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|
#! /bin/sh
#!perl -w # --*- Perl -*--
eval 'exec perl -x $0 ${1+"$@"}'
if 0;
#------------------------------------------------------------------------------
#$Author: antanas $
#$Date: 2017-07-20 13:13:16 +0300 (Kt, 20 liep. 2017) $
#$Revision: 5477 $
#$URL: svn://www.crystallography.net/cod-tools/tags/v2.3/scripts/cod_predeposition_check $
#------------------------------------------------------------------------------
#*
#* Filter and check pairs of CIF and Fobs files for suitability for
#* deposition to COD database.
#*
#* USAGE:
#* $0 --options input.cif input*.cif
#**
use strict;
use warnings;
use POSIX qw( strftime );
use COD::CIF::Data::CODPredepositionCheck qw( filter_and_check );
use COD::SOptions qw( getOptions get_value );
use COD::SUsage qw( usage options );
use COD::ToolsVersion;
my %database = (
host => 'www.crystallography.net',
user => 'cod_reader',
name => 'cod',
table => 'data',
password => '',
platform => 'mysql',
);
my @cif;
my @hkl;
my $deposition_type = 'published';
my $options;
$options->{'use_parser'} = 'c';
my $print_timestamps = 0;
my $tmp_dir;
my $tmp_file = "tmp-cod_predeposition_check-$$.tmp";
#* OPTIONS:
#* -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 (default 3306) to query
#* structures.
#*
#* -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 (default empty) to connect.
#*
#* --platform 'SQLite'
#* Use the SQL database platform 'SQLite' to query
#* structures (default 'mysql').
#*
#* --cif input1.cif
#* Specify a CIF file to be deposited. Multiple CIF files
#* can be provided in a way like this:
#* $0 --cif input1.cif --cif input2.cif
#*
#* --hkl, --fobs input1.hkl
#* Specify a Fobs file to be deposited. Multiple Fobs files
#* can be provided in way like this:
#* $0 --hkl input1.hkl --hkl input2.hkl
#* The order of the files is important in order to pair CIF
#* and Fobs files correctly.
#*
#* --type, --deposition-type 'prepublication'
#* Specify the deposition type under which the structure
#* is to be deposited (default 'published').
#*
#* --author-name 'Doe, J.'
#* Use the specified name as the name of the person
#* depositing the files.
#*
#* --journal 'The Journal'
#* Use the specified journal name as if it was supplied
#* by the depositor during the 'prepublication' type
#* deposition.
#*
#* --hold-period 3
#* Use the specified hold period as if it was supplied by
#* the depositor.
#*
#* --replace
#* Treat given files as replacements for previously
#* deposited data.
#* --no-replace, --dont-replace
#* Do not treat given files as replacements for previously
#* deposited data (default).
#*
#* --release
#* Treat given files as if they were previously deposited
#* as prepublication material and should now be released
#* into the public domain.
#* --no-release, --dont-release
#* Do not treat given files as if they were previously
#* deposited as prepublication material and should now
#* be released into the public domain (default).
#*
#* --bypass-checks
#* Do not check CIF files for compliance with COD
#* requirements.
#* --dont-bypass-checks, --no-bypass-checks
#* Check CIF files for compliance with COD requirements
#* (default).
#*
#* --split-pdcif
#* Output powder diffraction data blocks as a HKL file.
#* --dont-split-pdcif, --no-split-pdcif
#* Output powder diffraction data blocks as part of the
#* CIF file (default).
#*
#* --print-timestamps
#* Print timestamps to STDOUT at the start and end of
#* each CIF file deposition.
#* --no-print-timestamps, --dont-print-timestamps
#* Do not print timestamps to STDOUT at the start and end
#* of each CIF file deposition (default)
#*
#* --tmp-dir, --temp-dir
#* Use the specified temporary directory (default './').
#*
#* --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(
'-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},
'--cif' => sub { push @cif, get_value() },
'--hkl,--fobs' => sub { @hkl[(@cif-1 > 0) ? @cif-1 : 0] = get_value() },
'--type,--deposition-type' => \$deposition_type,
'--bypass-checks' => sub { $options->{bypass_checks} = 1 },
'--dont-bypass-checks' => sub { delete( $options->{bypass_checks} ) },
'--no-bypass-checks' => sub { delete( $options->{bypass_checks} ) },
'--replace' => sub { $options->{replace} = 1 },
'--dont-replace' => sub { delete( $options->{replace} ) },
'--no-replace' => sub { delete( $options->{replace} ) },
'--release' => sub { $options->{release} = 1 },
'--dont-release' => sub { delete( $options->{release} ) },
'--no-release' => sub { delete( $options->{release} ) },
'--hold-period' => \$options->{hold_period},
'--journal' => \$options->{journal},
'--author-name' => \$options->{author_name},
'--split-pdcif' => sub { $options->{split_pdcif} = 1 },
'--dont-split-pdcif' => sub { delete( $options->{split_pdcif} ) },
'--no-split-pdcif' => sub { delete( $options->{split_pdcif} ) },
'--print-timestamps' => sub { $print_timestamps = 1 },
'--dont-print-timestamps' => sub { $print_timestamps = 0 },
'--no-print-timestamps' => sub { $print_timestamps = 0 },
'--tmp-dir,--temp-dir' => \$tmp_dir,
'--use-perl-parser' => sub { $options->{use_parser} = 'perl' },
'--use-c-parser' => sub { $options->{use_parser} = 'c' },
'--options' => sub { options; exit },
'--help,--usage' => sub { usage; exit },
'--version' => sub { print 'cod-tools version ',
$COD::ToolsVersion::Version, "\n";
exit }
);
push @cif, @ARGV;
@cif = ('-') unless @cif;
binmode STDOUT, ':encoding(UTF-8)';
binmode STDERR, ':encoding(UTF-8)';
if( $tmp_dir ) {
$tmp_file = $tmp_dir . '/' . $tmp_file;
}
if( exists $options->{release} ) {
$options->{replace} = 1;
}
if( $options->{release} && $deposition_type eq 'prepublication' ) {
die "$0:: ERROR, structure can be released either as published or " .
'personal communication.' . "\n";
}
for my $i (0..@cif-1) {
print "START $cif[$i] " . strftime( "%Y-%m-%d %T\n", localtime )
if $print_timestamps;
my( $cif, $hkl );
eval {
( $cif, $hkl ) =
filter_and_check( $cif[$i],
$cif[$i],
$hkl[$i],
$hkl[$i],
\%database,
$deposition_type,
$tmp_file,
$options );
};
if( $@ ) {
if ( $@ =~ /[^.]\n$/ ) {
$@ =~ s/\n$/.\n/
};
print {*STDERR} $@;
} else {
if ( defined $cif ) { print map { "CIF $_\n" } split m/\n/, $cif };
if ( defined $hkl ) { print map { "HKL $_\n" } split m/\n/, $hkl };
}
print "FINISH $cif[$i] " . strftime( "%Y-%m-%d %T\n", localtime )
if $print_timestamps;
unlink $tmp_file if -e $tmp_file;
}
|
