Update scripts and sgbr test suite

Change-Id: I3d584fd559d84eca80da6c5fbe257edab79b1017
diff --git a/script/korapxml2krill_dir b/script/korapxml2krill_dir
new file mode 100644
index 0000000..7c38efc
--- /dev/null
+++ b/script/korapxml2krill_dir
@@ -0,0 +1,105 @@
+#!/usr/bin/env perl
+use strict;
+use warnings;
+use FindBin;
+use Getopt::Long;
+use Directory::Iterator;
+
+my $local = $FindBin::Bin;
+
+# Changes
+# 2013/11/25
+# - Initial release
+#
+# 2016/02/04
+# - Rename to korapxml2krill_dir
+
+sub printhelp {
+  print <<'EOHELP';
+
+Merge foundry data based on a tokenization and create indexer friendly documents
+for whole directories.
+
+Call:
+korapxml2krill_dir -z --input <directory> --output <directory>
+
+--input|-i <directory>          Directory of documents to index
+--output|-o <directory>         Name of output folder
+--token|-t <foundry>[#<layer>]  Define the default tokenization by specifying
+                                the name of the foundry and optionally the name
+                                of the layer. Defaults to OpenNLP#tokens.
+--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.
+--allow|-a <foundry>#<layer>    Allow specific foundries and layers by defining them
+                                combining the foundry name with a # and the layer name.
+--primary|-p                    Output primary data or not. Defaults to true.
+                                Can be flagged using --no-primary as well.
+--human|-m                      Represent the data human friendly,
+                                while the output defaults to JSON
+--pretty|-y                     Pretty print json output
+--gzip|-z                       Compress the output
+                                (expects a defined output file)
+--log|-l                        The Log4perl log level, defaults to ERROR.
+--help|-h                       Print this document (optional)
+
+diewald@ids-mannheim.de, 2016/02/04
+
+EOHELP
+
+  exit(defined $_[0] ? $_[0] : 0);
+};
+
+my ($input, $output, $text, $gzip, $log_level, @skip, $token_base, $primary, @allow, $pretty);
+GetOptions(
+  'input|i=s'   => \$input,
+  'output|o=s'  => \$output,
+  'human|m'     => \$text,
+  'token|t=s'   => \$token_base,
+  'gzip|z'      => \$gzip,
+  'skip|s=s'    => \@skip,
+  'log|l=s'     => \$log_level,
+  'allow|a=s'   => \@allow,
+  'primary|p!'  => \$primary,
+  'pretty|y'    => \$pretty,
+  'help|h'      => sub { printhelp }
+);
+
+printhelp(1) if !$input || !$output;
+
+
+sub write_file {
+  my $anno = shift;
+  my $file = $anno;
+  $file =~ s/^?\/?$input//;
+  $file =~ tr/\//-/;
+  $file =~ s{^-+}{};
+
+  my $call = 'perl ' . $local . '/korapxml2krill -i ' . $anno . ' -o ' . $output . '/' . $file . '.json';
+  $call .= '.gz -z' if $gzip;
+  $call .= ' -m' if $text;
+  $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;
+  print "Convert $file\n";
+  system($call);
+};
+
+
+my $it = Directory::Iterator->new($input);
+my $dir;
+while (1) {
+
+    if (!$it->is_directory && ($dir = $it->get) && $dir =~ s{/data\.xml$}{}) {
+	write_file($dir);
+	$it->prune;
+    };
+  last unless $it->next;
+};
+
+
+__END__