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 Cache::FastMmap;
use Directory::Iterator;
use KorAP::XML::Krill;
use KorAP::XML::Archive;
use KorAP::XML::Tokenizer;
use Parallel::ForkManager;
# TODO: use Parallel::Loops
# TODO: make output files

# 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
#
# 2016/02/27
# - Added extract function
#
# 2016/03/17
# - Added meta switch
#
# 2016/03/18
# - Added meta data caching
#
# 2016/06/27
# - Added multi archive support
# - Added prefix negation support
# - Added Malt#Dependency support
# ----------------------------------------------------------

our $LAST_CHANGE = '2016/03/17';
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;
};

my (@skip, @sigle, @input);
my $text;

# Parse options from the command line
GetOptions(
  'input|i=s'   => \@input,
  'output|o=s'  => \(my $output),
  'overwrite|w' => \(my $overwrite),
  'meta|m=s'    => \(my $meta),
  'token|t=s'   => \(my $token_base),
  'gzip|z'      => \(my $gzip),
  'skip|s=s'    => \@skip,
  'sigle|sg=s'  => \@sigle,
  'cache|c=s'   => \(my $cache_file = 'korapxml2krill.cache'),
  'cache-size|cs=s'   => \(my $cache_size = '50m'),
  'cache-delete|cd!' => \(my $cache_delete = 1),
  'cache-init|ci!'   => \(my $cache_init = 1),
  'log|l=s'     => \(my $log_level = 'ERROR'),
  'anno|a=s'    => \(my @anno),
  '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 $i = $input[0];
  my $file = shift;
  $file =~ s!^/?tmp/[^/]+!!;
  $file =~ s/^?\/?$i//;
  $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';
  $call .= ' -i ' . $anno;
  $call .= ' -o ' . $output . '/' . $file . '.json';
  $call .= '.gz -z' if $gzip;
  $call .= ' -m ' . $meta if $meta;
  $call .= ' -w' if $overwrite;
  $call .= ' -t ' . $token_base if $token_base;
  $call .= ' -l ' . $log_level if $log_level;
  $call .= ' -c ' . $cache_file;
  $call .= ' -cs ' . $cache_size;
  $call .= ' --no-cache-delete'; # Don't delete the cache
  $call .= ' --no-cache-init'; # Don't initialize the cache
  $call .= ' --no-primary ' if $primary;
  $call .= ' -y ' . $pretty if $pretty;
  $call .= ' -a ' . $_ foreach @anno;
  $call .= ' -s ' . $_ foreach @skip;
  system($call);
  return "$file";
};


# Convert sigle to path construct
s!^\s*([^_]+?)_([^\.]+?)\.(.+?)\s*$!$1/$2/$3! foreach @sigle;

# Process a single file
unless ($cmd) {
  my $input = $input[0];

  # 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 => $input,
    meta_type => ($meta // 'I5'),
    cache => Cache::FastMmap->new(
      share_file => $cache_file,
      cache_size => $cache_size,
      init_file => $cache_init
    )
  );

  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 (@anno) {
      $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 $print_text = ($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";
  };

  # Delete cache file
  unlink($cache_file) if $cache_delete;

  stop_time;
}

# Extract XML files
elsif ($cmd eq 'extract') {

  my $input = $input[0];

  pod2usage(%ERROR_HASH) unless $output;

  # TODO: Support sigles and full archives

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

#TODOOOOOO

  if (-f($input) && (my $archive = KorAP::XML::Archive->new($input))) {

    unless ($archive->test_unzip) {
      print "Unzip is not installed or incompatible.\n\n";
      exit(1);
    };

    # Iterate over all given sigles and extract
    foreach (@sigle) {
      print "$_ ";
      print '' . ($archive->extract('./'. $_, $output) ? '' : 'not ');
      print "extracted.\n";
    };

    print "\n";
    exit(1);
  };
}

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

  # TODO: Support sigles

  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";

  unless (Cache::FastMmap->new(
    share_file => $cache_file,
    cache_size => $cache_size,
    init_file => $cache_init
  )) {
    print "Unable to intialize cache '$cache_file'\n\n";
    exit(1);
  };

  # Input is a directory
  if (-d $input[0]) {
    my $it = Directory::Iterator->new($input[0]);
    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[0]) && (my $archive = KorAP::XML::Archive->new($input[0]))) {
    unless ($archive->test_unzip) {
      print "Unzip is not installed or incompatible.\n\n";
      exit(1);
    };

    # Add further annotation archived
    $archive->attach($_) foreach @input;

    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) {

	# This is not correct!!
	my $filename = catfile(
	  $output,
	  get_file_name(
	    catfile($corpus, $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
	my $input = catdir("$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;

  # Delete cache file
  unlink($cache_file) if $cache_delete;

  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 documents


=head1 SYNOPSIS

  $ korapxml2krill -z --input <directory> --output <filename>
  $ korapxml2krill archive -z --input <directory> --output <directory>
  $ korapxml2krill extract --input <directory> --output <filename> --sigle <SIGLE>


=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.
The C<korapxml2krill> command line tool is a simple wrapper to the library.


