Notes to create web filter page multiple choice selectors for martview
http://eugenes.org/gmod/biomart/
D. Gilbert, Jan 2006

See biomart0_3.cvs.diff  for source differences below from this CVS release
:pserver:cvsuser@cvs.sanger.ac.uk:/cvsroot/CVSmaster/biomart-web -r release-0_3


:::::::::::: example meta.xml 
# Use internalName="..multi.." to trigger martview multi-selection

<FilterDescription displayName="Feature type" field="type_source" 
 internalName="biotype_multi_list" key="region_id_key" tableConstraint="dpul__features__dm"
 legal_qualifiers="=,in" qualifier="="  type="list">
  <Option displayName="Gene prediction SNAP.fly" internalName="gene_SNAPfly"  value="gene_SNAPfly" />
  <Option displayName="Gene prediction SNAP.generic" internalName="gene_SNAPmin"  value="gene_SNAPmin" />
  <Option displayName="Match Daphnia EST" internalName="match_blastn_WFes"  value="match_blastn_WFes" />
  <Option displayName="Match Daphnia microsat." internalName="match_blastn_WFms"  value="match_blastn_WFms" />
  <Option displayName="Match Daphnia genetic markers" internalName="match_blastn_genetic_markers"  value="match_blastn_genetic_markers" />
  <Option displayName="Match Mosquito gene" internalName="match_tblastn_ensAG"  value="match_tblastn_ensAG" />
  <Option displayName="Match Bee genes" internalName="match_tblastn_ensAM"  value="match_tblastn_ensAM" />
  <Option displayName="Match ZebraFish genes" internalName="match_tblastn_ensDR"  value="match_tblastn_ensDR" />
  <Option displayName="Match Human genes" internalName="match_tblastn_ensHS"  value="match_tblastn_ensHS" />
  <Option displayName="Match Worm genes" internalName="match_tblastn_modCE"  value="match_tblastn_modCE" />
  <Option displayName="Match Fruitfly genes" internalName="match_tblastn_modDM"  value="match_tblastn_modDM" />
  <Option displayName="Match Mouse genes" internalName="match_tblastn_modMM"  value="match_tblastn_modMM" />
  <Option displayName="Match Yeast genes" internalName="match_tblastn_modSC"  value="match_tblastn_modSC" />
  <Option displayName="Match Mustard Weed genes" internalName="match_tblastn_ncbAT"  value="match_tblastn_ncbAT" />
</FilterDescription>

:::::::::: BooleanListFilter

BioMart::Configuration::BooleanListFilter
# This combines parts of BooleanFilter + ValueFilter for query of several boolean fields (OR)

:::::::::: martview
# martview has various hacks to get multi-selection to work
# 1. sub get_main_panel: set $entry->set_cgi_multiple(1) if filter->name =~ /multi/
# 2. sub get_status_panel,initialise_results : 
#  2a. keep all @values from CGI->param(): my @values = $CGI->param( $dataSetName.'_'.$entry->name );
#  2b. for BooleanFilter, and multi-values, use BioMart::Configuration::BooleanListFilter instead
#  2c. for ValueFilter, add @values back into $value list before AttributeTable
# 3. sub validate_params: dont wipe out @values in CGI->param() with edits


sub get_main_panel{

				   # CHECKBOX WITH SELECT AND RADIO BUTTONS
				   if (($$options[0] && $$options[0]->filter && 
				       $$options[0]->filter->isa
				       ("BioMart::Configuration::BooleanFilter"))){
...							
							## dgg here; want multi-select lists;  
							if ($filter->name() =~ /multi/) { # fixme
							 $entry->set_cgi_multiple(1);  
							 $entry->set_cgi_size(5);
							 }
							##  
...
				   # CHECKBOX WITH SELECT (UNLESS NESTED OPTIONS - TREE ONTOLOGY FILTER)
				   #elsif (($$options[0] 
				   elsif ((($$options[0] && !$nested_option_flag) 
				          || $filter->name eq $ref || 
					  $filter->name eq $subRef || 
					  $filter->name eq $secondRef)){				       
...

							## dgg here; want multi-select lists;  
							if ($filter->name() =~ /multi/) { # fixme
							 $entry->set_cgi_multiple(1);  
							 $entry->set_cgi_size(5);
							 }
							##  


sub get_status_panel{
...

				    # Are there CGI values for this entry?
				    my @values = $CGI->param( $dataSetName.'_'.
							      $entry->name );
				    my $value  = $values[0] || next;
				    $value = unescapeHTML( $value );

#dgg debug where is multiselect list ?
  my @debugallvals= @values; # $CGI->param( $dataSetName.'_'. $entry->name );

...

					if ($$options[0] && $$options[0]->filter && 
					    $$options[0]->filter->isa
					    ("BioMart::Configuration::BooleanFilter")){


					    my $option_name = $CGI->param($dataSetName.
					       '_'.$entry->name.'_filter');

### dgg; need patch here? YES for multiselect list
## but boolfilter doesnt support multi-list; how to do?
## need to query->addFilter( join( ' OR ', @ entries ) );
## SEE BELOW; need this code twice ...

my @debug_allopts= $CGI->param( $dataSetName.'_'. $entry->name.'_filter' );
warn("DEBUG.in2 _filter=$option_name; allopts= @debug_allopts \n") if DEBUG;
if(@debug_allopts > 1) {

use BioMart::Configuration::BooleanListFilter; # should be in  BioMart::Configurator;
	  		    my $att_table = BioMart::AttributeTable->new();
            my $dnames="";
            my $entry1;
            
					  foreach my $oname (@debug_allopts){
					    my $option = $ct->getOptionByName($oname);
					    next if (!$option);
					    $dnames .= $option->displayName.", ";
					    my $bentry = $option->filter;
					    if ($value ne 'Only'){ $bentry->setExcluded; }
					    else{ $bentry->setIncluded; }
					    $bentry->displayName($option->displayName);
						  $att_table->addRow( [ $bentry ] );
						  $entry1= $bentry unless($entry1);
					    }

            my $blistentry = BioMart::Configuration::BooleanListFilter->new(); #$entry1
            $blistentry->initFromBoolFilter($entry1); # this fixes it

