--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lib/output.pm	Mon Dec 05 08:32:04 2016 -0500
@@ -0,0 +1,536 @@
+package lib::output ;
+
+use strict;
+use warnings ;
+use Exporter ;
+use Carp ;
+use HTML::Template ;
+use JSON ;
+
+use FindBin ;
+use lib $FindBin::Bin ;
+my $binPath = $FindBin::Bin ;
+
+use Data::Dumper ;
+
+use vars qw($VERSION @ISA @EXPORT %EXPORT_TAGS);
+
+our $VERSION = "1.0";
+our @ISA = qw(Exporter);
+our @EXPORT = qw(build_json_res_object excel_output write_html_body add_entries_to_tbody_object write_json_skel write_ajax_data_source excel_like_output);
+our %EXPORT_TAGS = ( ALL => [qw(build_json_res_object excel_output write_html_body add_entries_to_tbody_object write_json_skel write_ajax_data_source excel_like_output)] );
+
+=head1 NAME
+My::Module - An example module
+
+=head1 SYNOPSIS
+
+    use My::Module;
+    my $object = My::Module->new();
+    print $object->as_string;
+
+=head1 DESCRIPTION
+
+This module does not really exist, it
+was made for the sole purpose of
+demonstrating how POD works.
+
+=head1 METHODS
+
+Methods are :
+
+=head2 METHOD new
+
+	## Description : new
+	## Input : $self
+	## Ouput : bless $self ;
+	## Usage : new() ;
+
+=cut
+
+sub new {
+    ## Variables
+    my $self={};
+    bless($self) ;
+    return $self ;
+}
+### END of SUB
+
+
+
+=head2 METHOD build_json_res_object
+
+	## Description : build json from array of hits
+	## Input : $results
+	## Output : \@json_results 
+	## Usage : my ( \@json_results ) = build_json_res_object( $results ) ;
+	## JSON structure: [
+#							{
+#								'id' : 'int',
+#								'nb_hits' : int, 
+#								'searchResults'	:	[
+#														{
+#															'metaboliteID' : GUID
+#															'distance_scores' : {
+#																					'EuclideanDistance' : float
+#																					'DotproductDistance' : int
+#																					'HammingDistance' : int
+#																					'JaccardDistance' : int
+#																					's12GowerLegendreDistance' : int
+#																				}
+#															'ri_infos' : {
+#																			'ri' : float
+#																			'riDiscrepancy' : float
+#																		 }
+#															'analyte' : {
+#																			'id' : GUID
+#																			'name' : string
+#																		 }
+#															'spectrum' : {
+#																			'id' : GUID
+#																			'name' : string
+#																		 }
+#														},
+#														.
+#														.
+#														.
+#													]
+#							}
+#							.
+#							.
+#							.
+#						]
+=cut
+## START of SUB
+sub build_json_res_object {
+	## Retrieve Values
+    my $self = shift ;
+    my ( $results ) = @_ ;
+  	
+	my @json_results ;
+	my @array_results = @$results ;
+	
+	my $nb_hits = 0 ;
+	my $i = 0 ;
+	my $spectrumID = 1 ;
+	
+	
+	
+	## Loop on each spectra
+	foreach my $res (@array_results) {
+		
+		if (@$res[0] eq 'no results'){
+		
+			my %hit_infos = () ;
+			
+			$json_results[$i]{'id'} = $spectrumID++ ;
+			$json_results[$i]{'nb_hits'} = $nb_hits ;
+			$hit_infos{'metaboliteID'} = "" ;
+			$hit_infos{'distance_scores'}{'EuclideanDistance'} = "" ;
+			$hit_infos{'distance_scores'}{'DotproductDistance'} = "" ;
+			$hit_infos{'distance_scores'}{'HammingDistance'} = "" ;
+			$hit_infos{'distance_scores'}{'JaccardDistance'} = "" ;
+			$hit_infos{'distance_scores'}{'s12GowerLegendreDistance'} = "" ;
+			$hit_infos{'ri_infos'}{'ri'} = "" ;
