script/korapxml2krill

#!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
BEGIN { unshift @INC, "$FindBin::Bin/../lib" };
use File::Spec::Functions qw/catfile catdir/;
use Getopt::Long qw/GetOptions :config no_auto_abbrev/;
use Benchmark qw/:hireswallclock/;
use IO::Compress::Gzip qw/$GzipError/;
use Log::Log4perl;
use Pod::Usage;
use Directory::Iterator;
use KorAP::XML::Krill;
use KorAP::XML::Archive;
use KorAP::XML::Tokenizer;
use Parallel::ForkManager;

# CHANGES:
# ----------------------------------------------------------
# 2013/11/25
# - Initial release
#
# 2014/10/29
# - Merges foundry data to create indexer friendly documents
#
# 2016/02/04
# - renamed to korapxml2krill
# - added Schreibgebrauch support
#
# 2016/02/12
# - fixed foundry skipping
# - Support overwrite in archive processing
#
# 2016/02/14
# - Added version information
# - Added support for archive files
#
# 2016/02/15
# - Fixed temporary directory bug
# - Improved skipping before unzipping
# - Added EXPERIMENTAL concurrency support
#
# 2016/02/23
# - Merge korapxml2krill and korapxml2krill_dir
# ----------------------------------------------------------

our $LAST_CHANGE = '2016/02/23';
our $LOCAL = $FindBin::Bin;
our $VERSION_MSG = <<"VERSION";
Version $KorAP::XML::Krill::VERSION - diewald\@ids-mannheim.de - $LAST_CHANGE
VERSION


# Parse comand
my $cmd;
our @ARGV;
if ($ARGV[0] && index($ARGV[0], '-') != 0) {
  $cmd = shift @ARGV;
};

# Parse options from the command line
GetOptions(
  'input|i=s'   => \(my $input),
  'output|o=s'  => \(my $output),
  'overwrite|w' => \(my $overwrite),
  'human|m'     => \(my $text),
  'token|t=s'   => \(my $token_base),
  'gzip|z'      => \(my $gzip),
  'skip|s=s'    => \(my @skip),
  'log|l=s'     => \(my $log_level = 'ERROR'),
  'allow|a=s'   => \(my @allow),
  'primary|p!'  => \(my $primary),
  'pretty|y'    => \(my $pretty),
  'jobs|j=i'    => \(my $jobs = 0),
  'help|h'      => sub {
    pod2usage(
      -sections => 'NAME|SYNOPSIS|ARGUMENTS|OPTIONS',
      -verbose => 99,
      -msg => $VERSION_MSG,
    );
  },
  'version|v'   => sub {
    pod2usage(
      -verbose => 0,
      -msg => $VERSION_MSG
    )
  }
);

my %ERROR_HASH = (
  -sections => 'NAME|SYNOPSIS|ARGUMENTS|OPTIONS',
  -verbose => 99,
  -msg => $VERSION_MSG,
  -exit => 1
);

# Input has to be defined
pod2usage(%ERROR_HASH) unless $input;


# Initialize log4perl object
Log::Log4perl->init({
  'log4perl.rootLogger' => uc($log_level) . ', STDERR',
  'log4perl.appender.STDERR' => 'Log::Log4perl::Appender::ScreenColoredLevels',
  'log4perl.appender.STDERR.layout' => 'PatternLayout',
  'log4perl.appender.STDERR.layout.ConversionPattern' => '[%r] %F %L %c - %m%n'
});

my $log = Log::Log4perl->get_logger('main');


# Get file name based on path information
sub get_file_name ($) {
  my $file = shift;
  $file =~ s/^?\/?$input//;
  $file =~ tr/\//-/;
  $file =~ s{^-+}{};
  return $file;
};