  				  $blistentry->name($entry->name.'_blist'); ## fixme...
  				  $blistentry->displayName($dnames);
  				  $blistentry->setTable($att_table);
            if ($value ne 'Only'){ $blistentry->setExcluded; }
            else{ $blistentry->setIncluded; }
            $entry= $blistentry;
} else {   ######
  ... orig code ...
} # dgg 					    
					    
					}
					elsif ($$options[0] && $$options[0]->filter
					       && $$options[0]->filter->isa
					       ("BioMart::Configuration::ValueFilter")){
					    my $option_name = $CGI->param($dataSetName.
					       '_'.$entry->name);#.'_filter');
					    my $option = $ct->getOptionByName($option_name);
					    next if (!$option); 
					    $entry = $option->filter;
					    $entry->displayName($option->displayName);
					    my $att_table = BioMart::AttributeTable->new();
					    $value = $CGI->param( $dataSetName.'_'.$name.
								  '_list' );
								  
## dgg patch for multilist all values
             if(@debugallvals>1) { 
                shift @debugallvals;
                foreach( @debugallvals) { $value .= ','.$_ ; }
                warn "DEBUG.in6: value=$value\n" if DEBUG;
                }
            
...
					    
## dgg patch for multilist all values
             my $ismultilist= 0;
             if(@debugallvals>1) { 
                shift @debugallvals;
                foreach( @debugallvals) { $value .= ','.$_ ; }
                warn "DEBUG.in7: value=$value\n" if DEBUG; ## this is it
                $ismultilist= 1;   
                }

					    my $att_table = BioMart::AttributeTable->new();
					    my @values = split('\,',$value);
					    foreach (@values){
						$att_table->addRow([$_]);
					    }
					    
					    if( $ismultilist) { ## dgg
					    $value =~ s/,/, /g; #??
					    $value = substr($value,0,75)."..." if(length($value)>80);
					    }
					    if (!$ismultilist && $option && !$nested_option_flag  ) {
						  $value = $option->displayName;# for status panel below
					    }
					    next if ($entry->isa("BioMart::Configuration::BooleanFilter"));
					    $entry->setTable($att_table);
					}


sub validate_params{# deals with the add_cgi_processing and add_error aspects of MetaData
...

## dgg; is below cgi-set wiping out array vals? YES
my @debugvals= $martview::CGI->param( $dataset.'_'. $name );
warn("DEBUG.in4 ",$dataset.'_'. $name," vals=",@debugvals,"\n") if DEBUG;

			      my $val = $martview::CGI->param($dataset.'_'.$name);
            my $oldval= $val; #dgg
            
...
				  # substitute any stars back to spaces
				  $val =~ s/\*/ /g;
			      }
			      
			      $martview::CGI->param($dataset.'_'.$name, $val)
			        unless($oldval eq $val); #dgg; dont wipe out array params ! 
			        

sub initialise_results{
...

			   # Are there CGI values for this entry?
			   my @values = $CGI->param( $dataSetName.'_'.$entry->name );
			   my $value  = $values[0] || next;

my @debugallvals= @values; # dgg

...
			       my $options = $entry->getAllOptions;
			       if ($$options[0] && $$options[0]->filter && 
				   $$options[0]->filter->isa
				   ("BioMart::Configuration::BooleanFilter")){
				   
				   my $option_name = $CGI->param($dataSetName.'_'.
								 $entry->name.'_filter');

## dgg; fixme again same as above
## dgg; need patch here? YES for multiselect list
## but boolfilter doesnt support multi-list; how to do?
## need to query->addFilter( join( ' OR ', @ entries ) );
my @debug_allopts= $CGI->param( $dataSetName.'_'. $entry->name.'_filter' );
if(@debug_allopts > 1) {
## use BioMart::Configuration::BooleanListFilter; # should be in  BioMart::Configurator;
	  		    my $att_table = BioMart::AttributeTable->new();
            my $dnames="";
            my $entry1;
            
					  foreach my $oname (@debug_allopts){
					    my $option = $ct->getOptionByName($oname);
					    next if (!$option);
					    $dnames .= $option->displayName.", ";
					    my $bentry = $option->filter;
					    if ($value ne 'Only'){ $bentry->setExcluded; }
					    else{ $bentry->setIncluded; }
					    $bentry->displayName($option->displayName);
						  $att_table->addRow( [ $bentry ] );
						  $entry1= $bentry unless($entry1);
					    }

            my $blistentry = BioMart::Configuration::BooleanListFilter->new(); #$entry1
            $blistentry->initFromBoolFilter($entry1); # this fixes it

  				  $blistentry->name($entry->name.'_blist'); ## fixme...
  				  $blistentry->displayName($dnames);
  				  $blistentry->setTable($att_table);
            if ($value ne 'Only'){ $blistentry->setExcluded; }
            else{ $blistentry->setIncluded; }
            $entry= $blistentry;
} else {   ######
  ...
}   ###### end dgg
			       }

...
         my $ismultilist= 0;
         if(@debugallvals>1) { 
            shift @debugallvals;
            foreach( @debugallvals) { $value .= ','.$_ ; }
            warn "DEBUG.in10: value=$value\n" if DEBUG; ## this is it
            $ismultilist= 1;   
            }