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revision 1.40, Tue Apr 29 20:52:05 2008 UTC revision 1.44, Thu Feb 5 07:17:03 2009 UTC
# Line 19  Line 19 
19      use URI::Escape;      use URI::Escape;
20      use PageBuilder;      use PageBuilder;
21      use AliasAnalysis;      use AliasAnalysis;
22        use CGI::Cookie;
23      use FreezeThaw qw(freeze thaw);      use FreezeThaw qw(freeze thaw);
24    
25  =head1 Search Helper Base Class  =head1 Search Helper Base Class
# Line 85  Line 86 
86    
87  List of the parameters that are used to select multiple genomes.  List of the parameters that are used to select multiple genomes.
88    
89    =item notices
90    
91    A list of messages to be put in the notice file.
92    
93  =back  =back
94    
95  =head2 Adding a new Search Tool  =head2 Adding a new Search Tool
# Line 258  Line 263 
263  sub new {  sub new {
264      # Get the parameters.      # Get the parameters.
265      my ($class, $cgi) = @_;      my ($class, $cgi) = @_;
266      # Check for a session ID.      # Check for a session ID. First we look in the CGI parameters.
267      my $session_id = $cgi->param("SessionID");      my $session_id = $cgi->param("SessionID");
268      my $type = "old";      my $type = "old";
269      if (! $session_id) {      if (! $session_id) {
270            # We need a session ID. Try to get it from the cookies.
271            my %cookies = fetch CGI::Cookie;
272            my $session_cookie = $cookies{$class};
273            if (! $session_cookie) {
274          Trace("No session ID found.") if T(3);          Trace("No session ID found.") if T(3);
275          # Here we're starting a new session. We create the session ID and          # Here we're starting a new session. We create the session ID and
276          # store it in the query object.              # store it in a cookie.
277          $session_id = FIGRules::NewSessionID();          $session_id = FIGRules::NewSessionID();
278          Trace("New session ID is $session_id.") if T(3);          Trace("New session ID is $session_id.") if T(3);
279                $session_cookie = new CGI::Cookie(-name => $class,
280                                                  -value => $session_id);
281                $session_cookie->bake();
282            } else {
283                # Here we're recovering an old session. The session ID is
284                # used to find any old search options lying around, but we're
285                # still considered a new session.
286                $session_id = $session_cookie->value();
287                Trace("Session $session_id recovered from cookie.") if T(3);
288            }
289            # Denote this is a new session.
290          $type = "new";          $type = "new";
291            # Put the session IS in the parameters.
292          $cgi->param(-name => 'SessionID', -value => $session_id);          $cgi->param(-name => 'SessionID', -value => $session_id);
293      } else {      } else {
294          Trace("Session ID is $session_id.") if T(3);          Trace("Session ID is $session_id.") if T(3);
# Line 303  Line 324 
324                    scriptQueue => [],                    scriptQueue => [],
325                    genomeList => undef,                    genomeList => undef,
326                    genomeParms => [],                    genomeParms => [],
327                      notices => [],
328                   };                   };
329      # Bless and return it.      # Bless and return it.
330      bless $retVal, $class;      bless $retVal, $class;
# Line 325  Line 347 
347  }  }
348    
349    
   
350  =head3 DB  =head3 DB
351    
352      my $sprout = $shelp->DB();      my $sprout = $shelp->DB();
# Line 460  Line 481 
481      # Start the form. Note we use the override option on the Class value, in      # Start the form. Note we use the override option on the Class value, in
482      # case the Advanced button was used.      # case the Advanced button was used.
483      my $retVal = "<div class=\"search\">\n" .      my $retVal = "<div class=\"search\">\n" .
484                   $cgi->start_form(-method => 'POST',                   CGI::start_form(-method => 'POST',
485                                    -action => $cgi->url(-relative => 1),                                    -action => "$FIG_Config::cgi_url/wiki/rest.cgi/NmpdrPlugin/search",
486                                    -name => $self->FormName()) .                                    -name => $self->FormName()) .
487                   $cgi->hidden(-name => 'Class',                   CGI::hidden(-name => 'Class',
488                                -value => $self->{class},                                -value => $self->{class}) .
489                                -override => 1) .                   CGI::hidden(-name => 'SPROUT',
                  $cgi->hidden(-name => 'SPROUT',  
490                                -value => 1) .                                -value => 1) .
491                   $cgi->h3("$title" . Hint($self->{class}, "Click here for more information."));                   CGI::h3("$title" . Hint($self->{class}, "Click here for more information."));
492      # Put in an anchor tag in case there's a table of contents.      # Put in an anchor tag in case there's a table of contents.
