#!/usr/bin/perl -W

use CGI qw(:standard :cgi-lib);
#use CGI::Carp qw//;
use CGI::Pretty;
use Data::Dumper;

use strict;

my %Input=Vars();

# process the inputs whose keys match the regex pattern
my @single_keys = grep (/^single_/, keys %Input);
my @single_list;
map { if ($Input{$_} eq 'on') { $_=~s/^single_//; push @single_list, $_; } } @single_keys;
my $single_list = join ',', @single_list;

map { delete $Input{$_} } @single_keys;
if ($single_list ne '') { $Input{fastq_file_list1} = $single_list; }

# process paired runs
my @paired_keys = grep (/^paired_/, keys %Input);
my @paired_list;
map { if ($Input{$_} eq 'on') { my $key = $_; $key =~s/^paired_//; push @paired_list, [split ',', $key]; } } @paired_keys;

if (@paired_list) {
  $Input{fastq_file_list1} = join ',', (map {sprintf "%s", $_->[0]} @paired_list);
  $Input{fastq_file_list2} = join ',', (map {sprintf "%s", $_->[1]} @paired_list);
}

# make a checksum of the input files only.  Further checksums will be
# calculated by the backend script when it is launched
my $paired_end_mode = (exists $Input{fastq_file_list2}) ? 1 : 0;


my $source_files = $paired_end_mode ?
  $Input{fastq_file_list1} . ',' . $Input{fastq_file_list2} :
  $Input{fastq_file_list1};

$Input{source_files} = $source_files;
#$Input{reads_checksum} = qx%echo "$source_files" | cksum - | cut -f 1 -d " "%;

#chomp $Input{reads_checksum};

# Now delete irrelevant options for single_end mode
my @paired_end_only_keys = qw/map_2 map_a map_A assemble_s pileup_s pileup_p/;
if (! $paired_end_mode){
  map { delete $Input{$_} } @paired_end_only_keys;
}

map { delete $Input{$_} } @paired_keys;

my $op;
# clone options from map for mapcheck.  Specific for maq version 0.7.1
for $op (qw/s Q m q/){ 
  if (exists $Input{'assemble_'.$op}) { 
    $Input{'mapcheck_'.$op} = $Input{'assemble_'.$op};
  }
}

$Input{mapcheck_c} = 'on';

my $Error = '';

# check that the filename prefix is valid
# this is now handled by the run_maq.sh script

# Substitute space with underscore
chomp $Input{outfile_prefix};

if ($Input{outfile_prefix} eq ''){
    $Error = sprintf "You did not specify an output file prefix.  (See General Settings section)";
    $Error .= sprintf Dumper \%Input;
}

# Translate all illegal characters
$Input{outfile_prefix} =~ s/[^a-zA-Z0-9_]+/_/g;

# Disallow dots at beginning
$Input{outfile_prefix} =~ s/^\.+//g;


#  $Error = sprintf "The output file prefix you specified, '%s', contains disallowed characters\n",
#  $Input{outfile_prefix};
#}

 
# For those, collect them into a comma separated list

my $argstring = '';


for my $k (keys %Input){
  $argstring .= sprintf "%s\t%s\n", $k, $Input{$k};
}

my $outfile_subdir = $Input{outfile_prefix};
my $outfile_stub = $Input{outfile_prefix};


my $outuri = "/$ENV{MAQGENE_OUT_ALIAS}/$Input{user_results_dir}/$outfile_subdir";
my $outdir = "$ENV{MAQGENE_OUT_DIR}/$Input{user_results_dir}/$outfile_subdir";

# For easy deleting of these files by non-root
umask 0000;
mkdir $outdir;

if ($Error eq ''){

  open O, ">$outdir/$outfile_stub.input";
  printf O "%s", $argstring;
  close O;
  system "$ENV{MAQGENE_EXE_DIR}/run_maq.sh $outdir/$outfile_stub.input nosave > $outdir/${outfile_stub}_messages.txt 2>&1 &";
  
  print &redirect($outuri);

  #&PrintPage($message);

} else {
  &PrintPage($Error);
}



sub PrintPage {

  my $message = $_[0];
  print 
    &header(),
    &start_html(-title=>'MAQGene Results',
                -dtd=>['-//W3C//DTD XHTML 1.0 Strict//EN',
                       'http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd'],
                -style=>{-src=>"../../run/maqgene.css"}
                #-head=>meta({-http_equiv=>'refresh', -content=>'10'})
    ),
  
  &pre($message),
  #&pre(`env`);
  &end_html;
}