#!/opt/conda/conda-bld/meme_1618213960901/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/bin/perl
=head1 NAME

dreme_xml_to_html - Make a DREME HTML output from a DREME XML output.

=head1 SYNOPSIS

dreme_xml_to_html <DREME XML file> <DREME HTML file>
=cut

use strict;
use warnings;

use Cwd qw(abs_path);
use Fcntl qw(O_RDONLY SEEK_SET);
use File::Basename qw(fileparse);
use File::Spec::Functions qw(tmpdir);
use File::Temp qw(tempfile);
use Getopt::Long;
use Pod::Usage;
use XML::Parser::Expat;

use lib '/opt/conda/conda-bld/meme_1618213960901/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/lib/meme-5.3.0/perl';

my $etc_dir;
my $temp_dir;
my $scripts_dir;

#
# initialise the global constants
# 
sub initialise {
  # setup etc dir
  $etc_dir = defined($ENV{MEME_DATA_DIR}) ? $ENV{MEME_DATA_DIR} : '/opt/conda/conda-bld/meme_1618213960901/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/share/meme-5.3.0';
  # setup temporary directory
  $temp_dir = '';
  # use the perl default if none is supplied or the replace fails
  $temp_dir = tmpdir() if ($temp_dir eq '' || $temp_dir =~ m/^\@TMP[_]DIR\@$/);

  # find the location of the script
  my $script_name;
  ($script_name, $scripts_dir) = fileparse(__FILE__);
  $scripts_dir = abs_path($scripts_dir);

  # add script location to search path
  unshift(@INC, $scripts_dir);

  require HtmlMonolithWr;
  require DremeSAX;
}

sub arguments {
  # Set Option Defaults
  my $options = {XML_PATH => undef, HTML_PATH => undef};
  # General Options
  my $help = 0; # FALSE
  my @errors = ();
  my @dbs = ();

  # get the options from the arguments
  my $options_success = 0; # FALSE
  # redirect stderr to a temp file so we can get the error message from GetOptions
  my $olderr;
  my $tmperr = tempfile('GetOptions_XXXXXXXXXX', DIR => $temp_dir, UNLINK => 1);
  open($olderr, ">&STDERR") or die("Can't dup STDERR: $!");
  open(STDERR, '>&', $tmperr) or die("Can't redirect STDERR to temp file: $!");
  # parse options
  $options_success = GetOptions(
    'help|?'          => \$help,
  );
  ($options->{XML_PATH}, $options->{HTML_PATH}) = @ARGV;
  # display help
  pod2usage(1) if $help;
  # reset STDERR
  open(STDERR, ">&", $olderr) or die("Can't reset STDERR: $!");
  # read argument parsing errors
  seek($tmperr, 0, SEEK_SET);
  while (<$tmperr>) {chomp; push(@errors, $_);}
  close($tmperr);
  # check source XML file
  unless (defined($options->{XML_PATH})) {
    push(@errors, "No DREME XML file specified");
  } elsif (not -e $options->{XML_PATH}) {
    push(@errors, "The DREME XML file specified does not exist");
  }
  unless (defined($options->{HTML_PATH})) {
    push(@errors, "No output file specified");
  }
  # print errors
  foreach my $error (@errors) {
    print STDERR $error, "\n";
  }
  pod2usage(2) if @errors;
  # return options
  return $options;
}

sub start_dreme {
  my ($info, $vmajor, $vminor, $vpatch, $release_date) = @_;
  my $wr = $info->{wr};
  $wr->str_prop('program', 'dreme');
  $wr->str_prop('version', "$vmajor.$vminor.$vpatch");
  # dreme doesn't include the revision information in the XML
  $wr->str_prop('release', $release_date);
}

sub end_dreme {
  my ($info) = @_;
  my $wr = $info->{wr};
}

sub start_model {
  my ($info) = @_;
  $info->{model} = {};
}

sub end_model {
  my ($info) = @_;
  my $wr = $info->{wr};