493      my $anchorName = $self->FormName();      my $anchorName = $self->FormName();
494      $retVal .= "<a name=\"$anchorName\"></a>\n";      $retVal .= "<a name=\"$anchorName\"></a>\n";
# Line 666  Line 686 
686      $self->{fileHandle} = Open(undef, "| sort | cut --fields=2- >>$fileName");      $self->{fileHandle} = Open(undef, "| sort | cut --fields=2- >>$fileName");
687  }  }
688    
689    =head3 SetNotice
690    
691        $shelp->SetNotice($message);
692    
693    This method creates a notice that will be displayed on the search results
694    page. After the search is complete, notices are placed in a small temporary
695    file that is checked by the results display engine.
696    
697    =over 4
698    
699    =item message
700    
701    Message to write to the notice file.
702    
703    =back
704    
705    =cut
706    
707    sub SetNotice {
708        # Get the parameters.
709        my ($self, $message) = @_;
710        # Save the message.
711        push @{$self->{notices}}, $message;
712    }
713    
714    
715  =head3 ReadColumnHeaders  =head3 ReadColumnHeaders
716    
717      my @colHdrs = $shelp->ReadColumnHeaders($fh);      my @colHdrs = $shelp->ReadColumnHeaders($fh);
# Line 747  Line 793 
793          my $cgi = $self->Q();          my $cgi = $self->Q();
794          $self->PrintLine("Output formatting complete.<br />");          $self->PrintLine("Output formatting complete.<br />");
795      }      }
796        # Check for notices.
797        my @notices = @{$self->{notices}};
798        if (scalar @notices) {
799            # We have some, so put then in a notice file.
800            my $noticeFile = $self->GetTempFileName('notices');
801            my $nh = Open(undef, ">$noticeFile");
802            print $nh join("\n", @notices, "");
803            close $nh;
804            $self->PrintLine(scalar(@notices) . " notices saved.<br />");
805        }
806  }  }
807    
808  =head3 OrganismData  =head3 OrganismData
# Line 833  Line 889 
889    
890  =head3 ComputeFASTA  =head3 ComputeFASTA
891    
892      my $fasta = $shelp->ComputeFASTA($desiredType, $sequence, $flankingWidth);      my $fasta = $shelp->ComputeFASTA($desiredType, $sequence, $flankingWidth, $comments);
893    
894  Parse a sequence input and convert it into a FASTA string of the desired type with  Parse a sequence input and convert it into a FASTA string of the desired type with
895  the desired flanking width.  the desired flanking width.
# Line 860  Line 916 
916  protein translation of a feature doesn't always match the DNA and is taken directly  protein translation of a feature doesn't always match the DNA and is taken directly
917  from the database.  from the database.
918    
919    =item comments
920    
921    Comment string to be added to the FASTA header.
922    
923  =item RETURN  =item RETURN
924    
925  Returns a string in FASTA format representing the content of the desired sequence with  Returns a string in FASTA format representing the content of the desired sequence with
# Line 872  Line 932 
932    
933  sub ComputeFASTA {  sub ComputeFASTA {
934      # Get the parameters.      # Get the parameters.
935      my ($self, $desiredType, $sequence, $flankingWidth) = @_;      my ($self, $desiredType, $sequence, $flankingWidth, $comment) = @_;
936      # Declare the return variable. If an error occurs, it will remain undefined.      # Declare the return variable. If an error occurs, it will remain undefined.
937      my $retVal;      my $retVal;
938      # This variable will be cleared if an error is detected.      # This variable will be cleared if an error is detected.
# Line 903  Line 963 
963                  # In an emergency, fall back to the original ID.                  # In an emergency, fall back to the original ID.
964                  $fastaLabel = $fid;                  $fastaLabel = $fid;
965              }              }
966                # Add any specified comments.
967                if ($comment) {
968                    $fastaLabel .= " $comment";
969                }
970              # Now proceed according to the sequence type.              # Now proceed according to the sequence type.
971              if ($desiredType =~ /prot/) {              if ($desiredType =~ /prot/) {
972                  # We want protein, so get the translation.                  # We want protein, so get the translation.
# Line 1052  Line 1116 
1116              push @subs, $classLess;              push @subs, $classLess;
1117          }          }
1118      }      }
1119        # Get the seedviewer URL.
1120        my $svURL = $FIG_Config::linkinSV || "$FIG_Config::cgi_url/seedviewer.cgi";
1121        Trace("Seed Viewer URL is $svURL.") if T(3);
1122      # Declare the return variable.      # Declare the return variable.
1123      my @retVal = ();      my @retVal = ();
1124      # Each element in @subs represents a leaf node, so as we loop through it we will be      # Each element in @subs represents a leaf node, so as we loop through it we will be
# Line 1126  Line 1193 
1193              if ($optionThing->{links}) {              if ($optionThing->{links}) {
1194                  # Compute the link value.                  # Compute the link value.
1195                  my $linkable = uri_escape($id);                  my $linkable = uri_escape($id);
1196                  $nodeContent->{link} = "../FIG/seedviewer.cgi?page=Subsystems;subsystem=$linkable";                  $nodeContent->{link} = "$svURL?page=Subsystems;subsystem=$linkable";
1197              }              }
1198              if ($optionThing->{radio}) {              if ($optionThing->{radio}) {
1199                  # Compute the radio value.                  # Compute the radio value.