+			$hit_infos{'ri_infos'}{'riDiscrepancy'} = "" ;
+			$hit_infos{'analyte'}{'id'} = "" ;
+			$hit_infos{'analyte'}{'name'} = "" ;
+			$hit_infos{'spectrum'}{'id'} = "" ;
+			$hit_infos{'spectrum'}{'name'} = "no results" ;
+			
+			push ( @{ $json_results[$i]{'searchResults'} } , \%hit_infos );
+		}
+		else {
+			
+			$nb_hits = scalar @$res;
+			
+			$json_results[$i]{'id'} = $spectrumID++ ;
+			$json_results[$i]{'nb_hits'} = $nb_hits ;
+			
+			## Loop on each hit of a spectrum + build json
+			foreach my $href (@$res) {
+				
+				if (!defined $href){
+					
+					last ;
+				}
+				else {
+					my %hash_res = %$href ;
+					my %hit_infos = () ;
+					# Get rid of false results
+					if ($hash_res{'metaboliteID'} eq '00000000-0000-0000-0000-000000000000') {
+						--$json_results[$i]{'nb_hits'} ;
+					}
+					else {
+						$hit_infos{'metaboliteID'} = $hash_res{'metaboliteID'} ;
+						$hit_infos{'distance_scores'}{'EuclideanDistance'} = $hash_res{'EuclideanDistance'} ;
+						$hit_infos{'distance_scores'}{'DotproductDistance'} = $hash_res{'DotproductDistance'} ;
+						$hit_infos{'distance_scores'}{'HammingDistance'} = $hash_res{'HammingDistance'} ;
+						$hit_infos{'distance_scores'}{'JaccardDistance'} = $hash_res{'JaccardDistance'} ;
+						$hit_infos{'distance_scores'}{'s12GowerLegendreDistance'} = $hash_res{'s12GowerLegendreDistance'} ;
+						$hit_infos{'ri_infos'}{'ri'} = $hash_res{'ri'} ;
+						$hit_infos{'ri_infos'}{'riDiscrepancy'} = $hash_res{'riDiscrepancy'} ;
+						$hit_infos{'analyte'}{'id'} = $hash_res{'analyteID'} ;
+						$hit_infos{'analyte'}{'name'} = $hash_res{'analyteName'} ;
+						$hit_infos{'spectrum'}{'id'} = $hash_res{'spectrumID'} ;
+						$hit_infos{'spectrum'}{'name'} = $hash_res{'spectrumName'} ;
+						
+						push ( @{ $json_results[$i]{'searchResults'} } , \%hit_infos );
+					}
+				}
+			}
+		}
+		$i++ ;
+	}
+    return \@json_results ;
+}
+## END of SUB
+
+
+
+=head2 METHOD add_entries_to_tbody_object
+
+	## Description : initialize and build the entries object needed by HTML::Template 
+	## Input : $results
+	## Output : \@tbody_entries
+	## Usage : my ( $tbody_entries ) = add_entries_to_tbody_object( $results ) ;
+=cut
+## START of SUB
+sub add_entries_to_tbody_object {
+	## Retrieve Values
+    my $self = shift ;
+    my ( $results ) = @_ ;
+    
+    my @tbody_entries = () ;
+								
+		foreach my $href_grp (@$results) {
+			
+				foreach my $hit ( @{$href_grp->{'searchResults'}} ){
+					my %grp_res = () ;
+					
+					## Add hyperlinks
+					if ( $hit->{'spectrum'}{'name'} ne 'no results') {
+						%grp_res = (
+							ID => $href_grp->{id} ,
+							ANALYTE_NAME => $hit->{analyte}{name} ,
+							SPECTRUM_NAME => $hit->{spectrum}{name} ,
+							RI => $hit->{ri_infos}{ri} ,
+							RI_DISCREPANCY => $hit->{ri_infos}{riDiscrepancy} ,
+							DOT_PRODUCT_DISTANCE => $hit->{distance_scores}{DotproductDistance} ,
+							EUCLIDEAN_DISTANCE => $hit->{distance_scores}{EuclideanDistance} ,
+							JACCARD_DISTANCE => $hit->{distance_scores}{JaccardDistance} ,
+							HAMMING_DISTANCE => $hit->{distance_scores}{HammingDistance} ,
+							S12_GOWER_LEGENDRE_DISTANCE => $hit->{distance_scores}{s12GowerLegendreDistance} ,
+							SPECTRUM_ID => $hit->{spectrum}{id} ,
+							METABOLITE_ID => $hit->{metaboliteID} ,
+							ANALYTE_ID => $hit->{analyte}{id},
+							ANALYTE_REF => 'http://gmd.mpimp-golm.mpg.de/Analytes/'.$hit->{analyte}{id}.'.aspx',
