#! /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/cif_cod_numbers $
#------------------------------------------------------------------------------
#*
#* Find COD numbers for the CIF files in given directories of file lists.
#*
#* USAGE:
#*    $0 --options input1.cif input*.cif
#**

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

my %database = (
        host  => 'www.crystallography.net',
        user  => 'cod_reader',
        name  => 'cod',
        table => 'data',
        password => '',
        platform => 'mysql',
    );

my $use_parser = 'c';
my $input_format = 'cif';

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

my $print_datablock_name = 0;

my %options = (
    'check_bibliography' => 1,
    'check_compound_source' => 0,
    'check_sample_history' => 0,
    'use_su' => 1,
    'max_cell_length_diff' => 0.5, # angstrom
    'max_cell_angle_diff'  => 1.2, # degree of arc
);
my %cif_fill_data_options = (
    'use_attached_hydrogens' => 1,
);

#* OPTIONS:
#*   --platform 'SQLite'
#*                     Use the SQL database platform 'SQLite' to query structures
#*                     (default: 'mysql').
#*
#*   -d, --database  cod
#*                     Use database "cod" to query for structures.
#*
#*   -h, --host   www.crystallography.net
#*   -s, --server www.crystallography.net
#*                     Query COD database on the host 'www.crystallography.net'.
#*
#*   -l, --localhost
#*                     Use database server on the localhost to query the
#*                     COD database.
#*
#*   -p, --port 3306
#*                     Use use the specified port to query structures
#*                     (default: 3306).
#*
#*   -t, --table  data
#*                     Use SQL table "data" to query for structures.
#*
#*   -u, --user cod_reader
#*                     Use user name "cod_reader" to access COD database;
#*                     this reader should be granted SELECT privilege, i.e.
#*                     should be able to read the COD database without
#*                     supplying a password.
#*
#*   --password
#*                     Use the specified password to connect (default: '').
#*
#*   -P, --print-datablock-name
#*                     Print data block name as the fifth column.
#*   -P-, --no-print-datablock-name, --dont-print-datablock-name
#*                     Do not print data block names (default).
#*
#*   -S, --series 9
#*                     Check only COD entries starting with 9 (so called 9* series).
#*                     Default: check the whole COD database. Set series to
#*                     "" (empty string) to restore the default behaviour.
#*
#*   --max-cell-length-difference 0.5
#*                     Maximum difference of unit cell lengths allowed
#*                     for entries regarded as the same, in angstroms
#*                     (default: 0.5).
#*
#*   --max-cell-angle-difference 1.2
#*                     Maximum difference of unit cell angles allowed for
#*                     entries regarded as the same, in angstroms
#*                     (default: 1.2).
#*
#*   --check-bibliography
#*                     Only CIFs that have different bibliography data are
#*                     declared different if all other parameters match
#*                     CIFs with missing bibliographies are assumed to
#*                     have matching bibliographies (default).
#*   --no-check-bibliography, --dont-check-bibliography
#*                     Ignore bibliographic data of all CIFs; thus even files
#*                     with different bibliographies will be regarded the same
#*                     if their cells, chemical formulae and measurement
#*                     conditions match.
#*
#*   --use-sigma, --no-ignore-sigma, --dont-ignore-sigma
#*                     Use standard deviations (sigmas) when comparing unit
#*                     cell constants (default).
#*   --no-use-sigma, --dont-use-sigma, --ignore-sigma
#*                     Ignore standard deviations (sigmas) when comparing unit
#*                     cell constants.
#*
#*   --check-sample-history
#*                     Only CIFs that have different sample history data
#*                     (as recorded in the _exptl_crystal_thermal_history
#*                     and _exptl_crystal_pressure_history tags) are declared
#*                     different if all other parameters match.
#*   --no-check-sample-history,
#*   --dont-check-sample-history,
#*   --disregard-sample-history
#*                     Ignore sample history of all CIFs; thus even files
#*                     with different sample histories will be regarded the
#*                     same if their cells, chemical formulae and measurement
#*                     conditions match (default).
#*
#*   --check-compound-source
#*                     Only CIFs that have different compound source
#*                     (as recorded in the _chemical_compound_source)
#*                     are declared different if all other parameters
#*                     match.
#*   --no-check-compound-source,
#*   --dont-check-compound-source,
#*   --disregard-compound-source
#*                     Ignore compound source of all CIFs; thus even files
#*                     with different compound sources will be regarded the
#*                     same if other conditions match (default).
#*
#*   --use-attached-hydrogens
#*                     Include number of implicit hydrogens, specified using
#*                     _atom_site_attached_hydrogens tag, into the formula
#*                     sum (default).
#*   --no-use-attached-hydrogens,
#*   --dont-use-attached-hydrogens,
#*   --ignore-attached-hydrogens
#*                     Ignore number of implicit hydrogens, specified using
#*                     _atom_site_attached_hydrogens tag, in calculation of
#*                     the formula sum.
#*
#*   --use-perl-parser
#*                     Use the Perl-only CIF parser.
#*   --use-c-parser
#*                     Use the speed-optimised C/Perl parser (default).
#*
#*   --cif-input
#*                     Use CIF format for input (default).
#*   --json-input
#*                     Use JSON format for input.
#*
#*   --help, --usage
#*                     Output a short usage message (this message) and exit.
#*   --version
#*                     Output version information and exit.
#**
@ARGV = getOptions(
    '-d,--database'  => \$database{'name'},
    '-l,--localhost' => sub { $database{'host'} = 'localhost' },
    '-h,--host'      => \$database{'host'},
    '-p,--port'      => \$database{'port'},
    '-s,--server'    => \$database{'host'},
    '-t,--table'     => \$database{'table'},
    '-u,--user'      => \$database{'user'},
    '--password'     => \$database{'password'},
    '--platform'     => \$database{'platform'},