# Line 1173  Line 1240 
1240    
1241  =item crossMenu (optional)  =item crossMenu (optional)
1242    
1243  If specified, is presumed to be the name of another genome menu whose contents  This is currently not supported.
 are to be mutually exclusive with the contents of this menu. As a result, instead  
 of the standard onChange event, the onChange event will deselect any entries in  
 the other menu.  
1244    
1245  =item RETURN  =item RETURN
1246    
# Line 1196  Line 1260 
1260      if (! defined $rows) {      if (! defined $rows) {
1261          $rows = ($multiple ? 10 : 1);          $rows = ($multiple ? 10 : 1);
1262      }      }
1263      # Create the multiple tag.      # Get a comma-delimited list of the preselected genomes.
1264      my $multipleTag = ($multiple ? " multiple" : "");      my $preselected = "";
1265      # Get the form name.      if ($selected) {
1266      my $formName = $self->FormName();          $preselected = join(", ", @$selected);
1267      # Check to see if we already have a genome list in memory.      }
1268      my $groupHash;      # Ask Sprout for a genome menu.
1269      my @groups;      my $retVal = $sprout->GenomeMenu(name => $menuName,
1270      my $nmpdrGroupCount;                                       multiSelect => $multiple,
1271      my $genomes = $self->{genomeList};                                       selected => $preselected,
1272      if (defined $genomes) {                                       size => $rows);
         # We have a list ready to use.  
         $groupHash = $genomes;  
         @groups = @{$self->{groupList}};  
         $nmpdrGroupCount = $self->{groupCount};  
     } else {  
         # Get a list of all the genomes in group order. In fact, we only need them ordered  
         # by name (genus,species,strain), but putting primary-group in front enables us to  
         # take advantage of an existing index.  
         my @genomeList = $sprout->GetAll(['Genome'],  
                                          "ORDER BY Genome(primary-group), Genome(genus), Genome(species), Genome(unique-characterization)",  
                                          [], ['Genome(primary-group)', 'Genome(id)',  
                                               'Genome(genus)', 'Genome(species)',  
                                               'Genome(unique-characterization)',  
                                               'Genome(taxonomy)']);  
         # Create a hash to organize the genomes by group. Each group will contain a list of  
         # 2-tuples, the first element being the genome ID and the second being the genome  
         # name.  
         my %gHash = ();  
         for my $genome (@genomeList) {  
             # Get the genome data.  
             my ($group, $genomeID, $genus, $species, $strain, $taxonomy) = @{$genome};  
             # Compute and cache its name and display group.  
             my ($name, $displayGroup, $domain) = $self->SaveOrganismData($group, $genomeID, $genus, $species,  
                                                                          $strain, $taxonomy);  
             # Push the genome into the group's list. Note that we use the real group  
             # name here, not the display group name.  
             push @{$gHash{$group}}, [$genomeID, $name, $domain];  
         }  
         # We are almost ready to unroll the menu out of the group hash. The final step is to separate  
         # the supporting genomes by domain. First, we extract the NMPDR groups and sort them. They  
         # are sorted by the first capitalized word. Groups with "other" are sorted after groups  
         # that aren't "other". At some point, we will want to make this less complicated.  
         my %sortGroups = map { $_ =~ /(other)?(.*)([A-Z].+)/; "$3$1$2" => $_ }  
                              grep { $_ ne $FIG_Config::otherGroup } keys %gHash;  
         @groups = map { $sortGroups{$_} } sort keys %sortGroups;  
         # Remember the number of NMPDR groups.  
         $nmpdrGroupCount = scalar @groups;  
         # Loop through the supporting genomes, classifying them by domain. We'll also keep a list  
         # of the domains found.  
         my @otherGenomes = @{$gHash{$FIG_Config::otherGroup}};  
         my @domains = ();  
         for my $genomeData (@otherGenomes) {  
             my ($genomeID, $name, $domain) = @{$genomeData};  
             if (exists $gHash{$domain}) {  
                 push @{$gHash{$domain}}, $genomeData;  
             } else {  
                 $gHash{$domain} = [$genomeData];  
                 push @domains, $domain;  
             }  
         }  
         # Add the domain groups at the end of the main group list. The main group list will now  
         # contain all the categories we need to display the genomes.  
         push @groups, sort @domains;  
         # Delete the supporting group.  
         delete $gHash{$FIG_Config::otherGroup};  