# Write file
sub write_file {
  my $anno = shift;
  my $file = get_file_name $anno;

  # TODO: This should be done directly with a data structure! KorAP::XML::Wrap

  my $call = 'perl ' . $LOCAL . '/korapxml2krill -i ' .
    $anno . ' -o ' . $output . '/' . $file . '.json';
  $call .= '.gz -z' if $gzip;
  $call .= ' -m' if $text;
  $call .= ' -w' if $overwrite;
  $call .= ' -t ' . $token_base if $token_base;
  $call .= ' -l ' . $log_level if $log_level;
  $call .= ' --no-primary ' if $primary;
  $call .= ' -y ' . $pretty if $pretty;
  $call .= ' -a ' . $_ foreach @allow;
  $call .= ' -s ' . $_ foreach @skip;
  system($call);
  return "$file";
};


# Process a single file
unless ($cmd) {

  # Can't print gzip to STDOUT
  pod2usage(%ERROR_HASH) if $gzip && !$output;

  my %skip;
  $skip{lc($_)} = 1 foreach @skip;


  # Ignore processing
  if (!$overwrite && $output && -e $output) {
    $log->trace($output . ' already exists');
    exit(0);
  };

  BEGIN {
    $main::TIME = Benchmark->new;
    $main::LAST_STOP = Benchmark->new;
  };

  sub stop_time {
    my $new = Benchmark->new;
    $log->trace(
      'The code took: '.
	timestr(timediff($new, $main::LAST_STOP)) .
	  ' (overall: ' . timestr(timediff($new, $main::TIME)) . ')'
	);
    $main::LAST_STOP = $new;
  };

  # Create and parse new document
  $input =~ s{([^/])$}{$1/};
  my $doc = KorAP::XML::Krill->new( path => $input );

  unless ($doc->parse) {
    $log->warn($output . " can't be processed - no document data");
    exit(0);
  };

  my ($token_base_foundry, $token_base_layer) = (qw/OpenNLP Tokens/);
  if ($token_base) {
    ($token_base_foundry, $token_base_layer) = split /#/, $token_base;
  };

  # Get tokenization
  my $tokens = KorAP::XML::Tokenizer->new(
    path => $doc->path,
    doc => $doc,
    foundry => $token_base_foundry,
    layer => $token_base_layer,
    name => 'tokens'
  );

  # Unable to process base tokenization
  unless ($tokens->parse) {
    $log->error($output . " can't be processed - no base tokenization");
    exit(0);
  };

  my @layers;
  push(@layers, ['Base', 'Sentences']);
  push(@layers, ['Base', 'Paragraphs']);

  # Connexor
  push(@layers, ['Connexor', 'Morpho']);
  push(@layers, ['Connexor', 'Syntax']);
  push(@layers, ['Connexor', 'Phrase']);
  push(@layers, ['Connexor', 'Sentences']);

  # CoreNLP
  push(@layers, ['CoreNLP', 'NamedEntities']);
  push(@layers, ['CoreNLP', 'Sentences']);
  push(@layers, ['CoreNLP', 'Morpho']);
  push(@layers, ['CoreNLP', 'Constituency']);

  # DeReKo
  push(@layers, ['DeReKo', 'Structure']);

  # Glemm
  push(@layers, ['Glemm', 'Morpho']);

  # Malt
  # push(@layers, ['Malt', 'Dependency']);

  # Mate
  push(@layers, ['Mate', 'Morpho']);
  push(@layers, ['Mate', 'Dependency']);

  # OpenNLP
  push(@layers, ['OpenNLP', 'Morpho']);
  push(@layers, ['OpenNLP', 'Sentences']);

  # Schreibgebrauch
  push(@layers, ['Sgbr', 'Lemma']);
  push(@layers, ['Sgbr', 'Morpho']);

  # TreeTagger
  push(@layers, ['TreeTagger', 'Morpho']);
  push(@layers, ['TreeTagger', 'Sentences']);

  # XIP
  push(@layers, ['XIP', 'Morpho']);
  push(@layers, ['XIP', 'Constituency']);
  push(@layers, ['XIP', 'Sentences']);
  push(@layers, ['XIP', 'Dependency']);


