#! /bin/sh
#!perl -w # --*- Perl -*--
eval 'exec perl -x $0 ${1+"$@"}'
    if 0;
#------------------------------------------------------------------------------
#$Author: antanas $
#$Date: 2020-09-29 10:54:47 +0300 (Tue, 29 Sep 2020) $
#$Revision: 8533 $
#$URL: svn+ssh://www.crystallography.net/home/coder/svn-repositories/cod-tools/tags/v3.8.0/scripts/find_numbers $
#------------------------------------------------------------------------------
#*
#* Find COD numbers for the .cif files in given directories of file lists.
#*
#* USAGE:
#*    $0 my-cif-dir1/ my-cif-dir2/files*.cif COD-cif-dir/
#* USAGE:
#*    $0 input1.cif input1_alt.cif
#**

use strict;
use warnings;
use COD::CIF::Data::CODNumbers qw( cif_fill_data
                                   entries_are_the_same );
use COD::CIF::Parser qw( parse_cif );
use COD::CIF::Tags::CanonicalNames qw( canonicalize_all_names );
use COD::ErrorHandler qw( process_warnings
                          process_errors
                          process_parser_messages
                          report_message );
use COD::SOptions qw( getOptions );
use COD::SUsage qw( usage );
use COD::ToolsVersion qw( get_version_string );

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

#* OPTIONS:
#*   --help, --usage
#*                     Output a short usage message (this message) and exit.
#*   --version
#*                     Output version information and exit.
#**
@ARGV = getOptions(
    '--help,--usage' => sub { usage; exit },
    '--version'      => sub { print get_version_string(), "\n"; exit }
);

my $check_bibliography = 1;

my $max_cell_length_diff = 0.5; # Angstroems
my $max_cell_angle_diff  = 1.2; # degrees

my %has_numeric_value = (
    '_journal_year'   => 1,
    '_journal_volume' => 1,
    '_journal_issue'  => 1,
);

my %skip_tag = (
    '_journal_name_full' => 0,
);

my %COD = ();

if( @ARGV < 2 ) {
    report_message( {
        'program'   => $0,
        'err_level' => 'ERROR',
        'message'   => 'please supply at least two directory names on the '
                     . 'command line -- names of directories with the '
                     . 'analysed CIF files come first and the name of the '
                     . 'directory with COD CIF files comes last'
    }, 1 );
}

my $COD_cif_dir = pop @ARGV;
my @COD_cif_files = `find $COD_cif_dir -name "*.cif" -o -name "*.CIF"`;

do {
    print int @COD_cif_files . "\n";
    print "@COD_cif_files";
} if 0;

for my $file (sort @COD_cif_files) {

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

    chomp $file;
    my %structures = ();
    eval {
        my $structures = structures_from_cif_file( $file );
        %structures = %$structures;
    }; # end of eval
    if ($@) {
        process_errors( {
          'program'       => $0,
          'filename'      => $file,
          'message'       => $@,
        }, $die_on_error_level->{'ERROR'} )
    };

    for my $id (sort keys %structures) {
        my $formula = $structures{$id}{chemical_formula_sum};

        $formula = '?' unless defined $formula;

        push( @{$COD{$formula}}, $structures{$id} );
    }
}

do {
    use COD::Serialise qw( serialiseRef );
    serialiseRef( \%COD );
} if 0;

#------------------------------------------------------------------------------

my @cif_files = `find @ARGV -name "*.cif" -o -name "*.CIF"`;

for my $file (sort @cif_files) {

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

    chomp $file;
    my %structures = ();
    eval {
        my $structures = structures_from_cif_file( $file );
        %structures = %$structures;
    }; # end of eval
    if ($@) {
        process_errors( {
          'program'       => $0,
          'filename'      => $file,
          'message'       => $@,
        }, $die_on_error_level->{'ERROR'} )
    };

    for my $id (sort keys %structures) {
        my $formula = $structures{$id}{chemical_formula_sum};

        $formula = '?' unless defined $formula;

        my $final_formula = $formula;
        $final_formula =~ s/\s/_/g;

        my $n = 0;
        if( defined $COD{$formula} ) {
            for my $COD_entry (@{$COD{$formula}}) {
                if( entries_are_the_same( $structures{$id},
                                          $COD_entry,
                                          {  check_bibliography =>
                                            $check_bibliography } ) ) {
                    $n++;
                }
            }
        }
        if( $n > 0 ) {
            for my $COD_entry (@{$COD{$formula}}) {
                if( entries_are_the_same( $structures{$id},
                                          $COD_entry,
                                          {  check_bibliography =>
                                            $check_bibliography } ) ) {
                    printf
                        "%-35s %15s %3d %s\n",
                        $final_formula,
                        $COD_entry->{filename}, $n, $file;
                }
            }
        } else {
            printf "%-35s %15s %3d %s\n", $final_formula, '?', 0, $file;
        }
    }

}

#------------------------------------------------------------------------------

sub structures_from_cif_file
{
    my( $filename ) = @_;

    my $options = { 'no_print' => 1 };
    my ( $data, $err_count, $messages ) = parse_cif( $filename, $options );
    process_parser_messages( $messages, $die_on_error_level );

    return {} if $err_count > 0;

    canonicalize_all_names( $data );

    my %structures;
    for my $datablock (@$data) {
        my $structure = cif_fill_data( $datablock, $filename );
        $structures{$datablock->{name}} = $structure;
    }

    return \%structures;
}
