#!@WHICHPERL@

use strict;
use warnings;

use Cwd qw(abs_path getcwd);
use File::Basename qw(dirname fileparse);
use File::Copy::Recursive qw(rmove);
use File::Path qw(remove_tree);
use File::Spec::Functions qw(catfile catdir);
use File::Temp qw(tempdir);
use Getopt::Long;
use Pod::Usage;


=head1 SYNOPSIS

create_examples [options] [list of examples to generate]

  If no examples are listed then all will be generated and a tar file will be created.

  Possible examples to generate are:
    ame
    centrimo
    dreme
    fimo
    glam2
    glam2scan
    gomo
    mast
    mcast
    meme
    meme-chip
    momo
    motiph
    spamo
    streme
    tgene
    tomtom

  Options:
    -not              generate examples not in the list
    -tar              generates examples.tgz for uploading
    -debug            skip various cleanup related functions to help with debugging
    -help             displays this help message.
=cut

my @example_dirs = (
  'ame_example_output_files',
  'centrimo_example_output_files',
  'tgene_example_output_files',
  'dreme_example_output_files',
  'fimo_example_output_files',
  'glam2_example_output_files',
  'glam2scan_example_output_files',
  'gomo_example_output_files',
  'mast_example_output_files',
  'mcast_example_output_files',
  'meme_example_output_files',
  'memechip_example_output_files',
  'momo_example_output_files',
  'motiph_example_output_files',
  'spamo_example_output_files',
  'streme_example_output_files',
  'tomtom_example_output_files'
);
my $negate_list = 0; #FALSE
my $tar = 0; #FALSE
my $debug = 0; #FALSE
my $help = 0; #FALSE
my %listed_examples = ();

GetOptions("not" => \$negate_list, "tar" => \$tar, "debug" => \$debug, "help|?" => \$help) or pod2usage(2);
pod2usage(1) if $help;
if (@ARGV) {
  for (my $i = 0; $i < scalar(@ARGV); $i++) {
    $listed_examples{$ARGV[$i]} = 1;
  }
} else {
  # no examples specified, so generate everything and tar it
  $negate_list = 1;
  $tar = 1;
}

create_examples($negate_list, \%listed_examples);
tar_examples() if $tar;
update_makefile();
exit(0);