  if (defined($info->{model}->{description})) {
    $wr->str_prop("description", $info->{model}->{description});
  }
  $wr->str_array_prop("cmd", split(/\s+/, $info->{model}->{command_line}));
  $wr->property("options");
  $wr->start_object_value();
  $wr->bool_prop("revcomp", $info->{model}->{strands} eq 'both');
  $wr->num_prop("ngen", $info->{model}->{ngen});
  $wr->num_prop("add_pv_thresh", $info->{model}->{pv_thresh});
  $wr->num_prop("seed", $info->{model}->{seed});
  $wr->property("stop");
  $wr->start_object_value();
  $wr->str_prop("evalue", $info->{model}->{stop}->{evalue});
  if (defined($info->{model}->{stop}->{count})) {
    $wr->num_prop("count", $info->{model}->{stop}->{count});
  }
  if (defined($info->{model}->{stop}->{time})) {
    $wr->num_prop("time", $info->{model}->{stop}->{time});
  }
  $wr->end_object_value();
  # more options to be put here
  $wr->end_object_value();
  $wr->property("alphabet");
  $info->{alph}->to_json($wr);
  $wr->property("background");
  $wr->start_object_value();
  $wr->num_array_prop("freqs", @{$info->{model}->{background}});
  $wr->end_object_value();
  $wr->property("sequence_db");
  $wr->start_object_value();
  $wr->str_prop("name", $info->{model}->{positives}->{name});
  $wr->str_prop("file", $info->{model}->{positives}->{file});
  $wr->str_prop("lmod", $info->{model}->{positives}->{last_mod_date});
  $wr->num_prop("count", $info->{model}->{positives}->{count});
  $wr->end_object_value();
  $wr->property("control_db");
  $wr->start_object_value();
  $wr->str_prop("name", $info->{model}->{negatives}->{name});
  $wr->str_prop("from", $info->{model}->{negatives}->{from});
  if ($info->{model}->{negatives}->{from} eq 'file') {
    $wr->str_prop("file", $info->{model}->{negatives}->{file});
    $wr->str_prop("lmod", $info->{model}->{negatives}->{last_mod_date});
  }
  $wr->num_prop("count", $info->{model}->{negatives}->{count});
  $wr->num_array_prop("freqs", @{$info->{model}->{background}});
  $wr->end_object_value();
}

sub handle_command_line {
  my ($info, $command_line) = @_;
  $info->{model}->{command_line} = $command_line;
}

sub handle_positives {
  my ($info, $name, $count, $file, $last_mod_date) = @_;
  $info->{model}->{positives} = {
    name => $name, count => $count, file => $file,
    last_mod_date => $last_mod_date};
}

sub handle_negatives {
  my ($info, $name, $count, $from, $file, $last_mod) = @_;
  $info->{model}->{negatives} = {
    name => $name, count => $count, from => $from,
    file => $file, last_mod_date => $last_mod};
}

sub handle_alphabet {
  my ($info, $alphabet) = @_;
  $info->{alph} = $alphabet;
}

sub handle_strands {
  my ($info, $strands) = @_;
  $info->{model}->{strands} = $strands;
}

sub handle_background {
  my ($info, @probs) = @_;
  $info->{model}->{background} = [@probs];
}

sub handle_stop {
  my ($info, $evalue, $count, $time) = @_;
  $info->{model}->{stop} = {evalue => $evalue, count => $count, time => $time};
}

sub handle_ngen {
  my ($info, $ngen) = @_;
  $info->{model}->{ngen} = $ngen;
}

sub handle_add_pv_thresh {
  my ($info, $pv_thresh) = @_;
  $info->{model}->{pv_thresh} = $pv_thresh;
}

sub handle_seed {
  my ($info, $seed) = @_;
  $info->{model}->{seed} = $seed;
}

sub handle_host {
  my ($info, $host) = @_;
  $info->{model}->{host} = $host;
}

sub handle_when {
  my ($info, $when) = @_;
  $info->{model}->{when} = $when;
}

sub handle_description {
  my ($info, $description) = @_;
  $info->{model}->{description} = $description;
}

sub start_motifs {
  my ($info) = @_;
  my $wr = $info->{wr};
  $wr->property("motifs");
  $wr->start_array_value();
}

sub end_motifs {
  my ($info) = @_;
  my $wr = $info->{wr};
  $wr->end_array_value();
}