         # Save the genome list for future use.  
         $self->{genomeList} = \%gHash;  
         $self->{groupList} = \@groups;  
         $self->{groupCount} = $nmpdrGroupCount;  
         $groupHash = \%gHash;  
     }  
     # Next, create a hash that specifies the pre-selected entries. Note that we need to deal  
     # with the possibility of undefined values in the incoming list.  
     my %selectedHash = ();  
     if (defined $selected) {  
         %selectedHash = map { $_ => 1 } grep { defined($_) } @{$selected};  
     }  
     # Now it gets complicated. We need a way to mark all the NMPDR genomes. We take advantage  
     # of the fact they come first in the list. We'll accumulate a count of the NMPDR genomes  
     # and use that to make the selections.  
     my $nmpdrCount = 0;  
     # Create the type counters.  
     my $groupCount = 1;  
     # Compute the ID for the status display.  
     my $divID = "${formName}_${menuName}_status";  
     # Compute the JavaScript call for updating the status.  
     my $showSelect = "showSelected($menuName, '$divID', 1000);";  
     # If multiple selection is supported, create an onChange event.  
     my $onChange = "";  
     if ($cross) {  
         # Here we have a paired menu. Selecting something in our menu unselects it in the  
         # other and redisplays the status of both.  
         $onChange = " onChange=\"crossUnSelect($menuName, '$divID', $cross, '${formName}_${cross}_status', 1000)\"";  
     } elsif ($multiple) {  
         # This is an unpaired menu, so all we do is redisplay our status.  
         $onChange = " onChange=\"$showSelect\"";  
     }  
     # Create the SELECT tag and stuff it into the output array.  
     my @lines = ("<SELECT name=\"$menuName\"$onChange$multipleTag size=\"$rows\">");  
     # Loop through the groups.  
     for my $group (@groups) {  
         # Create the option group tag.  
         my $tag = "<OPTGROUP label=\"$group\">";  
         push @lines, "  $tag";  
         # Get the genomes in the group.  
         for my $genome (@{$groupHash->{$group}}) {  
             # Count this organism if it's NMPDR.  
             if ($nmpdrGroupCount > 0) {  
                 $nmpdrCount++;  
             }  
             # Get the organism ID, name, and domain.  
             my ($genomeID, $name, $domain) = @{$genome};  
             # See if it's selected.  
             my $select = ($selectedHash{$genomeID} ? " selected" : "");  
             # Generate the option tag.  
             my $optionTag = "<OPTION class=\"$domain\" value=\"$genomeID\"$select>$name <em>($genomeID)</em></OPTION>";  
             push @lines, "    $optionTag";  
         }  
         # Close the option group.  
         push @lines, "  </OPTGROUP>";  
         # Record this group in the nmpdrGroup count. When that gets to 0, we've finished the NMPDR  
         # groups.  
         $nmpdrGroupCount--;  
     }  
     # Close the SELECT tag.  
     push @lines, "</SELECT>";  
     # Check for multiple selection.  
     if ($multiple) {  
         # Multi-select is on, so we need to add some selection helpers. First is  
         # the search box. This allows the user to type text and have all genomes containing  
         # the text selected automatically.  
         my $searchThingName = "${menuName}_SearchThing";  
         push @lines, "<br />" .  
                      "<INPUT type=\"button\" name=\"MacroSearch\" class=\"button\" value=\"Select genomes containing\" onClick=\"selectViaSearch($menuName, $searchThingName); $showSelect\" />&nbsp;" .  
                      "<INPUT type=\"text\" name=\"$searchThingName\" size=\"30\" />" . Hint("Genome Control",  
                                                                                             "Enter a genome number, then click the button to the left " .  
                                                                                             "in order to select the genome with that number. " .  
                                                                                             "Enter a genus, species, or strain and click the " .  
                                                                                             "button to select all genomes with that genus, species, " .  
                                                                                             "or strain name.");  
         # Next are the buttons to set and clear selections.  
         push @lines, "<br />";  
         push @lines, "<INPUT type=\"button\" name=\"ClearAll\" class=\"bigButton\"  value=\"Clear All\" onClick=\"clearAll($menuName); $showSelect\" />";  
         push @lines, "<INPUT type=\"button\" name=\"SelectAll\" class=\"bigButton\" value=\"Select All\" onClick=\"selectAll($menuName); $showSelect\" />";  
         push @lines, "<INPUT type=\"button\" name=\"NMPDROnly\" class=\"bigButton\"  value=\"Select NMPDR\" onClick=\"selectSome($menuName, $nmpdrCount, true); $showSelect\" />";  
         # push @lines, "<INPUT type=\"button\" name=\"OtherOnly\" class=\"bigButton\" value=\"Select Supporting\" onClick=\"selectSome($menuName, $nmpdrCount, false); $showSelect\" />";  
         # Add the status display, too.  
         push @lines, "<DIV id=\"$divID\" class=\"selectStatus\"></DIV>";  
         # Queue to update the status display when the form loads. We need to modify the show statement  
         # slightly because the queued statements are executed outside the form. This may seem like a lot of  
         # trouble, but we want all of the show statement calls to be generated from a single line of code,  
         # in case we decide to twiddle the parameters.  
         $showSelect =~ s/showSelected\(/showSelected\(thisForm\./;  
         $self->QueueFormScript($showSelect);  
         # Finally, add this parameter to the list of genome parameters. This enables us to  
         # easily find all the parameters used to select one or more genomes.  
         push @{$self->{genomeParms}}, $menuName;  
     }  
     # Assemble all the lines into a string.  
     my $retVal = join("\n", @lines, "");  
1273      # Return the result.      # Return the result.