=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> tool will
be available on your command line immediately.


=head1 ARGUMENTS

=over 2

=item B<archive>

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

=item B<extract>

Extract KorAP-XML files from a Zip-file.

=back


=head1 OPTIONS

=over 2

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

Directory or archive file of documents to convert.

Multiple input archives are supported for archiving,
with the constraint,
that the first archive listed contains all primary data files
and all meta data files.
The directory structure follows the base directory format,
starting with a C<.> root folder.
In case an attached archive has no C<.> root folder,
the archive path should start with a hash.

  -i file/news.zip -i file/news.malt.zip -i #file/news.tt.zip


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

Output folder for archive processing or
document name for single output (optional),
writes to C<STDOUT> by default
(in case C<output> is not mandatory due to further options).

=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 C<OpenNLP#tokens>.

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

Skip specific annotations by specifying the foundry
(and optionally the layer with a C<#>-prefix),
e.g. C<Mate> or C<Mate#Morpho>. Alternatively you can skip C<#ALL>.
Can be set multiple times.

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

Convert specific annotations by specifying the foundry
(and optionally the layer with a C<#>-prefix),
e.g. C<Mate> or C<Mate#Morpho>.
Can be set multiple times.

=item B<--primary|-p>

Output primary data or not. Defaults to C<true>.
Can be flagged using C<--no-primary> as well.
This is I<deprecated>.

=item B<--jobs|-j>

Define the number of concurrent jobs in seperated forks
for archive processing.
Defaults to C<0> (everything runs in a single process).
This is I<experimental>.

=item B<--meta|-m>

Define the metadata parser to use. Defaults to C<I5>.
Metadata parsers can be defined in the C<KorAP::XML::Meta> namespace.
This is I<experimental>.

=item B<--pretty|-y>

Pretty print JSON output. Defaults to C<false>.
This is I<deprecated>.

=item B<--gzip|-z>

Compress the output.
Expects a defined C<output> file in single processing.

=item B<--cache|-c>

File to mmap a cache (using L<Cache::FastMmap>).
Defaults to C<korapxml2krill.cache> in the calling directory.

=item B<--cache-size|-cs>

Size of the cache. Defaults to C<50m>.

=item B<--cache-init|-ci>

Initialize cache file.
Can be flagged using C<--no-cache-init> as well.
Defaults to C<true>.

=item B<--cache-delete|-cd>

Delete cache file after processing.
Can be flagged using C<--no-cache-delete> as well.
Defaults to C<true>.

=item B<--sigle|-sg>

Extract the given text sigles.
Can be set multiple times.
I<Currently only supported on C<extract>.>

=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 ANNOTATION SUPPORT

L<KorAP::XML::Krill> has built-in importer for some annotation foundries and layers
developed in the KorAP project that are part of the KorAP preprocessing pipeline.
The base foundry with paragraphs, sentences, and the text element are mandatory for
L<Krill|https://github.com/KorAP/Krill>.

=over 2

=item B<Base>

=over 4

=item #Paragraphs

=item #Sentences

=back

=item B<Connexor>

=over 4

=item #Morpho

=item #Phrase

=item #Sentences

=item #Syntax

=back

=item B<CoreNLP>

=over 4

=item #Constituency

=item #Morpho

=item #NamedEntities

=item #Sentences

=back

=item B<DeReKo>

=over 4

=item #Structure

=back

=item B<Glemm>

=over 4

=item #Morpho

=back

=item B<Mate>

=over 4

=item #Dependency

=item #Morpho

=back

=item B<OpenNLP>

=over 4

=item #Morpho

=item #Sentences

=back

=item B<Sgbr>

=over 4

=item #Lemma

=item #Morpho

=back

=item B<TreeTagger>

=over 4

=item #Morpho

=item #Sentences

=back

=item B<XIP>

=over 4

=item #Constituency

=item #Morpho

=item #Sentences

=back

=back

More importers are in preparation.
New annotation importers can be defined in the C<KorAP::XML::Annotation> namespace.
See the built-in annotation importers as examples.

=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