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|
#! /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) $
#$Rev: 8533 $
#$URL: svn+ssh://www.crystallography.net/home/coder/svn-repositories/cod-tools/tags/v3.7.0/scripts/cod_manage_related $
#------------------------------------------------------------------------------
#*
#* Embed provided relationships between databases into a CIF file using
#* the COD notation described in the 'cod_cif.dic' dictionary.
#*
#* USAGE:
#* $0 --options input1.cif
#**
use strict;
use warnings;
use List::Util qw( max );
use COD::CIF::Parser qw( parse_cif );
use COD::CIF::Tags::Print qw( print_cif );
use COD::CIF::Tags::Manage qw( set_loop_tag );
use COD::CIF::Tags::CanonicalNames qw( canonicalize_all_names );
use COD::SOptions qw( getOptions get_value );
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 $use_parser = 'c';
my $die_on_error_level = {
'ERROR' => 1,
'WARNING' => 0,
'NOTE' => 0
};
my $key_data_name = '_cod_related_entry_id';
my %cif_tags = (
'database' => '_cod_related_entry_database',
'code' => '_cod_related_entry_code',
'description' => '_cod_related_entry_description',
'uri' => '_cod_related_entry_uri'
);
my @ordered_keys = qw( database code description uri );
my %related;
#* OPTIONS:
#* --related-entry-code
#* Code of the related entry in the external database.
#* --related-entry-database
#* Name of the database that the related entry belong to.
#* --related-entry-description
#* Description of the related entry.
#* --related-entry-uri
#* The URI pointing to the related entry.
#*
#* --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(
'--related-entry-database' => sub { $related{'database'} = get_value() },
'--related-entry-code' => sub { $related{'code'} = get_value() },
'--related-entry-description' => sub { $related{'description'} = get_value() },
'--related-entry-uri' => sub { $related{'uri'} = get_value() },
'--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 }
);
@ARGV = ( '-' ) unless @ARGV;
binmode STDOUT, ':encoding(UTF-8)';
binmode STDERR, ':encoding(UTF-8)';
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 );
for my $dataset (@{$data}) {
my $dataname = 'data_' . $dataset->{'name'};
canonicalize_all_names( $data );
local $SIG{__WARN__} = sub { process_warnings( {
'message' => @_,
'program' => $0,
'filename' => $filename,
'add_pos' => $dataname
}, $die_on_error_level ) };
eval {
foreach( keys %related ) {
$related{$_} = [$related{$_}];
}
my $related_defined;
my $related_size = 0;
for ( @ordered_keys ) {
if ( defined $related{$_} ) {
$related_size = @{$related{$_}};
$related_defined = 1;
}
}
if ($related_defined) {
my $initial_loop_size = get_initial_entry_count(
$dataset,
[ $key_data_name, sort values %cif_tags ]
);
my @initial_loop_neighbours;
foreach ( $key_data_name, values %cif_tags ) {
if ( defined $dataset->{'inloop'}{$_} ) {
my $initial_loop_no = $dataset->{'inloop'}{$_};
@initial_loop_neighbours =
@{$dataset->{'loops'}[$initial_loop_no]};
last;
}
}
my @entry_ids = @{
generate_loop_key( $dataset, {
'key_data_name' => $key_data_name,
'initial_entry_count' => $initial_loop_size,
'addition_entry_count' => $related_size,
} )
};
my $target_loop_size = @entry_ids;
# Use the loop of other item in the same category
# if the key data item is currently not looped
my $loop_tag = $key_data_name;
set_loop_tag(
$dataset,
$key_data_name,
$loop_tag,
\@entry_ids
);
for ( @ordered_keys ) {
if ( !( defined $related{$_} ||
defined $dataset->{'values'}{$cif_tags{$_}} ) ) {
next;
}
my @new_data_values = @{ generate_loop_values(
$dataset, {
'data_name' => $cif_tags{$_},
'initial_loop_size' => $initial_loop_size,
'target_loop_size' => $target_loop_size,
'additional_values' => $related{$_},
}
) };
set_loop_tag(
$dataset,
$cif_tags{$_},
$key_data_name,
\@new_data_values
);
}
# Add unknown values to other data items in the loop
for my $data_name ( @initial_loop_neighbours ) {
my @padded_data_values = @{ generate_loop_values(
$dataset, {
'data_name' => $data_name,
'initial_loop_size' => $initial_loop_size,
'target_loop_size' => $target_loop_size,
}
) };
set_loop_tag(
$dataset,
$data_name,
$key_data_name,
\@padded_data_values
);
}
} else {
warn 'WARNING, no related entry information was provided -- ' .