1274      return $retVal;      return $retVal;
1275  }  }
# Line 1404  Line 1318 
1318      # Get all the property names, putting them after the null choice if one exists.      # Get all the property names, putting them after the null choice if one exists.
1319      push @propNames, $sprout->GetChoices('Property', 'property-name');      push @propNames, $sprout->GetChoices('Property', 'property-name');
1320      # Create a menu from them.      # Create a menu from them.
1321      my $retVal = $cgi->popup_menu(-name=> $menuName, -values => \@propNames,      my $retVal = CGI::popup_menu(-name=> $menuName, -values => \@propNames,
1322                                    -default => $selected);                                    -default => $selected);
1323      # Return the result.      # Return the result.
1324      return $retVal;      return $retVal;
# Line 1466  Line 1380 
1380          }          }
1381      }      }
1382      # Create the table.      # Create the table.
1383      my $retVal = $cgi->table({border => 2, cellspacing => 2,      my $retVal = CGI::table({border => 2, cellspacing => 2,
1384                                width => 700, class => 'search'},                                width => 700, class => 'search'},
1385                               @{$rows});                               @{$rows});
1386      # Return the result.      # Return the result.
# Line 1507  Line 1421 
1421      # Get the current feature ID type.      # Get the current feature ID type.
1422      my $aliasType = $self->GetPreferredAliasType();      my $aliasType = $self->GetPreferredAliasType();
1423      # Create the rows.      # Create the rows.
1424      my $retVal = $cgi->Tr($cgi->td("Identifier Type "),      my $retVal = CGI::Tr(CGI::td("Identifier Type "),
1425                            $cgi->td({ colspan => 2 },                            CGI::td({ colspan => 2 },
1426                                     $cgi->popup_menu(-name => 'AliasType',                                     CGI::popup_menu(-name => 'AliasType',
1427                                                      -values => ['FIG', AliasAnalysis::AliasTypes() ],                                                      -values => ['FIG', AliasAnalysis::AliasTypes() ],
1428                                                      -default => $aliasType) .                                                      -default => $aliasType) .
1429                                     Hint("Identifier Type", "Specify how you want gene names to be displayed."))) .                                     Hint("Identifier Type", "Specify how you want gene names to be displayed."))) .
1430                   "\n" .                   "\n" .
1431                   $cgi->Tr($cgi->td("Results/Page"),                   CGI::Tr(CGI::td("Results/Page"),
1432                            $cgi->td($cgi->popup_menu(-name => 'PageSize',                            CGI::td(CGI::popup_menu(-name => 'PageSize',
1433                                                      -values => [10, 25, 50, 100, 1000],                                                      -values => [10, 25, 50, 100, 1000],
1434                                                      -default => $pageSize)),                                                      -default => $pageSize)),
1435                            $cgi->td($cgi->submit(-class => 'goButton',                            CGI::td(CGI::submit(-class => 'goButton',
1436                                                  -name => 'Search',                                                  -name => 'Search',
1437                                                  -value => $realCaption)));                                                  -value => $realCaption)));
1438      # Return the result.      # Return the result.
# Line 1569  Line 1483 
1483      return @retVal;      return @retVal;
1484  }  }
1485    
 =head3 GetHelpText  
   
     my $htmlText = $shelp->GetHelpText();  
   
 Get the help text for this search. The help text is stored in files on the template  
 server. The help text for a specific search is taken from a file named  
 C<SearchHelp_>I<class>C<.inc> in the template directory C<$FIG_Config::template_url>.  
 There are also three standard help files: C<SearchHelp1_Filtering.inc> describes the  
 feature filtering performed by the B<RHFeatures> object, C<SearchHelp1_GenomeControl.inc>  
 describes how to use a multiple-selection genome control, and C<SearchHelp1_Standard.inc>  
 describes the standard controls for a search, such as page size, URL display, and  
 external alias display.  
