pop_list) {
 552             print "<hr />\n $pop_list";
 553         }
 554
 555         $page->footer();
 556 }
 557
 558 sub owner_populations {
 559     my $self = shift;
 560     my $sp_person_id = $self->get_object_id();
 561     my @pops = CXGN::Phenome::Population->my_populations($sp_person_id);
 562     my $pop_list = 'Populations:<br/>';
 563
 564     if (@pops) {
 565         foreach my $pops (@pops) {
 566             my $pop_name = $pops->get_name();
 567             my $pop_id = $pops->get_population_id();
 568             #my $is_public = $pops->get_privacy_status();
 569             #if ($is_public) {$is_public = 'is publicly available';}
 570             #if (!$is_public) {$is_public = 'is not publicly available yet';}
 571             $pop_list .= qq |<a href="/phenome/population.pl?population_id=$pop_id">$pop_name</a><br/>|;
 572         }
 573         return $pop_list;
 574
 575     } else {
 576         return;
 577     }
 578
 579 }