sub create_examples {
  my ($negate_list, $listed_examples) = @_;
  # ame
  if ($negate_list xor $listed_examples->{"ame"}) {
    print "Creating AME example\n";
    create_example(
      ["ame", "-oc", "ame_example_output_files", "-control", "--shuffle--",
        "-scoring", "avg", "-method", "fisher", "Klf1.fna", "JASPAR2018_CORE_non-redundant.meme"],
      "ame_example_output_files",
      ["example-datasets/Klf1.fna",
        "example-datasets/JASPAR2018_CORE_non-redundant.meme"],
      [\&test_html, "ame.html", \&test_exists, "ame.tsv", \&test_exists, "sequences.tsv"]);
  }
  # centrimo
  if ($negate_list xor $listed_examples->{"centrimo"}) {
    print "Creating CentriMo example\n";
    create_example(
      ["centrimo", "--oc", "centrimo_example_output_files", "--local",
        "--ethresh", "1", "mm9_tss_500bp_sampled_1000.fna", "some_vertebrates.meme"],
      "centrimo_example_output_files",
      [ "example-datasets/mm9_tss_500bp_sampled_1000.fna",
        "example-datasets/some_vertebrates.meme"],
      [\&test_html, "centrimo.html", \&test_exists, "centrimo.tsv",
        \&test_exists, "site_counts.txt"]);
  }
  # tgene
  if ($negate_list xor $listed_examples->{"tgene"}) {
    print "Creating T-Gene example\n";
    create_example(
      ["tgene", 
        "-oc", "tgene_example_output_files",
	"-max-link-distances", "500000,1000",
	"-tissues", "A549,Bj,H1hesc,Hepg2,Hsmm,K562,Nhek,Sknshra,Ag04450,Gm12878,Helas3,Hmec,Huvec,Mcf7,Nhlf",
        "-histone-root", "Histone",
	"-histones", "H3k27ac,H3k4me3",
	"--rna-source", "Cage",
        "-expression-root", "Expression",
	"--lecat", "6",
	"--no-closest-locus",
	"-desc", "Predicted links from P300 binding sites to genes on human chromosome 21",
        "P300.chr21.bed", "gencode.v7.transcripts.chr21.gtf"
      ],
      "tgene_example_output_files",
      [ "example-datasets/P300.chr21.bed",
        "../../tests/tgene/Histone",
        "../../tests/tgene/Expression",
        "../../tests/tgene/gencode.v7.transcripts.chr21.gtf"
      ],
      [\&test_html, "tgene.html", 
        \&test_exists, "links.tsv",
	\&test_exists, "HistLev+noise.H3k27ac.tsv",
	\&test_exists, "HistLev+noise.H3k4me3.tsv",
	\&test_exists, "TrExp+noise.tsv",
	\&test_exists, "TrExp.tsv"
      ]
    );
  }
  # dreme
  if ($negate_list xor $listed_examples->{"dreme"}) {
    print "Creating DREME example\n";
    create_example(
      ["dreme", "-oc", "dreme_example_output_files", "-png", "-p", "Klf1.fna"],
      "dreme_example_output_files",
      ["example-datasets/Klf1.fna"],
      [\&test_html, "dreme.html", \&test_exists, "dreme.txt",
        \&test_exists, "dreme.xml"]);
  }
  # fimo
  if ($negate_list xor $listed_examples->{"fimo"}) {
    print "Creating FIMO example\n";
    create_example(
      ["fimo", "--oc", "fimo_example_output_files", "--parse-genomic-coord",
        "some_vertebrates.meme", "mm9_tss_500bp_sampled_1000.fna"
      ],
      "fimo_example_output_files",
      [ "example-datasets/mm9_tss_500bp_sampled_1000.fna",
        "example-datasets/some_vertebrates.meme"],
      [\&test_html, "fimo.html", \&test_exists, "fimo.tsv",
        \&test_exists, "fimo.gff", \&test_exists, "fimo.xml",
        \&test_exists, "cisml.xml"
      ]);
  }
  # glam2
  if ($negate_list xor $listed_examples->{"glam2"}) {
    print "Creating GLAM2 example\n";
    create_example(
      ["glam2", "-O", "glam2_example_output_files", "-M", "p", "At.faa"],
      "glam2_example_output_files",
      ["example-datasets/At.faa"],
      [\&test_html, "glam2.html", \&test_exists, "glam2.meme", \&test_exists, "glam2.txt"]);
  }
  # glam2scan -n 25 p aln /home/tbailey/trunk/INSTALLED/db/fasta_databases/c_elegans.aa
  if ($negate_list xor $listed_examples->{"glam2scan"}) {
    print "Creating GLAM2Scan example\n";
    create_example(
      ["glam2scan", "-O", "glam2scan_example_output_files", "p", "At.glam2", "At.faa"],
      "glam2scan_example_output_files",
      [ "example-datasets/At.glam2",
        "example-datasets/At.faa"],
      [\&test_html, "glam2scan.html", \&test_exists, "glam2scan.txt"]);
  }
  # gomo
  if ($negate_list xor $listed_examples->{"gomo"}) {
    print "Creating GOMo example\n";
    create_example(
      [\&gomo_runner, 
      "dpinteract_subset.meme", # motifs for AMA & meme2images
      "bacteria_escherichia_coli_k12_1000_199.na", # sequences for AMA
      "bacteria_escherichia_coli_k12_1000_199.na.bfile", # background for AMA
      "bacteria_escherichia_coli_k12_1000_199.na.csv", # gene map for GOMo
      "go.dag" # GO DAG for GOMo
      ],
      "gomo_example_output_files", 
      [
        "example-datasets/dpinteract_subset.meme",
        "example-datasets/bacteria_escherichia_coli_k12_1000_199.na",
        "example-datasets/bacteria_escherichia_coli_k12_1000_199.na.bfile",
        "example-datasets/bacteria_escherichia_coli_k12_1000_199.na.csv",
        "example-datasets/go.dag"
      ],
      [\&test_html, "gomo.html", \&test_exists, "gomo.xml"]);
  }
  # mast
  if ($negate_list xor $listed_examples->{"mast"}) {
    print "Creating MAST example\n";
    create_example(
      ["mast", "-oc", "mast_example_output_files", "-dl", "http://www.uniprot.org/uniprot/?query=SEQUENCEID&sort=score", "adh.meme", "adh.faa"],
      "mast_example_output_files", [
        "example-datasets/adh.meme",
        "example-datasets/adh.faa"],
      [\&test_html, "mast.html", \&test_exists, "mast.txt", \&test_exists, "mast.xml"]);
  }
  # mcast
  if ($negate_list xor $listed_examples->{"mcast"}) {
    print "Creating MCAST example\n";
    create_example(
      ["mcast", "-oc", "mcast_example_output_files", "-parse-genomic-coord", "Klf1.dreme", "Klf1.fna"],
      "mcast_example_output_files",
      ["example-datasets/Klf1.dreme",
       "example-datasets/Klf1.fna"],
      [\&test_html, "mcast.html", \&test_exists, "mcast.tsv",
        \&test_exists, "mcast.xml", \&test_exists, "cisml.xml"]);
  }
  # meme
  if ($negate_list xor $listed_examples->{"meme"}) {
    print "Creating MEME example\n";
    create_example(
      ["meme", "lex0.fna", "-oc", "meme_example_output_files",
        "-dna", "-mod", "zoops", "-nmotifs", "3", "-revcomp"],
      "meme_example_output_files",
      ["example-datasets/lex0.fna"],
      [\&test_html, "meme.html", \&test_exists, "meme.txt", \&test_exists, "meme.xml"]);
  }
  # meme-chip
  if ($negate_list xor $listed_examples->{"meme-chip"}) {
    print "Creating MEME-ChIP example\n";
    create_example(
      ["meme-chip", "-meme-p", "6", "-oc", "memechip_example_output_files",
        "-db", "JASPAR2018_CORE_non-redundant.meme", "Klf1.fna"],
      "memechip_example_output_files",
      [ "example-datasets/JASPAR2018_CORE_non-redundant.meme",
        "example-datasets/Klf1.fna"],
      [\&test_html, "index.html"]);
  }
  # momo
  if ($negate_list xor $listed_examples->{"momo"}) {
    print "Creating MoMo example\n";
    create_example(
    ["momo", "motifx", "-oc", "momo_example_output_files",
    "--sequence-column", "Motif Peptide",
    "--width", "13", "--min-occurrences", "5", "--min-occurrences", "20",
    "--protein-database", "ensembl_Plasmodium_falciparum_38.200.fa",
    "pr8b00062_si_002.ptm"],
    "momo_example_output_files",
    [ "example-datasets/ensembl_Plasmodium_falciparum_38.200.fa",
      "example-datasets/pr8b00062_si_002.ptm"],
    [\&test_html, "momo.html", \&test_exists, "momo.txt"]);
  }