  if ($skip{'#all'}) {
    foreach (@allow) {
      $tokens->add(split('#', $_));
      stop_time;
    };
  }
  else {
    # Add to index file - respect skipping
    foreach my $info (@layers) {
      # Skip if Foundry or Foundry#Layer should be skipped
      unless ($skip{lc($info->[0])} || $skip{lc($info->[0]) . '#' . lc($info->[1])}) {
	$tokens->add(@$info);
	stop_time;
      };
    };
  };

  my $file;

  my $print_text = $text ? $tokens->to_string($primary) :
    ($pretty ? $tokens->to_pretty_json($primary) : $tokens->to_json($primary));

  if ($output) {

    if ($gzip) {
      $file = IO::Compress::Gzip->new($output, Minimal => 1);
    }
    else {
      $file = IO::File->new($output, "w");
    };

    $file->print($print_text);
    $file->close;
  }

  else {
    print $print_text . "\n";
  };

  stop_time;
}

# Process an archive
elsif ($cmd eq 'archive') {

  pod2usage(%ERROR_HASH) unless $output;

  if ($output && (!-e $output || !-d $output)) {
    print "Directory '$output' does not exist.\n\n";
    exit(0);
  };

  # Zero means: everything runs in the parent process
  my $pool = Parallel::ForkManager->new($jobs);

  my $count = 0; # Texts to process
  my $iter  = 1;  # Current text in process

  # Report on fork message
  $pool->run_on_finish (
    sub {
      my ($pid, $code) = shift;
      my $data = pop;
      print 'Convert ['. ($jobs > 0 ? "$pid:" : '') .
	($iter++) . "/$count]" .
	  ($code ? " $code" : '') .
	    " $$data\n";
    }
  );

  my $t;
  print "Reading data ...\n";

  # Input is a directory
  if (-d $input) {
    my $it = Directory::Iterator->new($input);
    my @dirs;
    my $dir;

    while (1) {
      if (!$it->is_directory && ($dir = $it->get) && $dir =~ s{/data\.xml$}{}) {
	push @dirs, $dir;
	$it->prune;
      };
      last unless $it->next;
    };

    print "Start processing ...\n";
    $t = Benchmark->new;
    $count = scalar @dirs;

  DIRECTORY_LOOP:
    for (my $i = 0; $i < $count; $i++) {

      unless ($overwrite) {
	my $filename = catfile(
	  $output,
	  get_file_name($dirs[$i]) . '.json' . ($gzip ? '.gz' : '')
	);

	if (-e $filename) {
	  $iter++;
	  print "Skip $filename\n";
	  next;
	};
      };

      # Get the next fork
      my $pid = $pool->start and next DIRECTORY_LOOP;
      my $msg;

      $msg = write_file($dirs[$i]);
      $pool->finish(0, \$msg);
    };
  }

  # Input is a file
  elsif (-f($input) && (my $archive = KorAP::XML::Archive->new($input))) {
    unless ($archive->test_unzip) {
      print "Unzip is not installed or incompatible.\n\n";
      exit(1);
    };

    unless ($archive->test) {
      print "Zip archive not compatible.\n\n";
      exit(1);
    };

    print "Start processing ...\n";
    $t = Benchmark->new;
    my @dirs = $archive->list_texts;
    $count = scalar @dirs;

  ARCHIVE_LOOP:
    for (my $i = 0; $i < $count; $i++) {

      # Split path information
      my ($prefix, $corpus, $doc, $text) = $archive->split_path($dirs[$i]);

      unless ($overwrite) {
	my $filename = catfile(
	  $output,
	  get_file_name(catdir($doc, $text)) . '.json' . ($gzip ? '.gz' : '')
	);

	if (-e $filename) {
	  $iter++;
	  print "Skip $filename\n";
	  next;
	};
      };

      # Get the next fork
      my $pid = $pool->start and next ARCHIVE_LOOP;

      # Create temporary file
      my $temp = File::Temp->newdir;

      my $msg;

