#! /bin/sh
#!perl -w # --*- Perl -*--
eval 'exec perl -x $0 ${1+"$@"}'
    if 0;
#------------------------------------------------------------------------------
#$Author: antanas $
#$Date: 2021-04-28 19:35:53 +0300 (Wed, 28 Apr 2021) $
#$Revision: 8738 $
#$URL: svn+ssh://www.crystallography.net/home/coder/svn-repositories/cod-tools/tags/v3.8.1/scripts/cif_merge $
#------------------------------------------------------------------------------
#*
#* Merge data values in identical data blocks of multiple CIFs. Unique
#* data items are combined into a single data block of the output CIF;
#* data items with equivalent values are silently merged into one. When
#* a value differs for the same data item and the same data block in two
#* files, a warning (error) is issued.
#*
#* USAGE:
#*    $0 --options input1.cif input*.cif
#**

use strict;
use warnings;
use COD::CIF::Parser qw( parse_cif );
use COD::CIF::Tags::CanonicalNames qw( canonicalize_all_names );
use COD::CIF::Tags::Merge qw( merge_datablocks );
use COD::CIF::Tags::Print qw( print_cif );
use COD::SOptions qw( getOptions );
use COD::SUsage qw( usage options );
use COD::SUsage qw(usage options);
use COD::ErrorHandler qw( process_warnings
                          process_errors
                          process_parser_messages
                          report_message );
use COD::ToolsVersion qw( get_version_string );

my $use_parser = 'c';
my $override_tags;
my $override_all = 0;
my $merge_tags;

my $die_on_error_level = {
    ERROR   => 1,
    WARNING => 0,
    NOTE    => 0
};

#* OPTIONS:
#*   --override-all
#*                     Override all data items in the recipient CIF.
#*   --dont-override-all
#*                     Do not override all data items in the recipient CIF
#*                     (default).
#*
#*   --override-tags  _tag1,_tag2
#*                     Replace the values of the provided data items
#*                     (_tag1 and _tag2 in this example) with the new ones
#*                     instead of keeping the old values.
#*
#*   --merge-tags  _tag1,_tag2
#*                     Merge the values of the provided data items
#*                     (_tag1 and _tag2 in this example).
#*
#*   --use-perl-parser
#*                     Use Perl parser to parse CIF files.
#*   --use-c-parser
#*                     Use C parser to parse CIF files (default).
#*
#*   --help, --usage
#*                     Output a short usage message (this message) and exit.
#*   --version
#*                     Output version information and exit.
#**
@ARGV = getOptions(
    "--merge-tags"         => \$merge_tags,
    "--override-tags"      => \$override_tags,
    "--override-all"       => sub { $override_all = 1 },
    "--dont-override-all"  => sub { $override_all = 0 },
    "--use-perl-parser"    => sub { $use_parser = "perl" },
    "--use-c-parser"       => sub { $use_parser = "c" },

    '--options'      => sub { options; exit },
    '--help,--usage' => sub { usage; exit },
    '--version'      => sub { print get_version_string(), "\n"; exit }
);

my ( %override_tags, %merge_tags );

if( $override_tags ) {
    %override_tags =
        map {( lc($_), $_ )} split m/,/, $override_tags;
}

if( $merge_tags ) {
    %merge_tags =
        map {( lc($_), $_ )} split m/,/, $merge_tags;
}

@ARGV = ( "-" ) unless @ARGV;

binmode STDOUT, ':encoding(UTF-8)';
binmode STDERR, ':encoding(UTF-8)';

my %merged_datablocks;
my @merged_datablock_names;

for my $filename (@ARGV) {
    my $options = { parser => $use_parser, no_print   => 1 };
    my ($data, $err_count, $messages) = parse_cif($filename, $options);
    process_parser_messages( $messages, $die_on_error_level );

    canonicalize_all_names( $data );

    if( !@$data || !defined $data->[0] || !defined $data->[0]{name} ) {
        report_message( {
           'program'   => $0,
           'filename'  => $filename,
           'err_level' => 'WARNING',
           'message'   => 'file seems to be empty'
        }, $die_on_error_level->{'WARNING'} );
        next;
    }

    for my $datablock (@$data) {
        my $dataname = 'data_' . $datablock->{'name'};

        local $SIG{__WARN__} = sub {
            process_warnings( {
                'message'  => @_,
                'program'  => $0,
                'add_pos'  => $dataname,
                'filename' => $filename
            }, $die_on_error_level )
        };

        eval {

        if( !exists $merged_datablocks{$dataname} ) {
            push( @merged_datablock_names, $dataname );
            $merged_datablocks{$dataname} = $datablock;
        } else {
            merge_datablocks( $datablock,
                              $merged_datablocks{$dataname},
                              { merge_tags      => \%merge_tags,
                                override_tags   => \%override_tags,
                                override_all    => $override_all,
                                source_filename => $filename } );
        }

    };
    if ($@) {
        process_errors( {
            'message'       => $@,
            'program'       => $0,
            'filename'      => $filename,
            'add_pos'       => $dataname
        }, $die_on_error_level->{'ERROR'} );
    };

    }
}

## use COD::Serialise qw( serialiseRef );
## serialiseRef( \%merged_datablocks );

for my $dataname (@merged_datablock_names) {
    print_cif( $merged_datablocks{$dataname},
               { keep_tag_order => 1, preserve_loop_order => 1 } );
}