  # motiph
  if ($negate_list xor $listed_examples->{"motiph"}) {
    print "Creating MOTIPH example\n";
    create_example(
      ['motiph', "-oc", "motiph_example_output_files", 
        '--seed', 0, '--bg', 2.0, '--pseudocount', 0.01,
        'spiked.aln', 'yeast.tree', 'MCM1.meme.html'],
      "motiph_example_output_files",
      [ "example-datasets/spiked.aln",
        "example-datasets/yeast.tree",
        "example-datasets/MCM1.meme.html"],
      [\&test_html, "motiph.html", \&test_exists, "motiph.txt",
        \&test_exists, "motiph.xml", \&test_exists, "motiph.gff"]);
  }
  # spamo
  if ($negate_list xor $listed_examples->{"spamo"}) {
    print "Creating SpaMo example\n";
    create_example(
      ["spamo", "-oc", "spamo_example_output_files", "-png", 
        "Klf1.fna", "Klf1.meme", "JASPAR2018_CORE_non-redundant.meme"],
      "spamo_example_output_files",
      [ "example-datasets/Klf1.fna",
        "example-datasets/Klf1.meme",
        "example-datasets/JASPAR2018_CORE_non-redundant.meme"],
      [\&test_html, "spamo.html", \&test_exists, "spamo.tsv"]);
  }
  # streme
  if ($negate_list xor $listed_examples->{"streme"}) {
    print "Creating STREME example\n";
    create_example(
      ["streme", "-oc", "streme_example_output_files", "-p", "Klf1.fna"],
      "streme_example_output_files",
      ["example-datasets/Klf1.fna"],
      [\&test_html, "streme.html", \&test_exists, "streme.txt",
        \&test_exists, "streme.xml"]);
  }
  # tomtom
  if ($negate_list xor $listed_examples->{"tomtom"}) {
    print "Creating Tomtom example\n";
    create_example(
      ["tomtom", "-oc", "tomtom_example_output_files", "-min-overlap", "5",
        "-dist", "pearson", "-evalue", "-thresh", "10", "-no-ssc",
        "STRGGTCAN.meme", "JASPAR2018_CORE_non-redundant.meme"],
      "tomtom_example_output_files", 
      [ "example-datasets/STRGGTCAN.meme", 
        "example-datasets/JASPAR2018_CORE_non-redundant.meme"],
      [\&test_html, "tomtom.html", \&test_exists, "tomtom.tsv", \&test_exists, "tomtom.xml"]);
  }
}

sub create_example {
  my ($cmd, $output_directory, $inputs, $validation_tests) = @_;

  my $cwd = getcwd;

  my $example_area = abs_path(dirname(__FILE__));
  print "Using example area $example_area\n";
  chdir($example_area);

