#!/usr/bin/perl
=head1 NAME

tomtom_xml_to_html - Make a Tomtom HTML output from a Tomtom XML output.

=head1 SYNOPSIS

tomtom_xml_to_html <Tomtom XML file> <Tomtom 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 '/mit/meme_v4.11.4/lib/perl';

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

#
# initialise the global constants
# 
sub initialise {
  # setup etc dir
  $etc_dir = defined($ENV{MEME_ETC_DIR}) ? $ENV{MEME_ETC_DIR} : '/mit/meme_v4.11.4/etc';
  # 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 TomtomSAX;
}

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 Tomtom XML file specified");
  } elsif (not -e $options->{XML_PATH}) {
    push(@errors, "The Tomtom XML file specified does not exist");
  }
  unless (defined($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_tomtom {
  my ($info, $vmajor, $vminor, $vpatch, $release_date) = @_;
  my $wr = $info->{wr};
  $wr->str_prop('program', 'Tomtom');
  $wr->str_prop('version', "$vmajor.$vminor.$vpatch");
  # tomtom doesn't include the revision information in the XML
  $wr->str_prop('release', $release_date);
}

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

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

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

  $wr->str_array_prop("cmd", split(/\s+/, $info->{model}->{command_line}));
  $wr->property("options");
  $wr->start_object_value();
  $wr->str_prop("strands", $info->{model}->{strands});
  $wr->str_prop("distance_measure", $info->{model}->{distance_measure});
  $wr->str_prop("threshold_type", $info->{model}->{threshold}->{type});
  $wr->num_prop("threshold_value", $info->{model}->{threshold}->{value});
  $wr->str_prop("background_source", $info->{model}->{background}->{source});
  if (defined($info->{model}->{background}->{file})) {
    $wr->str_prop("background_file", $info->{model}->{background}->{file});
  }
  # more options to be put here
  $wr->end_object_value();
  $wr->property("alphabet");
  $info->{alphabet}->to_json($wr);
  $wr->num_array_prop("background", @{$info->{model}->{background}->{probs}});
}

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

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

sub handle_threshold {
  my ($info, $type, $value) = @_;
  $info->{model}->{threshold} = {type => $type, value => $value};
}

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

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

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

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

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

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

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

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

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

sub handle_db {
  my ($info, $source, $name, $loaded, $excluded, $last_mod) = @_;
  my $wr = $info->{wr};
  $wr->start_object_value();
  $wr->str_prop("source", $source);
  $wr->str_prop("name", $name);
  $wr->num_prop("loaded", $loaded);
  $wr->num_prop("excluded", $excluded);
  $wr->str_prop("last_modified", $last_mod);
  $wr->end_object_value();
}

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

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

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

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

sub start_motif {
  my ($info, $db, $id, $alt, $len, $nsites, $evalue, $url) = @_;
  my $wr = $info->{wr};
  $wr->start_object_value();
  $wr->num_prop("db", $db);
  $wr->str_prop("id", $id);
  $wr->str_prop("alt", $alt) if (defined($alt));
  $wr->num_prop("len", $len);
  $wr->num_prop("nsites", $nsites) if (defined($nsites));
  $wr->str_prop("evalue", $evalue) if (defined($evalue));
  $wr->str_prop("url", $url) if $url;
  $wr->property("pwm");
  $wr->start_array_value();
}

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

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

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

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

sub start_query {
  my ($info, $idx) = @_;
  my $wr = $info->{wr};
  $wr->start_object_value();
  $wr->num_prop("idx", $idx);
  $wr->property("matches");
  $wr->start_array_value();
}

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

sub handle_target {
  my ($info, $idx, $rc, $off, $pvalue, $evalue, $qvalue) = @_;
  my $wr = $info->{wr};
  $wr->start_object_value();
  $wr->num_prop("idx", $idx);
  $wr->bool_prop("rc", $rc) if (defined($rc));
  $wr->num_prop("off", $off);
  $wr->str_prop("pv", $pvalue);
  $wr->str_prop("ev", $evalue);
  $wr->str_prop("qv", $qvalue);
  $wr->end_object_value();
}

sub handle_runtime {
  my ($info, $cycles, $seconds) = @_;
  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("cycles", $cycles);
  $wr->num_prop("seconds", $seconds);
  $wr->end_object_value();
}


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

  my $sax = new TomtomSAX($info,
    start_tomtom => \&start_tomtom,
    end_tomtom => \&end_tomtom,
    start_model => \&start_model,
    end_model => \&end_model,
    handle_command_line => \&handle_command_line,
    handle_distance_measure => \&handle_distance_measure,
    handle_threshold => \&handle_threshold,
    handle_alphabet => \&handle_alphabet,
    handle_strands => \&handle_strands,
    handle_background => \&handle_background,
    handle_host => \&handle_host,
    handle_when => \&handle_when,
    start_query_dbs => \&start_query_dbs,
    end_query_dbs => \&end_query_dbs,
    start_target_dbs => \&start_target_dbs,
    end_target_dbs => \&end_target_dbs,
    handle_db => \&handle_db,
    start_queries => \&start_queries,
    end_queries => \&end_queries,
    start_targets => \&start_targets,
    end_targets => \&end_targets,
    start_motif => \&start_motif,
    end_motif => \&end_motif,
    handle_pos => \&handle_pos,
    start_matches => \&start_matches,
    end_matches => \&end_matches,
    start_query => \&start_query,
    end_query => \&end_query,
    handle_target => \&handle_target,
    handle_runtime => \&handle_runtime
  );
  my $fh;
  sysopen($fh, $opts->{XML_PATH}, O_RDONLY) or die("Failed to open file \"$opts->{XML_PATH}\"\n");
  while (<$fh>) {
    $sax->parse_more($_);
  }
  $sax->parse_done();
  my @errors = $sax->get_errors();
  foreach my $error (@errors) {
    print $error, "\n";
  }
}

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

&main();
1;