+							SPECTRUM_REF => 'http://gmd.mpimp-golm.mpg.de/Spectrums/'.$hit->{spectrum}{id}.'.aspx',
+							METABOLITE_REF => 'http://gmd.mpimp-golm.mpg.de/Metabolites/'.$hit->{metaboliteID}.'.aspx',
+						) ;
+					}
+					else {
+						%grp_res = (
+							ID => $href_grp->{id} ,
+							ANALYTE_NAME => $hit->{analyte}{name} ,
+							SPECTRUM_NAME => $hit->{spectrum}{name} ,
+							RI => $hit->{ri_infos}{ri} ,
+							RI_DISCREPANCY => $hit->{ri_infos}{riDiscrepancy} ,
+							DOT_PRODUCT_DISTANCE => $hit->{distance_scores}{DotproductDistance} ,
+							EUCLIDEAN_DISTANCE => $hit->{distance_scores}{EuclideanDistance} ,
+							JACCARD_DISTANCE => $hit->{distance_scores}{JaccardDistance} ,
+							HAMMING_DISTANCE => $hit->{distance_scores}{HammingDistance} ,
+							S12_GOWER_LEGENDRE_DISTANCE => $hit->{distance_scores}{s12GowerLegendreDistance} ,
+							SPECTRUM_ID => $hit->{spectrum}{id} ,
+							METABOLITE_ID => $hit->{metaboliteID} ,
+							ANALYTE_ID => $hit->{analyte}{id},
+							ANALYTE_REF => 'http://gmd.mpimp-golm.mpg.de/',
+							SPECTRUM_REF => 'http://gmd.mpimp-golm.mpg.de/',
+							METABOLITE_REF => 'http://gmd.mpimp-golm.mpg.de/',
+						) ;
+					}
+					push (@tbody_entries , \%grp_res) ;
+				}
+		}
+	return \@tbody_entries ;
+}
+## END of SUB
+   
+   
+   
+ 
+    
+    
+=head2 METHOD write_html_body
+
+	## Description : Write the html output file 
+	## Input : $results, $tbody_entries, $html_file, $html_template
+	## Output :  $html_file
+	## Usage : $o_output->write_html_body( $results, $tbody_entries, $html_file, $html_template ) ;
+=cut
+## START of SUB
+sub write_html_body {
+	## Retrieve Values
+    my $self = shift ;
+    my ( $results, $tbody_entries, $html_file_name, $html_template, $default_entries, $jsons_obj ) = @_ ;
+    
+    if (defined $html_file_name){
+    	
+	    	open (HTML, '>', $html_file_name) or die "Failed to open filehandle: $!" ;
+	    
+		    if (-e $html_template) {
+		    	
+		    	my $ohtml = HTML::Template->new(filename => $html_template) ;
+#		    	$ohtml->param( DATA => $jsons_obj ) ;
+				$ohtml->param( GROUPS => $tbody_entries ) ;
+		    	$ohtml->param( DEFAULT_ENTRIES => $default_entries ) ;
+		    	print HTML $ohtml->output ;
+		    }	
+	    	else {
+				croak "Problem about your html template: no html template available\n" ;
+			}
+			close (HTML) ;
+    }
+    else {
+    	croak "Problem with the html output file: $html_file_name is not defined\n" ;
+    }
+}
+## END of SUB
+
+
+
+=head2 METHOD excel_output
+
+	## Description : create an excel XLS output of the results
+	## Input : $jsons, $excel_file
+	## Output :  excel file
+	## Usage : $o_output->excel_output( $jsons, $excel_file ) ;
+=cut
+## START of SUB
+#sub excel_output {
+#	## Retrieve Values
+#    my $self = shift ;
+#    my ( $excel_file, $jsons ) = @_ ;
+#        
+#    # Create a new workbook and add a worksheet
+#    my $workbook  = Excel::Writer::XLSX->new( $excel_file ) ;
+#    my $worksheet = $workbook->add_worksheet() ;
+#    
+#    my $i = 0 ;
+#    
+#    # Create a format for the headings
+#    my $format = $workbook->add_format() ;
+#    $format->set_bold() ;
+#    
+#   $worksheet->write( $i, 0, "Num Spectre" , $format);
+#	$worksheet->write( $i, 1, "Analyte Name" , $format);
+#	$worksheet->write( $i, 2, "Spectrum Name" , $format);
+#	$worksheet->write( $i, 3, "Retention Index" , $format);