      # Extract from archive
      if ($archive->extract($dirs[$i], $temp)) {

	# Create corpus directory
	$input = catdir("$temp", $corpus);

	# Temporary directory
	my $dir = catdir($input, $doc, $text);

	# Write file
	$msg = write_file($dir);

	$temp = undef;
	$pool->finish(0, \$msg);
      }
      else {

	$temp = undef;
	$msg = "Unable to extract " . $dirs[$i] . "\n";
	$pool->finish(1, \$msg);
      };
    };
  }

  else {
    print "Input is neither a directory nor an archive.\n\n";
  };

  $pool->wait_all_children;

  print "Done.\n";
  print timestr(timediff(Benchmark->new, $t))."\n\n";
}

# Unknown command
else {
  warn "Unknown command '$cmd'.\n\n";
  pod2usage(%ERROR_HASH);
}

__END__

=pod

=encoding utf8

=head1 NAME

korapxml2krill - Merge KorapXML data and create Krill friendly documents


=head1 SYNOPSIS

  $ korapxml2krill [archive] -z --input <directory> --output <filename>


=head1 DESCRIPTION

L<KorAP::XML::Krill> is a library to convert KorAP-XML documents to files
compatible with the L<Krill|https://github.com/KorAP/Krill> indexer.


=head1 INSTALLATION

The preferred way to install L<KorAP::XML::Krill> is to use L<cpanm|App::cpanminus>.

  $ cpanm https://github.com/KorAP/KorAP-XML-Krill

In case everything went well, the C<korapxml2krill> command line tool will
be available.


=head1 ARGUMENTS

=over 2

=item B<archive>

Process an archive as a Zip-File or a folder of KorAP-XML documents.

=back


=head1 OPTIONS

=over 2

=item B<--input|-i> <directory|file>

Directory or archive file of documents to index.

=item B<--output|-o> <directory|file>

Output folder for archive processing or
document name for single output (optional),
writes to <STDOUT> by default.

=item B<--overwrite|-w>

Overwrite files that already exist.

=item B<--token|-t> <foundry>[#<file>]

Define the default tokenization by specifying
the name of the foundry and optionally the name
of the layer-file. Defaults to OpenNLP#tokens.

=item B<--skip|-s> <foundry>[#<layer>]

Skip specific foundries by specifying the name
or specific layers by defining the name
with a # in front of the foundry,
e.g. Mate#Morpho. Alternatively you can skip #ALL.
Can be set multiple times.

=item B<--allow|-a> <foundry>#<layer>

Allow specific foundries and layers by defining them
combining the foundry name with a # and the layer name.

=item B<--primary|-p>

Output primary data or not. Defaults to true.
Can be flagged using --no-primary as well.

=item B<--jobs|-j>

Define the number of concurrent jobs in seperated forks
for archive processing, defaults to 0. This is B<EXPERIMENTAL>!

=item B<--human|-m>

Represent the data human friendly, while the output defaults to JSON.

=item B<--pretty|-y>

Pretty print JSON output.

=item B<--gzip|-z>

Compress the output (expects a defined output file in single processing).

=item B<--log|-l>

The L<Log4perl> log level, defaults to C<ERROR>.

=item B<--help|-h>

Print this document.

=item B<--version|-v>

Print version information.

=back

=head1 AVAILABILITY

  https://github.com/KorAP/KorAP-XML-Krill


=head1 COPYRIGHT AND LICENSE

Copyright (C) 2015-2016, L<IDS Mannheim|http://www.ids-mannheim.de/>
Author: L<Nils Diewald|http://nils-diewald.de/>

L<KorAP::XML::Krill> is developed as part of the L<KorAP|http://korap.ids-mannheim.de/>
Corpus Analysis Platform at the
L<Institute for the German Language (IDS)|http://ids-mannheim.de/>,
member of the
L<Leibniz-Gemeinschaft|http://www.leibniz-gemeinschaft.de/en/about-us/leibniz-competition/projekte-2011/2011-funding-line-2/>.

This program is free software published under the
L<BSD-2 License|https://raw.githubusercontent.com/KorAP/KorAP-XML-Krill/master/LICENSE>.

=cut