'the data block will not be modified' . "\n";
}
print_cif( $dataset,
{
'preserve_loop_order' => 1,
'keep_tag_order' => 1
}
);
};
if ( $@ ) {
process_errors( {
'message' => $@,
'program' => $0,
'filename' => $filename,
'add_pos' => $dataname
}, $die_on_error_level->{'ERROR'} )
}
}
}
##
# Returns the number of values associated with any of the given data names.
# It is expected that all of the given data items either belong to the same
# loop or contain only a single value. An error message is raised in case
# the data items contain differing numbers of values.
#
# @param $dataset
# Reference to a data block as returned by the COD::CIF::Parser.
# @param $data_names
# Reference to an array of data names that should be examined.
# @return
# The number of values associated with the given data names.
##
sub get_initial_entry_count
{
my ( $dataset, $data_names ) = @_;
my $count;
foreach ( @{$data_names} ) {
if (exists $dataset->{'values'}{$_}) {
$count = @{$dataset->{'values'}{$_}} if !defined $count;
if ( @{$dataset->{'values'}{$_}} ne $count ) {
die 'ERROR, data items [' .
( join ', ', map { "'$_'" } @{$data_names} ) . '] ' .
'do not contain the same number of values' . "\n";
}
}
}
$count = 0 if !defined $count;
return $count;
}
##
# Generates the list of loop identifiers based on the already existing
# values.
#
# @param $dataset
# Reference to a data block as returned by the COD::CIF::Parser.
# @param $options
# Reference to a hash of options. The following options are recognised:
# {
# # Data name of the loop identifiers
# 'key_data_name' => '_cod_related_entry_id',
# # The initial size of the identifier loop. This option is
# # ignored if the 'key_data_name' data item is defined
# 'initial_entry_count' => '5'
# # The number additional identifiers that need to be generated
# 'addition_entry_count' => '7'
# }
# @return
# Reference to an array of loop identifiers.
##
sub generate_loop_key
{
my ( $dataset, $options ) = @_;
my $key_data_name = $options->{'key_data_name'};
my $existing_entry_count = $options->{'initial_entry_count'};
my $addition_entry_count = $options->{'addition_entry_count'};
my @loop_key;
if ( defined $dataset->{'values'}{$key_data_name} ) {
push @loop_key, @{$dataset->{'values'}{$key_data_name}};
my $max_value = max( @{$dataset->{'values'}{$key_data_name}} );
push @loop_key, map { $max_value + $_ } 1..$addition_entry_count;
} else {
push @loop_key, (1..$existing_entry_count + $addition_entry_count);
}
return \@loop_key;
}
##
# Constructs a new list of values based on the existing one by padding CIF
# special values where needed.
#
# @param $dataset
# Reference to a data block as returned by the COD::CIF::Parser.
# @param $options
# Reference to a hash of options. The following options are recognised:
# {
# # Data name of the data item containing the original values
# 'key_data_name' => '_cod_related_entry_id',
# # The initial size of the data item loop. This option is
# # ignored if the 'key_data_name' data item is defined
# 'initial_loop_size' => '5'
# # The desired size of the new value list
# 'target_loop_size' => '7'
# # A list of additional data values that should be appended to the list
# 'additional_values' => [1, 2, 3 ,4]
# }
# @return
# Reference to an array of loop identifiers.
##
sub generate_loop_values
{
my ( $dataset, $options ) = @_;
my $data_name = $options->{'data_name'};
my $initial_loop_size = $options->{'initial_loop_size'};
my $target_loop_size = $options->{'target_loop_size'};
my $additional_values = $options->{'additional_values'};
my @new_data_values;
if ( defined $dataset->{'values'}{$data_name} ) {
@new_data_values = @{$dataset->{'values'}{$data_name}};
} else {
@new_data_values = ('?') x $initial_loop_size;
}
if ( defined $additional_values ) {
push @new_data_values, @{$additional_values};
}
my $diff = $target_loop_size - @new_data_values;
push @new_data_values, ('?') x $diff;
return \@new_data_values;
}
|