   
 =cut  
   
 sub GetHelpText {  
     # Get the parameters.  
     my ($self) = @_;  
     # Create a list to hold the pieces of the help.  
     my @helps = ();  
     # Get the template directory URL.  
     my $urlBase = $FIG_Config::template_url;  
     # Start with the specific help.  
     my $class = $self->{class};  
     push @helps, PageBuilder::GetPage("$urlBase/SearchHelp_$class.inc");  
     # Add the genome control help if needed.  
     if (scalar @{$self->{genomeParms}}) {  
         push @helps, PageBuilder::GetPage("$urlBase/SearchHelp1_GenomeControl.inc");  
     }  
     # Next the filter help.  
     if ($self->{filtered}) {  
         push @helps, PageBuilder::GetPage("$urlBase/SearchHelp1_Filtering.inc");  
     }  
     # Finally, the standard help.  
     push @helps, PageBuilder::GetPage("$urlBase/SearchHelp1_Standard.inc");  
     # Assemble the pieces.  
     my $retVal = join("\n<p>&nbsp;</p>\n", @helps);  
     # Return the result.  
     return $retVal;  
 }  
   
1486  =head3 ComputeSearchURL  =head3 ComputeSearchURL
1487    
1488      my $url = $shelp->ComputeSearchURL(%overrides);      my $url = $shelp->ComputeSearchURL(%overrides);
# Line 1645  Line 1518 
1518      my $cgi = $self->Q();      my $cgi = $self->Q();
1519      my $sprout = $self->DB();      my $sprout = $self->DB();
1520      # Start with the full URL.      # Start with the full URL.
1521      my $retVal = $cgi->url(-full => 1);      my $retVal = "$FIG_Config::cgi_url/SearchSkeleton.cgi";
1522      # Get all the query parameters in a hash.      # Get all the query parameters in a hash.
1523      my %parms = $cgi->Vars();      my %parms = $cgi->Vars();
1524      # Now we need to do some fixing. Each multi-valued parameter is encoded as a string with null      # Now we need to do some fixing. Each multi-valued parameter is encoded as a string with null
# Line 1837  Line 1710 
1710  =item nodeImageClosed  =item nodeImageClosed
1711    
1712  URL of the image to display next to the tree nodes when they are collapsed. Clicking  URL of the image to display next to the tree nodes when they are collapsed. Clicking
1713  on the image will expand a section of the tree. The default is C<../FIG/Html/plus.gif>.  on the image will expand a section of the tree. The default is C<plus.gif>.
1714    
1715  =item nodeImageOpen  =item nodeImageOpen
1716    
1717  URL of the image to display next to the tree nodes when they are expanded. Clicking  URL of the image to display next to the tree nodes when they are expanded. Clicking
1718  on the image will collapse a section of the tree. The default is C<../FIG/Html/minus.gif>.  on the image will collapse a section of the tree. The default is C<minus.gif>.
1719    
1720  =item style  =item style
1721    
# Line 1882  Line 1755 
1755      my ($cgi, $tree, %options) = @_;      my ($cgi, $tree, %options) = @_;
1756      # Get the options.      # Get the options.
1757      my $optionThing = Tracer::GetOptions({ name => 'selection',      my $optionThing = Tracer::GetOptions({ name => 'selection',
1758                                             nodeImageClosed => '../FIG/Html/plus.gif',                                             nodeImageClosed => "$FIG_Config::cgi_url/Html/plus.gif",
1759                                             nodeImageOpen => '../FIG/Html/minus.gif',                                             nodeImageOpen => "$FIG_Config::cgi_url/Html/minus.gif",
1760                                             style => 'tree',                                             style => 'tree',
1761                                             target => '_self',                                             target => '_self',
1762                                             selected => undef},                                             selected => undef},
# Line 1902  Line 1775 
1775              Confess("Hash reference found at start of selection tree. The tree as a whole cannot have attributes, only tree nodes.");              Confess("Hash reference found at start of selection tree. The tree as a whole cannot have attributes, only tree nodes.");
1776          } else {          } else {
1777              # Here we have a real tree. Apply the tree style.              # Here we have a real tree. Apply the tree style.
1778              push @retVal, $cgi->start_div({ class => $optionThing->{style} });              push @retVal, CGI::start_div({ class => $optionThing->{style} });
1779              # Give us a DIV ID.              # Give us a DIV ID.
1780              my $divID = GetDivID($optionThing->{name});              my $divID = GetDivID($optionThing->{name});
1781              # Show the tree.              # Show the tree.
1782              push @retVal, ShowBranch($cgi, "(root)", $divID, $tree, $optionThing, 'block');              push @retVal, ShowBranch($cgi, "(root)", $divID, $tree, $optionThing, 'block');
1783              # Close the DIV block.              # Close the DIV block.
1784              push @retVal, $cgi->end_div();              push @retVal, CGI::end_div();
1785          }          }
1786      }      }
1787      # Return the result.      # Return the result.
# Line 1966  Line 1839 
1839      # Declare the return variable.      # Declare the return variable.
1840      my @retVal = ();      my @retVal = ();
1841      # Start the branch.      # Start the branch.
1842      push @retVal, $cgi->start_ul({ id => $id, style => "display:$displayType" });      push @retVal, CGI::start_ul({ id => $id, style => "display:$displayType" });
1843      # Check for the hash and choose the start location accordingly.      # Check for the hash and choose the start location accordingly.
