#Declaration de l espace de travail et du chemin de l executable R :
use strict;
use Carp;
use Statistics::R;
use Cwd qw(abs_path);
use File::Basename;

my ($working_dir,$r_bin,$log_dir,$R,$cmd,$line);

#pour voir ce que le xml renvoie au wrapper perl. Sachant que $0 est la ligne de commande et @ARGV les arguments
#printf STDERR "%s\n",join("***** ",$0,@ARGV);

# Parameters :
  # - count.file : input count file name
  # - group.member.file : input sapmle/tag group member file name
  # - output.file : output file name
  # - formatformat.image.out : graphic format of the output file. This must be one of "png", "jpeg", "tiff", "pdf"
  # - transformation.method : count data transformation for graphical display. This must be one of "none", "rld", "vsd"
  # - distance.method : the distance measure to be used. This must be one of "euclidean", "correlation", "maximum", "manhattan", "canberra", "binary" or "minkowski"
  # - agglomeration.method : the agglomeration method to be used. This should be one of "ward", "single", "complete", "average", "mcquitty", "median" or "centroid"
  # - sample.clustering : if TRUE clustering is performed on the samples
  # - select : number of top genes to use for clustering, selected by highest row variance. If NULL all the genes are selected 
  # - plot.title : an overall title for the plot
  # - xlab : a title for the x axis
  # - ylab : a title for the y axis
  # - width : the width of the graphics region in inches
  # - height : the height of the graphics region in inches
  # - ppi : the nominal resolution in ppi 


#Parametres d'entree
my $count_file               =$ARGV[0]; #input count file name
my $group_member_file        =$ARGV[1]; #input sapmle/tag group member file name
#my $conditional              =$ARGV[2];
my $output_file              =$ARGV[2]; #output file name
my $transformation_method    =$ARGV[3]; #count data transformation for graphical display. This must be one of "none", "rld", "vsd"
my $distance_method          =$ARGV[4]; #the distance measure to be used. This must be one of "euclidean", "correlation", "maximum", "manhattan", "canberra", "binary" or "minkowski"
my $agglomeration_method     =$ARGV[5]; #the agglomeration method to be used. This should be one of "ward", "single", "complete", "average", "mcquitty", "median" or "centroid"
my $sample_clustering        =$ARGV[6]; #if TRUE clustering is performed on the samples
my $select                   =$ARGV[7]; #number of top genes to use for clustering, selected by highest row variance. If NULL all the genes are selected 
my $plot_title               =$ARGV[8]; #an overall title for the plot
my $xlab                     =$ARGV[9]; #a title for the x axis
my $ylab                     =$ARGV[10];#a title for the y axis
my $width                    =$ARGV[11];#the width of the graphics region in inches
my $height                   =$ARGV[12];#the height of the graphics region in inches
my $ppi                      =$ARGV[13];#the nominal resolution in ppi 


#ligne de commande test :
#perl sm_hclustfun.pl Data/gene_counts.txt Data/member.csv outfile none  euclidean  ward TRUE 100 titre x y 7 7 300

#Récuperer le numero (unique) de l'output
my ($nb) = ($output_file=~/galaxy_dataset_(\d+)\.\S+$/);

#remplacer les espaces par des underscores
$plot_title =~ s/@$§/ /g;
$xlab =~ s/@$§/ /g;
$ylab =~ s/@$§/ /g;



#On suppose que le fichier de donnees en entree a ete place dans un repertoire
#de travail working_dir
## smaman : $working_dir=abs_path($file_in);
#Repertoire de sortie cree par le script, verif des droits d'ecriture sur ce repertoire de sortie
`cd /galaxydata/database/files/workspace/; mkdir $nb; chmod -R 777 $nb/; cd $nb/;`;
my $working_dir= "/galaxydata/database/files/workspace/$nb";
#$working_dir=~s/\/[^\/]*$//;
#$file_in=~s/^.*\///;


#Recuperation de la matrice entrante dans le repertoir de travail
#`cp $group_member_file $working_dir/group_member_file`;

#Fichier de sortie des donnees de description statistiques
#$stat_out = "$working_dir/stat_out";


# Rbin path
$r_bin   = '/usr/local/bioinfo/src/R/current/bin/R';
#Log dir
$log_dir = $working_dir;

#déaration de l'objet $R et ouverture du pont :
$R = Statistics::R->new(
    "r_bin"   => $r_bin,
    "log_dir" => $log_dir,
) or die "Problem with R : $!\n";
# Ouverture du pont
$R->startR;