+#	$worksheet->write( $i, 4, "RI Discrepancy" , $format);
+#	$worksheet->write( $i, 5, "DotproductDistance" , $format);
+#	$worksheet->write( $i, 6, "EuclideanDistance" , $format);
+#	$worksheet->write( $i, 7, "JaccardDistance" , $format);
+#	$worksheet->write( $i, 8, "HammingDistance" , $format);
+#	$worksheet->write( $i, 9, "s12GowerLegendreDistance" , $format);
+#	$worksheet->write( $i, 10, "Spectrum ID" , $format);
+#	$worksheet->write( $i, 11, "Metabolite ID" , $format);
+#   $worksheet->write( $i, 12, "Analyte ID" , $format);
+#   $i++;
+#    
+#   foreach my $href_grp (@$jsons) {
+#		
+#			foreach my $hit ( @{$href_grp->{'searchResults'}} ){
+#				
+#					$worksheet->write( $i, 0, $href_grp->{id} );
+#			   		$worksheet->write( $i, 1, $hit->{analyte}{name} );
+#			   		$worksheet->write( $i, 2, $hit->{spectrum}{name} );
+#			   		$worksheet->write( $i, 3, $hit->{ri_infos}{ri} );
+#			   		$worksheet->write( $i, 4, $hit->{ri_infos}{riDiscrepancy} );
+#			   		$worksheet->write( $i, 5, $hit->{distance_scores}{DotproductDistance} );
+#			   		$worksheet->write( $i, 6, $hit->{distance_scores}{EuclideanDistance} );
+#			   		$worksheet->write( $i, 7, $hit->{distance_scores}{JaccardDistance} );
+#			   		$worksheet->write( $i, 8, $hit->{distance_scores}{HammingDistance} );
+#			   		$worksheet->write( $i, 9, $hit->{distance_scores}{s12GowerLegendreDistance} );
+#			   		$worksheet->write( $i, 10, $hit->{spectrum}{id} );
+#			   		$worksheet->write( $i, 11, $hit->{metaboliteID} );
+#			   		$worksheet->write( $i, 12, $hit->{analyte}{id});
+#			   		$i++;
+#			}
+#	}
+#
+#   $workbook->close();
+#}
+## END of SUB
+
+
+
+
+=head2 METHOD excel_like_output
+
+	## Description : create an excel like output of the results
+	## Input : $jsons, $excel_file
+	## Output :  excel file
+	## Usage : $o_output->excel_like_output( $jsons, $excel_file ) ;
+=cut
+## START of SUB
+sub excel_like_output {
+	## Retrieve Values
+    my $self = shift ;
+    my ( $excel_file, $jsons ) = @_ ;
+	
+	open (OUT , ">" , $excel_file) or die "Error at opening file $excel_file" ;
+	
+	print OUT "Num Spectre\tAnalyte Name\tSpectrum Name\tRetention Index\tRI Discrepancy\tDotproductDistance\tEuclideanDistance\tJaccardDistance\tHammingDistance\ts12GowerLegendreDistance\tSpectrum ID\tMetabolite ID\tAnalyte ID\n" ;
+	
+	foreach my $href_grp (@$jsons) {
+		
+			foreach my $hit ( @{$href_grp->{'searchResults'}} ){
+				
+					print OUT "$href_grp->{id}\t$hit->{analyte}{name}\t$hit->{spectrum}{name}\t$hit->{ri_infos}{ri}\t$hit->{ri_infos}{riDiscrepancy}\t$hit->{distance_scores}{DotproductDistance}\t$hit->{distance_scores}{EuclideanDistance}\t$hit->{distance_scores}{JaccardDistance}\t$hit->{distance_scores}{HammingDistance}\t$hit->{distance_scores}{s12GowerLegendreDistance}\t$hit->{spectrum}{id}\t$hit->{metaboliteID}\t$hit->{analyte}{id}\n";
+			}
+	}
+	close (OUT) ;
+	
+}
+## END of SUB
+
+
+=head2 METHOD write_json_skel
+
+	## Description : prepare and write json output file
+	## Input : $json_file, $scalar
+	## Output : json file
+	## Usage : $o_output->write_json_skel( $csv_file, $scalar ) ;
+	
+=cut
+## START of SUB
+sub write_json_skel {
+	## Retrieve Values
+    my $self = shift ;
+    my ( $json_file, $json_obj ) = @_ ;
+    
+    my $utf8_encoded_json_text = encode_json $json_obj ;
+    open(JSON, '>:utf8', $$json_file) or die "Can't create the file $$json_file\n" ;
+    print JSON $utf8_encoded_json_text ;
+    close(JSON) ;