1844      my $i0 = (ref $branch->[0] eq 'HASH' ? 1 : 0);      my $i0 = (ref $branch->[0] eq 'HASH' ? 1 : 0);
1845      # Get the list length.      # Get the list length.
# Line 2012  Line 1885 
1885                      # If we have children, create the child list with a recursive call.                      # If we have children, create the child list with a recursive call.
1886                      if ($hasChildren) {                      if ($hasChildren) {
1887                          Trace("Processing children of $myLabel.") if T(4);                          Trace("Processing children of $myLabel.") if T(4);
1888                          push @childHtml, ShowBranch($cgi, $myLabel, $myID, $myContent, $options, 'none');                          push @childHtml, ShowBranch($cgi, $myLabel, $myID, $myContent, $options, 'block');
1889                          Trace("Children of $myLabel finished.") if T(4);                          Trace("Children of $myLabel finished.") if T(4);
1890                      }                      }
1891                  }                  }
# Line 2024  Line 1897 
1897              # closed images.              # closed images.
1898              my @images = ($options->{nodeImageOpen}, $options->{nodeImageClosed});              my @images = ($options->{nodeImageOpen}, $options->{nodeImageClosed});
1899              my $image = $images[$hasChildren];              my $image = $images[$hasChildren];
1900              my $prefixHtml = $cgi->img({src => $image, id => "${myID}img"});              my $prefixHtml = CGI::img({src => $image, id => "${myID}img"});
1901              if ($hasChildren) {              if ($hasChildren) {
1902                  # If there are children, we wrap the image in a toggle hyperlink.                  # If there are children, we wrap the image in a toggle hyperlink.
1903                  $prefixHtml = $cgi->a({ onClick => "javascript:treeToggle('$myID','$images[0]', '$images[1]')" },                  $prefixHtml = CGI::a({ onClick => "javascript:treeToggle('$myID','$images[0]', '$images[1]')" },
1904                                        $prefixHtml);                                        $prefixHtml);
1905              }              }
1906              # Now the radio button, if any. Note we use "defined" in case the user wants the              # Now the radio button, if any. Note we use "defined" in case the user wants the
# Line 2044  Line 1917 
1917                  if (defined $options->{selected} && $options->{selected} eq $attrHash->{value}) {                  if (defined $options->{selected} && $options->{selected} eq $attrHash->{value}) {
1918                      $radioParms->{checked} = undef;                      $radioParms->{checked} = undef;
1919                  }                  }
1920                  $prefixHtml .= $cgi->input($radioParms);                  $prefixHtml .= CGI::input($radioParms);
1921              }              }
1922              # Next, we format the label.              # Next, we format the label.
1923              my $labelHtml = $myLabel;              my $labelHtml = $myLabel;
1924              Trace("Formatting tree node for \"$myLabel\".") if T(4);              Trace("Formatting tree node for \"$myLabel\".") if T(4);
1925              # Apply a hyperlink if necessary.              # Apply a hyperlink if necessary.
1926              if (defined $attrHash->{link}) {              if (defined $attrHash->{link}) {
1927                  $labelHtml = $cgi->a({ href => $attrHash->{link}, target => $options->{target} },                  $labelHtml = CGI::a({ href => $attrHash->{link}, target => $options->{target} },
1928                                       $labelHtml);                                       $labelHtml);
1929              }              }
1930              # Finally, roll up the child HTML. If there are no children, we'll get a null string              # Finally, roll up the child HTML. If there are no children, we'll get a null string
1931              # here.              # here.
1932              my $childHtml = join("\n", @childHtml);              my $childHtml = join("\n", @childHtml);
1933              # Now we have all the pieces, so we can put them together.              # Now we have all the pieces, so we can put them together.
1934              push @retVal, $cgi->li("$prefixHtml$labelHtml$childHtml");              push @retVal, CGI::li("$prefixHtml$labelHtml$childHtml");
1935          }          }
1936      }      }
1937      # Close the tree branch.      # Close the tree branch.
1938      push @retVal, $cgi->end_ul();      push @retVal, CGI::end_ul();
1939      # Return the result.      # Return the result.
1940      return @retVal;      return @retVal;
1941  }  }
# Line 2118  Line 1991 
1991  sub PrintLine {  sub PrintLine {
1992      # Get the parameters.      # Get the parameters.
1993      my ($self, $message) = @_;      my ($self, $message) = @_;
1994      # Send them to the output.      # Send the message to the output.
1995      print "$message\n";      print "$message\n";
1996  }  }
1997    
# Line 2170  Line 2043 
2043          # Commit suicide if it didn't work.          # Commit suicide if it didn't work.
2044          if (! defined $retVal) {          if (! defined $retVal) {
2045              die "Could not find a $type handler of type $className.";              die "Could not find a $type handler of type $className.";
2046            } else {
2047                # Perform any necessary subclass initialization.
2048                $retVal->Initialize();
2049          }          }
2050      };      };
2051      # Check for errors.      # Check for errors.