sub start_motif {
  my ($info, $id, $alt, $seq, $len, $nsites, $p, $n, $pvalue, $evalue, $unerased_evalue) = @_;
  my $wr = $info->{wr};
  $wr->start_object_value();
  $wr->num_prop("db", 0);
  $wr->str_prop("id", $seq);
  $wr->str_prop("alt", $alt);
  $wr->num_prop("len", $len);
  $wr->num_prop("nsites", $nsites);
  $wr->str_prop("evalue", $evalue);
  $wr->num_prop("p", $p);
  $wr->num_prop("n", $n);
  $wr->str_prop("pvalue", $pvalue);
  $wr->str_prop("unerased_evalue", $unerased_evalue);
  $wr->property("pwm");
  $wr->start_array_value();
  $info->{seen_match} = 0;
}

sub end_motif {
  my ($info) = @_;
  my $wr = $info->{wr};
  if (!$info->{seen_match}) {
    $wr->end_array_value();
    $wr->property("matches");
    $wr->start_array_value();
  }
  $wr->end_array_value();
  $wr->end_object_value();
}

sub handle_pos {
  my ($info, @probs) = @_;
  my $wr = $info->{wr};
  $wr->num_array_value(@probs);
}

sub handle_match {
  my ($info, $seq, $p, $n, $pvalue, $evalue) = @_;
  my $wr = $info->{wr};
  if (!$info->{seen_match}) {
    $wr->end_array_value();
    $wr->property("matches");
    $wr->start_array_value();
    $info->{seen_match} = 1;
  }
  $wr->start_object_value();
  $wr->str_prop("seq", $seq);
  $wr->num_prop("p", $p);
  $wr->num_prop("n", $n);
  $wr->str_prop("pvalue", $pvalue);
  $wr->str_prop("evalue", $evalue);
  $wr->end_object_value();
}

sub handle_run_time {
  my ($info, $cpu, $real, $stop) = @_;
  my $wr = $info->{wr};
  $wr->property("runtime");
  $wr->start_object_value();
  $wr->str_prop("host", $info->{model}->{host});
  $wr->str_prop("when", $info->{model}->{when});
  $wr->num_prop("cpu", $cpu);
  $wr->num_prop("real", $real);
  $wr->str_prop("stop", $stop);
  $wr->end_object_value();
}

sub transform_data {
  my ($opts, $jsonwr) = @_;
  my $info = {wr => $jsonwr};

  my $sax = new DremeSAX($info,
    start_dreme => \&start_dreme,
    end_dreme=> \&end_dreme,
    start_model => \&start_model,
    end_model => \&end_model,
    handle_command_line => \&handle_command_line,
    handle_positives => \&handle_positives,
    handle_negatives => \&handle_negatives,
    handle_alphabet => \&handle_alphabet,
    handle_strands => \&handle_strands,
    handle_background => \&handle_background,
    handle_stop => \&handle_stop,
    handle_ngen => \&handle_ngen,
    handle_add_pv_thresh => \&handle_add_pv_thresh,
    handle_seed => \&handle_seed,
    handle_host => \&handle_host,
    handle_when => \&handle_when,
    handle_description => \&handle_description,
    start_motifs => \&start_motifs,
    end_motifs => \&end_motifs,
    start_motif => \&start_motif,
    end_motif => \&end_motif,
    handle_pos => \&handle_pos,
    handle_match => \&handle_match,
    handle_run_time => \&handle_run_time
  );
  my $fh;
  sysopen($fh, $opts->{XML_PATH}, O_RDONLY) or die("Failed to open file \"$opts->{XML_PATH}\"\n");
  while (<$fh>) {
    $sax->parse_more($_);
    if ($sax->has_errors()) {
      die("Failed to write HTML output due to errors processing the XML:\n" . join("\n", $sax->get_errors()));
    }
  }
  $sax->parse_done();
  if ($sax->has_errors()) {
    die("Failed to write HTML output due to errors processing the XML:\n" . join("\n", $sax->get_errors()));
  }  
}

sub main {
  &initialise();
  my $opts = &arguments();
  # start writing HTML
  my $htmlwr = new HtmlMonolithWr($etc_dir, 'dreme_template.html', 
    $opts->{HTML_PATH}, 'dreme_data.js' => 'data');
  # transform the XML into JSON
  &transform_data($opts, $htmlwr->output());
  # finish writing HTML
  $htmlwr->output();
}

&main();
1;