#envoi du repertoire de travail
$R->send(
   qq`
        setwd("$working_dir")
    `);

#Read R script
$cmd="";
open IN,"< /usr/local/bioinfo/src/galaxy-dev/galaxy-dist/tools/sm_R_stats/hclustfun.R"
	or die "Unable to read R script : $!\n";
while ($line=<IN>) {
	$cmd.=$line;
}
close(IN);

#Declare R function
$R->send($cmd);



if ($group_member_file eq "NO"){
print STDOUT "Group member file NO \n\n";
    $R->send(
	    qq`
     hclustfun(
      count.file = "$count_file",
      group.member.file = NULL,
      format.image.out = "jpeg",
      transformation.method = "$transformation_method",
      sample.clustering = $sample_clustering,
      select = $select,
      distance.method = "$distance_method",
      agglomeration.method = "$agglomeration_method",
      plot.title = "$plot_title",
      xlab = "$xlab",
      ylab = "$ylab",
      output.file = "$working_dir/out",
      width = $width, 
      height = $height,
      ppi = $ppi)
      	`
    );
    print STDOUT "\n hclustfun(
      count.file = \"$count_file\",
      group.member.file = NULL,
      format.image.out = \"jpeg\",
      transformation.method = \"$transformation_method\",
      sample.clustering = $sample_clustering,
      select = $select,
      distance.method = \"$distance_method\",
      agglomeration.method = \"$agglomeration_method\",
      plot.title = \"$plot_title\",
      xlab = \"$xlab\",
      ylab = \"$ylab\",
      output.file = \"$working_dir/out\",
      width = $width, 
      height = $height,
      ppi = $ppi)";
}
else {
print STDOUT "group member file YES \n";
        $R->send(
	        qq`
         hclustfun(
          count.file = "$count_file",
          group.member.file = "$group_member_file",
          format.image.out = "jpeg",
          transformation.method = "$transformation_method",
          sample.clustering = $sample_clustering,
          select = $select,
          distance.method = "$distance_method",
          agglomeration.method = "$agglomeration_method",
          plot.title = "$plot_title",
          xlab = "$xlab",
          ylab = "$ylab",
          output.file = "$working_dir/out",
          width = $width, 
          height = $height,
          ppi = $ppi)
          	`
        );
        print STDOUT "\n hclustfun(
          count.file = \"$count_file\",
          group.member.file = \"$group_member_file\",
          format.image.out = \"jpeg\",
          transformation.method = \"$transformation_method\",
          sample.clustering = $sample_clustering,
          select = $select,
          distance.method = \"$distance_method\",
          agglomeration.method = \"$agglomeration_method\",
          plot.title = \"$plot_title\",
          xlab = \"$xlab\",
          ylab = \"$ylab\",
          output.file = \"$working_dir/out\",
          width = $width, 
          height = $height,
          ppi = $ppi)";
}


#Fermeture du pont
$R->stopR();

#Mise en forme d'un rapport HTML
open OUT,"> $working_dir/statistics_report.html"
	or die "Unable to create HTML output file : $!\n";
print OUT "<HTML><HEAD><TITLE>Descriptive statistics</TITLE></HEAD>\n";
print OUT "<BODY>\n";

#if (-f "$working_dir/$stat_out" ) {
if (-f "$working_dir/out.jpeg" ) {
	print OUT "<H1>Hierarchical classification :</H1>\n";
		my $file_url = "$working_dir/out.jpeg";
        my $tar = "$file_url.zip";
        `cp $file_url $tar`;
		$file_url =~s/^\/galaxydata\/database\/files\/workspace/\/galaxy-dev\/download/;
        print OUT "<A HREF=\"$file_url\"><IMG  height=\"700\" width=\"700\" src=\"$file_url\"></A>";
        print OUT "<BR /><BR /><BR />";
        $tar =~s/^\/galaxydata\/database\/files\/workspace/\/galaxy-dev\/download/;
        print OUT "<A HREF=\"$file_url\">Download here your hierarchical classification map.</A>";
        print OUT "</HTML>\n";
        print OUT "</BODY>\n";
}

#Recuperation des outputs dans Galaxy
my $cmdhtml ='';
my $out= "$working_dir/statistics_report.html";
if (! -e $out){print STDERR "Pas de fichier html produit \n";}
else {$cmdhtml = "(mv $out $output_file) >& ./cp_html.log 2>&1";
system $cmdhtml;}