# Line 2367  Line 2243 
2243      return $retVal;      return $retVal;
2244  }  }
2245    
2246    =head3 Hint
2247    
2248        my $htmlText = SearchHelper::Hint($wikiPage, $hintText);
2249    
2250    Return the HTML for a small question mark that displays the specified hint text when it is clicked.
2251    This HTML can be put in forms to provide a useful hinting mechanism.
2252    
2253    =over 4
2254    
2255    =item wikiPage
2256    
2257    Name of the wiki page to be popped up when the hint mark is clicked.
2258    
2259    =item hintText
2260    
2261    Text to display for the hint. It is raw html, but may not contain any double quotes.
2262    
2263    =item RETURN
2264    
2265    Returns the html for the hint facility. The resulting html shows a small button-like thing that
2266    uses the standard FIG popup technology.
2267    
2268    =back
2269    
2270    =cut
2271    
2272    sub Hint {
2273        # Get the parameters.
2274        my ($wikiPage, $hintText) = @_;
2275        # Ask Sprout to draw the hint button for us.
2276        return Sprout::Hint($wikiPage, $hintText);
2277    }
2278    
2279    
2280    
2281  =head2 Virtual Methods  =head2 Virtual Methods
2282    
2283    =head3 HeaderHtml
2284    
2285        my $html = $shelp->HeaderHtml();
2286    
2287    Generate HTML for the HTML header. If extra styles or javascript are required,
2288    they should go in here.
2289    
2290    =cut
2291    
2292    sub HeaderHtml {
2293        return "";
2294    }
2295    
2296  =head3 Form  =head3 Form
2297    
2298      my $html = $shelp->Form();      my $html = $shelp->Form($mode);
2299    
2300    Generate the HTML for a form to request a new search. If the subclass does not
2301    override this method, then the search is formless, and must be started from an
2302    external page.
2303    
2304  Generate the HTML for a form to request a new search.  =cut
2305    
2306    sub Form {
2307        # Get the parameters.
2308        my ($self) = @_;
2309        return "";
2310    }
2311    
2312  =head3 Find  =head3 Find
2313    
# Line 2456  Line 2390 
2390      $rhelp->SetColumns(@cols);      $rhelp->SetColumns(@cols);
2391  }  }
2392    
 =head3 Hint  
2393    
2394      my $htmlText = SearchHelper::Hint($wikiPage, $hintText);  =head3 Initialize
2395    
2396  Return the HTML for a small question mark that displays the specified hint text when it is clicked.      $shelp->Initialize();
 This HTML can be put in forms to provide a useful hinting mechanism.  
2397    
2398  =over 4  Perform any initialization required after construction of the helper.
2399    
2400  =item wikiPage  =cut
2401    
2402  Name of the wiki page to be popped up when the hint mark is clicked.  sub Initialize {
2403        # The default is to do nothing.
2404    }
2405    
2406  =item hintText  =head3 GetResultHelper
2407    
2408  Text to display for the hint. It is raw html, but may not contain any double quotes.      my $rhelp = $shelp->GetResultHelper($className);
2409    
2410    Return a result helper for this search helper. The default action is to create
2411    a result helper from scratch; however, if the subclass has an internal result
2412    helper it can override this method to return it without having to create a new
2413    one.
2414    
2415    =over 4
2416    
2417    =item className
2418    
2419    Result helper class name.
2420    
2421  =item RETURN  =item RETURN
2422    
2423  Returns the html for the hint facility. The resulting html shows a small button-like thing that  Returns a result helper of the specified class connected to this search helper.
 uses the standard FIG popup technology.  
2424    
2425  =back  =back
2426    
2427  =cut  =cut
2428    
2429  sub Hint {  sub GetResultHelper {
2430      # Get the parameters.      # Get the parameters.
2431      my ($wikiPage, $hintText) = @_;      my ($self, $className) = @_;
2432      # Escape the single quotes in the hint text.      # Create the helper.
2433      my $quotedText = $hintText;      my $retVal = GetHelper($self, RH => $className);
2434      $quotedText =~ s/'/\\'/g;      # return it.
     # Convert the wiki page name to a URL.  
     my $wikiURL = join("", map { ucfirst $_ } split /\s+/, $wikiPage);  
     $wikiURL = "wiki/view.cgi/FIG/$wikiURL";  
     # Create the html.  
     my $retVal = "&nbsp;<input type=\"button\" class=\"hintbutton\" onMouseOver=\"javascript:if (!this.tooltip) { " .  
                  "this.tooltip = new Popup_Tooltip(this, 'Search Hint', '$quotedText', '', 1); this.tooltip.addHandler(); } " .  
                  "return false;\" value=\"?\" onClick=\"javascript:window.open('$wikiURL', 'nmpdrHelp');\" />";  
     # Return it.  
2435      return $retVal;      return $retVal;
2436  }  }
2437    
   
2438  1;  1;

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