    '-P,--print-datablock-name'     => sub{ $print_datablock_name = 1 },
    '-P-,--no-print-datablock-name' => sub{ $print_datablock_name = 0 },
    '--dont-print-datablock-name'   => sub{ $print_datablock_name = 0 },

    '-S,--series' => \$options{'cod_series_prefix'},

    '--max-cell-length-difference' => \$options{'max_cell_length_diff'},
    '--max-cell-angle-difference'  => \$options{'max_cell_angle_diff'},

    '--check-bibliography'      => sub { $options{'check_bibliography'} = 1 },
    '--dont-check-bibliography' => sub { $options{'check_bibliography'} = 0 },
    '--no-check-bibliography'   => sub { $options{'check_bibliography'} = 0 },

    '--check-sample-history'
                            => sub { $options{'check_sample_history'} = 1 },
    '--dont-check-sample-history'
                            => sub { $options{'check_sample_history'} = 0 },
    '--no-check-sample-history'
                            => sub { $options{'check_sample_history'} = 0 },
    '--disregard-sample-history'
                            => sub { $options{'check_sample_history'} = 0 },

    '--check-compound-source'
                            => sub { $options{'check_compound_source'} = 1 },
    '--dont-check-compound-source'
                            => sub { $options{'check_compound_source'} = 0 },
    '--no-check-compound-source'
                            => sub { $options{'check_compound_source'} = 0 },
    '--disregard-compound-source'
                            => sub { $options{'check_compound_source'} = 0 },

    '--ignore-sigma'        => sub{ $options{'use_su'} = 0 },
    '--dont-ignore-sigma'   => sub{ $options{'use_su'} = 1 },
    '--no-ignore-sigma'     => sub{ $options{'use_su'} = 1 },

    '--use-sigma'           => sub{ $options{'use_su'} = 1 },
    '--dont-use-sigma'      => sub{ $options{'use_su'} = 0 },
    '--no-use-sigma'        => sub{ $options{'use_su'} = 0 },

    '--use-attached-hydrogens' =>
            sub { $cif_fill_data_options{'use_attached_hydrogens'} = 1 },
    '--dont-use-attached-hydrogens' =>
            sub { $cif_fill_data_options{'use_attached_hydrogens'} = 0 },
    '--no-use-attached-hydrogens' =>
            sub { $cif_fill_data_options{'use_attached_hydrogens'} = 0 },
    '--ignore-attached-hydrogens' =>
            sub { $cif_fill_data_options{'use_attached_hydrogens'} = 0 },

    '--use-perl-parser'       => sub{ $use_parser = 'perl' },
    '--use-c-parser'          => sub{ $use_parser = 'c' },

    '--cif-input'  => sub { $input_format = 'cif' },
    '--json-input' => sub { $input_format = 'json' },

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

if( $input_format eq 'json' ) {
    $use_parser = 'json';
}

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

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

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

    canonicalize_all_names( $data );

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

    if( !defined $data->[0] || !defined $data->[0]{name} ) {
        warn "WARNING, file seems to be empty\n";
        next;
    }

    my %structures = ();
    my $index = 0;
    foreach my $dataset ( @{$data} ) {

        my $dataname = 'data_' . $dataset->{name};

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

        eval {
            my $structure = cif_fill_data( $dataset,
                                           $filename,
                                           $index,
                                           \%cif_fill_data_options );
            if ( defined $structure ) {
                $structures{$structure->{id}} = $structure;
                $index++;
            }
        };
        if ($@) {
            process_errors( {
              'message'  => $@,
              'program'  => $0,
              'filename' => $filename,
              'add_pos'  => $dataname
            }, $die_on_error_level->{'ERROR'} );
        };
    }

    my $duplicates;
    eval {
        $duplicates = fetch_duplicates( \%structures, \%database, \%options );
    };
    if ($@) {
        process_errors( {
            'message'  => $@,
            'program'  => $0,
            'filename' => $filename,
            }, $die_on_error_level->{'ERROR'} );
    };

    for my $datablock ( @{$duplicates} ) {
        if( keys %{ $datablock->{duplicates} } > 0 ) {
            for my $key (sort keys %{ $datablock->{duplicates} } ) {
                my $cod_entry = $datablock->{duplicates}{$key};
                printf
                    '%-35s %15s %3d %s',
                    $datablock->{formula},
                    $cod_entry->{filename},
                    scalar keys %{ $datablock->{duplicates} },
                    $filename;
                if( $print_datablock_name ) {
                    printf ' %s', $datablock->{datablock}{id};
                }
                print "\n"
            }
        } else {
            printf
                '%-35s %15s %3d %s',
                $datablock->{formula}, '?', 0,
                $filename;
            if( $print_datablock_name ) {
                printf ' %s', $datablock->{datablock}{id};
            }
            print "\n"
        }
    }
}