  # create a temporary folder
  my $work_area = tempdir("create_examples_XXXXXXXXXX", TMPDIR => 1);
  print "Created working area $work_area\n";

  # copy all required files into the work area
  print "Copying inputs to working area\n";
  for (my $i = 0; $i < scalar(@{$inputs}); $i++) {
    my $input = $inputs->[$i];
    if (ref $input eq "HASH") {
      die("Input method undefined!\n") unless defined $input->{method};
      if ($input->{method} eq "wget") {
        my $wget_status = system("wget", "-nv", "-P", $work_area, $input->{url});
        die("wget failed!") if ($wget_status != 0);
      } else {
        die("Unknown input method!\n");
      }
    } elsif (ref $input eq "") {
      # assume this is a file name relative to the current directory
      my ($input_name, $input_path) = fileparse($input);
      #link $input, catfile($work_area, $input_name);	# DANGER-- if this is a directory, cleanup will wipe it out!
      symlink "$cwd/$input", catfile($work_area, $input_name);
    } else {
      die("Unknown input file type!\n");
    }
  }

  # change to work area
  chdir($work_area);

  # run program
  print "Running program\n";
  my $status;
  if (ref $cmd->[0] eq "CODE") {
    my @args = @{$cmd};
    my $fn = shift @args;
    $status = $fn->($output_directory, @args);
  } else {
    $status = system(@{$cmd});
  }

  # change back to where the examples are
  chdir($example_area);

  #check outputs
  goto cleanup if $status;
  for (my $i = 1; $i < scalar(@{$validation_tests}); $i += 2) {
    my $test = $validation_tests->[$i-1];
    my $file_name = $validation_tests->[$i];
    unless ($test->(catfile($work_area, $output_directory, $file_name))) {
      warn("Test failed on $file_name\n");
      goto cleanup;
    }
  }

  # replace example
  print "Output tests pass, replacing $output_directory\n";
  my $from_dir = catdir($work_area, $output_directory);
  my $to_dir = catdir($example_area, $output_directory);
  rmove($from_dir, $to_dir ) or die("failure: $!");

  cleanup:
  unless ($debug) {
    print "Deleting work area: $work_area\n";
    remove_tree($work_area);
  }
}

sub tar_examples {
  system('tar -czf examples.tgz ' . join(' ', @example_dirs));
}

sub update_makefile {
  # update examples.mk which is included by Makefile.am
  system('echo "EXAMPLE_OUTPUT_FILES = \\\\" > examples.mk');
  my $cmd = 'find ' . join(' ', @example_dirs) . q( -type f ! -iname '*.orig' | sed -e 's/^/  /' -e '$q;s/$/ \\\\/' >> examples.mk);
  system($cmd);
  # must run automake in top level dir
  my $example_area = abs_path(dirname(__FILE__));
  chdir(catdir($example_area, '..', '..'));
  # regenerate Makefile.in
  system('automake doc/examples/Makefile');
  # change back to examples dir
  chdir($example_area);
}

sub gomo_runner {
  my ($out, $motifs, $sequences, $bfile, $map, $dag, @ids) = @_;
  my @motif_ids = ();
  foreach my $id (@ids) {
    push(@motif_ids, '-motif', $id);
  }
  my $status;
  my @args = ();
  # run AMA
  push(@args, 'ama', '-oc', '.', '-pvalues', @motif_ids, $motifs, $sequences, $bfile);
  print join(" ", @args), "\n";
  $status = system(@args);
  return $status if $status;
  if (!&test_exists('ama.xml')) {
    warn("Test failed on ama.xml");
    return 1;
  }
  # run GOMo
  @args = ("gomo", '--oc', $out, '--dag', $dag, '--motifs', $motifs, $map, 'ama.xml');
  print join(" ", @args), "\n";
  $status = system(@args);
  return $status;
}

sub test_exists {
  my ($file) = @_;
  return (-e $file);
}

sub test_html {
  my ($file) = @_;
  # we assume the html is correct if it has a closing tag.
  return !! `grep "</html>" $file 2> /dev/null | wc -l`;
}

1;
