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|
#! /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/v3.7.0/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 } );
}
|