+    
+}
+## END of SUB
+
+
+
+=head2 METHOD write_csv
+
+	## Description : write csv output file
+	## Input : $xlsx_file, $csv_file
+	## Output : csv file
+	## Usage : $o_output->write_csv( $xlsx_file, $csv_file ) ;
+	
+=cut
+## START of SUB
+sub write_csv {
+	## Retrieve Values
+    my $self = shift ;
+    my ( $csv_file, $jsons ) = @_ ;
+    
+    open (CSV , ">" , $csv_file) or die "Can't create the file $csv_file\n" ;
+     
+    print CSV "\"Num Spectre\"\t\"Analyte Name\"\t\"Spectrum Name\"\t\"Retention Index\"\t\"RI Discrepancy\"\t\"DotproductDistance\"\t\"EuclideanDistance\"\t\"JaccardDistance\"\t\"HammingDistance\"\t\"s12GowerLegendreDistance\"\t\"Spectrum ID\"\t\"Metabolite ID\"\t\"Analyte ID\"\n" ;
+			   		
+    foreach my $href_grp (@$jsons) {
+		
+			foreach my $hit ( @{$href_grp->{'searchResults'}} ){
+				
+					print CSV "\"$href_grp->{id}\"\t\"$hit->{analyte}{name}\"\t\"$hit->{spectrum}{name}\"\t\"$hit->{ri_infos}{ri}\"\t\"$hit->{ri_infos}{riDiscrepancy}\"\t\"$hit->{distance_scores}{DotproductDistance}\"\t\"$hit->{distance_scores}{EuclideanDistance}\"\t\"$hit->{distance_scores}{JaccardDistance}\"\t\"$hit->{distance_scores}{HammingDistance}\"\t\"$hit->{distance_scores}{s12GowerLegendreDistance}\"\t\"$hit->{spectrum}{id}\"\t\"$hit->{metaboliteID}\"\t\"$hit->{analyte}{id}\"\n" ;
+			}
+	}
+    close(CSV) ;
+    
+}
+## END of SUB
+
+
+
+
+=head2 METHOD write_ajax_data_source
+
+	## Description : write csv output file
+	## Input : $jsons_obj
+	## Output : 
+	## Usage : $o_output->write_ajax_data_source( $jsons_obj ) ;
+	
+=cut
+## START of SUB
+sub write_ajax_data_source {
+	## Retrieve Values
+    my $self = shift ;
+    my ( $jsons_obj ) = @_ ;
+
+	my %ajax = () ;
+	my $i = 0 ;
+	            
+	#open (AJAX,">ajax.txt") or die "ERROR at opening file" ;
+	            
+	foreach my $href_grp (@$jsons_obj) {
+			
+				foreach my $hit ( @{$href_grp->{'searchResults'}} ){
+		            	
+					push (@{$ajax{ 'data' }[$i]} , $href_grp->{id}) ;
+					push (@{$ajax{ 'data' }[$i]} , $hit->{spectrum}{name}) ;
+					push (@{$ajax{ 'data' }[$i]} , $hit->{analyte}{name}) ;
+					push (@{$ajax{ 'data' }[$i]} , $hit->{ri_infos}{ri}) ;
+					push (@{$ajax{ 'data' }[$i]} , $hit->{ri_infos}{riDiscrepancy}) ;
+					push (@{$ajax{ 'data' }[$i]} , $hit->{distance_scores}{DotproductDistance}) ;
+					push (@{$ajax{ 'data' }[$i]} , $hit->{distance_scores}{EuclideanDistance}) ;
+					push (@{$ajax{ 'data' }[$i]} , $hit->{distance_scores}{JaccardDistance}) ;
+					push (@{$ajax{ 'data' }[$i]} , $hit->{distance_scores}{HammingDistance}) ;
+					push (@{$ajax{ 'data' }[$i]} , $hit->{distance_scores}{s12GowerLegendreDistance}) ;
+					push (@{$ajax{ 'data' }[$i]} , $hit->{spectrum}{id}) ;
+					push (@{$ajax{ 'data' }[$i]} , $hit->{metaboliteID}) ;
+					push (@{$ajax{ 'data' }[$i]} , $hit->{analyte}{ID}) ;
+					$i++ ;
+				}
+		}
+	
+	my $ajax = encode_json \%ajax ;
+	return $ajax ;
+	#print AJAX $ajax ;
+
+}
+#END of SUB
+
+
+
+1 ;
+
+
+__END__
+
+=head1 SUPPORT
+
+You can find documentation for this module with the perldoc command.
+
+ perldoc csv.pm
+
+=head1 Exports
+
+=over 4
+
+=item :ALL is get_spectra
+
+=back
+
+=head1 AUTHOR
+
+Gabriel Cretin E<lt>gabriel.cretin@clermont.inra.frE<gt>
+Franck Giacomoni E<lt>franck.giacomoni@clermont.inra.frE<gt>
+
+=head1 LICENSE
+
+This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.
+
+=head1 VERSION
+
+version 1 : ??
+
+=cut